diff --git a/.gitignore b/.gitignore index 57a83bd..714233b 100644 --- a/.gitignore +++ b/.gitignore @@ -1,8 +1,28 @@ -*.o -*.out +*.o[0-9]* +*.e[0-9]* *.exe *.log -*.txt tags -TriBITS/ +grad.py +example.tgz +gstring.cpp_1 BUILD/ +TriBITS/ +getOptEnergy +makeXYZ +*.qsh +gfstringq.exe +*.qsh.* +gsmdone +qmaked +qmakeg +reset +status +tmp/ +r +fort* +mxyzfile* +test_output +gsmdone1 +stringfile.xyz0001* +compare_output diff --git a/CMakeLists.txt b/CMakeLists.txt new file mode 100644 index 0000000..72bf75a --- /dev/null +++ b/CMakeLists.txt @@ -0,0 +1,31 @@ +# Declare minimum required CMake version before anything to avoid problems. +SET(GSM_TRIBITS_CMAKE_MINIMUM_REQUIRED 2.8.11) +CMAKE_MINIMUM_REQUIRED(VERSION ${GSM_TRIBITS_CMAKE_MINIMUM_REQUIRED}) + +# Define project name and set up major options +INCLUDE(${CMAKE_SOURCE_DIR}/ProjectName.cmake) + +#Indicate to TriBITS that we might use Python +SET(${PROJECT_NAME}_USES_PYTHON TRUE) + +set(TARGET_NAME "gsm" CACHE STRING "Description") + +PROJECT(${PROJECT_NAME} NONE) +SET(${PROJECT_NAME}_ENABLE_gsm ON CACHE BOOL "") +SET(TPL_ENABLE_MPI OFF ) + +#Pull in TriBITS for the project +SET(${PROJECT_NAME}_TRIBITS_DIR +"${CMAKE_CURRENT_SOURCE_DIR}/cmake/tribits" + CACHE PATH "" ) +INCLUDE (${${PROJECT_NAME}_TRIBITS_DIR}/TriBITS.cmake) + +list(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake") +include(GetGitRevisionDescription) +get_git_head_revision(GIT_REFSPEC GIT_SHA1) + +#Process the TriBITS Project +TRIBITS_PROJECT() + +ADD_SUBDIRECTORY(TEST) +ADD_SUBDIRECTORY(docs) diff --git a/CTestConfig.cmake b/CTestConfig.cmake new file mode 100644 index 0000000..4605772 --- /dev/null +++ b/CTestConfig.cmake @@ -0,0 +1,27 @@ +## Gives access to SET_DEFAULT_AND_FROM_ENV function +## This is file defined in TriBITS. Like a header file in C. +#INCLUDE(SetDefaultAndFromEnv) +# +## Settings for CTest/CDash +#IF(NOT DEFINED CTEST_DROP_METHOD) +# SET_DEFAULT_AND_FROM_ENV(CTEST_DROP_METHOD "https") +#ENDIF() +# +#IF(CTEST_DROP_METHOD STREQUAL "https") +# # The normal default is ${HOST_TYPE}-${COMPUTER_VERSION}-${BUILD_DIR} +# # We are over-riding it by using set. +# SET(CTEST_BUILD_NAME "Linux-HW2-mjafari") +# +# # To learn more about this function look at the TriBits documentation +# SET_DEFAULT_AND_FROM_ENV(CTEST_PROJECT_NAME "GSM") +# SET_DEFAULT_AND_FROM_ENV(CTEST_TRIGGER_SITE "") +# +# # CDash server hostname +# SET_DEFAULT_AND_FROM_ENV(CTEST_DROP_SITE "cdash-ners590.aura.arc-ts.umich.edu") +# +# # The rest of the web address +# SET_DEFAULT_AND_FROM_ENV(CTEST_DROP_LOCATION "/submit.php?project=GSM") +# +# # YES SUBMIT RESULTS! I WANT MY 10 POINTS! +# SET_DEFAULT_AND_FROM_ENV(CTEST_DROP_SITE_CDASH TRUE) +#ENDIF() diff --git a/GSM/CMakeLists.txt b/GSM/CMakeLists.txt new file mode 100644 index 0000000..70d09d4 --- /dev/null +++ b/GSM/CMakeLists.txt @@ -0,0 +1,71 @@ +TRIBITS_PACKAGE(gsm) + +# setting different energy calculators that GSM will use +if(NOT DEFINED GSM_ENABLE_QCHEM) + SET(GSM_ENABLE_QCHEM 0) +else() + set(CALCULATOR "qchem" CACHE STRING "Calculator") +endif() + +if(NOT DEFINED GSM_ENABLE_QCHEM_SF) + SET(GSM_ENABLE_QCHEM_SF 0) +else() + set(CALCULATOR "qchem_sf" CACHE STRING "Calculator") +endif() + +if(NOT DEFINED GSM_ENABLE_MOLPRO) + SET(GSM_ENABLE_MOLPRO 0) +else() + set(CALCULATOR "molpro" CACHE STRING "Calculator") +endif() + +if(NOT DEFINED GSM_ENABLE_ASE) + SET(GSM_ENABLE_ASE 0) +else() + set(CALCULATOR "ase" CACHE STRING "Calculator") +endif() + +if(NOT DEFINED GSM_ENABLE_GAUSSIAN) + SET(GSM_ENABLE_GAUSSIAN 0) +else() + set(CALCULATOR "gaussian" CACHE STRING "Calculator") +endif() + +if(NOT DEFINED GSM_ENABLE_ORCA) + SET(GSM_ENABLE_ORCA 0) +else() + set(CALCULATOR "orca" CACHE STRING "Calculator") +endif() + +if( NOT(GSM_ENABLE_QCHEM EQUAL 1 OR GSM_ENABLE_QCHEM_SF EQUAL 1 OR GSM_ENABLE_MOLPRO EQUAL 1 OR GSM_ENABLE_ASE EQUAL 1 OR GSM_ENABLE_GAUSSIAN EQUAL 1 OR GSM_ENABLE_ORCA EQUAL 1)) + set(CALCULATOR "mopac" CACHE STRING "Calculator") +endif() + + + + +CONFIGURE_FILE( + "${CMAKE_CURRENT_SOURCE_DIR}/qchem.h.in" + "${CMAKE_CURRENT_BINARY_DIR}/qchem.h" + ) +CONFIGURE_FILE("${CMAKE_CURRENT_SOURCE_DIR}/GitSHA1.cpp.in" "${CMAKE_CURRENT_BINARY_DIR}/GitSHA1.cpp") + +# source files +file(GLOB GSM_SRC + "qchem.h" + "*.h" + "*.cpp" +) + +list(APPEND GSM_SRC "${CMAKE_CURRENT_BINARY_DIR}/GitSHA1.cpp" GitSHA1.h) + +# set up libraries +find_package(MKL REQUIRED) +include_directories(${MKL_INCLUDE_DIRS}) +set(LIBS ${LIBS} ${MKL_LIBRARIES}) +include_directories(${CMAKE_CURRENT_BINARY_DIR}) +include_directories(${CMAKE_CURRENT_SOURCE_DIR}) +MESSAGE("-- Calculator is ${CALCULATOR}") +# set target name +TRIBITS_ADD_EXECUTABLE(${TARGET_NAME}.${CALCULATOR} NOEXEPREFIX SOURCES ${GSM_SRC} IMPORTEDLIBS ${LIBS}) +TRIBITS_PACKAGE_POSTPROCESS() diff --git a/GSM/GitSHA1.cpp.in b/GSM/GitSHA1.cpp.in new file mode 100644 index 0000000..b71e706 --- /dev/null +++ b/GSM/GitSHA1.cpp.in @@ -0,0 +1,3 @@ +#include "GitSHA1.h" +#define GIT_SHA1 "@GIT_SHA1@" +const char g_GIT_SHA1[] = GIT_SHA1; diff --git a/GSM/GitSHA1.h b/GSM/GitSHA1.h new file mode 100644 index 0000000..8e02c57 --- /dev/null +++ b/GSM/GitSHA1.h @@ -0,0 +1 @@ +extern const char g_GIT_SHA1[]; diff --git a/ase.cpp b/GSM/ase.cpp similarity index 100% rename from ase.cpp rename to GSM/ase.cpp diff --git a/ase.h b/GSM/ase.h similarity index 100% rename from ase.h rename to GSM/ase.h diff --git a/bmat.cpp b/GSM/bmat.cpp similarity index 99% rename from bmat.cpp rename to GSM/bmat.cpp index e0a93a0..6957849 100644 --- a/bmat.cpp +++ b/GSM/bmat.cpp @@ -129,7 +129,7 @@ int ICoord::bmat_free() { return 0; } - +///forms the original B matrix int ICoord::bmatp_create() { // printf(" in bmatp_create \n"); @@ -282,7 +282,7 @@ int ICoord::bmatp_create() { return 0; } - +///Diagonalizes G to form U int ICoord::bmatp_to_U() { // printf(" in bmatp_to_U \n"); @@ -457,6 +457,7 @@ int ICoord::bmatp_to_U() } +///Determines q the components of the molecular geometry in the DI space. Also forms the active B matrix. int ICoord::bmat_create() { @@ -1684,7 +1685,6 @@ void ICoord::make_Hint() - void ICoord::opt_constraint(double* C) { int len = nbonds+nangles+ntor; @@ -1703,9 +1703,10 @@ void ICoord::opt_constraint(double* C) nicd--; //printf(" nicd: %i \n",nicd); - //take constraint vector, project it out of all Ut - //orthonormalize vectors - //last vector becomes C (projection onto space) + /** take constraint vector, project it out of all Ut + * orthonormalize vectors + * last vector becomes C (projection onto space) + */ double norm = 0.; for (int i=0;i=nnmax0) @@ -2986,7 +3004,11 @@ void GString::opt_r() return; } - +/** + * Optimizes each active node. + * osteps is the number of optimization steps for the nodes + * oesteps is the number of eigenvector following steps for the TS + */ void GString::opt_steps(double** dqa, double** ictan, int osteps, int oesteps) { printf("\n"); fflush(stdout); @@ -3406,7 +3428,7 @@ void GString::add_angles(int nadd, int* newangles) return; } - +///reparametrizes the string along the constraint during the growth phase, only used by DE void GString::ic_reparam_g(double** dqa, double* dqmaga) { close_dist_fix(0); @@ -3576,7 +3598,7 @@ void GString::ic_reparam_g(double** dqa, double* dqmaga) return; } - +///reparametrizes the string along the constraint after the growth phase void GString::ic_reparam(double** dqa, double* dqmaga, int rtype) { int size_ic = newic.nbonds+newic.nangles+newic.ntor; @@ -3660,7 +3682,7 @@ void GString::ic_reparam(double** dqa, double* dqmaga, int rtype) } - //using average + ///rtype==0 using average if (rtype==0 && i==0) { if (!climb) @@ -4922,7 +4944,7 @@ int GString::find_uphill(double cutoff) return nup; } - +///Finds peaks, used by opt_iters to know which node to climb. int GString::find_peaks(int type) { printf(" in find_peaks (%i) \n",type); @@ -5085,6 +5107,7 @@ int GString::find_peaks(int type) return npeaks; } +///tangents pairwise, returns distance magnitudes also void GString::get_tangents_1(double** dqa, double* dqmaga, double** ictan) { int nbonds = newic.nbonds; @@ -5162,7 +5185,7 @@ void GString::get_tangents_1(double** dqa, double* dqmaga, double** ictan) return; } - +///Finds the tangents during the growth phase. Tangents referenced to left or right during growing phase void GString::get_tangents_1g(double** dqa, double* dqmaga, double** ictan) { int nbonds = newic.nbonds; @@ -6505,6 +6528,7 @@ void GString::set_ssm_bonds(ICoord &ic1) return; } +///Checks if string is past_ts. Used by SSM. int GString::past_ts() { int ispast = 0; //return value @@ -6592,7 +6616,11 @@ int GString::past_ts() return ispast; } - +/** + * Optimization and add node driver for SE and DE during growth phase. + * max_iter is the max number of iterations for the entire calculation (growth and + * optimiazation) + */ void GString::growth_iters(int max_iter, double& totalgrad, double& gradrms, double endenergy, string strfileg, int& tscontinue, double gaddmax, int osteps, int oesteps, double** dqa, double* dqmaga, double** ictan) { double rn3m6 = sqrt(3*natoms-6); @@ -6854,7 +6882,10 @@ void GString::print_em(int nmaxp) return; } - +/**Optimization driver for DE and SE during the optimization phase. + * climber=1 uses climbing image, + * finder=1 finds the exact TS + */ void GString::opt_iters(int max_iter, double& totalgrad, double& gradrms, double endenergy, string strfileg, int& tscontinue, double gaddmax, int osteps, int oesteps, double** dqa, double* dqmaga, double** ictan, int finder, int climber, int do_tp, int& tp) { double rn3m6 = sqrt(3*natoms-6); diff --git a/gstring.h b/GSM/gstring.h similarity index 100% rename from gstring.h rename to GSM/gstring.h diff --git a/icoord.cpp b/GSM/icoord.cpp similarity index 99% rename from icoord.cpp rename to GSM/icoord.cpp index 76d4cc7..5e7cadd 100644 --- a/icoord.cpp +++ b/GSM/icoord.cpp @@ -175,7 +175,7 @@ void ICoord::create_xyz() return; } - +///creates the internal coordinates int ICoord::ic_create() { make_bonds(); diff --git a/icoord.h b/GSM/icoord.h similarity index 100% rename from icoord.h rename to GSM/icoord.h diff --git a/knnr.cpp b/GSM/knnr.cpp similarity index 100% rename from knnr.cpp rename to GSM/knnr.cpp diff --git a/knnr.h b/GSM/knnr.h similarity index 100% rename from knnr.h rename to GSM/knnr.h diff --git a/GSM/main.cpp b/GSM/main.cpp new file mode 100644 index 0000000..be8f4d8 --- /dev/null +++ b/GSM/main.cpp @@ -0,0 +1,283 @@ +/*! + * \mainpage Growing String Method + * + * The Growing String Method (GSM) is a reaction path (RP) and transition state (TS) finding tool. + * GSM is utilized in two main fashions, double-ended (DE) and single-ended (SE). + * DE requires a reactant and product pair, wheras SE only requires a reactant and a driving + * coorindate. The driving coordinate are internal coordinates (angles, bonds, and torsions) + * corresponding to the assumed ideal reaction coordinate. + * + * GSM is written in C++11, and requires the Intel C++ Composer XE 2013 and higher + * as well as the MKL library. Furthermore, GSM requires an electronic structure package that is + * properly sourced, and available at the command line. The following electronic structure packages + * are implemented with GSM: + * - QChem + * - ORCA + * - GAUSSIAN + * - Mopac + * - Molpro + * + * For more information, check out the wiki page: + * https://github.com/ZimmermanGroup/molecularGSM/wiki + * + * We recommend running CTest to check that the executable was linked properly to the electronic + * structure package and MKL. The TEST folders also provide a "template" for performing calculations + * i.e. it has the requisite input files necessary for the calculation. + * + * Common build errors are + * 1. INTEL is not loaded or MKLROOT is not set as an environment variable. + * + * + * @PROJECT_NUMBER + * \date 2016-12-1 + * \copyright MIT Licence + */ +#include +#include +#include + +#include "gstring.h" + + +using namespace std; + +int main(int argc, char* argv[]){ + string inpfile; + string xyzfile; + string nprocs; + switch (argc){ + case 1: + inpfile="inpfileq"; + xyzfile="initial.xyz"; + nprocs="1"; + break; + case 2: + inpfile="inpfileq"; + xyzfile=argv[1]; + nprocs="1"; + break; + case 3: + inpfile="inpfileq"; + xyzfile=argv[1]; + nprocs=argv[2]; + break; + default: + cout << "Invalid command line options." << endl; + return -1; + } + + int nnprocs = atoi(nprocs.c_str()); + printf(" Number of QC processors: %i \n",nnprocs); + int name = atoi(xyzfile.c_str()); + GString gstr; + gstr.init(inpfile, name, nnprocs); + gstr.String_Method_Optimization(); + + + return 0; +} + + +/*! + * \page page1 Delocalized Internal Coordinates + * \section Overview + *Delocalized internal coordinates are fundamental to the GSM because they + *enable direct and efficient constrained optimization. + *Furthermore, delocalized internal coordinates are a more natural + *coordinate system with less coupling in the Hessian + *because they are linear combinations of bonds, angles and torsions. + *Cartesian coordinates, on the other hand, are highly coupled coordinate + *system. + *On this page we will describe the generation of delocalized internal + *coordinatess, and how they are used in the GSM. + * + * \subsection secg Generation + * GString#structure_init reads the xyzfile for the atom names and + * Cartesian coordinates. + * ICoord#alloc allocates memory and ICoord#reset sets the coordinates and atom information + * in the ICoord class. + * To construct delocalized internal coordinates, we require a complete set of + * internal coordinates. Internal coordinates are bonds, angles, and + * torsions and as such can be measured using atom-connectivity. + * The function responsible for forming the internal coorindates is + * ICoord#ic_create. + * In DE GSM, ICoord#union_ic forms the union of reactant and product + * internal cooridnates as the full set of internal coordinates. + * The linear transformation describing the transformation from Cartesian + * coordinates to internal coordinates is the Wilson B matrix. + * ICoord#bmat_alloc allocates memory for the B matrix, delocalized internal + * coordinates U, and other important variables, and ICoord#bmatp_create + * creates the B matrix. + * The function ICoord#bmatp_to_U diagonalizes G=BTB to provide two sets of + * eigenvectors; a set of m=3N-6 eigenvectors with eigenvalues λ>0 + * called U and a set of n-m eigenvectors with eigenvalues λ=0 (to + * numerical precision) called R. + * The set U exactly spans the 3N-6 molecular + * space and are therefore a non-redundant coordinate system. + * The coordinates U are saved as the transpose ICoord#Ut. + * The component of each coordinate (ICoord#q) in U is formed in + * ICoord#bmat_create. Additionally, the B matrix—which was constructed + * from the original primitive internals—is transformed to the active + * coordinate set according to B=(UT)Bp. + * This active B matrx is used by ICoord#grad_to_q to transform a gradient + * calculated in Cartesian coordinates, to a gradient described in + * delocalized internal coordinates. The back transformation from + * delocalized internal coordinates to Cartesian coordinates + * also uses the B matrix, and is performed in ICoord#ic_to_xyz and + * ICoord#ic_to_xyz_opt. + * + * \subsection secI Constrained Optimization and Linear Interpolation + * One of the main advantages of delocalized internal coordinates is their + * ease of use for constrained optimization and linear interpolation. + * Linear interpolation and constrained optimization begins by forming an + * internal coordinate constraint vector. In DE GSM, the + * constraint vector is the tangent vector between reactant and product, and + * is calculated by GString#tangent_1. + * In SE GSM the constraint vector is the driving coordinate scaled appropriately, + * and is calculated by GString#tangent_1b. + * The internal coordinate constraint vector is projected into the coordinate + * space defined by the primitive internal coordinates. A set V containting + * U and the constraint vector is formed. This set is redundant because it contains + * the 3N-6 non-redundant set U and the constraint vector. Therefore, it can be + * Schmidt orthogonalized to make the vectors U and the constraint vector orthogonal + * and the space non-redundant. + * This procedure is performed in ICoord#opt_constraint. + * The new non-redundant molecular space obtained from ICoord#opt_constraint contains + * 3N-7 adjustable degrees of freedom + * and one degree of freedom corresponding to the constraint vector. The constraint + * vector can either be kept constant to perform a constrained optimization, or incremented + * to linearly interpret along the constraint vector. Both are done in the GSM. + * Constrained optimization is performed in ICoord#opt_c, and linear interpolation + * is performed when adding nodes (GString#starting_string and GString#addNode), when + * reparametrizing the string (GString#ic_reparam_g and GString#ic_reparam), and when + * performing climbing image (ICoord#walk_up). + * + * + * \subsection ref1 References + * + * Baker, Jon and Kessi, Alain and Delley, Bernard, "The generation and use of delocalized internal coordinates in geometry optimization" The Journal of Chemical Physics, 105, 192-212 (1996), DOI:http://dx.doi.org/10.1063/1.471864\n + * http://scitation.aip.org/content/aip/journal/jcp/105/1/10.1063/1.471864 + * + * \page page2 Double-Ended GSM + * \tableofcontents + *\section sec Description + * DE GSM grows and optimizes a string of molecular geometries called nodes between a + * reactant and product pair and finds the exact transition state (TS) structure between them. + * This is done in two phases called the growth and optimization + * phase. The growth phase grows the string of nodes from the outside-in, and performs + * initial optimization. The optimization phase finishes optimizing the string + * and when the string is sufficiently optimized and behaving, + * the node with the highest energy is optimized to the exact transition state using climbing + * image and eigenvector following optimization. The driver for both DE and SE methods and growth and + * optimization phases is the GString#String_Method_Optimization. + * + *\subsection subsection1 Growth Phase + * The growth phase begins in GString#starting_string which grows two nodes along the tangent vector connecting + * the reactant product pair, one on the reactant side and the other on the product side. + * The new nodes can be optimized subject to the tangent vector + * constraint, and a new tangent vector formed between them. Two more nodes can be + * added and the process repeated until the number of nodes requested are formed. + * A description of how delocalized internal coordinates, are formed and used to add nodes + * and perform constrained optimization is given in \ref page1. + * + * The driver for adding nodes (GString#addNode) and node optimization (GString#opt_steps) + * during the growth phase is GString#growth_iters. + * GString#opt_steps sends each active node to be optimized in ICoord#opt_c. + * In DE the added nodes are active, whereas in SE only + * frontier nodes are active (see \ref page3). The ICoord#opt_c function optimizes the node + * subject to the constraint, formed in ICoord#opt_constraint. Each node is optimized + * at least one time and at most + * three times. If the node converges to within GString#CONV_TOL it will optimize less than + * three times. The maximum number of iterations are hard-coded + * for DE but can be changed via the inpfileq for SE. ICoord#opt_c uses ICoord#update_ic_eigen + * to take Newton-Raphson Steps in the 3N-7 degrees of freedom corresponding to the nuclear + * space orthogonal to the constraint vector. GString#ic_reparam_g repositions the nodes evenly + * along the string by adjusting the position of the nodes along the constraint vector. + * + *\subsection subsection2 Optimization Phase + * GString#opt_iters is the driver for optimizing the string of nodes subject to the constraint + * vectors and for finding the exact TS structure. + * Finding the exact TS structure is done in two steps that locates the TS structure efficiently + * and eliminates the possibility the TS search finds the wrong TS structure. + * The first step is the climbing image and the second step is a modified eigenvector following + * optimization. + * + * Climbing image allows the node corresponding the TS structure to move upward in energy towards + * the maximum using the component of the gradient that is in the direction of the reaction path. + * The maximum along the RP is a better structure for a local TS search. + * The local TS search is a modified eigenvector following approach. While + * conventional eigenvector following will ascend along the lowest + * eigenvalue vector of the Hessian, this criterion can be modified + * for increased stability since the approximate reaction path + * direction is known in GSM. To ensure that the correct mode is + * followed, the eigenvector of the Hessian with the highest + * overlap with the string tangent at the TS is targeted. + * Once the exact TS search commences, string optimization + * continues to proceed as usual. The TS node itself is not + * reparameterized, but equal spacing of nodes on either side of + * the string is still enforced (GString#ic_reparam). Because the maximized eigenvector of the TS node must overlap + * with the reaction path tangent, the TS node remains effectively constrained within the + * reaction path. + * + * Climbing image will be activated (GString#climb will equal 1) once the totalgrad < 0.3 and one peak is found + * (GString#find_peaks). When GString#opt_steps is called + * the function GString#get_tangents_1e will form a three-way tangent on the TS node. This forms a + * more accurate RP direction for climbing image and approximating the Hessian. + * The function which performs the climbing image is ICoord#walk_up, and is called within + * ICoord#update_ic_eigen_h. + * + * The local TS search (GString#find = 1) will commence once the gradient of + * the TS node is small, the totalgrad is small, and the gradient in the + * direction of the RP at the TS node is smalll. + * GString#get_eigenv_finite forms the eigenvectors corresponding to the imaginary frequencies. + * The eigenvector corresponding to the greatest overlap with the RP is used in the local TS + * search as described above. + * The function ICoord#opt_eigen_ts is responsible for performing the local TS search. + * Convergence of the reaction path is + * considered complete when the TS node has a small root + * mean squared (RMS) gradient of GString#CONV_TOL (usually 0.0005 hartree/Å). The same + * RMS gradient threshold is used to temporarily cease node + * optimization during each string iteration. + * + * \subsection ref2 References: + * P. M. Zimmerman, “Reliable Transition State Searches Integrated with the Growing String Method,” Journal of Chemical Theory and Computation, 9, 3043-3050 (2013)\n + * http://pubs.acs.org.proxy.lib.umich.edu/doi/full/10.1021/ct400319w\n + * + * \page page3 Single-Ended GSM + * \tableofcontents + * \section gen Overview + * SE operates using the same drivers as DE (GString#growth_iters and GString#opt_iters), + * but has some differences that are particular to SE. + * Some of the differences have already been discussed in \ref page1 and \ref page2. + * On this page we will further highlight the differences. + * + * \subsection sec3 General Description and Differences + * Unlike DE, which requires a reactant and a product, SE only requires the reactant and + * driving coordinates which are internal coordinates e.g. add/break bond. Therefore, + * SE can be used to search for pruducts that haven't been found yet. + * But because SE doesn't have a product structure, it can't form the internal coordinate + * tangent in the same way as DE. Instead, SE uses the GString#tangent_1b function to form the + * constrain vector using the driving coordinate . + * As the reaction proceeds,the tangent vector is scalled appropriately using atom-connectivity + * measurements. + * Another differences between SE and DE is that SE only optimizes the frontier node during the growth phase + * and doesn't undergo string reparametrization until the string is done growing. Nodes are set as active + * using GString#set_fsm_active and the variable GString#nnR keeps track of the reactant node. + * + * Besides those differences, SSM must keep careful track of how the string is being grown because the + * number of nodes it uses is not constant like DE and it needs to detect when it has passed a TS to finish growing. + * In GString#growth_iters, the function GString#past_ts checks if the string has grown + * over the TS. GString#opt_iters checks if the TS node is the second to last node and will + * add another node to the string. The function GString#addCNode, will add a node if more space + * between the TS and product is needed, i.e. if the distance from the TS to product requires more than + * two nodes for the overall string spacing to remain even. + * When the product node is found, it undergoes optimization using ICoord#opt_b. + * After the string is fully grown it behaves identically to DE because the string is fully grown and the + * product is optimized. + * + * \subsection ref3 References: + * P. M. Zimmerman "Single-ended transition state finding with the growing string method" J. Comput. Chem. 2015, 36, 601–611. DOI: 10.1002/jcc.23833\n + * http://onlinelibrary.wiley.com/doi/10.1002/jcc.23833/abstract + **/ + + diff --git a/mem.cpp b/GSM/mem.cpp similarity index 100% rename from mem.cpp rename to GSM/mem.cpp diff --git a/mm_grad.cpp b/GSM/mm_grad.cpp similarity index 100% rename from mm_grad.cpp rename to GSM/mm_grad.cpp diff --git a/molpro.cpp b/GSM/molpro.cpp similarity index 98% rename from molpro.cpp rename to GSM/molpro.cpp index 3adc890..a1c69bd 100644 --- a/molpro.cpp +++ b/GSM/molpro.cpp @@ -172,7 +172,8 @@ table, GRADX, GRADY, GRADZ #if !SAFE_MODE //printf(" executing molpro \n"); fflush(stdout); // string cmd = "/export/zimmerman/paulzim/Molpro_serial/bin/molpro "+filename; - string cmd = "/export/applications/Molpro/2012.1.9/molprop_2012_1_Linux_x86_64_i8/bin/molpro"; + //string cmd = "/export/applications/Molpro/2012.1.9/molprop_2012_1_Linux_x86_64_i8/bin/molpro"; + string cmd = "molpro"; // string cmd = "/export/applications/MolproCopy/2012.1.9/molprop_2012_1_Linux_x86_64_i8/bin/molpro"; string nstr = StringTools::int2str(NPROCS,1,"0"); cmd = cmd + " -W scratch"; @@ -265,7 +266,8 @@ int Molpro::seed() #if !SAFE_MODE //printf(" executing molpro \n"); fflush(stdout); // string cmd = "/export/zimmerman/paulzim/Molpro_serial/bin/molpro "+filename; - string cmd = "/export/applications/Molpro/2012.1.9/molprop_2012_1_Linux_x86_64_i8/bin/molpro"; + //string cmd = "/export/applications/Molpro/2012.1.9/molprop_2012_1_Linux_x86_64_i8/bin/molpro"; + string cmd = "molpro"; // string cmd = "/export/applications/MolproCopy/2012.1.9/molprop_2012_1_Linux_x86_64_i8/bin/molpro"; string nstr = StringTools::int2str(NPROCS,1,"0"); cmd = cmd + " -W scratch"; diff --git a/molpro.h b/GSM/molpro.h similarity index 100% rename from molpro.h rename to GSM/molpro.h diff --git a/mopac.cpp b/GSM/mopac.cpp similarity index 97% rename from mopac.cpp rename to GSM/mopac.cpp index 5b9c155..d183d9c 100644 --- a/mopac.cpp +++ b/GSM/mopac.cpp @@ -156,7 +156,9 @@ double Mopac::opt(string filename, ICoord icoords) { xyzfile << " " << anames[i] << " " << xyz[3*i+0] << " " << xyz[3*i+1] << " " << xyz[3*i+2] << endl; } - string cmd = "/tmp/MOPAC2016.exe "+filename; + //string cmd = "/tmp/MOPAC2016.exe "+filename; + //CRA 12/8/2016 why is this referencing /tmp/? + string cmd = "mopac "+filename; system(cmd.c_str()); energy = read_output(filename); @@ -220,7 +222,8 @@ double Mopac::opt(string filename) { } // xyzfile << " " << natoms << endl << endl; - string cmd = "/tmp/MOPAC2016.exe "+filename; + //string cmd = "/tmp/MOPAC2016.exe "+filename; + string cmd = "mopac "+filename; system(cmd.c_str()); energy = read_output(filename); @@ -282,7 +285,8 @@ double Mopac::grads(string filename) // xyzfile << " " << anames[i] << " " << xyz[3*i+0] << " " << xyz[3*i+1] << " " << xyz[3*i+2] << endl; } - string cmd = "/tmp/MOPAC2016.exe "+filename; + //string cmd = "/tmp/MOPAC2016.exe "+filename; + string cmd = "mopac "+filename; system(cmd.c_str()); //sleep(1); diff --git a/mopac.h b/GSM/mopac.h similarity index 100% rename from mopac.h rename to GSM/mopac.h diff --git a/optic.cpp b/GSM/optic.cpp similarity index 100% rename from optic.cpp rename to GSM/optic.cpp diff --git a/orca.cpp b/GSM/orca.cpp similarity index 100% rename from orca.cpp rename to GSM/orca.cpp diff --git a/orca.h b/GSM/orca.h similarity index 100% rename from orca.h rename to GSM/orca.h diff --git a/pTable.cpp b/GSM/pTable.cpp similarity index 100% rename from pTable.cpp rename to GSM/pTable.cpp diff --git a/pTable.h b/GSM/pTable.h similarity index 100% rename from pTable.h rename to GSM/pTable.h diff --git a/print.cpp b/GSM/print.cpp similarity index 100% rename from print.cpp rename to GSM/print.cpp diff --git a/qchem.cpp b/GSM/qchem.cpp similarity index 100% rename from qchem.cpp rename to GSM/qchem.cpp diff --git a/qchem.h b/GSM/qchem.h.in similarity index 85% rename from qchem.h rename to GSM/qchem.h.in index e992563..e365765 100644 --- a/qchem.h +++ b/GSM/qchem.h.in @@ -1,12 +1,12 @@ #ifndef QCHEM_H #define QCHEM_H -#define QCHEM 0 -#define QCHEMSF 0 -#define USE_MOLPRO 0 -#define USE_ASE 0 -#define USE_GAUSSIAN 0 -#define USE_ORCA 0 +#define QCHEM ${GSM_ENABLE_QCHEM} +#define QCHEMSF ${GSM_ENABLE_QCHEM_SF} +#define USE_MOLPRO ${GSM_ENABLE_MOLPRO} +#define USE_ASE ${GSM_ENABLE_ASE} +#define USE_GAUSSIAN ${GSM_ENABLE_GAUSSIAN} +#define USE_ORCA ${GSM_ENABLE_ORCA} #define THREADS_ON 0 #define WRITE_FILES 0 #define USE_KNNR 0 diff --git a/qchemsf.cpp b/GSM/qchemsf.cpp similarity index 100% rename from qchemsf.cpp rename to GSM/qchemsf.cpp diff --git a/qchemsf.h b/GSM/qchemsf.h similarity index 100% rename from qchemsf.h rename to GSM/qchemsf.h diff --git a/stringtools.cpp b/GSM/stringtools.cpp similarity index 100% rename from stringtools.cpp rename to GSM/stringtools.cpp diff --git a/stringtools.h b/GSM/stringtools.h similarity index 100% rename from stringtools.h rename to GSM/stringtools.h diff --git a/utils.cpp b/GSM/utils.cpp similarity index 100% rename from utils.cpp rename to GSM/utils.cpp diff --git a/utils.h b/GSM/utils.h similarity index 100% rename from utils.h rename to GSM/utils.h diff --git a/GetGitRevisionDescription.cmake b/GetGitRevisionDescription.cmake new file mode 100644 index 0000000..2666bc5 --- /dev/null +++ b/GetGitRevisionDescription.cmake @@ -0,0 +1,261 @@ + +# - Returns a version string from Git +# +# These functions force a re-configure on each git commit so that you can +# trust the values of the variables in your build system. +# +# get_git_head_revision( [ ...]) +# +# Returns the refspec and sha hash of the current head revision +# +# git_describe( [ ...]) +# +# Returns the results of git describe on the source tree, and adjusting +# the output so that it tests false if an error occurs. +# +# git_get_exact_tag( [ ...]) +# +# Returns the results of git describe --exact-match on the source tree, +# and adjusting the output so that it tests false if there was no exact +# matching tag. +# +# Requires CMake 2.6 or newer (uses the 'function' command) +# +# Original Author: +# 2009-2010 Ryan Pavlik +# http://academic.cleardefinition.com +# Iowa State University HCI Graduate Program/VRAC +# +# Copyright Iowa State University 2009-2010. +# Distributed under the Boost Software License, Version 1.0. +# (See accompanying file LICENSE_1_0.txt or copy at +# http://www.boost.org/LICENSE_1_0.txt) + +if(__get_git_revision_description) + return() +endif() +set(__get_git_revision_description YES) + +# We must run the following at "include" time, not at function call time, +# to find the path to this module rather than the path to a calling list file +get_filename_component(_gitdescmoddir ${CMAKE_CURRENT_LIST_FILE} PATH) + +function(get_git_head_revision _refspecvar _hashvar) + set(GIT_PARENT_DIR "${CMAKE_CURRENT_SOURCE_DIR}") + set(GIT_DIR "${GIT_PARENT_DIR}/.git") + while(NOT EXISTS "${GIT_DIR}") # .git dir not found, search parent directories + set(GIT_PREVIOUS_PARENT "${GIT_PARENT_DIR}") + get_filename_component(GIT_PARENT_DIR ${GIT_PARENT_DIR} PATH) + if(GIT_PARENT_DIR STREQUAL GIT_PREVIOUS_PARENT) + # We have reached the root directory, we are not in git + set(${_refspecvar} "GITDIR-NOTFOUND" PARENT_SCOPE) + set(${_hashvar} "GITDIR-NOTFOUND" PARENT_SCOPE) + return() + endif() + set(GIT_DIR "${GIT_PARENT_DIR}/.git") + endwhile() + # check if this is a submodule + if(NOT IS_DIRECTORY ${GIT_DIR}) + file(READ ${GIT_DIR} submodule) + string(REGEX REPLACE "gitdir: (.*)\n$" "\\1" GIT_DIR_RELATIVE ${submodule}) + get_filename_component(SUBMODULE_DIR ${GIT_DIR} PATH) + get_filename_component(GIT_DIR ${SUBMODULE_DIR}/${GIT_DIR_RELATIVE} ABSOLUTE) + endif() + set(GIT_DATA "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/git-data") + if(NOT EXISTS "${GIT_DATA}") + file(MAKE_DIRECTORY "${GIT_DATA}") + endif() + + if(NOT EXISTS "${GIT_DIR}/HEAD") + return() + endif() + set(HEAD_FILE "${GIT_DATA}/HEAD") + configure_file("${GIT_DIR}/HEAD" "${HEAD_FILE}" COPYONLY) + + configure_file("${_gitdescmoddir}/GetGitRevisionDescription.cmake.in" + "${GIT_DATA}/grabRef.cmake" + @ONLY) + include("${GIT_DATA}/grabRef.cmake") + + set(${_refspecvar} "${HEAD_REF}" PARENT_SCOPE) + set(${_hashvar} "${HEAD_HASH}" PARENT_SCOPE) +endfunction() + +function(git_describe _var) + if(NOT GIT_FOUND) + find_package(Git QUIET) + endif() + get_git_head_revision(refspec hash) + if(NOT GIT_FOUND) + set(${_var} "GIT-NOTFOUND" PARENT_SCOPE) + return() + endif() + if(NOT hash) + set(${_var} "HEAD-HASH-NOTFOUND" PARENT_SCOPE) + return() + endif() + + # TODO sanitize + #if((${ARGN}" MATCHES "&&") OR + # (ARGN MATCHES "||") OR + # (ARGN MATCHES "\\;")) + # message("Please report the following error to the project!") + # message(FATAL_ERROR "Looks like someone's doing something nefarious with git_describe! Passed arguments ${ARGN}") + #endif() + + #message(STATUS "Arguments to execute_process: ${ARGN}") + + execute_process(COMMAND + "${GIT_EXECUTABLE}" + describe + ${hash} + ${ARGN} + WORKING_DIRECTORY + "${CMAKE_CURRENT_SOURCE_DIR}" + RESULT_VARIABLE + res + OUTPUT_VARIABLE + out + ERROR_QUIET + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(NOT res EQUAL 0) + set(out "${out}-${res}-NOTFOUND") + endif() + + set(${_var} "${out}" PARENT_SCOPE) +endfunction() + +function(git_get_exact_tag _var) + git_describe(out --exact-match ${ARGN}) + set(${_var} "${out}" PARENT_SCOPE) +endfunction() +# - Returns a version string from Git +# +# These functions force a re-configure on each git commit so that you can +# trust the values of the variables in your build system. +# +# get_git_head_revision( [ ...]) +# +# Returns the refspec and sha hash of the current head revision +# +# git_describe( [ ...]) +# +# Returns the results of git describe on the source tree, and adjusting +# the output so that it tests false if an error occurs. +# +# git_get_exact_tag( [ ...]) +# +# Returns the results of git describe --exact-match on the source tree, +# and adjusting the output so that it tests false if there was no exact +# matching tag. +# +# Requires CMake 2.6 or newer (uses the 'function' command) +# +# Original Author: +# 2009-2010 Ryan Pavlik +# http://academic.cleardefinition.com +# Iowa State University HCI Graduate Program/VRAC +# +# Copyright Iowa State University 2009-2010. +# Distributed under the Boost Software License, Version 1.0. +# (See accompanying file LICENSE_1_0.txt or copy at +# http://www.boost.org/LICENSE_1_0.txt) + +if(__get_git_revision_description) + return() +endif() +set(__get_git_revision_description YES) + +# We must run the following at "include" time, not at function call time, +# to find the path to this module rather than the path to a calling list file +get_filename_component(_gitdescmoddir ${CMAKE_CURRENT_LIST_FILE} PATH) + +function(get_git_head_revision _refspecvar _hashvar) + set(GIT_PARENT_DIR "${CMAKE_CURRENT_SOURCE_DIR}") + set(GIT_DIR "${GIT_PARENT_DIR}/.git") + while(NOT EXISTS "${GIT_DIR}") # .git dir not found, search parent directories + set(GIT_PREVIOUS_PARENT "${GIT_PARENT_DIR}") + get_filename_component(GIT_PARENT_DIR ${GIT_PARENT_DIR} PATH) + if(GIT_PARENT_DIR STREQUAL GIT_PREVIOUS_PARENT) + # We have reached the root directory, we are not in git + set(${_refspecvar} "GITDIR-NOTFOUND" PARENT_SCOPE) + set(${_hashvar} "GITDIR-NOTFOUND" PARENT_SCOPE) + return() + endif() + set(GIT_DIR "${GIT_PARENT_DIR}/.git") + endwhile() + # check if this is a submodule + if(NOT IS_DIRECTORY ${GIT_DIR}) + file(READ ${GIT_DIR} submodule) + string(REGEX REPLACE "gitdir: (.*)\n$" "\\1" GIT_DIR_RELATIVE ${submodule}) + get_filename_component(SUBMODULE_DIR ${GIT_DIR} PATH) + get_filename_component(GIT_DIR ${SUBMODULE_DIR}/${GIT_DIR_RELATIVE} ABSOLUTE) + endif() + set(GIT_DATA "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/git-data") + if(NOT EXISTS "${GIT_DATA}") + file(MAKE_DIRECTORY "${GIT_DATA}") + endif() + + if(NOT EXISTS "${GIT_DIR}/HEAD") + return() + endif() + set(HEAD_FILE "${GIT_DATA}/HEAD") + configure_file("${GIT_DIR}/HEAD" "${HEAD_FILE}" COPYONLY) + + configure_file("${_gitdescmoddir}/GetGitRevisionDescription.cmake.in" + "${GIT_DATA}/grabRef.cmake" + @ONLY) + include("${GIT_DATA}/grabRef.cmake") + + set(${_refspecvar} "${HEAD_REF}" PARENT_SCOPE) + set(${_hashvar} "${HEAD_HASH}" PARENT_SCOPE) +endfunction() + +function(git_describe _var) + if(NOT GIT_FOUND) + find_package(Git QUIET) + endif() + get_git_head_revision(refspec hash) + if(NOT GIT_FOUND) + set(${_var} "GIT-NOTFOUND" PARENT_SCOPE) + return() + endif() + if(NOT hash) + set(${_var} "HEAD-HASH-NOTFOUND" PARENT_SCOPE) + return() + endif() + + # TODO sanitize + #if((${ARGN}" MATCHES "&&") OR + # (ARGN MATCHES "||") OR + # (ARGN MATCHES "\\;")) + # message("Please report the following error to the project!") + # message(FATAL_ERROR "Looks like someone's doing something nefarious with git_describe! Passed arguments ${ARGN}") + #endif() + + #message(STATUS "Arguments to execute_process: ${ARGN}") + + execute_process(COMMAND + "${GIT_EXECUTABLE}" + describe + ${hash} + ${ARGN} + WORKING_DIRECTORY + "${CMAKE_CURRENT_SOURCE_DIR}" + RESULT_VARIABLE + res + OUTPUT_VARIABLE + out + ERROR_QUIET + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(NOT res EQUAL 0) + set(out "${out}-${res}-NOTFOUND") + endif() + + set(${_var} "${out}" PARENT_SCOPE) +endfunction() + +function(git_get_exact_tag _var) + git_describe(out --exact-match ${ARGN}) + set(${_var} "${out}" PARENT_SCOPE) +endfunction() diff --git a/GetGitRevisionDescription.cmake.in b/GetGitRevisionDescription.cmake.in new file mode 100644 index 0000000..6d8b708 --- /dev/null +++ b/GetGitRevisionDescription.cmake.in @@ -0,0 +1,41 @@ +# +# Internal file for GetGitRevisionDescription.cmake +# +# Requires CMake 2.6 or newer (uses the 'function' command) +# +# Original Author: +# 2009-2010 Ryan Pavlik +# http://academic.cleardefinition.com +# Iowa State University HCI Graduate Program/VRAC +# +# Copyright Iowa State University 2009-2010. +# Distributed under the Boost Software License, Version 1.0. +# (See accompanying file LICENSE_1_0.txt or copy at +# http://www.boost.org/LICENSE_1_0.txt) + +set(HEAD_HASH) + +file(READ "@HEAD_FILE@" HEAD_CONTENTS LIMIT 1024) + +string(STRIP "${HEAD_CONTENTS}" HEAD_CONTENTS) +if(HEAD_CONTENTS MATCHES "ref") + # named branch + string(REPLACE "ref: " "" HEAD_REF "${HEAD_CONTENTS}") + if(EXISTS "@GIT_DIR@/${HEAD_REF}") + configure_file("@GIT_DIR@/${HEAD_REF}" "@GIT_DATA@/head-ref" COPYONLY) + else() + configure_file("@GIT_DIR@/packed-refs" "@GIT_DATA@/packed-refs" COPYONLY) + file(READ "@GIT_DATA@/packed-refs" PACKED_REFS) + if(${PACKED_REFS} MATCHES "([0-9a-z]*) ${HEAD_REF}") + set(HEAD_HASH "${CMAKE_MATCH_1}") + endif() + endif() +else() + # detached HEAD + configure_file("@GIT_DIR@/HEAD" "@GIT_DATA@/head-ref" COPYONLY) +endif() + +if(NOT HEAD_HASH) + file(READ "@GIT_DATA@/head-ref" HEAD_HASH LIMIT 1024) + string(STRIP "${HEAD_HASH}" HEAD_HASH) +endif() diff --git a/LST.cpp b/LST.cpp deleted file mode 100644 index 186591b..0000000 --- a/LST.cpp +++ /dev/null @@ -1,735 +0,0 @@ -#include "LST.h" - -using namespace std; - -void LST::getTangents_withLST_from_nodes_only(double** angs, double** dangstromsds, int nstring, int num_interp, int natoms, double* masses, int max_iters, double lst_grad_tol){ - - double** interp_string = new double*[1+num_interp]; - for (int i=1;i<=num_interp;i++){ - interp_string[i] = new double[1+natoms*3]; - } - - double* SS = new double[1+num_interp]; - Utils::S_from_angs(angs, SS, masses, nstring, natoms); - - int* nodes_picked = new int[1+nstring]; - - LST_stringbuild(interp_string, angs, nstring, nodes_picked, num_interp, masses, natoms, max_iters, lst_grad_tol); - - double temp1, temp2; - - double* y = new double[1+num_interp]; - double* y1 = new double[1+num_interp]; - double* y2 = new double[1+num_interp]; - - Utils::S_from_angs(interp_string, SS, masses, num_interp, natoms); - - for(int k=1;k<=natoms*3;k++){ - for(int j=1;j<=num_interp;j++){ - y[j] = interp_string[j][k]; - } - Utils::getSpline(num_interp, SS, y, y2); - Utils::splineTangents(num_interp, SS, y, y2, y1); - for(int j=1;j<=nstring;j++){ - dangstromsds[j][k] = y1[nodes_picked[j]]; - } - } - - for(int i=1;i<=nstring;i++){ - temp1 = Utils::vecMag(dangstromsds[i],natoms*3); - for(int j=1;j<=natoms*3;j++){ - dangstromsds[i][j] = dangstromsds[i][j]/temp1; - } - } - - cout << "The tangents calculated are: " << endl; - for (int i=1;i<=nstring;i++){ - cout << "image " << i << endl; - Utils::display_structure_nonames(dangstromsds[i], natoms); - } - - - for (int i=1;i<=num_interp;i++){ - delete [] interp_string[i]; - } - delete [] interp_string; - - delete [] nodes_picked; - delete [] y; - delete [] y1; - delete [] y2; - delete [] SS; - -} - -void LST::get_single_tangent_from_fstring(double** interp_string, double* dangstromds, int node_picked, int num_interp, double* masses, int natoms){ - - double* y = new double[1+num_interp]; - double* y1 = new double[1+num_interp]; - double* y2 = new double[1+num_interp]; - double* SS = new double[1+num_interp]; - - Utils::S_from_angs(interp_string, SS, masses, num_interp, natoms); - - double temp = 0; - for(int k=1;k<=natoms*3;k++){ - for(int j=1;j<=num_interp;j++){ - y[j] = interp_string[j][k]; - } - Utils::getSpline(num_interp, SS, y, y2); - Utils::splineTangents(num_interp, SS, y, y2, y1); - dangstromds[k] = y1[node_picked]; - } - - double temp1 = Utils::vecMag(dangstromds ,natoms*3); - for(int j=1;j<=natoms*3;j++){ - dangstromds[j] *= 1/temp1; - } - - delete [] y; - delete [] y1; - delete [] y2; - delete [] SS; - -} - -void LST::getTangents_from_fstring(double** interp_string, double** dangstromsds, int* nodes_picked, int nstring, int num_interp, double* masses, int natoms){ - - double temp1, temp2; - - double* y = new double[1+num_interp]; - double* y1 = new double[1+num_interp]; - double* y2 = new double[1+num_interp]; - double* SS = new double[1+num_interp]; - - Utils::S_from_angs(interp_string, SS, masses, num_interp, natoms); - - for(int k=1;k<=natoms*3;k++){ - for(int j=1;j<=num_interp;j++){ - y[j] = interp_string[j][k]; - } - Utils::getSpline(num_interp, SS, y, y2); - Utils::splineTangents(num_interp, SS, y, y2, y1); - for(int j=1;j<=nstring;j++){ - dangstromsds[j][k] = y1[nodes_picked[j]]; - } - } - - for(int i=1;i<=nstring;i++){ - temp1 = Utils::vecMag(dangstromsds[i],natoms*3); - for(int j=1;j<=natoms*3;j++){ - dangstromsds[i][j] = dangstromsds[i][j]/temp1; - } - } - - delete [] y; - delete [] y1; - delete [] y2; - delete [] SS; - -} - -void LST::LST_stringbuild(double** interp_string, double** ang_coords, int nstring, int* nodes_picked, int num_interp, double* masses, int natoms, int max_iters, double lst_grad_tol){ - - //initialize the fstring - for (int i=1;i<=num_interp;i++){ - for (int j=1;j<=natoms*3;j++){ - interp_string[i][j]=0.0; - } - } - - //The f array will hold the f values for each piece of the fstring - double* f= new double[1+num_interp]; - f[1]=0; - - double* SS = new double[1+nstring]; - - Utils::S_from_angs(ang_coords, SS, masses, nstring, natoms); - - //Normalize SS into norm_s - double* norm_s = new double[1+nstring]; - - for (int i=1;i<=nstring;i++){ - norm_s[i] = SS[i]/SS[nstring]; - } - - //Utils::normalize_S(norm_s, SS, nstring); - - //Figure out what values of the interpolation factor f we should use for each piece of the fstring - //First - determine the number of interpolations to do between each pair of nodes based on node spacing - double* f_distribute = new double[1+nstring-1]; - - for (int i=1;i<=nstring-1;i++){ - f_distribute[i]=(num_interp-nstring)*(norm_s[i+1]-norm_s[i]); - if (f_distribute[i]>=ceil(f_distribute[i]-0.5000000000000)){ - f_distribute[i]=ceil(f_distribute[i]); - } - else { - f_distribute[i]=floor(f_distribute[i]); - } - } - - fflush(stdout); - - - //OK - this really requires some comments. Due to the above scheme to distribute the number of nodes - //in a given interval, there is a chance that we can end up with something greater than num_interp - //as the sum of all elements in f_distribute. If we do, the code below will find the interval with the - //most interpolations and take out one. This will iterate until the sum of f_distribute equals num_interp. - - //find some of f_distribute pieces. - int sum=nstring; - for (int i=1;i<=nstring-1;i++){ - sum+=(int)f_distribute[i]; - } - - int interval_with_max=1; - if (sum>num_interp){ - for (int i=1;i<=sum-num_interp;i++){ - for (int j=1;j<=nstring-1;j++){ - if (f_distribute[j] > f_distribute[interval_with_max]){ - interval_with_max=j; - } - } - f_distribute[interval_with_max]=f_distribute[interval_with_max]-1; - } - } - - - int interval_with_min=1; - if (sum S_return){ - if (fabs(fstr_S[i-1]-S_return) < fabs(fstr_S[i]-S_return)){ - *picked = i-1; - } - else{ - *picked = i; - } - break; - } - } - - for (int i=1;i<=natoms*3;i++){ - return_struct[i] = fstring[*picked][i]; - } - - delete [] fstr_S; - delete [] diff; - - -} - -//pickes new nodes based on nnNew, S_new and the fstring, and then places them angspos -void LST::LST_pickout(double** fstring, double* s_new, int nnOld, int nnNew, int* nodes_picked, int num_interp, int natoms, double* masses, double** angs_pos) { - - double** angspos_old = new double*[1+nnOld]; - for (int i=1;i<=nnOld;i++){ - angspos_old[i] = new double[1+natoms*3]; - } - - for (int i=1;i<=nnOld;i++){ - for (int j=1;j<=natoms*3;j++){ - angspos_old[i][j] = angs_pos[i][j]; - } - } - - double* fstr_S = new double[1+num_interp]; - - Utils::S_from_angs(fstring, fstr_S, masses, num_interp, natoms); - - //normalize fstr_S - for (int i=1;i<=num_interp;i++){ - fstr_S[i]*=(1/fstr_S[num_interp]); - } - - //Pick out new nodes from the fstring by comparing actual and desired ss_new values. - for (int i=1;i<=nnNew;i++){ - // cout <<"Now searching where to place new node: " << i << endl << endl; - for (int j=1;j<=num_interp-1;j++){ - if (s_new[i]>=fstr_S[j] && s_new[i]<=fstr_S[j+1]) { - //cout <<"success! at interpolation number: "; - if ((s_new[i]-fstr_S[j])/(fstr_S[j+1]-fstr_S[j])<0.50000){ - // cout << j << endl;; - nodes_picked[i]=j; - for (int m=1;m<=natoms*3;m++){ - angs_pos[i][m]=fstring[j][m]; - } - } - else { - // cout << j+1 << endl;; - nodes_picked[i]=j+1; - for (int m=1;m<=natoms*3;m++){ - angs_pos[i][m]=fstring[j+1][m]; - } - } - } - } - if (i==nnNew){ - for (int j=1;j<=natoms*3;j++){ - angs_pos[i][j]=fstring[num_interp][j]; - } - } - } - - for (int i=1;i<=nnOld;i++){ - delete [] angspos_old[i]; - } - delete [] angspos_old; - delete [] fstr_S; - -} - - - -void LST::LSTinterpolate(double* xyz1, double* xyz2, double* xyzf, double f, int max_iter, int natoms, double grad_tol) { - - double** r_1 = new double*[1+natoms]; - double** r_2 = new double*[1+natoms]; - double** r_c = new double*[1+natoms]; - double** r_i = new double*[1+natoms]; - for (int i=1;i<=natoms;i++){ - r_1[i] = new double[1+natoms]; - r_2[i] = new double[1+natoms]; - r_c[i] = new double[1+natoms]; - r_i[i] = new double[1+natoms]; - } - - double* dS = new double[1+natoms*3]; - double* step = new double[1+natoms*3]; - - double** d2S = new double*[1+natoms*3]; - double** d2S_inv = new double*[1+natoms*3]; - for (int i=1;i<=natoms*3;i++){ - d2S[i] = new double[1+natoms*3]; - d2S_inv[i] = new double[1+natoms*3]; - } - - double* xyz_stor = new double[1+natoms*3]; - - //Interpolate cartesian distances to get initial cartesian guess - for (int i=1;i<=natoms*3;i++) { - xyzf[i]=xyz1[i] + f*(xyz2[i]-xyz1[i]); - xyz_stor[i] = xyzf[i]; - } - - //construct r matrices of reference structures from cartesian information - Utils::Rmat_from_lincart(r_1, xyz1, natoms); - Utils::Rmat_from_lincart(r_2, xyz2, natoms); - Utils::Rmat_from_lincart(r_c, xyzf, natoms); - - //Interpolate r matrices to get r_i - for (int i=1;i<=natoms;i++){ - for (int j=1;j<=natoms;j++){ - r_i[i][j]=r_1[i][j] + f*(r_2[i][j]-r_1[i][j]); - } - } - - // cout << "LST minimization attempted........." << endl; - - //Loop through the gradient based optimization scheme - for (int iter=1;iter<=max_iter;iter++) { - - //Initialize dS and d2S - for (int i=1;i<=natoms*3;i++){ - dS[i]=0; - for (int j=1;j<=natoms*3;j++){ - d2S[i][j]=0; - } - } - - //evaluate 1st derivative of S wrt cartesians - for (int i=1;i<=natoms;i++){ - for (int j=1;j<=3;j++){ - for (int k=1;k<=natoms;k++){ - if (i!=k){ - dS[3*(i-1)+j]+=2*((r_c[k][i]-r_i[k][i])/(pow(r_i[k][i],4)))*(1/r_c[k][i])*(xyzf[3*(i-1)+j]-xyzf[3*(k-1)+j]); - } - } - dS[3*(i-1)+j]+=2*(10e-3)*(xyzf[3*(i-1)+j]-xyz_stor[3*(i-1)+j]); - } - } - - //evaluate 2nd derivative of S wrt cartesians - //first, let's do the diagonal elements of the matrix - for (int i=1;i<=natoms;i++){ - for (int j=1;j<=3;j++){ - for (int k=1;k<=natoms;k++){ - if (i!=k){ - d2S[3*(i-1)+j][3*(i-1)+j]+=2*((1/pow(r_i[i][k], 4)) + (1/pow(r_i[i][k], 3))*(1/r_c[i][k]) + (1/pow(r_i[i][k]*r_c[i][k], 3))*pow(xyzf[3*(i-1)+j]-xyzf[3*(k-1)+j], 2)); - } - } - } - } - - //Next, evaluate pieces that are wrt the same cartesian component on different atomic centers - for (int i=1;i<=natoms;i++){ - for (int j=1;j<=natoms;j++){ - for (int k=1;k<=3;k++){ - if (i!=j){ - d2S[3*(i-1)+k][3*(j-1)+k]=-2*((1/pow(r_i[i][j], 4))-(1/pow(r_i[i][j], 3))*(1/r_c[i][j])+(1/pow(r_i[i][j]*r_c[i][j], 3))*(xyzf[3*(i-1)+k]-xyzf[3*(j-1)+k])); - } - } - } - } - - //Now, evaluate pieces that are wrt different cartesian components, but same atomic center - for (int i=1;i<=natoms;i++){ - for (int j=1;j<=3;j++){ - for (int k=1;k<=3;k++){ - for (int m=1;m<=natoms;m++){ - if (i!=m && k!=j){ - d2S[3*(i-1)+j][3*(i-1)+k]+=2*(1/pow(r_i[i][m]*r_c[i][m],3))*(xyzf[3*(i-1)+j]-xyzf[3*(m-1)+j])*(xyzf[3*(i-1)+k]-xyzf[3*(m-1)+k]); - } - } - } - } - } - - //Now, evaluate pieces that are wrt to different cartesian components on different atomic centers - for (int i=1;i<=natoms;i++){ - for (int j=1;j<=natoms;j++){ - for (int k=1;k<=3;k++){ - for (int m=1;m<=3;m++){ - if (i!=j && k!=m){ - d2S[3*(i-1)+k][3*(j-1)+m]=-2*(1/pow(r_i[i][j]*r_c[i][j], 3))*(xyzf[3*(i-1)+k]-xyzf[3*(j-1)+k])*(xyzf[3*(i-1)+m]-xyzf[3*(j-1)+m]); - } - } - } - } - } - - for (int i=1;i<=natoms*3;i++){ - for (int j=1;j<=natoms*3;j++){ - d2S[i][j]+=2*(10e-3); - } - } - - Utils::invertNxN(d2S, d2S_inv, natoms*3); - - Utils::Mat_times_vec(d2S_inv, dS, step, natoms*3); - - for (int i=1;i<=natoms*3;i++){ - step[i]*=-1; - } - - //Check for convergence based on magnitude of gradient - double dSmag=Utils::vecMag(dS, natoms*3); - double SCALING = Utils::vecMag(step, natoms*3); - //if the mag. of the 1st der is less than threshold, break out of loop - // cout << "dSmag = " << dSmag << " tol = " << grad_tol << endl; - - if ((dSmag < grad_tol)){ // || (Utils::vecMag(step, natoms*3)<0.00000000001)){ - // cout << "********** LST minimization successful! ***********" << endl; - //cout << "It took " << iter << " steps" << endl; - // cout << "dSmag is: " << dSmag << " SCALING is: " << SCALING; - //cout << "and occured at step number: " << iter << endl; - // cout << "the structure is: " << endl; - // Utils::display_structure_nonames(xyzf, natoms); - break; - } - else if(iter==max_iter){ - cout << "LST minimization failed! dSmag = " << dSmag << " and the tolerance is: " << grad_tol << endl; - } - - //update working cartesians - for (int i=1;i<=natoms*3;i++){ - xyzf[i]+=step[i]; - } - - Utils::Rmat_from_lincart(r_c, xyzf, natoms); - } - - delete [] dS; - delete [] step; - delete [] xyz_stor; - - for (int i=1;i<=natoms*3;i++){ - delete [] d2S[i]; - delete [] d2S_inv[i]; - } - delete [] d2S; - delete [] d2S_inv; - - for (int i=1;i<=natoms;i++){ - delete [] r_1[i]; - delete [] r_2[i]; - delete [] r_i[i]; - delete [] r_c[i]; - } - delete [] r_1; - delete [] r_2; - delete [] r_i; - delete [] r_c; - -} - -void LST::LSTinterpolate(double* xyz1, double* xyz2, double* xyzf, double f, int max_iter, int natoms, double grad_tol, double* initial_guess) { - - double** r_1 = new double*[1+natoms]; - double** r_2 = new double*[1+natoms]; - double** r_c = new double*[1+natoms]; - double** r_i = new double*[1+natoms]; - for (int i=1;i<=natoms;i++){ - r_1[i] = new double[1+natoms]; - r_2[i] = new double[1+natoms]; - r_c[i] = new double[1+natoms]; - r_i[i] = new double[1+natoms]; - } - - double* dS = new double[1+natoms*3]; - double* step = new double[1+natoms*3]; - - double** d2S = new double*[1+natoms*3]; - double** d2S_inv = new double*[1+natoms*3]; - for (int i=1;i<=natoms*3;i++){ - d2S[i] = new double[1+natoms*3]; - d2S_inv[i] = new double[1+natoms*3]; - } - - double* xyz_stor = new double[1+natoms*3]; - - //Interpolate cartesian distances to get initial cartesian guess - for (int i=1;i<=natoms*3;i++) { - // xyzf[i]=xyz1[i] + f*(xyz2[i]-xyz1[i]); - xyzf[i] = initial_guess[i]; - - xyz_stor[i] = xyzf[i]; - } - - //construct r matrices of reference structures from cartesian information - Utils::Rmat_from_lincart(r_1, xyz1, natoms); - Utils::Rmat_from_lincart(r_2, xyz2, natoms); - Utils::Rmat_from_lincart(r_c, xyzf, natoms); - - //Interpolate r matrices to get r_i - for (int i=1;i<=natoms;i++){ - for (int j=1;j<=natoms;j++){ - r_i[i][j]=r_1[i][j] + f*(r_2[i][j]-r_1[i][j]); - } - } - - // cout << "LST minimization attempted........." << endl; - - //Loop through the gradient based optimization scheme - for (int iter=1;iter<=max_iter;iter++) { - - //Initialize dS and d2S - for (int i=1;i<=natoms*3;i++){ - dS[i]=0; - for (int j=1;j<=natoms*3;j++){ - d2S[i][j]=0; - } - } - - //evaluate 1st derivative of S wrt cartesians - for (int i=1;i<=natoms;i++){ - for (int j=1;j<=3;j++){ - for (int k=1;k<=natoms;k++){ - if (i!=k){ - dS[3*(i-1)+j]+=2*((r_c[k][i]-r_i[k][i])/(pow(r_i[k][i],4)))*(1/r_c[k][i])*(xyzf[3*(i-1)+j]-xyzf[3*(k-1)+j]); - } - } - dS[3*(i-1)+j]+=2*(10e-3)*(xyzf[3*(i-1)+j]-xyz_stor[3*(i-1)+j]); - } - } - - //evaluate 2nd derivative of S wrt cartesians - //first, let's do the diagonal elements of the matrix - for (int i=1;i<=natoms;i++){ - for (int j=1;j<=3;j++){ - for (int k=1;k<=natoms;k++){ - if (i!=k){ - d2S[3*(i-1)+j][3*(i-1)+j]+=2*((1/pow(r_i[i][k], 4)) + (1/pow(r_i[i][k], 3))*(1/r_c[i][k]) + (1/pow(r_i[i][k]*r_c[i][k], 3))*pow(xyzf[3*(i-1)+j]-xyzf[3*(k-1)+j], 2)); - } - } - } - } - - //Next, evaluate pieces that are wrt the same cartesian component on different atomic centers - for (int i=1;i<=natoms;i++){ - for (int j=1;j<=natoms;j++){ - for (int k=1;k<=3;k++){ - if (i!=j){ - d2S[3*(i-1)+k][3*(j-1)+k]=-2*((1/pow(r_i[i][j], 4))-(1/pow(r_i[i][j], 3))*(1/r_c[i][j])+(1/pow(r_i[i][j]*r_c[i][j], 3))*(xyzf[3*(i-1)+k]-xyzf[3*(j-1)+k])); - } - } - } - } - - //Now, evaluate pieces that are wrt different cartesian components, but same atomic center - for (int i=1;i<=natoms;i++){ - for (int j=1;j<=3;j++){ - for (int k=1;k<=3;k++){ - for (int m=1;m<=natoms;m++){ - if (i!=m && k!=j){ - d2S[3*(i-1)+j][3*(i-1)+k]+=2*(1/pow(r_i[i][m]*r_c[i][m],3))*(xyzf[3*(i-1)+j]-xyzf[3*(m-1)+j])*(xyzf[3*(i-1)+k]-xyzf[3*(m-1)+k]); - } - } - } - } - } - - //Now, evaluate pieces that are wrt to different cartesian components on different atomic centers - for (int i=1;i<=natoms;i++){ - for (int j=1;j<=natoms;j++){ - for (int k=1;k<=3;k++){ - for (int m=1;m<=3;m++){ - if (i!=j && k!=m){ - d2S[3*(i-1)+k][3*(j-1)+m]=-2*(1/pow(r_i[i][j]*r_c[i][j], 3))*(xyzf[3*(i-1)+k]-xyzf[3*(j-1)+k])*(xyzf[3*(i-1)+m]-xyzf[3*(j-1)+m]); - } - } - } - } - } - - for (int i=1;i<=natoms*3;i++){ - for (int j=1;j<=natoms*3;j++){ - d2S[i][j]+=2*(10e-3); - } - } - - Utils::invertNxN(d2S, d2S_inv, natoms*3); - - Utils::Mat_times_vec(d2S_inv, dS, step, natoms*3); - - for (int i=1;i<=natoms*3;i++){ - step[i]*=-1; - } - - //Check for convergence based on magnitude of gradient - double dSmag=Utils::vecMag(dS, natoms*3); - double SCALING = Utils::vecMag(step, natoms*3); - //if the mag. of the 1st der is less than threshold, break out of loop - // cout << "\tdSmag = " << dSmag << " tol = " << grad_tol << endl; - if ((dSmag < grad_tol)){ // || (Utils::vecMag(step, natoms*3)<0.00000000001)){ - // cout << "********** LST minimization successful! ***********" << endl; - //cout << "It took " << iter << " steps" << endl; - // cout << "dSmag is: " << dSmag << " SCALING is: " << SCALING; - //cout << "and occured at step number: " << iter << endl; - break; - } - else if(iter==max_iter){ - cout << "LST minimization failed!" << endl; - } - - //update working cartesians - for (int i=1;i<=natoms*3;i++){ - xyzf[i]+=step[i]; - } - - Utils::Rmat_from_lincart(r_c, xyzf, natoms); - } - - delete [] dS; - delete [] step; - delete [] xyz_stor; - - for (int i=1;i<=natoms*3;i++){ - delete [] d2S[i]; - delete [] d2S_inv[i]; - } - delete [] d2S; - delete [] d2S_inv; - - for (int i=1;i<=natoms;i++){ - delete [] r_1[i]; - delete [] r_2[i]; - delete [] r_i[i]; - delete [] r_c[i]; - } - delete [] r_1; - delete [] r_2; - delete [] r_i; - delete [] r_c; - -} diff --git a/LST.h b/LST.h deleted file mode 100644 index 93cce83..0000000 --- a/LST.h +++ /dev/null @@ -1,31 +0,0 @@ -#ifndef LST_H -#define LST_H - -#include -#include -#include -#include -#include -#include - -#include "constants.h" -#include "utils.h" - -using namespace std; - -namespace LST -{ - void getTangents_withLST_from_nodes_only(double** angs, double** dangstromsds, int nstring, int num_interp, int natoms, double* masses, int max_iters, double lst_grad_tol); - void LST_perpgrads_from_mwcoords(double** mw_coords, double** mw_grads, double** mw_perp_grads, int num_interp, int natoms, double* masses, int nstring, int max_iters, double lst_grad_tol); - void get_single_tangent_from_fstring(double** interp_string, double* dangstromds, int node_picked, int num_interp, double* masses, int natoms); - void getTangents_from_fstring(double** interp_string, double** dangstromsds, int* nodes_picked, int nstring, int num_interp, double* masses, int natoms); - void LST_stringbuild(double** interp_string, double** ang_coords, int nstring, int* nodes_picked, int num_interp, double* masses, int natoms, int max_iters, double lst_grad_tol); - void LST_pickout(double** fstring, double* s_new, int nnOld, int nnNew, int* nodes_picked, int num_interp, int natoms, double* masses, double** angs_pos); - void simple_LST_pickout(double** fstring, int natoms, int num_interp, double s_return, double* return_struct, int* picked); - void LSTinterpolate(double* xyz1, double* xyz2, double* xyzf, double f, int max_iter, int natoms, double grad_tol); - void LSTinterpolate(double* xyz1, double* xyz2, double* xyzf, double f, int max_iter, int natoms, double grad_tol, double* initial_guess); -}; - -#endif - - diff --git a/PackagesList.cmake b/PackagesList.cmake new file mode 100644 index 0000000..cff33be --- /dev/null +++ b/PackagesList.cmake @@ -0,0 +1,3 @@ +TRIBITS_REPOSITORY_DEFINE_PACKAGES( + gsm GSM PT + ) diff --git a/ProjectName.cmake b/ProjectName.cmake new file mode 100644 index 0000000..71ed899 --- /dev/null +++ b/ProjectName.cmake @@ -0,0 +1 @@ +SET(PROJECT_NAME GSM) diff --git a/README.md b/README.md index dcc0256..4c38aa7 100644 --- a/README.md +++ b/README.md @@ -11,43 +11,50 @@ Sample tutorial files can be found under the tutorial folder: https://github.com/ZimmermanGroup/molecularGSM/tree/master/tutorial ## Installation -To compile: - -1. Set FC and LINKERFLAGS in Makefile - --I have used Intel 12 and 13 compilers -2. type: make -3. copy gfstringq.exe to run directory -4. copy nwchem.py to your ase/calculators/ directory - - -To run gfstringq.exe: - -1. Setup grad.py by setting scratch directory to local scratch - --default is $PBSTMPDIR -2. Set XC and basis in grad.py - --default B3LYP/6-31G** -3. Check inpfileq for string method settings -4. To run: - a. NWChem must be available at command line (e.g. source setnw) - b. export OMP_NUM_THREADS=1 - c. to execute: ./gfstringq.exe jobnumber numberofcores > scratch/paragsmXXXX - d. initialXXXX.xyz and ISOMERSXXXX must be present in scratch -5. example/qmakeg can create a queuing script in scratch/ called go_gsm_dft.qsh - --add "#PBS -t jobnumber1,jobnumber2,..." at the top of go_gsm_dft.qsh - - -Analysis: - -1. stringfile.xyz#### contains the reaction path and TS - --variants on this file w/"g" at the end are growth phase strings - --"fr" at the end is a partial Hessian analysis, showing the first 3 vibrational modes - --comment lines are energies relative to first structure in kcal/mol -2. paragsm#### contains the optimization output -3. ./status shows the current state of the various runs - - -Examples in example/ directory: - -0007: This is a Diels-Alder reaction. initial0007.xyz contains input for SE-GSM (SSM) or DE-GSM (GSM) - -0076: H2 addition to SiH2. initial0076.xyz contains SSM and GSM input. +This code can be built using CMake. To do so: + +1. Load/install CMake +2. Load Intel compilers (if not loaded) +3. Clone this repository and checkout tribits branch + +```bash + $ git clone https://github.com/ZimmermanGroup/molecularGSM.git + $ cd molecularGSM + $ git checkout tribits +``` + +4. Clone TriBITS repository +```bash + $ git clone https://github.com/TriBITSPub/TriBITS.git +``` + +5. Create a BUILD directory at the same level as GSM +```bash + $ mkdir BUILD + $ cd BUILD +``` + +6. Configure using CMake +```bash + $ cmake -D GSM_ENABLE_QCHEM=1 ../ +``` + - other options: + - GSM_ENABLE_QCHEM_SF=1 + - GSM_ENABLE_ORCA=1 + - GSM_ENABLE_GAUSSIAN=1 + - GSM_ENABLE_MOLPRO=1 + - GSM_ENABLE_ASE=1 + - If no option is specified, the code will use MOPAC as its energy calculator. Check mopac.cpp to make sure charge/multiplicity is correct, since that is hard-coded. + +7. After successful configuration. To compile: +```bash + $make -j8 +``` + +8. An executable named "gsm.${CALCULATOR}.exe" will be created in BUILD/GSM directory, where ${CALCULATOR} is the name of the QM package. + +To run gsm, copy the executable to the working directory (where the input files are) or reference it using the full path. + +##CTest + +There are five test examples: alanine dipeptide isomerization, ammonia borane reactions, diels alder reaction, ethylene rotation, and methanol formaldehyde reaction. After building the executable you can use type $ ctest to run the tests. When each test is complete, the output will be compared with the standard output in each test directory. If the difference in coordinates of a each atom is more than 0.001, the test will fail. diff --git a/TEST/CMakeLists.txt b/TEST/CMakeLists.txt new file mode 100644 index 0000000..b7c26d4 --- /dev/null +++ b/TEST/CMakeLists.txt @@ -0,0 +1,94 @@ +# TEST_DIR is passed as an argument to GFSTRINGQ_TEST function +FUNCTION(GFSTRINGQ_TEST TEST_DIR TEST_NAME) + + #copy input files to the testing folder + file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/${TEST_DIR}/ DESTINATION +${CMAKE_CURRENT_BINARY_DIR}/${TEST_DIR}) + + TRIBITS_ADD_ADVANCED_TEST( + ${TEST_NAME} + TEST_0 + MESSAGE "-- Working directory is + ${CMAKE_CURRENT_SOURCE_DIR}/${TEST_DIR}" + # the execution command + EXEC gsm.${CALCULATOR} NOEXEPREFIX + DIRECTORY ${PROJECT_BINARY_DIR}/${PROJECT_NAME} + # the args for gstringq, 1 is the file name and 4 is the number of processors + ARGS 1 1 + # where it executes + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${TEST_DIR} + # don't clean it because we copied things there that it needs + SKIP_CLEAN_WORKING_DIRECTORY + OUTPUT_FILE + ${CMAKE_CURRENT_BINARY_DIR}/${TEST_DIR}/scratch/test_output + NO_ECHO_OUTPUT + PASS_ANY + COMM serial + TIMEOUT 100000 + + TEST_1 + MESSAGE "-- Comparing output in ${CMAKE_CURRENT_BINARY_DIR}/${TEST_DIR}" + # the execution command + CMND python + # the args for CMND + ARGS compare.py + # where it executes + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${TEST_DIR} + SKIP_CLEAN_WORKING_DIRECTORY + # where the output should go + OUTPUT_FILE + ${CMAKE_CURRENT_BINARY_DIR}/${TEST_DIR}/scratch/compare_output + #NO_ECHO_OUTPUT + # don't clean it because we copied things there that it needs + SKIP_CLEAN_WORKING_DIRECTORY + FAIL_FAST + NUM_TOTAL_CORES_USED 1 + CATEGORIES BASIC + COMM serial + + ) +ENDFUNCTION() + +#call the function +if(GSM_ENABLE_QCHEM) + MESSAGE(STATUS "QCHEM is enabled.") + #don't run because it crashes + #GFSTRINGQ_TEST(alanineDipeptideIsomerization/qchem/de-gsm alanine) + GFSTRINGQ_TEST(ammoniaBorane/qchem/de-gsm ammonia) + GFSTRINGQ_TEST(dielsAlder/qchem/de-gsm diels) + # + ##don't run ethylene because it crashes + #GFSTRINGQ_TEST(ethyleneRotation/qchem/de-gsm ethylene) + GFSTRINGQ_TEST(methanolFormaldehydeHydTransfer/qchem/de-gsm methanol) + +elseif(GSM_ENABLE_GAUSSIAN) + MESSAGE(STATUS "GAUSSIAN is enabled.") + GFSTRINGQ_TEST(alanineDipeptideIsomerization/gaussian/de-gsm alanine) + GFSTRINGQ_TEST(ammoniaBorane/gaussian/de-gsm ammonia) + GFSTRINGQ_TEST(dielsAlder/gaussian/de-gsm diels) + GFSTRINGQ_TEST(ethyleneRotation/gaussian/de-gsm ethylene) + GFSTRINGQ_TEST(methanolFormaldehydeHydTransfer/gaussian/de-gsm methanol) + +elseif(GSM_ENABLE_ORCA) + MESSAGE(STATUS "ORCA is enabled.") + # + # Don't run alanine --causes GSM to stall + #GFSTRINGQ_TEST(alanineDipeptideIsomerization/orca/de-gsm alanine) + GFSTRINGQ_TEST(ammoniaBorane/orca/de-gsm ammonia) + GFSTRINGQ_TEST(dielsAlder/orca/de-gsm diels) + # + #Don't run ethene --causes GSM to stall + #GFSTRINGQ_TEST(ethyleneRotation/orca/de-gsm ethylene) + GFSTRINGQ_TEST(methanolFormaldehydeHydTransfer/orca/de-gsm methanol) + +else() + MESSAGE(STATUS "MOPAC is enabled.") + # + #GFSTRINGQ_TEST(alanineDipeptideIsomerization/mopac/de-gsm alanine) + #GFSTRINGQ_TEST(ammoniaBorane/mopac/de-gsm ammonia) + #GFSTRINGQ_TEST(ethyleneRotation/mopac/de-gsm ethene) + #GFSTRINGQ_TEST(methanolFormaldehydeHydTransfer/mopac/de-gsm methanol) + #GFSTRINGQ_TEST(dielsAlder/mopac/de-gsm diels) + GFSTRINGQ_TEST(ethyleneRotation/mopac/de-gsm ethylene) + GFSTRINGQ_TEST(methanolFormaldehydeHydTransfer/mopac/de-gsm methanol) +endif() diff --git a/TEST/alanineDipeptideIsomerization/mopac/de-gsm/compare.py b/TEST/alanineDipeptideIsomerization/mopac/de-gsm/compare.py new file mode 100644 index 0000000..8bc4f62 --- /dev/null +++ b/TEST/alanineDipeptideIsomerization/mopac/de-gsm/compare.py @@ -0,0 +1,41 @@ +# for reading csv format files +import csv + +# function to convert strings to float and skip conversion if the value is not a float +def convertToFloat(inList): + for element in inList: + try: + yield float(element) + except ValueError: + yield element + +# subtract two floats and skip if string +def subtractFloat(number1, number2): + try: + return (number1 - number2) + except TypeError: + pass + +def main(): + threshold = 0.001 + try: + # read standard and output files + standard = csv.reader(open('stringfile.standard', 'r'), delimiter=' ') + currentOutput = csv.reader(open('stringfile.xyz0001', 'r'), delimiter=' ') + # error if file does not exist + except IOError: + print("Error: File cannot be found!") + exit(1) + # loop over elements of two files simultaneously + for rowStd, rowOut in zip(standard, currentOutput): + rowStd = filter(None, rowStd) + rowOut = filter(None, rowOut) + for valStd, valOut in zip(list(convertToFloat(rowStd)), list(convertToFloat(rowOut))): + # error if difference larger than threshold + if ((subtractFloat(valStd, valOut)) > threshold): + print ((subtractFloat(valStd, valOut))) + exit(2) + return 0 + +if __name__ == "__main__": + main() diff --git a/TEST/alanineDipeptideIsomerization/mopac/de-gsm/gscreate b/TEST/alanineDipeptideIsomerization/mopac/de-gsm/gscreate new file mode 100755 index 0000000..2648cf0 --- /dev/null +++ b/TEST/alanineDipeptideIsomerization/mopac/de-gsm/gscreate @@ -0,0 +1,16 @@ +#!/bin/bash + +file=molecule + +#nl $file > tmp.mole +#nl link > tmp.link +#join tmp.mole tmp.link > tmp.geom2 +#awk '{ print $2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10 }' tmp.geom2 > tmp.geom + +#cat qstart tmp.geom qend > qcin +#cat qstart molecule$1 qend > scratch/qcin$1 +cat qstart $QCSCRATCH/molecule$1 qend > $QCSCRATCH/qcin$1 + +#rm tmp.geom tmp.geom2 tmp.link tmp.mole + + diff --git a/TEST/alanineDipeptideIsomerization/mopac/de-gsm/inpfileq b/TEST/alanineDipeptideIsomerization/mopac/de-gsm/inpfileq new file mode 100644 index 0000000..83a96a1 --- /dev/null +++ b/TEST/alanineDipeptideIsomerization/mopac/de-gsm/inpfileq @@ -0,0 +1,27 @@ + +# FSM/GSM/SSM inpfileq + +------------- QCHEM Scratch Info ------------------------ +$QCSCRATCH/ # path for scratch dir. end with "/" +GSM_go1q # name of run +--------------------------------------------------------- + +------------ String Info -------------------------------- +SM_TYPE GSM # SSM, FSM or GSM +RESTART 0 # read restart.xyz +MAX_OPT_ITERS 80 # maximum iterations +STEP_OPT_ITERS 30 # for FSM/SSM +CONV_TOL 0.0005 # perp grad +ADD_NODE_TOL 0.1 # for GSM +SCALING 1.0 # for opt steps +SSM_DQMAX 0.8 # add step size +GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 +INT_THRESH 2.0 # intermediate detection +MIN_SPACING 5.0 # node spacing SSM +BOND_FRAGMENTS 1 # make IC's for fragments +INITIAL_OPT 0 # opt steps first node +FINAL_OPT 150 # opt steps last SSM node +PRODUCT_LIMIT 100.0 # kcal/mol +TS_FINAL_TYPE 1 # any/delta bond: 0/1 +NNODES 9 # including endpoints +--------------------------------------------------------- diff --git a/TEST/alanineDipeptideIsomerization/mopac/de-gsm/scratch/initial0001.xyz b/TEST/alanineDipeptideIsomerization/mopac/de-gsm/scratch/initial0001.xyz new file mode 100644 index 0000000..46879e0 --- /dev/null +++ b/TEST/alanineDipeptideIsomerization/mopac/de-gsm/scratch/initial0001.xyz @@ -0,0 +1,48 @@ +22 + + C 3.229500143 -1.189208873 0.139884199 + C 2.146015609 -0.205277340 0.472350600 + N 1.118945963 -0.112570225 -0.476082396 + C -0.047243882 0.763674630 -0.244060076 + C -1.303372401 -0.141988306 -0.210244508 + N -2.291823409 0.245144133 0.683372021 + C -3.533352727 -0.542642118 0.823358708 + O 2.135600863 0.498914065 1.468642050 + C -0.213883265 1.775303506 -1.377215496 + O -1.430938786 -1.114644891 -0.937948112 + H 3.761964341 -0.925904727 -0.783924677 + H 2.849246312 -2.213259730 0.027908378 + H 3.977199149 -1.208576837 0.950327781 + H 1.044378979 -0.752094793 -1.266196463 + H 0.102202311 1.303404325 0.735056289 + H -2.174667309 1.020034576 1.323554728 + H -4.416281800 0.081571617 0.609553525 + H -3.620828522 -0.960320632 1.839472047 + H -3.535367434 -1.390382715 0.106911648 + H -1.058895373 2.448597515 -1.192128572 + H -0.391966619 1.284864578 -2.344308637 + H 0.688253393 2.392712099 -1.487113804 +22 + + C 2.631040800 -1.106006186 -1.087251446 + C 1.455433960 -0.247406296 -0.720351447 + N 1.111330581 -0.245040965 0.632617367 + C 0.013296964 0.566859303 1.209728990 + C -1.371253959 -0.047197126 0.856896402 + N -1.758278255 -0.027353669 -0.465545904 + C -3.048601731 -0.606776565 -0.886889731 + O 0.828411740 0.404243419 -1.546049991 + C 0.093495718 2.034730623 0.807075902 + O -2.076272130 -0.498913473 1.749500783 + H 2.309296004 -1.912838255 -1.766184327 + H 3.154692233 -1.571597680 -0.246396909 + H 3.367552489 -0.509479586 -1.650547015 + H 1.622930701 -0.819779117 1.296556514 + H 0.101544644 0.488022293 2.332977571 + H -1.131843859 0.311497590 -1.206453969 + H -2.896398772 -1.545093253 -1.446399685 + H -3.596199978 0.105940393 -1.525332072 + H -3.681066939 -0.836997366 -0.005680182 + H -0.743521789 2.607399517 1.225766714 + H 0.068112285 2.166270013 -0.287358711 + H 1.024023911 2.496248786 1.159830035 diff --git a/TEST/alanineDipeptideIsomerization/mopac/de-gsm/stringfile.standard b/TEST/alanineDipeptideIsomerization/mopac/de-gsm/stringfile.standard new file mode 100644 index 0000000..fd1f17b --- /dev/null +++ b/TEST/alanineDipeptideIsomerization/mopac/de-gsm/stringfile.standard @@ -0,0 +1,216 @@ + 22 + 0.000000 + C 3.229500 -1.189209 0.139884 + C 2.146016 -0.205277 0.472351 + N 1.118946 -0.112570 -0.476082 + C -0.047244 0.763675 -0.244060 + C -1.303372 -0.141988 -0.210245 + N -2.291823 0.245144 0.683372 + C -3.533353 -0.542642 0.823359 + O 2.135601 0.498914 1.468642 + C -0.213883 1.775304 -1.377215 + O -1.430939 -1.114645 -0.937948 + H 3.761964 -0.925905 -0.783925 + H 2.849246 -2.213260 0.027908 + H 3.977199 -1.208577 0.950328 + H 1.044379 -0.752095 -1.266196 + H 0.102202 1.303404 0.735056 + H -2.174667 1.020035 1.323555 + H -4.416282 0.081572 0.609554 + H -3.620829 -0.960321 1.839472 + H -3.535367 -1.390383 0.106912 + H -1.058895 2.448598 -1.192129 + H -0.391967 1.284865 -2.344309 + H 0.688253 2.392712 -1.487114 + 22 + 0.298410 + C 3.325460 -1.142474 -0.140776 + C 2.270105 -0.188658 0.340035 + N 1.067277 -0.229555 -0.374060 + C -0.076117 0.617469 0.026728 + C -1.356872 -0.236733 -0.121053 + N -2.473222 0.242180 0.548060 + C -3.756622 -0.487029 0.495527 + O 2.418788 0.595190 1.265068 + C -0.183722 1.856335 -0.863400 + O -1.392043 -1.256777 -0.792504 + H 3.719047 -0.853943 -1.125182 + H 2.967405 -2.177648 -0.212922 + H 4.177450 -1.140756 0.559353 + H 0.879856 -0.924203 -1.099577 + H 0.074073 0.930938 1.100542 + H -2.444793 1.067346 1.132686 + H -4.544949 0.144570 0.053998 + H -4.069289 -0.805501 1.503428 + H -3.659301 -1.396684 -0.133028 + H -1.009971 2.507362 -0.559221 + H -0.339764 1.593345 -1.917937 + H 0.741550 2.448789 -0.812765 + 22 + 1.094410 + C 3.358560 -1.047944 -0.333222 + C 2.319563 -0.095315 0.184416 + N 1.014911 -0.358920 -0.238301 + C -0.111964 0.481405 0.231444 + C -1.409153 -0.327954 0.008550 + N -2.586441 0.293291 0.397530 + C -3.885859 -0.394524 0.255603 + O 2.561893 0.857567 0.902526 + C -0.147025 1.812497 -0.519415 + O -1.401784 -1.458790 -0.464788 + H 3.602098 -0.842849 -1.385202 + H 3.062091 -2.101418 -0.257036 + H 4.292593 -0.928703 0.240413 + H 0.768156 -1.180679 -0.795899 + H 0.026582 0.675102 1.334206 + H -2.603696 1.216001 0.812441 + H -4.546036 0.158254 -0.433136 + H -4.384912 -0.495227 1.233203 + H -3.741534 -1.414080 -0.159190 + H -0.947986 2.469806 -0.170240 + H -0.272595 1.672935 -1.600451 + H 0.805489 2.349979 -0.372836 + 22 + 2.104370 + C 3.319214 -1.014736 -0.485114 + C 2.324715 0.003283 0.003038 + N 0.992647 -0.416198 -0.042853 + C -0.124097 0.441683 0.429419 + C -1.424031 -0.365460 0.195197 + N -2.615613 0.341435 0.211065 + C -3.907600 -0.353519 0.038517 + O 2.637030 1.121679 0.401544 + C -0.126985 1.797031 -0.272617 + O -1.401541 -1.584312 0.038327 + H 3.403076 -0.989305 -1.581111 + H 3.084156 -2.044449 -0.191045 + H 4.318933 -0.779402 -0.084412 + H 0.732624 -1.366470 -0.329868 + H -0.007967 0.593611 1.541036 + H -2.651773 1.345039 0.340639 + H -4.409113 -0.021798 -0.885830 + H -4.570557 -0.164418 0.898434 + H -3.751556 -1.450156 -0.036944 + H -0.918355 2.458307 0.088876 + H -0.225419 1.700378 -1.360430 + H 0.835884 2.315469 -0.089134 + 22 + 3.478930 + C 3.220833 -1.055902 -0.615840 + C 2.286396 0.049840 -0.200194 + N 1.011759 -0.386302 0.166698 + C -0.093215 0.498753 0.622630 + C -1.390756 -0.327661 0.409840 + N -2.539132 0.335364 0.009524 + C -3.807605 -0.401573 -0.176941 + O 2.611336 1.225663 -0.192024 + C -0.096582 1.855965 -0.066715 + O -1.393228 -1.532922 0.629263 + H 3.145593 -1.239590 -1.697765 + H 3.054732 -2.009565 -0.102342 + H 4.262591 -0.753931 -0.418574 + H 0.790283 -1.389844 0.199146 + H 0.010140 0.643863 1.737865 + H -2.554806 1.325843 -0.201413 + H -4.112808 -0.395273 -1.236671 + H -4.609401 0.044074 0.434137 + H -3.690652 -1.461450 0.133473 + H -0.889142 2.511657 0.303499 + H 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1.159830 diff --git a/TEST/alanineDipeptideIsomerization/qchem/.q002.product.inp.9354.qcin.1 b/TEST/alanineDipeptideIsomerization/qchem/.q002.product.inp.9354.qcin.1 new file mode 100644 index 0000000..c88b92b --- /dev/null +++ b/TEST/alanineDipeptideIsomerization/qchem/.q002.product.inp.9354.qcin.1 @@ -0,0 +1,47 @@ + $rem + JOBTYPE OPT + EXCHANGE B3LYP +! CORRELATION PBE +! UNRESTRICTED TRUE + SCF_ALGORITHM rca_diis + SCF_MAX_CYCLES 150 +! BASIS LANL2DZ +! ECP LANL2DZ + BASIS 6-31G* + WAVEFUNCTION_ANALYSIS FALSE + GEOM_OPT_MAX_CYCLES 300 + +scf_convergence 6 + + SYM_IGNORE TRUE + SYMMETRY FALSE + +molden_format true + $end + + +$molecule +0 1 + C 2.643785 -1.121028 -1.073991 + C 1.440890 -0.257653 -0.731562 + N 1.113549 -0.198238 0.587618 + C -0.002980 0.568839 1.173333 + C -1.390825 -0.048391 0.863046 + N -1.768439 -0.012358 -0.441195 + C -3.015698 -0.602464 -0.893016 + O 0.822529 0.344445 -1.613501 + C 0.081155 2.065992 0.847556 + O -2.082502 -0.492329 1.775255 + H 2.323771 -1.914876 -1.754602 + H 3.131647 -1.568635 -0.204417 + H 3.369802 -0.505402 -1.611088 + H 1.593996 -0.829628 1.210337 + H 0.094656 0.439609 2.253020 + H -1.059273 0.248575 -1.122879 + H -2.849726 -1.546821 -1.426538 + H -3.545070 0.084690 -1.560948 + H -3.631817 -0.800937 -0.015503 + H -0.734906 2.593966 1.349942 + H 0.013387 2.248453 -0.224778 + H 1.029499 2.473951 1.210080 +$end diff --git a/TEST/alanineDipeptideIsomerization/qchem/de-gsm/gscreate b/TEST/alanineDipeptideIsomerization/qchem/de-gsm/gscreate new file mode 100755 index 0000000..119b132 --- /dev/null +++ b/TEST/alanineDipeptideIsomerization/qchem/de-gsm/gscreate @@ -0,0 +1,14 @@ +#!/bin/bash + +file=molecule + +#nl $file > tmp.mole +#nl link > tmp.link +#join tmp.mole tmp.link > tmp.geom2 +#awk '{ print $2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10 }' tmp.geom2 > tmp.geom + +#cat qstart tmp.geom qend > qcin +#cat qstart molecule$1 qend > scratch/qcin$1 +cat qstart $QCSCRATCH/molecule$1 qend > $QCSCRATCH/qcin$1 + +#rm tmp.geom tmp.geom2 tmp.link tmp.mole diff --git a/TEST/alanineDipeptideIsomerization/qchem/de-gsm/inpfileq b/TEST/alanineDipeptideIsomerization/qchem/de-gsm/inpfileq new file mode 100644 index 0000000..83a96a1 --- /dev/null +++ b/TEST/alanineDipeptideIsomerization/qchem/de-gsm/inpfileq @@ -0,0 +1,27 @@ + +# FSM/GSM/SSM inpfileq + +------------- QCHEM Scratch Info ------------------------ +$QCSCRATCH/ # path for scratch dir. end with "/" +GSM_go1q # name of run +--------------------------------------------------------- + +------------ String Info -------------------------------- +SM_TYPE GSM # SSM, FSM or GSM +RESTART 0 # read restart.xyz +MAX_OPT_ITERS 80 # maximum iterations +STEP_OPT_ITERS 30 # for FSM/SSM +CONV_TOL 0.0005 # perp grad +ADD_NODE_TOL 0.1 # for GSM +SCALING 1.0 # for opt steps +SSM_DQMAX 0.8 # add step size +GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 +INT_THRESH 2.0 # intermediate detection +MIN_SPACING 5.0 # node spacing SSM +BOND_FRAGMENTS 1 # make IC's for fragments +INITIAL_OPT 0 # opt steps first node +FINAL_OPT 150 # opt steps last SSM node +PRODUCT_LIMIT 100.0 # kcal/mol +TS_FINAL_TYPE 1 # any/delta bond: 0/1 +NNODES 9 # including endpoints +--------------------------------------------------------- diff --git a/TEST/alanineDipeptideIsomerization/qchem/de-gsm/qend b/TEST/alanineDipeptideIsomerization/qchem/de-gsm/qend new file mode 100644 index 0000000..b39a0e1 --- /dev/null +++ b/TEST/alanineDipeptideIsomerization/qchem/de-gsm/qend @@ -0,0 +1 @@ +$end diff --git a/TEST/alanineDipeptideIsomerization/qchem/de-gsm/qstart b/TEST/alanineDipeptideIsomerization/qchem/de-gsm/qstart new file mode 100644 index 0000000..afa463a --- /dev/null +++ b/TEST/alanineDipeptideIsomerization/qchem/de-gsm/qstart @@ -0,0 +1,24 @@ + $rem + JOBTYPE FORCE + EXCHANGE B3LYP +! CORRELATION PBE +! UNRESTRICTED TRUE + SCF_ALGORITHM rca_diis + SCF_MAX_CYCLES 150 + BASIS 6-31G* +! BASIS LANL2DZ +! ECP LANL2DZ + WAVEFUNCTION_ANALYSIS FALSE + GEOM_OPT_MAX_CYCLES 300 + +scf_convergence 6 + + SYM_IGNORE TRUE + SYMMETRY FALSE + +molden_format true + $end + + +$molecule +0 1 diff --git a/TEST/alanineDipeptideIsomerization/qchem/de-gsm/scratch/gsmdone1 b/TEST/alanineDipeptideIsomerization/qchem/de-gsm/scratch/gsmdone1 new file mode 100644 index 0000000..4d56f1d --- /dev/null +++ b/TEST/alanineDipeptideIsomerization/qchem/de-gsm/scratch/gsmdone1 @@ -0,0 +1 @@ +done with paragsm0001 diff --git a/TEST/alanineDipeptideIsomerization/qchem/de-gsm/scratch/initial0001.xyz b/TEST/alanineDipeptideIsomerization/qchem/de-gsm/scratch/initial0001.xyz new file mode 100644 index 0000000..199953f --- /dev/null +++ b/TEST/alanineDipeptideIsomerization/qchem/de-gsm/scratch/initial0001.xyz @@ -0,0 +1,48 @@ + 22 +Step 12 + C 3.31502854 -1.14428477 -0.07833863 + C 2.27368191 -0.08290184 0.24400427 + N 1.01775129 -0.33119131 -0.22147007 + C -0.09692549 0.54620720 0.07392889 + C -1.37806532 -0.29036768 -0.08159080 + N -2.49539554 0.26339992 0.46063556 + C -3.80842307 -0.35269813 0.36912712 + O 2.55113792 0.93207195 0.87781597 + C -0.12012907 1.78271184 -0.84626356 + O -1.37498666 -1.36563041 -0.67688002 + H 4.12904645 -0.68104364 -0.64462588 + H 2.91918708 -1.98892782 -0.65070653 + H 3.74116590 -1.51580717 0.85884633 + H 0.76711436 -1.20387519 -0.67179930 + H 0.00211259 0.88849993 1.11214377 + H -2.40559063 1.13949554 0.95541137 + H -4.51802867 0.30542439 -0.14557452 + H -4.20267956 -0.59135411 1.36362200 + H -3.69646626 -1.27532171 -0.20134847 + H -0.94802578 2.45554030 -0.59367880 + H -0.22744645 1.47893665 -1.89284377 + H 0.81910346 2.32835004 -0.72656094 + 22 +Step 17 + C 2.68428027 -1.08649423 -1.07658991 + C 1.43764723 -0.27868144 -0.75112617 + N 1.08519533 -0.23939519 0.56148774 + C -0.01031015 0.54587042 1.16150592 + C -1.43096499 -0.00151903 0.86895844 + N -1.75019004 -0.13876441 -0.44216906 + C -3.04815983 -0.61836881 -0.87853737 + O 0.80778926 0.29847342 -1.64193616 + C 0.09832240 2.04645209 0.84778740 + O -2.19309694 -0.23708699 1.80258638 + H 2.43759533 -1.81684693 -1.85267184 + H 3.11428148 -1.60798951 -0.21610339 + H 3.43919152 -0.41166148 -1.49301489 + H 1.62727464 -0.80165380 1.20111399 + H 0.09578035 0.40749321 2.23935300 + H -1.03119692 0.08231800 -1.12897404 + H -2.94961330 -1.53114107 -1.47879225 + H -3.56725345 0.13836900 -1.47944033 + H -3.64161887 -0.83639523 0.01057400 + H -0.71006138 2.58100721 1.35732517 + H 0.02781624 2.23620201 -0.22458996 + H 1.05472179 2.43957276 1.20942233 diff --git a/TEST/alanineDipeptideIsomerization/qchem/de-gsm/scratch/paragsm0001 b/TEST/alanineDipeptideIsomerization/qchem/de-gsm/scratch/paragsm0001 new file mode 100644 index 0000000..0f94f7b --- /dev/null +++ b/TEST/alanineDipeptideIsomerization/qchem/de-gsm/scratch/paragsm0001 @@ -0,0 +1,932 @@ + Number of QC processors: 4 +***** Starting Initialization ***** + runend 1 + -structure filename from input: scratch/initial0001.xyz +Initializing Tolerances and Parameters... + -Opening inpfileq + -reading file... + -using GSM + -RESTART: 0 + -MAX_OPT_ITERS: 80 + -STEP_OPT_ITERS: 30 + -CONV_TOL = 0.0005 + -ADD_NODE_TOL = 0.1 + -SCALING = 1 + -SSM_DQMAX: 0.8 + -SSM_DQMIN: 0.2 + -GROWTH_DIRECTION = 0 + -INT_THRESH: 2 + -SSM_MIN_SPACING: 5 + -BOND_FRAGMENTS = 1 + -INITIAL_OPT: 0 + -FINAL_OPT: 150 + -PRODUCT_LIMIT: 100 + -TS_FINAL_TYPE: 1 + -NNODES = 9 + Done reading inpfileq + + reading isomers + WARNING: ignoring BONDS in ISOMERS file because BOND_FRAGMENTS == 0 or 1 + couldn't find ISOMERS file: scratch/ISOMERS0001 +Reading and initializing string coordinates + -Opening structure file + -reading file... + -The number of atoms is: 22 + -Reading the atomic names... -Reading coordinates...Opening xyz file +Finished reading information from structure file + +**************************************** +**************************************** +****** Starting IC-GSM calculation ***** +**************************************** +**************************************** + + skipped Eckart_align + 22 + +C 3.315029 -1.144285 -0.078339 +C 2.273682 -0.082902 0.244004 +N 1.017751 -0.331191 -0.221470 +C -0.096925 0.546207 0.073929 +C -1.378065 -0.290368 -0.081591 +N -2.495396 0.263400 0.460636 +C -3.808423 -0.352698 0.369127 +O 2.551138 0.932072 0.877816 +C -0.120129 1.782712 -0.846264 +O -1.374987 -1.365630 -0.676880 +H 4.129046 -0.681044 -0.644626 +H 2.919187 -1.988928 -0.650707 +H 3.741166 -1.515807 0.858846 +H 0.767114 -1.203875 -0.671799 +H 0.002113 0.888500 1.112144 +H -2.405591 1.139496 0.955411 +H -4.518029 0.305424 -0.145575 +H -4.202680 -0.591354 1.363622 +H -3.696466 -1.275322 -0.201348 +H -0.948026 2.455540 -0.593679 +H -0.227446 1.478937 -1.892844 +H 0.819103 2.328350 -0.726561 + 22 + +C 2.684280 -1.086494 -1.076590 +C 1.437647 -0.278681 -0.751126 +N 1.085195 -0.239395 0.561488 +C -0.010310 0.545870 1.161506 +C -1.430965 -0.001519 0.868958 +N -1.750190 -0.138764 -0.442169 +C -3.048160 -0.618369 -0.878537 +O 0.807789 0.298473 -1.641936 +C 0.098322 2.046452 0.847787 +O -2.193097 -0.237087 1.802586 +H 2.437595 -1.816847 -1.852672 +H 3.114281 -1.607990 -0.216103 +H 3.439192 -0.411661 -1.493015 +H 1.627275 -0.801654 1.201114 +H 0.095780 0.407493 2.239353 +H -1.031197 0.082318 -1.128974 +H -2.949613 -1.531141 -1.478792 +H -3.567253 0.138369 -1.479440 +H -3.641619 -0.836395 0.010574 +H -0.710061 2.581007 1.357325 +H 0.027816 2.236202 -0.224590 +H 1.054722 2.439573 1.209422 + + NOTICES + Not using Davidson + Not using close dist add + Not using ONE_SKIP + Using HESS_TANG + END NOTICES + + isOpt: 1 + in make_frags() + merging: + atom[0] frag: 0 + atom[1] frag: 0 + atom[2] frag: 0 + atom[3] frag: 0 + atom[4] frag: 0 + atom[5] frag: 0 + atom[6] frag: 0 + atom[7] frag: 0 + atom[8] frag: 0 + atom[9] frag: 0 + atom[10] frag: 0 + atom[11] frag: 0 + atom[12] frag: 0 + atom[13] frag: 0 + atom[14] frag: 0 + atom[15] frag: 0 + atom[16] frag: 0 + atom[17] frag: 0 + atom[18] frag: 0 + atom[19] frag: 0 + atom[20] frag: 0 + atom[21] frag: 0 + nfrags: 1 + in bond_frags() + linear ties complete + isOpt: 1 + in make_frags() + merging: + atom[0] frag: 0 + atom[1] frag: 0 + atom[2] frag: 0 + atom[3] frag: 0 + atom[4] frag: 0 + atom[5] frag: 0 + atom[6] frag: 0 + atom[7] frag: 0 + atom[8] frag: 0 + atom[9] frag: 0 + atom[10] frag: 0 + atom[11] frag: 0 + atom[12] frag: 0 + atom[13] frag: 0 + atom[14] frag: 0 + atom[15] frag: 0 + atom[16] frag: 0 + atom[17] frag: 0 + atom[18] frag: 0 + atom[19] frag: 0 + atom[20] frag: 0 + atom[21] frag: 0 + nfrags: 1 + in bond_frags() + linear ties complete + + setting SSM bonds + nbonds: 21 nangles: 36 ntor: 41 + printing ic1 ic's + + printing internals + number of bonds: 21 + bond 1: 2 to 1: 1.52 + bond 2: 3 to 2: 1.36 + bond 3: 4 to 3: 1.45 + bond 4: 5 to 4: 1.54 + bond 5: 6 to 5: 1.36 + bond 6: 7 to 6: 1.45 + bond 7: 8 to 2: 1.23 + bond 8: 9 to 4: 1.54 + bond 9: 10 to 5: 1.23 + bond 10: 11 to 1: 1.09 + bond 11: 12 to 1: 1.09 + bond 12: 13 to 1: 1.09 + bond 13: 14 to 3: 1.01 + bond 14: 15 to 4: 1.10 + bond 15: 16 to 6: 1.01 + bond 16: 17 to 7: 1.10 + bond 17: 18 to 7: 1.10 + bond 18: 19 to 7: 1.09 + bond 19: 20 to 9: 1.10 + bond 20: 21 to 9: 1.10 + bond 21: 22 to 9: 1.09 + + number of angles: 36 + angle 1: 3 2 1: 115.6 + angle 2: 4 3 2: 122.0 + angle 3: 5 4 3: 106.9 + angle 4: 6 5 4: 115.0 + angle 5: 7 6 5: 123.0 + angle 6: 8 2 1: 122.1 + angle 7: 8 2 3: 122.4 + angle 8: 9 4 3: 112.1 + angle 9: 9 4 5: 111.3 + angle 10: 10 5 4: 121.5 + angle 11: 10 5 6: 123.5 + angle 12: 11 1 2: 108.9 + angle 13: 12 1 2: 113.7 + angle 14: 12 1 11: 109.0 + angle 15: 13 1 2: 108.8 + angle 16: 13 1 11: 107.3 + angle 17: 13 1 12: 109.1 + angle 18: 14 3 2: 122.5 + angle 19: 14 3 4: 114.9 + angle 20: 15 4 3: 108.2 + angle 21: 15 4 5: 109.9 + angle 22: 15 4 9: 108.4 + angle 23: 16 6 5: 118.4 + angle 24: 16 6 7: 118.6 + angle 25: 17 7 6: 111.1 + angle 26: 18 7 6: 111.1 + angle 27: 18 7 17: 108.9 + angle 28: 19 7 6: 107.4 + angle 29: 19 7 17: 109.2 + angle 30: 19 7 18: 109.1 + angle 31: 20 9 4: 111.5 + angle 32: 21 9 4: 110.5 + angle 33: 21 9 20: 108.4 + angle 34: 22 9 4: 108.8 + angle 35: 22 9 20: 108.5 + angle 36: 22 9 21: 109.1 + + number of torsions: 41 + torsion 1: 4 3 2 1: 176.2 + torsion 2: 5 4 3 2: -157.1 + torsion 3: 6 5 4 3: 164.9 + torsion 4: 7 6 5 4: 177.6 + torsion 5: 8 2 3 4: -4.0 + torsion 6: 9 4 3 2: 80.7 + torsion 7: 9 4 5 6: -72.5 + torsion 8: 10 5 4 3: -16.4 + torsion 9: 10 5 4 9: 106.3 + torsion 10: 10 5 6 7: -1.1 + torsion 11: 11 1 2 3: 121.5 + torsion 12: 11 1 2 8: -58.2 + torsion 13: 12 1 2 3: -0.1 + torsion 14: 12 1 2 8: -179.9 + torsion 15: 13 1 2 3: -121.9 + torsion 16: 13 1 2 8: 58.4 + torsion 17: 14 3 2 1: 5.9 + torsion 18: 14 3 2 8: -174.4 + torsion 19: 14 3 4 5: 13.9 + torsion 20: 14 3 4 9: -108.3 + torsion 21: 15 4 3 2: -38.8 + torsion 22: 15 4 3 14: 132.3 + torsion 23: 15 4 5 6: 47.7 + torsion 24: 15 4 5 10: -133.6 + torsion 25: 16 6 5 4: -2.9 + torsion 26: 16 6 5 10: 178.4 + torsion 27: 17 7 6 5: -120.2 + torsion 28: 17 7 6 16: 60.3 + torsion 29: 18 7 6 5: 118.4 + torsion 30: 18 7 6 16: -61.1 + torsion 31: 19 7 6 5: -0.8 + torsion 32: 19 7 6 16: 179.7 + torsion 33: 20 9 4 3: -178.2 + torsion 34: 20 9 4 5: 62.2 + torsion 35: 20 9 4 15: -58.8 + torsion 36: 21 9 4 3: 61.2 + torsion 37: 21 9 4 5: -58.5 + torsion 38: 21 9 4 15: -179.5 + torsion 39: 22 9 4 3: -58.6 + torsion 40: 22 9 4 5: -178.2 + torsion 41: 22 9 4 15: 60.8 + + number of improper torsions: 4 + imptor 1: 3 8 2 1: 179.7 + imptor 2: 4 10 5 6: 178.6 + imptor 3: 4 14 3 2: 171.0 + imptor 4: 5 16 6 7: 179.5 + + number of nonbonds: 174 + + printing ic2 ic's + + printing internals + number of bonds: 21 + bond 1: 2 to 1: 1.52 + bond 2: 3 to 2: 1.36 + bond 3: 4 to 3: 1.48 + bond 4: 5 to 4: 1.55 + bond 5: 6 to 5: 1.36 + bond 6: 7 to 6: 1.45 + bond 7: 8 to 2: 1.23 + bond 8: 9 to 4: 1.54 + bond 9: 10 to 5: 1.23 + bond 10: 11 to 1: 1.09 + bond 11: 12 to 1: 1.09 + bond 12: 13 to 1: 1.09 + bond 13: 14 to 3: 1.01 + bond 14: 15 to 4: 1.09 + bond 15: 16 to 6: 1.02 + bond 16: 17 to 7: 1.10 + bond 17: 18 to 7: 1.10 + bond 18: 19 to 7: 1.09 + bond 19: 20 to 9: 1.09 + bond 20: 21 to 9: 1.09 + bond 21: 22 to 9: 1.10 + + number of angles: 36 + angle 1: 3 2 1: 115.8 + angle 2: 4 3 2: 126.9 + angle 3: 5 4 3: 114.6 + angle 4: 6 5 4: 115.7 + angle 5: 7 6 5: 122.3 + angle 6: 8 2 1: 120.8 + angle 7: 8 2 3: 123.4 + angle 8: 9 4 3: 112.6 + angle 9: 9 4 5: 111.8 + angle 10: 10 5 4: 119.5 + angle 11: 10 5 6: 124.7 + angle 12: 11 1 2: 108.8 + angle 13: 12 1 2: 114.0 + angle 14: 12 1 11: 109.2 + angle 15: 13 1 2: 108.6 + angle 16: 13 1 11: 107.3 + angle 17: 13 1 12: 108.8 + angle 18: 14 3 2: 117.2 + angle 19: 14 3 4: 115.9 + angle 20: 15 4 3: 105.2 + angle 21: 15 4 5: 103.3 + angle 22: 15 4 9: 108.6 + angle 23: 16 6 5: 117.6 + angle 24: 16 6 7: 120.0 + angle 25: 17 7 6: 111.1 + angle 26: 18 7 6: 111.1 + angle 27: 18 7 17: 108.5 + angle 28: 19 7 6: 107.9 + angle 29: 19 7 17: 109.2 + angle 30: 19 7 18: 109.1 + angle 31: 20 9 4: 109.2 + angle 32: 21 9 4: 111.5 + angle 33: 21 9 20: 108.9 + angle 34: 22 9 4: 110.2 + angle 35: 22 9 20: 108.4 + angle 36: 22 9 21: 108.6 + + number of torsions: 41 + torsion 1: 4 3 2 1: 175.1 + torsion 2: 5 4 3 2: 73.7 + torsion 3: 6 5 4 3: -56.5 + torsion 4: 7 6 5 4: -179.0 + torsion 5: 8 2 3 4: -4.7 + torsion 6: 9 4 3 2: -55.5 + torsion 7: 9 4 5 6: 73.1 + torsion 8: 10 5 4 3: 125.8 + torsion 9: 10 5 4 9: -104.6 + torsion 10: 10 5 6 7: -1.4 + torsion 11: 11 1 2 3: 126.4 + torsion 12: 11 1 2 8: -53.9 + torsion 13: 12 1 2 3: 4.3 + torsion 14: 12 1 2 8: -175.9 + torsion 15: 13 1 2 3: -117.1 + torsion 16: 13 1 2 8: 62.6 + torsion 17: 14 3 2 1: -4.7 + torsion 18: 14 3 2 8: 175.6 + torsion 19: 14 3 4 5: -106.6 + torsion 20: 14 3 4 9: 124.2 + torsion 21: 15 4 3 2: -173.6 + torsion 22: 15 4 3 14: 6.2 + torsion 23: 15 4 5 6: -170.3 + torsion 24: 15 4 5 10: 12.0 + torsion 25: 16 6 5 4: 2.8 + torsion 26: 16 6 5 10: -179.7 + torsion 27: 17 7 6 5: -120.5 + torsion 28: 17 7 6 16: 57.7 + torsion 29: 18 7 6 5: 118.7 + torsion 30: 18 7 6 16: -63.1 + torsion 31: 19 7 6 5: -0.8 + torsion 32: 19 7 6 16: 177.3 + torsion 33: 20 9 4 3: -177.3 + torsion 34: 20 9 4 5: 52.1 + torsion 35: 20 9 4 15: -61.2 + torsion 36: 21 9 4 3: 62.3 + torsion 37: 21 9 4 5: -68.3 + torsion 38: 21 9 4 15: 178.3 + torsion 39: 22 9 4 3: -58.3 + torsion 40: 22 9 4 5: 171.1 + torsion 41: 22 9 4 15: 57.7 + + number of improper torsions: 4 + imptor 1: 1 8 2 3: 179.7 + imptor 2: 6 10 5 4: 177.5 + imptor 3: 4 14 3 2: 179.8 + imptor 4: 7 16 6 5: 178.3 + + number of nonbonds: 174 + + ic1.nbonds: 21 ic2.nbonds: 21 + saving bond union: 21 saving angle union: 36 saving torsion union: 41 total number of coordinates: 98 + + + actual IC's + + printing internals + number of bonds: 21 + bond 1: 2 to 1: 1.52 + bond 2: 3 to 2: 1.36 + bond 3: 4 to 3: 1.45 + bond 4: 5 to 4: 1.54 + bond 5: 6 to 5: 1.36 + bond 6: 7 to 6: 1.45 + bond 7: 8 to 2: 1.23 + bond 8: 9 to 4: 1.54 + bond 9: 10 to 5: 1.23 + bond 10: 11 to 1: 1.09 + bond 11: 12 to 1: 1.09 + bond 12: 13 to 1: 1.09 + bond 13: 14 to 3: 1.01 + bond 14: 15 to 4: 1.10 + bond 15: 16 to 6: 1.01 + bond 16: 17 to 7: 1.10 + bond 17: 18 to 7: 1.10 + bond 18: 19 to 7: 1.09 + bond 19: 20 to 9: 1.10 + bond 20: 21 to 9: 1.10 + bond 21: 22 to 9: 1.09 + + number of angles: 36 + angle 1: 3 2 1: 115.6 + angle 2: 4 3 2: 122.0 + angle 3: 5 4 3: 106.9 + angle 4: 6 5 4: 115.0 + angle 5: 7 6 5: 123.0 + angle 6: 8 2 1: 122.1 + angle 7: 8 2 3: 122.4 + angle 8: 9 4 3: 112.1 + angle 9: 9 4 5: 111.3 + angle 10: 10 5 4: 121.5 + angle 11: 10 5 6: 123.5 + angle 12: 11 1 2: 108.9 + angle 13: 12 1 2: 113.7 + angle 14: 12 1 11: 109.0 + angle 15: 13 1 2: 108.8 + angle 16: 13 1 11: 107.3 + angle 17: 13 1 12: 109.1 + angle 18: 14 3 2: 122.5 + angle 19: 14 3 4: 114.9 + angle 20: 15 4 3: 108.2 + angle 21: 15 4 5: 109.9 + angle 22: 15 4 9: 108.4 + angle 23: 16 6 5: 118.4 + angle 24: 16 6 7: 118.6 + angle 25: 17 7 6: 111.1 + angle 26: 18 7 6: 111.1 + angle 27: 18 7 17: 108.9 + angle 28: 19 7 6: 107.4 + angle 29: 19 7 17: 109.2 + angle 30: 19 7 18: 109.1 + angle 31: 20 9 4: 111.5 + angle 32: 21 9 4: 110.5 + angle 33: 21 9 20: 108.4 + angle 34: 22 9 4: 108.8 + angle 35: 22 9 20: 108.5 + angle 36: 22 9 21: 109.1 + + number of torsions: 41 + torsion 1: 4 3 2 1: 176.2 + torsion 2: 5 4 3 2: -157.1 + torsion 3: 6 5 4 3: 164.9 + torsion 4: 7 6 5 4: 177.6 + torsion 5: 8 2 3 4: -4.0 + torsion 6: 9 4 3 2: 80.7 + torsion 7: 9 4 5 6: -72.5 + torsion 8: 10 5 4 3: -16.4 + torsion 9: 10 5 4 9: 106.3 + torsion 10: 10 5 6 7: -1.1 + torsion 11: 11 1 2 3: 121.5 + torsion 12: 11 1 2 8: -58.2 + torsion 13: 12 1 2 3: -0.1 + torsion 14: 12 1 2 8: -179.9 + torsion 15: 13 1 2 3: -121.9 + torsion 16: 13 1 2 8: 58.4 + torsion 17: 14 3 2 1: 5.9 + torsion 18: 14 3 2 8: -174.4 + torsion 19: 14 3 4 5: 13.9 + torsion 20: 14 3 4 9: -108.3 + torsion 21: 15 4 3 2: -38.8 + torsion 22: 15 4 3 14: 132.3 + torsion 23: 15 4 5 6: 47.7 + torsion 24: 15 4 5 10: -133.6 + torsion 25: 16 6 5 4: -2.9 + torsion 26: 16 6 5 10: 178.4 + torsion 27: 17 7 6 5: -120.2 + torsion 28: 17 7 6 16: 60.3 + torsion 29: 18 7 6 5: 118.4 + torsion 30: 18 7 6 16: -61.1 + torsion 31: 19 7 6 5: -0.8 + torsion 32: 19 7 6 16: 179.7 + torsion 33: 20 9 4 3: -178.2 + torsion 34: 20 9 4 5: 62.2 + torsion 35: 20 9 4 15: -58.8 + torsion 36: 21 9 4 3: 61.2 + torsion 37: 21 9 4 5: -58.5 + torsion 38: 21 9 4 15: -179.5 + torsion 39: 22 9 4 3: -58.6 + torsion 40: 22 9 4 5: -178.2 + torsion 41: 22 9 4 15: 60.8 + + number of improper torsions: 0 + + number of nonbonds: 0 + + + ic1.nbonds: 21 ic2.nbonds: 21 + saving bond union: 21 saving angle union: 36 saving torsion union: 41 total number of coordinates: 98 + + Number of OpenMP threads: 1 + + + ---- Now preparing gradients ---- + Q-Chem initialized + -run name set to: GSM_go1q0001.001 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.000 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.001 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.002 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.003 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.004 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.005 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.006 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.007 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.008 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.009 + grad initiated: Q-Chem mode + ---- Done preparing gradients ---- + + + + Begin Growing the String + creating R node: 1 iR,iP: 0 8 wR,wP: 1 -1 iN: 1 bdist: 0.000 + dqmag: 8.28 dq0[constraint]: -1.18 + creating P node: 7 iR,iP: 1 8 wR,wP: -1 7 iN: 7 bdist: 0.000 + dqmag: 7.10 dq0[constraint]: -1.18 + nnR: 2 nnP: 2 + rpart: 0.50 0.00 0.00 0.00 0.00 0.00 0.50 0.00 + spacings (end ic_reparam, steps: 4): 1.09 2.43 0.00 0.00 0.00 0.00 0.00 2.43 1.09 disprms: 0.000 + eg eg setting V0 to: -311147.7 (-495.85286790 au) + + at beginning, starting V's are 0.000000 1.185552 + + growing iter: 1 + rpart: 0.50 0.00 0.00 0.00 0.00 0.00 0.50 0.00 + spacings (end ic_reparam, steps: 4): 1.09 2.43 0.00 0.00 0.00 0.00 0.00 2.43 1.09 disprms: 0.000 + + eg eg eg eg + + Opt step: 1 gqc: 0.005 ss: 0.030 (DMAX: 0.100) predE: -0.28 E(M): 1.48 gRMS: 0.0026 ratio: 0.899 + Opt step: 2 gqc: 0.004 ss: 0.025 (DMAX: 0.100) predE: -0.14 E(M): 1.23 gRMS: 0.0016 + + Opt step: 1 gqc: 0.009 ss: 0.053 (DMAX: 0.100) predE: -0.74 E(M): 5.40 gRMS: 0.0043 ratio: 0.840 + Opt step: 2 gqc: 0.008 ss: 0.046 (DMAX: 0.100) predE: -0.35 E(M): 4.78 gRMS: 0.0024 + + gopt_iter: 1 totalgrad: 0.031 gradrms: 0.0020 tgrads: 6 max E: 4.8 + printing string to scratch/stringfile.xyz0001g1 + + growing iter: 2 + adding node: 2 between 1 7 + iR,iP: 1 7 iN: 2 dqmag: 1.00 dq0[constraint]: -0.20 + initial Hint ev: 0.035 0.035 0.035 0.035 + adding node: 6 between 7 2 + iR,iP: 7 2 iN: 6 dqmag: 1.00 dq0[constraint]: -0.25 + initial Hint ev: 0.035 0.035 0.035 0.035 + rpart: 0.25 0.25 0.00 0.00 0.00 0.25 0.25 0.00 + spacings (end ic_reparam, steps: 4): 1.09 0.91 2.06 0.00 0.00 0.00 2.06 0.91 1.09 disprms: 0.177 + + eg eg eg eg eg eg eg eg + + Opt step: 1 gqc: 0.004 ss: 0.019 (DMAX: 0.100) predE: -0.07 E(M): 1.10 gRMS: 0.0012 ratio: 0.965 + Opt step: 2 gqc: 0.003 ss: 0.022 (DMAX: 0.100) predE: -0.06 E(M): 1.03 gRMS: 0.0008 + + Opt step: 1 gqc: 0.007 ss: 0.057 (DMAX: 0.100) predE: -1.13 E(M): 4.37 gRMS: 0.0055 ratio: 0.808 + Opt step: 2 gqc: 0.006 ss: 0.032 (DMAX: 0.100) predE: -0.29 E(M): 3.45 gRMS: 0.0027 + + Opt step: 1 gqc: 0.007 ss: 0.064 (DMAX: 0.100) predE: -1.62 E(M): 9.06 gRMS: 0.0069 ratio: 0.703 + Opt step: 2 gqc: 0.005 ss: 0.038 (DMAX: 0.100) predE: -0.40 E(M): 7.92 gRMS: 0.0029 + + Opt step: 1 gqc: 0.008 ss: 0.038 (DMAX: 0.100) predE: -0.22 E(M): 4.45 gRMS: 0.0021 ratio: 0.996 + Opt step: 2 gqc: 0.008 ss: 0.046 (DMAX: 0.100) predE: -0.21 E(M): 4.22 gRMS: 0.0017 + + gopt_iter: 2 totalgrad: 0.063 gradrms: 0.0022 tgrads: 14 max E: 7.9 + printing string to scratch/stringfile.xyz0001g1 + + growing iter: 3 + adding node: 3 between 2 6 + iR,iP: 2 6 iN: 3 dqmag: 1.00 dq0[constraint]: -0.33 + initial Hint ev: 0.035 0.035 0.035 0.035 + adding node: 5 between 6 3 + iR,iP: 6 3 iN: 5 dqmag: 1.00 dq0[constraint]: -0.50 + initial Hint ev: 0.035 0.035 0.035 0.035 + rpart: 0.17 0.17 0.17 0.00 0.17 0.17 0.17 0.00 + spacings (end ic_reparam, steps: 4): 1.09 0.97 0.93 1.52 0.00 1.52 0.93 0.97 1.09 disprms: 0.166 + + eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 gqc: 0.003 ss: 0.019 (DMAX: 0.100) predE: -0.04 E(M): 0.97 gRMS: 0.0006 ratio: 1.001 + Opt step: 2 gqc: 0.003 ss: 0.025 (DMAX: 0.100) predE: -0.03 E(M): 0.94 gRMS: 0.0005 * + + Opt step: 1 gqc: 0.005 ss: 0.025 (DMAX: 0.100) predE: -0.14 E(M): 3.36 gRMS: 0.0025 ratio: 0.997 + Opt step: 2 gqc: 0.005 ss: 0.030 (DMAX: 0.100) predE: -0.13 E(M): 3.22 gRMS: 0.0022 + + Opt step: 1 gqc: 0.005 ss: 0.060 (DMAX: 0.100) predE: -1.54 E(M): 6.60 gRMS: 0.0067 ratio: 0.732 + Opt step: 2 gqc: 0.004 ss: 0.032 (DMAX: 0.100) predE: -0.33 E(M): 5.47 gRMS: 0.0028 + + Opt step: 1 gqc: 0.002 ss: 0.048 (DMAX: 0.100) predE: -1.07 E(M): 9.32 gRMS: 0.0057 ratio: 0.747 + Opt step: 2 gqc: 0.001 ss: 0.034 (DMAX: 0.100) predE: -0.38 E(M): 8.52 gRMS: 0.0029 + + Opt step: 1 gqc: 0.004 ss: 0.029 (DMAX: 0.100) predE: -0.20 E(M): 7.73 gRMS: 0.0027 ratio: 0.866 + Opt step: 2 gqc: 0.004 ss: 0.035 (DMAX: 0.100) predE: -0.17 E(M): 7.56 gRMS: 0.0021 + + Opt step: 1 gqc: 0.007 ss: 0.038 (DMAX: 0.100) predE: -0.15 E(M): 4.01 gRMS: 0.0018 ratio: 0.968 + Opt step: 2 gqc: 0.007 ss: 0.057 (DMAX: 0.100) predE: -0.17 E(M): 3.86 gRMS: 0.0013 + + gopt_iter: 3 totalgrad: 0.092 gradrms: 0.0022 tgrads: 26 max E: 8.5 + printing string to scratch/stringfile.xyz0001g1 + + growing iter: 4 + adding node: 4 between 3 5 + iR,iP: 3 5 iN: 4 dqmag: 1.00 dq0[constraint]: -0.50 + initial Hint ev: 0.035 0.035 0.035 0.035 + gopt_iter: string done growing + writing grown string scratch/stringfile.xyz0001g + Warning: last added node(s) do not have energies yet + + initial ic_reparam + TSn: 0 rpart: 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.12 + disp[1]: -0.08 disp[2]: -0.06 disp[3]: -0.00 disp[4]: 0.30 disp[5]: 0.02 disp[6]: 0.07 disp[7]: 0.19 + disp[1]: -0.04 disp[2]: -0.01 disp[3]: 0.02 disp[4]: 0.14 disp[5]: -0.02 disp[6]: 0.02 disp[7]: -0.00 + disp[1]: -0.02 disp[2]: -0.00 disp[3]: 0.02 disp[4]: 0.08 disp[5]: -0.01 disp[6]: 0.01 disp[7]: -0.01 + disp[1]: -0.01 disp[2]: -0.00 disp[3]: 0.01 disp[4]: 0.04 disp[5]: -0.01 disp[6]: 0.00 disp[7]: -0.00 + disp[1]: -0.00 disp[2]: -0.00 disp[3]: 0.01 disp[4]: 0.02 disp[5]: -0.01 disp[6]: 0.00 disp[7]: -0.00 + disp[1]: -0.00 disp[2]: -0.00 disp[3]: 0.00 disp[4]: 0.01 disp[5]: -0.00 disp[6]: 0.00 disp[7]: -0.00 + spacings (end ic_reparam, steps: 25): 1.02 1.02 1.02 1.01 1.04 1.02 1.02 1.02 disprms: 0.013 + + + Starting String opt + V_profile: 0.0 0.9 3.2 5.5 0.0 8.5 7.6 3.9 1.2 + 3 way tangent (3): f1: 0.29 + 3 way tangent (4): f1: 0.61 + 3 way tangent (5): f1: 0.90 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 10 (0.69) ss: 0.019 (DMAX: 0.100) predE: -0.03 E(M): 0.70 gRMS: 0.0007 ratio: 0.007 + Opt step: 2 gqc: 0.002 ss: 0.040 (DMAX: 0.100) predE: -0.10 E(M): 0.70 gRMS: 0.0018 ratio: -1.305 dE>0, decreasing DMAX + Opt step: 3 gqc: 0.002 ss: 0.037 (DMAX: 0.027) predE: -0.16 E(M): 0.84 gRMS: 0.0053 +r + Opt step: 1 t/ol: 10 (0.93) ss: 0.032 (0.100) predE: -0.11 Hint ev: 0.032 0.035 E(M): 2.90 gRMS: 0.0018 ratio: 1.028 + Opt step: 2 t/ol: 10 (0.92) ss: 0.046 (0.100) predE: -0.13 Hint ev: 0.032 0.035 E(M): 2.79 gRMS: 0.0015 ratio: 0.960 + Opt step: 3 t/ol: 10 (0.92) ss: 0.092 (0.100) predE: -0.20 Hint ev: 0.030 0.034 E(M): 2.67 gRMS: 0.0019 + + Opt step: 1 t/ol: 10 (0.87) ss: 0.027 (0.100) predE: -0.15 Hint ev: 0.033 0.035 E(M): 5.33 gRMS: 0.0025 ratio: 0.929 + Opt step: 2 t/ol: 10 (0.84) ss: 0.034 (0.100) predE: -0.14 Hint ev: 0.033 0.035 E(M): 5.19 gRMS: 0.0021 ratio: 0.957 + Opt step: 3 t/ol: 10 (0.77) ss: 0.048 (0.100) predE: -0.15 Hint ev: 0.032 0.035 E(M): 5.06 gRMS: 0.0022 + + Opt step: 1 t/ol: 1 (0.67) ss: 0.031 (DMAX: 0.100) predE: -0.47 E(M): 7.54 gRMS: 0.0039 ratio: 0.755 + Opt step: 2 gqc: 0.002 ss: 0.024 (DMAX: 0.100) predE: -0.20 E(M): 7.18 gRMS: 0.0022 ratio: 0.754 + Opt step: 3 gqc: 0.002 ss: 0.019 (DMAX: 0.100) predE: -0.10 E(M): 7.03 gRMS: 0.0019 + + Opt step: 1 t/ol: 10 (0.69) ss: 0.023 (DMAX: 0.100) predE: -0.17 E(M): 8.23 gRMS: 0.0029 ratio: 0.820 + Opt step: 2 gqc: 0.000 ss: 0.027 (DMAX: 0.100) predE: -0.13 E(M): 8.09 gRMS: 0.0020 ratio: 0.910 + Opt step: 3 gqc: 0.000 ss: 0.032 (DMAX: 0.100) predE: -0.10 E(M): 7.98 gRMS: 0.0022 + + Opt step: 1 t/ol: 10 (0.91) ss: 0.037 (0.100) predE: -0.14 Hint ev: 0.033 0.035 E(M): 7.18 gRMS: 0.0023 ratio: 1.035 + Opt step: 2 t/ol: 9 (0.72) ss: 0.044 (DMAX: 0.100) predE: -0.11 E(M): 7.04 gRMS: 0.0015 ratio: 0.623 + Opt step: 3 gqc: -0.004 ss: 0.082 (DMAX: 0.100) predE: -0.13 E(M): 6.97 gRMS: 0.0016 + + Opt step: 1 t/ol: 10 (0.78) ss: 0.077 (0.100) predE: -0.29 Hint ev: 0.030 0.035 E(M): 3.10 gRMS: 0.0018 ratio: 0.995 + Opt step: 2 t/ol: 10 (0.61) ss: 0.091 (DMAX: 0.100) predE: -0.17 E(M): 2.81 gRMS: 0.0014 ratio: -0.184 dE>0, decreasing DMAX + Opt step: 3 gqc: -0.006 ss: 0.081 (DMAX: 0.061) predE: -0.20 E(M): 2.84 gRMS: 0.0033 +r + opt_iter: 4 totalgrad: 0.091 gradrms: 0.0017 tgrads: 47 ol(0): 0.00 max E: 8.0 + in find_peaks (2) + V_profile: 0.0 0.7 2.7 5.1 7.0 8.0 7.0 2.8 1.2 + min nodes: max nodes: 5 + found 1 significant peak(s). TOL: 0.50 + ** starting climb ** + printing string to stringfile.xyz0001 + V_profile: 0.0 0.7 2.7 5.1 7.0 8.0 7.0 2.8 1.2 + TSn: 5 rpart: 0.20 0.20 0.20 0.20 0.00 0.33 0.33 0.33 + disp[1]: 0.00 disp[2]: 0.01 disp[3]: 0.02 disp[4]: 0.01 disp[5]: 0.00 disp[6]: 0.02 disp[7]: -0.03 + disp[1]: 0.00 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.01 disp[5]: 0.00 disp[6]: 0.01 disp[7]: -0.00 + disp[1]: 0.00 disp[2]: 0.00 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.00 disp[6]: 0.01 disp[7]: -0.00 + spacings (end ic_reparam, steps: 5): 1.02 1.02 1.02 1.03 1.03 1.02 1.03 1.02 disprms: 0.012 + V_profile: 0.0 0.7 2.7 5.1 7.0 8.0 7.0 2.8 1.2 + 3 way tangent (5): f1: 0.49 + + slowing down climb optimization + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 10 (0.70) ss: 0.046 (DMAX: 0.020) predE: -0.02 E(M): 0.70 gRMS: 0.0007 * + + Opt step: 1 t/ol: 10 (0.90) ss: 0.098 (0.100) predE: -1.04 Hint ev: 0.030 0.034 E(M): 2.70 gRMS: 0.0057 ratio: -2.016 dE>0, decreasing DMAX + Opt step: 2 t/ol: 10 (0.89) ss: 0.133 (0.066) predE: -1.76 Hint ev: 0.029 0.034 E(M): 4.80 gRMS: 0.0175 ratio: 1.030 + Opt step: 3 t/ol: 10 (0.89) ss: 0.071 (0.066) predE: -1.05 Hint ev: 0.024 0.034 E(M): 2.99 gRMS: 0.0098 +S + Opt step: 1 t/ol: 10 (0.74) ss: 0.029 (DMAX: 0.100) predE: -0.10 E(M): 4.99 gRMS: 0.0019 ratio: 0.439 + Opt step: 2 gqc: 0.004 ss: 0.053 (DMAX: 0.100) predE: -0.12 E(M): 4.95 gRMS: 0.0025 ratio: 0.494 + Opt step: 3 gqc: 0.004 ss: 0.053 (DMAX: 0.100) predE: -0.11 E(M): 4.89 gRMS: 0.0029 +S + Opt step: 1 t/ol: 7 (0.65) ss: 0.014 (DMAX: 0.100) predE: -0.04 E(M): 6.97 gRMS: 0.0011 ratio: 0.933 + Opt step: 2 gqc: 0.002 ss: 0.017 (DMAX: 0.100) predE: -0.03 E(M): 6.93 gRMS: 0.0007 * + + Opt step: 1 gqc: 0.000 ss: 0.029 (DMAX: 0.050) gts: 0.0001 predE: -0.06 E(M): 7.88 gRMS: 0.0012 ratio: 1.068 + Opt step: 2 gqc: 0.000 ss: 0.054 (DMAX: 0.050) gts: 0.0001 predE: -0.06 E(M): 7.81 gRMS: 0.0012 ratio: 1.347 + Opt step: 3 gqc: 0.000 ss: 0.056 (DMAX: 0.050) gts: 0.0001 predE: -0.06 E(M): 7.73 gRMS: 0.0009 * + + Opt step: 1 t/ol: 1 (0.88) ss: 0.098 (0.100) predE: -0.30 Hint ev: 0.030 0.034 E(M): 6.79 gRMS: 0.0021 ratio: -1.850 dE>0, decreasing DMAX + Opt step: 2 t/ol: 2 (0.89) ss: 0.164 (0.066) predE: -0.60 Hint ev: 0.022 0.033 E(M): 7.34 gRMS: 0.0103 ratio: 0.997 + Opt step: 3 t/ol: 2 (0.88) ss: 0.102 (0.066) predE: -0.42 Hint ev: 0.018 0.033 E(M): 6.74 gRMS: 0.0064 +r + Opt step: 1 t/ol: 1 (0.70) ss: 0.081 (DMAX: 0.041) predE: -0.10 E(M): 2.92 gRMS: 0.0014 ratio: 1.023 increasing DMAX + Opt step: 2 gqc: -0.006 ss: 0.078 (DMAX: 0.045) predE: -0.10 E(M): 2.82 gRMS: 0.0011 ratio: 0.908 increasing DMAX + Opt step: 3 gqc: -0.006 ss: 0.079 (DMAX: 0.049) predE: -0.13 E(M): 2.73 gRMS: 0.0014 + +c opt_iter: 5 totalgrad: 0.144 gradrms: 0.0040 tgrads: 65 ol(0): 0.00 max E: 7.7 + in find_peaks (2) + V_profile: 0.0 0.7 3.0 4.9 6.9 7.7 6.8 2.7 1.2 + min nodes: max nodes: 5 + found 1 significant peak(s). TOL: 0.50 + ** starting exact TS search at node 5 ** + totalgrad: 0.1440 gradrms: 0.0009 gts: 0.0001 + TS Hess init'd w/existing Hintp + tHt: 0.035 a: 1.1 b: 1.0 C: -0.003 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.7 3.0 4.9 6.9 7.7 6.8 2.7 1.2 + TSn: 5 rpart: 0.20 0.20 0.20 0.20 0.00 0.33 0.33 0.33 + disp[1]: 0.01 disp[2]: 0.02 disp[3]: 0.00 disp[4]: 0.00 disp[5]: 0.00 disp[6]: 0.01 disp[7]: 0.02 + disp[1]: 0.00 disp[2]: 0.01 disp[3]: 0.00 disp[4]: 0.00 disp[5]: 0.00 disp[6]: 0.01 disp[7]: 0.00 + spacings (end ic_reparam, steps: 5): 1.03 1.03 1.04 1.03 1.03 1.03 1.04 1.03 disprms: 0.012 + V_profile: 0.0 0.7 3.0 4.9 6.9 7.7 6.8 2.7 1.2 + 3 way tangent (5): f1: 0.46 + + eg eg eg eg eg eg TS Hess init'd w/existing Hintp + tHt: 0.035 a: 1.1 b: 1.0 C: -0.003 + eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 10 (0.70) ss: 0.046 (DMAX: 0.020) predE: -0.02 E(M): 0.69 gRMS: 0.0005 * + + Opt step: 1 t/ol: 10 (0.83) ss: 0.337 (0.052) predE: -3.53 Hint ev: 0.024 0.034 E(M): 4.16 gRMS: 0.0178 ratio: 0.518 + Opt step: 2 t/ol: 10 (0.85) ss: 0.096 (0.052) predE: -0.16 Hint ev: 0.024 0.034 E(M): 2.32 gRMS: 0.0017 ratio: 0.481 + Opt step: 3 t/ol: 10 (0.83) ss: 0.088 (0.052) predE: -0.11 Hint ev: 0.022 0.034 E(M): 2.25 gRMS: 0.0018 + + Opt step: 1 t/ol: 1 (0.68) ss: 0.028 (DMAX: 0.043) predE: -0.02 E(M): 4.78 gRMS: 0.0010 * + + Opt step: 1 t/ol: 6 (0.85) ss: 0.018 (0.100) predE: -0.02 Hint ev: 0.035 0.035 E(M): 6.90 gRMS: 0.0005 * + + Opt step: 1 S: 5.0 ol: 1.00 0.00 0.00 0.00 + max ol: 0 (f0) ss: 0.011 (DMAX: 0.050) predE: -0.06 Hint ev: -0.003 0.031 0.035 0.035 ratio: 0.528 decreasing DMAX E(M): 7.66 gRMS: 0.0021 + Opt step: 2 S: 4.0 ol: 0.28 0.96 0.01 0.00 + max ol: 1 (f1) ss: 0.057 (DMAX: 0.010) predE: 0.00 Hint ev: -0.414 -0.000 0.035 0.035 ratio: 0.942 increasing DMAX E(M): 7.66 gRMS: 0.0011 + Opt step: 3 S: 3.0 ol: 0.22 0.97 0.02 0.00 + max ol: 1 (f1) ss: 0.029 (DMAX: 0.011) predE: 0.00 Hint ev: -0.414 -0.007 0.035 0.035 ratio: 1.263 increasing DMAX E(M): 7.66 gRMS: 0.0010 + Opt step: 4 S: 2.0 ol: 0.12 0.99 0.01 0.00 + max ol: 1 (f1) ss: 0.027 (DMAX: 0.013) predE: -0.00 Hint ev: -0.411 -0.005 0.035 0.035 ratio: 0.676 E(M): 7.66 gRMS: 0.0009 + Opt step: 5 S: 1.0 ol: 0.07 0.97 0.01 0.02 + max ol: 1 (f1) ss: 0.007 (DMAX: 0.013) predE: -0.01 Hint ev: -0.404 -0.036 0.035 0.035 ratio: 0.297 E(M): 7.65 gRMS: 0.0006 + Opt step: 6 S: 1.0 ol: 0.18 0.89 0.28 0.02 + max ol: 1 (f1) ss: 0.012 (DMAX: 0.013) predE: -0.03 Hint ev: -0.211 -0.053 0.027 0.035 E(M): 7.65 gRMS: 0.0005 + + Opt step: 1 t/ol: 2 (0.88) ss: 0.165 (0.044) predE: -0.12 Hint ev: 0.018 0.033 E(M): 6.77 gRMS: 0.0021 ratio: 0.983 increasing DMAX + Opt step: 2 t/ol: 2 (0.86) ss: 0.155 (0.048) predE: -0.11 Hint ev: 0.017 0.033 E(M): 6.64 gRMS: 0.0012 ratio: 1.048 increasing DMAX + Opt step: 3 t/ol: 2 (0.86) ss: 0.147 (0.053) predE: -0.10 Hint ev: 0.017 0.033 E(M): 6.53 gRMS: 0.0007 * + + Opt step: 1 t/ol: 1 (0.73) ss: 0.079 (DMAX: 0.049) predE: -0.26 E(M): 2.64 gRMS: 0.0028 ratio: -0.382 dE>0, decreasing DMAX + Opt step: 2 gqc: -0.006 ss: 0.079 (DMAX: 0.033) predE: -0.15 E(M): 2.74 gRMS: 0.0055 ratio: 1.014 + Opt step: 3 gqc: -0.006 ss: 0.069 (DMAX: 0.033) predE: -0.08 E(M): 2.59 gRMS: 0.0036 + +x opt_iter: 6 totalgrad: 0.067 gradrms: 0.0016 tgrads: 86 ol(1): 0.89 max E: 7.7 + in find_peaks (2) + V_profile: 0.0 0.7 2.2 4.8 6.9 7.7 6.5 2.6 1.2 + min nodes: max nodes: 5 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.7 2.2 4.8 6.9 7.7 6.5 2.6 1.2 + TSn: 5 rpart: 0.20 0.20 0.20 0.20 0.00 0.33 0.33 0.33 + disp[1]: 0.01 disp[2]: 0.03 disp[3]: 0.00 disp[4]: 0.01 disp[5]: 0.00 disp[6]: 0.01 disp[7]: 0.04 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.00 disp[4]: 0.01 disp[5]: 0.00 disp[6]: 0.00 disp[7]: 0.00 + spacings (end ic_reparam, steps: 5): 1.03 1.03 1.05 1.03 1.05 1.03 1.03 1.04 disprms: 0.020 + V_profile: 0.0 0.7 2.2 4.8 6.9 7.7 6.5 2.6 1.2 + 3 way tangent (5): f1: 0.40 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 10 (0.69) ss: 0.046 (DMAX: 0.020) predE: -0.02 E(M): 0.68 gRMS: 0.0004 * + + Opt step: 1 t/ol: 10 (0.64) ss: 0.040 (DMAX: 0.052) predE: -0.04 E(M): 2.19 gRMS: 0.0009 * + + Opt step: 1 t/ol: 1 (0.67) ss: 0.054 (DMAX: 0.043) predE: -0.25 E(M): 4.80 gRMS: 0.0022 ratio: -3.319 dE>0, decreasing DMAX + Opt step: 2 gqc: 0.004 ss: 0.042 (DMAX: 0.028) predE: -0.78 E(M): 5.63 gRMS: 0.0123 ratio: 0.973 + Opt step: 3 gqc: 0.004 ss: 0.025 (DMAX: 0.028) predE: -0.15 E(M): 4.87 gRMS: 0.0044 +r + Opt step: 1 t/ol: 6 (0.81) ss: 0.016 (0.100) predE: -0.02 Hint ev: 0.035 0.035 E(M): 6.90 gRMS: 0.0005 * + + Opt step: 1 S: 1.0 ol: 0.87 0.05 0.37 0.03 + max ol: 0 (f0) ss: 0.022 (DMAX: 0.020) predE: -0.04 Hint ev: -0.089 -0.056 0.026 0.035 ratio: 0.408 E(M): 7.63 gRMS: 0.0008 + Opt step: 2 S: 1.0 ol: 0.57 0.65 0.41 0.03 + max ol: 1 (f1) ss: 0.036 (DMAX: 0.020) predE: -0.02 Hint ev: -0.118 -0.080 0.026 0.035 ratio: 0.015 E(M): 7.63 gRMS: 0.0010 + Opt step: 3 S: 1.0 ol: 0.51 0.83 0.10 0.02 + max ol: 1 (f1) ss: 0.128 (DMAX: 0.020) predE: 0.01 Hint ev: -0.146 -0.006 0.029 0.035 ratio: 1.086 increasing DMAX E(M): 7.64 gRMS: 0.0007 + Opt step: 4 S: 1.0 ol: 0.44 0.88 0.05 0.03 + max ol: 1 (f1) ss: 0.035 (DMAX: 0.022) predE: -0.01 Hint ev: -0.144 -0.011 0.030 0.035 ratio: -0.691 E(M): 7.65 gRMS: 0.0008 + Opt step: 5 S: 1.0 ol: 0.95 0.04 0.07 0.05 + max ol: 0 (f0) ss: 0.017 (DMAX: 0.022) predE: -0.02 Hint ev: -0.158 -0.128 0.030 0.035 ratio: 0.863 E(M): 7.63 gRMS: 0.0011 + Opt step: 6 E(M): 7.63 gRMS: 0.0004 * + + Opt step: 1 t/ol: 2 (0.83) ss: 0.140 (0.053) predE: -0.10 Hint ev: 0.017 0.033 E(M): 6.40 gRMS: 0.0006 * + + Opt step: 1 t/ol: 1 (0.73) ss: 0.065 (DMAX: 0.033) predE: -0.05 E(M): 2.41 gRMS: 0.0020 ratio: 1.077 increasing DMAX + Opt step: 2 gqc: -0.005 ss: 0.056 (DMAX: 0.036) predE: -0.03 E(M): 2.36 gRMS: 0.0012 ratio: 1.177 increasing DMAX + Opt step: 3 gqc: -0.005 ss: 0.050 (DMAX: 0.040) predE: -0.03 E(M): 2.32 gRMS: 0.0006 * + +x opt_iter: 7 totalgrad: 0.043 gradrms: 0.0010 tgrads: 102 ol(0): 0.95 max E: 7.6 + in find_peaks (2) + V_profile: 0.0 0.7 2.2 4.8 6.9 7.6 6.4 2.3 1.2 + min nodes: max nodes: 5 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + check_for_reaction wts: 0 wint: 8 isrxn: 0 + + opt_iters over: totalgrad: 0.043 gradrms: 0.0010 tgrads: 102 ol(0): 0.95 max E: 7.6 Erxn: 1.2 nmax: 5 TSnode: 5 -XTS- + + oi: 6 nmax: 5 TSnode0: 5 overlapn: 0 + string E (kcal/mol): 0.0 0.7 2.2 4.8 6.9 7.6 6.4 2.3 1.2 + string E (au): -495.85286790 -495.85179208 -495.84937291 -495.84522060 -495.84187107 -495.84070228 -495.84267114 -495.84917138 -495.85097857 + string E (au) - force*distance: -495.85286790 -495.85179208 -495.84937291 -495.84522060 -495.84187107 -495.84070228 -495.84267114 -495.84917138 -495.85097857 + max E: 7.633926 for node: 5 + + creating 3 lowest eigenvectors + Hint eigenvalues: -0.141 -0.082 0.030 0.035 0.035 + maximum number of iterations: 20 + + Davidson iteration 1 + eg eg eg eg eg eg + mag/DTHRESH: 0.951320 0.000050 lamb/lambp: 0.011 0.000 + mag/DTHRESH: 883.373865 0.000050 lamb/lambp: 0.071 0.000 + mag/DTHRESH: 47.412090 0.000050 lamb/lambp: 0.128 0.000 + + Davidson iteration 2 + eg eg eg eg eg eg + mag/DTHRESH: 0.100300 0.000050 lamb/lambp: 0.010 0.011 + mag/DTHRESH: 150.491353 0.000050 lamb/lambp: 0.045 0.071 + mag/DTHRESH: 683.990985 0.000050 lamb/lambp: 0.098 0.128 + + Davidson iteration 3 + eg eg eg eg eg eg + mag/DTHRESH: 0.193664 0.000050 lamb/lambp: 0.010 0.010 + vector 0 converged + mag/DTHRESH: 3.986337 0.000050 lamb/lambp: 0.025 0.045 + mag/DTHRESH: 107.707542 0.000050 lamb/lambp: 0.077 0.098 + + Davidson iteration 4 + eg eg eg eg + mag/DTHRESH: 1.244779 0.000050 lamb/lambp: 0.005 0.010 + mag/DTHRESH: 0.050858 0.000050 lamb/lambp: 0.010 0.025 + mag/DTHRESH: 1658411.888841 0.000050 lamb/lambp: 0.035 0.077 + + Davidson iteration 5 + eg eg eg eg eg eg + mag/DTHRESH: 0.054534 0.000050 lamb/lambp: 0.001 0.005 + mag/DTHRESH: 0.008234 0.000050 lamb/lambp: 0.010 0.010 + vector 1 converged + mag/DTHRESH: 6.145364 0.000050 lamb/lambp: 0.026 0.035 + + Davidson iteration 6 + eg eg eg eg + mag/DTHRESH: 0.015777 0.000050 lamb/lambp: 0.000 0.001 + mag/DTHRESH: 0.084797 0.000050 lamb/lambp: 0.010 0.010 + vector 1 converged + mag/DTHRESH: 0.212866 0.000050 lamb/lambp: 0.017 0.026 + + Davidson iteration 7 + eg eg eg eg + mag/DTHRESH: 0.010836 0.000050 lamb/lambp: 0.000 0.000 + vector 0 converged + mag/DTHRESH: 0.204703 0.000050 lamb/lambp: 0.006 0.010 + mag/DTHRESH: 0.003792 0.000050 lamb/lambp: 0.010 0.017 + + Davidson iteration 8 + eg eg eg eg + mag/DTHRESH: 0.001533 0.000050 lamb/lambp: -0.000 0.000 + vector 0 converged + mag/DTHRESH: 0.036228 0.000050 lamb/lambp: 0.003 0.006 + mag/DTHRESH: 0.002584 0.000050 lamb/lambp: 0.010 0.010 + vector 2 converged + + Davidson iteration 9 + eg eg + mag/DTHRESH: 0.000368 0.000050 lamb/lambp: -0.000 -0.000 + vector 0 converged + mag/DTHRESH: 0.026228 0.000050 lamb/lambp: 0.003 0.003 + vector 1 converged + mag/DTHRESH: 0.002521 0.000050 lamb/lambp: 0.010 0.010 + vector 2 converged + Davidson converged + + now saving vibrations to stringfile.xyz0001fr + Hessian eigenvalues: -0.000 0.003 0.010 + + Updating Hint with new vectors + updating vector: 1 with curvature: -0.00007 + updating vector: 2 with curvature: 0.00257 + updating vector: 3 with curvature: 0.01014 + + Davidson required 42 gradients + + found 1 negative eigenvalue + creating final string file + + about to write tsq.xyz, tscontinue: 1 endearly: 0 + check_for_reaction wts: 0 wint: 8 isrxn: 0 + E of min node before TS: 0.0 diff --git a/TEST/alanineDipeptideIsomerization/qchem/de-gsm/scratch/stringfile.xyz0001g b/TEST/alanineDipeptideIsomerization/qchem/de-gsm/scratch/stringfile.xyz0001g new file mode 100644 index 0000000..3a51484 --- /dev/null +++ b/TEST/alanineDipeptideIsomerization/qchem/de-gsm/scratch/stringfile.xyz0001g @@ -0,0 +1,216 @@ + 22 + 0.000000 + C 3.315029 -1.144285 -0.078339 + C 2.273682 -0.082902 0.244004 + N 1.017751 -0.331191 -0.221470 + C -0.096925 0.546207 0.073929 + C -1.378065 -0.290368 -0.081591 + N -2.495396 0.263400 0.460636 + C -3.808423 -0.352698 0.369127 + O 2.551138 0.932072 0.877816 + C -0.120129 1.782712 -0.846264 + O -1.374987 -1.365630 -0.676880 + H 4.129046 -0.681044 -0.644626 + H 2.919187 -1.988928 -0.650707 + H 3.741166 -1.515807 0.858846 + H 0.767114 -1.203875 -0.671799 + H 0.002113 0.888500 1.112144 + H -2.405591 1.139496 0.955411 + H -4.518029 0.305424 -0.145575 + H -4.202680 -0.591354 1.363622 + H -3.696466 -1.275322 -0.201348 + H -0.948026 2.455540 -0.593679 + H -0.227446 1.478937 -1.892844 + H 0.819103 2.328350 -0.726561 + 22 + 0.938886 + C 3.289421 -1.109019 -0.306348 + C 2.283004 -0.036613 0.089220 + N 0.975326 -0.375072 -0.086071 + C -0.131502 0.483858 0.293381 + C -1.413209 -0.351047 0.083841 + N -2.583243 0.306837 0.291404 + C -3.881755 -0.328763 0.142081 + O 2.641018 1.051201 0.537895 + C -0.138284 1.809942 -0.489198 + O -1.357679 -1.535671 -0.236405 + H 3.966286 -0.696576 -1.060898 + H 2.830561 -2.021389 -0.699495 + H 3.894755 -1.362617 0.569633 + H 0.702526 -1.311677 -0.362688 + H -0.045592 0.712292 1.367204 + H -2.548678 1.276733 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1.161506 + C -1.430965 -0.001519 0.868958 + N -1.750190 -0.138764 -0.442169 + C -3.048160 -0.618369 -0.878537 + O 0.807789 0.298473 -1.641936 + C 0.098322 2.046452 0.847787 + O -2.193097 -0.237087 1.802586 + H 2.437595 -1.816847 -1.852672 + H 3.114281 -1.607990 -0.216103 + H 3.439192 -0.411661 -1.493015 + H 1.627275 -0.801654 1.201114 + H 0.095780 0.407493 2.239353 + H -1.031197 0.082318 -1.128974 + H -2.949613 -1.531141 -1.478792 + H -3.567253 0.138369 -1.479440 + H -3.641619 -0.836395 0.010574 + H -0.710061 2.581007 1.357325 + H 0.027816 2.236202 -0.224590 + H 1.054722 2.439573 1.209422 diff --git a/TEST/alanineDipeptideIsomerization/qchem/de-gsm/scratch/tsq0001.xyz b/TEST/alanineDipeptideIsomerization/qchem/de-gsm/scratch/tsq0001.xyz new file mode 100644 index 0000000..a1b721c --- /dev/null +++ b/TEST/alanineDipeptideIsomerization/qchem/de-gsm/scratch/tsq0001.xyz @@ -0,0 +1,25 @@ + 22 +-495.840702 -495.852868 -495.850979 +C 2.982354 -1.210447 -0.786149 +C 1.975805 -0.078568 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+def convertToFloat(inList): + for element in inList: + try: + yield float(element) + except ValueError: + yield element + +# subtract two floats and skip if string +def subtractFloat(number1, number2): + try: + return (number1 - number2) + except TypeError: + pass + +def main(): + threshold = 0.001 + try: + # read standard and output files + standard = csv.reader(open('stringfile.standard', 'r'), delimiter=' ') + currentOutput = csv.reader(open('stringfile.xyz0001', 'r'), delimiter=' ') + # error if file does not exist + except IOError: + print("Error: File cannot be found!") + exit(1) + # loop over elements of two files simultaneously + for rowStd, rowOut in zip(standard, currentOutput): + rowStd = filter(None, rowStd) + rowOut = filter(None, rowOut) + for valStd, valOut in zip(list(convertToFloat(rowStd)), list(convertToFloat(rowOut))): + # error if difference larger than threshold + if ((subtractFloat(valStd, valOut)) > threshold): + print ((subtractFloat(valStd, valOut))) + exit(2) + return 0 + +if __name__ == "__main__": + main() diff --git a/TEST/ammoniaBorane/mopac/de-gsm/inpfileq b/TEST/ammoniaBorane/mopac/de-gsm/inpfileq new file mode 100644 index 0000000..d2a54ff --- /dev/null +++ b/TEST/ammoniaBorane/mopac/de-gsm/inpfileq @@ -0,0 +1,26 @@ +# FSM/GSM/SSM inpfileq + +------------- QCHEM Scratch Info ------------------------ +$QCSCRATCH/ # path for scratch dir. end with "/" +GSM_go1q # name of run +--------------------------------------------------------- + +------------ String Info -------------------------------- +SM_TYPE GSM # SSM, FSM or GSM +RESTART 0 # read restart.xyz +MAX_OPT_ITERS 80 # maximum iterations +STEP_OPT_ITERS 30 # for FSM/SSM +CONV_TOL 0.0005 # perp grad +ADD_NODE_TOL 0.1 # for GSM +SCALING 1.0 # for opt steps +SSM_DQMAX 0.8 # add step size +GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 +INT_THRESH 2.0 # intermediate detection +MIN_SPACING 5.0 # node spacing SSM +BOND_FRAGMENTS 1 # make IC's for fragments +INITIAL_OPT 0 # opt steps first node +FINAL_OPT 150 # opt steps last SSM node +PRODUCT_LIMIT 100.0 # kcal/mol +TS_FINAL_TYPE 1 # any/delta bond: 0/1 +NNODES 9 # including endpoints +--------------------------------------------------------- diff --git a/TEST/ammoniaBorane/mopac/de-gsm/scratch/initial0001.xyz b/TEST/ammoniaBorane/mopac/de-gsm/scratch/initial0001.xyz new file mode 100644 index 0000000..e11902e --- /dev/null +++ b/TEST/ammoniaBorane/mopac/de-gsm/scratch/initial0001.xyz @@ -0,0 +1,32 @@ + 14 + + N 1.383770091 -0.954052038 -0.151204418 + B 1.683770235 0.579434831 0.094123862 + B -1.913335463 -0.414385322 0.080253305 + N -1.573330405 0.917724710 -0.082088716 + H 0.362958858 -1.152502256 0.029547531 + H 1.952511500 -1.518899363 0.471861584 + H 1.603727220 -1.200723305 -1.111645175 + H 1.685884747 0.794108260 1.271411505 + H 2.747766790 0.856233208 -0.377519758 + H 0.828804768 1.233683197 -0.444071342 + H -1.033174789 -1.228986125 0.127204910 + H -3.042894590 -0.772202593 0.166197022 + H -2.251075338 1.648451353 -0.119053483 + H -0.592044246 1.235067187 -0.144664561 + 14 + + N 0.776258143 -1.811801030 1.790990171 + B 0.716713960 1.226549327 -0.934956367 + B -1.014127649 0.539764998 -1.284401998 + N -0.301678868 0.653213154 0.099092833 + H 0.134910972 -2.386711679 2.314896494 + H 1.496448836 -1.504069465 2.425932533 + H 1.215582738 -2.403268982 1.101520813 + H 0.869063818 2.408771659 -0.895903859 + H 1.661925807 0.530875691 -1.147253283 + H -0.027246135 1.067121234 -2.073276994 + H -1.912840870 1.304309832 -1.458957446 + H -1.112481269 -0.571146366 -1.707139061 + H -0.046671886 -0.221234397 0.565424944 + H -0.692576571 1.307804790 0.761430894 diff --git a/TEST/ammoniaBorane/mopac/de-gsm/stringfile.standard b/TEST/ammoniaBorane/mopac/de-gsm/stringfile.standard new file mode 100644 index 0000000..9eb73c3 --- /dev/null +++ b/TEST/ammoniaBorane/mopac/de-gsm/stringfile.standard @@ -0,0 +1,144 @@ + 14 + 0.000000 + N 1.383770 -0.954052 -0.151204 + B 1.683770 0.579435 0.094124 + B -1.913335 -0.414385 0.080253 + N -1.573330 0.917725 -0.082089 + H 0.362959 -1.152502 0.029548 + H 1.952511 -1.518899 0.471862 + H 1.603727 -1.200723 -1.111645 + H 1.685885 0.794108 1.271412 + H 2.747767 0.856233 -0.377520 + H 0.828805 1.233683 -0.444071 + H -1.033175 -1.228986 0.127205 + H -3.042895 -0.772203 0.166197 + H -2.251075 1.648451 -0.119053 + H -0.592044 1.235067 -0.144665 + 14 + 3.215260 + N 1.611639 -1.180262 0.062477 + B 1.771299 0.391804 -0.053884 + B -2.301420 0.027218 0.224064 + N -1.500284 1.060630 -0.237339 + H 0.697786 -1.429552 0.437188 + H 2.336197 -1.547210 0.675055 + H 1.715808 -1.599713 -0.858499 + H 1.783410 0.865336 1.045198 + H 2.798155 0.626495 -0.621569 + H 0.842616 0.805598 -0.693006 + H -1.821243 -0.800644 0.931150 + H -3.454598 -0.019265 -0.061770 + H -1.832386 1.777772 -0.845227 + H -0.495459 1.092739 -0.041914 + 14 + 18.208530 + N 1.822987 -1.227330 0.248078 + B 1.834923 0.471821 0.128015 + B -2.604282 0.268874 0.025559 + N -1.522893 0.987839 -0.483776 + H 1.031844 -1.716630 0.643202 + H 2.635783 -1.409901 0.840574 + H 2.028787 -1.590892 -0.676815 + H 1.913462 1.056711 1.159602 + H 2.835893 0.458892 -0.530853 + H 0.737084 0.512262 -0.350175 + H -2.497568 -0.165859 1.134972 + H -3.635624 0.211709 -0.564024 + H -1.525954 1.381233 -1.394456 + H -0.577390 0.783993 -0.137069 + 14 + 53.824930 + N 1.347470 -1.857039 0.345380 + B 2.035774 1.481577 0.242721 + B -2.420825 0.211511 -0.164943 + N -1.290338 0.610686 -0.867826 + H 0.552711 -2.286926 0.789346 + H 2.089240 -1.809456 1.022382 + H 1.650994 -2.465350 -0.396204 + H 2.221782 2.633115 0.415066 + H 2.944116 0.745754 0.414420 + H 1.010419 0.994359 -0.092466 + H -2.516101 0.469656 0.990963 + H -3.300378 -0.355250 -0.731476 + H -1.136559 0.331839 -1.813208 + H -0.456430 0.984914 -0.421514 + 14 + 51.280610 + N 1.235240 -1.335808 0.957553 + B 1.746627 1.713540 -0.028384 + B -2.406543 0.029159 -0.505538 + N -1.151432 -0.058781 -1.093132 + H 0.407998 -1.584049 1.476607 + H 1.953820 -1.099987 1.621721 + H 1.539613 -2.155974 0.460766 + H 1.702286 2.093474 1.087501 + H 2.788842 1.492998 -0.535497 + H 0.741541 1.567834 -0.638608 + H -2.514866 0.559659 0.555195 + H -3.358853 -0.415789 -1.062080 + H -1.003369 -0.493376 -1.976914 + H -0.310077 0.304941 -0.660795 + 14 + 53.138610 + N 1.035862 -1.462016 1.445476 + B 1.150064 1.927339 -0.474332 + B -1.885288 0.092936 -0.746053 + N -0.585397 -0.321500 -1.010257 + H 0.151507 -1.565504 1.918727 + H 1.701792 -1.117706 2.118711 + H 1.336896 -2.380999 1.163992 + H 1.019167 1.822922 0.693606 + H 2.167518 1.620891 -0.988983 + H 0.265252 2.347131 -1.134657 + H -2.103597 0.726939 0.237618 + H -2.755423 -0.171603 -1.511047 + H -0.339746 -0.887891 -1.791043 + H 0.154938 -0.205899 -0.339674 + 14 + 17.441480 + N 0.790413 -1.500913 1.892034 + B 0.571107 1.412403 -0.912726 + B -1.302949 0.395094 -0.983220 + N 0.065859 -0.158854 -0.776959 + H -0.150836 -1.585372 2.246941 + H 1.337740 -1.083538 2.630228 + H 1.147004 -2.429521 1.736014 + H 0.500352 1.874379 0.186873 + H 1.652616 1.367275 -1.416890 + H -0.210179 1.909473 -1.686593 + H -1.785828 1.003380 -0.086903 + H -1.870795 0.147897 -1.994083 + H 0.474818 -0.797000 -1.447067 + H 0.466756 -0.336392 0.159625 + 14 + -0.641950 + N 0.685498 -1.651150 2.060968 + B 0.695640 1.337923 -1.108185 + B -1.018213 0.538755 -1.236736 + N 0.125376 0.161777 -0.251958 + H -0.246963 -1.875871 2.374924 + H 1.189791 -1.291717 2.857193 + H 1.125665 -2.517929 1.792375 + H 0.722602 2.384545 -0.533552 + H 1.623380 1.057356 -1.802428 + H -0.314108 1.478389 -1.989857 + H -1.898273 1.198401 -0.773424 + H -1.254897 -0.259908 -2.088973 + H 0.558535 -0.748900 -0.367464 + H 0.012809 0.355732 0.736825 + 14 + -0.920680 + N 0.776258 -1.811801 1.790990 + B 0.716714 1.226549 -0.934956 + B -1.014128 0.539765 -1.284402 + N -0.301679 0.653213 0.099093 + H 0.134911 -2.386712 2.314896 + H 1.496449 -1.504069 2.425933 + H 1.215583 -2.403269 1.101521 + H 0.869064 2.408772 -0.895904 + H 1.661926 0.530876 -1.147253 + H -0.027246 1.067121 -2.073277 + H -1.912841 1.304310 -1.458957 + H -1.112481 -0.571146 -1.707139 + H -0.046672 -0.221234 0.565425 + H -0.692577 1.307805 0.761431 diff --git a/TEST/ammoniaBorane/mopac/de-gsm/stringfile.standard.fr b/TEST/ammoniaBorane/mopac/de-gsm/stringfile.standard.fr new file mode 100644 index 0000000..2dd77d6 --- /dev/null +++ b/TEST/ammoniaBorane/mopac/de-gsm/stringfile.standard.fr @@ -0,0 +1,144 @@ + 14 + + N 1.354486 -1.869638 0.342672 + B 2.029562 1.483705 0.244537 + B -2.416934 0.210520 -0.162772 + N -1.293976 0.630855 -0.866415 + H 0.558388 -2.300738 0.782941 + H 2.092499 -1.821713 1.023929 + H 1.661525 -2.475192 -0.399250 + H 2.228974 2.640783 0.350040 + H 2.921519 0.738304 0.460781 + H 1.004294 0.984006 -0.074390 + H -2.521967 0.466556 0.993272 + H -3.287546 -0.369691 -0.730017 + H -1.134353 0.355903 -1.811770 + H -0.464599 1.015729 -0.420917 + 14 + + N 1.347470 -1.857039 0.345380 + B 2.035774 1.481577 0.242721 + B -2.420825 0.211511 -0.164943 + N -1.290338 0.610686 -0.867826 + H 0.552711 -2.286926 0.789346 + H 2.089240 -1.809456 1.022382 + H 1.650994 -2.465350 -0.396204 + H 2.221782 2.633115 0.415066 + H 2.944116 0.745754 0.414420 + H 1.010419 0.994359 -0.092466 + H -2.516101 0.469656 0.990963 + H -3.300378 -0.355250 -0.731476 + H -1.136559 0.331839 -1.813208 + H -0.456430 0.984914 -0.421514 + 14 + + N 1.339765 -1.842487 0.348688 + B 2.042652 1.479057 0.240619 + B -2.425581 0.211841 -0.167239 + N -1.285618 0.588814 -0.870544 + H 0.546820 -2.271047 0.796827 + H 2.085698 -1.795413 1.020934 + H 1.638999 -2.453789 -0.392708 + H 2.215793 2.619956 0.487296 + H 2.967796 0.755243 0.362022 + H 1.015635 1.007365 -0.111024 + H -2.509976 0.472288 0.989466 + H -3.314677 -0.340307 -0.732803 + H -1.138461 0.305978 -1.815322 + H -0.446971 0.951888 -0.423571 + 14 + + N 1.339045 -1.862137 0.343494 + B 2.035998 1.484587 0.248975 + B -2.415273 0.212834 -0.163278 + N -1.288664 0.609350 -0.870898 + H 0.545149 -2.290052 0.788811 + H 2.083501 -1.820258 1.018528 + H 1.640532 -2.469458 -0.400276 + H 2.226737 2.638059 0.419780 + H 2.954624 0.760751 0.417906 + H 1.016371 0.995882 -0.084124 + H -2.515770 0.475014 0.990037 + H -3.288398 -0.379384 -0.718103 + H -1.140894 0.321918 -1.814941 + H -0.461083 1.012282 -0.443269 + 14 + + N 1.347470 -1.857039 0.345380 + B 2.035774 1.481577 0.242721 + B -2.420825 0.211511 -0.164943 + N -1.290338 0.610686 -0.867826 + H 0.552711 -2.286926 0.789346 + H 2.089240 -1.809456 1.022382 + H 1.650994 -2.465350 -0.396204 + H 2.221782 2.633115 0.415066 + H 2.944116 0.745754 0.414420 + H 1.010419 0.994359 -0.092466 + H -2.516101 0.469656 0.990963 + H -3.300378 -0.355250 -0.731476 + H -1.136559 0.331839 -1.813208 + H -0.456430 0.984914 -0.421514 + 14 + + N 1.356002 -1.851866 0.347182 + B 2.035306 1.478344 0.236910 + B -2.426305 0.210185 -0.166412 + N -1.291931 0.612047 -0.865115 + H 0.560413 -2.283510 0.789981 + H 2.095195 -1.798472 1.025963 + H 1.661353 -2.461386 -0.392110 + H 2.216455 2.627912 0.411051 + H 2.933204 0.730649 0.411325 + H 1.004221 0.992575 -0.100591 + H -2.516112 0.464485 0.992118 + H -3.312047 -0.331010 -0.743807 + H -1.132614 0.341672 -1.811681 + H -0.451266 0.957763 -0.402173 + 14 + + N 1.366252 -1.868753 0.344036 + B 2.036837 1.479322 0.240894 + B -2.432779 0.222666 -0.164501 + N -1.288270 0.586679 -0.859740 + H 0.567207 -2.296526 0.782033 + H 2.102448 -1.822301 1.027236 + H 1.675454 -2.480928 -0.391852 + H 2.208789 2.636516 0.392288 + H 2.943239 0.746572 0.429996 + H 1.000792 1.006461 -0.085778 + H -2.528050 0.480352 0.990876 + H -3.320521 -0.322215 -0.740072 + H -1.140158 0.344619 -1.816120 + H -0.459365 0.976924 -0.416654 + 14 + + N 1.347470 -1.857039 0.345380 + B 2.035774 1.481577 0.242721 + B -2.420825 0.211511 -0.164943 + N -1.290338 0.610686 -0.867826 + H 0.552711 -2.286926 0.789346 + H 2.089240 -1.809456 1.022382 + H 1.650994 -2.465350 -0.396204 + H 2.221782 2.633115 0.415066 + H 2.944116 0.745754 0.414420 + H 1.010419 0.994359 -0.092466 + H -2.516101 0.469656 0.990963 + H -3.300378 -0.355250 -0.731476 + H -1.136559 0.331839 -1.813208 + H -0.456430 0.984914 -0.421514 + 14 + + N 1.329162 -1.845404 0.346779 + B 2.033538 1.483542 0.244392 + B -2.408379 0.200747 -0.165888 + N -1.293498 0.635127 -0.875000 + H 0.538629 -2.277340 0.796359 + H 2.076297 -1.796392 1.017692 + H 1.627548 -2.449832 -0.400197 + H 2.235148 2.628593 0.437643 + H 2.943741 0.745011 0.398906 + H 1.020360 0.980959 -0.100437 + H -2.503832 0.459103 0.989730 + H -3.279173 -0.387796 -0.723280 + H -1.133420 0.318994 -1.808514 + H -0.454246 0.994076 -0.425543 diff --git a/TEST/ammoniaBorane/qchem/de-gsm/compare.py b/TEST/ammoniaBorane/qchem/de-gsm/compare.py new file mode 100644 index 0000000..8bc4f62 --- /dev/null +++ b/TEST/ammoniaBorane/qchem/de-gsm/compare.py @@ -0,0 +1,41 @@ +# for reading csv format files +import csv + +# function to convert strings to float and skip conversion if the value is not a float +def convertToFloat(inList): + for element in inList: + try: + yield float(element) + except ValueError: + yield element + +# subtract two floats and skip if string +def subtractFloat(number1, number2): + try: + return (number1 - number2) + except TypeError: + pass + +def main(): + threshold = 0.001 + try: + # read standard and output files + standard = csv.reader(open('stringfile.standard', 'r'), delimiter=' ') + currentOutput = csv.reader(open('stringfile.xyz0001', 'r'), delimiter=' ') + # error if file does not exist + except IOError: + print("Error: File cannot be found!") + exit(1) + # loop over elements of two files simultaneously + for rowStd, rowOut in zip(standard, currentOutput): + rowStd = filter(None, rowStd) + rowOut = filter(None, rowOut) + for valStd, valOut in zip(list(convertToFloat(rowStd)), list(convertToFloat(rowOut))): + # error if difference larger than threshold + if ((subtractFloat(valStd, valOut)) > threshold): + print ((subtractFloat(valStd, valOut))) + exit(2) + return 0 + +if __name__ == "__main__": + main() diff --git a/TEST/ammoniaBorane/qchem/de-gsm/gscreate b/TEST/ammoniaBorane/qchem/de-gsm/gscreate new file mode 100755 index 0000000..119b132 --- /dev/null +++ b/TEST/ammoniaBorane/qchem/de-gsm/gscreate @@ -0,0 +1,14 @@ +#!/bin/bash + +file=molecule + +#nl $file > tmp.mole +#nl link > tmp.link +#join tmp.mole tmp.link > tmp.geom2 +#awk '{ print $2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10 }' tmp.geom2 > tmp.geom + +#cat qstart tmp.geom qend > qcin +#cat qstart molecule$1 qend > scratch/qcin$1 +cat qstart $QCSCRATCH/molecule$1 qend > $QCSCRATCH/qcin$1 + +#rm tmp.geom tmp.geom2 tmp.link tmp.mole diff --git a/TEST/ammoniaBorane/qchem/de-gsm/inpfileq b/TEST/ammoniaBorane/qchem/de-gsm/inpfileq new file mode 100644 index 0000000..83a96a1 --- /dev/null +++ b/TEST/ammoniaBorane/qchem/de-gsm/inpfileq @@ -0,0 +1,27 @@ + +# FSM/GSM/SSM inpfileq + +------------- QCHEM Scratch Info ------------------------ +$QCSCRATCH/ # path for scratch dir. end with "/" +GSM_go1q # name of run +--------------------------------------------------------- + +------------ String Info -------------------------------- +SM_TYPE GSM # SSM, FSM or GSM +RESTART 0 # read restart.xyz +MAX_OPT_ITERS 80 # maximum iterations +STEP_OPT_ITERS 30 # for FSM/SSM +CONV_TOL 0.0005 # perp grad +ADD_NODE_TOL 0.1 # for GSM +SCALING 1.0 # for opt steps +SSM_DQMAX 0.8 # add step size +GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 +INT_THRESH 2.0 # intermediate detection +MIN_SPACING 5.0 # node spacing SSM +BOND_FRAGMENTS 1 # make IC's for fragments +INITIAL_OPT 0 # opt steps first node +FINAL_OPT 150 # opt steps last SSM node +PRODUCT_LIMIT 100.0 # kcal/mol +TS_FINAL_TYPE 1 # any/delta bond: 0/1 +NNODES 9 # including endpoints +--------------------------------------------------------- diff --git a/TEST/ammoniaBorane/qchem/de-gsm/qend b/TEST/ammoniaBorane/qchem/de-gsm/qend new file mode 100644 index 0000000..b39a0e1 --- /dev/null +++ b/TEST/ammoniaBorane/qchem/de-gsm/qend @@ -0,0 +1 @@ +$end diff --git a/TEST/ammoniaBorane/qchem/de-gsm/qstart b/TEST/ammoniaBorane/qchem/de-gsm/qstart new file mode 100644 index 0000000..afa463a --- /dev/null +++ b/TEST/ammoniaBorane/qchem/de-gsm/qstart @@ -0,0 +1,24 @@ + $rem + JOBTYPE FORCE + EXCHANGE B3LYP +! CORRELATION PBE +! UNRESTRICTED TRUE + SCF_ALGORITHM rca_diis + SCF_MAX_CYCLES 150 + BASIS 6-31G* +! BASIS LANL2DZ +! ECP LANL2DZ + WAVEFUNCTION_ANALYSIS FALSE + GEOM_OPT_MAX_CYCLES 300 + +scf_convergence 6 + + SYM_IGNORE TRUE + SYMMETRY FALSE + +molden_format true + $end + + +$molecule +0 1 diff --git a/TEST/ammoniaBorane/qchem/de-gsm/scratch/initial0001.xyz b/TEST/ammoniaBorane/qchem/de-gsm/scratch/initial0001.xyz new file mode 100644 index 0000000..6c4ca24 --- /dev/null +++ b/TEST/ammoniaBorane/qchem/de-gsm/scratch/initial0001.xyz @@ -0,0 +1,32 @@ +14 +Step 4 + N 1.42404391 -0.81362238 0.16432836 + B 1.91120439 0.72094317 -0.22413883 + B -2.35330285 -0.36214677 -0.26327912 + N -1.42908691 0.56361934 0.22417517 + H 0.42248853 -0.81199165 0.38582555 + H 1.93282356 -1.17333424 0.97200968 + H 1.57373286 -1.46150641 -0.60975022 + H 1.69255432 1.37924732 0.77052984 + H 3.08350510 0.63770092 -0.50771637 + H 1.21661838 1.03584692 -1.17276368 + H -2.23026857 -0.76469220 -1.38406550 + H -3.22416240 -0.75303043 0.45855394 + H -1.50321926 0.98359541 1.14279875 + H -0.69850405 0.99200398 -0.33889060 + 14 +Step 18 + N 0.67997031 -1.68795249 1.58958866 + B 0.75189698 1.24383924 -0.89412778 + B -0.94827614 0.38622710 -1.13772599 + N -0.23816136 0.74860471 0.19709107 + H -0.04839454 -2.25921752 2.01513996 + H 1.44294111 -1.63283109 2.26235003 + H 1.03293400 -2.21598277 0.79266125 + H 0.82297709 2.43387009 -1.00501563 + H 1.74137707 0.57557798 -0.99743196 + H 0.00591577 0.87195915 -1.95520338 + H -1.90677014 1.05629824 -1.39466826 + H -0.95908370 -0.78743159 -1.38072218 + H 0.07355444 -0.04777152 0.77821649 + H -0.68183590 1.47227448 0.75078672 diff --git a/TEST/ammoniaBorane/qchem/de-gsm/stringfile.standard b/TEST/ammoniaBorane/qchem/de-gsm/stringfile.standard new file mode 100644 index 0000000..f06baf2 --- /dev/null +++ b/TEST/ammoniaBorane/qchem/de-gsm/stringfile.standard @@ -0,0 +1,144 @@ + 14 + 0.000000 + N 1.424044 -0.813622 0.164328 + B 1.911204 0.720943 -0.224139 + B -2.353303 -0.362147 -0.263279 + N -1.429087 0.563619 0.224175 + H 0.422489 -0.811992 0.385826 + H 1.932824 -1.173334 0.972010 + H 1.573733 -1.461506 -0.609750 + H 1.692554 1.379247 0.770530 + H 3.083505 0.637701 -0.507716 + H 1.216618 1.035847 -1.172764 + H -2.230269 -0.764692 -1.384065 + H -3.224162 -0.753030 0.458554 + H -1.503219 0.983595 1.142799 + H -0.698504 0.992004 -0.338891 + 14 + 1.030116 + N 1.387924 -0.796895 0.316176 + B 1.900219 0.649500 -0.312526 + B -2.247689 -0.274713 -0.368981 + N -1.376442 0.606436 0.271641 + H 0.387382 -0.746233 0.527017 + H 1.900003 -1.036682 1.165562 + H 1.532730 -1.548926 -0.357671 + H 1.707083 1.468758 0.562764 + H 3.071781 0.486945 -0.566966 + H 1.201164 0.813170 -1.291393 + H -2.228353 -0.346838 -1.561889 + H -2.970588 -0.958205 0.297676 + H -1.384296 0.760263 1.271384 + H -0.743349 1.232306 -0.216516 + 14 + 6.561957 + N 1.329973 -0.839574 0.452457 + B 1.827775 0.568864 -0.376863 + B -2.065768 -0.185139 -0.459225 + N -1.414596 0.779467 0.305341 + H 0.345757 -0.914697 0.706672 + H 1.934709 -0.947617 1.264451 + H 1.553126 -1.577291 -0.214061 + H 1.723914 1.485459 0.409892 + H 2.978203 0.242325 -0.584935 + H 1.111624 0.643690 -1.345890 + H -2.237388 0.011022 -1.624666 + H -2.431284 -1.193299 0.078351 + H -1.224196 0.696404 1.294278 + H -1.041718 1.638126 -0.072321 + 14 + 26.578206 + N 1.188402 -0.981890 0.732609 + B 1.861115 0.770441 -0.522700 + B -1.977323 -0.116173 -0.553410 + N -1.365177 0.843507 0.248327 + H 0.322379 -1.398120 1.075304 + H 1.932691 -1.080457 1.417375 + H 1.467195 -1.530761 -0.077810 + H 1.882690 1.633731 0.307720 + H 2.828468 0.067221 -0.629069 + H 1.088060 0.863429 -1.435742 + H -2.422317 0.207110 -1.615680 + H -2.059038 -1.244581 -0.148263 + H -0.896327 0.647736 1.119901 + H -1.239457 1.808832 -0.020344 + 14 + 31.410545 + N 1.088765 -1.208783 1.139950 + B 1.859222 1.118609 -0.800762 + B -2.008890 -0.051930 -0.624440 + N -1.156273 0.720389 0.157579 + H 0.320760 -1.782136 1.489532 + H 1.848006 -1.305476 1.811843 + H 1.404304 -1.654438 0.280879 + H 1.851823 1.842236 0.149010 + H 2.638139 0.213640 -0.847674 + H 1.164942 1.354239 -1.741550 + H -2.767815 0.479310 -1.383714 + H -1.966814 -1.245977 -0.514334 + H -0.446047 0.308269 0.759537 + H -1.098321 1.726286 0.075693 + 14 + 30.194854 + N 0.996811 -1.490662 1.271656 + B 1.312799 1.234283 -0.968175 + B -1.659851 -0.024051 -0.708877 + N -0.922106 0.797614 0.154008 + H 0.149978 -1.969502 1.578786 + H 1.713181 -1.746020 1.950478 + H 1.256302 -1.928232 0.389626 + H 1.433632 2.031658 -0.084129 + H 1.945888 0.224478 -0.926998 + H 0.735744 1.549372 -1.964265 + H -2.294785 0.473156 -1.591218 + H -1.638227 -1.208029 -0.532079 + H -0.393896 0.420581 0.938114 + H -0.927236 1.806965 0.080137 + 14 + 22.832646 + N 0.936775 -1.525646 1.369134 + B 0.913751 1.141270 -0.941646 + B -1.340542 0.097476 -0.833864 + N -0.636066 0.821793 0.173890 + H 0.079674 -2.005145 1.647418 + H 1.621108 -1.774971 2.081730 + H 1.232316 -1.962424 0.498393 + H 1.266873 2.109692 -0.320224 + H 1.581683 0.153378 -0.865162 + H 0.380517 1.396648 -1.991496 + H -2.044846 0.679051 -1.596690 + H -1.220824 -1.089684 -0.844173 + H -0.200342 0.341272 0.965238 + H -0.781036 1.816352 0.291288 + 14 + 7.919647 + N 0.879581 -1.550891 1.509633 + B 0.753192 1.068553 -0.861120 + B -1.073316 0.305224 -1.055694 + N -0.442868 0.790678 0.217581 + H 0.038997 -2.077506 1.746967 + H 1.536169 -1.736741 2.266123 + H 1.254920 -1.980643 0.666393 + H 1.128895 2.195199 -0.676722 + H 1.549764 0.176344 -0.878413 + H 0.046345 1.085661 -1.916469 + H -1.949025 0.959387 -1.539185 + H -0.947139 -0.858748 -1.284865 + H -0.076619 0.182137 0.960196 + H -0.700324 1.715430 0.539413 + 14 + -2.432273 + N 0.679970 -1.687952 1.589589 + B 0.751897 1.243839 -0.894128 + B -0.948276 0.386227 -1.137726 + N -0.238161 0.748605 0.197091 + H -0.048395 -2.259218 2.015140 + H 1.442941 -1.632831 2.262350 + H 1.032934 -2.215983 0.792661 + H 0.822977 2.433870 -1.005016 + H 1.741377 0.575578 -0.997432 + H 0.005916 0.871959 -1.955203 + H -1.906770 1.056298 -1.394668 + H -0.959084 -0.787432 -1.380722 + H 0.073554 -0.047772 0.778216 + H -0.681836 1.472274 0.750787 diff --git a/TEST/dielsAlder/gaussian/ggrad b/TEST/dielsAlder/gaussian/ggrad new file mode 100644 index 0000000..5f630d2 --- /dev/null +++ b/TEST/dielsAlder/gaussian/ggrad @@ -0,0 +1,55 @@ +#!/bin/bash +# The path to Gaussian should be added to PATH +# If using another version of Gaussian, change g09 to your version + +if [ -z $2 ] +then + echo " need two arguments! " + exit +fi + +#echo " in ggrad: $1 $2 " + +# Remove check files if starting a new calculation +chkfile=scratch/gfs$1.chk +fchkfile=scratch/gfs$1.fchk +gfile=scratch/gin$1.gjf +molfile=scratch/structure$1 +ncpu=$2 + +chkexists=0 +if [ -e $chkfile ] +then + chkexists=1 +fi + +#echo " chkfile: $chkfile gfile: $gfile molfile: $molfile ncpu: $ncpu" + +echo "%nprocshared=$ncpu " > $gfile +echo "%chk=$chkfile " >> $gfile +if [ $chkexists -eq 1 ] +then + echo "# guess=(read)" >> $gfile +fi +cat gstart >> $gfile +cat $molfile >> $gfile +echo " " >> $gfile +echo " " >> $gfile +echo " " >> $gfile +echo " " >> $gfile +echo " " >> $gfile +echo " " >> $gfile + +#echo "running: g09 < $gfile >& $gfile.log" +g09 < $gfile >& $gfile.log + +#check for SCF failure here +gfail=`grep -c "Convergence failure" $gfile.log` +if [ $gfail -ge 1 ] +then + echo " SCF failure in Gaussian " + #present fix: use previous gradient +else + #echo "running: formchk $chkfile $fchkfile" + formchk $chkfile $fchkfile > scratch/fchkout +fi diff --git a/TEST/dielsAlder/gaussian/gstart b/TEST/dielsAlder/gaussian/gstart new file mode 100644 index 0000000..921af62 --- /dev/null +++ b/TEST/dielsAlder/gaussian/gstart @@ -0,0 +1,5 @@ +# B3LYP/6-31G** nosymm Force test + +Title Card Required + +0 1 diff --git a/TEST/dielsAlder/mopac/de-gsm/compare.py b/TEST/dielsAlder/mopac/de-gsm/compare.py new file mode 100644 index 0000000..8bc4f62 --- /dev/null +++ b/TEST/dielsAlder/mopac/de-gsm/compare.py @@ -0,0 +1,41 @@ +# for reading csv format files +import csv + +# function to convert strings to float and skip conversion if the value is not a float +def convertToFloat(inList): + for element in inList: + try: + yield float(element) + except ValueError: + yield element + +# subtract two floats and skip if string +def subtractFloat(number1, number2): + try: + return (number1 - number2) + except TypeError: + pass + +def main(): + threshold = 0.001 + try: + # read standard and output files + standard = csv.reader(open('stringfile.standard', 'r'), delimiter=' ') + currentOutput = csv.reader(open('stringfile.xyz0001', 'r'), delimiter=' ') + # error if file does not exist + except IOError: + print("Error: File cannot be found!") + exit(1) + # loop over elements of two files simultaneously + for rowStd, rowOut in zip(standard, currentOutput): + rowStd = filter(None, rowStd) + rowOut = filter(None, rowOut) + for valStd, valOut in zip(list(convertToFloat(rowStd)), list(convertToFloat(rowOut))): + # error if difference larger than threshold + if ((subtractFloat(valStd, valOut)) > threshold): + print ((subtractFloat(valStd, valOut))) + exit(2) + return 0 + +if __name__ == "__main__": + main() diff --git a/TEST/dielsAlder/mopac/de-gsm/inpfileq b/TEST/dielsAlder/mopac/de-gsm/inpfileq new file mode 100644 index 0000000..d2a54ff --- /dev/null +++ b/TEST/dielsAlder/mopac/de-gsm/inpfileq @@ -0,0 +1,26 @@ +# FSM/GSM/SSM inpfileq + +------------- QCHEM Scratch Info ------------------------ +$QCSCRATCH/ # path for scratch dir. end with "/" +GSM_go1q # name of run +--------------------------------------------------------- + +------------ String Info -------------------------------- +SM_TYPE GSM # SSM, FSM or GSM +RESTART 0 # read restart.xyz +MAX_OPT_ITERS 80 # maximum iterations +STEP_OPT_ITERS 30 # for FSM/SSM +CONV_TOL 0.0005 # perp grad +ADD_NODE_TOL 0.1 # for GSM +SCALING 1.0 # for opt steps +SSM_DQMAX 0.8 # add step size +GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 +INT_THRESH 2.0 # intermediate detection +MIN_SPACING 5.0 # node spacing SSM +BOND_FRAGMENTS 1 # make IC's for fragments +INITIAL_OPT 0 # opt steps first node +FINAL_OPT 150 # opt steps last SSM node +PRODUCT_LIMIT 100.0 # kcal/mol +TS_FINAL_TYPE 1 # any/delta bond: 0/1 +NNODES 9 # including endpoints +--------------------------------------------------------- diff --git a/TEST/dielsAlder/mopac/de-gsm/scratch/initial0001.xyz b/TEST/dielsAlder/mopac/de-gsm/scratch/initial0001.xyz new file mode 100644 index 0000000..27b6078 --- /dev/null +++ b/TEST/dielsAlder/mopac/de-gsm/scratch/initial0001.xyz @@ -0,0 +1,36 @@ + 16 + + C -1.037225935 -1.575057079 0.267707912 + C -1.708337045 -0.692852836 -0.473272941 + C -1.940300404 0.707404075 -0.088479364 + C -1.009041948 1.497621701 0.446255054 + C 2.732868692 -0.399002174 0.382328885 + C 2.511914031 0.465946545 -0.599791985 + H -2.143698307 -0.972175001 -1.437026627 + H -0.604491208 -1.340650761 1.230189495 + H -0.877954350 -2.600126276 -0.033220247 + H 3.637983428 -0.412060550 0.974372413 + H 2.025495997 -1.165771090 0.670414088 + H 1.605947473 0.476343117 -1.192479427 + H 3.218026083 1.231192741 -0.891866332 + H -1.184626031 2.531163345 0.706314557 + H 0.000968997 1.169351717 0.656481639 + H -2.951061069 1.071129245 -0.293712793 +16 + + C 0.020341526 -1.496218373 0.058645511 + C -1.252780557 -0.711946442 -0.072432699 + C -1.293528451 0.622754843 -0.135300138 + C -0.070828081 1.489109844 -0.053029021 + C 1.214362608 -0.621210736 0.473790004 + C 1.222148922 0.698487297 -0.309128963 + H -2.158648998 -1.313484501 -0.128547977 + H -0.114950764 -2.316203080 0.791886225 + H 0.235607739 -1.989611408 -0.913009420 + H 1.160153427 -0.406733507 1.558378455 + H 2.159983399 -1.169252234 0.309815327 + H 1.318154252 0.486249766 -1.391273973 + H 2.102026514 1.305572159 -0.030670432 + H -0.148426579 2.325855087 -0.774547169 + H -0.035454506 1.955341019 0.954403786 + H -2.233314668 1.162539924 -0.235848986 diff --git a/TEST/dielsAlder/mopac/de-gsm/scratch/paragsm0001 b/TEST/dielsAlder/mopac/de-gsm/scratch/paragsm0001 new file mode 100644 index 0000000..e6c25b3 --- /dev/null +++ b/TEST/dielsAlder/mopac/de-gsm/scratch/paragsm0001 @@ -0,0 +1,1792 @@ + Number of QC processors: 4 +***** Starting Initialization ***** + runend 1 + -structure filename from input: scratch/initial0001.xyz +Initializing Tolerances and Parameters... + -Opening inpfileq + -reading file... + -using GSM + -RESTART: 0 + -MAX_OPT_ITERS: 80 + -STEP_OPT_ITERS: 30 + -CONV_TOL = 0.0005 + -ADD_NODE_TOL = 0.1 + -SCALING = 1 + -SSM_DQMAX: 0.8 + -SSM_DQMIN: 0.2 + -GROWTH_DIRECTION = 0 + -INT_THRESH: 2 + -SSM_MIN_SPACING: 5 + -BOND_FRAGMENTS = 1 + -INITIAL_OPT: 0 + -FINAL_OPT: 150 + -PRODUCT_LIMIT: 100 + -TS_FINAL_TYPE: 1 + -NNODES = 9 + Done reading inpfileq + + reading isomers + WARNING: ignoring BONDS in ISOMERS file because BOND_FRAGMENTS == 0 or 1 + couldn't find ISOMERS file: scratch/ISOMERS0001 +Reading and initializing string coordinates + -Opening structure file + -reading file... + -The number of atoms is: 16 + -Reading the atomic names... -Reading coordinates...Opening xyz file +Finished reading information from structure file + +**************************************** +**************************************** +****** Starting IC-GSM calculation ***** +**************************************** +**************************************** + + skipped Eckart_align + 16 + +C -1.060017 -1.517146 0.052887 +C -1.829554 -0.594086 -0.539688 +C -2.012604 0.793709 -0.089780 +C -1.097406 1.540951 0.541104 +C 3.018414 -0.332740 0.534205 +C 2.482680 0.169904 -0.576610 +H -2.400633 -0.882356 -1.423216 +H -0.513652 -1.303832 0.968289 +H -0.966890 -2.521220 -0.351177 +H 3.891712 0.112541 1.005362 +H 2.608491 -1.215917 1.019022 +H 1.608060 -0.276406 -1.043738 +H 2.895264 1.050961 -1.063014 +H -1.320890 2.556285 0.856673 +H -0.094545 1.173901 0.744815 +H -2.981424 1.238281 -0.320708 + 16 + +C 0.018565 -1.505102 0.071755 +C -1.254726 -0.702912 -0.048283 +C -1.285511 0.633242 -0.085278 +C -0.048111 1.496966 -0.044220 +C 1.216014 -0.631689 0.479480 +C 1.229452 0.684821 -0.310339 +H -2.187944 -1.262829 -0.104375 +H -0.121338 -2.316354 0.799873 +H 0.226636 -2.006431 -0.887349 +H 1.148348 -0.405323 1.552809 +H 2.153272 -1.182597 0.331990 +H 1.295645 0.458374 -1.383898 +H 2.115916 1.280139 -0.058569 +H -0.137620 2.309803 -0.778494 +H 0.019570 1.995007 0.936447 +H -2.244815 1.145933 -0.151545 + + NOTICES + Not using Davidson + Not using close dist add + Not using ONE_SKIP + Using HESS_TANG + END NOTICES + + isOpt: 1 + in make_frags() + merging: + atom[0] frag: 0 + atom[1] frag: 0 + atom[2] frag: 0 + atom[3] frag: 0 + atom[4] frag: 1 + atom[5] frag: 1 + atom[6] frag: 0 + atom[7] frag: 0 + atom[8] frag: 0 + atom[9] frag: 1 + atom[10] frag: 1 + atom[11] frag: 1 + atom[12] frag: 1 + atom[13] frag: 0 + atom[14] frag: 0 + atom[15] frag: 0 + nfrags: 2 + in bond_frags() + connecting frag 1 to frag 0: bond pair1 added : 12 15 + linear ties complete + isOpt: 1 + in make_frags() + merging: + atom[0] frag: 0 + atom[1] frag: 0 + atom[2] frag: 0 + atom[3] frag: 0 + atom[4] frag: 0 + atom[5] frag: 0 + atom[6] frag: 0 + atom[7] frag: 0 + atom[8] frag: 0 + atom[9] frag: 0 + atom[10] frag: 0 + atom[11] frag: 0 + atom[12] frag: 0 + atom[13] frag: 0 + atom[14] frag: 0 + atom[15] frag: 0 + nfrags: 1 + in bond_frags() + linear ties complete + + setting SSM bonds + nbonds: 15 nangles: 20 ntor: 21 + printing ic1 ic's + + printing internals + number of bonds: 15 + bond 1: 2 to 1: 1.34 + bond 2: 3 to 2: 1.47 + bond 3: 4 to 3: 1.34 + bond 4: 6 to 5: 1.33 + bond 5: 7 to 2: 1.09 + bond 6: 8 to 1: 1.09 + bond 7: 9 to 1: 1.09 + bond 8: 10 to 5: 1.09 + bond 9: 11 to 5: 1.09 + bond 10: 12 to 6: 1.09 + bond 11: 13 to 6: 1.09 + bond 12: 14 to 4: 1.09 + bond 13: 15 to 4: 1.09 + bond 14: 16 to 3: 1.09 + bond 15: 12 to 15: 2.86 + + number of angles: 20 + angle 1: 3 2 1: 125.9 + angle 2: 4 3 2: 125.8 + angle 3: 7 2 1: 118.5 + angle 4: 7 2 3: 115.6 + angle 5: 8 1 2: 121.7 + angle 6: 9 1 2: 121.4 + angle 7: 9 1 8: 116.8 + angle 8: 10 5 6: 122.0 + angle 9: 11 5 6: 121.8 + angle 10: 11 5 10: 116.2 + angle 11: 12 6 5: 121.8 + angle 12: 13 6 5: 121.7 + angle 13: 13 6 12: 116.5 + angle 14: 14 4 3: 121.2 + angle 15: 15 4 3: 122.0 + angle 16: 15 4 14: 116.8 + angle 17: 16 3 2: 115.5 + angle 18: 16 3 4: 118.6 + angle 19: 15 12 6: 90.1 + angle 20: 12 15 4: 127.0 + + number of torsions: 21 + torsion 1: 4 3 2 1: 31.5 + torsion 2: 7 2 3 4: -150.1 + torsion 3: 8 1 2 3: 1.9 + torsion 4: 8 1 2 7: -176.4 + torsion 5: 9 1 2 3: -179.1 + torsion 6: 9 1 2 7: 2.5 + torsion 7: 12 6 5 10: -179.9 + torsion 8: 12 6 5 11: 0.4 + torsion 9: 13 6 5 10: -0.0 + torsion 10: 13 6 5 11: -179.8 + torsion 11: 14 4 3 2: -178.9 + torsion 12: 15 4 3 2: 2.4 + torsion 13: 16 3 2 1: -149.8 + torsion 14: 16 3 2 7: 28.6 + torsion 15: 16 3 4 14: 2.5 + torsion 16: 16 3 4 15: -176.3 + torsion 17: 15 12 6 5: 83.8 + torsion 18: 15 12 6 13: -96.0 + torsion 19: 12 15 4 3: 43.6 + torsion 20: 12 15 4 14: -135.2 + torsion 21: 4 15 12 6: 148.8 + + number of improper torsions: 6 + imptor 1: 3 7 2 1: 178.5 + imptor 2: 2 9 1 8: 179.0 + imptor 3: 10 11 5 6: 179.7 + imptor 4: 5 13 6 12: 179.8 + imptor 5: 14 15 4 3: 178.8 + imptor 6: 2 16 3 4: 178.8 + + number of nonbonds: 85 + + printing ic2 ic's + + printing internals + number of bonds: 16 + bond 1: 2 to 1: 1.51 + bond 2: 3 to 2: 1.34 + bond 3: 4 to 3: 1.51 + bond 4: 5 to 1: 1.54 + bond 5: 6 to 4: 1.54 + bond 6: 6 to 5: 1.54 + bond 7: 7 to 2: 1.09 + bond 8: 8 to 1: 1.10 + bond 9: 9 to 1: 1.10 + bond 10: 10 to 5: 1.10 + bond 11: 11 to 5: 1.10 + bond 12: 12 to 6: 1.10 + bond 13: 13 to 6: 1.10 + bond 14: 14 to 4: 1.10 + bond 15: 15 to 4: 1.10 + bond 16: 16 to 3: 1.09 + + number of angles: 30 + angle 1: 3 2 1: 123.5 + angle 2: 4 3 2: 123.5 + angle 3: 5 1 2: 112.1 + angle 4: 6 4 3: 112.0 + angle 5: 6 5 1: 111.0 + angle 6: 5 6 4: 110.9 + angle 7: 7 2 1: 117.0 + angle 8: 7 2 3: 119.5 + angle 9: 8 1 2: 109.7 + angle 10: 8 1 5: 110.1 + angle 11: 9 1 2: 109.4 + angle 12: 9 1 5: 110.0 + angle 13: 9 1 8: 105.4 + angle 14: 10 5 1: 109.2 + angle 15: 10 5 6: 109.0 + angle 16: 11 5 1: 110.2 + angle 17: 11 5 6: 110.7 + angle 18: 11 5 10: 106.7 + angle 19: 12 6 4: 109.1 + angle 20: 12 6 5: 109.0 + angle 21: 13 6 4: 110.2 + angle 22: 13 6 5: 110.8 + angle 23: 13 6 12: 106.7 + angle 24: 14 4 3: 109.8 + angle 25: 14 4 6: 110.0 + angle 26: 15 4 3: 109.5 + angle 27: 15 4 6: 110.0 + angle 28: 15 4 14: 105.4 + angle 29: 16 3 2: 119.5 + angle 30: 16 3 4: 117.0 + + number of torsions: 43 + torsion 1: 4 3 2 1: 1.5 + torsion 2: 5 1 2 3: 13.6 + torsion 3: 6 4 3 2: 14.3 + torsion 4: 6 5 1 2: -43.9 + torsion 5: 5 6 4 3: -44.6 + torsion 6: 4 6 5 1: 60.6 + torsion 7: 7 2 1 5: -166.2 + torsion 8: 7 2 3 4: -178.6 + torsion 9: 8 1 2 3: 136.2 + torsion 10: 8 1 2 7: -43.6 + torsion 11: 8 1 5 6: -166.3 + torsion 12: 9 1 2 3: -108.7 + torsion 13: 9 1 2 7: 71.5 + torsion 14: 9 1 5 6: 78.1 + torsion 15: 10 5 1 2: 76.3 + torsion 16: 10 5 1 8: -46.1 + torsion 17: 10 5 1 9: -161.8 + torsion 18: 10 5 6 4: -59.7 + torsion 19: 11 5 1 2: -166.9 + torsion 20: 11 5 1 8: 70.7 + torsion 21: 11 5 1 9: -44.9 + torsion 22: 11 5 6 4: -176.8 + torsion 23: 12 6 4 3: 75.6 + torsion 24: 12 6 5 1: -59.7 + torsion 25: 12 6 5 10: -179.9 + torsion 26: 12 6 5 11: 63.0 + torsion 27: 13 6 4 3: -167.5 + torsion 28: 13 6 5 1: -176.8 + torsion 29: 13 6 5 10: 63.0 + torsion 30: 13 6 5 11: -54.1 + torsion 31: 14 4 3 2: 136.9 + torsion 32: 14 4 6 5: -166.9 + torsion 33: 14 4 6 12: -46.8 + torsion 34: 14 4 6 13: 70.1 + torsion 35: 15 4 3 2: -107.9 + torsion 36: 15 4 6 5: 77.4 + torsion 37: 15 4 6 12: -162.5 + torsion 38: 15 4 6 13: -45.6 + torsion 39: 16 3 2 1: -178.7 + torsion 40: 16 3 2 7: 1.2 + torsion 41: 16 3 4 6: -165.5 + torsion 42: 16 3 4 14: -42.9 + torsion 43: 16 3 4 15: 72.3 + + number of improper torsions: 2 + imptor 1: 3 7 2 1: 179.9 + imptor 2: 2 16 3 4: 179.8 + + number of nonbonds: 74 + + ic1.nbonds: 15 ic2.nbonds: 16 + saving bond union: 17 saving angle union: 32 saving torsion union: 48 total number of coordinates: 97 + + + actual IC's + + printing internals + number of bonds: 17 + bond 1: 2 to 1: 1.34 + bond 2: 3 to 2: 1.47 + bond 3: 4 to 3: 1.34 + bond 4: 6 to 5: 1.33 + bond 5: 7 to 2: 1.09 + bond 6: 8 to 1: 1.09 + bond 7: 9 to 1: 1.09 + bond 8: 10 to 5: 1.09 + bond 9: 11 to 5: 1.09 + bond 10: 12 to 6: 1.09 + bond 11: 13 to 6: 1.09 + bond 12: 14 to 4: 1.09 + bond 13: 15 to 4: 1.09 + bond 14: 16 to 3: 1.09 + bond 15: 12 to 15: 2.86 + bond 16: 5 to 1: 4.27 + bond 17: 6 to 4: 3.99 + + number of angles: 32 + angle 1: 3 2 1: 125.9 + angle 2: 4 3 2: 125.8 + angle 3: 7 2 1: 118.5 + angle 4: 7 2 3: 115.6 + angle 5: 8 1 2: 121.7 + angle 6: 9 1 2: 121.4 + angle 7: 9 1 8: 116.8 + angle 8: 10 5 6: 122.0 + angle 9: 11 5 6: 121.8 + angle 10: 11 5 10: 116.2 + angle 11: 12 6 5: 121.8 + angle 12: 13 6 5: 121.7 + angle 13: 13 6 12: 116.5 + angle 14: 14 4 3: 121.2 + angle 15: 15 4 3: 122.0 + angle 16: 15 4 14: 116.8 + angle 17: 16 3 2: 115.5 + angle 18: 16 3 4: 118.6 + angle 19: 15 12 6: 90.1 + angle 20: 12 15 4: 127.0 + angle 21: 5 1 2: 114.0 + angle 22: 6 4 3: 106.8 + angle 23: 6 5 1: 68.1 + angle 24: 5 6 4: 104.9 + angle 25: 8 1 5: 51.0 + angle 26: 9 1 5: 102.5 + angle 27: 10 5 1: 158.2 + angle 28: 11 5 1: 57.7 + angle 29: 12 6 4: 62.6 + angle 30: 13 6 4: 100.8 + angle 31: 14 4 6: 125.9 + angle 32: 15 4 6: 27.1 + + number of torsions: 48 + torsion 1: 4 3 2 1: 31.5 + torsion 2: 7 2 3 4: -150.1 + torsion 3: 8 1 2 3: 1.9 + torsion 4: 8 1 2 7: -176.4 + torsion 5: 9 1 2 3: -179.1 + torsion 6: 9 1 2 7: 2.5 + torsion 7: 12 6 5 10: -179.9 + torsion 8: 12 6 5 11: 0.4 + torsion 9: 13 6 5 10: -0.0 + torsion 10: 13 6 5 11: -179.8 + torsion 11: 14 4 3 2: -178.9 + torsion 12: 15 4 3 2: 2.4 + torsion 13: 16 3 2 1: -149.8 + torsion 14: 16 3 2 7: 28.6 + torsion 15: 16 3 4 14: 2.5 + torsion 16: 16 3 4 15: -176.3 + torsion 17: 15 12 6 5: 83.8 + torsion 18: 15 12 6 13: -96.0 + torsion 19: 12 15 4 3: 43.6 + torsion 20: 12 15 4 14: -135.2 + torsion 21: 4 15 12 6: 148.8 + torsion 22: 5 1 2 3: -55.8 + torsion 23: 6 4 3 2: 27.1 + torsion 24: 6 5 1 2: -33.3 + torsion 25: 5 6 4 3: -114.4 + torsion 26: 4 6 5 1: 45.1 + torsion 27: 7 2 1 5: 125.8 + torsion 28: 8 1 5 6: -145.7 + torsion 29: 9 1 5 6: 99.8 + torsion 30: 10 5 1 2: 88.8 + torsion 31: 10 5 1 8: -23.5 + torsion 32: 10 5 1 9: -138.1 + torsion 33: 10 5 6 4: -113.1 + torsion 34: 11 5 1 2: 168.9 + torsion 35: 11 5 1 8: 56.5 + torsion 36: 11 5 1 9: -58.0 + torsion 37: 11 5 6 4: 67.1 + torsion 38: 12 6 4 3: 4.0 + torsion 39: 12 6 5 1: -21.6 + torsion 40: 13 6 4 3: 118.3 + torsion 41: 13 6 5 1: 158.2 + torsion 42: 14 4 6 5: 93.1 + torsion 43: 14 4 6 12: -148.4 + torsion 44: 14 4 6 13: -34.1 + torsion 45: 15 4 6 5: 14.3 + torsion 46: 15 4 6 12: 132.8 + torsion 47: 15 4 6 13: -112.9 + torsion 48: 16 3 4 6: -151.5 + + number of improper torsions: 0 + + number of nonbonds: 0 + + + ic1.nbonds: 14 ic2.nbonds: 16 + saving bond union: 16 saving angle union: 30 saving torsion union: 43 total number of coordinates: 89 + + Number of OpenMP threads: 1 + + + ---- Now preparing gradients ---- + Q-Chem initialized + -run name set to: GSM_go1q0001.001 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.000 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.001 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.002 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.003 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.004 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.005 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.006 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.007 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.008 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.009 + grad initiated: Q-Chem mode + ---- Done preparing gradients ---- + + + + Begin Growing the String + creating R node: 1 iR,iP: 0 8 wR,wP: 1 -1 iN: 1 bdist: 0.000 + dqmag: 9.10 dq0[constraint]: -1.30 + creating P node: 7 iR,iP: 1 8 wR,wP: -1 7 iN: 7 bdist: 0.000 + dqmag: 7.82 dq0[constraint]: -1.30 + nnR: 2 nnP: 2 + rpart: 0.50 0.00 0.00 0.00 0.00 0.00 0.50 0.00 + spacings (end ic_reparam, steps: 4): 1.14 2.58 0.00 0.00 0.00 0.00 0.00 2.59 1.14 disprms: 0.001 + eg eg setting V0 to: -147166.0 (-234.52746107 au) + + at beginning, starting V's are 0.000000 -40.719351 + + growing iter: 1 + rpart: 0.50 0.00 0.00 0.00 0.00 0.00 0.50 0.00 + spacings (end ic_reparam, steps: 4): 1.14 2.58 0.00 0.00 0.00 0.00 0.00 2.59 1.14 disprms: 0.001 + + eg eg eg eg + + Opt step: 1 gqc: 0.019 ss: 0.065 (DMAX: 0.100) predE: -2.12 E(M): 7.80 gRMS: 0.0115 ratio: 0.659 + Opt step: 2 gqc: 0.016 ss: 0.058 (DMAX: 0.100) predE: -0.50 E(M): 6.40 gRMS: 0.0033 + + Opt step: 1 gqc: 0.088 ss: 0.147 (DMAX: 0.100) predE: -8.74 E(M): 7.27 gRMS: 0.0258 ratio: 0.974 increasing DMAX + Opt step: 2 gqc: 0.085 ss: 0.201 (DMAX: 0.110) predE: -7.79 E(M): -1.23 gRMS: 0.0214 + + gopt_iter: 1 totalgrad: 0.160 gradrms: 0.0153 tgrads: 6 max E: 6.4 + printing string to scratch/stringfile.xyz0001g1 + + growing iter: 2 + adding node: 2 between 1 7 + iR,iP: 1 7 iN: 2 dqmag: 0.98 dq0[constraint]: -0.20 + initial Hint ev: 0.035 0.035 0.036 0.036 + rpart: 0.33 0.33 0.00 0.00 0.00 0.00 0.33 0.00 + spacings (end ic_reparam, steps: 4): 1.14 1.01 2.39 0.00 0.00 0.00 0.00 2.40 1.15 disprms: 0.112 + + eg eg eg eg eg eg + + Opt step: 1 gqc: 0.016 ss: 0.052 (DMAX: 0.100) predE: -0.35 E(M): 5.92 gRMS: 0.0025 ratio: 1.047 + Opt step: 2 gqc: 0.015 ss: 0.065 (DMAX: 0.100) predE: -0.39 E(M): 5.56 gRMS: 0.0023 + + Opt step: 1 gqc: 0.030 ss: 0.089 (DMAX: 0.100) predE: -2.77 E(M): 22.01 gRMS: 0.0122 ratio: 0.738 + Opt step: 2 gqc: 0.027 ss: 0.097 (DMAX: 0.100) predE: -1.19 E(M): 19.97 gRMS: 0.0044 + + Opt step: 1 gqc: 0.084 ss: 0.199 (DMAX: 0.110) predE: -6.90 E(M): -9.00 gRMS: 0.0187 ratio: 0.980 increasing DMAX + Opt step: 2 gqc: 0.077 ss: 0.178 (DMAX: 0.121) predE: -5.77 E(M): -15.76 gRMS: 0.0162 + + gopt_iter: 2 totalgrad: 0.148 gradrms: 0.0098 tgrads: 12 max E: 20.0 + printing string to scratch/stringfile.xyz0001g1 + + growing iter: 3 + adding node: 3 between 2 7 + iR,iP: 2 7 iN: 3 dqmag: 0.99 dq0[constraint]: -0.25 + initial Hint ev: 0.035 0.035 0.035 0.036 + rpart: 0.25 0.25 0.25 0.00 0.00 0.00 0.25 0.00 + spacings (end ic_reparam, steps: 4): 1.15 1.06 1.01 2.16 0.00 0.00 0.00 2.16 1.17 disprms: 0.132 + + eg eg eg eg eg eg eg eg + + Opt step: 1 gqc: 0.014 ss: 0.064 (DMAX: 0.100) predE: -0.37 E(M): 5.13 gRMS: 0.0022 ratio: 1.086 + Opt step: 2 gqc: 0.013 ss: 0.089 (DMAX: 0.100) predE: -0.43 E(M): 4.73 gRMS: 0.0020 + + Opt step: 1 gqc: 0.028 ss: 0.088 (DMAX: 0.100) predE: -0.95 E(M): 19.77 gRMS: 0.0041 ratio: 1.052 + Opt step: 2 gqc: 0.027 ss: 0.103 (DMAX: 0.100) predE: -1.01 E(M): 18.76 gRMS: 0.0039 + + Opt step: 1 gqc: 0.040 ss: 0.107 (DMAX: 0.100) predE: -3.12 E(M): 42.95 gRMS: 0.0126 ratio: 0.824 increasing DMAX + Opt step: 2 gqc: 0.037 ss: 0.107 (DMAX: 0.110) predE: -1.70 E(M): 40.37 gRMS: 0.0053 + + Opt step: 1 gqc: 0.072 ss: 0.169 (DMAX: 0.121) predE: -4.54 E(M): -21.52 gRMS: 0.0130 ratio: 0.998 increasing DMAX + Opt step: 2 gqc: 0.062 ss: 0.165 (DMAX: 0.133) predE: -3.36 E(M): -26.05 gRMS: 0.0101 + + gopt_iter: 3 totalgrad: 0.138 gradrms: 0.0061 tgrads: 20 max E: 40.4 + printing string to scratch/stringfile.xyz0001g1 + + growing iter: 4 + adding node: 4 between 3 7 + iR,iP: 3 7 iN: 4 dqmag: 0.99 dq0[constraint]: -0.33 + initial Hint ev: 0.035 0.035 0.035 0.036 + adding node: 6 between 7 4 + iR,iP: 7 4 iN: 6 dqmag: 0.99 dq0[constraint]: -0.49 + initial Hint ev: 0.035 0.035 0.035 0.035 + rpart: 0.17 0.17 0.17 0.17 0.00 0.17 0.17 0.00 + spacings (end ic_reparam, steps: 4): 1.16 1.08 1.05 0.99 1.62 0.00 1.62 1.01 1.22 disprms: 0.193 + + eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 gqc: 0.012 ss: 0.081 (DMAX: 0.100) predE: -0.36 E(M): 4.23 gRMS: 0.0019 ratio: 1.163 + Opt step: 2 gqc: 0.011 ss: 0.125 (DMAX: 0.100) predE: -0.37 E(M): 3.80 gRMS: 0.0017 + + Opt step: 1 gqc: 0.026 ss: 0.101 (DMAX: 0.100) predE: -0.94 E(M): 17.68 gRMS: 0.0038 ratio: 1.089 increasing DMAX + Opt step: 2 gqc: 0.025 ss: 0.121 (DMAX: 0.110) predE: -0.97 E(M): 16.65 gRMS: 0.0035 + + Opt step: 1 gqc: 0.038 ss: 0.102 (DMAX: 0.110) predE: -1.44 E(M): 40.10 gRMS: 0.0050 ratio: 1.051 + Opt step: 2 gqc: 0.037 ss: 0.114 (DMAX: 0.110) predE: -1.50 E(M): 38.59 gRMS: 0.0049 + + Opt step: 1 gqc: 0.038 ss: 0.115 (DMAX: 0.100) predE: -2.73 E(M): 66.53 gRMS: 0.0108 ratio: 0.921 increasing DMAX + Opt step: 2 gqc: 0.037 ss: 0.113 (DMAX: 0.110) predE: -2.03 E(M): 64.02 gRMS: 0.0061 + + Opt step: 1 gqc: 0.091 ss: 0.145 (DMAX: 0.100) predE: -6.01 E(M): 28.18 gRMS: 0.0194 ratio: 0.999 increasing DMAX + Opt step: 2 gqc: 0.090 ss: 0.186 (DMAX: 0.110) predE: -6.10 E(M): 22.17 gRMS: 0.0166 + + Opt step: 1 gqc: 0.053 ss: 0.147 (DMAX: 0.133) predE: -2.17 E(M): -29.48 gRMS: 0.0072 ratio: 1.100 increasing DMAX + Opt step: 2 gqc: 0.043 ss: 0.187 (DMAX: 0.146) predE: -1.46 E(M): -31.86 gRMS: 0.0049 + + gopt_iter: 4 totalgrad: 0.244 gradrms: 0.0079 tgrads: 32 max E: 64.0 + printing string to scratch/stringfile.xyz0001g1 + + growing iter: 5 + adding node: 5 between 4 6 + iR,iP: 4 6 iN: 5 dqmag: 1.00 dq0[constraint]: -0.50 + initial Hint ev: 0.035 0.035 0.035 0.036 + gopt_iter: string done growing + writing grown string scratch/stringfile.xyz0001g + Warning: last added node(s) do not have energies yet + + initial ic_reparam + TSn: 0 rpart: 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.12 + disp[1]: -0.09 disp[2]: -0.08 disp[3]: -0.06 disp[4]: 0.01 disp[5]: 0.41 disp[6]: 0.00 disp[7]: 0.11 + disp[1]: -0.04 disp[2]: -0.02 disp[3]: 0.01 disp[4]: 0.05 disp[5]: 0.18 disp[6]: -0.04 disp[7]: 0.00 + disp[1]: -0.02 disp[2]: -0.01 disp[3]: 0.01 disp[4]: 0.03 disp[5]: 0.09 disp[6]: -0.02 disp[7]: -0.01 + disp[1]: -0.01 disp[2]: -0.00 disp[3]: 0.01 disp[4]: 0.02 disp[5]: 0.05 disp[6]: -0.01 disp[7]: -0.00 + disp[1]: -0.01 disp[2]: -0.00 disp[3]: 0.01 disp[4]: 0.01 disp[5]: 0.02 disp[6]: -0.01 disp[7]: -0.00 + disp[1]: -0.00 disp[2]: -0.00 disp[3]: 0.00 disp[4]: 0.01 disp[5]: 0.01 disp[6]: -0.01 disp[7]: -0.00 + spacings (end ic_reparam, steps: 25): 1.24 1.24 1.24 1.24 1.24 1.26 1.24 1.24 disprms: 0.015 + + + Starting String opt + V_profile: 0.0 3.8 16.7 38.6 64.0 0.0 22.2 -31.9 -40.7 + 3 way tangent (4): f1: 0.28 + 3 way tangent (5): f1: 0.26 + 3 way tangent (6): f1: 0.29 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 5 (0.53) ss: 0.116 (DMAX: 0.100) predE: -0.39 E(M): 2.66 gRMS: 0.0022 ratio: 0.175 decreasing DMAX + Opt step: 2 gqc: 0.008 ss: 0.110 (DMAX: 0.083) predE: -0.50 E(M): 2.59 gRMS: 0.0074 ratio: 1.123 + Opt step: 3 gqc: 0.007 ss: 0.086 (DMAX: 0.083) predE: -0.18 E(M): 2.04 gRMS: 0.0025 + + Opt step: 1 t/ol: 4 (0.59) ss: 0.113 (DMAX: 0.110) predE: -0.83 E(M): 14.15 gRMS: 0.0031 ratio: 1.160 increasing DMAX + Opt step: 2 gqc: 0.022 ss: 0.173 (DMAX: 0.121) predE: -0.80 E(M): 13.18 gRMS: 0.0027 ratio: 1.296 + Opt step: 3 gqc: 0.021 ss: 0.162 (DMAX: 0.121) predE: -0.77 E(M): 12.15 gRMS: 0.0028 + + Opt step: 1 t/ol: 4 (0.50) ss: 0.109 (DMAX: 0.110) predE: -1.38 E(M): 36.29 gRMS: 0.0047 ratio: 1.085 + Opt step: 2 gqc: 0.035 ss: 0.136 (DMAX: 0.110) predE: -1.32 E(M): 34.80 gRMS: 0.0044 ratio: 1.145 increasing DMAX + Opt step: 3 gqc: 0.034 ss: 0.206 (DMAX: 0.121) predE: -1.28 E(M): 33.28 gRMS: 0.0040 + + Opt step: 1 t/ol: 4 (0.40) ss: 0.110 (DMAX: 0.110) predE: -1.93 E(M): 64.35 gRMS: 0.0063 ratio: 1.082 increasing DMAX + Opt step: 2 gqc: 0.034 ss: 0.128 (DMAX: 0.121) predE: -2.06 E(M): 62.26 gRMS: 0.0061 ratio: 1.112 increasing DMAX + Opt step: 3 gqc: 0.033 ss: 0.168 (DMAX: 0.133) predE: -2.14 E(M): 59.96 gRMS: 0.0058 + + Opt step: 1 t/ol: 27 (0.36) ss: 0.121 (DMAX: 0.100) predE: -3.21 E(M): 71.29 gRMS: 0.0106 ratio: 1.046 increasing DMAX + Opt step: 2 gqc: -0.033 ss: 0.153 (DMAX: 0.110) predE: -3.70 E(M): 67.94 gRMS: 0.0098 ratio: 1.066 increasing DMAX + Opt step: 3 gqc: -0.037 ss: 0.180 (DMAX: 0.121) predE: -3.92 E(M): 63.99 gRMS: 0.0094 + + Opt step: 1 t/ol: 0 (0.69) ss: 0.181 (DMAX: 0.110) predE: -5.63 E(M): 19.91 gRMS: 0.0153 ratio: 1.021 increasing DMAX + Opt step: 2 gqc: -0.089 ss: 0.199 (DMAX: 0.121) predE: -5.33 E(M): 14.16 gRMS: 0.0139 ratio: 1.032 increasing DMAX + Opt step: 3 gqc: -0.087 ss: 0.213 (DMAX: 0.133) predE: -4.75 E(M): 8.66 gRMS: 0.0123 + + Opt step: 1 t/ol: 0 (0.57) ss: 0.148 (DMAX: 0.146) predE: -1.01 E(M): -34.27 gRMS: 0.0046 ratio: 1.119 increasing DMAX + Opt step: 2 gqc: -0.028 ss: 0.142 (DMAX: 0.161) predE: -0.87 E(M): -35.40 gRMS: 0.0040 ratio: 1.101 + Opt step: 3 gqc: -0.020 ss: 0.123 (DMAX: 0.161) predE: -0.51 E(M): -36.36 gRMS: 0.0026 + + opt_iter: 5 totalgrad: 0.256 gradrms: 0.0067 tgrads: 53 ol(0): 0.00 max E: 64.0 + in find_peaks (2) + V_profile: 0.0 2.0 12.2 33.3 60.0 64.0 8.7 -36.4 -40.7 + min nodes: max nodes: 5 + found 1 significant peak(s). TOL: 0.50 + ** starting climb ** + printing string to stringfile.xyz0001 + V_profile: 0.0 2.0 12.2 33.3 60.0 64.0 8.7 -36.4 -40.7 + TSn: 5 rpart: 0.20 0.20 0.20 0.20 0.00 0.33 0.33 0.33 + disp[1]: -0.02 disp[2]: -0.01 disp[3]: 0.01 disp[4]: 0.04 disp[5]: 0.00 disp[6]: -0.01 disp[7]: 0.12 + disp[1]: -0.01 disp[2]: -0.01 disp[3]: 0.01 disp[4]: 0.02 disp[5]: 0.00 disp[6]: -0.01 disp[7]: 0.04 + disp[1]: -0.01 disp[2]: -0.00 disp[3]: 0.00 disp[4]: 0.01 disp[5]: 0.00 disp[6]: -0.01 disp[7]: 0.02 + disp[1]: -0.00 disp[2]: -0.00 disp[3]: 0.00 disp[4]: 0.01 disp[5]: 0.00 disp[6]: -0.01 disp[7]: 0.01 + spacings (end ic_reparam, steps: 5): 1.27 1.26 1.26 1.26 1.27 1.27 1.26 1.27 disprms: 0.012 + V_profile: 0.0 2.0 12.2 33.3 60.0 64.0 8.7 -36.4 -40.7 + 3 way tangent (5): f1: 0.07 + + slowing down climb optimization + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 5 (0.57) ss: 0.090 (DMAX: 0.083) predE: -0.24 E(M): 1.71 gRMS: 0.0019 ratio: 0.066 decreasing DMAX + Opt step: 2 gqc: 0.006 ss: 0.085 (DMAX: 0.069) predE: -0.29 E(M): 1.70 gRMS: 0.0052 ratio: 1.180 + Opt step: 3 gqc: 0.005 ss: 0.072 (DMAX: 0.069) predE: -0.16 E(M): 1.36 gRMS: 0.0022 + + Opt step: 1 t/ol: 4 (0.60) ss: 0.177 (DMAX: 0.121) predE: -1.38 E(M): 11.15 gRMS: 0.0052 ratio: -0.441 dE>0, decreasing DMAX + Opt step: 2 gqc: 0.020 ss: 0.145 (DMAX: 0.081) predE: -1.39 E(M): 11.76 gRMS: 0.0151 ratio: 1.078 + Opt step: 3 gqc: 0.019 ss: 0.137 (DMAX: 0.081) predE: -0.84 E(M): 10.26 gRMS: 0.0085 +S + Opt step: 1 t/ol: 4 (0.49) ss: 0.181 (DMAX: 0.121) predE: -1.23 E(M): 32.16 gRMS: 0.0037 ratio: 1.223 increasing DMAX + Opt step: 2 gqc: 0.032 ss: 0.173 (DMAX: 0.133) predE: -1.24 E(M): 30.66 gRMS: 0.0034 ratio: 1.243 increasing DMAX + Opt step: 3 gqc: 0.031 ss: 0.167 (DMAX: 0.146) predE: -1.30 E(M): 29.12 gRMS: 0.0035 + + Opt step: 1 t/ol: 27 (0.44) ss: 0.152 (DMAX: 0.133) predE: -1.82 E(M): 58.65 gRMS: 0.0053 ratio: 1.181 increasing DMAX + Opt step: 2 gqc: 0.032 ss: 0.204 (DMAX: 0.146) predE: -1.76 E(M): 56.50 gRMS: 0.0050 ratio: 1.234 increasing DMAX + Opt step: 3 gqc: 0.030 ss: 0.171 (DMAX: 0.161) predE: -1.82 E(M): 54.33 gRMS: 0.0046 + + Opt step: 1 gqc: -0.044 ss: 0.182 (DMAX: 0.061) gts: -0.0439 predE: -0.67 E(M): 59.80 gRMS: 0.0087 ratio: 1.083 increasing DMAX + Opt step: 2 gqc: -0.042 ss: 0.219 (DMAX: 0.067) gts: -0.0416 predE: -0.87 E(M): 59.08 gRMS: 0.0083 ratio: 1.065 increasing DMAX + Opt step: 3 gqc: -0.040 ss: 0.245 (DMAX: 0.073) gts: -0.0395 predE: -0.98 E(M): 58.15 gRMS: 0.0079 + + Opt step: 1 t/ol: 0 (0.68) ss: 0.186 (DMAX: 0.133) predE: -3.85 E(M): 5.18 gRMS: 0.0105 ratio: 1.059 increasing DMAX + Opt step: 2 gqc: -0.082 ss: 0.229 (DMAX: 0.146) predE: -2.91 E(M): 1.09 gRMS: 0.0089 ratio: 1.131 increasing DMAX + Opt step: 3 gqc: -0.076 ss: 0.188 (DMAX: 0.161) predE: -2.63 E(M): -2.20 gRMS: 0.0077 + + Opt step: 1 t/ol: 0 (0.49) ss: 0.093 (DMAX: 0.161) predE: -0.25 E(M): -37.65 gRMS: 0.0020 ratio: 0.974 + Opt step: 2 gqc: -0.014 ss: 0.091 (DMAX: 0.161) predE: -0.28 E(M): -37.89 gRMS: 0.0029 ratio: 0.938 + Opt step: 3 gqc: -0.012 ss: 0.069 (DMAX: 0.161) predE: -0.13 E(M): -38.15 gRMS: 0.0023 + +c opt_iter: 6 totalgrad: 0.237 gradrms: 0.0058 tgrads: 74 ol(0): 0.00 max E: 58.1 + in find_peaks (2) + V_profile: 0.0 1.4 10.3 29.1 54.3 58.1 -2.2 -38.2 -40.7 + min nodes: max nodes: 5 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 1.4 10.3 29.1 54.3 58.1 -2.2 -38.2 -40.7 + TSn: 5 rpart: 0.20 0.20 0.20 0.20 0.00 0.33 0.33 0.33 + disp[1]: -0.03 disp[2]: -0.04 disp[3]: -0.04 disp[4]: -0.08 disp[5]: 0.00 disp[6]: -0.05 disp[7]: 0.01 + disp[1]: -0.02 disp[2]: -0.02 disp[3]: -0.02 disp[4]: -0.04 disp[5]: 0.00 disp[6]: -0.03 disp[7]: 0.01 + disp[1]: -0.01 disp[2]: -0.01 disp[3]: -0.01 disp[4]: -0.02 disp[5]: 0.00 disp[6]: -0.02 disp[7]: 0.01 + disp[1]: -0.01 disp[2]: -0.01 disp[3]: -0.01 disp[4]: -0.01 disp[5]: 0.00 disp[6]: -0.01 disp[7]: 0.01 + spacings (end ic_reparam, steps: 5): 1.28 1.27 1.27 1.27 1.26 1.33 1.31 1.32 disprms: 0.019 + V_profile: 0.0 1.4 10.3 29.1 54.3 58.1 -2.2 -38.2 -40.7 + 3 way tangent (5): f1: 0.06 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 5 (0.58) ss: 0.070 (DMAX: 0.069) predE: -0.31 E(M): 1.17 gRMS: 0.0030 ratio: -0.632 dE>0, decreasing DMAX + Opt step: 2 gqc: 0.005 ss: 0.072 (DMAX: 0.046) predE: -0.34 E(M): 1.37 gRMS: 0.0064 ratio: 1.076 + Opt step: 3 gqc: 0.004 ss: 0.052 (DMAX: 0.046) predE: -0.13 E(M): 1.00 gRMS: 0.0030 + + Opt step: 1 t/ol: 4 (0.59) ss: 0.160 (DMAX: 0.065) predE: -0.73 E(M): 8.92 gRMS: 0.0053 ratio: 0.539 + Opt step: 2 gqc: 0.015 ss: 0.139 (DMAX: 0.065) predE: -0.46 E(M): 8.53 gRMS: 0.0050 ratio: 1.108 increasing DMAX + Opt step: 3 gqc: 0.015 ss: 0.133 (DMAX: 0.071) predE: -0.39 E(M): 8.02 gRMS: 0.0032 + + Opt step: 1 t/ol: 6 (0.44) ss: 0.166 (DMAX: 0.146) predE: -1.50 E(M): 26.38 gRMS: 0.0053 ratio: 0.675 + Opt step: 2 gqc: 0.029 ss: 0.142 (DMAX: 0.146) predE: -1.53 E(M): 25.37 gRMS: 0.0087 ratio: 1.210 + Opt step: 3 gqc: 0.028 ss: 0.144 (DMAX: 0.146) predE: -1.01 E(M): 23.51 gRMS: 0.0030 + + Opt step: 1 t/ol: 0 (0.52) ss: 0.160 (DMAX: 0.161) predE: -1.21 E(M): 49.96 gRMS: 0.0040 ratio: 1.090 + Opt step: 2 gqc: 0.033 ss: 0.133 (DMAX: 0.161) predE: -1.08 E(M): 48.63 gRMS: 0.0064 ratio: 1.212 + Opt step: 3 gqc: 0.031 ss: 0.124 (DMAX: 0.161) predE: -0.96 E(M): 47.33 gRMS: 0.0041 + + Opt step: 1 gqc: -0.030 ss: 0.236 (DMAX: 0.073) gts: -0.0304 predE: -1.42 E(M): 57.10 gRMS: 0.0083 ratio: 1.035 increasing DMAX + Opt step: 2 gqc: -0.030 ss: 0.234 (DMAX: 0.081) gts: -0.0304 predE: -1.52 E(M): 55.64 gRMS: 0.0080 ratio: 1.075 increasing DMAX + Opt step: 3 gqc: -0.031 ss: 0.233 (DMAX: 0.089) gts: -0.0307 predE: -1.58 E(M): 54.00 gRMS: 0.0076 + + Opt step: 1 t/ol: 0 (0.44) ss: 0.168 (DMAX: 0.161) predE: -2.18 E(M): -0.77 gRMS: 0.0069 ratio: 1.045 increasing DMAX + Opt step: 2 gqc: -0.075 ss: 0.152 (DMAX: 0.177) predE: -1.89 E(M): -3.05 gRMS: 0.0053 ratio: 1.003 + Opt step: 3 gqc: -0.070 ss: 0.147 (DMAX: 0.177) predE: -1.56 E(M): -4.95 gRMS: 0.0051 + + Opt step: 1 t/ol: 0 (0.54) ss: 0.051 (DMAX: 0.161) predE: -0.07 E(M): -38.36 gRMS: 0.0011 ratio: 1.073 + Opt step: 2 gqc: -0.009 ss: 0.047 (DMAX: 0.161) predE: -0.08 E(M): -38.43 gRMS: 0.0014 ratio: 0.455 + Opt step: 3 gqc: -0.009 ss: 0.038 (DMAX: 0.161) predE: -0.08 E(M): -38.47 gRMS: 0.0020 +r +c opt_iter: 7 totalgrad: 0.176 gradrms: 0.0043 tgrads: 95 ol(0): 0.00 max E: 54.0 + in find_peaks (2) + V_profile: 0.0 1.0 8.0 23.5 47.3 54.0 -4.9 -38.4 -40.7 + min nodes: max nodes: 5 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 1.0 8.0 23.5 47.3 54.0 -4.9 -38.4 -40.7 + TSn: 5 rpart: 0.20 0.20 0.20 0.20 0.00 0.33 0.33 0.33 + disp[1]: -0.01 disp[2]: 0.00 disp[3]: -0.01 disp[4]: -0.06 disp[5]: 0.00 disp[6]: -0.02 disp[7]: -0.01 + disp[1]: -0.01 disp[2]: -0.00 disp[3]: -0.01 disp[4]: -0.03 disp[5]: 0.00 disp[6]: -0.01 disp[7]: -0.00 + disp[1]: -0.00 disp[2]: -0.00 disp[3]: -0.01 disp[4]: -0.02 disp[5]: 0.00 disp[6]: -0.01 disp[7]: -0.00 + disp[1]: -0.00 disp[2]: -0.00 disp[3]: -0.00 disp[4]: -0.01 disp[5]: 0.00 disp[6]: -0.01 disp[7]: -0.00 + spacings (end ic_reparam, steps: 5): 1.29 1.28 1.29 1.29 1.28 1.33 1.32 1.32 disprms: 0.012 + V_profile: 0.0 1.0 8.0 23.5 47.3 54.0 -4.9 -38.4 -40.7 + 3 way tangent (5): f1: 0.10 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 5 (0.60) ss: 0.055 (DMAX: 0.046) predE: -0.08 E(M): 0.85 gRMS: 0.0012 ratio: 0.625 + Opt step: 2 gqc: 0.003 ss: 0.053 (DMAX: 0.046) predE: -0.10 E(M): 0.80 gRMS: 0.0016 ratio: 0.800 increasing DMAX + Opt step: 3 gqc: 0.003 ss: 0.046 (DMAX: 0.051) predE: -0.05 E(M): 0.72 gRMS: 0.0011 + + Opt step: 1 t/ol: 4 (0.50) ss: 0.148 (DMAX: 0.071) predE: -0.43 E(M): 7.56 gRMS: 0.0025 ratio: 1.135 increasing DMAX + Opt step: 2 gqc: 0.012 ss: 0.142 (DMAX: 0.078) predE: -0.42 E(M): 7.08 gRMS: 0.0020 ratio: 1.175 increasing DMAX + Opt step: 3 gqc: 0.012 ss: 0.134 (DMAX: 0.086) predE: -0.41 E(M): 6.59 gRMS: 0.0018 + + Opt step: 1 t/ol: 6 (0.42) ss: 0.141 (DMAX: 0.146) predE: -1.06 E(M): 21.89 gRMS: 0.0035 ratio: 0.916 + Opt step: 2 gqc: 0.026 ss: 0.137 (DMAX: 0.146) predE: -1.08 E(M): 20.92 gRMS: 0.0058 ratio: 1.256 + Opt step: 3 gqc: 0.025 ss: 0.144 (DMAX: 0.146) predE: -1.00 E(M): 19.56 gRMS: 0.0034 + + Opt step: 1 t/ol: 0 (0.58) ss: 0.116 (DMAX: 0.161) predE: -0.76 E(M): 44.72 gRMS: 0.0035 ratio: 0.574 + Opt step: 2 gqc: 0.032 ss: 0.097 (DMAX: 0.161) predE: -0.79 E(M): 44.28 gRMS: 0.0067 ratio: 1.001 + Opt step: 3 gqc: 0.032 ss: 0.109 (DMAX: 0.161) predE: -0.69 E(M): 43.49 gRMS: 0.0039 + + Opt step: 1 gqc: -0.028 ss: 0.238 (DMAX: 0.089) gts: -0.0283 predE: -1.55 E(M): 52.27 gRMS: 0.0075 ratio: 1.090 increasing DMAX + Opt step: 2 gqc: -0.029 ss: 0.234 (DMAX: 0.097) gts: -0.0290 predE: -1.60 E(M): 50.58 gRMS: 0.0073 ratio: 1.105 increasing DMAX + Opt step: 3 gqc: -0.030 ss: 0.224 (DMAX: 0.107) gts: -0.0299 predE: -1.65 E(M): 48.81 gRMS: 0.0070 + + Opt step: 1 t/ol: 9 (0.49) ss: 0.182 (DMAX: 0.177) predE: -1.17 E(M): -5.37 gRMS: 0.0031 ratio: 1.192 increasing DMAX + Opt step: 2 gqc: -0.068 ss: 0.172 (DMAX: 0.195) predE: -1.11 E(M): -6.76 gRMS: 0.0040 ratio: 0.951 + Opt step: 3 gqc: -0.065 ss: 0.156 (DMAX: 0.195) predE: -0.85 E(M): -7.82 gRMS: 0.0039 + + Opt step: 1 t/ol: 0 (0.65) ss: 0.074 (DMAX: 0.025) predE: -0.07 E(M): -38.30 gRMS: 0.0014 ratio: 0.994 increasing DMAX + Opt step: 2 gqc: -0.009 ss: 0.067 (DMAX: 0.028) predE: -0.06 E(M): -38.37 gRMS: 0.0011 ratio: 1.042 increasing DMAX + Opt step: 3 gqc: -0.009 ss: 0.061 (DMAX: 0.030) predE: -0.06 E(M): -38.44 gRMS: 0.0010 + +c opt_iter: 8 totalgrad: 0.143 gradrms: 0.0037 tgrads: 116 ol(0): 0.00 max E: 48.8 + in find_peaks (2) + V_profile: 0.0 0.7 6.6 19.6 43.5 48.8 -7.8 -38.4 -40.7 + min nodes: max nodes: 5 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.7 6.6 19.6 43.5 48.8 -7.8 -38.4 -40.7 + TSn: 5 rpart: 0.20 0.20 0.20 0.20 0.00 0.33 0.33 0.33 + disp[1]: -0.00 disp[2]: 0.02 disp[3]: 0.00 disp[4]: -0.04 disp[5]: 0.00 disp[6]: 0.03 disp[7]: -0.03 + disp[1]: -0.00 disp[2]: 0.01 disp[3]: 0.00 disp[4]: -0.02 disp[5]: 0.00 disp[6]: 0.02 disp[7]: -0.01 + disp[1]: -0.00 disp[2]: 0.01 disp[3]: 0.00 disp[4]: -0.01 disp[5]: 0.00 disp[6]: 0.02 disp[7]: -0.00 + disp[1]: -0.00 disp[2]: 0.01 disp[3]: 0.00 disp[4]: -0.01 disp[5]: 0.00 disp[6]: 0.01 disp[7]: -0.00 + spacings (end ic_reparam, steps: 5): 1.31 1.30 1.31 1.32 1.30 1.34 1.36 1.35 disprms: 0.015 + V_profile: 0.0 0.7 6.6 19.6 43.5 48.8 -7.8 -38.4 -40.7 + 3 way tangent (5): f1: 0.09 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 5 (0.58) ss: 0.045 (DMAX: 0.051) predE: -0.04 E(M): 0.65 gRMS: 0.0007 * + + Opt step: 1 t/ol: 4 (0.44) ss: 0.129 (DMAX: 0.086) predE: -0.44 E(M): 6.32 gRMS: 0.0019 ratio: 1.199 increasing DMAX + Opt step: 2 gqc: 0.010 ss: 0.119 (DMAX: 0.094) predE: -0.43 E(M): 5.79 gRMS: 0.0018 ratio: 1.242 increasing DMAX + Opt step: 3 gqc: 0.009 ss: 0.111 (DMAX: 0.104) predE: -0.43 E(M): 5.25 gRMS: 0.0018 + + Opt step: 1 t/ol: 6 (0.44) ss: 0.160 (DMAX: 0.146) predE: -1.90 E(M): 18.88 gRMS: 0.0074 ratio: -0.024 dE>0, decreasing DMAX + Opt step: 2 gqc: 0.027 ss: 0.149 (DMAX: 0.098) predE: -1.30 E(M): 18.93 gRMS: 0.0112 ratio: 1.054 + Opt step: 3 gqc: 0.025 ss: 0.133 (DMAX: 0.098) predE: -0.70 E(M): 17.55 gRMS: 0.0054 + + Opt step: 1 t/ol: 7 (0.47) ss: 0.150 (DMAX: 0.161) predE: -1.26 E(M): 42.01 gRMS: 0.0048 ratio: 0.032 decreasing DMAX + Opt step: 2 gqc: 0.031 ss: 0.137 (DMAX: 0.136) predE: -1.40 E(M): 41.97 gRMS: 0.0101 ratio: 1.164 + Opt step: 3 gqc: 0.029 ss: 0.122 (DMAX: 0.136) predE: -0.62 E(M): 40.34 gRMS: 0.0033 + + Opt step: 1 gqc: -0.031 ss: 0.218 (DMAX: 0.107) gts: -0.0313 predE: -1.43 E(M): 46.95 gRMS: 0.0067 ratio: 1.133 increasing DMAX + Opt step: 2 gqc: -0.032 ss: 0.217 (DMAX: 0.118) gts: -0.0316 predE: -1.47 E(M): 45.33 gRMS: 0.0064 ratio: 1.151 increasing DMAX + Opt step: 3 gqc: -0.032 ss: 0.209 (DMAX: 0.130) gts: -0.0316 predE: -1.53 E(M): 43.63 gRMS: 0.0061 + + Opt step: 1 t/ol: 9 (0.46) ss: 0.162 (DMAX: 0.195) predE: -1.19 E(M): -10.15 gRMS: 0.0032 ratio: 1.108 + Opt step: 2 gqc: -0.059 ss: 0.127 (DMAX: 0.195) predE: -0.87 E(M): -11.47 gRMS: 0.0030 ratio: 0.951 + Opt step: 3 gqc: -0.059 ss: 0.118 (DMAX: 0.195) predE: -0.83 E(M): -12.29 gRMS: 0.0035 + + Opt step: 1 t/ol: 0 (0.71) ss: 0.061 (DMAX: 0.030) predE: -0.08 E(M): -38.29 gRMS: 0.0013 ratio: 1.080 increasing DMAX + Opt step: 2 gqc: -0.008 ss: 0.054 (DMAX: 0.033) predE: -0.07 E(M): -38.38 gRMS: 0.0011 ratio: 1.160 increasing DMAX + Opt step: 3 gqc: -0.007 ss: 0.046 (DMAX: 0.037) predE: -0.06 E(M): -38.46 gRMS: 0.0010 * + +c opt_iter: 9 totalgrad: 0.141 gradrms: 0.0037 tgrads: 135 ol(0): 0.00 max E: 43.6 + in find_peaks (2) + V_profile: 0.0 0.7 5.3 17.6 40.3 43.6 -12.3 -38.5 -40.7 + min nodes: max nodes: 5 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.7 5.3 17.6 40.3 43.6 -12.3 -38.5 -40.7 + TSn: 5 rpart: 0.20 0.20 0.20 0.20 0.00 0.33 0.33 0.33 + disp[1]: 0.01 disp[2]: 0.03 disp[3]: -0.00 disp[4]: -0.05 disp[5]: 0.00 disp[6]: -0.00 disp[7]: 0.05 + disp[1]: 0.00 disp[2]: 0.02 disp[3]: -0.00 disp[4]: -0.03 disp[5]: 0.00 disp[6]: -0.00 disp[7]: 0.02 + disp[1]: 0.00 disp[2]: 0.01 disp[3]: -0.00 disp[4]: -0.01 disp[5]: 0.00 disp[6]: -0.00 disp[7]: 0.01 + spacings (end ic_reparam, steps: 5): 1.32 1.31 1.33 1.33 1.31 1.34 1.33 1.34 disprms: 0.019 + V_profile: 0.0 0.7 5.3 17.6 40.3 43.6 -12.3 -38.5 -40.7 + 3 way tangent (5): f1: 0.06 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 5 (0.53) ss: 0.055 (DMAX: 0.051) predE: -0.08 E(M): 0.61 gRMS: 0.0011 ratio: 0.291 + Opt step: 2 gqc: 0.002 ss: 0.054 (DMAX: 0.051) predE: -0.12 E(M): 0.59 gRMS: 0.0022 ratio: 0.697 + Opt step: 3 gqc: 0.002 ss: 0.042 (DMAX: 0.051) predE: -0.05 E(M): 0.51 gRMS: 0.0013 + + Opt step: 1 t/ol: 22 (0.43) ss: 0.110 (DMAX: 0.104) predE: -0.45 E(M): 4.95 gRMS: 0.0023 ratio: 0.924 increasing DMAX + Opt step: 2 gqc: 0.009 ss: 0.098 (DMAX: 0.114) predE: -0.44 E(M): 4.54 gRMS: 0.0034 ratio: 1.182 + Opt step: 3 gqc: 0.008 ss: 0.091 (DMAX: 0.114) predE: -0.28 E(M): 4.01 gRMS: 0.0013 + + Opt step: 1 t/ol: 27 (0.39) ss: 0.143 (DMAX: 0.098) predE: -0.74 E(M): 16.93 gRMS: 0.0041 ratio: 0.876 increasing DMAX + Opt step: 2 gqc: 0.023 ss: 0.133 (DMAX: 0.107) predE: -0.57 E(M): 16.28 gRMS: 0.0034 ratio: 1.268 + Opt step: 3 gqc: 0.023 ss: 0.122 (DMAX: 0.107) predE: -0.45 E(M): 15.56 gRMS: 0.0017 + + Opt step: 1 t/ol: 0 (0.48) ss: 0.150 (DMAX: 0.136) predE: -0.83 E(M): 38.59 gRMS: 0.0036 ratio: 0.813 increasing DMAX + Opt step: 2 gqc: 0.028 ss: 0.138 (DMAX: 0.150) predE: -0.75 E(M): 37.92 gRMS: 0.0049 ratio: 1.242 + Opt step: 3 gqc: 0.027 ss: 0.120 (DMAX: 0.150) predE: -0.46 E(M): 36.99 gRMS: 0.0019 + + Opt step: 1 gqc: -0.031 ss: 0.209 (DMAX: 0.130) gts: -0.0313 predE: -1.53 E(M): 41.84 gRMS: 0.0060 ratio: 1.144 increasing DMAX + Opt step: 2 gqc: -0.032 ss: 0.195 (DMAX: 0.143) gts: -0.0320 predE: -1.75 E(M): 40.09 gRMS: 0.0060 ratio: 1.158 increasing DMAX + Opt step: 3 gqc: -0.034 ss: 0.192 (DMAX: 0.157) gts: -0.0335 predE: -1.82 E(M): 38.06 gRMS: 0.0059 + + Opt step: 1 t/ol: 6 (0.47) ss: 0.159 (DMAX: 0.195) predE: -1.07 E(M): -12.92 gRMS: 0.0030 ratio: 1.155 + Opt step: 2 gqc: -0.054 ss: 0.145 (DMAX: 0.195) predE: -0.89 E(M): -14.15 gRMS: 0.0028 ratio: 1.056 + Opt step: 3 gqc: -0.053 ss: 0.138 (DMAX: 0.195) predE: -0.86 E(M): -15.09 gRMS: 0.0033 + + Opt step: 1 t/ol: 0 (0.68) ss: 0.045 (DMAX: 0.037) predE: -0.04 E(M): -38.69 gRMS: 0.0008 * + +c opt_iter: 10 totalgrad: 0.105 gradrms: 0.0028 tgrads: 154 ol(0): 0.00 max E: 38.1 + in find_peaks (2) + V_profile: 0.0 0.5 4.0 15.6 37.0 38.1 -15.1 -38.7 -40.7 + min nodes: max nodes: 5 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.5 4.0 15.6 37.0 38.1 -15.1 -38.7 -40.7 + TSn: 5 rpart: 0.20 0.20 0.20 0.20 0.00 0.33 0.33 0.33 + disp[1]: 0.01 disp[2]: 0.04 disp[3]: 0.00 disp[4]: -0.04 disp[5]: 0.00 disp[6]: 0.03 disp[7]: -0.04 + disp[1]: 0.01 disp[2]: 0.02 disp[3]: 0.00 disp[4]: -0.02 disp[5]: 0.00 disp[6]: 0.02 disp[7]: -0.01 + disp[1]: 0.00 disp[2]: 0.01 disp[3]: 0.00 disp[4]: -0.01 disp[5]: 0.00 disp[6]: 0.02 disp[7]: -0.01 + disp[1]: 0.00 disp[2]: 0.01 disp[3]: 0.00 disp[4]: -0.01 disp[5]: 0.00 disp[6]: 0.01 disp[7]: -0.00 + spacings (end ic_reparam, steps: 5): 1.34 1.34 1.35 1.35 1.33 1.34 1.37 1.35 disprms: 0.016 + V_profile: 0.0 0.5 4.0 15.6 37.0 38.1 -15.1 -38.7 -40.7 + 3 way tangent (5): f1: 0.02 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 5 (0.50) ss: 0.040 (DMAX: 0.051) predE: -0.03 E(M): 0.47 gRMS: 0.0004 * + + Opt step: 1 t/ol: 22 (0.48) ss: 0.093 (DMAX: 0.114) predE: -0.27 E(M): 3.98 gRMS: 0.0013 ratio: 1.315 + Opt step: 2 gqc: 0.007 ss: 0.092 (DMAX: 0.114) predE: -0.27 E(M): 3.62 gRMS: 0.0015 ratio: 1.101 + Opt step: 3 gqc: 0.007 ss: 0.090 (DMAX: 0.114) predE: -0.28 E(M): 3.32 gRMS: 0.0023 +S + Opt step: 1 t/ol: 27 (0.42) ss: 0.146 (DMAX: 0.107) predE: -0.52 E(M): 15.00 gRMS: 0.0021 ratio: 1.133 increasing DMAX + Opt step: 2 gqc: 0.021 ss: 0.142 (DMAX: 0.118) predE: -0.52 E(M): 14.41 gRMS: 0.0024 ratio: 1.238 increasing DMAX + Opt step: 3 gqc: 0.021 ss: 0.129 (DMAX: 0.130) predE: -0.47 E(M): 13.77 gRMS: 0.0022 + + Opt step: 1 t/ol: 8 (0.40) ss: 0.176 (DMAX: 0.150) predE: -0.88 E(M): 35.47 gRMS: 0.0026 ratio: 1.118 increasing DMAX + Opt step: 2 gqc: 0.026 ss: 0.166 (DMAX: 0.165) predE: -0.83 E(M): 34.49 gRMS: 0.0030 ratio: 1.053 increasing DMAX + Opt step: 3 gqc: 0.025 ss: 0.158 (DMAX: 0.181) predE: -0.71 E(M): 33.62 gRMS: 0.0042 +S + Opt step: 1 gqc: -0.036 ss: 0.186 (DMAX: 0.157) gts: -0.0358 predE: -1.89 E(M): 35.96 gRMS: 0.0059 ratio: 1.148 increasing DMAX + Opt step: 2 gqc: -0.037 ss: 0.174 (DMAX: 0.173) gts: -0.0372 predE: -1.98 E(M): 33.79 gRMS: 0.0053 ratio: 1.166 increasing DMAX + Opt step: 3 gqc: -0.038 ss: 0.194 (DMAX: 0.190) gts: -0.0378 predE: -1.73 E(M): 31.48 gRMS: 0.0053 + + Opt step: 1 t/ol: 11 (0.55) ss: 0.160 (DMAX: 0.195) predE: -1.26 E(M): -16.98 gRMS: 0.0037 ratio: 1.059 + Opt step: 2 gqc: -0.046 ss: 0.147 (DMAX: 0.195) predE: -1.30 E(M): -18.31 gRMS: 0.0037 ratio: 1.000 + Opt step: 3 gqc: -0.045 ss: 0.138 (DMAX: 0.195) predE: -1.21 E(M): -19.61 gRMS: 0.0035 + + Opt step: 1 t/ol: 0 (0.73) ss: 0.050 (DMAX: 0.037) predE: -0.06 E(M): -38.57 gRMS: 0.0009 * + +c opt_iter: 11 totalgrad: 0.122 gradrms: 0.0031 tgrads: 171 ol(0): 0.00 max E: 33.6 + in find_peaks (2) + V_profile: 0.0 0.5 3.3 13.8 33.6 31.5 -19.6 -38.6 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.5 3.3 13.8 33.6 31.5 -19.6 -38.6 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.03 disp[2]: 0.05 disp[3]: 0.02 disp[4]: 0.00 disp[5]: 0.03 disp[6]: 0.02 disp[7]: 0.00 + disp[1]: 0.02 disp[2]: 0.03 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.02 disp[6]: 0.02 disp[7]: 0.00 + disp[1]: 0.01 disp[2]: 0.02 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.01 disp[7]: 0.00 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.00 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.01 disp[7]: 0.00 + spacings (end ic_reparam, steps: 5): 1.36 1.36 1.37 1.37 1.35 1.35 1.36 1.36 disprms: 0.019 + V_profile: 0.0 0.5 3.3 13.8 33.6 31.5 -19.6 -38.6 -40.7 + 3 way tangent (4): f1: 0.90 + + slowing down climb optimization + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 5 (0.46) ss: 0.043 (DMAX: 0.051) predE: -0.03 E(M): 0.47 gRMS: 0.0005 * + + Opt step: 1 t/ol: 22 (0.49) ss: 0.091 (DMAX: 0.072) predE: -0.23 E(M): 3.35 gRMS: 0.0018 ratio: 1.165 increasing DMAX + Opt step: 2 gqc: 0.006 ss: 0.089 (DMAX: 0.079) predE: -0.20 E(M): 3.08 gRMS: 0.0012 ratio: 1.229 increasing DMAX + Opt step: 3 gqc: 0.006 ss: 0.088 (DMAX: 0.087) predE: -0.20 E(M): 2.84 gRMS: 0.0014 + + Opt step: 1 t/ol: 27 (0.43) ss: 0.151 (DMAX: 0.130) predE: -0.58 E(M): 13.44 gRMS: 0.0021 ratio: 1.309 + Opt step: 2 gqc: 0.020 ss: 0.129 (DMAX: 0.130) predE: -0.52 E(M): 12.68 gRMS: 0.0019 ratio: 1.233 + Opt step: 3 gqc: 0.019 ss: 0.120 (DMAX: 0.130) predE: -0.53 E(M): 12.04 gRMS: 0.0029 +S + Opt step: 1 gqc: 0.023 ss: 0.178 (DMAX: 0.042) gts: 0.0227 predE: -0.01 E(M): 32.75 gRMS: 0.0035 ratio: 2.174 + Opt step: 2 gqc: 0.022 ss: 0.177 (DMAX: 0.042) gts: 0.0222 predE: 0.01 E(M): 32.72 gRMS: 0.0028 ratio: -2.987 + Opt step: 3 gqc: 0.022 ss: 0.173 (DMAX: 0.042) gts: 0.0217 predE: 0.01 E(M): 32.70 gRMS: 0.0025 + + Opt step: 1 t/ol: 0 (0.47) ss: 0.206 (DMAX: 0.190) predE: -2.72 E(M): 28.47 gRMS: 0.0065 ratio: 0.911 increasing DMAX + Opt step: 2 gqc: -0.046 ss: 0.198 (DMAX: 0.209) predE: -2.56 E(M): 25.99 gRMS: 0.0076 ratio: 1.170 + Opt step: 3 gqc: -0.048 ss: 0.168 (DMAX: 0.209) predE: -2.10 E(M): 22.99 gRMS: 0.0047 + + Opt step: 1 t/ol: 11 (0.56) ss: 0.186 (DMAX: 0.195) predE: -1.62 E(M): -21.38 gRMS: 0.0043 ratio: 1.181 + Opt step: 2 gqc: -0.037 ss: 0.170 (DMAX: 0.195) predE: -1.19 E(M): -23.30 gRMS: 0.0036 ratio: 1.038 + Opt step: 3 gqc: -0.035 ss: 0.145 (DMAX: 0.195) predE: -1.11 E(M): -24.54 gRMS: 0.0042 + + Opt step: 1 t/ol: 0 (0.79) ss: 0.075 (0.037) predE: -0.09 Hint ev: 0.018 0.032 E(M): -38.65 gRMS: 0.0010 ratio: 1.045 increasing DMAX + Opt step: 2 t/ol: 0 (0.80) ss: 0.059 (0.040) predE: -0.07 Hint ev: 0.018 0.031 E(M): -38.74 gRMS: 0.0010 * + +c opt_iter: 12 totalgrad: 0.112 gradrms: 0.0029 tgrads: 189 ol(0): 0.00 max E: 32.7 + in find_peaks (2) + V_profile: 0.0 0.5 2.8 12.0 32.7 23.0 -24.5 -38.7 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.5 2.8 12.0 32.7 23.0 -24.5 -38.7 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.03 disp[2]: 0.04 disp[3]: 0.03 disp[4]: 0.00 disp[5]: -0.02 disp[6]: 0.02 disp[7]: -0.06 + disp[1]: 0.02 disp[2]: 0.02 disp[3]: 0.02 disp[4]: 0.00 disp[5]: -0.01 disp[6]: 0.01 disp[7]: -0.02 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: -0.01 disp[6]: 0.01 disp[7]: -0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: -0.00 disp[6]: 0.01 disp[7]: -0.00 + spacings (end ic_reparam, steps: 5): 1.38 1.38 1.39 1.39 1.38 1.36 1.39 1.37 disprms: 0.016 + V_profile: 0.0 0.5 2.8 12.0 32.7 23.0 -24.5 -38.7 -40.7 + 3 way tangent (4): f1: 0.68 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 5 (0.43) ss: 0.043 (DMAX: 0.051) predE: -0.05 E(M): 0.47 gRMS: 0.0009 * + + Opt step: 1 t/ol: 22 (0.51) ss: 0.091 (DMAX: 0.087) predE: -0.24 E(M): 2.86 gRMS: 0.0017 ratio: 0.900 increasing DMAX + Opt step: 2 gqc: 0.005 ss: 0.089 (DMAX: 0.096) predE: -0.25 E(M): 2.64 gRMS: 0.0025 ratio: 1.132 + Opt step: 3 gqc: 0.005 ss: 0.085 (DMAX: 0.096) predE: -0.16 E(M): 2.36 gRMS: 0.0014 + + Opt step: 1 t/ol: 27 (0.43) ss: 0.123 (DMAX: 0.096) predE: -0.32 E(M): 12.06 gRMS: 0.0026 ratio: 0.971 increasing DMAX + Opt step: 2 gqc: 0.020 ss: 0.100 (DMAX: 0.105) predE: -0.21 E(M): 11.75 gRMS: 0.0018 ratio: 1.396 + Opt step: 3 gqc: 0.020 ss: 0.097 (DMAX: 0.105) predE: -0.18 E(M): 11.46 gRMS: 0.0014 + + Opt step: 1 gqc: 0.020 ss: 0.156 (DMAX: 0.042) gts: 0.0195 predE: -0.09 E(M): 32.68 gRMS: 0.0026 ratio: 1.227 increasing DMAX + Opt step: 2 gqc: 0.019 ss: 0.153 (DMAX: 0.046) gts: 0.0189 predE: -0.13 E(M): 32.57 gRMS: 0.0026 ratio: 1.187 increasing DMAX + Opt step: 3 gqc: 0.018 ss: 0.151 (DMAX: 0.051) gts: 0.0182 predE: -0.16 E(M): 32.42 gRMS: 0.0025 + + Opt step: 1 t/ol: 12 (0.43) ss: 0.201 (DMAX: 0.209) predE: -1.87 E(M): 21.69 gRMS: 0.0043 ratio: 0.749 + Opt step: 2 gqc: -0.054 ss: 0.203 (DMAX: 0.209) predE: -1.89 E(M): 20.29 gRMS: 0.0077 ratio: 1.129 + Opt step: 3 gqc: -0.055 ss: 0.173 (DMAX: 0.209) predE: -1.10 E(M): 18.15 gRMS: 0.0028 + + Opt step: 1 t/ol: 1 (0.51) ss: 0.165 (DMAX: 0.195) predE: -1.16 E(M): -26.03 gRMS: 0.0035 ratio: 0.983 + Opt step: 2 gqc: -0.027 ss: 0.146 (DMAX: 0.195) predE: -0.90 E(M): -27.18 gRMS: 0.0040 ratio: 0.967 + Opt step: 3 gqc: -0.028 ss: 0.156 (DMAX: 0.195) predE: -0.86 E(M): -28.05 gRMS: 0.0028 + + Opt step: 1 t/ol: 0 (0.80) ss: 0.056 (0.040) predE: -0.07 Hint ev: 0.018 0.031 E(M): -38.63 gRMS: 0.0010 * + +c opt_iter: 13 totalgrad: 0.083 gradrms: 0.0020 tgrads: 206 ol(0): 0.00 max E: 32.4 + in find_peaks (2) + V_profile: 0.0 0.5 2.4 11.5 32.4 18.2 -28.0 -38.6 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + ** starting exact TS search at node 4 ** + totalgrad: 0.0829 gradrms: 0.0025 gts: 0.0182 + TS Hess init'd w/existing Hintp + tHt: 0.118 a: 1.3 b: 1.1 C: -0.039 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.5 2.4 11.5 32.4 18.2 -28.0 -38.6 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.03 disp[2]: 0.04 disp[3]: 0.02 disp[4]: 0.00 disp[5]: 0.02 disp[6]: 0.02 disp[7]: -0.04 + disp[1]: 0.02 disp[2]: 0.02 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.01 disp[7]: -0.02 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.01 disp[7]: -0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.00 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.01 disp[7]: -0.00 + spacings (end ic_reparam, steps: 5): 1.40 1.41 1.41 1.41 1.39 1.39 1.40 1.39 disprms: 0.017 + V_profile: 0.0 0.5 2.4 11.5 32.4 18.2 -28.0 -38.6 -40.7 + 3 way tangent (4): f1: 0.60 + + eg eg eg eg eg eg eg eg eg TS Hess init'd w/existing Hintp + tHt: 0.117 a: 1.2 b: 1.2 C: -0.039 + eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.43) ss: 0.053 (DMAX: 0.051) predE: -0.19 E(M): 0.51 gRMS: 0.0021 ratio: -0.860 dE>0, decreasing DMAX + Opt step: 2 gqc: 0.001 ss: 0.044 (DMAX: 0.034) predE: -0.21 E(M): 0.67 gRMS: 0.0048 ratio: 1.113 + Opt step: 3 gqc: 0.001 ss: 0.027 (DMAX: 0.034) predE: -0.05 E(M): 0.44 gRMS: 0.0019 + + Opt step: 1 t/ol: 22 (0.49) ss: 0.085 (DMAX: 0.096) predE: -0.15 E(M): 2.35 gRMS: 0.0012 ratio: 1.233 + Opt step: 2 gqc: 0.005 ss: 0.086 (DMAX: 0.096) predE: -0.17 E(M): 2.17 gRMS: 0.0017 ratio: 0.905 + Opt step: 3 gqc: 0.004 ss: 0.085 (DMAX: 0.096) predE: -0.17 E(M): 2.02 gRMS: 0.0022 +r + Opt step: 1 t/ol: 27 (0.46) ss: 0.056 (DMAX: 0.105) predE: -0.13 E(M): 11.53 gRMS: 0.0017 ratio: 0.388 + Opt step: 2 gqc: 0.020 ss: 0.051 (DMAX: 0.105) predE: -0.16 E(M): 11.48 gRMS: 0.0030 ratio: 1.142 + Opt step: 3 gqc: 0.020 ss: 0.046 (DMAX: 0.105) predE: -0.06 E(M): 11.30 gRMS: 0.0009 * + + Opt step: 1 S: 5.0 ol: 0.95 0.13 0.08 0.07 + max ol: 0 (f0) ss: 0.075 (DMAX: 0.051) predE: 0.06 Hint ev: -0.071 0.015 0.027 0.030 ratio: 1.089 increasing DMAX E(M): 32.29 gRMS: 0.0036 + Opt step: 2 S: 4.0 ol: 0.85 0.45 0.03 0.02 + max ol: 0 (f0) ss: 0.146 (DMAX: 0.056) predE: 0.34 Hint ev: -0.037 -0.006 0.024 0.028 ratio: 0.983 increasing DMAX E(M): 32.63 gRMS: 0.0035 + Opt step: 3 S: 3.0 ol: 0.96 0.12 0.02 0.00 + max ol: 0 (f0) ss: 0.178 (DMAX: 0.062) predE: -0.22 Hint ev: -0.030 -0.017 0.024 0.028 ratio: 0.853 increasing DMAX E(M): 32.44 gRMS: 0.0034 + Opt step: 4 S: 2.0 ol: 0.97 0.01 0.05 0.01 + max ol: 0 (f0) ss: 0.353 (DMAX: 0.068) predE: -0.14 Hint ev: -0.035 0.000 0.024 0.028 ratio: 0.513 decreasing DMAX E(M): 32.37 gRMS: 0.0031 + Opt step: 5 S: 1.0 ol: 0.68 0.68 0.06 0.03 + max ol: 0 (f0) ss: 0.355 (DMAX: 0.057) predE: -0.64 Hint ev: -0.099 -0.017 0.024 0.028 ratio: 0.966 E(M): 31.75 gRMS: 0.0044 + Opt step: 6 S: 1.0 ol: 0.87 0.38 0.00 0.10 + max ol: 0 (f0) ss: 0.391 (DMAX: 0.057) predE: -0.50 Hint ev: -0.129 -0.010 0.025 0.027 E(M): 31.75 gRMS: 0.0037 + + Opt step: 1 t/ol: 8 (0.37) ss: 0.189 (DMAX: 0.209) predE: -1.22 E(M): 16.27 gRMS: 0.0037 ratio: 0.852 + Opt step: 2 gqc: -0.058 ss: 0.166 (DMAX: 0.209) predE: -0.97 E(M): 15.24 gRMS: 0.0056 ratio: 1.081 + Opt step: 3 gqc: -0.059 ss: 0.130 (DMAX: 0.209) predE: -0.49 E(M): 14.19 gRMS: 0.0026 + + Opt step: 1 t/ol: 1 (0.47) ss: 0.136 (DMAX: 0.195) predE: -0.88 E(M): -29.13 gRMS: 0.0031 ratio: 1.197 + Opt step: 2 gqc: -0.021 ss: 0.125 (DMAX: 0.195) predE: -0.71 E(M): -30.18 gRMS: 0.0027 ratio: 0.922 + Opt step: 3 gqc: -0.019 ss: 0.123 (DMAX: 0.195) predE: -0.73 E(M): -30.83 gRMS: 0.0038 + + Opt step: 1 t/ol: 0 (0.79) ss: 0.049 (0.040) predE: -0.06 Hint ev: 0.018 0.031 E(M): -38.57 gRMS: 0.0010 * + +x opt_iter: 14 totalgrad: 0.097 gradrms: 0.0024 tgrads: 231 ol(0): 0.87 max E: 31.8 + in find_peaks (2) + V_profile: 0.0 0.4 2.4 11.3 31.8 14.2 -30.8 -38.6 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 2.4 11.3 31.8 14.2 -30.8 -38.6 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.02 disp[2]: 0.03 disp[3]: 0.01 disp[4]: 0.00 disp[5]: -0.01 disp[6]: 0.04 disp[7]: -0.02 + disp[1]: 0.01 disp[2]: 0.02 disp[3]: 0.01 disp[4]: 0.00 disp[5]: -0.01 disp[6]: 0.03 disp[7]: -0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.00 disp[4]: 0.00 disp[5]: -0.01 disp[6]: 0.02 disp[7]: -0.00 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.00 disp[4]: 0.00 disp[5]: -0.00 disp[6]: 0.02 disp[7]: 0.00 + disp[1]: 0.00 disp[2]: 0.00 disp[3]: 0.00 disp[4]: 0.00 disp[5]: -0.00 disp[6]: 0.01 disp[7]: 0.00 + spacings (end ic_reparam, steps: 5): 1.41 1.42 1.42 1.42 1.40 1.38 1.41 1.40 disprms: 0.017 + V_profile: 0.0 0.4 2.4 11.3 31.8 14.2 -30.8 -38.6 -40.7 + 3 way tangent (4): f1: 0.54 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.39) ss: 0.026 (DMAX: 0.034) predE: -0.02 E(M): 0.41 gRMS: 0.0005 * + + Opt step: 1 t/ol: 22 (0.48) ss: 0.086 (DMAX: 0.057) predE: -0.13 E(M): 2.51 gRMS: 0.0013 ratio: 1.191 increasing DMAX + Opt step: 2 gqc: 0.005 ss: 0.085 (DMAX: 0.062) predE: -0.12 E(M): 2.35 gRMS: 0.0010 ratio: 1.273 + Opt step: 3 gqc: 0.004 ss: 0.084 (DMAX: 0.062) predE: -0.11 E(M): 2.20 gRMS: 0.0010 * + + Opt step: 1 t/ol: 27 (0.49) ss: 0.095 (DMAX: 0.105) predE: -0.15 E(M): 11.46 gRMS: 0.0009 * + + Opt step: 1 S: 1.0 ol: 0.79 0.48 0.15 0.08 + max ol: 0 (f0) ss: 0.193 (DMAX: 0.057) predE: -0.68 Hint ev: -0.128 -0.048 0.024 0.027 ratio: 0.718 decreasing DMAX E(M): 30.81 gRMS: 0.0044 + Opt step: 2 S: 1.0 ol: 0.93 0.13 0.10 0.11 + max ol: 0 (f0) ss: 0.153 (DMAX: 0.047) predE: 0.25 Hint ev: -0.131 -0.063 0.023 0.027 ratio: 1.523 decreasing DMAX E(M): 31.19 gRMS: 0.0038 + Opt step: 3 S: 1.0 ol: 0.95 0.19 0.03 0.09 + max ol: 0 (f0) ss: 0.143 (DMAX: 0.039) predE: 0.06 Hint ev: -0.117 -0.063 0.024 0.027 ratio: 2.159 decreasing DMAX E(M): 31.32 gRMS: 0.0042 + Opt step: 4 S: 1.0 ol: 0.40 0.88 0.01 0.06 + max ol: 1 (f1) ss: 0.203 (DMAX: 0.033) predE: -0.23 Hint ev: -0.075 -0.064 0.023 0.028 ratio: 0.777 E(M): 31.14 gRMS: 0.0031 + Opt step: 5 S: 1.0 ol: 0.95 0.13 0.10 0.05 + max ol: 0 (f0) ss: 0.227 (DMAX: 0.033) predE: -0.02 Hint ev: -0.068 -0.034 0.017 0.028 ratio: 0.135 E(M): 31.14 gRMS: 0.0029 + Opt step: 6 S: 1.0 ol: 0.95 0.02 0.05 0.06 + max ol: 0 (f0) ss: 0.422 (DMAX: 0.033) predE: -0.02 Hint ev: -0.082 -0.004 0.020 0.028 E(M): 31.14 gRMS: 0.0027 + + Opt step: 1 t/ol: 10 (0.42) ss: 0.202 (DMAX: 0.209) predE: -2.10 E(M): 14.28 gRMS: 0.0041 ratio: 1.118 + Opt step: 2 gqc: -0.056 ss: 0.193 (DMAX: 0.209) predE: -1.92 E(M): 11.93 gRMS: 0.0045 ratio: 1.108 + Opt step: 3 gqc: -0.057 ss: 0.186 (DMAX: 0.209) predE: -1.79 E(M): 9.80 gRMS: 0.0044 + + Opt step: 1 t/ol: 11 (0.52) ss: 0.138 (DMAX: 0.195) predE: -0.45 E(M): -32.08 gRMS: 0.0017 ratio: 0.999 + Opt step: 2 gqc: -0.017 ss: 0.115 (DMAX: 0.195) predE: -0.31 E(M): -32.53 gRMS: 0.0023 ratio: 1.098 + Opt step: 3 gqc: -0.016 ss: 0.117 (DMAX: 0.195) predE: -0.27 E(M): -32.87 gRMS: 0.0020 + + Opt step: 1 t/ol: 0 (0.79) ss: 0.038 (0.040) predE: -0.04 Hint ev: 0.018 0.031 E(M): -38.61 gRMS: 0.0008 * + +x opt_iter: 15 totalgrad: 0.079 gradrms: 0.0022 tgrads: 249 ol(0): 0.95 max E: 31.1 + in find_peaks (2) + V_profile: 0.0 0.4 2.2 11.5 31.1 9.8 -32.9 -38.6 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 2.2 11.5 31.1 9.8 -32.9 -38.6 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.03 disp[2]: 0.04 disp[3]: 0.04 disp[4]: 0.00 disp[5]: 0.02 disp[6]: 0.07 disp[7]: -0.01 + disp[1]: 0.02 disp[2]: 0.02 disp[3]: 0.02 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.06 disp[7]: 0.00 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.04 disp[7]: 0.00 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.03 disp[7]: 0.01 + disp[1]: 0.00 disp[2]: 0.01 disp[3]: 0.00 disp[4]: 0.00 disp[5]: 0.00 disp[6]: 0.02 disp[7]: 0.01 + spacings (end ic_reparam, steps: 5): 1.43 1.44 1.44 1.44 1.39 1.37 1.41 1.40 disprms: 0.026 + V_profile: 0.0 0.4 2.2 11.5 31.1 9.8 -32.9 -38.6 -40.7 + 3 way tangent (4): f1: 0.48 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.44) ss: 0.028 (DMAX: 0.034) predE: -0.03 E(M): 0.43 gRMS: 0.0007 * + + Opt step: 1 t/ol: 22 (0.50) ss: 0.084 (DMAX: 0.062) predE: -0.10 E(M): 2.28 gRMS: 0.0010 * + + Opt step: 1 t/ol: 27 (0.50) ss: 0.102 (DMAX: 0.105) predE: -0.20 E(M): 12.21 gRMS: 0.0015 ratio: 1.265 + Opt step: 2 gqc: 0.021 ss: 0.102 (DMAX: 0.105) predE: -0.25 E(M): 11.96 gRMS: 0.0021 ratio: 1.007 + Opt step: 3 gqc: 0.020 ss: 0.098 (DMAX: 0.105) predE: -0.20 E(M): 11.71 gRMS: 0.0023 +S + Opt step: 1 S: 1.0 ol: 0.94 0.04 0.10 0.00 + max ol: 0 (f0) ss: 0.303 (DMAX: 0.033) predE: -0.09 Hint ev: -0.083 -0.014 0.020 0.028 ratio: 0.757 E(M): 31.06 gRMS: 0.0029 + Opt step: 2 S: 1.0 ol: 0.94 0.09 0.12 0.02 + max ol: 0 (f0) ss: 0.163 (DMAX: 0.033) predE: -0.12 Hint ev: -0.079 -0.048 0.019 0.028 ratio: 0.664 decreasing DMAX E(M): 30.98 gRMS: 0.0031 + Opt step: 3 S: 1.0 ol: 0.92 0.16 0.11 0.03 + max ol: 0 (f0) ss: 0.173 (DMAX: 0.027) predE: -0.20 Hint ev: -0.097 -0.036 0.020 0.027 ratio: 0.794 E(M): 30.82 gRMS: 0.0029 + Opt step: 4 S: 1.0 ol: 0.93 0.13 0.11 0.03 + max ol: 0 (f0) ss: 0.207 (DMAX: 0.027) predE: -0.07 Hint ev: -0.090 -0.024 0.019 0.027 ratio: 0.694 decreasing DMAX E(M): 30.77 gRMS: 0.0027 + Opt step: 5 S: 1.0 ol: 0.93 0.23 0.03 0.01 + max ol: 0 (f0) ss: 0.156 (DMAX: 0.023) predE: 0.01 Hint ev: -0.079 -0.048 0.021 0.027 ratio: 1.465 E(M): 30.79 gRMS: 0.0026 + Opt step: 6 S: 1.0 ol: 0.92 0.30 0.01 0.03 + max ol: 0 (f0) ss: 0.153 (DMAX: 0.023) predE: 0.00 Hint ev: -0.080 -0.044 0.022 0.027 E(M): 30.79 gRMS: 0.0024 + + Opt step: 1 t/ol: 11 (0.43) ss: 0.190 (DMAX: 0.209) predE: -1.54 E(M): 6.64 gRMS: 0.0041 ratio: 0.625 + Opt step: 2 gqc: -0.058 ss: 0.165 (DMAX: 0.209) predE: -1.38 E(M): 5.68 gRMS: 0.0069 ratio: 1.014 + Opt step: 3 gqc: -0.059 ss: 0.139 (DMAX: 0.209) predE: -0.73 E(M): 4.28 gRMS: 0.0034 + + Opt step: 1 t/ol: 1 (0.49) ss: 0.114 (DMAX: 0.195) predE: -0.31 E(M): -33.78 gRMS: 0.0017 ratio: 1.146 + Opt step: 2 gqc: -0.011 ss: 0.117 (DMAX: 0.195) predE: -0.26 E(M): -34.13 gRMS: 0.0018 ratio: 1.011 + Opt step: 3 gqc: -0.011 ss: 0.112 (DMAX: 0.195) predE: -0.24 E(M): -34.39 gRMS: 0.0024 + + Opt step: 1 t/ol: 0 (0.81) ss: 0.028 (0.040) predE: -0.02 Hint ev: 0.018 0.031 E(M): -38.67 gRMS: 0.0006 * + +x opt_iter: 16 totalgrad: 0.083 gradrms: 0.0021 tgrads: 267 ol(0): 0.92 max E: 30.8 + in find_peaks (2) + V_profile: 0.0 0.4 2.3 11.7 30.8 4.3 -34.4 -38.7 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 2.3 11.7 30.8 4.3 -34.4 -38.7 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.03 disp[2]: 0.04 disp[3]: 0.02 disp[4]: 0.00 disp[5]: 0.03 disp[6]: 0.04 disp[7]: -0.04 + disp[1]: 0.02 disp[2]: 0.02 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.02 disp[6]: 0.03 disp[7]: -0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.02 disp[7]: -0.00 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.02 disp[7]: 0.00 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.00 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.02 disp[7]: 0.00 + spacings (end ic_reparam, steps: 5): 1.45 1.46 1.46 1.46 1.40 1.40 1.42 1.41 disprms: 0.020 + V_profile: 0.0 0.4 2.3 11.7 30.8 4.3 -34.4 -38.7 -40.7 + 3 way tangent (4): f1: 0.42 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.45) ss: 0.035 (DMAX: 0.034) predE: -0.08 E(M): 0.45 gRMS: 0.0014 ratio: -0.863 dE>0, decreasing DMAX + Opt step: 2 gqc: 0.001 ss: 0.030 (DMAX: 0.023) predE: -0.12 E(M): 0.52 gRMS: 0.0032 ratio: 0.939 + Opt step: 3 gqc: 0.001 ss: 0.020 (DMAX: 0.023) predE: -0.02 E(M): 0.41 gRMS: 0.0009 * + + Opt step: 1 t/ol: 22 (0.49) ss: 0.086 (DMAX: 0.062) predE: -0.13 E(M): 2.36 gRMS: 0.0011 ratio: 1.248 increasing DMAX + Opt step: 2 gqc: 0.004 ss: 0.084 (DMAX: 0.068) predE: -0.12 E(M): 2.20 gRMS: 0.0010 * + + Opt step: 1 t/ol: 27 (0.41) ss: 0.036 (DMAX: 0.079) predE: -0.04 E(M): 12.00 gRMS: 0.0011 ratio: 1.336 + Opt step: 2 gqc: 0.021 ss: 0.030 (DMAX: 0.079) predE: -0.04 E(M): 11.95 gRMS: 0.0007 * + + Opt step: 1 S: 1.0 ol: 0.96 0.17 0.05 0.01 + max ol: 0 (f0) ss: 0.142 (DMAX: 0.023) predE: -0.04 Hint ev: -0.085 -0.043 0.021 0.027 ratio: 0.693 E(M): 30.78 gRMS: 0.0023 + Opt step: 2 S: 1.0 ol: 0.94 0.27 0.10 0.01 + max ol: 0 (f0) ss: 0.143 (DMAX: 0.023) predE: -0.02 Hint ev: -0.079 -0.044 0.022 0.027 ratio: 0.632 E(M): 30.77 gRMS: 0.0021 + Opt step: 3 S: 1.0 ol: 0.93 0.30 0.07 0.00 + max ol: 0 (f0) ss: 0.151 (DMAX: 0.023) predE: -0.05 Hint ev: -0.084 -0.035 0.022 0.027 ratio: 0.816 E(M): 30.72 gRMS: 0.0020 + Opt step: 4 S: 1.0 ol: 0.95 0.21 0.08 0.01 + max ol: 0 (f0) ss: 0.133 (DMAX: 0.023) predE: -0.09 Hint ev: -0.086 -0.042 0.022 0.027 ratio: 0.810 E(M): 30.65 gRMS: 0.0019 + Opt step: 5 S: 1.0 ol: 0.97 0.04 0.07 0.00 + max ol: 0 (f0) ss: 0.155 (DMAX: 0.023) predE: -0.15 Hint ev: -0.103 -0.035 0.022 0.027 ratio: 0.822 E(M): 30.52 gRMS: 0.0018 + Opt step: 6 S: 1.0 ol: 0.97 0.08 0.07 0.00 + max ol: 0 (f0) ss: 0.200 (DMAX: 0.023) predE: -0.16 Hint ev: -0.108 -0.025 0.022 0.027 E(M): 30.52 gRMS: 0.0018 + + Opt step: 1 t/ol: 10 (0.52) ss: 0.192 (DMAX: 0.209) predE: -1.33 E(M): 1.97 gRMS: 0.0030 ratio: 0.923 + Opt step: 2 gqc: -0.058 ss: 0.166 (DMAX: 0.209) predE: -0.99 E(M): 0.74 gRMS: 0.0039 ratio: 0.924 + Opt step: 3 gqc: -0.059 ss: 0.151 (DMAX: 0.209) predE: -0.72 E(M): -0.18 gRMS: 0.0038 + + Opt step: 1 t/ol: 1 (0.49) ss: 0.112 (DMAX: 0.195) predE: -0.18 E(M): -34.82 gRMS: 0.0015 ratio: 0.616 + Opt step: 2 gqc: -0.007 ss: 0.070 (DMAX: 0.195) predE: -0.13 E(M): -34.93 gRMS: 0.0022 ratio: 0.934 + Opt step: 3 gqc: -0.007 ss: 0.071 (DMAX: 0.195) predE: -0.06 E(M): -35.05 gRMS: 0.0012 + + Opt step: 1 t/ol: 0 (0.79) ss: 0.023 (0.040) predE: -0.02 Hint ev: 0.018 0.031 E(M): -38.63 gRMS: 0.0005 * + +x opt_iter: 17 totalgrad: 0.064 gradrms: 0.0018 tgrads: 287 ol(0): 0.97 max E: 30.5 + in find_peaks (2) + V_profile: 0.0 0.4 2.2 11.9 30.5 -0.2 -35.1 -38.6 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 2.2 11.9 30.5 -0.2 -35.1 -38.6 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.03 disp[2]: 0.03 disp[3]: 0.03 disp[4]: 0.00 disp[5]: 0.03 disp[6]: 0.07 disp[7]: 0.01 + disp[1]: 0.02 disp[2]: 0.02 disp[3]: 0.02 disp[4]: 0.00 disp[5]: 0.02 disp[6]: 0.05 disp[7]: 0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.04 disp[7]: 0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.03 disp[7]: 0.01 + disp[1]: 0.01 disp[2]: 0.00 disp[3]: 0.00 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.02 disp[7]: 0.01 + spacings (end ic_reparam, steps: 5): 1.47 1.47 1.47 1.48 1.39 1.38 1.41 1.40 disprms: 0.026 + V_profile: 0.0 0.4 2.2 11.9 30.5 -0.2 -35.1 -38.6 -40.7 + 3 way tangent (4): f1: 0.38 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.47) ss: 0.019 (DMAX: 0.023) predE: -0.01 E(M): 0.42 gRMS: 0.0004 * + + Opt step: 1 t/ol: 22 (0.51) ss: 0.085 (DMAX: 0.068) predE: -0.12 E(M): 2.21 gRMS: 0.0011 ratio: 1.183 increasing DMAX + Opt step: 2 gqc: 0.004 ss: 0.085 (DMAX: 0.075) predE: -0.13 E(M): 2.07 gRMS: 0.0013 ratio: 0.990 increasing DMAX + Opt step: 3 gqc: 0.004 ss: 0.077 (DMAX: 0.083) predE: -0.13 E(M): 1.94 gRMS: 0.0018 +S + Opt step: 1 t/ol: 27 (0.42) ss: 0.063 (DMAX: 0.079) predE: -0.10 E(M): 12.61 gRMS: 0.0014 ratio: 0.145 decreasing DMAX + Opt step: 2 gqc: 0.022 ss: 0.059 (DMAX: 0.057) predE: -0.15 E(M): 12.59 gRMS: 0.0028 ratio: 0.973 + Opt step: 3 gqc: 0.021 ss: 0.047 (DMAX: 0.057) predE: -0.04 E(M): 12.45 gRMS: 0.0008 * + + Opt step: 1 S: 1.0 ol: 0.97 0.04 0.03 0.04 + max ol: 0 (f0) ss: 0.258 (DMAX: 0.023) predE: -0.13 Hint ev: -0.108 -0.014 0.022 0.027 ratio: 0.853 increasing DMAX E(M): 30.28 gRMS: 0.0018 + Opt step: 2 S: 1.0 ol: 0.97 0.04 0.03 0.04 + max ol: 0 (f0) ss: 0.297 (DMAX: 0.025) predE: -0.13 Hint ev: -0.108 -0.010 0.022 0.027 ratio: 0.838 E(M): 30.17 gRMS: 0.0019 + Opt step: 3 S: 1.0 ol: 0.96 0.13 0.03 0.04 + max ol: 0 (f0) ss: 0.202 (DMAX: 0.025) predE: -0.17 Hint ev: -0.110 -0.023 0.022 0.027 ratio: 0.823 E(M): 30.03 gRMS: 0.0023 + Opt step: 4 S: 1.0 ol: 0.97 0.11 0.01 0.01 + max ol: 0 (f0) ss: 0.148 (DMAX: 0.025) predE: -0.18 Hint ev: -0.111 -0.035 0.022 0.027 ratio: 0.815 E(M): 29.89 gRMS: 0.0022 + Opt step: 5 S: 1.0 ol: 0.97 0.09 0.02 0.02 + max ol: 0 (f0) ss: 0.200 (DMAX: 0.025) predE: -0.16 Hint ev: -0.111 -0.022 0.022 0.027 ratio: 0.846 E(M): 29.75 gRMS: 0.0021 + Opt step: 6 S: 1.0 ol: 0.97 0.06 0.02 0.02 + max ol: 0 (f0) ss: 0.274 (DMAX: 0.025) predE: -0.12 Hint ev: -0.111 -0.011 0.022 0.027 E(M): 29.75 gRMS: 0.0021 + + Opt step: 1 t/ol: 7 (0.43) ss: 0.199 (DMAX: 0.209) predE: -1.72 E(M): -2.46 gRMS: 0.0034 ratio: 0.859 + Opt step: 2 gqc: -0.054 ss: 0.176 (DMAX: 0.209) predE: -1.24 E(M): -3.94 gRMS: 0.0044 ratio: 1.045 + Opt step: 3 gqc: -0.057 ss: 0.153 (DMAX: 0.209) predE: -0.86 E(M): -5.23 gRMS: 0.0029 + + Opt step: 1 t/ol: 1 (0.54) ss: 0.090 (DMAX: 0.195) predE: -0.09 E(M): -35.39 gRMS: 0.0011 ratio: 0.700 + Opt step: 2 gqc: -0.006 ss: 0.062 (DMAX: 0.195) predE: -0.09 E(M): -35.46 gRMS: 0.0017 ratio: 0.476 + Opt step: 3 gqc: -0.006 ss: 0.040 (DMAX: 0.195) predE: -0.06 E(M): -35.50 gRMS: 0.0017 +S + Opt step: 1 t/ol: 0 (0.78) ss: 0.019 (0.040) predE: -0.02 Hint ev: 0.018 0.031 E(M): -38.71 gRMS: 0.0007 * + +x opt_iter: 18 totalgrad: 0.067 gradrms: 0.0017 tgrads: 307 ol(0): 0.97 max E: 29.8 + in find_peaks (2) + V_profile: 0.0 0.4 1.9 12.5 29.8 -5.2 -35.5 -38.7 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 1.9 12.5 29.8 -5.2 -35.5 -38.7 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.02 disp[2]: 0.01 disp[3]: -0.01 disp[4]: 0.00 disp[5]: -0.02 disp[6]: 0.00 disp[7]: -0.04 + disp[1]: 0.01 disp[2]: 0.00 disp[3]: -0.01 disp[4]: 0.00 disp[5]: -0.01 disp[6]: 0.00 disp[7]: -0.01 + disp[1]: 0.01 disp[2]: 0.00 disp[3]: -0.01 disp[4]: 0.00 disp[5]: -0.01 disp[6]: 0.00 disp[7]: -0.01 + spacings (end ic_reparam, steps: 5): 1.48 1.49 1.49 1.48 1.42 1.41 1.42 1.41 disprms: 0.014 + V_profile: 0.0 0.4 1.9 12.5 29.8 -5.2 -35.5 -38.7 -40.7 + 3 way tangent (4): f1: 0.33 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.53) ss: 0.020 (DMAX: 0.023) predE: -0.02 E(M): 0.42 gRMS: 0.0006 * + + Opt step: 1 t/ol: 22 (0.51) ss: 0.060 (DMAX: 0.061) predE: -0.09 E(M): 1.81 gRMS: 0.0015 ratio: 1.165 + Opt step: 2 gqc: 0.004 ss: 0.059 (DMAX: 0.061) predE: -0.07 E(M): 1.70 gRMS: 0.0013 ratio: 1.244 + Opt step: 3 gqc: 0.003 ss: 0.050 (DMAX: 0.061) predE: -0.07 E(M): 1.61 gRMS: 0.0011 + + Opt step: 1 t/ol: 27 (0.42) ss: 0.035 (DMAX: 0.057) predE: -0.03 E(M): 12.22 gRMS: 0.0006 * + + Opt step: 1 S: 1.0 ol: 0.96 0.18 0.06 0.01 + max ol: 0 (f0) ss: 0.125 (DMAX: 0.025) predE: -0.18 Hint ev: -0.112 -0.041 0.022 0.027 ratio: 0.816 E(M): 29.50 gRMS: 0.0025 + Opt step: 2 S: 1.0 ol: 0.96 0.11 0.11 0.04 + max ol: 0 (f0) ss: 0.174 (DMAX: 0.025) predE: -0.17 Hint ev: -0.113 -0.027 0.022 0.025 ratio: 0.835 E(M): 29.36 gRMS: 0.0023 + Opt step: 3 S: 1.0 ol: 0.96 0.17 0.06 0.01 + max ol: 0 (f0) ss: 0.255 (DMAX: 0.025) predE: -0.13 Hint ev: -0.113 -0.012 0.021 0.025 ratio: 0.832 E(M): 29.26 gRMS: 0.0022 + Opt step: 4 S: 1.0 ol: 0.97 0.05 0.07 0.00 + max ol: 0 (f0) ss: 0.274 (DMAX: 0.025) predE: -0.10 Hint ev: -0.112 -0.011 0.022 0.026 ratio: 0.857 increasing DMAX E(M): 29.17 gRMS: 0.0025 + Opt step: 5 S: 1.0 ol: 0.97 0.01 0.06 0.01 + max ol: 0 (f0) ss: 0.438 (DMAX: 0.028) predE: -0.02 Hint ev: -0.112 -0.000 0.022 0.025 ratio: 0.908 increasing DMAX E(M): 29.15 gRMS: 0.0029 + Opt step: 6 S: 1.0 ol: 0.96 0.12 0.07 0.00 + max ol: 0 (f0) ss: 0.373 (DMAX: 0.030) predE: -0.03 Hint ev: -0.124 -0.004 0.022 0.026 E(M): 29.15 gRMS: 0.0041 + + Opt step: 1 t/ol: 11 (0.42) ss: 0.202 (DMAX: 0.209) predE: -1.76 E(M): -5.24 gRMS: 0.0044 ratio: 0.445 + Opt step: 2 gqc: -0.053 ss: 0.176 (DMAX: 0.209) predE: -1.48 E(M): -6.02 gRMS: 0.0080 ratio: 1.019 + Opt step: 3 gqc: -0.055 ss: 0.144 (DMAX: 0.209) predE: -0.63 E(M): -7.53 gRMS: 0.0026 + + Opt step: 1 t/ol: 1 (0.55) ss: 0.047 (DMAX: 0.032) predE: -0.04 E(M): -35.56 gRMS: 0.0009 * + + Opt step: 1 t/ol: 0 (0.77) ss: 0.025 (0.040) predE: -0.05 Hint ev: 0.018 0.031 E(M): -38.63 gRMS: 0.0011 ratio: -0.658 dE>0, decreasing DMAX + Opt step: 2 t/ol: 0 (0.77) ss: 0.022 (0.020) predE: -0.08 Hint ev: 0.018 0.031 E(M): -38.59 gRMS: 0.0022 ratio: 0.648 + Opt step: 3 t/ol: 0 (0.77) ss: 0.009 (0.020) predE: -0.01 Hint ev: 0.018 0.031 E(M): -38.65 gRMS: 0.0006 * + +x opt_iter: 19 totalgrad: 0.068 gradrms: 0.0020 tgrads: 325 ol(0): 0.96 max E: 29.1 + in find_peaks (2) + V_profile: 0.0 0.4 1.6 12.2 29.1 -7.5 -35.6 -38.6 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 1.6 12.2 29.1 -7.5 -35.6 -38.6 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.02 disp[2]: 0.01 disp[3]: -0.01 disp[4]: 0.00 disp[5]: -0.02 disp[6]: 0.02 disp[7]: 0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: -0.01 disp[4]: 0.00 disp[5]: -0.01 disp[6]: 0.02 disp[7]: 0.01 + disp[1]: 0.01 disp[2]: 0.00 disp[3]: -0.00 disp[4]: 0.00 disp[5]: -0.01 disp[6]: 0.01 disp[7]: 0.01 + disp[1]: 0.01 disp[2]: 0.00 disp[3]: -0.00 disp[4]: 0.00 disp[5]: -0.01 disp[6]: 0.01 disp[7]: 0.01 + spacings (end ic_reparam, steps: 5): 1.49 1.50 1.50 1.49 1.41 1.39 1.41 1.41 disprms: 0.017 + V_profile: 0.0 0.4 1.6 12.2 29.1 -7.5 -35.6 -38.6 -40.7 + 3 way tangent (4): f1: 0.32 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.57) ss: 0.026 (DMAX: 0.023) predE: -0.05 E(M): 0.43 gRMS: 0.0011 ratio: -0.260 dE>0, decreasing DMAX + Opt step: 2 gqc: 0.001 ss: 0.024 (DMAX: 0.020) predE: -0.07 E(M): 0.44 gRMS: 0.0019 ratio: 0.594 + Opt step: 3 gqc: 0.001 ss: 0.015 (DMAX: 0.020) predE: -0.01 E(M): 0.40 gRMS: 0.0007 * + + Opt step: 1 t/ol: 22 (0.51) ss: 0.047 (DMAX: 0.061) predE: -0.10 E(M): 1.58 gRMS: 0.0015 ratio: 0.007 decreasing DMAX + Opt step: 2 gqc: 0.003 ss: 0.044 (DMAX: 0.043) predE: -0.13 E(M): 1.58 gRMS: 0.0028 ratio: 1.031 + Opt step: 3 gqc: 0.003 ss: 0.037 (DMAX: 0.043) predE: -0.03 E(M): 1.45 gRMS: 0.0006 * + + Opt step: 1 t/ol: 27 (0.43) ss: 0.087 (DMAX: 0.057) predE: -0.10 E(M): 12.06 gRMS: 0.0010 ratio: 0.883 increasing DMAX + Opt step: 2 gqc: 0.021 ss: 0.078 (DMAX: 0.063) predE: -0.10 E(M): 11.97 gRMS: 0.0013 ratio: 0.959 increasing DMAX + Opt step: 3 gqc: 0.021 ss: 0.071 (DMAX: 0.069) predE: -0.09 E(M): 11.87 gRMS: 0.0013 + + Opt step: 1 S: 1.0 ol: 0.95 0.18 0.02 0.01 + max ol: 0 (f0) ss: 0.324 (DMAX: 0.030) predE: -0.08 Hint ev: -0.133 0.003 0.022 0.026 ratio: 0.868 increasing DMAX E(M): 29.06 gRMS: 0.0051 + Opt step: 2 S: 1.0 ol: 0.97 0.03 0.01 0.03 + max ol: 0 (f0) ss: 0.292 (DMAX: 0.033) predE: -0.09 Hint ev: -0.133 0.006 0.022 0.027 ratio: 0.936 increasing DMAX E(M): 28.98 gRMS: 0.0053 + Opt step: 3 S: 1.0 ol: 0.97 0.04 0.00 0.03 + max ol: 0 (f0) ss: 0.423 (DMAX: 0.037) predE: 0.02 Hint ev: -0.132 -0.000 0.022 0.027 ratio: 0.966 increasing DMAX E(M): 28.99 gRMS: 0.0058 + Opt step: 4 S: 1.0 ol: 0.97 0.01 0.01 0.02 + max ol: 0 (f0) ss: 0.292 (DMAX: 0.040) predE: -0.13 Hint ev: -0.136 0.005 0.022 0.026 ratio: 0.907 increasing DMAX E(M): 28.88 gRMS: 0.0066 + Opt step: 5 S: 1.0 ol: 0.97 0.09 0.00 0.02 + max ol: 0 (f0) ss: 0.320 (DMAX: 0.044) predE: -0.09 Hint ev: -0.134 0.002 0.022 0.026 ratio: 0.925 increasing DMAX E(M): 28.79 gRMS: 0.0068 + Opt step: 6 S: 1.0 ol: 0.95 0.21 0.00 0.02 + max ol: 0 (f0) ss: 0.400 (DMAX: 0.049) predE: -0.02 Hint ev: -0.131 -0.002 0.022 0.026 E(M): 28.79 gRMS: 0.0072 + + Opt step: 1 t/ol: 7 (0.42) ss: 0.170 (DMAX: 0.209) predE: -1.13 E(M): -6.85 gRMS: 0.0028 ratio: 0.959 + Opt step: 2 gqc: -0.055 ss: 0.160 (DMAX: 0.209) predE: -0.92 E(M): -7.93 gRMS: 0.0036 ratio: 0.819 + Opt step: 3 gqc: -0.055 ss: 0.117 (DMAX: 0.209) predE: -0.63 E(M): -8.69 gRMS: 0.0035 + + Opt step: 1 t/ol: 1 (0.56) ss: 0.059 (DMAX: 0.032) predE: -0.03 E(M): -35.65 gRMS: 0.0007 * + + Opt step: 1 t/ol: 0 (0.77) ss: 0.007 (0.020) predE: -0.00 Hint ev: 0.018 0.031 E(M): -38.69 gRMS: 0.0002 * + +x opt_iter: 20 totalgrad: 0.091 gradrms: 0.0031 tgrads: 345 ol(0): 0.95 max E: 28.8 + in find_peaks (2) + V_profile: 0.0 0.4 1.4 11.9 28.8 -8.7 -35.6 -38.7 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 1.4 11.9 28.8 -8.7 -35.6 -38.7 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.03 disp[2]: 0.02 disp[3]: -0.00 disp[4]: 0.00 disp[5]: -0.01 disp[6]: -0.01 disp[7]: -0.02 + disp[1]: 0.02 disp[2]: 0.01 disp[3]: -0.00 disp[4]: 0.00 disp[5]: -0.01 disp[6]: -0.01 disp[7]: -0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: -0.00 disp[4]: 0.00 disp[5]: -0.00 disp[6]: -0.01 disp[7]: -0.00 + spacings (end ic_reparam, steps: 5): 1.50 1.51 1.52 1.51 1.42 1.42 1.41 1.42 disprms: 0.016 + V_profile: 0.0 0.4 1.4 11.9 28.8 -8.7 -35.6 -38.7 -40.7 + 3 way tangent (4): f1: 0.31 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.58) ss: 0.015 (DMAX: 0.020) predE: -0.01 E(M): 0.40 gRMS: 0.0003 * + + Opt step: 1 t/ol: 22 (0.50) ss: 0.043 (DMAX: 0.043) predE: -0.03 E(M): 1.44 gRMS: 0.0006 * + + Opt step: 1 t/ol: 8 (0.40) ss: 0.059 (DMAX: 0.069) predE: -0.08 E(M): 11.73 gRMS: 0.0011 ratio: 1.419 + Opt step: 2 gqc: 0.021 ss: 0.056 (DMAX: 0.069) predE: -0.06 E(M): 11.62 gRMS: 0.0009 * + + Opt step: 1 S: 1.0 ol: 0.94 0.24 0.05 0.02 + max ol: 0 (f0) ss: 0.424 (DMAX: 0.049) predE: -0.01 Hint ev: -0.130 -0.000 0.022 0.026 ratio: 0.933 increasing DMAX E(M): 28.77 gRMS: 0.0081 + Opt step: 2 S: 1.0 ol: 0.93 0.26 0.07 0.01 + max ol: 0 (f0) ss: 0.421 (DMAX: 0.054) predE: 0.03 Hint ev: -0.129 -0.002 0.022 0.026 ratio: 0.989 increasing DMAX E(M): 28.80 gRMS: 0.0087 + Opt step: 3 S: 1.0 ol: 0.94 0.23 0.07 0.01 + max ol: 0 (f0) ss: 0.309 (DMAX: 0.059) predE: -0.19 Hint ev: -0.130 0.003 0.022 0.026 ratio: 0.956 increasing DMAX E(M): 28.62 gRMS: 0.0096 + Opt step: 4 S: 1.0 ol: 0.96 0.10 0.05 0.01 + max ol: 0 (f0) ss: 0.226 (DMAX: 0.065) predE: -0.34 Hint ev: -0.136 0.006 0.022 0.026 ratio: 0.967 increasing DMAX E(M): 28.29 gRMS: 0.0098 + Opt step: 5 S: 1.0 ol: 0.97 0.04 0.04 0.00 + max ol: 0 (f0) ss: 0.205 (DMAX: 0.071) predE: -0.35 Hint ev: -0.135 0.007 0.022 0.026 ratio: 0.970 increasing DMAX E(M): 27.95 gRMS: 0.0094 + Opt step: 6 S: 1.0 ol: 0.96 0.12 0.05 0.02 + max ol: 0 (f0) ss: 0.204 (DMAX: 0.079) predE: -0.33 Hint ev: -0.131 0.006 0.022 0.026 E(M): 27.95 gRMS: 0.0086 + + Opt step: 1 t/ol: 11 (0.38) ss: 0.172 (DMAX: 0.209) predE: -1.27 E(M): -9.01 gRMS: 0.0026 ratio: 0.957 + Opt step: 2 gqc: -0.051 ss: 0.164 (DMAX: 0.209) predE: -0.98 E(M): -10.22 gRMS: 0.0030 ratio: 0.846 + Opt step: 3 gqc: -0.055 ss: 0.152 (DMAX: 0.209) predE: -0.84 E(M): -11.05 gRMS: 0.0037 + + Opt step: 1 t/ol: 1 (0.59) ss: 0.043 (DMAX: 0.032) predE: -0.03 E(M): -35.62 gRMS: 0.0006 * + + Opt step: 1 t/ol: 0 (0.76) ss: 0.006 (0.020) predE: -0.00 Hint ev: 0.018 0.031 E(M): -38.64 gRMS: 0.0001 * + +x opt_iter: 21 totalgrad: 0.096 gradrms: 0.0036 tgrads: 360 ol(0): 0.96 max E: 27.9 + in find_peaks (2) + V_profile: 0.0 0.4 1.4 11.6 27.9 -11.0 -35.6 -38.6 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 1.4 11.6 27.9 -11.0 -35.6 -38.6 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.02 disp[2]: 0.01 disp[3]: -0.00 disp[4]: 0.00 disp[5]: -0.04 disp[6]: 0.01 disp[7]: 0.00 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: -0.00 disp[4]: 0.00 disp[5]: -0.02 disp[6]: 0.01 disp[7]: 0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: -0.00 disp[4]: 0.00 disp[5]: -0.01 disp[6]: 0.01 disp[7]: 0.01 + spacings (end ic_reparam, steps: 5): 1.50 1.51 1.52 1.51 1.42 1.39 1.42 1.41 disprms: 0.019 + V_profile: 0.0 0.4 1.4 11.6 27.9 -11.0 -35.6 -38.6 -40.7 + 3 way tangent (4): f1: 0.30 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.58) ss: 0.015 (DMAX: 0.020) predE: -0.01 E(M): 0.40 gRMS: 0.0004 * + + Opt step: 1 t/ol: 22 (0.50) ss: 0.044 (DMAX: 0.043) predE: -0.04 E(M): 1.43 gRMS: 0.0008 * + + Opt step: 1 t/ol: 8 (0.44) ss: 0.099 (DMAX: 0.069) predE: -0.17 E(M): 11.49 gRMS: 0.0011 ratio: 1.199 increasing DMAX + Opt step: 2 gqc: 0.020 ss: 0.096 (DMAX: 0.076) predE: -0.17 E(M): 11.29 gRMS: 0.0010 ratio: 1.226 increasing DMAX + Opt step: 3 gqc: 0.020 ss: 0.093 (DMAX: 0.084) predE: -0.17 E(M): 11.08 gRMS: 0.0011 + + Opt step: 1 S: 1.0 ol: 0.97 0.08 0.03 0.03 + max ol: 0 (f0) ss: 0.214 (DMAX: 0.079) predE: -0.27 Hint ev: -0.129 0.007 0.022 0.026 ratio: 0.967 increasing DMAX E(M): 27.37 gRMS: 0.0080 + Opt step: 2 S: 1.0 ol: 0.97 0.07 0.02 0.03 + max ol: 0 (f0) ss: 0.206 (DMAX: 0.086) predE: -0.33 Hint ev: -0.129 0.008 0.022 0.026 ratio: 0.976 increasing DMAX E(M): 27.05 gRMS: 0.0077 + Opt step: 3 S: 1.0 ol: 0.96 0.08 0.03 0.02 + max ol: 0 (f0) ss: 0.213 (DMAX: 0.095) predE: -0.28 Hint ev: -0.129 0.009 0.022 0.026 ratio: 0.992 increasing DMAX E(M): 26.77 gRMS: 0.0074 + Opt step: 4 S: 1.0 ol: 0.96 0.09 0.02 0.02 + max ol: 0 (f0) ss: 0.212 (DMAX: 0.105) predE: -0.32 Hint ev: -0.128 0.008 0.022 0.026 ratio: 1.018 increasing DMAX E(M): 26.44 gRMS: 0.0075 + Opt step: 5 S: 1.0 ol: 0.96 0.12 0.02 0.01 + max ol: 0 (f0) ss: 0.227 (DMAX: 0.115) predE: -0.23 Hint ev: -0.128 0.007 0.022 0.026 ratio: 1.042 increasing DMAX E(M): 26.20 gRMS: 0.0074 + Opt step: 6 S: 1.0 ol: 0.95 0.15 0.01 0.00 + max ol: 0 (f0) ss: 0.202 (DMAX: 0.126) predE: -0.42 Hint ev: -0.127 0.006 0.022 0.026 E(M): 26.20 gRMS: 0.0078 + + Opt step: 1 t/ol: 11 (0.36) ss: 0.179 (DMAX: 0.209) predE: -1.75 E(M): -9.84 gRMS: 0.0035 ratio: 0.989 + Opt step: 2 gqc: -0.051 ss: 0.159 (DMAX: 0.209) predE: -1.27 E(M): -11.58 gRMS: 0.0037 ratio: 0.964 + Opt step: 3 gqc: -0.051 ss: 0.159 (DMAX: 0.209) predE: -1.29 E(M): -12.80 gRMS: 0.0038 + + Opt step: 1 t/ol: 1 (0.57) ss: 0.073 (DMAX: 0.032) predE: -0.02 E(M): -35.66 gRMS: 0.0005 * + + Opt step: 1 t/ol: 0 (0.76) ss: 0.006 (0.020) predE: -0.00 Hint ev: 0.018 0.031 E(M): -38.66 gRMS: 0.0001 * + +x opt_iter: 22 totalgrad: 0.095 gradrms: 0.0033 tgrads: 376 ol(0): 0.95 max E: 26.2 + in find_peaks (2) + V_profile: 0.0 0.4 1.4 11.1 26.2 -12.8 -35.7 -38.7 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 1.4 11.1 26.2 -12.8 -35.7 -38.7 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.00 disp[2]: -0.01 disp[3]: -0.04 disp[4]: 0.00 disp[5]: -0.05 disp[6]: -0.04 disp[7]: -0.05 + disp[1]: 0.00 disp[2]: -0.01 disp[3]: -0.02 disp[4]: 0.00 disp[5]: -0.03 disp[6]: -0.03 disp[7]: -0.01 + disp[1]: 0.00 disp[2]: -0.01 disp[3]: -0.01 disp[4]: 0.00 disp[5]: -0.02 disp[6]: -0.02 disp[7]: -0.00 + disp[1]: 0.00 disp[2]: -0.01 disp[3]: -0.01 disp[4]: 0.00 disp[5]: -0.01 disp[6]: -0.01 disp[7]: 0.00 + spacings (end ic_reparam, steps: 5): 1.50 1.51 1.51 1.50 1.44 1.43 1.42 1.43 disprms: 0.019 + V_profile: 0.0 0.4 1.4 11.1 26.2 -12.8 -35.7 -38.7 -40.7 + 3 way tangent (4): f1: 0.28 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.59) ss: 0.019 (DMAX: 0.020) predE: -0.03 E(M): 0.40 gRMS: 0.0008 * + + Opt step: 1 t/ol: 22 (0.47) ss: 0.050 (DMAX: 0.043) predE: -0.10 E(M): 1.38 gRMS: 0.0014 ratio: -0.100 dE>0, decreasing DMAX + Opt step: 2 gqc: 0.003 ss: 0.046 (DMAX: 0.028) predE: -0.11 E(M): 1.39 gRMS: 0.0028 ratio: 0.889 + Opt step: 3 gqc: 0.003 ss: 0.036 (DMAX: 0.028) predE: -0.03 E(M): 1.29 gRMS: 0.0009 * + + Opt step: 1 t/ol: 27 (0.48) ss: 0.112 (DMAX: 0.084) predE: -0.35 E(M): 10.30 gRMS: 0.0018 ratio: 0.989 increasing DMAX + Opt step: 2 gqc: 0.018 ss: 0.104 (DMAX: 0.092) predE: -0.36 E(M): 9.95 gRMS: 0.0019 ratio: 1.031 increasing DMAX + Opt step: 3 gqc: 0.018 ss: 0.094 (DMAX: 0.101) predE: -0.33 E(M): 9.58 gRMS: 0.0017 + + Opt step: 1 S: 1.0 ol: 0.96 0.08 0.05 0.01 + max ol: 0 (f0) ss: 0.202 (DMAX: 0.126) predE: -0.32 Hint ev: -0.125 0.004 0.022 0.026 ratio: 0.922 increasing DMAX E(M): 25.50 gRMS: 0.0073 + Opt step: 2 S: 1.0 ol: 0.95 0.11 0.05 0.01 + max ol: 0 (f0) ss: 0.203 (DMAX: 0.139) predE: -0.39 Hint ev: -0.124 0.004 0.022 0.026 ratio: 0.863 increasing DMAX E(M): 25.16 gRMS: 0.0072 + Opt step: 3 S: 1.0 ol: 0.95 0.10 0.05 0.01 + max ol: 0 (f0) ss: 0.184 (DMAX: 0.150) predE: -0.46 Hint ev: -0.125 0.003 0.022 0.026 ratio: 0.797 E(M): 24.79 gRMS: 0.0067 + Opt step: 4 S: 1.0 ol: 0.95 0.13 0.05 0.01 + max ol: 0 (f0) ss: 0.198 (DMAX: 0.150) predE: -0.25 Hint ev: -0.125 0.001 0.022 0.026 ratio: 0.418 decreasing DMAX E(M): 24.69 gRMS: 0.0060 + Opt step: 5 S: 1.0 ol: 0.96 0.04 0.05 0.02 + max ol: 0 (f0) ss: 0.227 (DMAX: 0.125) predE: -0.05 Hint ev: -0.126 -0.002 0.022 0.026 ratio: -1.210 E(M): 24.75 gRMS: 0.0066 + Opt step: 6 S: 1.0 ol: 0.95 0.08 0.06 0.02 + max ol: 0 (f0) ss: 0.111 (DMAX: 0.125) predE: -0.77 Hint ev: -0.127 -0.002 0.022 0.026 E(M): 24.75 gRMS: 0.0068 + + Opt step: 1 t/ol: 22 (0.33) ss: 0.184 (DMAX: 0.209) predE: -1.85 E(M): -11.14 gRMS: 0.0048 ratio: 0.964 + Opt step: 2 gqc: -0.048 ss: 0.156 (DMAX: 0.209) predE: -1.45 E(M): -12.92 gRMS: 0.0046 ratio: 1.051 + Opt step: 3 gqc: -0.047 ss: 0.148 (DMAX: 0.209) predE: -1.27 E(M): -14.45 gRMS: 0.0035 + + Opt step: 1 t/ol: 2 (0.57) ss: 0.073 (DMAX: 0.032) predE: -0.05 E(M): -35.44 gRMS: 0.0009 * + + Opt step: 1 t/ol: 0 (0.76) ss: 0.006 (0.020) predE: -0.00 Hint ev: 0.018 0.031 E(M): -38.56 gRMS: 0.0002 * + +x opt_iter: 23 totalgrad: 0.096 gradrms: 0.0030 tgrads: 394 ol(0): 0.95 max E: 24.7 + in find_peaks (2) + V_profile: 0.0 0.4 1.3 9.6 24.7 -14.4 -35.4 -38.6 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 1.3 9.6 24.7 -14.4 -35.4 -38.6 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.01 disp[2]: 0.00 disp[3]: 0.01 disp[4]: 0.00 disp[5]: -0.06 disp[6]: -0.07 disp[7]: -0.06 + disp[1]: 0.01 disp[2]: 0.00 disp[3]: 0.00 disp[4]: 0.00 disp[5]: -0.04 disp[6]: -0.04 disp[7]: -0.02 + disp[1]: 0.01 disp[2]: 0.00 disp[3]: 0.00 disp[4]: 0.00 disp[5]: -0.02 disp[6]: -0.03 disp[7]: -0.00 + disp[1]: 0.00 disp[2]: 0.00 disp[3]: 0.00 disp[4]: 0.00 disp[5]: -0.02 disp[6]: -0.02 disp[7]: 0.00 + disp[1]: 0.00 disp[2]: 0.00 disp[3]: 0.00 disp[4]: 0.00 disp[5]: -0.01 disp[6]: -0.01 disp[7]: 0.00 + spacings (end ic_reparam, steps: 5): 1.51 1.52 1.51 1.52 1.46 1.45 1.44 1.45 disprms: 0.014 + V_profile: 0.0 0.4 1.3 9.6 24.7 -14.4 -35.4 -38.6 -40.7 + 3 way tangent (4): f1: 0.28 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.61) ss: 0.033 (DMAX: 0.020) predE: -0.09 E(M): 0.42 gRMS: 0.0017 ratio: 0.088 decreasing DMAX + Opt step: 2 gqc: 0.001 ss: 0.018 (DMAX: 0.020) predE: -0.05 E(M): 0.41 gRMS: 0.0016 ratio: 0.580 + Opt step: 3 gqc: 0.000 ss: 0.013 (DMAX: 0.020) predE: -0.01 E(M): 0.38 gRMS: 0.0008 * + + Opt step: 1 t/ol: 22 (0.46) ss: 0.037 (DMAX: 0.028) predE: -0.02 E(M): 1.27 gRMS: 0.0005 * + + Opt step: 1 t/ol: 27 (0.52) ss: 0.146 (DMAX: 0.101) predE: -0.49 E(M): 9.31 gRMS: 0.0019 ratio: 1.156 increasing DMAX + Opt step: 2 gqc: 0.015 ss: 0.121 (DMAX: 0.111) predE: -0.49 E(M): 8.74 gRMS: 0.0018 ratio: 1.223 increasing DMAX + Opt step: 3 gqc: 0.015 ss: 0.108 (DMAX: 0.122) predE: -0.46 E(M): 8.14 gRMS: 0.0017 + + Opt step: 1 S: 1.0 ol: 0.93 0.09 0.06 0.11 + max ol: 0 (f0) ss: 0.168 (DMAX: 0.125) predE: -0.49 Hint ev: -0.129 -0.014 0.022 0.026 ratio: 0.471 decreasing DMAX E(M): 23.70 gRMS: 0.0031 + Opt step: 2 S: 1.0 ol: 0.95 0.11 0.09 0.12 + max ol: 0 (f0) ss: 0.226 (DMAX: 0.104) predE: -0.44 Hint ev: -0.150 -0.012 0.017 0.022 ratio: 0.731 decreasing DMAX E(M): 23.37 gRMS: 0.0061 + Opt step: 3 S: 1.0 ol: 0.92 0.20 0.13 0.16 + max ol: 0 (f0) ss: 0.341 (DMAX: 0.087) predE: -0.14 Hint ev: -0.142 -0.005 0.017 0.022 ratio: 0.671 decreasing DMAX E(M): 23.28 gRMS: 0.0054 + Opt step: 4 S: 1.0 ol: 0.92 0.22 0.13 0.12 + max ol: 0 (f0) ss: 0.332 (DMAX: 0.072) predE: -0.12 Hint ev: -0.142 0.001 0.017 0.023 ratio: 0.882 increasing DMAX E(M): 23.17 gRMS: 0.0059 + Opt step: 5 S: 1.0 ol: 0.92 0.22 0.14 0.11 + max ol: 0 (f0) ss: 0.215 (DMAX: 0.080) predE: -0.32 Hint ev: -0.142 0.006 0.017 0.023 ratio: 0.972 increasing DMAX E(M): 22.86 gRMS: 0.0061 + Opt step: 6 S: 1.0 ol: 0.94 0.11 0.12 0.12 + max ol: 0 (f0) ss: 0.185 (DMAX: 0.088) predE: -0.24 Hint ev: -0.151 0.006 0.017 0.023 E(M): 22.86 gRMS: 0.0050 + + Opt step: 1 t/ol: 10 (0.39) ss: 0.207 (DMAX: 0.209) predE: -2.17 E(M): -11.75 gRMS: 0.0054 ratio: 1.083 + Opt step: 2 gqc: -0.047 ss: 0.169 (DMAX: 0.209) predE: -1.57 E(M): -14.10 gRMS: 0.0045 ratio: 0.984 + Opt step: 3 gqc: -0.043 ss: 0.154 (DMAX: 0.209) predE: -1.31 E(M): -15.64 gRMS: 0.0047 + + Opt step: 1 t/ol: 2 (0.68) ss: 0.098 (DMAX: 0.032) predE: -0.10 E(M): -35.04 gRMS: 0.0014 ratio: 0.933 increasing DMAX + Opt step: 2 gqc: -0.006 ss: 0.095 (DMAX: 0.035) predE: -0.08 E(M): -35.14 gRMS: 0.0011 ratio: 0.980 increasing DMAX + Opt step: 3 gqc: -0.005 ss: 0.089 (DMAX: 0.039) predE: -0.07 E(M): -35.22 gRMS: 0.0011 + + Opt step: 1 t/ol: 0 (0.77) ss: 0.008 (0.020) predE: -0.00 Hint ev: 0.018 0.031 E(M): -38.45 gRMS: 0.0002 * + +x opt_iter: 24 totalgrad: 0.091 gradrms: 0.0027 tgrads: 414 ol(0): 0.94 max E: 22.9 + in find_peaks (2) + V_profile: 0.0 0.4 1.3 8.1 22.9 -15.6 -35.2 -38.4 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 1.3 8.1 22.9 -15.6 -35.2 -38.4 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.02 disp[2]: 0.03 disp[3]: 0.07 disp[4]: 0.00 disp[5]: -0.02 disp[6]: -0.03 disp[7]: -0.03 + disp[1]: 0.02 disp[2]: 0.02 disp[3]: 0.04 disp[4]: 0.00 disp[5]: -0.01 disp[6]: -0.02 disp[7]: -0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.02 disp[4]: 0.00 disp[5]: -0.01 disp[6]: -0.01 disp[7]: -0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: -0.01 disp[6]: -0.01 disp[7]: -0.00 + spacings (end ic_reparam, steps: 5): 1.52 1.53 1.52 1.54 1.47 1.47 1.46 1.47 disprms: 0.020 + V_profile: 0.0 0.4 1.3 8.1 22.9 -15.6 -35.2 -38.4 -40.7 + 3 way tangent (4): f1: 0.28 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.60) ss: 0.012 (DMAX: 0.020) predE: -0.01 E(M): 0.38 gRMS: 0.0003 * + + Opt step: 1 t/ol: 22 (0.45) ss: 0.040 (DMAX: 0.028) predE: -0.03 E(M): 1.31 gRMS: 0.0006 * + + Opt step: 1 t/ol: 23 (0.42) ss: 0.107 (DMAX: 0.122) predE: -0.53 E(M): 8.80 gRMS: 0.0027 ratio: 0.962 + Opt step: 2 gqc: 0.015 ss: 0.103 (DMAX: 0.122) predE: -0.55 E(M): 8.29 gRMS: 0.0032 ratio: 1.041 + Opt step: 3 gqc: 0.014 ss: 0.097 (DMAX: 0.122) predE: -0.42 E(M): 7.72 gRMS: 0.0020 + + Opt step: 1 S: 1.0 ol: 0.94 0.14 0.04 0.11 + max ol: 0 (f0) ss: 0.167 (DMAX: 0.088) predE: -0.22 Hint ev: -0.152 0.006 0.017 0.023 ratio: 0.966 increasing DMAX E(M): 22.41 gRMS: 0.0048 + Opt step: 2 S: 1.0 ol: 0.95 0.07 0.04 0.11 + max ol: 0 (f0) ss: 0.163 (DMAX: 0.096) predE: -0.19 Hint ev: -0.152 0.004 0.018 0.023 ratio: 0.966 increasing DMAX E(M): 22.23 gRMS: 0.0044 + Opt step: 3 S: 1.0 ol: 0.95 0.08 0.03 0.11 + max ol: 0 (f0) ss: 0.157 (DMAX: 0.106) predE: -0.21 Hint ev: -0.152 0.004 0.018 0.023 ratio: 0.957 increasing DMAX E(M): 22.02 gRMS: 0.0042 + Opt step: 4 S: 1.0 ol: 0.94 0.11 0.02 0.12 + max ol: 0 (f0) ss: 0.143 (DMAX: 0.117) predE: -0.23 Hint ev: -0.153 0.004 0.018 0.023 ratio: 0.961 increasing DMAX E(M): 21.80 gRMS: 0.0038 + Opt step: 5 S: 1.0 ol: 0.94 0.16 0.01 0.11 + max ol: 0 (f0) ss: 0.139 (DMAX: 0.128) predE: -0.22 Hint ev: -0.153 0.004 0.018 0.023 ratio: 0.977 increasing DMAX E(M): 21.58 gRMS: 0.0032 + Opt step: 6 S: 1.0 ol: 0.94 0.19 0.01 0.10 + max ol: 0 (f0) ss: 0.138 (DMAX: 0.141) predE: -0.19 Hint ev: -0.153 0.002 0.018 0.023 E(M): 21.58 gRMS: 0.0026 + + Opt step: 1 t/ol: 17 (0.45) ss: 0.194 (DMAX: 0.209) predE: -1.99 E(M): -16.09 gRMS: 0.0049 ratio: 1.021 + Opt step: 2 gqc: -0.040 ss: 0.179 (DMAX: 0.209) predE: -1.79 E(M): -18.12 gRMS: 0.0052 ratio: 1.078 + Opt step: 3 gqc: -0.041 ss: 0.160 (DMAX: 0.209) predE: -1.46 E(M): -20.04 gRMS: 0.0034 + + Opt step: 1 t/ol: 2 (0.74) ss: 0.092 (DMAX: 0.039) predE: -0.09 E(M): -35.14 gRMS: 0.0012 ratio: 1.004 increasing DMAX + Opt step: 2 gqc: -0.004 ss: 0.087 (DMAX: 0.042) predE: -0.08 E(M): -35.23 gRMS: 0.0011 ratio: 1.042 increasing DMAX + Opt step: 3 gqc: -0.004 ss: 0.085 (DMAX: 0.047) predE: -0.07 E(M): -35.31 gRMS: 0.0011 + + Opt step: 1 t/ol: 0 (0.75) ss: 0.009 (0.020) predE: -0.00 Hint ev: 0.018 0.031 E(M): -38.38 gRMS: 0.0003 * + +x opt_iter: 25 totalgrad: 0.067 gradrms: 0.0019 tgrads: 432 ol(0): 0.94 max E: 21.6 + in find_peaks (2) + V_profile: 0.0 0.4 1.3 7.7 21.6 -20.0 -35.3 -38.4 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 1.3 7.7 21.6 -20.0 -35.3 -38.4 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.02 disp[2]: 0.04 disp[3]: 0.07 disp[4]: 0.00 disp[5]: -0.05 disp[6]: -0.04 disp[7]: -0.05 + disp[1]: 0.02 disp[2]: 0.02 disp[3]: 0.04 disp[4]: 0.00 disp[5]: -0.03 disp[6]: -0.03 disp[7]: -0.02 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.02 disp[4]: 0.00 disp[5]: -0.02 disp[6]: -0.02 disp[7]: -0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: -0.01 disp[6]: -0.01 disp[7]: -0.00 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: -0.01 disp[6]: -0.01 disp[7]: 0.00 + spacings (end ic_reparam, steps: 5): 1.53 1.54 1.54 1.55 1.50 1.48 1.48 1.49 disprms: 0.016 + V_profile: 0.0 0.4 1.3 7.7 21.6 -20.0 -35.3 -38.4 -40.7 + 3 way tangent (4): f1: 0.25 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.61) ss: 0.013 (DMAX: 0.020) predE: -0.01 E(M): 0.38 gRMS: 0.0003 * + + Opt step: 1 t/ol: 0 (0.46) ss: 0.041 (DMAX: 0.028) predE: -0.03 E(M): 1.37 gRMS: 0.0007 * + + Opt step: 1 t/ol: 0 (0.46) ss: 0.146 (DMAX: 0.122) predE: -0.63 E(M): 8.29 gRMS: 0.0025 ratio: 1.244 increasing DMAX + Opt step: 2 gqc: 0.013 ss: 0.145 (DMAX: 0.134) predE: -0.60 E(M): 7.51 gRMS: 0.0020 ratio: 1.305 + Opt step: 3 gqc: 0.012 ss: 0.141 (DMAX: 0.134) predE: -0.55 E(M): 6.72 gRMS: 0.0019 + + Opt step: 1 S: 1.0 ol: 0.91 0.30 0.12 0.03 + max ol: 0 (f0) ss: 0.158 (DMAX: 0.141) predE: -0.15 Hint ev: -0.153 0.000 0.019 0.023 ratio: 0.680 decreasing DMAX E(M): 21.31 gRMS: 0.0026 + Opt step: 2 S: 1.0 ol: 0.91 0.32 0.14 0.00 + max ol: 0 (f0) ss: 0.180 (DMAX: 0.117) predE: -0.10 Hint ev: -0.153 -0.003 0.019 0.023 ratio: 0.289 decreasing DMAX E(M): 21.28 gRMS: 0.0030 + Opt step: 3 S: 1.0 ol: 0.90 0.32 0.14 0.02 + max ol: 0 (f0) ss: 0.142 (DMAX: 0.098) predE: -0.28 Hint ev: -0.153 -0.006 0.018 0.023 ratio: 0.723 decreasing DMAX E(M): 21.08 gRMS: 0.0039 + Opt step: 4 S: 1.0 ol: 0.93 0.20 0.15 0.01 + max ol: 0 (f0) ss: 0.115 (DMAX: 0.082) predE: -0.13 Hint ev: -0.154 -0.006 0.019 0.023 ratio: 0.647 decreasing DMAX E(M): 20.99 gRMS: 0.0022 + Opt step: 5 S: 1.0 ol: 0.94 0.12 0.16 0.01 + max ol: 0 (f0) ss: 0.142 (DMAX: 0.068) predE: -0.07 Hint ev: -0.151 -0.004 0.019 0.023 ratio: 0.734 decreasing DMAX E(M): 20.94 gRMS: 0.0016 + Opt step: 6 S: 1.0 ol: 0.93 0.17 0.17 0.01 + max ol: 0 (f0) ss: 0.147 (DMAX: 0.057) predE: -0.05 Hint ev: -0.153 -0.002 0.019 0.023 E(M): 20.94 gRMS: 0.0013 + + Opt step: 1 t/ol: 15 (0.42) ss: 0.171 (DMAX: 0.209) predE: -1.83 E(M): -18.73 gRMS: 0.0053 ratio: 0.793 + Opt step: 2 gqc: -0.035 ss: 0.143 (DMAX: 0.209) predE: -1.39 E(M): -20.18 gRMS: 0.0057 ratio: 0.997 + Opt step: 3 gqc: -0.036 ss: 0.137 (DMAX: 0.209) predE: -1.05 E(M): -21.57 gRMS: 0.0039 + + Opt step: 1 t/ol: 2 (0.83) ss: 0.165 (0.047) predE: -0.11 Hint ev: 0.007 0.009 E(M): -35.19 gRMS: 0.0013 ratio: 0.921 increasing DMAX + Opt step: 2 t/ol: 2 (0.83) ss: 0.133 (0.051) predE: -0.10 Hint ev: 0.007 0.009 E(M): -35.29 gRMS: 0.0013 ratio: 1.061 increasing DMAX + Opt step: 3 t/ol: 2 (0.82) ss: 0.109 (0.056) predE: -0.10 Hint ev: 0.007 0.009 E(M): -35.39 gRMS: 0.0013 + + Opt step: 1 t/ol: 0 (0.74) ss: 0.066 (DMAX: 0.020) predE: -0.02 E(M): -38.28 gRMS: 0.0005 * + +x opt_iter: 26 totalgrad: 0.064 gradrms: 0.0018 tgrads: 450 ol(0): 0.93 max E: 20.9 + in find_peaks (2) + V_profile: 0.0 0.4 1.4 6.7 20.9 -21.6 -35.4 -38.3 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 1.4 6.7 20.9 -21.6 -35.4 -38.3 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.03 disp[2]: 0.04 disp[3]: 0.08 disp[4]: 0.00 disp[5]: -0.05 disp[6]: -0.09 disp[7]: -0.07 + disp[1]: 0.02 disp[2]: 0.03 disp[3]: 0.05 disp[4]: 0.00 disp[5]: -0.04 disp[6]: -0.06 disp[7]: -0.03 + disp[1]: 0.01 disp[2]: 0.02 disp[3]: 0.03 disp[4]: 0.00 disp[5]: -0.02 disp[6]: -0.04 disp[7]: -0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.02 disp[4]: 0.00 disp[5]: -0.02 disp[6]: -0.02 disp[7]: -0.00 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: -0.01 disp[6]: -0.02 disp[7]: -0.00 + spacings (end ic_reparam, steps: 5): 1.55 1.55 1.55 1.57 1.52 1.52 1.50 1.51 disprms: 0.023 + V_profile: 0.0 0.4 1.4 6.7 20.9 -21.6 -35.4 -38.3 -40.7 + 3 way tangent (4): f1: 0.25 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.61) ss: 0.014 (DMAX: 0.020) predE: -0.01 E(M): 0.39 gRMS: 0.0005 * + + Opt step: 1 t/ol: 0 (0.58) ss: 0.040 (DMAX: 0.028) predE: -0.04 E(M): 1.43 gRMS: 0.0009 * + + Opt step: 1 t/ol: 0 (0.51) ss: 0.153 (DMAX: 0.134) predE: -0.58 E(M): 7.25 gRMS: 0.0027 ratio: 1.346 + Opt step: 2 gqc: 0.012 ss: 0.149 (DMAX: 0.134) predE: -0.52 E(M): 6.46 gRMS: 0.0022 ratio: 1.322 + Opt step: 3 gqc: 0.011 ss: 0.141 (DMAX: 0.134) predE: -0.50 E(M): 5.77 gRMS: 0.0024 + + Opt step: 1 S: 1.0 ol: 0.92 0.27 0.12 0.00 + max ol: 0 (f0) ss: 0.098 (DMAX: 0.057) predE: -0.05 Hint ev: -0.154 0.001 0.019 0.023 ratio: 0.952 increasing DMAX E(M): 20.85 gRMS: 0.0010 + Opt step: 2 S: 1.0 ol: 0.91 0.29 0.11 0.02 + max ol: 0 (f0) ss: 0.090 (DMAX: 0.062) predE: -0.05 Hint ev: -0.154 0.002 0.019 0.023 ratio: 0.941 increasing DMAX E(M): 20.81 gRMS: 0.0007 + Opt step: 3 E(M): 20.81 gRMS: 0.0003 * + + Opt step: 1 t/ol: 15 (0.44) ss: 0.175 (DMAX: 0.209) predE: -2.10 E(M): -19.32 gRMS: 0.0059 ratio: 0.839 + Opt step: 2 gqc: -0.034 ss: 0.139 (DMAX: 0.209) predE: -1.21 E(M): -21.08 gRMS: 0.0054 ratio: 1.008 + Opt step: 3 gqc: -0.034 ss: 0.123 (DMAX: 0.209) predE: -0.89 E(M): -22.29 gRMS: 0.0043 + + Opt step: 1 t/ol: 2 (0.86) ss: 0.124 (0.056) predE: -0.16 Hint ev: 0.007 0.009 E(M): -35.07 gRMS: 0.0015 ratio: 1.035 increasing DMAX + Opt step: 2 t/ol: 2 (0.86) ss: 0.093 (0.062) predE: -0.13 Hint ev: 0.007 0.009 E(M): -35.23 gRMS: 0.0015 ratio: 1.246 increasing DMAX + Opt step: 3 t/ol: 2 (0.85) ss: 0.077 (0.068) predE: -0.10 Hint ev: 0.007 0.009 E(M): -35.39 gRMS: 0.0013 + + Opt step: 1 t/ol: 0 (0.72) ss: 0.062 (DMAX: 0.020) predE: -0.02 E(M): -38.14 gRMS: 0.0004 * + +x opt_iter: 27 totalgrad: 0.065 gradrms: 0.0020 tgrads: 465 ol(0): 0.91 max E: 20.8 + in find_peaks (2) + V_profile: 0.0 0.4 1.4 5.8 20.8 -22.3 -35.4 -38.1 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + check_for_reaction wts: 4 wint: 8 isrxn: 2 + + opt_iters over: totalgrad: 0.065 gradrms: 0.0020 tgrads: 465 ol(0): 0.91 max E: 20.8 Erxn: -40.7 nmax: 4 TSnode: 4 -XTS- + + oi: 26 nmax: 4 TSnode0: 4 overlapn: 0 + string E (kcal/mol): 0.0 0.4 1.4 5.8 20.8 -22.3 -35.4 -38.1 -40.7 + string E (au): -234.52746107 -234.52683350 -234.52517957 -234.51825956 -234.49429816 -234.56298985 -234.58385452 -234.58824697 -234.59235246 + string E (au) - force*distance: -234.52746107 -234.52683350 -234.52517957 -234.51825956 -234.49429816 -234.56298985 -234.58385452 -234.58824697 -234.59235246 + max E: 20.809724 for node: 4 + + creating 3 lowest eigenvectors + Hint eigenvalues: -0.154 0.002 0.019 0.023 0.028 + maximum number of iterations: 14 + + Davidson iteration 1 + eg eg eg eg eg eg + mag/DTHRESH: 24.567981 0.000050 lamb/lambp: -0.005 0.000 + mag/DTHRESH: 36.177103 0.000050 lamb/lambp: 0.003 0.000 + mag/DTHRESH: 7.581765 0.000050 lamb/lambp: 0.015 0.000 + + Davidson iteration 2 + eg eg eg eg eg eg + mag/DTHRESH: 1.692984 0.000050 lamb/lambp: -0.038 -0.005 + mag/DTHRESH: 0.123915 0.000050 lamb/lambp: 0.002 0.003 + vector 1 converged + mag/DTHRESH: 1.570284 0.000050 lamb/lambp: 0.010 0.015 + + Davidson iteration 3 + eg eg eg eg + mag/DTHRESH: 0.644502 0.000050 lamb/lambp: -0.049 -0.038 + mag/DTHRESH: 0.015935 0.000050 lamb/lambp: 0.002 0.002 + vector 1 converged + mag/DTHRESH: 0.240628 0.000050 lamb/lambp: 0.010 0.010 + vector 2 converged + + Davidson iteration 4 + eg eg + mag/DTHRESH: 0.061932 0.000050 lamb/lambp: -0.062 -0.049 + mag/DTHRESH: 0.013643 0.000050 lamb/lambp: 0.002 0.002 + vector 1 converged + mag/DTHRESH: 0.132474 0.000050 lamb/lambp: 0.009 0.010 + vector 2 converged + + Davidson iteration 5 + eg eg + mag/DTHRESH: 0.028382 0.000050 lamb/lambp: -0.064 -0.062 + mag/DTHRESH: 0.013669 0.000050 lamb/lambp: 0.002 0.002 + vector 1 converged + mag/DTHRESH: 0.161569 0.000050 lamb/lambp: 0.009 0.009 + vector 2 converged + + Davidson iteration 6 + eg eg + mag/DTHRESH: 0.034854 0.000050 lamb/lambp: -0.066 -0.064 + mag/DTHRESH: 0.013035 0.000050 lamb/lambp: 0.002 0.002 + vector 1 converged + mag/DTHRESH: 0.129058 0.000050 lamb/lambp: 0.009 0.009 + vector 2 converged + + Davidson iteration 7 + eg eg + mag/DTHRESH: 0.016568 0.000050 lamb/lambp: -0.068 -0.066 + mag/DTHRESH: 0.010106 0.000050 lamb/lambp: 0.002 0.002 + vector 1 converged + mag/DTHRESH: 0.110299 0.000050 lamb/lambp: 0.009 0.009 + vector 2 converged + + Davidson iteration 8 + eg eg + mag/DTHRESH: 0.007269 0.000050 lamb/lambp: -0.069 -0.068 + mag/DTHRESH: 0.009062 0.000050 lamb/lambp: 0.002 0.002 + vector 1 converged + mag/DTHRESH: 0.050872 0.000050 lamb/lambp: 0.009 0.009 + vector 2 converged + + Davidson iteration 9 + eg eg + mag/DTHRESH: 0.001885 0.000050 lamb/lambp: -0.069 -0.069 + vector 0 converged + mag/DTHRESH: 0.008598 0.000050 lamb/lambp: 0.002 0.002 + vector 1 converged + mag/DTHRESH: 0.046156 0.000050 lamb/lambp: 0.009 0.009 + vector 2 converged + Davidson converged + + now saving vibrations to stringfile.xyz0001fr + Hessian eigenvalues: -0.069 0.002 0.009 + + Updating Hint with new vectors + updating vector: 1 with curvature: -0.06896 + updating vector: 2 with curvature: 0.00213 + updating vector: 3 with curvature: 0.00877 + + Davidson required 28 gradients + + found 1 negative eigenvalue + creating final string file + + about to write tsq.xyz, tscontinue: 1 endearly: 0 + check_for_reaction wts: 4 wint: 8 isrxn: 2 + E of min node before TS: 0.0 diff --git a/TEST/dielsAlder/mopac/de-gsm/stringfile.standard b/TEST/dielsAlder/mopac/de-gsm/stringfile.standard new file mode 100644 index 0000000..5e13690 --- /dev/null +++ b/TEST/dielsAlder/mopac/de-gsm/stringfile.standard @@ -0,0 +1,162 @@ + 16 + 0.000000 + C -1.037226 -1.575057 0.267708 + C -1.708337 -0.692853 -0.473273 + C -1.940300 0.707404 -0.088479 + C -1.009042 1.497622 0.446255 + C 2.732869 -0.399002 0.382329 + C 2.511914 0.465947 -0.599792 + H -2.143698 -0.972175 -1.437027 + H -0.604491 -1.340651 1.230189 + H -0.877954 -2.600126 -0.033220 + H 3.637983 -0.412061 0.974372 + H 2.025496 -1.165771 0.670414 + H 1.605947 0.476343 -1.192479 + H 3.218026 1.231193 -0.891866 + H -1.184626 2.531163 0.706315 + H 0.000969 1.169352 0.656482 + H -2.951061 1.071129 -0.293713 + 16 + 0.065310 + C -0.881227 -1.557393 0.272088 + C -1.610064 -0.713467 -0.460324 + C -1.801024 0.711054 -0.152196 + C -0.890612 1.487041 0.437951 + C 2.516894 -0.421962 0.383741 + C 2.332001 0.487098 -0.565349 + H -2.131418 -1.053644 -1.358624 + H -0.360952 -1.269568 1.174926 + H -0.761400 -2.601536 0.023569 + H 3.282981 -0.341264 1.145961 + H 1.919776 -1.320261 0.475426 + H 1.563600 0.411668 -1.325032 + H 2.931619 1.380162 -0.657183 + H -1.050398 2.537562 0.636875 + H 0.082037 1.136030 0.758548 + H -2.766779 1.113634 -0.463469 + 16 + 0.506110 + C -0.796213 -1.546366 0.316857 + C -1.581470 -0.741371 -0.402069 + C -1.689394 0.712253 -0.231819 + C -0.804860 1.477922 0.409772 + C 2.400950 -0.465178 0.325678 + C 2.196365 0.542582 -0.513453 + H -2.215361 -1.148859 -1.197479 + H -0.163997 -1.207652 1.125446 + H -0.738437 -2.611869 0.147557 + H 2.978108 -0.369047 1.235955 + H 2.015322 -1.464875 0.172962 + H 1.613410 0.461604 -1.420321 + H 2.595213 1.535082 -0.355424 + H -0.906494 2.551454 0.489679 + H 0.083333 1.097796 0.898836 + H -2.571812 1.156786 -0.702092 + 16 + 0.880430 + C -0.773656 -1.546591 0.472532 + C -1.491325 -0.778970 -0.351364 + C -1.516592 0.689471 -0.330509 + C -0.734188 1.456596 0.432272 + C 2.272667 -0.488455 0.166942 + C 2.053222 0.632231 -0.510071 + H -2.118514 -1.231139 -1.125406 + H -0.146620 -1.158463 1.263531 + H -0.766659 -2.625765 0.414225 + H 2.685318 -0.509616 1.165315 + H 2.054867 -1.473402 -0.223612 + H 1.633976 0.653653 -1.508679 + H 2.286377 1.616590 -0.127518 + H -0.766468 2.535261 0.411078 + H -0.011460 1.064033 1.135358 + H -2.234327 1.140548 -1.022353 + 16 + 4.734660 + C -0.878653 -1.655783 0.622469 + C -1.425230 -0.866669 -0.308849 + C -1.251858 0.587183 -0.380542 + C -0.488954 1.298446 0.454910 + C 2.132875 -0.307538 0.035760 + C 1.822029 0.839205 -0.565831 + H -2.036980 -1.298229 -1.109032 + H -0.268635 -1.292091 1.440143 + H -1.007304 -2.729808 0.625769 + H 2.531295 -0.358842 1.038453 + H 1.963165 -1.279964 -0.411926 + H 1.453384 0.882774 -1.581722 + H 2.114963 1.803252 -0.172116 + H -0.410434 2.376656 0.387283 + H -0.075423 0.897178 1.369427 + H -1.751796 1.073410 -1.226178 + 16 + 19.862190 + C -0.936904 -1.758158 0.666023 + C -1.403170 -0.931289 -0.304680 + C -1.096471 0.459894 -0.432923 + C -0.208516 1.170519 0.387715 + C 2.083203 -0.140715 0.019883 + C 1.544146 1.014178 -0.514757 + H -2.076998 -1.336546 -1.068278 + H -0.282889 -1.436396 1.459186 + H -1.194052 -2.804456 0.699992 + H 2.648762 -0.143011 0.934258 + H 1.912961 -1.111272 -0.410950 + H 1.176104 1.022702 -1.538194 + H 1.911065 1.985654 -0.189011 + H -0.229192 2.256279 0.365238 + H 0.074000 0.770541 1.357724 + H -1.556636 0.985251 -1.269557 + 16 + 9.543110 + C -0.259513 -1.416306 0.561108 + C -1.184493 -0.746664 -0.327551 + C -1.215408 0.595876 -0.463874 + C -0.190163 1.308990 0.299073 + C 1.483214 -0.546741 0.097788 + C 1.188923 0.810311 -0.426922 + H -1.789512 -1.378472 -0.983300 + H 0.066218 -1.074205 1.538478 + H -0.219200 -2.489995 0.457589 + H 2.005453 -0.582724 1.041541 + H 1.528331 -1.429858 -0.521695 + H 1.021584 0.864326 -1.508456 + H 1.854981 1.618954 -0.091635 + H -0.190559 2.404694 0.293960 + H -0.050903 0.958019 1.337631 + H -1.855245 1.110842 -1.164070 + 16 + -45.764830 + C -0.032995 -1.430824 0.318130 + C -1.213111 -0.716288 -0.273258 + C -1.279329 0.617461 -0.345462 + C -0.122122 1.445331 0.132950 + C 1.299930 -0.642627 0.279896 + C 1.179943 0.762785 -0.326191 + H -2.011589 -1.358452 -0.639483 + H -0.268867 -1.662777 1.379502 + H 0.104625 -2.407920 -0.185292 + H 1.698181 -0.567336 1.307960 + H 2.037251 -1.226545 -0.298564 + H 1.174664 0.683124 -1.431925 + H 2.053647 1.379201 -0.054076 + H -0.174029 2.486566 -0.226458 + H -0.141820 1.489050 1.241376 + H -2.124519 1.146835 -0.773733 + 16 + -48.332610 + C 0.020342 -1.496218 0.058646 + C -1.252781 -0.711946 -0.072433 + C -1.293528 0.622755 -0.135300 + C -0.070828 1.489110 -0.053029 + C 1.214363 -0.621211 0.473790 + C 1.222149 0.698487 -0.309129 + H -2.158649 -1.313485 -0.128548 + H -0.114951 -2.316203 0.791886 + H 0.235608 -1.989611 -0.913009 + H 1.160153 -0.406734 1.558378 + H 2.159983 -1.169252 0.309815 + H 1.318154 0.486250 -1.391274 + H 2.102027 1.305572 -0.030670 + H -0.148427 2.325855 -0.774547 + H -0.035455 1.955341 0.954404 + H -2.233315 1.162540 -0.235849 diff --git a/TEST/dielsAlder/orca/de-gsm/inpfileq b/TEST/dielsAlder/orca/de-gsm/inpfileq new file mode 100644 index 0000000..d2a54ff --- /dev/null +++ b/TEST/dielsAlder/orca/de-gsm/inpfileq @@ -0,0 +1,26 @@ +# FSM/GSM/SSM inpfileq + +------------- QCHEM Scratch Info ------------------------ +$QCSCRATCH/ # path for scratch dir. end with "/" +GSM_go1q # name of run +--------------------------------------------------------- + +------------ String Info -------------------------------- +SM_TYPE GSM # SSM, FSM or GSM +RESTART 0 # read restart.xyz +MAX_OPT_ITERS 80 # maximum iterations +STEP_OPT_ITERS 30 # for FSM/SSM +CONV_TOL 0.0005 # perp grad +ADD_NODE_TOL 0.1 # for GSM +SCALING 1.0 # for opt steps +SSM_DQMAX 0.8 # add step size +GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 +INT_THRESH 2.0 # intermediate detection +MIN_SPACING 5.0 # node spacing SSM +BOND_FRAGMENTS 1 # make IC's for fragments +INITIAL_OPT 0 # opt steps first node +FINAL_OPT 150 # opt steps last SSM node +PRODUCT_LIMIT 100.0 # kcal/mol +TS_FINAL_TYPE 1 # any/delta bond: 0/1 +NNODES 9 # including endpoints +--------------------------------------------------------- diff --git a/TEST/dielsAlder/orca/de-gsm/ograd b/TEST/dielsAlder/orca/de-gsm/ograd new file mode 100644 index 0000000..17b5945 --- /dev/null +++ b/TEST/dielsAlder/orca/de-gsm/ograd @@ -0,0 +1,34 @@ +#!/bin/bash +# The path to ORCA should be added to .bashrc or exported in command line + + +if [ -z $2 ] +then + echo " need two arguments! " + exit +fi + +#echo " in ograd: $1 $2 " + +ofile=scratch/orcain$1.in +ofileout=scratch/orcain$1.out +molfile=scratch/structure$1 +ncpu=$2 + +#echo " ofile: $ofile ofileout: $ofileout molfile: $molfile ncpu: $ncpu" + +########## DFT settings: ################# +#echo '! DFT BP86 ECP{LANL2} ENGRAD' > $ofile +echo '! DFT B3LYP ENGRAD' > $ofile +#echo '! veryslowconv SCFCONV6' >> $ofile +echo '! nomoprint' >> $ofile +echo '%scf' >> $ofile +echo ' maxiter 350' >> $ofile +echo 'end' >> $ofile +# charge and spin multiplicity +echo '* xyz 0 1' >> $ofile +cat $molfile >> $ofile +echo '*' >> $ofile + +#echo "running: orca $ofile > $ofileout" +orca $ofile > $ofileout diff --git a/TEST/dielsAlder/orca/de-gsm/scratch/initial0001.xyz b/TEST/dielsAlder/orca/de-gsm/scratch/initial0001.xyz new file mode 100644 index 0000000..4210d81 --- /dev/null +++ b/TEST/dielsAlder/orca/de-gsm/scratch/initial0001.xyz @@ -0,0 +1,36 @@ + 16 +Step 35 + C -1.06001665 -1.51714564 0.05288674 + C -1.82955412 -0.59408623 -0.53968755 + C -2.01260392 0.79370866 -0.08977969 + C -1.09740592 1.54095108 0.54110413 + C 3.01841440 -0.33274049 0.53420511 + C 2.48267950 0.16990394 -0.57660955 + H -2.40063347 -0.88235561 -1.42321617 + H -0.51365172 -1.30383154 0.96828855 + H -0.96688964 -2.52122005 -0.35117707 + H 3.89171154 0.11254122 1.00536203 + H 2.60849064 -1.21591676 1.01902222 + H 1.60806045 -0.27640639 -1.04373753 + H 2.89526366 1.05096138 -1.06301386 + H -1.32088987 2.55628492 0.85667305 + H -0.09454533 1.17390089 0.74481476 + H -2.98142355 1.23828062 -0.32070817 + 16 +Step 22 + C 0.01856467 -1.50510245 0.07175535 + C -1.25472580 -0.70291222 -0.04828280 + C -1.28551058 0.63324180 -0.08527776 + C -0.04811068 1.49696591 -0.04422009 + C 1.21601433 -0.63168912 0.47947978 + C 1.22945185 0.68482088 -0.31033881 + H -2.18794361 -1.26282927 -0.10437525 + H -0.12133841 -2.31635373 0.79987325 + H 0.22663560 -2.00643122 -0.88734886 + H 1.14834814 -0.40532251 1.55280900 + H 2.15327210 -1.18259709 0.33198960 + H 1.29564501 0.45837391 -1.38389788 + H 2.11591575 1.28013898 -0.05856919 + H -0.13761965 2.30980257 -0.77849415 + H 0.01956981 1.99500653 0.93644690 + H -2.24481452 1.14593304 -0.15154508 diff --git a/TEST/dielsAlder/orca/de-gsm/scratch/paragsm0001 b/TEST/dielsAlder/orca/de-gsm/scratch/paragsm0001 new file mode 100644 index 0000000..e6c25b3 --- /dev/null +++ b/TEST/dielsAlder/orca/de-gsm/scratch/paragsm0001 @@ -0,0 +1,1792 @@ + Number of QC processors: 4 +***** Starting Initialization ***** + runend 1 + -structure filename from input: scratch/initial0001.xyz +Initializing Tolerances and Parameters... + -Opening inpfileq + -reading file... + -using GSM + -RESTART: 0 + -MAX_OPT_ITERS: 80 + -STEP_OPT_ITERS: 30 + -CONV_TOL = 0.0005 + -ADD_NODE_TOL = 0.1 + -SCALING = 1 + -SSM_DQMAX: 0.8 + -SSM_DQMIN: 0.2 + -GROWTH_DIRECTION = 0 + -INT_THRESH: 2 + -SSM_MIN_SPACING: 5 + -BOND_FRAGMENTS = 1 + -INITIAL_OPT: 0 + -FINAL_OPT: 150 + -PRODUCT_LIMIT: 100 + -TS_FINAL_TYPE: 1 + -NNODES = 9 + Done reading inpfileq + + reading isomers + WARNING: ignoring BONDS in ISOMERS file because BOND_FRAGMENTS == 0 or 1 + couldn't find ISOMERS file: scratch/ISOMERS0001 +Reading and initializing string coordinates + -Opening structure file + -reading file... + -The number of atoms is: 16 + -Reading the atomic names... -Reading coordinates...Opening xyz file +Finished reading information from structure file + +**************************************** +**************************************** +****** Starting IC-GSM calculation ***** +**************************************** +**************************************** + + skipped Eckart_align + 16 + +C -1.060017 -1.517146 0.052887 +C -1.829554 -0.594086 -0.539688 +C -2.012604 0.793709 -0.089780 +C -1.097406 1.540951 0.541104 +C 3.018414 -0.332740 0.534205 +C 2.482680 0.169904 -0.576610 +H -2.400633 -0.882356 -1.423216 +H -0.513652 -1.303832 0.968289 +H -0.966890 -2.521220 -0.351177 +H 3.891712 0.112541 1.005362 +H 2.608491 -1.215917 1.019022 +H 1.608060 -0.276406 -1.043738 +H 2.895264 1.050961 -1.063014 +H -1.320890 2.556285 0.856673 +H -0.094545 1.173901 0.744815 +H -2.981424 1.238281 -0.320708 + 16 + +C 0.018565 -1.505102 0.071755 +C -1.254726 -0.702912 -0.048283 +C -1.285511 0.633242 -0.085278 +C -0.048111 1.496966 -0.044220 +C 1.216014 -0.631689 0.479480 +C 1.229452 0.684821 -0.310339 +H -2.187944 -1.262829 -0.104375 +H -0.121338 -2.316354 0.799873 +H 0.226636 -2.006431 -0.887349 +H 1.148348 -0.405323 1.552809 +H 2.153272 -1.182597 0.331990 +H 1.295645 0.458374 -1.383898 +H 2.115916 1.280139 -0.058569 +H -0.137620 2.309803 -0.778494 +H 0.019570 1.995007 0.936447 +H -2.244815 1.145933 -0.151545 + + NOTICES + Not using Davidson + Not using close dist add + Not using ONE_SKIP + Using HESS_TANG + END NOTICES + + isOpt: 1 + in make_frags() + merging: + atom[0] frag: 0 + atom[1] frag: 0 + atom[2] frag: 0 + atom[3] frag: 0 + atom[4] frag: 1 + atom[5] frag: 1 + atom[6] frag: 0 + atom[7] frag: 0 + atom[8] frag: 0 + atom[9] frag: 1 + atom[10] frag: 1 + atom[11] frag: 1 + atom[12] frag: 1 + atom[13] frag: 0 + atom[14] frag: 0 + atom[15] frag: 0 + nfrags: 2 + in bond_frags() + connecting frag 1 to frag 0: bond pair1 added : 12 15 + linear ties complete + isOpt: 1 + in make_frags() + merging: + atom[0] frag: 0 + atom[1] frag: 0 + atom[2] frag: 0 + atom[3] frag: 0 + atom[4] frag: 0 + atom[5] frag: 0 + atom[6] frag: 0 + atom[7] frag: 0 + atom[8] frag: 0 + atom[9] frag: 0 + atom[10] frag: 0 + atom[11] frag: 0 + atom[12] frag: 0 + atom[13] frag: 0 + atom[14] frag: 0 + atom[15] frag: 0 + nfrags: 1 + in bond_frags() + linear ties complete + + setting SSM bonds + nbonds: 15 nangles: 20 ntor: 21 + printing ic1 ic's + + printing internals + number of bonds: 15 + bond 1: 2 to 1: 1.34 + bond 2: 3 to 2: 1.47 + bond 3: 4 to 3: 1.34 + bond 4: 6 to 5: 1.33 + bond 5: 7 to 2: 1.09 + bond 6: 8 to 1: 1.09 + bond 7: 9 to 1: 1.09 + bond 8: 10 to 5: 1.09 + bond 9: 11 to 5: 1.09 + bond 10: 12 to 6: 1.09 + bond 11: 13 to 6: 1.09 + bond 12: 14 to 4: 1.09 + bond 13: 15 to 4: 1.09 + bond 14: 16 to 3: 1.09 + bond 15: 12 to 15: 2.86 + + number of angles: 20 + angle 1: 3 2 1: 125.9 + angle 2: 4 3 2: 125.8 + angle 3: 7 2 1: 118.5 + angle 4: 7 2 3: 115.6 + angle 5: 8 1 2: 121.7 + angle 6: 9 1 2: 121.4 + angle 7: 9 1 8: 116.8 + angle 8: 10 5 6: 122.0 + angle 9: 11 5 6: 121.8 + angle 10: 11 5 10: 116.2 + angle 11: 12 6 5: 121.8 + angle 12: 13 6 5: 121.7 + angle 13: 13 6 12: 116.5 + angle 14: 14 4 3: 121.2 + angle 15: 15 4 3: 122.0 + angle 16: 15 4 14: 116.8 + angle 17: 16 3 2: 115.5 + angle 18: 16 3 4: 118.6 + angle 19: 15 12 6: 90.1 + angle 20: 12 15 4: 127.0 + + number of torsions: 21 + torsion 1: 4 3 2 1: 31.5 + torsion 2: 7 2 3 4: -150.1 + torsion 3: 8 1 2 3: 1.9 + torsion 4: 8 1 2 7: -176.4 + torsion 5: 9 1 2 3: -179.1 + torsion 6: 9 1 2 7: 2.5 + torsion 7: 12 6 5 10: -179.9 + torsion 8: 12 6 5 11: 0.4 + torsion 9: 13 6 5 10: -0.0 + torsion 10: 13 6 5 11: -179.8 + torsion 11: 14 4 3 2: -178.9 + torsion 12: 15 4 3 2: 2.4 + torsion 13: 16 3 2 1: -149.8 + torsion 14: 16 3 2 7: 28.6 + torsion 15: 16 3 4 14: 2.5 + torsion 16: 16 3 4 15: -176.3 + torsion 17: 15 12 6 5: 83.8 + torsion 18: 15 12 6 13: -96.0 + torsion 19: 12 15 4 3: 43.6 + torsion 20: 12 15 4 14: -135.2 + torsion 21: 4 15 12 6: 148.8 + + number of improper torsions: 6 + imptor 1: 3 7 2 1: 178.5 + imptor 2: 2 9 1 8: 179.0 + imptor 3: 10 11 5 6: 179.7 + imptor 4: 5 13 6 12: 179.8 + imptor 5: 14 15 4 3: 178.8 + imptor 6: 2 16 3 4: 178.8 + + number of nonbonds: 85 + + printing ic2 ic's + + printing internals + number of bonds: 16 + bond 1: 2 to 1: 1.51 + bond 2: 3 to 2: 1.34 + bond 3: 4 to 3: 1.51 + bond 4: 5 to 1: 1.54 + bond 5: 6 to 4: 1.54 + bond 6: 6 to 5: 1.54 + bond 7: 7 to 2: 1.09 + bond 8: 8 to 1: 1.10 + bond 9: 9 to 1: 1.10 + bond 10: 10 to 5: 1.10 + bond 11: 11 to 5: 1.10 + bond 12: 12 to 6: 1.10 + bond 13: 13 to 6: 1.10 + bond 14: 14 to 4: 1.10 + bond 15: 15 to 4: 1.10 + bond 16: 16 to 3: 1.09 + + number of angles: 30 + angle 1: 3 2 1: 123.5 + angle 2: 4 3 2: 123.5 + angle 3: 5 1 2: 112.1 + angle 4: 6 4 3: 112.0 + angle 5: 6 5 1: 111.0 + angle 6: 5 6 4: 110.9 + angle 7: 7 2 1: 117.0 + angle 8: 7 2 3: 119.5 + angle 9: 8 1 2: 109.7 + angle 10: 8 1 5: 110.1 + angle 11: 9 1 2: 109.4 + angle 12: 9 1 5: 110.0 + angle 13: 9 1 8: 105.4 + angle 14: 10 5 1: 109.2 + angle 15: 10 5 6: 109.0 + angle 16: 11 5 1: 110.2 + angle 17: 11 5 6: 110.7 + angle 18: 11 5 10: 106.7 + angle 19: 12 6 4: 109.1 + angle 20: 12 6 5: 109.0 + angle 21: 13 6 4: 110.2 + angle 22: 13 6 5: 110.8 + angle 23: 13 6 12: 106.7 + angle 24: 14 4 3: 109.8 + angle 25: 14 4 6: 110.0 + angle 26: 15 4 3: 109.5 + angle 27: 15 4 6: 110.0 + angle 28: 15 4 14: 105.4 + angle 29: 16 3 2: 119.5 + angle 30: 16 3 4: 117.0 + + number of torsions: 43 + torsion 1: 4 3 2 1: 1.5 + torsion 2: 5 1 2 3: 13.6 + torsion 3: 6 4 3 2: 14.3 + torsion 4: 6 5 1 2: -43.9 + torsion 5: 5 6 4 3: -44.6 + torsion 6: 4 6 5 1: 60.6 + torsion 7: 7 2 1 5: -166.2 + torsion 8: 7 2 3 4: -178.6 + torsion 9: 8 1 2 3: 136.2 + torsion 10: 8 1 2 7: -43.6 + torsion 11: 8 1 5 6: -166.3 + torsion 12: 9 1 2 3: -108.7 + torsion 13: 9 1 2 7: 71.5 + torsion 14: 9 1 5 6: 78.1 + torsion 15: 10 5 1 2: 76.3 + torsion 16: 10 5 1 8: -46.1 + torsion 17: 10 5 1 9: -161.8 + torsion 18: 10 5 6 4: -59.7 + torsion 19: 11 5 1 2: -166.9 + torsion 20: 11 5 1 8: 70.7 + torsion 21: 11 5 1 9: -44.9 + torsion 22: 11 5 6 4: -176.8 + torsion 23: 12 6 4 3: 75.6 + torsion 24: 12 6 5 1: -59.7 + torsion 25: 12 6 5 10: -179.9 + torsion 26: 12 6 5 11: 63.0 + torsion 27: 13 6 4 3: -167.5 + torsion 28: 13 6 5 1: -176.8 + torsion 29: 13 6 5 10: 63.0 + torsion 30: 13 6 5 11: -54.1 + torsion 31: 14 4 3 2: 136.9 + torsion 32: 14 4 6 5: -166.9 + torsion 33: 14 4 6 12: -46.8 + torsion 34: 14 4 6 13: 70.1 + torsion 35: 15 4 3 2: -107.9 + torsion 36: 15 4 6 5: 77.4 + torsion 37: 15 4 6 12: -162.5 + torsion 38: 15 4 6 13: -45.6 + torsion 39: 16 3 2 1: -178.7 + torsion 40: 16 3 2 7: 1.2 + torsion 41: 16 3 4 6: -165.5 + torsion 42: 16 3 4 14: -42.9 + torsion 43: 16 3 4 15: 72.3 + + number of improper torsions: 2 + imptor 1: 3 7 2 1: 179.9 + imptor 2: 2 16 3 4: 179.8 + + number of nonbonds: 74 + + ic1.nbonds: 15 ic2.nbonds: 16 + saving bond union: 17 saving angle union: 32 saving torsion union: 48 total number of coordinates: 97 + + + actual IC's + + printing internals + number of bonds: 17 + bond 1: 2 to 1: 1.34 + bond 2: 3 to 2: 1.47 + bond 3: 4 to 3: 1.34 + bond 4: 6 to 5: 1.33 + bond 5: 7 to 2: 1.09 + bond 6: 8 to 1: 1.09 + bond 7: 9 to 1: 1.09 + bond 8: 10 to 5: 1.09 + bond 9: 11 to 5: 1.09 + bond 10: 12 to 6: 1.09 + bond 11: 13 to 6: 1.09 + bond 12: 14 to 4: 1.09 + bond 13: 15 to 4: 1.09 + bond 14: 16 to 3: 1.09 + bond 15: 12 to 15: 2.86 + bond 16: 5 to 1: 4.27 + bond 17: 6 to 4: 3.99 + + number of angles: 32 + angle 1: 3 2 1: 125.9 + angle 2: 4 3 2: 125.8 + angle 3: 7 2 1: 118.5 + angle 4: 7 2 3: 115.6 + angle 5: 8 1 2: 121.7 + angle 6: 9 1 2: 121.4 + angle 7: 9 1 8: 116.8 + angle 8: 10 5 6: 122.0 + angle 9: 11 5 6: 121.8 + angle 10: 11 5 10: 116.2 + angle 11: 12 6 5: 121.8 + angle 12: 13 6 5: 121.7 + angle 13: 13 6 12: 116.5 + angle 14: 14 4 3: 121.2 + angle 15: 15 4 3: 122.0 + angle 16: 15 4 14: 116.8 + angle 17: 16 3 2: 115.5 + angle 18: 16 3 4: 118.6 + angle 19: 15 12 6: 90.1 + angle 20: 12 15 4: 127.0 + angle 21: 5 1 2: 114.0 + angle 22: 6 4 3: 106.8 + angle 23: 6 5 1: 68.1 + angle 24: 5 6 4: 104.9 + angle 25: 8 1 5: 51.0 + angle 26: 9 1 5: 102.5 + angle 27: 10 5 1: 158.2 + angle 28: 11 5 1: 57.7 + angle 29: 12 6 4: 62.6 + angle 30: 13 6 4: 100.8 + angle 31: 14 4 6: 125.9 + angle 32: 15 4 6: 27.1 + + number of torsions: 48 + torsion 1: 4 3 2 1: 31.5 + torsion 2: 7 2 3 4: -150.1 + torsion 3: 8 1 2 3: 1.9 + torsion 4: 8 1 2 7: -176.4 + torsion 5: 9 1 2 3: -179.1 + torsion 6: 9 1 2 7: 2.5 + torsion 7: 12 6 5 10: -179.9 + torsion 8: 12 6 5 11: 0.4 + torsion 9: 13 6 5 10: -0.0 + torsion 10: 13 6 5 11: -179.8 + torsion 11: 14 4 3 2: -178.9 + torsion 12: 15 4 3 2: 2.4 + torsion 13: 16 3 2 1: -149.8 + torsion 14: 16 3 2 7: 28.6 + torsion 15: 16 3 4 14: 2.5 + torsion 16: 16 3 4 15: -176.3 + torsion 17: 15 12 6 5: 83.8 + torsion 18: 15 12 6 13: -96.0 + torsion 19: 12 15 4 3: 43.6 + torsion 20: 12 15 4 14: -135.2 + torsion 21: 4 15 12 6: 148.8 + torsion 22: 5 1 2 3: -55.8 + torsion 23: 6 4 3 2: 27.1 + torsion 24: 6 5 1 2: -33.3 + torsion 25: 5 6 4 3: -114.4 + torsion 26: 4 6 5 1: 45.1 + torsion 27: 7 2 1 5: 125.8 + torsion 28: 8 1 5 6: -145.7 + torsion 29: 9 1 5 6: 99.8 + torsion 30: 10 5 1 2: 88.8 + torsion 31: 10 5 1 8: -23.5 + torsion 32: 10 5 1 9: -138.1 + torsion 33: 10 5 6 4: -113.1 + torsion 34: 11 5 1 2: 168.9 + torsion 35: 11 5 1 8: 56.5 + torsion 36: 11 5 1 9: -58.0 + torsion 37: 11 5 6 4: 67.1 + torsion 38: 12 6 4 3: 4.0 + torsion 39: 12 6 5 1: -21.6 + torsion 40: 13 6 4 3: 118.3 + torsion 41: 13 6 5 1: 158.2 + torsion 42: 14 4 6 5: 93.1 + torsion 43: 14 4 6 12: -148.4 + torsion 44: 14 4 6 13: -34.1 + torsion 45: 15 4 6 5: 14.3 + torsion 46: 15 4 6 12: 132.8 + torsion 47: 15 4 6 13: -112.9 + torsion 48: 16 3 4 6: -151.5 + + number of improper torsions: 0 + + number of nonbonds: 0 + + + ic1.nbonds: 14 ic2.nbonds: 16 + saving bond union: 16 saving angle union: 30 saving torsion union: 43 total number of coordinates: 89 + + Number of OpenMP threads: 1 + + + ---- Now preparing gradients ---- + Q-Chem initialized + -run name set to: GSM_go1q0001.001 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.000 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.001 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.002 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.003 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.004 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.005 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.006 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.007 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.008 + grad initiated: Q-Chem mode + Q-Chem initialized + -run name set to: GSM_go1q0001.009 + grad initiated: Q-Chem mode + ---- Done preparing gradients ---- + + + + Begin Growing the String + creating R node: 1 iR,iP: 0 8 wR,wP: 1 -1 iN: 1 bdist: 0.000 + dqmag: 9.10 dq0[constraint]: -1.30 + creating P node: 7 iR,iP: 1 8 wR,wP: -1 7 iN: 7 bdist: 0.000 + dqmag: 7.82 dq0[constraint]: -1.30 + nnR: 2 nnP: 2 + rpart: 0.50 0.00 0.00 0.00 0.00 0.00 0.50 0.00 + spacings (end ic_reparam, steps: 4): 1.14 2.58 0.00 0.00 0.00 0.00 0.00 2.59 1.14 disprms: 0.001 + eg eg setting V0 to: -147166.0 (-234.52746107 au) + + at beginning, starting V's are 0.000000 -40.719351 + + growing iter: 1 + rpart: 0.50 0.00 0.00 0.00 0.00 0.00 0.50 0.00 + spacings (end ic_reparam, steps: 4): 1.14 2.58 0.00 0.00 0.00 0.00 0.00 2.59 1.14 disprms: 0.001 + + eg eg eg eg + + Opt step: 1 gqc: 0.019 ss: 0.065 (DMAX: 0.100) predE: -2.12 E(M): 7.80 gRMS: 0.0115 ratio: 0.659 + Opt step: 2 gqc: 0.016 ss: 0.058 (DMAX: 0.100) predE: -0.50 E(M): 6.40 gRMS: 0.0033 + + Opt step: 1 gqc: 0.088 ss: 0.147 (DMAX: 0.100) predE: -8.74 E(M): 7.27 gRMS: 0.0258 ratio: 0.974 increasing DMAX + Opt step: 2 gqc: 0.085 ss: 0.201 (DMAX: 0.110) predE: -7.79 E(M): -1.23 gRMS: 0.0214 + + gopt_iter: 1 totalgrad: 0.160 gradrms: 0.0153 tgrads: 6 max E: 6.4 + printing string to scratch/stringfile.xyz0001g1 + + growing iter: 2 + adding node: 2 between 1 7 + iR,iP: 1 7 iN: 2 dqmag: 0.98 dq0[constraint]: -0.20 + initial Hint ev: 0.035 0.035 0.036 0.036 + rpart: 0.33 0.33 0.00 0.00 0.00 0.00 0.33 0.00 + spacings (end ic_reparam, steps: 4): 1.14 1.01 2.39 0.00 0.00 0.00 0.00 2.40 1.15 disprms: 0.112 + + eg eg eg eg eg eg + + Opt step: 1 gqc: 0.016 ss: 0.052 (DMAX: 0.100) predE: -0.35 E(M): 5.92 gRMS: 0.0025 ratio: 1.047 + Opt step: 2 gqc: 0.015 ss: 0.065 (DMAX: 0.100) predE: -0.39 E(M): 5.56 gRMS: 0.0023 + + Opt step: 1 gqc: 0.030 ss: 0.089 (DMAX: 0.100) predE: -2.77 E(M): 22.01 gRMS: 0.0122 ratio: 0.738 + Opt step: 2 gqc: 0.027 ss: 0.097 (DMAX: 0.100) predE: -1.19 E(M): 19.97 gRMS: 0.0044 + + Opt step: 1 gqc: 0.084 ss: 0.199 (DMAX: 0.110) predE: -6.90 E(M): -9.00 gRMS: 0.0187 ratio: 0.980 increasing DMAX + Opt step: 2 gqc: 0.077 ss: 0.178 (DMAX: 0.121) predE: -5.77 E(M): -15.76 gRMS: 0.0162 + + gopt_iter: 2 totalgrad: 0.148 gradrms: 0.0098 tgrads: 12 max E: 20.0 + printing string to scratch/stringfile.xyz0001g1 + + growing iter: 3 + adding node: 3 between 2 7 + iR,iP: 2 7 iN: 3 dqmag: 0.99 dq0[constraint]: -0.25 + initial Hint ev: 0.035 0.035 0.035 0.036 + rpart: 0.25 0.25 0.25 0.00 0.00 0.00 0.25 0.00 + spacings (end ic_reparam, steps: 4): 1.15 1.06 1.01 2.16 0.00 0.00 0.00 2.16 1.17 disprms: 0.132 + + eg eg eg eg eg eg eg eg + + Opt step: 1 gqc: 0.014 ss: 0.064 (DMAX: 0.100) predE: -0.37 E(M): 5.13 gRMS: 0.0022 ratio: 1.086 + Opt step: 2 gqc: 0.013 ss: 0.089 (DMAX: 0.100) predE: -0.43 E(M): 4.73 gRMS: 0.0020 + + Opt step: 1 gqc: 0.028 ss: 0.088 (DMAX: 0.100) predE: -0.95 E(M): 19.77 gRMS: 0.0041 ratio: 1.052 + Opt step: 2 gqc: 0.027 ss: 0.103 (DMAX: 0.100) predE: -1.01 E(M): 18.76 gRMS: 0.0039 + + Opt step: 1 gqc: 0.040 ss: 0.107 (DMAX: 0.100) predE: -3.12 E(M): 42.95 gRMS: 0.0126 ratio: 0.824 increasing DMAX + Opt step: 2 gqc: 0.037 ss: 0.107 (DMAX: 0.110) predE: -1.70 E(M): 40.37 gRMS: 0.0053 + + Opt step: 1 gqc: 0.072 ss: 0.169 (DMAX: 0.121) predE: -4.54 E(M): -21.52 gRMS: 0.0130 ratio: 0.998 increasing DMAX + Opt step: 2 gqc: 0.062 ss: 0.165 (DMAX: 0.133) predE: -3.36 E(M): -26.05 gRMS: 0.0101 + + gopt_iter: 3 totalgrad: 0.138 gradrms: 0.0061 tgrads: 20 max E: 40.4 + printing string to scratch/stringfile.xyz0001g1 + + growing iter: 4 + adding node: 4 between 3 7 + iR,iP: 3 7 iN: 4 dqmag: 0.99 dq0[constraint]: -0.33 + initial Hint ev: 0.035 0.035 0.035 0.036 + adding node: 6 between 7 4 + iR,iP: 7 4 iN: 6 dqmag: 0.99 dq0[constraint]: -0.49 + initial Hint ev: 0.035 0.035 0.035 0.035 + rpart: 0.17 0.17 0.17 0.17 0.00 0.17 0.17 0.00 + spacings (end ic_reparam, steps: 4): 1.16 1.08 1.05 0.99 1.62 0.00 1.62 1.01 1.22 disprms: 0.193 + + eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 gqc: 0.012 ss: 0.081 (DMAX: 0.100) predE: -0.36 E(M): 4.23 gRMS: 0.0019 ratio: 1.163 + Opt step: 2 gqc: 0.011 ss: 0.125 (DMAX: 0.100) predE: -0.37 E(M): 3.80 gRMS: 0.0017 + + Opt step: 1 gqc: 0.026 ss: 0.101 (DMAX: 0.100) predE: -0.94 E(M): 17.68 gRMS: 0.0038 ratio: 1.089 increasing DMAX + Opt step: 2 gqc: 0.025 ss: 0.121 (DMAX: 0.110) predE: -0.97 E(M): 16.65 gRMS: 0.0035 + + Opt step: 1 gqc: 0.038 ss: 0.102 (DMAX: 0.110) predE: -1.44 E(M): 40.10 gRMS: 0.0050 ratio: 1.051 + Opt step: 2 gqc: 0.037 ss: 0.114 (DMAX: 0.110) predE: -1.50 E(M): 38.59 gRMS: 0.0049 + + Opt step: 1 gqc: 0.038 ss: 0.115 (DMAX: 0.100) predE: -2.73 E(M): 66.53 gRMS: 0.0108 ratio: 0.921 increasing DMAX + Opt step: 2 gqc: 0.037 ss: 0.113 (DMAX: 0.110) predE: -2.03 E(M): 64.02 gRMS: 0.0061 + + Opt step: 1 gqc: 0.091 ss: 0.145 (DMAX: 0.100) predE: -6.01 E(M): 28.18 gRMS: 0.0194 ratio: 0.999 increasing DMAX + Opt step: 2 gqc: 0.090 ss: 0.186 (DMAX: 0.110) predE: -6.10 E(M): 22.17 gRMS: 0.0166 + + Opt step: 1 gqc: 0.053 ss: 0.147 (DMAX: 0.133) predE: -2.17 E(M): -29.48 gRMS: 0.0072 ratio: 1.100 increasing DMAX + Opt step: 2 gqc: 0.043 ss: 0.187 (DMAX: 0.146) predE: -1.46 E(M): -31.86 gRMS: 0.0049 + + gopt_iter: 4 totalgrad: 0.244 gradrms: 0.0079 tgrads: 32 max E: 64.0 + printing string to scratch/stringfile.xyz0001g1 + + growing iter: 5 + adding node: 5 between 4 6 + iR,iP: 4 6 iN: 5 dqmag: 1.00 dq0[constraint]: -0.50 + initial Hint ev: 0.035 0.035 0.035 0.036 + gopt_iter: string done growing + writing grown string scratch/stringfile.xyz0001g + Warning: last added node(s) do not have energies yet + + initial ic_reparam + TSn: 0 rpart: 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.12 + disp[1]: -0.09 disp[2]: -0.08 disp[3]: -0.06 disp[4]: 0.01 disp[5]: 0.41 disp[6]: 0.00 disp[7]: 0.11 + disp[1]: -0.04 disp[2]: -0.02 disp[3]: 0.01 disp[4]: 0.05 disp[5]: 0.18 disp[6]: -0.04 disp[7]: 0.00 + disp[1]: -0.02 disp[2]: -0.01 disp[3]: 0.01 disp[4]: 0.03 disp[5]: 0.09 disp[6]: -0.02 disp[7]: -0.01 + disp[1]: -0.01 disp[2]: -0.00 disp[3]: 0.01 disp[4]: 0.02 disp[5]: 0.05 disp[6]: -0.01 disp[7]: -0.00 + disp[1]: -0.01 disp[2]: -0.00 disp[3]: 0.01 disp[4]: 0.01 disp[5]: 0.02 disp[6]: -0.01 disp[7]: -0.00 + disp[1]: -0.00 disp[2]: -0.00 disp[3]: 0.00 disp[4]: 0.01 disp[5]: 0.01 disp[6]: -0.01 disp[7]: -0.00 + spacings (end ic_reparam, steps: 25): 1.24 1.24 1.24 1.24 1.24 1.26 1.24 1.24 disprms: 0.015 + + + Starting String opt + V_profile: 0.0 3.8 16.7 38.6 64.0 0.0 22.2 -31.9 -40.7 + 3 way tangent (4): f1: 0.28 + 3 way tangent (5): f1: 0.26 + 3 way tangent (6): f1: 0.29 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 5 (0.53) ss: 0.116 (DMAX: 0.100) predE: -0.39 E(M): 2.66 gRMS: 0.0022 ratio: 0.175 decreasing DMAX + Opt step: 2 gqc: 0.008 ss: 0.110 (DMAX: 0.083) predE: -0.50 E(M): 2.59 gRMS: 0.0074 ratio: 1.123 + Opt step: 3 gqc: 0.007 ss: 0.086 (DMAX: 0.083) predE: -0.18 E(M): 2.04 gRMS: 0.0025 + + Opt step: 1 t/ol: 4 (0.59) ss: 0.113 (DMAX: 0.110) predE: -0.83 E(M): 14.15 gRMS: 0.0031 ratio: 1.160 increasing DMAX + Opt step: 2 gqc: 0.022 ss: 0.173 (DMAX: 0.121) predE: -0.80 E(M): 13.18 gRMS: 0.0027 ratio: 1.296 + Opt step: 3 gqc: 0.021 ss: 0.162 (DMAX: 0.121) predE: -0.77 E(M): 12.15 gRMS: 0.0028 + + Opt step: 1 t/ol: 4 (0.50) ss: 0.109 (DMAX: 0.110) predE: -1.38 E(M): 36.29 gRMS: 0.0047 ratio: 1.085 + Opt step: 2 gqc: 0.035 ss: 0.136 (DMAX: 0.110) predE: -1.32 E(M): 34.80 gRMS: 0.0044 ratio: 1.145 increasing DMAX + Opt step: 3 gqc: 0.034 ss: 0.206 (DMAX: 0.121) predE: -1.28 E(M): 33.28 gRMS: 0.0040 + + Opt step: 1 t/ol: 4 (0.40) ss: 0.110 (DMAX: 0.110) predE: -1.93 E(M): 64.35 gRMS: 0.0063 ratio: 1.082 increasing DMAX + Opt step: 2 gqc: 0.034 ss: 0.128 (DMAX: 0.121) predE: -2.06 E(M): 62.26 gRMS: 0.0061 ratio: 1.112 increasing DMAX + Opt step: 3 gqc: 0.033 ss: 0.168 (DMAX: 0.133) predE: -2.14 E(M): 59.96 gRMS: 0.0058 + + Opt step: 1 t/ol: 27 (0.36) ss: 0.121 (DMAX: 0.100) predE: -3.21 E(M): 71.29 gRMS: 0.0106 ratio: 1.046 increasing DMAX + Opt step: 2 gqc: -0.033 ss: 0.153 (DMAX: 0.110) predE: -3.70 E(M): 67.94 gRMS: 0.0098 ratio: 1.066 increasing DMAX + Opt step: 3 gqc: -0.037 ss: 0.180 (DMAX: 0.121) predE: -3.92 E(M): 63.99 gRMS: 0.0094 + + Opt step: 1 t/ol: 0 (0.69) ss: 0.181 (DMAX: 0.110) predE: -5.63 E(M): 19.91 gRMS: 0.0153 ratio: 1.021 increasing DMAX + Opt step: 2 gqc: -0.089 ss: 0.199 (DMAX: 0.121) predE: -5.33 E(M): 14.16 gRMS: 0.0139 ratio: 1.032 increasing DMAX + Opt step: 3 gqc: -0.087 ss: 0.213 (DMAX: 0.133) predE: -4.75 E(M): 8.66 gRMS: 0.0123 + + Opt step: 1 t/ol: 0 (0.57) ss: 0.148 (DMAX: 0.146) predE: -1.01 E(M): -34.27 gRMS: 0.0046 ratio: 1.119 increasing DMAX + Opt step: 2 gqc: -0.028 ss: 0.142 (DMAX: 0.161) predE: -0.87 E(M): -35.40 gRMS: 0.0040 ratio: 1.101 + Opt step: 3 gqc: -0.020 ss: 0.123 (DMAX: 0.161) predE: -0.51 E(M): -36.36 gRMS: 0.0026 + + opt_iter: 5 totalgrad: 0.256 gradrms: 0.0067 tgrads: 53 ol(0): 0.00 max E: 64.0 + in find_peaks (2) + V_profile: 0.0 2.0 12.2 33.3 60.0 64.0 8.7 -36.4 -40.7 + min nodes: max nodes: 5 + found 1 significant peak(s). TOL: 0.50 + ** starting climb ** + printing string to stringfile.xyz0001 + V_profile: 0.0 2.0 12.2 33.3 60.0 64.0 8.7 -36.4 -40.7 + TSn: 5 rpart: 0.20 0.20 0.20 0.20 0.00 0.33 0.33 0.33 + disp[1]: -0.02 disp[2]: -0.01 disp[3]: 0.01 disp[4]: 0.04 disp[5]: 0.00 disp[6]: -0.01 disp[7]: 0.12 + disp[1]: -0.01 disp[2]: -0.01 disp[3]: 0.01 disp[4]: 0.02 disp[5]: 0.00 disp[6]: -0.01 disp[7]: 0.04 + disp[1]: -0.01 disp[2]: -0.00 disp[3]: 0.00 disp[4]: 0.01 disp[5]: 0.00 disp[6]: -0.01 disp[7]: 0.02 + disp[1]: -0.00 disp[2]: -0.00 disp[3]: 0.00 disp[4]: 0.01 disp[5]: 0.00 disp[6]: -0.01 disp[7]: 0.01 + spacings (end ic_reparam, steps: 5): 1.27 1.26 1.26 1.26 1.27 1.27 1.26 1.27 disprms: 0.012 + V_profile: 0.0 2.0 12.2 33.3 60.0 64.0 8.7 -36.4 -40.7 + 3 way tangent (5): f1: 0.07 + + slowing down climb optimization + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 5 (0.57) ss: 0.090 (DMAX: 0.083) predE: -0.24 E(M): 1.71 gRMS: 0.0019 ratio: 0.066 decreasing DMAX + Opt step: 2 gqc: 0.006 ss: 0.085 (DMAX: 0.069) predE: -0.29 E(M): 1.70 gRMS: 0.0052 ratio: 1.180 + Opt step: 3 gqc: 0.005 ss: 0.072 (DMAX: 0.069) predE: -0.16 E(M): 1.36 gRMS: 0.0022 + + Opt step: 1 t/ol: 4 (0.60) ss: 0.177 (DMAX: 0.121) predE: -1.38 E(M): 11.15 gRMS: 0.0052 ratio: -0.441 dE>0, decreasing DMAX + Opt step: 2 gqc: 0.020 ss: 0.145 (DMAX: 0.081) predE: -1.39 E(M): 11.76 gRMS: 0.0151 ratio: 1.078 + Opt step: 3 gqc: 0.019 ss: 0.137 (DMAX: 0.081) predE: -0.84 E(M): 10.26 gRMS: 0.0085 +S + Opt step: 1 t/ol: 4 (0.49) ss: 0.181 (DMAX: 0.121) predE: -1.23 E(M): 32.16 gRMS: 0.0037 ratio: 1.223 increasing DMAX + Opt step: 2 gqc: 0.032 ss: 0.173 (DMAX: 0.133) predE: -1.24 E(M): 30.66 gRMS: 0.0034 ratio: 1.243 increasing DMAX + Opt step: 3 gqc: 0.031 ss: 0.167 (DMAX: 0.146) predE: -1.30 E(M): 29.12 gRMS: 0.0035 + + Opt step: 1 t/ol: 27 (0.44) ss: 0.152 (DMAX: 0.133) predE: -1.82 E(M): 58.65 gRMS: 0.0053 ratio: 1.181 increasing DMAX + Opt step: 2 gqc: 0.032 ss: 0.204 (DMAX: 0.146) predE: -1.76 E(M): 56.50 gRMS: 0.0050 ratio: 1.234 increasing DMAX + Opt step: 3 gqc: 0.030 ss: 0.171 (DMAX: 0.161) predE: -1.82 E(M): 54.33 gRMS: 0.0046 + + Opt step: 1 gqc: -0.044 ss: 0.182 (DMAX: 0.061) gts: -0.0439 predE: -0.67 E(M): 59.80 gRMS: 0.0087 ratio: 1.083 increasing DMAX + Opt step: 2 gqc: -0.042 ss: 0.219 (DMAX: 0.067) gts: -0.0416 predE: -0.87 E(M): 59.08 gRMS: 0.0083 ratio: 1.065 increasing DMAX + Opt step: 3 gqc: -0.040 ss: 0.245 (DMAX: 0.073) gts: -0.0395 predE: -0.98 E(M): 58.15 gRMS: 0.0079 + + Opt step: 1 t/ol: 0 (0.68) ss: 0.186 (DMAX: 0.133) predE: -3.85 E(M): 5.18 gRMS: 0.0105 ratio: 1.059 increasing DMAX + Opt step: 2 gqc: -0.082 ss: 0.229 (DMAX: 0.146) predE: -2.91 E(M): 1.09 gRMS: 0.0089 ratio: 1.131 increasing DMAX + Opt step: 3 gqc: -0.076 ss: 0.188 (DMAX: 0.161) predE: -2.63 E(M): -2.20 gRMS: 0.0077 + + Opt step: 1 t/ol: 0 (0.49) ss: 0.093 (DMAX: 0.161) predE: -0.25 E(M): -37.65 gRMS: 0.0020 ratio: 0.974 + Opt step: 2 gqc: -0.014 ss: 0.091 (DMAX: 0.161) predE: -0.28 E(M): -37.89 gRMS: 0.0029 ratio: 0.938 + Opt step: 3 gqc: -0.012 ss: 0.069 (DMAX: 0.161) predE: -0.13 E(M): -38.15 gRMS: 0.0023 + +c opt_iter: 6 totalgrad: 0.237 gradrms: 0.0058 tgrads: 74 ol(0): 0.00 max E: 58.1 + in find_peaks (2) + V_profile: 0.0 1.4 10.3 29.1 54.3 58.1 -2.2 -38.2 -40.7 + min nodes: max nodes: 5 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 1.4 10.3 29.1 54.3 58.1 -2.2 -38.2 -40.7 + TSn: 5 rpart: 0.20 0.20 0.20 0.20 0.00 0.33 0.33 0.33 + disp[1]: -0.03 disp[2]: -0.04 disp[3]: -0.04 disp[4]: -0.08 disp[5]: 0.00 disp[6]: -0.05 disp[7]: 0.01 + disp[1]: -0.02 disp[2]: -0.02 disp[3]: -0.02 disp[4]: -0.04 disp[5]: 0.00 disp[6]: -0.03 disp[7]: 0.01 + disp[1]: -0.01 disp[2]: -0.01 disp[3]: -0.01 disp[4]: -0.02 disp[5]: 0.00 disp[6]: -0.02 disp[7]: 0.01 + disp[1]: -0.01 disp[2]: -0.01 disp[3]: -0.01 disp[4]: -0.01 disp[5]: 0.00 disp[6]: -0.01 disp[7]: 0.01 + spacings (end ic_reparam, steps: 5): 1.28 1.27 1.27 1.27 1.26 1.33 1.31 1.32 disprms: 0.019 + V_profile: 0.0 1.4 10.3 29.1 54.3 58.1 -2.2 -38.2 -40.7 + 3 way tangent (5): f1: 0.06 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 5 (0.58) ss: 0.070 (DMAX: 0.069) predE: -0.31 E(M): 1.17 gRMS: 0.0030 ratio: -0.632 dE>0, decreasing DMAX + Opt step: 2 gqc: 0.005 ss: 0.072 (DMAX: 0.046) predE: -0.34 E(M): 1.37 gRMS: 0.0064 ratio: 1.076 + Opt step: 3 gqc: 0.004 ss: 0.052 (DMAX: 0.046) predE: -0.13 E(M): 1.00 gRMS: 0.0030 + + Opt step: 1 t/ol: 4 (0.59) ss: 0.160 (DMAX: 0.065) predE: -0.73 E(M): 8.92 gRMS: 0.0053 ratio: 0.539 + Opt step: 2 gqc: 0.015 ss: 0.139 (DMAX: 0.065) predE: -0.46 E(M): 8.53 gRMS: 0.0050 ratio: 1.108 increasing DMAX + Opt step: 3 gqc: 0.015 ss: 0.133 (DMAX: 0.071) predE: -0.39 E(M): 8.02 gRMS: 0.0032 + + Opt step: 1 t/ol: 6 (0.44) ss: 0.166 (DMAX: 0.146) predE: -1.50 E(M): 26.38 gRMS: 0.0053 ratio: 0.675 + Opt step: 2 gqc: 0.029 ss: 0.142 (DMAX: 0.146) predE: -1.53 E(M): 25.37 gRMS: 0.0087 ratio: 1.210 + Opt step: 3 gqc: 0.028 ss: 0.144 (DMAX: 0.146) predE: -1.01 E(M): 23.51 gRMS: 0.0030 + + Opt step: 1 t/ol: 0 (0.52) ss: 0.160 (DMAX: 0.161) predE: -1.21 E(M): 49.96 gRMS: 0.0040 ratio: 1.090 + Opt step: 2 gqc: 0.033 ss: 0.133 (DMAX: 0.161) predE: -1.08 E(M): 48.63 gRMS: 0.0064 ratio: 1.212 + Opt step: 3 gqc: 0.031 ss: 0.124 (DMAX: 0.161) predE: -0.96 E(M): 47.33 gRMS: 0.0041 + + Opt step: 1 gqc: -0.030 ss: 0.236 (DMAX: 0.073) gts: -0.0304 predE: -1.42 E(M): 57.10 gRMS: 0.0083 ratio: 1.035 increasing DMAX + Opt step: 2 gqc: -0.030 ss: 0.234 (DMAX: 0.081) gts: -0.0304 predE: -1.52 E(M): 55.64 gRMS: 0.0080 ratio: 1.075 increasing DMAX + Opt step: 3 gqc: -0.031 ss: 0.233 (DMAX: 0.089) gts: -0.0307 predE: -1.58 E(M): 54.00 gRMS: 0.0076 + + Opt step: 1 t/ol: 0 (0.44) ss: 0.168 (DMAX: 0.161) predE: -2.18 E(M): -0.77 gRMS: 0.0069 ratio: 1.045 increasing DMAX + Opt step: 2 gqc: -0.075 ss: 0.152 (DMAX: 0.177) predE: -1.89 E(M): -3.05 gRMS: 0.0053 ratio: 1.003 + Opt step: 3 gqc: -0.070 ss: 0.147 (DMAX: 0.177) predE: -1.56 E(M): -4.95 gRMS: 0.0051 + + Opt step: 1 t/ol: 0 (0.54) ss: 0.051 (DMAX: 0.161) predE: -0.07 E(M): -38.36 gRMS: 0.0011 ratio: 1.073 + Opt step: 2 gqc: -0.009 ss: 0.047 (DMAX: 0.161) predE: -0.08 E(M): -38.43 gRMS: 0.0014 ratio: 0.455 + Opt step: 3 gqc: -0.009 ss: 0.038 (DMAX: 0.161) predE: -0.08 E(M): -38.47 gRMS: 0.0020 +r +c opt_iter: 7 totalgrad: 0.176 gradrms: 0.0043 tgrads: 95 ol(0): 0.00 max E: 54.0 + in find_peaks (2) + V_profile: 0.0 1.0 8.0 23.5 47.3 54.0 -4.9 -38.4 -40.7 + min nodes: max nodes: 5 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 1.0 8.0 23.5 47.3 54.0 -4.9 -38.4 -40.7 + TSn: 5 rpart: 0.20 0.20 0.20 0.20 0.00 0.33 0.33 0.33 + disp[1]: -0.01 disp[2]: 0.00 disp[3]: -0.01 disp[4]: -0.06 disp[5]: 0.00 disp[6]: -0.02 disp[7]: -0.01 + disp[1]: -0.01 disp[2]: -0.00 disp[3]: -0.01 disp[4]: -0.03 disp[5]: 0.00 disp[6]: -0.01 disp[7]: -0.00 + disp[1]: -0.00 disp[2]: -0.00 disp[3]: -0.01 disp[4]: -0.02 disp[5]: 0.00 disp[6]: -0.01 disp[7]: -0.00 + disp[1]: -0.00 disp[2]: -0.00 disp[3]: -0.00 disp[4]: -0.01 disp[5]: 0.00 disp[6]: -0.01 disp[7]: -0.00 + spacings (end ic_reparam, steps: 5): 1.29 1.28 1.29 1.29 1.28 1.33 1.32 1.32 disprms: 0.012 + V_profile: 0.0 1.0 8.0 23.5 47.3 54.0 -4.9 -38.4 -40.7 + 3 way tangent (5): f1: 0.10 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 5 (0.60) ss: 0.055 (DMAX: 0.046) predE: -0.08 E(M): 0.85 gRMS: 0.0012 ratio: 0.625 + Opt step: 2 gqc: 0.003 ss: 0.053 (DMAX: 0.046) predE: -0.10 E(M): 0.80 gRMS: 0.0016 ratio: 0.800 increasing DMAX + Opt step: 3 gqc: 0.003 ss: 0.046 (DMAX: 0.051) predE: -0.05 E(M): 0.72 gRMS: 0.0011 + + Opt step: 1 t/ol: 4 (0.50) ss: 0.148 (DMAX: 0.071) predE: -0.43 E(M): 7.56 gRMS: 0.0025 ratio: 1.135 increasing DMAX + Opt step: 2 gqc: 0.012 ss: 0.142 (DMAX: 0.078) predE: -0.42 E(M): 7.08 gRMS: 0.0020 ratio: 1.175 increasing DMAX + Opt step: 3 gqc: 0.012 ss: 0.134 (DMAX: 0.086) predE: -0.41 E(M): 6.59 gRMS: 0.0018 + + Opt step: 1 t/ol: 6 (0.42) ss: 0.141 (DMAX: 0.146) predE: -1.06 E(M): 21.89 gRMS: 0.0035 ratio: 0.916 + Opt step: 2 gqc: 0.026 ss: 0.137 (DMAX: 0.146) predE: -1.08 E(M): 20.92 gRMS: 0.0058 ratio: 1.256 + Opt step: 3 gqc: 0.025 ss: 0.144 (DMAX: 0.146) predE: -1.00 E(M): 19.56 gRMS: 0.0034 + + Opt step: 1 t/ol: 0 (0.58) ss: 0.116 (DMAX: 0.161) predE: -0.76 E(M): 44.72 gRMS: 0.0035 ratio: 0.574 + Opt step: 2 gqc: 0.032 ss: 0.097 (DMAX: 0.161) predE: -0.79 E(M): 44.28 gRMS: 0.0067 ratio: 1.001 + Opt step: 3 gqc: 0.032 ss: 0.109 (DMAX: 0.161) predE: -0.69 E(M): 43.49 gRMS: 0.0039 + + Opt step: 1 gqc: -0.028 ss: 0.238 (DMAX: 0.089) gts: -0.0283 predE: -1.55 E(M): 52.27 gRMS: 0.0075 ratio: 1.090 increasing DMAX + Opt step: 2 gqc: -0.029 ss: 0.234 (DMAX: 0.097) gts: -0.0290 predE: -1.60 E(M): 50.58 gRMS: 0.0073 ratio: 1.105 increasing DMAX + Opt step: 3 gqc: -0.030 ss: 0.224 (DMAX: 0.107) gts: -0.0299 predE: -1.65 E(M): 48.81 gRMS: 0.0070 + + Opt step: 1 t/ol: 9 (0.49) ss: 0.182 (DMAX: 0.177) predE: -1.17 E(M): -5.37 gRMS: 0.0031 ratio: 1.192 increasing DMAX + Opt step: 2 gqc: -0.068 ss: 0.172 (DMAX: 0.195) predE: -1.11 E(M): -6.76 gRMS: 0.0040 ratio: 0.951 + Opt step: 3 gqc: -0.065 ss: 0.156 (DMAX: 0.195) predE: -0.85 E(M): -7.82 gRMS: 0.0039 + + Opt step: 1 t/ol: 0 (0.65) ss: 0.074 (DMAX: 0.025) predE: -0.07 E(M): -38.30 gRMS: 0.0014 ratio: 0.994 increasing DMAX + Opt step: 2 gqc: -0.009 ss: 0.067 (DMAX: 0.028) predE: -0.06 E(M): -38.37 gRMS: 0.0011 ratio: 1.042 increasing DMAX + Opt step: 3 gqc: -0.009 ss: 0.061 (DMAX: 0.030) predE: -0.06 E(M): -38.44 gRMS: 0.0010 + +c opt_iter: 8 totalgrad: 0.143 gradrms: 0.0037 tgrads: 116 ol(0): 0.00 max E: 48.8 + in find_peaks (2) + V_profile: 0.0 0.7 6.6 19.6 43.5 48.8 -7.8 -38.4 -40.7 + min nodes: max nodes: 5 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.7 6.6 19.6 43.5 48.8 -7.8 -38.4 -40.7 + TSn: 5 rpart: 0.20 0.20 0.20 0.20 0.00 0.33 0.33 0.33 + disp[1]: -0.00 disp[2]: 0.02 disp[3]: 0.00 disp[4]: -0.04 disp[5]: 0.00 disp[6]: 0.03 disp[7]: -0.03 + disp[1]: -0.00 disp[2]: 0.01 disp[3]: 0.00 disp[4]: -0.02 disp[5]: 0.00 disp[6]: 0.02 disp[7]: -0.01 + disp[1]: -0.00 disp[2]: 0.01 disp[3]: 0.00 disp[4]: -0.01 disp[5]: 0.00 disp[6]: 0.02 disp[7]: -0.00 + disp[1]: -0.00 disp[2]: 0.01 disp[3]: 0.00 disp[4]: -0.01 disp[5]: 0.00 disp[6]: 0.01 disp[7]: -0.00 + spacings (end ic_reparam, steps: 5): 1.31 1.30 1.31 1.32 1.30 1.34 1.36 1.35 disprms: 0.015 + V_profile: 0.0 0.7 6.6 19.6 43.5 48.8 -7.8 -38.4 -40.7 + 3 way tangent (5): f1: 0.09 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 5 (0.58) ss: 0.045 (DMAX: 0.051) predE: -0.04 E(M): 0.65 gRMS: 0.0007 * + + Opt step: 1 t/ol: 4 (0.44) ss: 0.129 (DMAX: 0.086) predE: -0.44 E(M): 6.32 gRMS: 0.0019 ratio: 1.199 increasing DMAX + Opt step: 2 gqc: 0.010 ss: 0.119 (DMAX: 0.094) predE: -0.43 E(M): 5.79 gRMS: 0.0018 ratio: 1.242 increasing DMAX + Opt step: 3 gqc: 0.009 ss: 0.111 (DMAX: 0.104) predE: -0.43 E(M): 5.25 gRMS: 0.0018 + + Opt step: 1 t/ol: 6 (0.44) ss: 0.160 (DMAX: 0.146) predE: -1.90 E(M): 18.88 gRMS: 0.0074 ratio: -0.024 dE>0, decreasing DMAX + Opt step: 2 gqc: 0.027 ss: 0.149 (DMAX: 0.098) predE: -1.30 E(M): 18.93 gRMS: 0.0112 ratio: 1.054 + Opt step: 3 gqc: 0.025 ss: 0.133 (DMAX: 0.098) predE: -0.70 E(M): 17.55 gRMS: 0.0054 + + Opt step: 1 t/ol: 7 (0.47) ss: 0.150 (DMAX: 0.161) predE: -1.26 E(M): 42.01 gRMS: 0.0048 ratio: 0.032 decreasing DMAX + Opt step: 2 gqc: 0.031 ss: 0.137 (DMAX: 0.136) predE: -1.40 E(M): 41.97 gRMS: 0.0101 ratio: 1.164 + Opt step: 3 gqc: 0.029 ss: 0.122 (DMAX: 0.136) predE: -0.62 E(M): 40.34 gRMS: 0.0033 + + Opt step: 1 gqc: -0.031 ss: 0.218 (DMAX: 0.107) gts: -0.0313 predE: -1.43 E(M): 46.95 gRMS: 0.0067 ratio: 1.133 increasing DMAX + Opt step: 2 gqc: -0.032 ss: 0.217 (DMAX: 0.118) gts: -0.0316 predE: -1.47 E(M): 45.33 gRMS: 0.0064 ratio: 1.151 increasing DMAX + Opt step: 3 gqc: -0.032 ss: 0.209 (DMAX: 0.130) gts: -0.0316 predE: -1.53 E(M): 43.63 gRMS: 0.0061 + + Opt step: 1 t/ol: 9 (0.46) ss: 0.162 (DMAX: 0.195) predE: -1.19 E(M): -10.15 gRMS: 0.0032 ratio: 1.108 + Opt step: 2 gqc: -0.059 ss: 0.127 (DMAX: 0.195) predE: -0.87 E(M): -11.47 gRMS: 0.0030 ratio: 0.951 + Opt step: 3 gqc: -0.059 ss: 0.118 (DMAX: 0.195) predE: -0.83 E(M): -12.29 gRMS: 0.0035 + + Opt step: 1 t/ol: 0 (0.71) ss: 0.061 (DMAX: 0.030) predE: -0.08 E(M): -38.29 gRMS: 0.0013 ratio: 1.080 increasing DMAX + Opt step: 2 gqc: -0.008 ss: 0.054 (DMAX: 0.033) predE: -0.07 E(M): -38.38 gRMS: 0.0011 ratio: 1.160 increasing DMAX + Opt step: 3 gqc: -0.007 ss: 0.046 (DMAX: 0.037) predE: -0.06 E(M): -38.46 gRMS: 0.0010 * + +c opt_iter: 9 totalgrad: 0.141 gradrms: 0.0037 tgrads: 135 ol(0): 0.00 max E: 43.6 + in find_peaks (2) + V_profile: 0.0 0.7 5.3 17.6 40.3 43.6 -12.3 -38.5 -40.7 + min nodes: max nodes: 5 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.7 5.3 17.6 40.3 43.6 -12.3 -38.5 -40.7 + TSn: 5 rpart: 0.20 0.20 0.20 0.20 0.00 0.33 0.33 0.33 + disp[1]: 0.01 disp[2]: 0.03 disp[3]: -0.00 disp[4]: -0.05 disp[5]: 0.00 disp[6]: -0.00 disp[7]: 0.05 + disp[1]: 0.00 disp[2]: 0.02 disp[3]: -0.00 disp[4]: -0.03 disp[5]: 0.00 disp[6]: -0.00 disp[7]: 0.02 + disp[1]: 0.00 disp[2]: 0.01 disp[3]: -0.00 disp[4]: -0.01 disp[5]: 0.00 disp[6]: -0.00 disp[7]: 0.01 + spacings (end ic_reparam, steps: 5): 1.32 1.31 1.33 1.33 1.31 1.34 1.33 1.34 disprms: 0.019 + V_profile: 0.0 0.7 5.3 17.6 40.3 43.6 -12.3 -38.5 -40.7 + 3 way tangent (5): f1: 0.06 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 5 (0.53) ss: 0.055 (DMAX: 0.051) predE: -0.08 E(M): 0.61 gRMS: 0.0011 ratio: 0.291 + Opt step: 2 gqc: 0.002 ss: 0.054 (DMAX: 0.051) predE: -0.12 E(M): 0.59 gRMS: 0.0022 ratio: 0.697 + Opt step: 3 gqc: 0.002 ss: 0.042 (DMAX: 0.051) predE: -0.05 E(M): 0.51 gRMS: 0.0013 + + Opt step: 1 t/ol: 22 (0.43) ss: 0.110 (DMAX: 0.104) predE: -0.45 E(M): 4.95 gRMS: 0.0023 ratio: 0.924 increasing DMAX + Opt step: 2 gqc: 0.009 ss: 0.098 (DMAX: 0.114) predE: -0.44 E(M): 4.54 gRMS: 0.0034 ratio: 1.182 + Opt step: 3 gqc: 0.008 ss: 0.091 (DMAX: 0.114) predE: -0.28 E(M): 4.01 gRMS: 0.0013 + + Opt step: 1 t/ol: 27 (0.39) ss: 0.143 (DMAX: 0.098) predE: -0.74 E(M): 16.93 gRMS: 0.0041 ratio: 0.876 increasing DMAX + Opt step: 2 gqc: 0.023 ss: 0.133 (DMAX: 0.107) predE: -0.57 E(M): 16.28 gRMS: 0.0034 ratio: 1.268 + Opt step: 3 gqc: 0.023 ss: 0.122 (DMAX: 0.107) predE: -0.45 E(M): 15.56 gRMS: 0.0017 + + Opt step: 1 t/ol: 0 (0.48) ss: 0.150 (DMAX: 0.136) predE: -0.83 E(M): 38.59 gRMS: 0.0036 ratio: 0.813 increasing DMAX + Opt step: 2 gqc: 0.028 ss: 0.138 (DMAX: 0.150) predE: -0.75 E(M): 37.92 gRMS: 0.0049 ratio: 1.242 + Opt step: 3 gqc: 0.027 ss: 0.120 (DMAX: 0.150) predE: -0.46 E(M): 36.99 gRMS: 0.0019 + + Opt step: 1 gqc: -0.031 ss: 0.209 (DMAX: 0.130) gts: -0.0313 predE: -1.53 E(M): 41.84 gRMS: 0.0060 ratio: 1.144 increasing DMAX + Opt step: 2 gqc: -0.032 ss: 0.195 (DMAX: 0.143) gts: -0.0320 predE: -1.75 E(M): 40.09 gRMS: 0.0060 ratio: 1.158 increasing DMAX + Opt step: 3 gqc: -0.034 ss: 0.192 (DMAX: 0.157) gts: -0.0335 predE: -1.82 E(M): 38.06 gRMS: 0.0059 + + Opt step: 1 t/ol: 6 (0.47) ss: 0.159 (DMAX: 0.195) predE: -1.07 E(M): -12.92 gRMS: 0.0030 ratio: 1.155 + Opt step: 2 gqc: -0.054 ss: 0.145 (DMAX: 0.195) predE: -0.89 E(M): -14.15 gRMS: 0.0028 ratio: 1.056 + Opt step: 3 gqc: -0.053 ss: 0.138 (DMAX: 0.195) predE: -0.86 E(M): -15.09 gRMS: 0.0033 + + Opt step: 1 t/ol: 0 (0.68) ss: 0.045 (DMAX: 0.037) predE: -0.04 E(M): -38.69 gRMS: 0.0008 * + +c opt_iter: 10 totalgrad: 0.105 gradrms: 0.0028 tgrads: 154 ol(0): 0.00 max E: 38.1 + in find_peaks (2) + V_profile: 0.0 0.5 4.0 15.6 37.0 38.1 -15.1 -38.7 -40.7 + min nodes: max nodes: 5 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.5 4.0 15.6 37.0 38.1 -15.1 -38.7 -40.7 + TSn: 5 rpart: 0.20 0.20 0.20 0.20 0.00 0.33 0.33 0.33 + disp[1]: 0.01 disp[2]: 0.04 disp[3]: 0.00 disp[4]: -0.04 disp[5]: 0.00 disp[6]: 0.03 disp[7]: -0.04 + disp[1]: 0.01 disp[2]: 0.02 disp[3]: 0.00 disp[4]: -0.02 disp[5]: 0.00 disp[6]: 0.02 disp[7]: -0.01 + disp[1]: 0.00 disp[2]: 0.01 disp[3]: 0.00 disp[4]: -0.01 disp[5]: 0.00 disp[6]: 0.02 disp[7]: -0.01 + disp[1]: 0.00 disp[2]: 0.01 disp[3]: 0.00 disp[4]: -0.01 disp[5]: 0.00 disp[6]: 0.01 disp[7]: -0.00 + spacings (end ic_reparam, steps: 5): 1.34 1.34 1.35 1.35 1.33 1.34 1.37 1.35 disprms: 0.016 + V_profile: 0.0 0.5 4.0 15.6 37.0 38.1 -15.1 -38.7 -40.7 + 3 way tangent (5): f1: 0.02 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 5 (0.50) ss: 0.040 (DMAX: 0.051) predE: -0.03 E(M): 0.47 gRMS: 0.0004 * + + Opt step: 1 t/ol: 22 (0.48) ss: 0.093 (DMAX: 0.114) predE: -0.27 E(M): 3.98 gRMS: 0.0013 ratio: 1.315 + Opt step: 2 gqc: 0.007 ss: 0.092 (DMAX: 0.114) predE: -0.27 E(M): 3.62 gRMS: 0.0015 ratio: 1.101 + Opt step: 3 gqc: 0.007 ss: 0.090 (DMAX: 0.114) predE: -0.28 E(M): 3.32 gRMS: 0.0023 +S + Opt step: 1 t/ol: 27 (0.42) ss: 0.146 (DMAX: 0.107) predE: -0.52 E(M): 15.00 gRMS: 0.0021 ratio: 1.133 increasing DMAX + Opt step: 2 gqc: 0.021 ss: 0.142 (DMAX: 0.118) predE: -0.52 E(M): 14.41 gRMS: 0.0024 ratio: 1.238 increasing DMAX + Opt step: 3 gqc: 0.021 ss: 0.129 (DMAX: 0.130) predE: -0.47 E(M): 13.77 gRMS: 0.0022 + + Opt step: 1 t/ol: 8 (0.40) ss: 0.176 (DMAX: 0.150) predE: -0.88 E(M): 35.47 gRMS: 0.0026 ratio: 1.118 increasing DMAX + Opt step: 2 gqc: 0.026 ss: 0.166 (DMAX: 0.165) predE: -0.83 E(M): 34.49 gRMS: 0.0030 ratio: 1.053 increasing DMAX + Opt step: 3 gqc: 0.025 ss: 0.158 (DMAX: 0.181) predE: -0.71 E(M): 33.62 gRMS: 0.0042 +S + Opt step: 1 gqc: -0.036 ss: 0.186 (DMAX: 0.157) gts: -0.0358 predE: -1.89 E(M): 35.96 gRMS: 0.0059 ratio: 1.148 increasing DMAX + Opt step: 2 gqc: -0.037 ss: 0.174 (DMAX: 0.173) gts: -0.0372 predE: -1.98 E(M): 33.79 gRMS: 0.0053 ratio: 1.166 increasing DMAX + Opt step: 3 gqc: -0.038 ss: 0.194 (DMAX: 0.190) gts: -0.0378 predE: -1.73 E(M): 31.48 gRMS: 0.0053 + + Opt step: 1 t/ol: 11 (0.55) ss: 0.160 (DMAX: 0.195) predE: -1.26 E(M): -16.98 gRMS: 0.0037 ratio: 1.059 + Opt step: 2 gqc: -0.046 ss: 0.147 (DMAX: 0.195) predE: -1.30 E(M): -18.31 gRMS: 0.0037 ratio: 1.000 + Opt step: 3 gqc: -0.045 ss: 0.138 (DMAX: 0.195) predE: -1.21 E(M): -19.61 gRMS: 0.0035 + + Opt step: 1 t/ol: 0 (0.73) ss: 0.050 (DMAX: 0.037) predE: -0.06 E(M): -38.57 gRMS: 0.0009 * + +c opt_iter: 11 totalgrad: 0.122 gradrms: 0.0031 tgrads: 171 ol(0): 0.00 max E: 33.6 + in find_peaks (2) + V_profile: 0.0 0.5 3.3 13.8 33.6 31.5 -19.6 -38.6 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.5 3.3 13.8 33.6 31.5 -19.6 -38.6 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.03 disp[2]: 0.05 disp[3]: 0.02 disp[4]: 0.00 disp[5]: 0.03 disp[6]: 0.02 disp[7]: 0.00 + disp[1]: 0.02 disp[2]: 0.03 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.02 disp[6]: 0.02 disp[7]: 0.00 + disp[1]: 0.01 disp[2]: 0.02 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.01 disp[7]: 0.00 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.00 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.01 disp[7]: 0.00 + spacings (end ic_reparam, steps: 5): 1.36 1.36 1.37 1.37 1.35 1.35 1.36 1.36 disprms: 0.019 + V_profile: 0.0 0.5 3.3 13.8 33.6 31.5 -19.6 -38.6 -40.7 + 3 way tangent (4): f1: 0.90 + + slowing down climb optimization + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 5 (0.46) ss: 0.043 (DMAX: 0.051) predE: -0.03 E(M): 0.47 gRMS: 0.0005 * + + Opt step: 1 t/ol: 22 (0.49) ss: 0.091 (DMAX: 0.072) predE: -0.23 E(M): 3.35 gRMS: 0.0018 ratio: 1.165 increasing DMAX + Opt step: 2 gqc: 0.006 ss: 0.089 (DMAX: 0.079) predE: -0.20 E(M): 3.08 gRMS: 0.0012 ratio: 1.229 increasing DMAX + Opt step: 3 gqc: 0.006 ss: 0.088 (DMAX: 0.087) predE: -0.20 E(M): 2.84 gRMS: 0.0014 + + Opt step: 1 t/ol: 27 (0.43) ss: 0.151 (DMAX: 0.130) predE: -0.58 E(M): 13.44 gRMS: 0.0021 ratio: 1.309 + Opt step: 2 gqc: 0.020 ss: 0.129 (DMAX: 0.130) predE: -0.52 E(M): 12.68 gRMS: 0.0019 ratio: 1.233 + Opt step: 3 gqc: 0.019 ss: 0.120 (DMAX: 0.130) predE: -0.53 E(M): 12.04 gRMS: 0.0029 +S + Opt step: 1 gqc: 0.023 ss: 0.178 (DMAX: 0.042) gts: 0.0227 predE: -0.01 E(M): 32.75 gRMS: 0.0035 ratio: 2.174 + Opt step: 2 gqc: 0.022 ss: 0.177 (DMAX: 0.042) gts: 0.0222 predE: 0.01 E(M): 32.72 gRMS: 0.0028 ratio: -2.987 + Opt step: 3 gqc: 0.022 ss: 0.173 (DMAX: 0.042) gts: 0.0217 predE: 0.01 E(M): 32.70 gRMS: 0.0025 + + Opt step: 1 t/ol: 0 (0.47) ss: 0.206 (DMAX: 0.190) predE: -2.72 E(M): 28.47 gRMS: 0.0065 ratio: 0.911 increasing DMAX + Opt step: 2 gqc: -0.046 ss: 0.198 (DMAX: 0.209) predE: -2.56 E(M): 25.99 gRMS: 0.0076 ratio: 1.170 + Opt step: 3 gqc: -0.048 ss: 0.168 (DMAX: 0.209) predE: -2.10 E(M): 22.99 gRMS: 0.0047 + + Opt step: 1 t/ol: 11 (0.56) ss: 0.186 (DMAX: 0.195) predE: -1.62 E(M): -21.38 gRMS: 0.0043 ratio: 1.181 + Opt step: 2 gqc: -0.037 ss: 0.170 (DMAX: 0.195) predE: -1.19 E(M): -23.30 gRMS: 0.0036 ratio: 1.038 + Opt step: 3 gqc: -0.035 ss: 0.145 (DMAX: 0.195) predE: -1.11 E(M): -24.54 gRMS: 0.0042 + + Opt step: 1 t/ol: 0 (0.79) ss: 0.075 (0.037) predE: -0.09 Hint ev: 0.018 0.032 E(M): -38.65 gRMS: 0.0010 ratio: 1.045 increasing DMAX + Opt step: 2 t/ol: 0 (0.80) ss: 0.059 (0.040) predE: -0.07 Hint ev: 0.018 0.031 E(M): -38.74 gRMS: 0.0010 * + +c opt_iter: 12 totalgrad: 0.112 gradrms: 0.0029 tgrads: 189 ol(0): 0.00 max E: 32.7 + in find_peaks (2) + V_profile: 0.0 0.5 2.8 12.0 32.7 23.0 -24.5 -38.7 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.5 2.8 12.0 32.7 23.0 -24.5 -38.7 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.03 disp[2]: 0.04 disp[3]: 0.03 disp[4]: 0.00 disp[5]: -0.02 disp[6]: 0.02 disp[7]: -0.06 + disp[1]: 0.02 disp[2]: 0.02 disp[3]: 0.02 disp[4]: 0.00 disp[5]: -0.01 disp[6]: 0.01 disp[7]: -0.02 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: -0.01 disp[6]: 0.01 disp[7]: -0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: -0.00 disp[6]: 0.01 disp[7]: -0.00 + spacings (end ic_reparam, steps: 5): 1.38 1.38 1.39 1.39 1.38 1.36 1.39 1.37 disprms: 0.016 + V_profile: 0.0 0.5 2.8 12.0 32.7 23.0 -24.5 -38.7 -40.7 + 3 way tangent (4): f1: 0.68 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 5 (0.43) ss: 0.043 (DMAX: 0.051) predE: -0.05 E(M): 0.47 gRMS: 0.0009 * + + Opt step: 1 t/ol: 22 (0.51) ss: 0.091 (DMAX: 0.087) predE: -0.24 E(M): 2.86 gRMS: 0.0017 ratio: 0.900 increasing DMAX + Opt step: 2 gqc: 0.005 ss: 0.089 (DMAX: 0.096) predE: -0.25 E(M): 2.64 gRMS: 0.0025 ratio: 1.132 + Opt step: 3 gqc: 0.005 ss: 0.085 (DMAX: 0.096) predE: -0.16 E(M): 2.36 gRMS: 0.0014 + + Opt step: 1 t/ol: 27 (0.43) ss: 0.123 (DMAX: 0.096) predE: -0.32 E(M): 12.06 gRMS: 0.0026 ratio: 0.971 increasing DMAX + Opt step: 2 gqc: 0.020 ss: 0.100 (DMAX: 0.105) predE: -0.21 E(M): 11.75 gRMS: 0.0018 ratio: 1.396 + Opt step: 3 gqc: 0.020 ss: 0.097 (DMAX: 0.105) predE: -0.18 E(M): 11.46 gRMS: 0.0014 + + Opt step: 1 gqc: 0.020 ss: 0.156 (DMAX: 0.042) gts: 0.0195 predE: -0.09 E(M): 32.68 gRMS: 0.0026 ratio: 1.227 increasing DMAX + Opt step: 2 gqc: 0.019 ss: 0.153 (DMAX: 0.046) gts: 0.0189 predE: -0.13 E(M): 32.57 gRMS: 0.0026 ratio: 1.187 increasing DMAX + Opt step: 3 gqc: 0.018 ss: 0.151 (DMAX: 0.051) gts: 0.0182 predE: -0.16 E(M): 32.42 gRMS: 0.0025 + + Opt step: 1 t/ol: 12 (0.43) ss: 0.201 (DMAX: 0.209) predE: -1.87 E(M): 21.69 gRMS: 0.0043 ratio: 0.749 + Opt step: 2 gqc: -0.054 ss: 0.203 (DMAX: 0.209) predE: -1.89 E(M): 20.29 gRMS: 0.0077 ratio: 1.129 + Opt step: 3 gqc: -0.055 ss: 0.173 (DMAX: 0.209) predE: -1.10 E(M): 18.15 gRMS: 0.0028 + + Opt step: 1 t/ol: 1 (0.51) ss: 0.165 (DMAX: 0.195) predE: -1.16 E(M): -26.03 gRMS: 0.0035 ratio: 0.983 + Opt step: 2 gqc: -0.027 ss: 0.146 (DMAX: 0.195) predE: -0.90 E(M): -27.18 gRMS: 0.0040 ratio: 0.967 + Opt step: 3 gqc: -0.028 ss: 0.156 (DMAX: 0.195) predE: -0.86 E(M): -28.05 gRMS: 0.0028 + + Opt step: 1 t/ol: 0 (0.80) ss: 0.056 (0.040) predE: -0.07 Hint ev: 0.018 0.031 E(M): -38.63 gRMS: 0.0010 * + +c opt_iter: 13 totalgrad: 0.083 gradrms: 0.0020 tgrads: 206 ol(0): 0.00 max E: 32.4 + in find_peaks (2) + V_profile: 0.0 0.5 2.4 11.5 32.4 18.2 -28.0 -38.6 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + ** starting exact TS search at node 4 ** + totalgrad: 0.0829 gradrms: 0.0025 gts: 0.0182 + TS Hess init'd w/existing Hintp + tHt: 0.118 a: 1.3 b: 1.1 C: -0.039 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.5 2.4 11.5 32.4 18.2 -28.0 -38.6 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.03 disp[2]: 0.04 disp[3]: 0.02 disp[4]: 0.00 disp[5]: 0.02 disp[6]: 0.02 disp[7]: -0.04 + disp[1]: 0.02 disp[2]: 0.02 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.01 disp[7]: -0.02 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.01 disp[7]: -0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.00 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.01 disp[7]: -0.00 + spacings (end ic_reparam, steps: 5): 1.40 1.41 1.41 1.41 1.39 1.39 1.40 1.39 disprms: 0.017 + V_profile: 0.0 0.5 2.4 11.5 32.4 18.2 -28.0 -38.6 -40.7 + 3 way tangent (4): f1: 0.60 + + eg eg eg eg eg eg eg eg eg TS Hess init'd w/existing Hintp + tHt: 0.117 a: 1.2 b: 1.2 C: -0.039 + eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.43) ss: 0.053 (DMAX: 0.051) predE: -0.19 E(M): 0.51 gRMS: 0.0021 ratio: -0.860 dE>0, decreasing DMAX + Opt step: 2 gqc: 0.001 ss: 0.044 (DMAX: 0.034) predE: -0.21 E(M): 0.67 gRMS: 0.0048 ratio: 1.113 + Opt step: 3 gqc: 0.001 ss: 0.027 (DMAX: 0.034) predE: -0.05 E(M): 0.44 gRMS: 0.0019 + + Opt step: 1 t/ol: 22 (0.49) ss: 0.085 (DMAX: 0.096) predE: -0.15 E(M): 2.35 gRMS: 0.0012 ratio: 1.233 + Opt step: 2 gqc: 0.005 ss: 0.086 (DMAX: 0.096) predE: -0.17 E(M): 2.17 gRMS: 0.0017 ratio: 0.905 + Opt step: 3 gqc: 0.004 ss: 0.085 (DMAX: 0.096) predE: -0.17 E(M): 2.02 gRMS: 0.0022 +r + Opt step: 1 t/ol: 27 (0.46) ss: 0.056 (DMAX: 0.105) predE: -0.13 E(M): 11.53 gRMS: 0.0017 ratio: 0.388 + Opt step: 2 gqc: 0.020 ss: 0.051 (DMAX: 0.105) predE: -0.16 E(M): 11.48 gRMS: 0.0030 ratio: 1.142 + Opt step: 3 gqc: 0.020 ss: 0.046 (DMAX: 0.105) predE: -0.06 E(M): 11.30 gRMS: 0.0009 * + + Opt step: 1 S: 5.0 ol: 0.95 0.13 0.08 0.07 + max ol: 0 (f0) ss: 0.075 (DMAX: 0.051) predE: 0.06 Hint ev: -0.071 0.015 0.027 0.030 ratio: 1.089 increasing DMAX E(M): 32.29 gRMS: 0.0036 + Opt step: 2 S: 4.0 ol: 0.85 0.45 0.03 0.02 + max ol: 0 (f0) ss: 0.146 (DMAX: 0.056) predE: 0.34 Hint ev: -0.037 -0.006 0.024 0.028 ratio: 0.983 increasing DMAX E(M): 32.63 gRMS: 0.0035 + Opt step: 3 S: 3.0 ol: 0.96 0.12 0.02 0.00 + max ol: 0 (f0) ss: 0.178 (DMAX: 0.062) predE: -0.22 Hint ev: -0.030 -0.017 0.024 0.028 ratio: 0.853 increasing DMAX E(M): 32.44 gRMS: 0.0034 + Opt step: 4 S: 2.0 ol: 0.97 0.01 0.05 0.01 + max ol: 0 (f0) ss: 0.353 (DMAX: 0.068) predE: -0.14 Hint ev: -0.035 0.000 0.024 0.028 ratio: 0.513 decreasing DMAX E(M): 32.37 gRMS: 0.0031 + Opt step: 5 S: 1.0 ol: 0.68 0.68 0.06 0.03 + max ol: 0 (f0) ss: 0.355 (DMAX: 0.057) predE: -0.64 Hint ev: -0.099 -0.017 0.024 0.028 ratio: 0.966 E(M): 31.75 gRMS: 0.0044 + Opt step: 6 S: 1.0 ol: 0.87 0.38 0.00 0.10 + max ol: 0 (f0) ss: 0.391 (DMAX: 0.057) predE: -0.50 Hint ev: -0.129 -0.010 0.025 0.027 E(M): 31.75 gRMS: 0.0037 + + Opt step: 1 t/ol: 8 (0.37) ss: 0.189 (DMAX: 0.209) predE: -1.22 E(M): 16.27 gRMS: 0.0037 ratio: 0.852 + Opt step: 2 gqc: -0.058 ss: 0.166 (DMAX: 0.209) predE: -0.97 E(M): 15.24 gRMS: 0.0056 ratio: 1.081 + Opt step: 3 gqc: -0.059 ss: 0.130 (DMAX: 0.209) predE: -0.49 E(M): 14.19 gRMS: 0.0026 + + Opt step: 1 t/ol: 1 (0.47) ss: 0.136 (DMAX: 0.195) predE: -0.88 E(M): -29.13 gRMS: 0.0031 ratio: 1.197 + Opt step: 2 gqc: -0.021 ss: 0.125 (DMAX: 0.195) predE: -0.71 E(M): -30.18 gRMS: 0.0027 ratio: 0.922 + Opt step: 3 gqc: -0.019 ss: 0.123 (DMAX: 0.195) predE: -0.73 E(M): -30.83 gRMS: 0.0038 + + Opt step: 1 t/ol: 0 (0.79) ss: 0.049 (0.040) predE: -0.06 Hint ev: 0.018 0.031 E(M): -38.57 gRMS: 0.0010 * + +x opt_iter: 14 totalgrad: 0.097 gradrms: 0.0024 tgrads: 231 ol(0): 0.87 max E: 31.8 + in find_peaks (2) + V_profile: 0.0 0.4 2.4 11.3 31.8 14.2 -30.8 -38.6 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 2.4 11.3 31.8 14.2 -30.8 -38.6 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.02 disp[2]: 0.03 disp[3]: 0.01 disp[4]: 0.00 disp[5]: -0.01 disp[6]: 0.04 disp[7]: -0.02 + disp[1]: 0.01 disp[2]: 0.02 disp[3]: 0.01 disp[4]: 0.00 disp[5]: -0.01 disp[6]: 0.03 disp[7]: -0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.00 disp[4]: 0.00 disp[5]: -0.01 disp[6]: 0.02 disp[7]: -0.00 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.00 disp[4]: 0.00 disp[5]: -0.00 disp[6]: 0.02 disp[7]: 0.00 + disp[1]: 0.00 disp[2]: 0.00 disp[3]: 0.00 disp[4]: 0.00 disp[5]: -0.00 disp[6]: 0.01 disp[7]: 0.00 + spacings (end ic_reparam, steps: 5): 1.41 1.42 1.42 1.42 1.40 1.38 1.41 1.40 disprms: 0.017 + V_profile: 0.0 0.4 2.4 11.3 31.8 14.2 -30.8 -38.6 -40.7 + 3 way tangent (4): f1: 0.54 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.39) ss: 0.026 (DMAX: 0.034) predE: -0.02 E(M): 0.41 gRMS: 0.0005 * + + Opt step: 1 t/ol: 22 (0.48) ss: 0.086 (DMAX: 0.057) predE: -0.13 E(M): 2.51 gRMS: 0.0013 ratio: 1.191 increasing DMAX + Opt step: 2 gqc: 0.005 ss: 0.085 (DMAX: 0.062) predE: -0.12 E(M): 2.35 gRMS: 0.0010 ratio: 1.273 + Opt step: 3 gqc: 0.004 ss: 0.084 (DMAX: 0.062) predE: -0.11 E(M): 2.20 gRMS: 0.0010 * + + Opt step: 1 t/ol: 27 (0.49) ss: 0.095 (DMAX: 0.105) predE: -0.15 E(M): 11.46 gRMS: 0.0009 * + + Opt step: 1 S: 1.0 ol: 0.79 0.48 0.15 0.08 + max ol: 0 (f0) ss: 0.193 (DMAX: 0.057) predE: -0.68 Hint ev: -0.128 -0.048 0.024 0.027 ratio: 0.718 decreasing DMAX E(M): 30.81 gRMS: 0.0044 + Opt step: 2 S: 1.0 ol: 0.93 0.13 0.10 0.11 + max ol: 0 (f0) ss: 0.153 (DMAX: 0.047) predE: 0.25 Hint ev: -0.131 -0.063 0.023 0.027 ratio: 1.523 decreasing DMAX E(M): 31.19 gRMS: 0.0038 + Opt step: 3 S: 1.0 ol: 0.95 0.19 0.03 0.09 + max ol: 0 (f0) ss: 0.143 (DMAX: 0.039) predE: 0.06 Hint ev: -0.117 -0.063 0.024 0.027 ratio: 2.159 decreasing DMAX E(M): 31.32 gRMS: 0.0042 + Opt step: 4 S: 1.0 ol: 0.40 0.88 0.01 0.06 + max ol: 1 (f1) ss: 0.203 (DMAX: 0.033) predE: -0.23 Hint ev: -0.075 -0.064 0.023 0.028 ratio: 0.777 E(M): 31.14 gRMS: 0.0031 + Opt step: 5 S: 1.0 ol: 0.95 0.13 0.10 0.05 + max ol: 0 (f0) ss: 0.227 (DMAX: 0.033) predE: -0.02 Hint ev: -0.068 -0.034 0.017 0.028 ratio: 0.135 E(M): 31.14 gRMS: 0.0029 + Opt step: 6 S: 1.0 ol: 0.95 0.02 0.05 0.06 + max ol: 0 (f0) ss: 0.422 (DMAX: 0.033) predE: -0.02 Hint ev: -0.082 -0.004 0.020 0.028 E(M): 31.14 gRMS: 0.0027 + + Opt step: 1 t/ol: 10 (0.42) ss: 0.202 (DMAX: 0.209) predE: -2.10 E(M): 14.28 gRMS: 0.0041 ratio: 1.118 + Opt step: 2 gqc: -0.056 ss: 0.193 (DMAX: 0.209) predE: -1.92 E(M): 11.93 gRMS: 0.0045 ratio: 1.108 + Opt step: 3 gqc: -0.057 ss: 0.186 (DMAX: 0.209) predE: -1.79 E(M): 9.80 gRMS: 0.0044 + + Opt step: 1 t/ol: 11 (0.52) ss: 0.138 (DMAX: 0.195) predE: -0.45 E(M): -32.08 gRMS: 0.0017 ratio: 0.999 + Opt step: 2 gqc: -0.017 ss: 0.115 (DMAX: 0.195) predE: -0.31 E(M): -32.53 gRMS: 0.0023 ratio: 1.098 + Opt step: 3 gqc: -0.016 ss: 0.117 (DMAX: 0.195) predE: -0.27 E(M): -32.87 gRMS: 0.0020 + + Opt step: 1 t/ol: 0 (0.79) ss: 0.038 (0.040) predE: -0.04 Hint ev: 0.018 0.031 E(M): -38.61 gRMS: 0.0008 * + +x opt_iter: 15 totalgrad: 0.079 gradrms: 0.0022 tgrads: 249 ol(0): 0.95 max E: 31.1 + in find_peaks (2) + V_profile: 0.0 0.4 2.2 11.5 31.1 9.8 -32.9 -38.6 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 2.2 11.5 31.1 9.8 -32.9 -38.6 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.03 disp[2]: 0.04 disp[3]: 0.04 disp[4]: 0.00 disp[5]: 0.02 disp[6]: 0.07 disp[7]: -0.01 + disp[1]: 0.02 disp[2]: 0.02 disp[3]: 0.02 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.06 disp[7]: 0.00 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.04 disp[7]: 0.00 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.03 disp[7]: 0.01 + disp[1]: 0.00 disp[2]: 0.01 disp[3]: 0.00 disp[4]: 0.00 disp[5]: 0.00 disp[6]: 0.02 disp[7]: 0.01 + spacings (end ic_reparam, steps: 5): 1.43 1.44 1.44 1.44 1.39 1.37 1.41 1.40 disprms: 0.026 + V_profile: 0.0 0.4 2.2 11.5 31.1 9.8 -32.9 -38.6 -40.7 + 3 way tangent (4): f1: 0.48 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.44) ss: 0.028 (DMAX: 0.034) predE: -0.03 E(M): 0.43 gRMS: 0.0007 * + + Opt step: 1 t/ol: 22 (0.50) ss: 0.084 (DMAX: 0.062) predE: -0.10 E(M): 2.28 gRMS: 0.0010 * + + Opt step: 1 t/ol: 27 (0.50) ss: 0.102 (DMAX: 0.105) predE: -0.20 E(M): 12.21 gRMS: 0.0015 ratio: 1.265 + Opt step: 2 gqc: 0.021 ss: 0.102 (DMAX: 0.105) predE: -0.25 E(M): 11.96 gRMS: 0.0021 ratio: 1.007 + Opt step: 3 gqc: 0.020 ss: 0.098 (DMAX: 0.105) predE: -0.20 E(M): 11.71 gRMS: 0.0023 +S + Opt step: 1 S: 1.0 ol: 0.94 0.04 0.10 0.00 + max ol: 0 (f0) ss: 0.303 (DMAX: 0.033) predE: -0.09 Hint ev: -0.083 -0.014 0.020 0.028 ratio: 0.757 E(M): 31.06 gRMS: 0.0029 + Opt step: 2 S: 1.0 ol: 0.94 0.09 0.12 0.02 + max ol: 0 (f0) ss: 0.163 (DMAX: 0.033) predE: -0.12 Hint ev: -0.079 -0.048 0.019 0.028 ratio: 0.664 decreasing DMAX E(M): 30.98 gRMS: 0.0031 + Opt step: 3 S: 1.0 ol: 0.92 0.16 0.11 0.03 + max ol: 0 (f0) ss: 0.173 (DMAX: 0.027) predE: -0.20 Hint ev: -0.097 -0.036 0.020 0.027 ratio: 0.794 E(M): 30.82 gRMS: 0.0029 + Opt step: 4 S: 1.0 ol: 0.93 0.13 0.11 0.03 + max ol: 0 (f0) ss: 0.207 (DMAX: 0.027) predE: -0.07 Hint ev: -0.090 -0.024 0.019 0.027 ratio: 0.694 decreasing DMAX E(M): 30.77 gRMS: 0.0027 + Opt step: 5 S: 1.0 ol: 0.93 0.23 0.03 0.01 + max ol: 0 (f0) ss: 0.156 (DMAX: 0.023) predE: 0.01 Hint ev: -0.079 -0.048 0.021 0.027 ratio: 1.465 E(M): 30.79 gRMS: 0.0026 + Opt step: 6 S: 1.0 ol: 0.92 0.30 0.01 0.03 + max ol: 0 (f0) ss: 0.153 (DMAX: 0.023) predE: 0.00 Hint ev: -0.080 -0.044 0.022 0.027 E(M): 30.79 gRMS: 0.0024 + + Opt step: 1 t/ol: 11 (0.43) ss: 0.190 (DMAX: 0.209) predE: -1.54 E(M): 6.64 gRMS: 0.0041 ratio: 0.625 + Opt step: 2 gqc: -0.058 ss: 0.165 (DMAX: 0.209) predE: -1.38 E(M): 5.68 gRMS: 0.0069 ratio: 1.014 + Opt step: 3 gqc: -0.059 ss: 0.139 (DMAX: 0.209) predE: -0.73 E(M): 4.28 gRMS: 0.0034 + + Opt step: 1 t/ol: 1 (0.49) ss: 0.114 (DMAX: 0.195) predE: -0.31 E(M): -33.78 gRMS: 0.0017 ratio: 1.146 + Opt step: 2 gqc: -0.011 ss: 0.117 (DMAX: 0.195) predE: -0.26 E(M): -34.13 gRMS: 0.0018 ratio: 1.011 + Opt step: 3 gqc: -0.011 ss: 0.112 (DMAX: 0.195) predE: -0.24 E(M): -34.39 gRMS: 0.0024 + + Opt step: 1 t/ol: 0 (0.81) ss: 0.028 (0.040) predE: -0.02 Hint ev: 0.018 0.031 E(M): -38.67 gRMS: 0.0006 * + +x opt_iter: 16 totalgrad: 0.083 gradrms: 0.0021 tgrads: 267 ol(0): 0.92 max E: 30.8 + in find_peaks (2) + V_profile: 0.0 0.4 2.3 11.7 30.8 4.3 -34.4 -38.7 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 2.3 11.7 30.8 4.3 -34.4 -38.7 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.03 disp[2]: 0.04 disp[3]: 0.02 disp[4]: 0.00 disp[5]: 0.03 disp[6]: 0.04 disp[7]: -0.04 + disp[1]: 0.02 disp[2]: 0.02 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.02 disp[6]: 0.03 disp[7]: -0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.02 disp[7]: -0.00 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.02 disp[7]: 0.00 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.00 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.02 disp[7]: 0.00 + spacings (end ic_reparam, steps: 5): 1.45 1.46 1.46 1.46 1.40 1.40 1.42 1.41 disprms: 0.020 + V_profile: 0.0 0.4 2.3 11.7 30.8 4.3 -34.4 -38.7 -40.7 + 3 way tangent (4): f1: 0.42 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.45) ss: 0.035 (DMAX: 0.034) predE: -0.08 E(M): 0.45 gRMS: 0.0014 ratio: -0.863 dE>0, decreasing DMAX + Opt step: 2 gqc: 0.001 ss: 0.030 (DMAX: 0.023) predE: -0.12 E(M): 0.52 gRMS: 0.0032 ratio: 0.939 + Opt step: 3 gqc: 0.001 ss: 0.020 (DMAX: 0.023) predE: -0.02 E(M): 0.41 gRMS: 0.0009 * + + Opt step: 1 t/ol: 22 (0.49) ss: 0.086 (DMAX: 0.062) predE: -0.13 E(M): 2.36 gRMS: 0.0011 ratio: 1.248 increasing DMAX + Opt step: 2 gqc: 0.004 ss: 0.084 (DMAX: 0.068) predE: -0.12 E(M): 2.20 gRMS: 0.0010 * + + Opt step: 1 t/ol: 27 (0.41) ss: 0.036 (DMAX: 0.079) predE: -0.04 E(M): 12.00 gRMS: 0.0011 ratio: 1.336 + Opt step: 2 gqc: 0.021 ss: 0.030 (DMAX: 0.079) predE: -0.04 E(M): 11.95 gRMS: 0.0007 * + + Opt step: 1 S: 1.0 ol: 0.96 0.17 0.05 0.01 + max ol: 0 (f0) ss: 0.142 (DMAX: 0.023) predE: -0.04 Hint ev: -0.085 -0.043 0.021 0.027 ratio: 0.693 E(M): 30.78 gRMS: 0.0023 + Opt step: 2 S: 1.0 ol: 0.94 0.27 0.10 0.01 + max ol: 0 (f0) ss: 0.143 (DMAX: 0.023) predE: -0.02 Hint ev: -0.079 -0.044 0.022 0.027 ratio: 0.632 E(M): 30.77 gRMS: 0.0021 + Opt step: 3 S: 1.0 ol: 0.93 0.30 0.07 0.00 + max ol: 0 (f0) ss: 0.151 (DMAX: 0.023) predE: -0.05 Hint ev: -0.084 -0.035 0.022 0.027 ratio: 0.816 E(M): 30.72 gRMS: 0.0020 + Opt step: 4 S: 1.0 ol: 0.95 0.21 0.08 0.01 + max ol: 0 (f0) ss: 0.133 (DMAX: 0.023) predE: -0.09 Hint ev: -0.086 -0.042 0.022 0.027 ratio: 0.810 E(M): 30.65 gRMS: 0.0019 + Opt step: 5 S: 1.0 ol: 0.97 0.04 0.07 0.00 + max ol: 0 (f0) ss: 0.155 (DMAX: 0.023) predE: -0.15 Hint ev: -0.103 -0.035 0.022 0.027 ratio: 0.822 E(M): 30.52 gRMS: 0.0018 + Opt step: 6 S: 1.0 ol: 0.97 0.08 0.07 0.00 + max ol: 0 (f0) ss: 0.200 (DMAX: 0.023) predE: -0.16 Hint ev: -0.108 -0.025 0.022 0.027 E(M): 30.52 gRMS: 0.0018 + + Opt step: 1 t/ol: 10 (0.52) ss: 0.192 (DMAX: 0.209) predE: -1.33 E(M): 1.97 gRMS: 0.0030 ratio: 0.923 + Opt step: 2 gqc: -0.058 ss: 0.166 (DMAX: 0.209) predE: -0.99 E(M): 0.74 gRMS: 0.0039 ratio: 0.924 + Opt step: 3 gqc: -0.059 ss: 0.151 (DMAX: 0.209) predE: -0.72 E(M): -0.18 gRMS: 0.0038 + + Opt step: 1 t/ol: 1 (0.49) ss: 0.112 (DMAX: 0.195) predE: -0.18 E(M): -34.82 gRMS: 0.0015 ratio: 0.616 + Opt step: 2 gqc: -0.007 ss: 0.070 (DMAX: 0.195) predE: -0.13 E(M): -34.93 gRMS: 0.0022 ratio: 0.934 + Opt step: 3 gqc: -0.007 ss: 0.071 (DMAX: 0.195) predE: -0.06 E(M): -35.05 gRMS: 0.0012 + + Opt step: 1 t/ol: 0 (0.79) ss: 0.023 (0.040) predE: -0.02 Hint ev: 0.018 0.031 E(M): -38.63 gRMS: 0.0005 * + +x opt_iter: 17 totalgrad: 0.064 gradrms: 0.0018 tgrads: 287 ol(0): 0.97 max E: 30.5 + in find_peaks (2) + V_profile: 0.0 0.4 2.2 11.9 30.5 -0.2 -35.1 -38.6 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 2.2 11.9 30.5 -0.2 -35.1 -38.6 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.03 disp[2]: 0.03 disp[3]: 0.03 disp[4]: 0.00 disp[5]: 0.03 disp[6]: 0.07 disp[7]: 0.01 + disp[1]: 0.02 disp[2]: 0.02 disp[3]: 0.02 disp[4]: 0.00 disp[5]: 0.02 disp[6]: 0.05 disp[7]: 0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.04 disp[7]: 0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.03 disp[7]: 0.01 + disp[1]: 0.01 disp[2]: 0.00 disp[3]: 0.00 disp[4]: 0.00 disp[5]: 0.01 disp[6]: 0.02 disp[7]: 0.01 + spacings (end ic_reparam, steps: 5): 1.47 1.47 1.47 1.48 1.39 1.38 1.41 1.40 disprms: 0.026 + V_profile: 0.0 0.4 2.2 11.9 30.5 -0.2 -35.1 -38.6 -40.7 + 3 way tangent (4): f1: 0.38 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.47) ss: 0.019 (DMAX: 0.023) predE: -0.01 E(M): 0.42 gRMS: 0.0004 * + + Opt step: 1 t/ol: 22 (0.51) ss: 0.085 (DMAX: 0.068) predE: -0.12 E(M): 2.21 gRMS: 0.0011 ratio: 1.183 increasing DMAX + Opt step: 2 gqc: 0.004 ss: 0.085 (DMAX: 0.075) predE: -0.13 E(M): 2.07 gRMS: 0.0013 ratio: 0.990 increasing DMAX + Opt step: 3 gqc: 0.004 ss: 0.077 (DMAX: 0.083) predE: -0.13 E(M): 1.94 gRMS: 0.0018 +S + Opt step: 1 t/ol: 27 (0.42) ss: 0.063 (DMAX: 0.079) predE: -0.10 E(M): 12.61 gRMS: 0.0014 ratio: 0.145 decreasing DMAX + Opt step: 2 gqc: 0.022 ss: 0.059 (DMAX: 0.057) predE: -0.15 E(M): 12.59 gRMS: 0.0028 ratio: 0.973 + Opt step: 3 gqc: 0.021 ss: 0.047 (DMAX: 0.057) predE: -0.04 E(M): 12.45 gRMS: 0.0008 * + + Opt step: 1 S: 1.0 ol: 0.97 0.04 0.03 0.04 + max ol: 0 (f0) ss: 0.258 (DMAX: 0.023) predE: -0.13 Hint ev: -0.108 -0.014 0.022 0.027 ratio: 0.853 increasing DMAX E(M): 30.28 gRMS: 0.0018 + Opt step: 2 S: 1.0 ol: 0.97 0.04 0.03 0.04 + max ol: 0 (f0) ss: 0.297 (DMAX: 0.025) predE: -0.13 Hint ev: -0.108 -0.010 0.022 0.027 ratio: 0.838 E(M): 30.17 gRMS: 0.0019 + Opt step: 3 S: 1.0 ol: 0.96 0.13 0.03 0.04 + max ol: 0 (f0) ss: 0.202 (DMAX: 0.025) predE: -0.17 Hint ev: -0.110 -0.023 0.022 0.027 ratio: 0.823 E(M): 30.03 gRMS: 0.0023 + Opt step: 4 S: 1.0 ol: 0.97 0.11 0.01 0.01 + max ol: 0 (f0) ss: 0.148 (DMAX: 0.025) predE: -0.18 Hint ev: -0.111 -0.035 0.022 0.027 ratio: 0.815 E(M): 29.89 gRMS: 0.0022 + Opt step: 5 S: 1.0 ol: 0.97 0.09 0.02 0.02 + max ol: 0 (f0) ss: 0.200 (DMAX: 0.025) predE: -0.16 Hint ev: -0.111 -0.022 0.022 0.027 ratio: 0.846 E(M): 29.75 gRMS: 0.0021 + Opt step: 6 S: 1.0 ol: 0.97 0.06 0.02 0.02 + max ol: 0 (f0) ss: 0.274 (DMAX: 0.025) predE: -0.12 Hint ev: -0.111 -0.011 0.022 0.027 E(M): 29.75 gRMS: 0.0021 + + Opt step: 1 t/ol: 7 (0.43) ss: 0.199 (DMAX: 0.209) predE: -1.72 E(M): -2.46 gRMS: 0.0034 ratio: 0.859 + Opt step: 2 gqc: -0.054 ss: 0.176 (DMAX: 0.209) predE: -1.24 E(M): -3.94 gRMS: 0.0044 ratio: 1.045 + Opt step: 3 gqc: -0.057 ss: 0.153 (DMAX: 0.209) predE: -0.86 E(M): -5.23 gRMS: 0.0029 + + Opt step: 1 t/ol: 1 (0.54) ss: 0.090 (DMAX: 0.195) predE: -0.09 E(M): -35.39 gRMS: 0.0011 ratio: 0.700 + Opt step: 2 gqc: -0.006 ss: 0.062 (DMAX: 0.195) predE: -0.09 E(M): -35.46 gRMS: 0.0017 ratio: 0.476 + Opt step: 3 gqc: -0.006 ss: 0.040 (DMAX: 0.195) predE: -0.06 E(M): -35.50 gRMS: 0.0017 +S + Opt step: 1 t/ol: 0 (0.78) ss: 0.019 (0.040) predE: -0.02 Hint ev: 0.018 0.031 E(M): -38.71 gRMS: 0.0007 * + +x opt_iter: 18 totalgrad: 0.067 gradrms: 0.0017 tgrads: 307 ol(0): 0.97 max E: 29.8 + in find_peaks (2) + V_profile: 0.0 0.4 1.9 12.5 29.8 -5.2 -35.5 -38.7 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 1.9 12.5 29.8 -5.2 -35.5 -38.7 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.02 disp[2]: 0.01 disp[3]: -0.01 disp[4]: 0.00 disp[5]: -0.02 disp[6]: 0.00 disp[7]: -0.04 + disp[1]: 0.01 disp[2]: 0.00 disp[3]: -0.01 disp[4]: 0.00 disp[5]: -0.01 disp[6]: 0.00 disp[7]: -0.01 + disp[1]: 0.01 disp[2]: 0.00 disp[3]: -0.01 disp[4]: 0.00 disp[5]: -0.01 disp[6]: 0.00 disp[7]: -0.01 + spacings (end ic_reparam, steps: 5): 1.48 1.49 1.49 1.48 1.42 1.41 1.42 1.41 disprms: 0.014 + V_profile: 0.0 0.4 1.9 12.5 29.8 -5.2 -35.5 -38.7 -40.7 + 3 way tangent (4): f1: 0.33 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.53) ss: 0.020 (DMAX: 0.023) predE: -0.02 E(M): 0.42 gRMS: 0.0006 * + + Opt step: 1 t/ol: 22 (0.51) ss: 0.060 (DMAX: 0.061) predE: -0.09 E(M): 1.81 gRMS: 0.0015 ratio: 1.165 + Opt step: 2 gqc: 0.004 ss: 0.059 (DMAX: 0.061) predE: -0.07 E(M): 1.70 gRMS: 0.0013 ratio: 1.244 + Opt step: 3 gqc: 0.003 ss: 0.050 (DMAX: 0.061) predE: -0.07 E(M): 1.61 gRMS: 0.0011 + + Opt step: 1 t/ol: 27 (0.42) ss: 0.035 (DMAX: 0.057) predE: -0.03 E(M): 12.22 gRMS: 0.0006 * + + Opt step: 1 S: 1.0 ol: 0.96 0.18 0.06 0.01 + max ol: 0 (f0) ss: 0.125 (DMAX: 0.025) predE: -0.18 Hint ev: -0.112 -0.041 0.022 0.027 ratio: 0.816 E(M): 29.50 gRMS: 0.0025 + Opt step: 2 S: 1.0 ol: 0.96 0.11 0.11 0.04 + max ol: 0 (f0) ss: 0.174 (DMAX: 0.025) predE: -0.17 Hint ev: -0.113 -0.027 0.022 0.025 ratio: 0.835 E(M): 29.36 gRMS: 0.0023 + Opt step: 3 S: 1.0 ol: 0.96 0.17 0.06 0.01 + max ol: 0 (f0) ss: 0.255 (DMAX: 0.025) predE: -0.13 Hint ev: -0.113 -0.012 0.021 0.025 ratio: 0.832 E(M): 29.26 gRMS: 0.0022 + Opt step: 4 S: 1.0 ol: 0.97 0.05 0.07 0.00 + max ol: 0 (f0) ss: 0.274 (DMAX: 0.025) predE: -0.10 Hint ev: -0.112 -0.011 0.022 0.026 ratio: 0.857 increasing DMAX E(M): 29.17 gRMS: 0.0025 + Opt step: 5 S: 1.0 ol: 0.97 0.01 0.06 0.01 + max ol: 0 (f0) ss: 0.438 (DMAX: 0.028) predE: -0.02 Hint ev: -0.112 -0.000 0.022 0.025 ratio: 0.908 increasing DMAX E(M): 29.15 gRMS: 0.0029 + Opt step: 6 S: 1.0 ol: 0.96 0.12 0.07 0.00 + max ol: 0 (f0) ss: 0.373 (DMAX: 0.030) predE: -0.03 Hint ev: -0.124 -0.004 0.022 0.026 E(M): 29.15 gRMS: 0.0041 + + Opt step: 1 t/ol: 11 (0.42) ss: 0.202 (DMAX: 0.209) predE: -1.76 E(M): -5.24 gRMS: 0.0044 ratio: 0.445 + Opt step: 2 gqc: -0.053 ss: 0.176 (DMAX: 0.209) predE: -1.48 E(M): -6.02 gRMS: 0.0080 ratio: 1.019 + Opt step: 3 gqc: -0.055 ss: 0.144 (DMAX: 0.209) predE: -0.63 E(M): -7.53 gRMS: 0.0026 + + Opt step: 1 t/ol: 1 (0.55) ss: 0.047 (DMAX: 0.032) predE: -0.04 E(M): -35.56 gRMS: 0.0009 * + + Opt step: 1 t/ol: 0 (0.77) ss: 0.025 (0.040) predE: -0.05 Hint ev: 0.018 0.031 E(M): -38.63 gRMS: 0.0011 ratio: -0.658 dE>0, decreasing DMAX + Opt step: 2 t/ol: 0 (0.77) ss: 0.022 (0.020) predE: -0.08 Hint ev: 0.018 0.031 E(M): -38.59 gRMS: 0.0022 ratio: 0.648 + Opt step: 3 t/ol: 0 (0.77) ss: 0.009 (0.020) predE: -0.01 Hint ev: 0.018 0.031 E(M): -38.65 gRMS: 0.0006 * + +x opt_iter: 19 totalgrad: 0.068 gradrms: 0.0020 tgrads: 325 ol(0): 0.96 max E: 29.1 + in find_peaks (2) + V_profile: 0.0 0.4 1.6 12.2 29.1 -7.5 -35.6 -38.6 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 1.6 12.2 29.1 -7.5 -35.6 -38.6 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.02 disp[2]: 0.01 disp[3]: -0.01 disp[4]: 0.00 disp[5]: -0.02 disp[6]: 0.02 disp[7]: 0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: -0.01 disp[4]: 0.00 disp[5]: -0.01 disp[6]: 0.02 disp[7]: 0.01 + disp[1]: 0.01 disp[2]: 0.00 disp[3]: -0.00 disp[4]: 0.00 disp[5]: -0.01 disp[6]: 0.01 disp[7]: 0.01 + disp[1]: 0.01 disp[2]: 0.00 disp[3]: -0.00 disp[4]: 0.00 disp[5]: -0.01 disp[6]: 0.01 disp[7]: 0.01 + spacings (end ic_reparam, steps: 5): 1.49 1.50 1.50 1.49 1.41 1.39 1.41 1.41 disprms: 0.017 + V_profile: 0.0 0.4 1.6 12.2 29.1 -7.5 -35.6 -38.6 -40.7 + 3 way tangent (4): f1: 0.32 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.57) ss: 0.026 (DMAX: 0.023) predE: -0.05 E(M): 0.43 gRMS: 0.0011 ratio: -0.260 dE>0, decreasing DMAX + Opt step: 2 gqc: 0.001 ss: 0.024 (DMAX: 0.020) predE: -0.07 E(M): 0.44 gRMS: 0.0019 ratio: 0.594 + Opt step: 3 gqc: 0.001 ss: 0.015 (DMAX: 0.020) predE: -0.01 E(M): 0.40 gRMS: 0.0007 * + + Opt step: 1 t/ol: 22 (0.51) ss: 0.047 (DMAX: 0.061) predE: -0.10 E(M): 1.58 gRMS: 0.0015 ratio: 0.007 decreasing DMAX + Opt step: 2 gqc: 0.003 ss: 0.044 (DMAX: 0.043) predE: -0.13 E(M): 1.58 gRMS: 0.0028 ratio: 1.031 + Opt step: 3 gqc: 0.003 ss: 0.037 (DMAX: 0.043) predE: -0.03 E(M): 1.45 gRMS: 0.0006 * + + Opt step: 1 t/ol: 27 (0.43) ss: 0.087 (DMAX: 0.057) predE: -0.10 E(M): 12.06 gRMS: 0.0010 ratio: 0.883 increasing DMAX + Opt step: 2 gqc: 0.021 ss: 0.078 (DMAX: 0.063) predE: -0.10 E(M): 11.97 gRMS: 0.0013 ratio: 0.959 increasing DMAX + Opt step: 3 gqc: 0.021 ss: 0.071 (DMAX: 0.069) predE: -0.09 E(M): 11.87 gRMS: 0.0013 + + Opt step: 1 S: 1.0 ol: 0.95 0.18 0.02 0.01 + max ol: 0 (f0) ss: 0.324 (DMAX: 0.030) predE: -0.08 Hint ev: -0.133 0.003 0.022 0.026 ratio: 0.868 increasing DMAX E(M): 29.06 gRMS: 0.0051 + Opt step: 2 S: 1.0 ol: 0.97 0.03 0.01 0.03 + max ol: 0 (f0) ss: 0.292 (DMAX: 0.033) predE: -0.09 Hint ev: -0.133 0.006 0.022 0.027 ratio: 0.936 increasing DMAX E(M): 28.98 gRMS: 0.0053 + Opt step: 3 S: 1.0 ol: 0.97 0.04 0.00 0.03 + max ol: 0 (f0) ss: 0.423 (DMAX: 0.037) predE: 0.02 Hint ev: -0.132 -0.000 0.022 0.027 ratio: 0.966 increasing DMAX E(M): 28.99 gRMS: 0.0058 + Opt step: 4 S: 1.0 ol: 0.97 0.01 0.01 0.02 + max ol: 0 (f0) ss: 0.292 (DMAX: 0.040) predE: -0.13 Hint ev: -0.136 0.005 0.022 0.026 ratio: 0.907 increasing DMAX E(M): 28.88 gRMS: 0.0066 + Opt step: 5 S: 1.0 ol: 0.97 0.09 0.00 0.02 + max ol: 0 (f0) ss: 0.320 (DMAX: 0.044) predE: -0.09 Hint ev: -0.134 0.002 0.022 0.026 ratio: 0.925 increasing DMAX E(M): 28.79 gRMS: 0.0068 + Opt step: 6 S: 1.0 ol: 0.95 0.21 0.00 0.02 + max ol: 0 (f0) ss: 0.400 (DMAX: 0.049) predE: -0.02 Hint ev: -0.131 -0.002 0.022 0.026 E(M): 28.79 gRMS: 0.0072 + + Opt step: 1 t/ol: 7 (0.42) ss: 0.170 (DMAX: 0.209) predE: -1.13 E(M): -6.85 gRMS: 0.0028 ratio: 0.959 + Opt step: 2 gqc: -0.055 ss: 0.160 (DMAX: 0.209) predE: -0.92 E(M): -7.93 gRMS: 0.0036 ratio: 0.819 + Opt step: 3 gqc: -0.055 ss: 0.117 (DMAX: 0.209) predE: -0.63 E(M): -8.69 gRMS: 0.0035 + + Opt step: 1 t/ol: 1 (0.56) ss: 0.059 (DMAX: 0.032) predE: -0.03 E(M): -35.65 gRMS: 0.0007 * + + Opt step: 1 t/ol: 0 (0.77) ss: 0.007 (0.020) predE: -0.00 Hint ev: 0.018 0.031 E(M): -38.69 gRMS: 0.0002 * + +x opt_iter: 20 totalgrad: 0.091 gradrms: 0.0031 tgrads: 345 ol(0): 0.95 max E: 28.8 + in find_peaks (2) + V_profile: 0.0 0.4 1.4 11.9 28.8 -8.7 -35.6 -38.7 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 1.4 11.9 28.8 -8.7 -35.6 -38.7 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.03 disp[2]: 0.02 disp[3]: -0.00 disp[4]: 0.00 disp[5]: -0.01 disp[6]: -0.01 disp[7]: -0.02 + disp[1]: 0.02 disp[2]: 0.01 disp[3]: -0.00 disp[4]: 0.00 disp[5]: -0.01 disp[6]: -0.01 disp[7]: -0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: -0.00 disp[4]: 0.00 disp[5]: -0.00 disp[6]: -0.01 disp[7]: -0.00 + spacings (end ic_reparam, steps: 5): 1.50 1.51 1.52 1.51 1.42 1.42 1.41 1.42 disprms: 0.016 + V_profile: 0.0 0.4 1.4 11.9 28.8 -8.7 -35.6 -38.7 -40.7 + 3 way tangent (4): f1: 0.31 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.58) ss: 0.015 (DMAX: 0.020) predE: -0.01 E(M): 0.40 gRMS: 0.0003 * + + Opt step: 1 t/ol: 22 (0.50) ss: 0.043 (DMAX: 0.043) predE: -0.03 E(M): 1.44 gRMS: 0.0006 * + + Opt step: 1 t/ol: 8 (0.40) ss: 0.059 (DMAX: 0.069) predE: -0.08 E(M): 11.73 gRMS: 0.0011 ratio: 1.419 + Opt step: 2 gqc: 0.021 ss: 0.056 (DMAX: 0.069) predE: -0.06 E(M): 11.62 gRMS: 0.0009 * + + Opt step: 1 S: 1.0 ol: 0.94 0.24 0.05 0.02 + max ol: 0 (f0) ss: 0.424 (DMAX: 0.049) predE: -0.01 Hint ev: -0.130 -0.000 0.022 0.026 ratio: 0.933 increasing DMAX E(M): 28.77 gRMS: 0.0081 + Opt step: 2 S: 1.0 ol: 0.93 0.26 0.07 0.01 + max ol: 0 (f0) ss: 0.421 (DMAX: 0.054) predE: 0.03 Hint ev: -0.129 -0.002 0.022 0.026 ratio: 0.989 increasing DMAX E(M): 28.80 gRMS: 0.0087 + Opt step: 3 S: 1.0 ol: 0.94 0.23 0.07 0.01 + max ol: 0 (f0) ss: 0.309 (DMAX: 0.059) predE: -0.19 Hint ev: -0.130 0.003 0.022 0.026 ratio: 0.956 increasing DMAX E(M): 28.62 gRMS: 0.0096 + Opt step: 4 S: 1.0 ol: 0.96 0.10 0.05 0.01 + max ol: 0 (f0) ss: 0.226 (DMAX: 0.065) predE: -0.34 Hint ev: -0.136 0.006 0.022 0.026 ratio: 0.967 increasing DMAX E(M): 28.29 gRMS: 0.0098 + Opt step: 5 S: 1.0 ol: 0.97 0.04 0.04 0.00 + max ol: 0 (f0) ss: 0.205 (DMAX: 0.071) predE: -0.35 Hint ev: -0.135 0.007 0.022 0.026 ratio: 0.970 increasing DMAX E(M): 27.95 gRMS: 0.0094 + Opt step: 6 S: 1.0 ol: 0.96 0.12 0.05 0.02 + max ol: 0 (f0) ss: 0.204 (DMAX: 0.079) predE: -0.33 Hint ev: -0.131 0.006 0.022 0.026 E(M): 27.95 gRMS: 0.0086 + + Opt step: 1 t/ol: 11 (0.38) ss: 0.172 (DMAX: 0.209) predE: -1.27 E(M): -9.01 gRMS: 0.0026 ratio: 0.957 + Opt step: 2 gqc: -0.051 ss: 0.164 (DMAX: 0.209) predE: -0.98 E(M): -10.22 gRMS: 0.0030 ratio: 0.846 + Opt step: 3 gqc: -0.055 ss: 0.152 (DMAX: 0.209) predE: -0.84 E(M): -11.05 gRMS: 0.0037 + + Opt step: 1 t/ol: 1 (0.59) ss: 0.043 (DMAX: 0.032) predE: -0.03 E(M): -35.62 gRMS: 0.0006 * + + Opt step: 1 t/ol: 0 (0.76) ss: 0.006 (0.020) predE: -0.00 Hint ev: 0.018 0.031 E(M): -38.64 gRMS: 0.0001 * + +x opt_iter: 21 totalgrad: 0.096 gradrms: 0.0036 tgrads: 360 ol(0): 0.96 max E: 27.9 + in find_peaks (2) + V_profile: 0.0 0.4 1.4 11.6 27.9 -11.0 -35.6 -38.6 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 1.4 11.6 27.9 -11.0 -35.6 -38.6 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.02 disp[2]: 0.01 disp[3]: -0.00 disp[4]: 0.00 disp[5]: -0.04 disp[6]: 0.01 disp[7]: 0.00 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: -0.00 disp[4]: 0.00 disp[5]: -0.02 disp[6]: 0.01 disp[7]: 0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: -0.00 disp[4]: 0.00 disp[5]: -0.01 disp[6]: 0.01 disp[7]: 0.01 + spacings (end ic_reparam, steps: 5): 1.50 1.51 1.52 1.51 1.42 1.39 1.42 1.41 disprms: 0.019 + V_profile: 0.0 0.4 1.4 11.6 27.9 -11.0 -35.6 -38.6 -40.7 + 3 way tangent (4): f1: 0.30 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.58) ss: 0.015 (DMAX: 0.020) predE: -0.01 E(M): 0.40 gRMS: 0.0004 * + + Opt step: 1 t/ol: 22 (0.50) ss: 0.044 (DMAX: 0.043) predE: -0.04 E(M): 1.43 gRMS: 0.0008 * + + Opt step: 1 t/ol: 8 (0.44) ss: 0.099 (DMAX: 0.069) predE: -0.17 E(M): 11.49 gRMS: 0.0011 ratio: 1.199 increasing DMAX + Opt step: 2 gqc: 0.020 ss: 0.096 (DMAX: 0.076) predE: -0.17 E(M): 11.29 gRMS: 0.0010 ratio: 1.226 increasing DMAX + Opt step: 3 gqc: 0.020 ss: 0.093 (DMAX: 0.084) predE: -0.17 E(M): 11.08 gRMS: 0.0011 + + Opt step: 1 S: 1.0 ol: 0.97 0.08 0.03 0.03 + max ol: 0 (f0) ss: 0.214 (DMAX: 0.079) predE: -0.27 Hint ev: -0.129 0.007 0.022 0.026 ratio: 0.967 increasing DMAX E(M): 27.37 gRMS: 0.0080 + Opt step: 2 S: 1.0 ol: 0.97 0.07 0.02 0.03 + max ol: 0 (f0) ss: 0.206 (DMAX: 0.086) predE: -0.33 Hint ev: -0.129 0.008 0.022 0.026 ratio: 0.976 increasing DMAX E(M): 27.05 gRMS: 0.0077 + Opt step: 3 S: 1.0 ol: 0.96 0.08 0.03 0.02 + max ol: 0 (f0) ss: 0.213 (DMAX: 0.095) predE: -0.28 Hint ev: -0.129 0.009 0.022 0.026 ratio: 0.992 increasing DMAX E(M): 26.77 gRMS: 0.0074 + Opt step: 4 S: 1.0 ol: 0.96 0.09 0.02 0.02 + max ol: 0 (f0) ss: 0.212 (DMAX: 0.105) predE: -0.32 Hint ev: -0.128 0.008 0.022 0.026 ratio: 1.018 increasing DMAX E(M): 26.44 gRMS: 0.0075 + Opt step: 5 S: 1.0 ol: 0.96 0.12 0.02 0.01 + max ol: 0 (f0) ss: 0.227 (DMAX: 0.115) predE: -0.23 Hint ev: -0.128 0.007 0.022 0.026 ratio: 1.042 increasing DMAX E(M): 26.20 gRMS: 0.0074 + Opt step: 6 S: 1.0 ol: 0.95 0.15 0.01 0.00 + max ol: 0 (f0) ss: 0.202 (DMAX: 0.126) predE: -0.42 Hint ev: -0.127 0.006 0.022 0.026 E(M): 26.20 gRMS: 0.0078 + + Opt step: 1 t/ol: 11 (0.36) ss: 0.179 (DMAX: 0.209) predE: -1.75 E(M): -9.84 gRMS: 0.0035 ratio: 0.989 + Opt step: 2 gqc: -0.051 ss: 0.159 (DMAX: 0.209) predE: -1.27 E(M): -11.58 gRMS: 0.0037 ratio: 0.964 + Opt step: 3 gqc: -0.051 ss: 0.159 (DMAX: 0.209) predE: -1.29 E(M): -12.80 gRMS: 0.0038 + + Opt step: 1 t/ol: 1 (0.57) ss: 0.073 (DMAX: 0.032) predE: -0.02 E(M): -35.66 gRMS: 0.0005 * + + Opt step: 1 t/ol: 0 (0.76) ss: 0.006 (0.020) predE: -0.00 Hint ev: 0.018 0.031 E(M): -38.66 gRMS: 0.0001 * + +x opt_iter: 22 totalgrad: 0.095 gradrms: 0.0033 tgrads: 376 ol(0): 0.95 max E: 26.2 + in find_peaks (2) + V_profile: 0.0 0.4 1.4 11.1 26.2 -12.8 -35.7 -38.7 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 1.4 11.1 26.2 -12.8 -35.7 -38.7 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.00 disp[2]: -0.01 disp[3]: -0.04 disp[4]: 0.00 disp[5]: -0.05 disp[6]: -0.04 disp[7]: -0.05 + disp[1]: 0.00 disp[2]: -0.01 disp[3]: -0.02 disp[4]: 0.00 disp[5]: -0.03 disp[6]: -0.03 disp[7]: -0.01 + disp[1]: 0.00 disp[2]: -0.01 disp[3]: -0.01 disp[4]: 0.00 disp[5]: -0.02 disp[6]: -0.02 disp[7]: -0.00 + disp[1]: 0.00 disp[2]: -0.01 disp[3]: -0.01 disp[4]: 0.00 disp[5]: -0.01 disp[6]: -0.01 disp[7]: 0.00 + spacings (end ic_reparam, steps: 5): 1.50 1.51 1.51 1.50 1.44 1.43 1.42 1.43 disprms: 0.019 + V_profile: 0.0 0.4 1.4 11.1 26.2 -12.8 -35.7 -38.7 -40.7 + 3 way tangent (4): f1: 0.28 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.59) ss: 0.019 (DMAX: 0.020) predE: -0.03 E(M): 0.40 gRMS: 0.0008 * + + Opt step: 1 t/ol: 22 (0.47) ss: 0.050 (DMAX: 0.043) predE: -0.10 E(M): 1.38 gRMS: 0.0014 ratio: -0.100 dE>0, decreasing DMAX + Opt step: 2 gqc: 0.003 ss: 0.046 (DMAX: 0.028) predE: -0.11 E(M): 1.39 gRMS: 0.0028 ratio: 0.889 + Opt step: 3 gqc: 0.003 ss: 0.036 (DMAX: 0.028) predE: -0.03 E(M): 1.29 gRMS: 0.0009 * + + Opt step: 1 t/ol: 27 (0.48) ss: 0.112 (DMAX: 0.084) predE: -0.35 E(M): 10.30 gRMS: 0.0018 ratio: 0.989 increasing DMAX + Opt step: 2 gqc: 0.018 ss: 0.104 (DMAX: 0.092) predE: -0.36 E(M): 9.95 gRMS: 0.0019 ratio: 1.031 increasing DMAX + Opt step: 3 gqc: 0.018 ss: 0.094 (DMAX: 0.101) predE: -0.33 E(M): 9.58 gRMS: 0.0017 + + Opt step: 1 S: 1.0 ol: 0.96 0.08 0.05 0.01 + max ol: 0 (f0) ss: 0.202 (DMAX: 0.126) predE: -0.32 Hint ev: -0.125 0.004 0.022 0.026 ratio: 0.922 increasing DMAX E(M): 25.50 gRMS: 0.0073 + Opt step: 2 S: 1.0 ol: 0.95 0.11 0.05 0.01 + max ol: 0 (f0) ss: 0.203 (DMAX: 0.139) predE: -0.39 Hint ev: -0.124 0.004 0.022 0.026 ratio: 0.863 increasing DMAX E(M): 25.16 gRMS: 0.0072 + Opt step: 3 S: 1.0 ol: 0.95 0.10 0.05 0.01 + max ol: 0 (f0) ss: 0.184 (DMAX: 0.150) predE: -0.46 Hint ev: -0.125 0.003 0.022 0.026 ratio: 0.797 E(M): 24.79 gRMS: 0.0067 + Opt step: 4 S: 1.0 ol: 0.95 0.13 0.05 0.01 + max ol: 0 (f0) ss: 0.198 (DMAX: 0.150) predE: -0.25 Hint ev: -0.125 0.001 0.022 0.026 ratio: 0.418 decreasing DMAX E(M): 24.69 gRMS: 0.0060 + Opt step: 5 S: 1.0 ol: 0.96 0.04 0.05 0.02 + max ol: 0 (f0) ss: 0.227 (DMAX: 0.125) predE: -0.05 Hint ev: -0.126 -0.002 0.022 0.026 ratio: -1.210 E(M): 24.75 gRMS: 0.0066 + Opt step: 6 S: 1.0 ol: 0.95 0.08 0.06 0.02 + max ol: 0 (f0) ss: 0.111 (DMAX: 0.125) predE: -0.77 Hint ev: -0.127 -0.002 0.022 0.026 E(M): 24.75 gRMS: 0.0068 + + Opt step: 1 t/ol: 22 (0.33) ss: 0.184 (DMAX: 0.209) predE: -1.85 E(M): -11.14 gRMS: 0.0048 ratio: 0.964 + Opt step: 2 gqc: -0.048 ss: 0.156 (DMAX: 0.209) predE: -1.45 E(M): -12.92 gRMS: 0.0046 ratio: 1.051 + Opt step: 3 gqc: -0.047 ss: 0.148 (DMAX: 0.209) predE: -1.27 E(M): -14.45 gRMS: 0.0035 + + Opt step: 1 t/ol: 2 (0.57) ss: 0.073 (DMAX: 0.032) predE: -0.05 E(M): -35.44 gRMS: 0.0009 * + + Opt step: 1 t/ol: 0 (0.76) ss: 0.006 (0.020) predE: -0.00 Hint ev: 0.018 0.031 E(M): -38.56 gRMS: 0.0002 * + +x opt_iter: 23 totalgrad: 0.096 gradrms: 0.0030 tgrads: 394 ol(0): 0.95 max E: 24.7 + in find_peaks (2) + V_profile: 0.0 0.4 1.3 9.6 24.7 -14.4 -35.4 -38.6 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 1.3 9.6 24.7 -14.4 -35.4 -38.6 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.01 disp[2]: 0.00 disp[3]: 0.01 disp[4]: 0.00 disp[5]: -0.06 disp[6]: -0.07 disp[7]: -0.06 + disp[1]: 0.01 disp[2]: 0.00 disp[3]: 0.00 disp[4]: 0.00 disp[5]: -0.04 disp[6]: -0.04 disp[7]: -0.02 + disp[1]: 0.01 disp[2]: 0.00 disp[3]: 0.00 disp[4]: 0.00 disp[5]: -0.02 disp[6]: -0.03 disp[7]: -0.00 + disp[1]: 0.00 disp[2]: 0.00 disp[3]: 0.00 disp[4]: 0.00 disp[5]: -0.02 disp[6]: -0.02 disp[7]: 0.00 + disp[1]: 0.00 disp[2]: 0.00 disp[3]: 0.00 disp[4]: 0.00 disp[5]: -0.01 disp[6]: -0.01 disp[7]: 0.00 + spacings (end ic_reparam, steps: 5): 1.51 1.52 1.51 1.52 1.46 1.45 1.44 1.45 disprms: 0.014 + V_profile: 0.0 0.4 1.3 9.6 24.7 -14.4 -35.4 -38.6 -40.7 + 3 way tangent (4): f1: 0.28 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.61) ss: 0.033 (DMAX: 0.020) predE: -0.09 E(M): 0.42 gRMS: 0.0017 ratio: 0.088 decreasing DMAX + Opt step: 2 gqc: 0.001 ss: 0.018 (DMAX: 0.020) predE: -0.05 E(M): 0.41 gRMS: 0.0016 ratio: 0.580 + Opt step: 3 gqc: 0.000 ss: 0.013 (DMAX: 0.020) predE: -0.01 E(M): 0.38 gRMS: 0.0008 * + + Opt step: 1 t/ol: 22 (0.46) ss: 0.037 (DMAX: 0.028) predE: -0.02 E(M): 1.27 gRMS: 0.0005 * + + Opt step: 1 t/ol: 27 (0.52) ss: 0.146 (DMAX: 0.101) predE: -0.49 E(M): 9.31 gRMS: 0.0019 ratio: 1.156 increasing DMAX + Opt step: 2 gqc: 0.015 ss: 0.121 (DMAX: 0.111) predE: -0.49 E(M): 8.74 gRMS: 0.0018 ratio: 1.223 increasing DMAX + Opt step: 3 gqc: 0.015 ss: 0.108 (DMAX: 0.122) predE: -0.46 E(M): 8.14 gRMS: 0.0017 + + Opt step: 1 S: 1.0 ol: 0.93 0.09 0.06 0.11 + max ol: 0 (f0) ss: 0.168 (DMAX: 0.125) predE: -0.49 Hint ev: -0.129 -0.014 0.022 0.026 ratio: 0.471 decreasing DMAX E(M): 23.70 gRMS: 0.0031 + Opt step: 2 S: 1.0 ol: 0.95 0.11 0.09 0.12 + max ol: 0 (f0) ss: 0.226 (DMAX: 0.104) predE: -0.44 Hint ev: -0.150 -0.012 0.017 0.022 ratio: 0.731 decreasing DMAX E(M): 23.37 gRMS: 0.0061 + Opt step: 3 S: 1.0 ol: 0.92 0.20 0.13 0.16 + max ol: 0 (f0) ss: 0.341 (DMAX: 0.087) predE: -0.14 Hint ev: -0.142 -0.005 0.017 0.022 ratio: 0.671 decreasing DMAX E(M): 23.28 gRMS: 0.0054 + Opt step: 4 S: 1.0 ol: 0.92 0.22 0.13 0.12 + max ol: 0 (f0) ss: 0.332 (DMAX: 0.072) predE: -0.12 Hint ev: -0.142 0.001 0.017 0.023 ratio: 0.882 increasing DMAX E(M): 23.17 gRMS: 0.0059 + Opt step: 5 S: 1.0 ol: 0.92 0.22 0.14 0.11 + max ol: 0 (f0) ss: 0.215 (DMAX: 0.080) predE: -0.32 Hint ev: -0.142 0.006 0.017 0.023 ratio: 0.972 increasing DMAX E(M): 22.86 gRMS: 0.0061 + Opt step: 6 S: 1.0 ol: 0.94 0.11 0.12 0.12 + max ol: 0 (f0) ss: 0.185 (DMAX: 0.088) predE: -0.24 Hint ev: -0.151 0.006 0.017 0.023 E(M): 22.86 gRMS: 0.0050 + + Opt step: 1 t/ol: 10 (0.39) ss: 0.207 (DMAX: 0.209) predE: -2.17 E(M): -11.75 gRMS: 0.0054 ratio: 1.083 + Opt step: 2 gqc: -0.047 ss: 0.169 (DMAX: 0.209) predE: -1.57 E(M): -14.10 gRMS: 0.0045 ratio: 0.984 + Opt step: 3 gqc: -0.043 ss: 0.154 (DMAX: 0.209) predE: -1.31 E(M): -15.64 gRMS: 0.0047 + + Opt step: 1 t/ol: 2 (0.68) ss: 0.098 (DMAX: 0.032) predE: -0.10 E(M): -35.04 gRMS: 0.0014 ratio: 0.933 increasing DMAX + Opt step: 2 gqc: -0.006 ss: 0.095 (DMAX: 0.035) predE: -0.08 E(M): -35.14 gRMS: 0.0011 ratio: 0.980 increasing DMAX + Opt step: 3 gqc: -0.005 ss: 0.089 (DMAX: 0.039) predE: -0.07 E(M): -35.22 gRMS: 0.0011 + + Opt step: 1 t/ol: 0 (0.77) ss: 0.008 (0.020) predE: -0.00 Hint ev: 0.018 0.031 E(M): -38.45 gRMS: 0.0002 * + +x opt_iter: 24 totalgrad: 0.091 gradrms: 0.0027 tgrads: 414 ol(0): 0.94 max E: 22.9 + in find_peaks (2) + V_profile: 0.0 0.4 1.3 8.1 22.9 -15.6 -35.2 -38.4 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 1.3 8.1 22.9 -15.6 -35.2 -38.4 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.02 disp[2]: 0.03 disp[3]: 0.07 disp[4]: 0.00 disp[5]: -0.02 disp[6]: -0.03 disp[7]: -0.03 + disp[1]: 0.02 disp[2]: 0.02 disp[3]: 0.04 disp[4]: 0.00 disp[5]: -0.01 disp[6]: -0.02 disp[7]: -0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.02 disp[4]: 0.00 disp[5]: -0.01 disp[6]: -0.01 disp[7]: -0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: -0.01 disp[6]: -0.01 disp[7]: -0.00 + spacings (end ic_reparam, steps: 5): 1.52 1.53 1.52 1.54 1.47 1.47 1.46 1.47 disprms: 0.020 + V_profile: 0.0 0.4 1.3 8.1 22.9 -15.6 -35.2 -38.4 -40.7 + 3 way tangent (4): f1: 0.28 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.60) ss: 0.012 (DMAX: 0.020) predE: -0.01 E(M): 0.38 gRMS: 0.0003 * + + Opt step: 1 t/ol: 22 (0.45) ss: 0.040 (DMAX: 0.028) predE: -0.03 E(M): 1.31 gRMS: 0.0006 * + + Opt step: 1 t/ol: 23 (0.42) ss: 0.107 (DMAX: 0.122) predE: -0.53 E(M): 8.80 gRMS: 0.0027 ratio: 0.962 + Opt step: 2 gqc: 0.015 ss: 0.103 (DMAX: 0.122) predE: -0.55 E(M): 8.29 gRMS: 0.0032 ratio: 1.041 + Opt step: 3 gqc: 0.014 ss: 0.097 (DMAX: 0.122) predE: -0.42 E(M): 7.72 gRMS: 0.0020 + + Opt step: 1 S: 1.0 ol: 0.94 0.14 0.04 0.11 + max ol: 0 (f0) ss: 0.167 (DMAX: 0.088) predE: -0.22 Hint ev: -0.152 0.006 0.017 0.023 ratio: 0.966 increasing DMAX E(M): 22.41 gRMS: 0.0048 + Opt step: 2 S: 1.0 ol: 0.95 0.07 0.04 0.11 + max ol: 0 (f0) ss: 0.163 (DMAX: 0.096) predE: -0.19 Hint ev: -0.152 0.004 0.018 0.023 ratio: 0.966 increasing DMAX E(M): 22.23 gRMS: 0.0044 + Opt step: 3 S: 1.0 ol: 0.95 0.08 0.03 0.11 + max ol: 0 (f0) ss: 0.157 (DMAX: 0.106) predE: -0.21 Hint ev: -0.152 0.004 0.018 0.023 ratio: 0.957 increasing DMAX E(M): 22.02 gRMS: 0.0042 + Opt step: 4 S: 1.0 ol: 0.94 0.11 0.02 0.12 + max ol: 0 (f0) ss: 0.143 (DMAX: 0.117) predE: -0.23 Hint ev: -0.153 0.004 0.018 0.023 ratio: 0.961 increasing DMAX E(M): 21.80 gRMS: 0.0038 + Opt step: 5 S: 1.0 ol: 0.94 0.16 0.01 0.11 + max ol: 0 (f0) ss: 0.139 (DMAX: 0.128) predE: -0.22 Hint ev: -0.153 0.004 0.018 0.023 ratio: 0.977 increasing DMAX E(M): 21.58 gRMS: 0.0032 + Opt step: 6 S: 1.0 ol: 0.94 0.19 0.01 0.10 + max ol: 0 (f0) ss: 0.138 (DMAX: 0.141) predE: -0.19 Hint ev: -0.153 0.002 0.018 0.023 E(M): 21.58 gRMS: 0.0026 + + Opt step: 1 t/ol: 17 (0.45) ss: 0.194 (DMAX: 0.209) predE: -1.99 E(M): -16.09 gRMS: 0.0049 ratio: 1.021 + Opt step: 2 gqc: -0.040 ss: 0.179 (DMAX: 0.209) predE: -1.79 E(M): -18.12 gRMS: 0.0052 ratio: 1.078 + Opt step: 3 gqc: -0.041 ss: 0.160 (DMAX: 0.209) predE: -1.46 E(M): -20.04 gRMS: 0.0034 + + Opt step: 1 t/ol: 2 (0.74) ss: 0.092 (DMAX: 0.039) predE: -0.09 E(M): -35.14 gRMS: 0.0012 ratio: 1.004 increasing DMAX + Opt step: 2 gqc: -0.004 ss: 0.087 (DMAX: 0.042) predE: -0.08 E(M): -35.23 gRMS: 0.0011 ratio: 1.042 increasing DMAX + Opt step: 3 gqc: -0.004 ss: 0.085 (DMAX: 0.047) predE: -0.07 E(M): -35.31 gRMS: 0.0011 + + Opt step: 1 t/ol: 0 (0.75) ss: 0.009 (0.020) predE: -0.00 Hint ev: 0.018 0.031 E(M): -38.38 gRMS: 0.0003 * + +x opt_iter: 25 totalgrad: 0.067 gradrms: 0.0019 tgrads: 432 ol(0): 0.94 max E: 21.6 + in find_peaks (2) + V_profile: 0.0 0.4 1.3 7.7 21.6 -20.0 -35.3 -38.4 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 1.3 7.7 21.6 -20.0 -35.3 -38.4 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.02 disp[2]: 0.04 disp[3]: 0.07 disp[4]: 0.00 disp[5]: -0.05 disp[6]: -0.04 disp[7]: -0.05 + disp[1]: 0.02 disp[2]: 0.02 disp[3]: 0.04 disp[4]: 0.00 disp[5]: -0.03 disp[6]: -0.03 disp[7]: -0.02 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.02 disp[4]: 0.00 disp[5]: -0.02 disp[6]: -0.02 disp[7]: -0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: -0.01 disp[6]: -0.01 disp[7]: -0.00 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: -0.01 disp[6]: -0.01 disp[7]: 0.00 + spacings (end ic_reparam, steps: 5): 1.53 1.54 1.54 1.55 1.50 1.48 1.48 1.49 disprms: 0.016 + V_profile: 0.0 0.4 1.3 7.7 21.6 -20.0 -35.3 -38.4 -40.7 + 3 way tangent (4): f1: 0.25 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.61) ss: 0.013 (DMAX: 0.020) predE: -0.01 E(M): 0.38 gRMS: 0.0003 * + + Opt step: 1 t/ol: 0 (0.46) ss: 0.041 (DMAX: 0.028) predE: -0.03 E(M): 1.37 gRMS: 0.0007 * + + Opt step: 1 t/ol: 0 (0.46) ss: 0.146 (DMAX: 0.122) predE: -0.63 E(M): 8.29 gRMS: 0.0025 ratio: 1.244 increasing DMAX + Opt step: 2 gqc: 0.013 ss: 0.145 (DMAX: 0.134) predE: -0.60 E(M): 7.51 gRMS: 0.0020 ratio: 1.305 + Opt step: 3 gqc: 0.012 ss: 0.141 (DMAX: 0.134) predE: -0.55 E(M): 6.72 gRMS: 0.0019 + + Opt step: 1 S: 1.0 ol: 0.91 0.30 0.12 0.03 + max ol: 0 (f0) ss: 0.158 (DMAX: 0.141) predE: -0.15 Hint ev: -0.153 0.000 0.019 0.023 ratio: 0.680 decreasing DMAX E(M): 21.31 gRMS: 0.0026 + Opt step: 2 S: 1.0 ol: 0.91 0.32 0.14 0.00 + max ol: 0 (f0) ss: 0.180 (DMAX: 0.117) predE: -0.10 Hint ev: -0.153 -0.003 0.019 0.023 ratio: 0.289 decreasing DMAX E(M): 21.28 gRMS: 0.0030 + Opt step: 3 S: 1.0 ol: 0.90 0.32 0.14 0.02 + max ol: 0 (f0) ss: 0.142 (DMAX: 0.098) predE: -0.28 Hint ev: -0.153 -0.006 0.018 0.023 ratio: 0.723 decreasing DMAX E(M): 21.08 gRMS: 0.0039 + Opt step: 4 S: 1.0 ol: 0.93 0.20 0.15 0.01 + max ol: 0 (f0) ss: 0.115 (DMAX: 0.082) predE: -0.13 Hint ev: -0.154 -0.006 0.019 0.023 ratio: 0.647 decreasing DMAX E(M): 20.99 gRMS: 0.0022 + Opt step: 5 S: 1.0 ol: 0.94 0.12 0.16 0.01 + max ol: 0 (f0) ss: 0.142 (DMAX: 0.068) predE: -0.07 Hint ev: -0.151 -0.004 0.019 0.023 ratio: 0.734 decreasing DMAX E(M): 20.94 gRMS: 0.0016 + Opt step: 6 S: 1.0 ol: 0.93 0.17 0.17 0.01 + max ol: 0 (f0) ss: 0.147 (DMAX: 0.057) predE: -0.05 Hint ev: -0.153 -0.002 0.019 0.023 E(M): 20.94 gRMS: 0.0013 + + Opt step: 1 t/ol: 15 (0.42) ss: 0.171 (DMAX: 0.209) predE: -1.83 E(M): -18.73 gRMS: 0.0053 ratio: 0.793 + Opt step: 2 gqc: -0.035 ss: 0.143 (DMAX: 0.209) predE: -1.39 E(M): -20.18 gRMS: 0.0057 ratio: 0.997 + Opt step: 3 gqc: -0.036 ss: 0.137 (DMAX: 0.209) predE: -1.05 E(M): -21.57 gRMS: 0.0039 + + Opt step: 1 t/ol: 2 (0.83) ss: 0.165 (0.047) predE: -0.11 Hint ev: 0.007 0.009 E(M): -35.19 gRMS: 0.0013 ratio: 0.921 increasing DMAX + Opt step: 2 t/ol: 2 (0.83) ss: 0.133 (0.051) predE: -0.10 Hint ev: 0.007 0.009 E(M): -35.29 gRMS: 0.0013 ratio: 1.061 increasing DMAX + Opt step: 3 t/ol: 2 (0.82) ss: 0.109 (0.056) predE: -0.10 Hint ev: 0.007 0.009 E(M): -35.39 gRMS: 0.0013 + + Opt step: 1 t/ol: 0 (0.74) ss: 0.066 (DMAX: 0.020) predE: -0.02 E(M): -38.28 gRMS: 0.0005 * + +x opt_iter: 26 totalgrad: 0.064 gradrms: 0.0018 tgrads: 450 ol(0): 0.93 max E: 20.9 + in find_peaks (2) + V_profile: 0.0 0.4 1.4 6.7 20.9 -21.6 -35.4 -38.3 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + V_profile: 0.0 0.4 1.4 6.7 20.9 -21.6 -35.4 -38.3 -40.7 + TSn: 4 rpart: 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.25 + disp[1]: 0.03 disp[2]: 0.04 disp[3]: 0.08 disp[4]: 0.00 disp[5]: -0.05 disp[6]: -0.09 disp[7]: -0.07 + disp[1]: 0.02 disp[2]: 0.03 disp[3]: 0.05 disp[4]: 0.00 disp[5]: -0.04 disp[6]: -0.06 disp[7]: -0.03 + disp[1]: 0.01 disp[2]: 0.02 disp[3]: 0.03 disp[4]: 0.00 disp[5]: -0.02 disp[6]: -0.04 disp[7]: -0.01 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.02 disp[4]: 0.00 disp[5]: -0.02 disp[6]: -0.02 disp[7]: -0.00 + disp[1]: 0.01 disp[2]: 0.01 disp[3]: 0.01 disp[4]: 0.00 disp[5]: -0.01 disp[6]: -0.02 disp[7]: -0.00 + spacings (end ic_reparam, steps: 5): 1.55 1.55 1.55 1.57 1.52 1.52 1.50 1.51 disprms: 0.023 + V_profile: 0.0 0.4 1.4 6.7 20.9 -21.6 -35.4 -38.3 -40.7 + 3 way tangent (4): f1: 0.25 + + eg eg eg eg eg eg eg eg eg eg eg eg eg eg eg + + Opt step: 1 t/ol: 0 (0.61) ss: 0.014 (DMAX: 0.020) predE: -0.01 E(M): 0.39 gRMS: 0.0005 * + + Opt step: 1 t/ol: 0 (0.58) ss: 0.040 (DMAX: 0.028) predE: -0.04 E(M): 1.43 gRMS: 0.0009 * + + Opt step: 1 t/ol: 0 (0.51) ss: 0.153 (DMAX: 0.134) predE: -0.58 E(M): 7.25 gRMS: 0.0027 ratio: 1.346 + Opt step: 2 gqc: 0.012 ss: 0.149 (DMAX: 0.134) predE: -0.52 E(M): 6.46 gRMS: 0.0022 ratio: 1.322 + Opt step: 3 gqc: 0.011 ss: 0.141 (DMAX: 0.134) predE: -0.50 E(M): 5.77 gRMS: 0.0024 + + Opt step: 1 S: 1.0 ol: 0.92 0.27 0.12 0.00 + max ol: 0 (f0) ss: 0.098 (DMAX: 0.057) predE: -0.05 Hint ev: -0.154 0.001 0.019 0.023 ratio: 0.952 increasing DMAX E(M): 20.85 gRMS: 0.0010 + Opt step: 2 S: 1.0 ol: 0.91 0.29 0.11 0.02 + max ol: 0 (f0) ss: 0.090 (DMAX: 0.062) predE: -0.05 Hint ev: -0.154 0.002 0.019 0.023 ratio: 0.941 increasing DMAX E(M): 20.81 gRMS: 0.0007 + Opt step: 3 E(M): 20.81 gRMS: 0.0003 * + + Opt step: 1 t/ol: 15 (0.44) ss: 0.175 (DMAX: 0.209) predE: -2.10 E(M): -19.32 gRMS: 0.0059 ratio: 0.839 + Opt step: 2 gqc: -0.034 ss: 0.139 (DMAX: 0.209) predE: -1.21 E(M): -21.08 gRMS: 0.0054 ratio: 1.008 + Opt step: 3 gqc: -0.034 ss: 0.123 (DMAX: 0.209) predE: -0.89 E(M): -22.29 gRMS: 0.0043 + + Opt step: 1 t/ol: 2 (0.86) ss: 0.124 (0.056) predE: -0.16 Hint ev: 0.007 0.009 E(M): -35.07 gRMS: 0.0015 ratio: 1.035 increasing DMAX + Opt step: 2 t/ol: 2 (0.86) ss: 0.093 (0.062) predE: -0.13 Hint ev: 0.007 0.009 E(M): -35.23 gRMS: 0.0015 ratio: 1.246 increasing DMAX + Opt step: 3 t/ol: 2 (0.85) ss: 0.077 (0.068) predE: -0.10 Hint ev: 0.007 0.009 E(M): -35.39 gRMS: 0.0013 + + Opt step: 1 t/ol: 0 (0.72) ss: 0.062 (DMAX: 0.020) predE: -0.02 E(M): -38.14 gRMS: 0.0004 * + +x opt_iter: 27 totalgrad: 0.065 gradrms: 0.0020 tgrads: 465 ol(0): 0.91 max E: 20.8 + in find_peaks (2) + V_profile: 0.0 0.4 1.4 5.8 20.8 -22.3 -35.4 -38.1 -40.7 + min nodes: max nodes: 4 + found 1 significant peak(s). TOL: 0.50 + printing string to stringfile.xyz0001 + check_for_reaction wts: 4 wint: 8 isrxn: 2 + + opt_iters over: totalgrad: 0.065 gradrms: 0.0020 tgrads: 465 ol(0): 0.91 max E: 20.8 Erxn: -40.7 nmax: 4 TSnode: 4 -XTS- + + oi: 26 nmax: 4 TSnode0: 4 overlapn: 0 + string E (kcal/mol): 0.0 0.4 1.4 5.8 20.8 -22.3 -35.4 -38.1 -40.7 + string E (au): -234.52746107 -234.52683350 -234.52517957 -234.51825956 -234.49429816 -234.56298985 -234.58385452 -234.58824697 -234.59235246 + string E (au) - force*distance: -234.52746107 -234.52683350 -234.52517957 -234.51825956 -234.49429816 -234.56298985 -234.58385452 -234.58824697 -234.59235246 + max E: 20.809724 for node: 4 + + creating 3 lowest eigenvectors + Hint eigenvalues: -0.154 0.002 0.019 0.023 0.028 + maximum number of iterations: 14 + + Davidson iteration 1 + eg eg eg eg eg eg + mag/DTHRESH: 24.567981 0.000050 lamb/lambp: -0.005 0.000 + mag/DTHRESH: 36.177103 0.000050 lamb/lambp: 0.003 0.000 + mag/DTHRESH: 7.581765 0.000050 lamb/lambp: 0.015 0.000 + + Davidson iteration 2 + eg eg eg eg eg eg + mag/DTHRESH: 1.692984 0.000050 lamb/lambp: -0.038 -0.005 + mag/DTHRESH: 0.123915 0.000050 lamb/lambp: 0.002 0.003 + vector 1 converged + mag/DTHRESH: 1.570284 0.000050 lamb/lambp: 0.010 0.015 + + Davidson iteration 3 + eg eg eg eg + mag/DTHRESH: 0.644502 0.000050 lamb/lambp: -0.049 -0.038 + mag/DTHRESH: 0.015935 0.000050 lamb/lambp: 0.002 0.002 + vector 1 converged + mag/DTHRESH: 0.240628 0.000050 lamb/lambp: 0.010 0.010 + vector 2 converged + + Davidson iteration 4 + eg eg + mag/DTHRESH: 0.061932 0.000050 lamb/lambp: -0.062 -0.049 + mag/DTHRESH: 0.013643 0.000050 lamb/lambp: 0.002 0.002 + vector 1 converged + mag/DTHRESH: 0.132474 0.000050 lamb/lambp: 0.009 0.010 + vector 2 converged + + Davidson iteration 5 + eg eg + mag/DTHRESH: 0.028382 0.000050 lamb/lambp: -0.064 -0.062 + mag/DTHRESH: 0.013669 0.000050 lamb/lambp: 0.002 0.002 + vector 1 converged + mag/DTHRESH: 0.161569 0.000050 lamb/lambp: 0.009 0.009 + vector 2 converged + + Davidson iteration 6 + eg eg + mag/DTHRESH: 0.034854 0.000050 lamb/lambp: -0.066 -0.064 + mag/DTHRESH: 0.013035 0.000050 lamb/lambp: 0.002 0.002 + vector 1 converged + mag/DTHRESH: 0.129058 0.000050 lamb/lambp: 0.009 0.009 + vector 2 converged + + Davidson iteration 7 + eg eg + mag/DTHRESH: 0.016568 0.000050 lamb/lambp: -0.068 -0.066 + mag/DTHRESH: 0.010106 0.000050 lamb/lambp: 0.002 0.002 + vector 1 converged + mag/DTHRESH: 0.110299 0.000050 lamb/lambp: 0.009 0.009 + vector 2 converged + + Davidson iteration 8 + eg eg + mag/DTHRESH: 0.007269 0.000050 lamb/lambp: -0.069 -0.068 + mag/DTHRESH: 0.009062 0.000050 lamb/lambp: 0.002 0.002 + vector 1 converged + mag/DTHRESH: 0.050872 0.000050 lamb/lambp: 0.009 0.009 + vector 2 converged + + Davidson iteration 9 + eg eg + mag/DTHRESH: 0.001885 0.000050 lamb/lambp: -0.069 -0.069 + vector 0 converged + mag/DTHRESH: 0.008598 0.000050 lamb/lambp: 0.002 0.002 + vector 1 converged + mag/DTHRESH: 0.046156 0.000050 lamb/lambp: 0.009 0.009 + vector 2 converged + Davidson converged + + now saving vibrations to stringfile.xyz0001fr + Hessian eigenvalues: -0.069 0.002 0.009 + + Updating Hint with new vectors + updating vector: 1 with curvature: -0.06896 + updating vector: 2 with curvature: 0.00213 + updating vector: 3 with curvature: 0.00877 + + Davidson required 28 gradients + + found 1 negative eigenvalue + creating final string file + + about to write tsq.xyz, tscontinue: 1 endearly: 0 + check_for_reaction wts: 4 wint: 8 isrxn: 2 + E of min node before TS: 0.0 diff --git a/TEST/dielsAlder/orca/de-gsm/scratch/stringfile.xyz0001g b/TEST/dielsAlder/orca/de-gsm/scratch/stringfile.xyz0001g new file mode 100644 index 0000000..455f70b --- /dev/null +++ b/TEST/dielsAlder/orca/de-gsm/scratch/stringfile.xyz0001g @@ -0,0 +1,162 @@ + 16 + 0.000000 + C -1.060017 -1.517146 0.052887 + C -1.829554 -0.594086 -0.539688 + C -2.012604 0.793709 -0.089780 + C -1.097406 1.540951 0.541104 + C 3.018414 -0.332740 0.534205 + C 2.482680 0.169904 -0.576610 + H 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a/TEST/dielsAlder/orca/de-gsm/stringfile.xyz0001fr b/TEST/dielsAlder/orca/de-gsm/stringfile.xyz0001fr new file mode 100644 index 0000000..64f4554 --- /dev/null +++ b/TEST/dielsAlder/orca/de-gsm/stringfile.xyz0001fr @@ -0,0 +1,162 @@ + 16 + + C -0.313183 -1.382053 0.648594 + C -1.225476 -0.788285 -0.245080 + C -1.275990 0.587002 -0.416007 + C -0.396109 1.436079 0.284923 + C 1.569631 -0.670055 -0.033038 + C 1.479822 0.720116 -0.305523 + H -1.745040 -1.421687 -0.961066 + H -0.067398 -0.899295 1.588763 + H -0.204492 -2.463906 0.658962 + H 2.078855 -0.996754 0.868505 + H 1.576240 -1.384735 -0.846687 + H 1.363395 1.051552 -1.332309 + H 1.987217 1.427333 0.345304 + H -0.368460 2.495620 0.045541 + H -0.115210 1.200940 1.308806 + H -1.837565 0.988439 -1.256272 + 16 + + C -0.379248 -1.407261 0.663075 + C -1.254539 -0.799703 -0.227493 + C -1.300292 0.597018 -0.401987 + C -0.453292 1.451289 0.293329 + C 1.658855 -0.651341 -0.053845 + C 1.565003 0.710674 -0.326124 + H -1.775048 -1.422776 -0.953449 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-1.230630 diff --git a/TEST/dielsAlder/qchem/de-gsm/compare.py b/TEST/dielsAlder/qchem/de-gsm/compare.py new file mode 100644 index 0000000..8bc4f62 --- /dev/null +++ b/TEST/dielsAlder/qchem/de-gsm/compare.py @@ -0,0 +1,41 @@ +# for reading csv format files +import csv + +# function to convert strings to float and skip conversion if the value is not a float +def convertToFloat(inList): + for element in inList: + try: + yield float(element) + except ValueError: + yield element + +# subtract two floats and skip if string +def subtractFloat(number1, number2): + try: + return (number1 - number2) + except TypeError: + pass + +def main(): + threshold = 0.001 + try: + # read standard and output files + standard = csv.reader(open('stringfile.standard', 'r'), delimiter=' ') + currentOutput = csv.reader(open('stringfile.xyz0001', 'r'), delimiter=' ') + # error if file does not exist + except IOError: + print("Error: File cannot be found!") + exit(1) + # loop over elements of two files simultaneously + for rowStd, rowOut in zip(standard, currentOutput): + rowStd = filter(None, rowStd) + rowOut = filter(None, rowOut) + for valStd, valOut in zip(list(convertToFloat(rowStd)), list(convertToFloat(rowOut))): + # error if difference larger than threshold + if ((subtractFloat(valStd, valOut)) > threshold): + print ((subtractFloat(valStd, valOut))) + exit(2) + return 0 + +if __name__ == "__main__": + main() diff --git a/TEST/dielsAlder/qchem/de-gsm/gscreate b/TEST/dielsAlder/qchem/de-gsm/gscreate new file mode 100755 index 0000000..119b132 --- /dev/null +++ b/TEST/dielsAlder/qchem/de-gsm/gscreate @@ -0,0 +1,14 @@ +#!/bin/bash + +file=molecule + +#nl $file > tmp.mole +#nl link > tmp.link +#join tmp.mole tmp.link > tmp.geom2 +#awk '{ print $2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10 }' tmp.geom2 > tmp.geom + +#cat qstart tmp.geom qend > qcin +#cat qstart molecule$1 qend > scratch/qcin$1 +cat qstart $QCSCRATCH/molecule$1 qend > $QCSCRATCH/qcin$1 + +#rm tmp.geom tmp.geom2 tmp.link tmp.mole diff --git a/TEST/dielsAlder/qchem/de-gsm/inpfileq b/TEST/dielsAlder/qchem/de-gsm/inpfileq new file mode 100644 index 0000000..83a96a1 --- /dev/null +++ b/TEST/dielsAlder/qchem/de-gsm/inpfileq @@ -0,0 +1,27 @@ + +# FSM/GSM/SSM inpfileq + +------------- QCHEM Scratch Info ------------------------ +$QCSCRATCH/ # path for scratch dir. end with "/" +GSM_go1q # name of run +--------------------------------------------------------- + +------------ String Info -------------------------------- +SM_TYPE GSM # SSM, FSM or GSM +RESTART 0 # read restart.xyz +MAX_OPT_ITERS 80 # maximum iterations +STEP_OPT_ITERS 30 # for FSM/SSM +CONV_TOL 0.0005 # perp grad +ADD_NODE_TOL 0.1 # for GSM +SCALING 1.0 # for opt steps +SSM_DQMAX 0.8 # add step size +GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 +INT_THRESH 2.0 # intermediate detection +MIN_SPACING 5.0 # node spacing SSM +BOND_FRAGMENTS 1 # make IC's for fragments +INITIAL_OPT 0 # opt steps first node +FINAL_OPT 150 # opt steps last SSM node +PRODUCT_LIMIT 100.0 # kcal/mol +TS_FINAL_TYPE 1 # any/delta bond: 0/1 +NNODES 9 # including endpoints +--------------------------------------------------------- diff --git a/TEST/dielsAlder/qchem/de-gsm/qend b/TEST/dielsAlder/qchem/de-gsm/qend new file mode 100644 index 0000000..b39a0e1 --- /dev/null +++ b/TEST/dielsAlder/qchem/de-gsm/qend @@ -0,0 +1 @@ +$end diff --git a/TEST/dielsAlder/qchem/de-gsm/qstart b/TEST/dielsAlder/qchem/de-gsm/qstart new file mode 100644 index 0000000..afa463a --- /dev/null +++ b/TEST/dielsAlder/qchem/de-gsm/qstart @@ -0,0 +1,24 @@ + $rem + JOBTYPE FORCE + EXCHANGE B3LYP +! CORRELATION PBE +! UNRESTRICTED TRUE + SCF_ALGORITHM rca_diis + SCF_MAX_CYCLES 150 + BASIS 6-31G* +! BASIS LANL2DZ +! ECP LANL2DZ + WAVEFUNCTION_ANALYSIS FALSE + GEOM_OPT_MAX_CYCLES 300 + +scf_convergence 6 + + SYM_IGNORE TRUE + SYMMETRY FALSE + +molden_format true + $end + + +$molecule +0 1 diff --git a/TEST/dielsAlder/qchem/de-gsm/scratch/initial0001.xyz b/TEST/dielsAlder/qchem/de-gsm/scratch/initial0001.xyz new file mode 100644 index 0000000..4210d81 --- /dev/null +++ b/TEST/dielsAlder/qchem/de-gsm/scratch/initial0001.xyz @@ -0,0 +1,36 @@ + 16 +Step 35 + C -1.06001665 -1.51714564 0.05288674 + C -1.82955412 -0.59408623 -0.53968755 + C -2.01260392 0.79370866 -0.08977969 + C -1.09740592 1.54095108 0.54110413 + C 3.01841440 -0.33274049 0.53420511 + C 2.48267950 0.16990394 -0.57660955 + H -2.40063347 -0.88235561 -1.42321617 + H -0.51365172 -1.30383154 0.96828855 + H -0.96688964 -2.52122005 -0.35117707 + H 3.89171154 0.11254122 1.00536203 + H 2.60849064 -1.21591676 1.01902222 + H 1.60806045 -0.27640639 -1.04373753 + H 2.89526366 1.05096138 -1.06301386 + H -1.32088987 2.55628492 0.85667305 + H -0.09454533 1.17390089 0.74481476 + H -2.98142355 1.23828062 -0.32070817 + 16 +Step 22 + C 0.01856467 -1.50510245 0.07175535 + C -1.25472580 -0.70291222 -0.04828280 + C -1.28551058 0.63324180 -0.08527776 + C -0.04811068 1.49696591 -0.04422009 + C 1.21601433 -0.63168912 0.47947978 + C 1.22945185 0.68482088 -0.31033881 + H -2.18794361 -1.26282927 -0.10437525 + H -0.12133841 -2.31635373 0.79987325 + H 0.22663560 -2.00643122 -0.88734886 + H 1.14834814 -0.40532251 1.55280900 + H 2.15327210 -1.18259709 0.33198960 + H 1.29564501 0.45837391 -1.38389788 + H 2.11591575 1.28013898 -0.05856919 + H -0.13761965 2.30980257 -0.77849415 + H 0.01956981 1.99500653 0.93644690 + H -2.24481452 1.14593304 -0.15154508 diff --git a/TEST/dielsAlder/qchem/de-gsm/stringfile.standard b/TEST/dielsAlder/qchem/de-gsm/stringfile.standard new file mode 100644 index 0000000..6ffd3b4 --- /dev/null +++ b/TEST/dielsAlder/qchem/de-gsm/stringfile.standard @@ -0,0 +1,162 @@ + 16 + 0.000000 + C -1.060017 -1.517146 0.052887 + C -1.829554 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H -0.663575 2.566203 0.244844 + H -0.129370 1.156221 1.302619 + H -2.016293 1.111057 -1.124126 + 16 + 21.280192 + C -0.420150 -1.451028 0.602280 + C -1.267940 -0.775051 -0.254681 + C -1.288366 0.627006 -0.367048 + C -0.402516 1.422120 0.345165 + C 1.704902 -0.591871 0.044956 + C 1.521726 0.701035 -0.418374 + H -1.793192 -1.349679 -1.016750 + H -0.131208 -1.042454 1.563221 + H -0.336585 -2.532324 0.524318 + H 2.140259 -0.749117 1.028793 + H 1.771581 -1.433531 -0.633717 + H 1.319710 0.855974 -1.473792 + H 1.998018 1.537045 0.085519 + H -0.380227 2.497200 0.180695 + H -0.083988 1.115028 1.335627 + H -1.844106 1.068089 -1.192926 + 16 + -19.377138 + C -0.124128 -1.362910 0.542966 + C -1.195103 -0.736543 -0.269685 + C -1.264899 0.603265 -0.366151 + C -0.175096 1.382278 0.265514 + C 1.374993 -0.676531 0.116026 + C 1.214711 0.747454 -0.389744 + H -1.805387 -1.375270 -0.910776 + H -0.093079 -1.082218 1.602865 + H -0.033271 -2.436084 0.391500 + H 1.930889 -0.731535 1.059052 + H 1.688393 -1.420128 -0.629494 + H 1.081894 0.864284 -1.463022 + H 1.914814 1.477007 0.037081 + H -0.156235 2.457680 0.081949 + H 0.020021 1.159262 1.326138 + H -1.927764 1.059928 -1.087913 + 16 + -40.167642 + C -0.043631 -1.423083 0.390027 + C -1.223129 -0.719727 -0.238834 + C -1.285440 0.614041 -0.305972 + C -0.110540 1.438090 0.163511 + C 1.318642 -0.663768 0.234854 + C 1.184563 0.760542 -0.336774 + H -2.032306 -1.333267 -0.630921 + H -0.241625 -1.544809 1.466733 + H 0.042182 -2.441174 -0.008400 + H 1.800563 -0.611322 1.218080 + H 1.981198 -1.254779 -0.407626 + H 1.146374 0.721416 -1.431358 + H 2.057487 1.364701 -0.059169 + H -0.174910 2.478099 -0.177659 + H -0.073662 1.464399 1.263033 + H -2.135959 1.108949 -0.769222 + 16 + -43.216128 + C -0.007642 -1.482522 0.230386 + C -1.237174 -0.698796 -0.159583 + C -1.283679 0.635141 -0.217067 + C -0.067734 1.480189 0.079068 + C 1.279494 -0.625940 0.387516 + C 1.200074 0.722413 -0.344946 + H -2.121765 -1.282024 -0.414727 + H -0.206083 -2.005829 1.177517 + H 0.151321 -2.282417 -0.507228 + H 1.466225 -0.438086 1.453022 + H 2.139116 -1.198938 0.019844 + H 1.161757 0.542476 -1.427966 + H 2.097421 1.320167 -0.141487 + H -0.136213 2.459801 -0.408798 + H -0.011175 1.675359 1.162303 + H -2.199839 1.133760 -0.529791 + 16 + -45.754017 + C 0.018565 -1.505102 0.071755 + C -1.254726 -0.702912 -0.048283 + C -1.285511 0.633242 -0.085278 + C -0.048111 1.496966 -0.044220 + C 1.216014 -0.631689 0.479480 + C 1.229452 0.684821 -0.310339 + H -2.187944 -1.262829 -0.104375 + H -0.121338 -2.316354 0.799873 + H 0.226636 -2.006431 -0.887349 + H 1.148348 -0.405323 1.552809 + H 2.153272 -1.182597 0.331990 + H 1.295645 0.458374 -1.383898 + H 2.115916 1.280139 -0.058569 + H -0.137620 2.309803 -0.778494 + H 0.019570 1.995007 0.936447 + H -2.244815 1.145933 -0.151545 diff --git a/TEST/ethyleneRotation/mopac/de-gsm/compare.py b/TEST/ethyleneRotation/mopac/de-gsm/compare.py new file mode 100644 index 0000000..8bc4f62 --- /dev/null +++ b/TEST/ethyleneRotation/mopac/de-gsm/compare.py @@ -0,0 +1,41 @@ +# for reading csv format files +import csv + +# function to convert strings to float and skip conversion if the value is not a float +def convertToFloat(inList): + for element in inList: + try: + yield float(element) + except ValueError: + yield element + +# subtract two floats and skip if string +def subtractFloat(number1, number2): + try: + return (number1 - number2) + except TypeError: + pass + +def main(): + threshold = 0.001 + try: + # read standard and output files + standard = csv.reader(open('stringfile.standard', 'r'), delimiter=' ') + currentOutput = csv.reader(open('stringfile.xyz0001', 'r'), delimiter=' ') + # error if file does not exist + except IOError: + print("Error: File cannot be found!") + exit(1) + # loop over elements of two files simultaneously + for rowStd, rowOut in zip(standard, currentOutput): + rowStd = filter(None, rowStd) + rowOut = filter(None, rowOut) + for valStd, valOut in zip(list(convertToFloat(rowStd)), list(convertToFloat(rowOut))): + # error if difference larger than threshold + if ((subtractFloat(valStd, valOut)) > threshold): + print ((subtractFloat(valStd, valOut))) + exit(2) + return 0 + +if __name__ == "__main__": + main() diff --git a/TEST/ethyleneRotation/mopac/de-gsm/gscreate b/TEST/ethyleneRotation/mopac/de-gsm/gscreate new file mode 100755 index 0000000..2648cf0 --- /dev/null +++ b/TEST/ethyleneRotation/mopac/de-gsm/gscreate @@ -0,0 +1,16 @@ +#!/bin/bash + +file=molecule + +#nl $file > tmp.mole +#nl link > tmp.link +#join tmp.mole tmp.link > tmp.geom2 +#awk '{ print $2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10 }' tmp.geom2 > tmp.geom + +#cat qstart tmp.geom qend > qcin +#cat qstart molecule$1 qend > scratch/qcin$1 +cat qstart $QCSCRATCH/molecule$1 qend > $QCSCRATCH/qcin$1 + +#rm tmp.geom tmp.geom2 tmp.link tmp.mole + + diff --git a/TEST/ethyleneRotation/mopac/de-gsm/inpfileq b/TEST/ethyleneRotation/mopac/de-gsm/inpfileq new file mode 100644 index 0000000..d2a54ff --- /dev/null +++ b/TEST/ethyleneRotation/mopac/de-gsm/inpfileq @@ -0,0 +1,26 @@ +# FSM/GSM/SSM inpfileq + +------------- QCHEM Scratch Info ------------------------ +$QCSCRATCH/ # path for scratch dir. end with "/" +GSM_go1q # name of run +--------------------------------------------------------- + +------------ String Info -------------------------------- +SM_TYPE GSM # SSM, FSM or GSM +RESTART 0 # read restart.xyz +MAX_OPT_ITERS 80 # maximum iterations +STEP_OPT_ITERS 30 # for FSM/SSM +CONV_TOL 0.0005 # perp grad +ADD_NODE_TOL 0.1 # for GSM +SCALING 1.0 # for opt steps +SSM_DQMAX 0.8 # add step size +GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 +INT_THRESH 2.0 # intermediate detection +MIN_SPACING 5.0 # node spacing SSM +BOND_FRAGMENTS 1 # make IC's for fragments +INITIAL_OPT 0 # opt steps first node +FINAL_OPT 150 # opt steps last SSM node +PRODUCT_LIMIT 100.0 # kcal/mol +TS_FINAL_TYPE 1 # any/delta bond: 0/1 +NNODES 9 # including endpoints +--------------------------------------------------------- diff --git a/TEST/ethyleneRotation/mopac/de-gsm/scratch/initial0001.xyz b/TEST/ethyleneRotation/mopac/de-gsm/scratch/initial0001.xyz new file mode 100644 index 0000000..40de4be --- /dev/null +++ b/TEST/ethyleneRotation/mopac/de-gsm/scratch/initial0001.xyz @@ -0,0 +1,16 @@ + 6 +Step 2 + C 0.66560204 0.00000000 0.00000000 + C -0.66555970 0.00000000 0.00000000 + H -1.23967945 0.92228617 -0.05058564 + H 1.23965778 -0.92231833 0.05060017 + H 1.23965778 0.92231833 -0.05060017 + H -1.23967945 -0.92228617 0.05058564 + 6 +Step 3 + C 0.66543421 0.00807607 0.00254083 + C -0.66543186 -0.00709879 -0.00260160 + H -1.23542454 -0.06339719 -0.92708417 + H 1.24370124 -0.03492594 -0.91749945 + H 1.23541877 0.06474270 0.92700959 + H -1.24367682 0.03648516 0.91742380 diff --git a/TEST/ethyleneRotation/mopac/de-gsm/stringfile.standard b/TEST/ethyleneRotation/mopac/de-gsm/stringfile.standard new file mode 100644 index 0000000..fdf38b5 --- /dev/null +++ b/TEST/ethyleneRotation/mopac/de-gsm/stringfile.standard @@ -0,0 +1,72 @@ + 6 + 0.000000 + C 0.665602 0.000000 0.000000 + C -0.665560 0.000000 0.000000 + H -1.239679 0.922286 -0.050586 + H 1.239658 -0.922318 0.050600 + H 1.239658 0.922318 -0.050600 + H -1.239679 -0.922286 0.050586 + 6 + 32.850548 + C 0.633732 0.000764 -0.000879 + C -0.695465 0.068320 -0.270271 + H -0.973380 -0.851843 0.341405 + H 1.278116 0.884774 0.077546 + H 1.186358 -0.936884 -0.112246 + H -1.429377 0.835391 -0.035587 + 6 + 110.921453 + C 0.480807 -0.087997 -0.020865 + C -0.819717 0.213910 -0.399085 + H -0.176616 -0.664485 0.741674 + H 1.255475 0.641274 0.287004 + H 0.972561 -0.997719 -0.426777 + H -1.711014 0.779445 -0.175673 + 6 + 113.680151 + C 0.439444 -0.185193 0.018729 + C -0.851332 0.330331 -0.269523 + H 0.140888 -0.822609 0.890009 + H 1.226628 0.491921 0.417973 + H 0.907501 -0.889049 -0.700492 + H -1.857235 0.683894 -0.335441 + 6 + 112.519457 + C 0.453427 -0.244936 0.014679 + C -0.844803 0.276209 -0.275144 + H 0.186310 -0.781462 0.951727 + H 1.245996 0.468540 0.314079 + H 0.897335 -1.023635 -0.640281 + H -1.920736 0.288635 -0.309631 + 6 + 82.477842 + C 0.366601 0.143813 -0.148378 + C -0.830211 -0.725317 -0.021263 + H -0.058040 1.080792 -0.571852 + H 1.098887 -0.211364 -0.879912 + H 0.875493 0.454637 0.778977 + H -1.458681 -0.330292 0.820009 + 6 + 89.261181 + C 0.449466 -0.024345 -0.081148 + C -0.901536 -0.500768 -0.053375 + H -0.289241 0.732602 -0.644215 + H 1.100404 -0.341416 -0.898686 + H 0.970037 0.513942 0.718387 + H -1.330436 -0.265647 0.952824 + 6 + 27.533917 + C 0.640136 -0.019431 -0.008104 + C -0.704888 -0.257028 -0.016075 + H -1.139216 0.322412 -0.870137 + H 1.249235 -0.265455 -0.877733 + H 1.202382 0.341793 0.852610 + H -1.247345 -0.129988 0.919858 + 6 + 0.001010 + C 0.665434 0.008076 0.002541 + C -0.665432 -0.007099 -0.002602 + H -1.235425 -0.063397 -0.927084 + H 1.243701 -0.034926 -0.917499 + H 1.235419 0.064743 0.927010 + H -1.243677 0.036485 0.917424 diff --git a/TEST/ethyleneRotation/qchem/de-gsm/compare.py b/TEST/ethyleneRotation/qchem/de-gsm/compare.py new file mode 100644 index 0000000..8bc4f62 --- /dev/null +++ b/TEST/ethyleneRotation/qchem/de-gsm/compare.py @@ -0,0 +1,41 @@ +# for reading csv format files +import csv + +# function to convert strings to float and skip conversion if the value is not a float +def convertToFloat(inList): + for element in inList: + try: + yield float(element) + except ValueError: + yield element + +# subtract two floats and skip if string +def subtractFloat(number1, number2): + try: + return (number1 - number2) + except TypeError: + pass + +def main(): + threshold = 0.001 + try: + # read standard and output files + standard = csv.reader(open('stringfile.standard', 'r'), delimiter=' ') + currentOutput = csv.reader(open('stringfile.xyz0001', 'r'), delimiter=' ') + # error if file does not exist + except IOError: + print("Error: File cannot be found!") + exit(1) + # loop over elements of two files simultaneously + for rowStd, rowOut in zip(standard, currentOutput): + rowStd = filter(None, rowStd) + rowOut = filter(None, rowOut) + for valStd, valOut in zip(list(convertToFloat(rowStd)), list(convertToFloat(rowOut))): + # error if difference larger than threshold + if ((subtractFloat(valStd, valOut)) > threshold): + print ((subtractFloat(valStd, valOut))) + exit(2) + return 0 + +if __name__ == "__main__": + main() diff --git a/TEST/ethyleneRotation/qchem/de-gsm/gscreate b/TEST/ethyleneRotation/qchem/de-gsm/gscreate new file mode 100755 index 0000000..119b132 --- /dev/null +++ b/TEST/ethyleneRotation/qchem/de-gsm/gscreate @@ -0,0 +1,14 @@ +#!/bin/bash + +file=molecule + +#nl $file > tmp.mole +#nl link > tmp.link +#join tmp.mole tmp.link > tmp.geom2 +#awk '{ print $2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10 }' tmp.geom2 > tmp.geom + +#cat qstart tmp.geom qend > qcin +#cat qstart molecule$1 qend > scratch/qcin$1 +cat qstart $QCSCRATCH/molecule$1 qend > $QCSCRATCH/qcin$1 + +#rm tmp.geom tmp.geom2 tmp.link tmp.mole diff --git a/TEST/ethyleneRotation/qchem/de-gsm/inpfileq b/TEST/ethyleneRotation/qchem/de-gsm/inpfileq new file mode 100644 index 0000000..83a96a1 --- /dev/null +++ b/TEST/ethyleneRotation/qchem/de-gsm/inpfileq @@ -0,0 +1,27 @@ + +# FSM/GSM/SSM inpfileq + +------------- QCHEM Scratch Info ------------------------ +$QCSCRATCH/ # path for scratch dir. end with "/" +GSM_go1q # name of run +--------------------------------------------------------- + +------------ String Info -------------------------------- +SM_TYPE GSM # SSM, FSM or GSM +RESTART 0 # read restart.xyz +MAX_OPT_ITERS 80 # maximum iterations +STEP_OPT_ITERS 30 # for FSM/SSM +CONV_TOL 0.0005 # perp grad +ADD_NODE_TOL 0.1 # for GSM +SCALING 1.0 # for opt steps +SSM_DQMAX 0.8 # add step size +GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 +INT_THRESH 2.0 # intermediate detection +MIN_SPACING 5.0 # node spacing SSM +BOND_FRAGMENTS 1 # make IC's for fragments +INITIAL_OPT 0 # opt steps first node +FINAL_OPT 150 # opt steps last SSM node +PRODUCT_LIMIT 100.0 # kcal/mol +TS_FINAL_TYPE 1 # any/delta bond: 0/1 +NNODES 9 # including endpoints +--------------------------------------------------------- diff --git a/TEST/ethyleneRotation/qchem/de-gsm/qend b/TEST/ethyleneRotation/qchem/de-gsm/qend new file mode 100644 index 0000000..b39a0e1 --- /dev/null +++ b/TEST/ethyleneRotation/qchem/de-gsm/qend @@ -0,0 +1 @@ +$end diff --git a/TEST/ethyleneRotation/qchem/de-gsm/qstart b/TEST/ethyleneRotation/qchem/de-gsm/qstart new file mode 100644 index 0000000..afa463a --- /dev/null +++ b/TEST/ethyleneRotation/qchem/de-gsm/qstart @@ -0,0 +1,24 @@ + $rem + JOBTYPE FORCE + EXCHANGE B3LYP +! CORRELATION PBE +! UNRESTRICTED TRUE + SCF_ALGORITHM rca_diis + SCF_MAX_CYCLES 150 + BASIS 6-31G* +! BASIS LANL2DZ +! ECP LANL2DZ + WAVEFUNCTION_ANALYSIS FALSE + GEOM_OPT_MAX_CYCLES 300 + +scf_convergence 6 + + SYM_IGNORE TRUE + SYMMETRY FALSE + +molden_format true + $end + + +$molecule +0 1 diff --git a/TEST/ethyleneRotation/qchem/de-gsm/scratch/initial0001.xyz b/TEST/ethyleneRotation/qchem/de-gsm/scratch/initial0001.xyz new file mode 100644 index 0000000..40de4be --- /dev/null +++ b/TEST/ethyleneRotation/qchem/de-gsm/scratch/initial0001.xyz @@ -0,0 +1,16 @@ + 6 +Step 2 + C 0.66560204 0.00000000 0.00000000 + C -0.66555970 0.00000000 0.00000000 + H -1.23967945 0.92228617 -0.05058564 + H 1.23965778 -0.92231833 0.05060017 + H 1.23965778 0.92231833 -0.05060017 + H -1.23967945 -0.92228617 0.05058564 + 6 +Step 3 + C 0.66543421 0.00807607 0.00254083 + C -0.66543186 -0.00709879 -0.00260160 + H -1.23542454 -0.06339719 -0.92708417 + H 1.24370124 -0.03492594 -0.91749945 + H 1.23541877 0.06474270 0.92700959 + H -1.24367682 0.03648516 0.91742380 diff --git a/TEST/ethyleneRotation/qchem/de-gsm/stringfile.standard b/TEST/ethyleneRotation/qchem/de-gsm/stringfile.standard new file mode 100644 index 0000000..fb5c9ac --- /dev/null +++ b/TEST/ethyleneRotation/qchem/de-gsm/stringfile.standard @@ -0,0 +1,72 @@ + 6 + 0.000000 + C 0.665602 0.000000 0.000000 + C -0.665560 0.000000 0.000000 + H -1.239679 0.922286 -0.050586 + H 1.239658 -0.922318 0.050600 + H 1.239658 0.922318 -0.050600 + H -1.239679 -0.922286 0.050586 + 6 + 13.780310 + C 0.653646 -0.003726 -0.026008 + C -0.677326 -0.060936 -0.158262 + H -1.225900 -0.874680 0.326709 + H 1.187267 0.935453 0.124372 + H 1.297798 -0.874092 -0.158918 + H -1.235501 0.878503 -0.107925 + 6 + 64.957763 + C 0.583732 -0.053826 -0.094747 + C -0.781241 -0.124982 -0.335798 + H -0.933431 -0.698520 0.639033 + H 1.150912 0.780481 0.350624 + H 1.228801 -0.868007 -0.429623 + H -1.247272 0.848457 -0.123169 + 6 + 82.231267 + C 0.443431 -0.128702 -0.153993 + C -0.937997 -0.085856 -0.461192 + H -0.216097 -0.643583 0.700610 + H 1.014154 0.555981 0.505279 + H 1.075829 -0.882850 -0.635303 + H -1.373418 0.792924 0.065924 + 6 + 101.332948 + C 0.525735 -0.259179 -0.208048 + C -0.851632 -0.309189 -0.305006 + H -0.415808 -0.310477 0.851697 + H 1.172016 0.360793 0.448167 + H 1.131256 -0.971982 -0.790717 + H -1.543790 0.459858 0.060083 + 6 + 62.641735 + C 0.665761 0.012589 0.010824 + C -0.634425 -0.078096 0.353322 + H -0.860351 0.463252 -0.636515 + H 1.044639 0.156556 -0.996924 + H 1.475231 -0.054488 0.753464 + H -1.696816 -0.086079 0.493335 + 6 + 51.876494 + C 0.687754 -0.004173 0.036113 + C -0.615077 -0.106980 0.334189 + H -0.939810 0.195644 -0.759277 + H 1.069172 0.041357 -0.971006 + H 1.471730 0.024343 0.808301 + H -1.675079 -0.034992 0.545425 + 6 + 21.666469 + C 0.673307 0.006328 0.033670 + C -0.646032 -0.190651 0.155559 + H -1.091926 -0.122435 -0.855914 + H 1.129602 0.125531 -0.945619 + H 1.374508 -0.057105 0.867102 + H -1.480625 0.219747 0.720185 + 6 + -0.000139 + C 0.665434 0.008076 0.002541 + C -0.665432 -0.007099 -0.002602 + H -1.235425 -0.063397 -0.927084 + H 1.243701 -0.034926 -0.917499 + H 1.235419 0.064743 0.927010 + H -1.243677 0.036485 0.917424 diff --git a/TEST/methanolFormaldehydeHydTransfer/mopac/de-gsm/compare.py b/TEST/methanolFormaldehydeHydTransfer/mopac/de-gsm/compare.py new file mode 100644 index 0000000..8bc4f62 --- /dev/null +++ b/TEST/methanolFormaldehydeHydTransfer/mopac/de-gsm/compare.py @@ -0,0 +1,41 @@ +# for reading csv format files +import csv + +# function to convert strings to float and skip conversion if the value is not a float +def convertToFloat(inList): + for element in inList: + try: + yield float(element) + except ValueError: + yield element + +# subtract two floats and skip if string +def subtractFloat(number1, number2): + try: + return (number1 - number2) + except TypeError: + pass + +def main(): + threshold = 0.001 + try: + # read standard and output files + standard = csv.reader(open('stringfile.standard', 'r'), delimiter=' ') + currentOutput = csv.reader(open('stringfile.xyz0001', 'r'), delimiter=' ') + # error if file does not exist + except IOError: + print("Error: File cannot be found!") + exit(1) + # loop over elements of two files simultaneously + for rowStd, rowOut in zip(standard, currentOutput): + rowStd = filter(None, rowStd) + rowOut = filter(None, rowOut) + for valStd, valOut in zip(list(convertToFloat(rowStd)), list(convertToFloat(rowOut))): + # error if difference larger than threshold + if ((subtractFloat(valStd, valOut)) > threshold): + print ((subtractFloat(valStd, valOut))) + exit(2) + return 0 + +if __name__ == "__main__": + main() diff --git a/TEST/methanolFormaldehydeHydTransfer/mopac/de-gsm/inpfileq b/TEST/methanolFormaldehydeHydTransfer/mopac/de-gsm/inpfileq new file mode 100644 index 0000000..5d94cdd --- /dev/null +++ b/TEST/methanolFormaldehydeHydTransfer/mopac/de-gsm/inpfileq @@ -0,0 +1,26 @@ +# FSM/GSM/SSM inpfileq + +------------- QCHEM Scratch Info ------------------------ +$QCSCRATCH/ # path for scratch dir. end with "/" +GSM_go1q # name of run +--------------------------------------------------------- + +------------ String Info -------------------------------- +SM_TYPE GSM # SSM, FSM or GSM +RESTART 0 # read restart.xyz +MAX_OPT_ITERS 120 # maximum iterations +STEP_OPT_ITERS 30 # for FSM/SSM +CONV_TOL 0.0005 # perp grad +ADD_NODE_TOL 0.1 # for GSM +SCALING 1.0 # for opt steps +SSM_DQMAX 0.8 # add step size +GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 +INT_THRESH 2.0 # intermediate detection +MIN_SPACING 5.0 # node spacing SSM +BOND_FRAGMENTS 1 # make IC's for fragments +INITIAL_OPT 0 # opt steps first node +FINAL_OPT 150 # opt steps last SSM node +PRODUCT_LIMIT 100.0 # kcal/mol +TS_FINAL_TYPE 1 # any/delta bond: 0/1 +NNODES 9 # including endpoints +--------------------------------------------------------- diff --git a/TEST/methanolFormaldehydeHydTransfer/mopac/de-gsm/scratch/initial0001.xyz b/TEST/methanolFormaldehydeHydTransfer/mopac/de-gsm/scratch/initial0001.xyz new file mode 100644 index 0000000..a47fe6a --- /dev/null +++ b/TEST/methanolFormaldehydeHydTransfer/mopac/de-gsm/scratch/initial0001.xyz @@ -0,0 +1,26 @@ + 11 +Step 5 + H 0.41797324 0.94736684 -0.39562105 + C 0.23463898 1.11282329 0.66131673 + C 0.64075280 0.23925801 1.58339559 + H -0.28695375 2.01445005 0.96002081 + H 0.46045309 0.40790985 2.64613421 + O 1.30089798 -0.91413688 1.27688069 + H 1.50257557 -1.39412410 2.10286864 + O 1.19203118 -2.73369610 3.40309101 + C 0.37322499 -3.45250540 2.86892341 + H -0.00656927 -4.36236697 3.36949173 + H -0.02689882 -3.23019659 1.86359922 + 11 +Step 20 + H -0.19936743 0.59407144 0.74388584 + C -0.40617656 -0.33905946 1.27660171 + C 0.86105725 -0.80690813 1.99099738 + H -1.21318809 -0.17115368 1.99621611 + H 1.15156591 -0.07305690 2.75681870 + O 1.87101317 -0.96523074 0.99795803 + H 2.71471571 -1.12994105 1.44729950 + O 0.30236175 -2.25148677 3.85738347 + C 0.59626418 -2.13750850 2.68899351 + H -0.73244687 -1.08584907 0.54426337 + H 0.68810598 -3.02017613 2.01425240 diff --git a/TEST/methanolFormaldehydeHydTransfer/mopac/de-gsm/stringfile.standard b/TEST/methanolFormaldehydeHydTransfer/mopac/de-gsm/stringfile.standard new file mode 100644 index 0000000..8374662 --- /dev/null +++ b/TEST/methanolFormaldehydeHydTransfer/mopac/de-gsm/stringfile.standard @@ -0,0 +1,117 @@ + 11 + 0.000000 + H 0.417973 0.947367 -0.395621 + C 0.234639 1.112823 0.661317 + C 0.640753 0.239258 1.583396 + H -0.286954 2.014450 0.960021 + H 0.460453 0.407910 2.646134 + O 1.300898 -0.914137 1.276881 + H 1.502576 -1.394124 2.102869 + O 1.192031 -2.733696 3.403091 + C 0.373225 -3.452505 2.868923 + H -0.006569 -4.362367 3.369492 + H -0.026899 -3.230197 1.863599 + 11 + -1.778260 + H 0.111327 0.636785 -0.190579 + C 0.040974 0.864117 0.862500 + C 0.711478 0.187246 1.794395 + H -0.607428 1.692746 1.088688 + H 0.698338 0.361907 2.864529 + O 1.516854 -0.853081 1.381077 + H 1.920053 -1.330146 2.167792 + O 1.125364 -2.659719 3.294191 + C 0.296988 -3.281424 2.657377 + H -0.365118 -4.009914 3.139672 + H 0.176767 -3.136448 1.574426 + 11 + -1.033450 + H -0.087848 0.446552 -0.033640 + C -0.085076 0.673037 1.022161 + C 0.753936 0.099332 1.883262 + H -0.809266 1.415397 1.311346 + H 0.826053 0.278284 2.950393 + O 1.640486 -0.839237 1.387051 + H 2.156558 -1.263501 2.126035 + O 1.027471 -2.641282 3.359284 + C 0.267116 -3.133161 2.549138 + H -0.689411 -3.575580 2.851542 + H 0.502343 -3.148496 1.475645 + 11 + -0.105310 + H -0.183695 0.360736 0.096163 + C -0.150842 0.530181 1.162503 + C 0.799268 0.025981 1.948054 + H -0.946239 1.157276 1.529410 + H 0.912011 0.159819 3.018312 + O 1.761517 -0.773773 1.351662 + H 2.383306 -1.140180 2.028229 + O 0.817701 -2.721676 3.475931 + C 0.205940 -3.027421 2.473289 + H -0.879122 -3.186939 2.484047 + H 0.708478 -3.148633 1.504071 + 11 + 0.434300 + H -0.189371 0.292847 0.113754 + C -0.144788 0.392189 1.188589 + C 0.888491 -0.032360 1.913642 + H -1.004014 0.879399 1.619297 + H 1.028303 0.064716 2.984550 + O 1.917867 -0.669075 1.236863 + H 2.627344 -0.956958 1.857129 + O 0.492148 -2.763683 3.504097 + C 0.094876 -2.881702 2.363649 + H -0.968464 -2.795551 2.109056 + H 0.780225 -3.071293 1.526792 + 11 + 1.949710 + H -0.236350 0.148334 0.163122 + C -0.137979 0.198566 1.238711 + C 0.975261 -0.154804 1.881689 + H -1.014395 0.578441 1.739369 + H 1.204047 -0.006497 2.931349 + O 2.021731 -0.629063 1.106947 + H 2.788385 -0.904088 1.659032 + O 0.177998 -2.682883 3.572604 + C 0.002824 -2.652281 2.373684 + H -0.945199 -2.313548 1.933323 + H 0.758329 -2.984207 1.649625 + 11 + 25.024590 + H -0.253306 0.071175 0.277171 + C -0.182918 0.032639 1.353095 + C 0.945358 -0.350696 1.981416 + H -1.022394 0.459258 1.881466 + H 1.224664 -0.000779 2.973857 + O 2.039316 -0.516626 1.121297 + H 2.811834 -0.885420 1.604189 + O -0.104373 -2.672826 3.470226 + C 0.120313 -2.447801 2.299781 + H -0.735920 -2.040600 1.690392 + H 0.771739 -3.009796 1.626475 + 11 + 47.522970 + H -0.329227 -0.092794 0.355220 + C -0.308691 -0.167614 1.428260 + C 0.926484 -0.662446 2.094527 + H -1.047840 0.372421 1.987658 + H 1.242637 -0.158530 3.022751 + O 1.979764 -0.666423 1.130689 + H 2.819279 -0.952095 1.548376 + O -0.060373 -2.450741 3.441762 + C 0.345547 -2.097429 2.284369 + H -0.798281 -1.796464 1.666270 + H 0.714650 -2.848192 1.568616 + 11 + -26.835910 + H -0.199367 0.594071 0.743886 + C -0.406177 -0.339059 1.276602 + C 0.861057 -0.806908 1.990997 + H -1.213188 -0.171154 1.996216 + H 1.151566 -0.073057 2.756819 + O 1.871013 -0.965231 0.997958 + H 2.714716 -1.129941 1.447299 + O 0.302362 -2.251487 3.857383 + C 0.596264 -2.137509 2.688994 + H -0.732447 -1.085849 0.544263 + H 0.688106 -3.020176 2.014252 diff --git a/TEST/methanolFormaldehydeHydTransfer/mopac/de-gsm/stringfile.standard.fr b/TEST/methanolFormaldehydeHydTransfer/mopac/de-gsm/stringfile.standard.fr new file mode 100644 index 0000000..3859d7a --- /dev/null +++ b/TEST/methanolFormaldehydeHydTransfer/mopac/de-gsm/stringfile.standard.fr @@ -0,0 +1,117 @@ + 11 + + H -0.351903 -0.148585 0.361989 + C -0.328870 -0.216962 1.435915 + C 0.938342 -0.675554 2.111141 + H -1.064777 0.328351 1.991568 + H 1.257067 -0.155880 3.027492 + O 1.985211 -0.675991 1.137653 + H 2.834259 -0.958079 1.549178 + O -0.041727 -2.456822 3.418630 + C 0.370913 -2.092781 2.313705 + H -0.841740 -1.632925 1.603866 + H 0.727175 -2.835079 1.577362 + 11 + + H -0.329227 -0.092794 0.355220 + C -0.308691 -0.167614 1.428260 + C 0.926484 -0.662446 2.094527 + H -1.047840 0.372421 1.987658 + H 1.242637 -0.158530 3.022751 + O 1.979764 -0.666423 1.130689 + H 2.819279 -0.952095 1.548376 + O -0.060373 -2.450741 3.441762 + C 0.345547 -2.097429 2.284369 + H -0.798281 -1.796464 1.666270 + H 0.714650 -2.848192 1.568616 + 11 + + H -0.306920 -0.033962 0.347192 + C -0.290397 -0.116611 1.419220 + C 0.912396 -0.649869 2.077276 + H -1.032408 0.419351 1.981630 + H 1.224676 -0.161866 3.017475 + O 1.972313 -0.657323 1.123502 + H 2.801968 -0.945823 1.547256 + O -0.077889 -2.447412 3.466224 + C 0.318098 -2.108167 2.254761 + H -0.738910 -1.951775 1.733496 + H 0.701022 -2.866849 1.560467 + 11 + + H -0.318026 -0.043148 0.363612 + C -0.314389 -0.165511 1.432695 + C 0.925601 -0.652826 2.094956 + H -1.076039 0.326511 2.005846 + H 1.247352 -0.145589 3.019876 + O 1.976148 -0.648083 1.127787 + H 2.794989 -1.022142 1.517493 + O -0.088437 -2.426415 3.438667 + C 0.350589 -2.090173 2.287836 + H -0.775772 -1.801681 1.632322 + H 0.761933 -2.851251 1.607410 + 11 + + H -0.329227 -0.092794 0.355220 + C -0.308691 -0.167614 1.428260 + C 0.926484 -0.662446 2.094527 + H -1.047840 0.372421 1.987658 + H 1.242637 -0.158530 3.022751 + O 1.979764 -0.666423 1.130689 + H 2.819279 -0.952095 1.548376 + O -0.060373 -2.450741 3.441762 + C 0.345547 -2.097429 2.284369 + H -0.798281 -1.796464 1.666270 + H 0.714650 -2.848192 1.568616 + 11 + + H -0.340269 -0.142213 0.349163 + C -0.301830 -0.170116 1.423786 + C 0.927760 -0.672306 2.094753 + H -1.017453 0.416599 1.966845 + H 1.237750 -0.171754 3.026439 + O 1.984630 -0.685643 1.135476 + H 2.838053 -0.880573 1.575932 + O -0.032608 -2.475371 3.443117 + C 0.340611 -2.104521 2.280873 + H -0.819344 -1.790957 1.700092 + H 0.666649 -2.843452 1.532022 + 11 + + H -0.298769 -0.036264 0.346633 + C -0.298887 -0.171207 1.413243 + C 0.928299 -0.665979 2.091062 + H -1.073688 0.311354 1.979336 + H 1.245026 -0.139954 3.006650 + O 1.988199 -0.683052 1.130762 + H 2.828038 -0.940608 1.563403 + O -0.037049 -2.451834 3.458021 + C 0.349298 -2.098613 2.294898 + H -0.809396 -1.801048 1.698217 + H 0.662879 -2.843100 1.546273 + 11 + + H -0.329227 -0.092794 0.355220 + C -0.308691 -0.167614 1.428260 + C 0.926484 -0.662446 2.094527 + H -1.047840 0.372421 1.987658 + H 1.242637 -0.158530 3.022751 + O 1.979764 -0.666423 1.130689 + H 2.819279 -0.952095 1.548376 + O -0.060373 -2.450741 3.441762 + C 0.345547 -2.097429 2.284369 + H -0.798281 -1.796464 1.666270 + H 0.714650 -2.848192 1.568616 + 11 + + H -0.360991 -0.149179 0.367896 + C -0.318139 -0.164197 1.443603 + C 0.924768 -0.659157 2.098189 + H -1.020774 0.430874 1.991869 + H 1.240406 -0.178212 3.038802 + O 1.971741 -0.649577 1.130889 + H 2.810479 -0.963299 1.532574 + O -0.083493 -2.449661 3.424464 + C 0.341925 -2.095930 2.273081 + H -0.786742 -1.790949 1.634190 + H 0.764770 -2.851018 1.592942 diff --git a/TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/compare.py b/TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/compare.py new file mode 100644 index 0000000..8bc4f62 --- /dev/null +++ b/TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/compare.py @@ -0,0 +1,41 @@ +# for reading csv format files +import csv + +# function to convert strings to float and skip conversion if the value is not a float +def convertToFloat(inList): + for element in inList: + try: + yield float(element) + except ValueError: + yield element + +# subtract two floats and skip if string +def subtractFloat(number1, number2): + try: + return (number1 - number2) + except TypeError: + pass + +def main(): + threshold = 0.001 + try: + # read standard and output files + standard = csv.reader(open('stringfile.standard', 'r'), delimiter=' ') + currentOutput = csv.reader(open('stringfile.xyz0001', 'r'), delimiter=' ') + # error if file does not exist + except IOError: + print("Error: File cannot be found!") + exit(1) + # loop over elements of two files simultaneously + for rowStd, rowOut in zip(standard, currentOutput): + rowStd = filter(None, rowStd) + rowOut = filter(None, rowOut) + for valStd, valOut in zip(list(convertToFloat(rowStd)), list(convertToFloat(rowOut))): + # error if difference larger than threshold + if ((subtractFloat(valStd, valOut)) > threshold): + print ((subtractFloat(valStd, valOut))) + exit(2) + return 0 + +if __name__ == "__main__": + main() diff --git a/TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/gscreate b/TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/gscreate new file mode 100755 index 0000000..119b132 --- /dev/null +++ b/TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/gscreate @@ -0,0 +1,14 @@ +#!/bin/bash + +file=molecule + +#nl $file > tmp.mole +#nl link > tmp.link +#join tmp.mole tmp.link > tmp.geom2 +#awk '{ print $2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10 }' tmp.geom2 > tmp.geom + +#cat qstart tmp.geom qend > qcin +#cat qstart molecule$1 qend > scratch/qcin$1 +cat qstart $QCSCRATCH/molecule$1 qend > $QCSCRATCH/qcin$1 + +#rm tmp.geom tmp.geom2 tmp.link tmp.mole diff --git a/TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/inpfileq b/TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/inpfileq new file mode 100644 index 0000000..83a96a1 --- /dev/null +++ b/TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/inpfileq @@ -0,0 +1,27 @@ + +# FSM/GSM/SSM inpfileq + +------------- QCHEM Scratch Info ------------------------ +$QCSCRATCH/ # path for scratch dir. end with "/" +GSM_go1q # name of run +--------------------------------------------------------- + +------------ String Info -------------------------------- +SM_TYPE GSM # SSM, FSM or GSM +RESTART 0 # read restart.xyz +MAX_OPT_ITERS 80 # maximum iterations +STEP_OPT_ITERS 30 # for FSM/SSM +CONV_TOL 0.0005 # perp grad +ADD_NODE_TOL 0.1 # for GSM +SCALING 1.0 # for opt steps +SSM_DQMAX 0.8 # add step size +GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 +INT_THRESH 2.0 # intermediate detection +MIN_SPACING 5.0 # node spacing SSM +BOND_FRAGMENTS 1 # make IC's for fragments +INITIAL_OPT 0 # opt steps first node +FINAL_OPT 150 # opt steps last SSM node +PRODUCT_LIMIT 100.0 # kcal/mol +TS_FINAL_TYPE 1 # any/delta bond: 0/1 +NNODES 9 # including endpoints +--------------------------------------------------------- diff --git a/TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/qend b/TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/qend new file mode 100644 index 0000000..b39a0e1 --- /dev/null +++ b/TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/qend @@ -0,0 +1 @@ +$end diff --git a/TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/qstart b/TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/qstart new file mode 100644 index 0000000..afa463a --- /dev/null +++ b/TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/qstart @@ -0,0 +1,24 @@ + $rem + JOBTYPE FORCE + EXCHANGE B3LYP +! CORRELATION PBE +! UNRESTRICTED TRUE + SCF_ALGORITHM rca_diis + SCF_MAX_CYCLES 150 + BASIS 6-31G* +! BASIS LANL2DZ +! ECP LANL2DZ + WAVEFUNCTION_ANALYSIS FALSE + GEOM_OPT_MAX_CYCLES 300 + +scf_convergence 6 + + SYM_IGNORE TRUE + SYMMETRY FALSE + +molden_format true + $end + + +$molecule +0 1 diff --git a/TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/scratch/initial0001.xyz b/TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/scratch/initial0001.xyz new file mode 100644 index 0000000..a47fe6a --- /dev/null +++ b/TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/scratch/initial0001.xyz @@ -0,0 +1,26 @@ + 11 +Step 5 + H 0.41797324 0.94736684 -0.39562105 + C 0.23463898 1.11282329 0.66131673 + C 0.64075280 0.23925801 1.58339559 + H -0.28695375 2.01445005 0.96002081 + H 0.46045309 0.40790985 2.64613421 + O 1.30089798 -0.91413688 1.27688069 + H 1.50257557 -1.39412410 2.10286864 + O 1.19203118 -2.73369610 3.40309101 + C 0.37322499 -3.45250540 2.86892341 + H -0.00656927 -4.36236697 3.36949173 + H -0.02689882 -3.23019659 1.86359922 + 11 +Step 20 + H -0.19936743 0.59407144 0.74388584 + C -0.40617656 -0.33905946 1.27660171 + C 0.86105725 -0.80690813 1.99099738 + H -1.21318809 -0.17115368 1.99621611 + H 1.15156591 -0.07305690 2.75681870 + O 1.87101317 -0.96523074 0.99795803 + H 2.71471571 -1.12994105 1.44729950 + O 0.30236175 -2.25148677 3.85738347 + C 0.59626418 -2.13750850 2.68899351 + H -0.73244687 -1.08584907 0.54426337 + H 0.68810598 -3.02017613 2.01425240 diff --git a/TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/stringfile.standard b/TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/stringfile.standard new file mode 100644 index 0000000..0a45bbe --- /dev/null +++ b/TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/stringfile.standard @@ -0,0 +1,117 @@ + 11 + 0.000000 + H 0.417973 0.947367 -0.395621 + C 0.234639 1.112823 0.661317 + C 0.640753 0.239258 1.583396 + H -0.286954 2.014450 0.960021 + H 0.460453 0.407910 2.646134 + O 1.300898 -0.914137 1.276881 + H 1.502576 -1.394124 2.102869 + O 1.192031 -2.733696 3.403091 + C 0.373225 -3.452505 2.868923 + H -0.006569 -4.362367 3.369492 + H -0.026899 -3.230197 1.863599 + 11 + 1.183521 + H 0.057002 0.595267 -0.191130 + C -0.003387 0.777347 0.877206 + C 0.767280 0.117186 1.739984 + H -0.691662 1.534591 1.233738 + H 0.712088 0.300942 2.813275 + O 1.686864 -0.814643 1.352529 + H 1.942388 -1.329380 2.138683 + O 1.117218 -2.702732 3.393627 + C 0.280384 -3.182516 2.658215 + H -0.523511 -3.834894 3.046809 + H 0.280934 -2.989098 1.571132 + 11 + 3.663935 + H -0.141515 0.244769 -0.001183 + C -0.134575 0.455592 1.063644 + C 0.847870 0.021751 1.852666 + H -0.929025 1.068741 1.473122 + H 0.864516 0.235909 2.920953 + O 1.912398 -0.696155 1.380422 + H 2.285659 -1.202061 2.120241 + O 1.001392 -2.735069 3.388092 + C 0.197633 -2.957360 2.508592 + H -0.863993 -3.183675 2.729672 + H 0.478390 -2.946580 1.439877 + 11 + 6.299598 + H -0.253855 -0.027399 0.166073 + C -0.180174 0.200305 1.225459 + C 0.932752 -0.050198 1.914933 + H -1.019093 0.687100 1.709026 + H 1.023311 0.199107 2.971869 + O 2.052544 -0.582489 1.336137 + H 2.566238 -1.036694 2.022298 + O 0.668716 -2.821995 3.482140 + C 0.091401 -2.785276 2.418695 + H -0.998230 -2.600422 2.335908 + H 0.613797 -2.947456 1.456165 + 11 + 12.231001 + H -0.328973 -0.139184 0.311313 + C -0.169929 -0.026186 1.378893 + C 1.040320 -0.175315 1.918571 + H -0.996282 0.315677 1.992176 + H 1.230496 0.106031 2.954067 + O 2.147984 -0.415065 1.144090 + H 2.817807 -0.859211 1.686625 + O -0.098206 -2.722568 3.564587 + C -0.053975 -2.579661 2.363167 + H -0.928880 -2.277058 1.755283 + H 0.807390 -2.874021 1.725809 + 11 + 59.288766 + H -0.310861 -0.214025 0.327418 + C -0.230984 -0.268496 1.410483 + C 1.023767 -0.517903 2.016150 + H -1.040617 0.143102 2.002421 + H 1.214175 -0.126767 3.014798 + O 2.102103 -0.561651 1.133236 + H 2.839307 -1.009742 1.576376 + O -0.210611 -2.315636 3.447231 + C 0.153329 -2.046875 2.294736 + H -0.755680 -1.807787 1.458835 + H 0.773773 -2.633029 1.600648 + 11 + -0.135269 + H -0.259437 -0.056381 0.284885 + C -0.369852 -0.287633 1.347242 + C 0.925920 -0.670216 2.076262 + H -1.096195 0.293488 1.916078 + H 1.110077 -0.162447 3.032330 + O 1.992644 -0.710165 1.150390 + H 2.788336 -1.110441 1.551736 + O 0.026206 -2.470974 3.511575 + C 0.454322 -2.093047 2.442330 + H -0.881014 -1.300029 1.285868 + H 0.906805 -2.788826 1.687472 + 11 + -19.289558 + H -0.120638 0.233386 0.407561 + C -0.433465 -0.336229 1.287044 + C 0.801128 -0.778072 2.076685 + H -1.113592 0.260693 1.900105 + H 0.998322 -0.122524 2.936271 + O 1.901943 -0.817993 1.166210 + H 2.691693 -1.086987 1.664403 + O 0.597693 -2.514138 3.770487 + C 0.600849 -2.193486 2.603488 + H -0.987107 -1.213194 0.928529 + H 0.547124 -2.951762 1.787715 + 11 + -21.526454 + H -0.199367 0.594071 0.743886 + C -0.406177 -0.339059 1.276602 + C 0.861057 -0.806908 1.990997 + H -1.213188 -0.171154 1.996216 + H 1.151566 -0.073057 2.756819 + O 1.871013 -0.965231 0.997958 + H 2.714716 -1.129941 1.447299 + O 0.302362 -2.251487 3.857383 + C 0.596264 -2.137509 2.688994 + H -0.732447 -1.085849 0.544263 + H 0.688106 -3.020176 2.014252 diff --git a/TPLsList.cmake b/TPLsList.cmake new file mode 100644 index 0000000..0a69c1d --- /dev/null +++ b/TPLsList.cmake @@ -0,0 +1,3 @@ +TRIBITS_REPOSITORY_DEFINE_TPLS( + MKL cmake/TPLS PT + ) diff --git a/Version.cmake b/Version.cmake new file mode 100644 index 0000000..809990a --- /dev/null +++ b/Version.cmake @@ -0,0 +1,13 @@ +# +# Single file that needs to be changed on when branching +# +IF("${REPOSITORY_NAME}" STREQUAL "") + # Need to set the repository name + SET(REPOSITORY_NAME molecularGSM) +ENDIF() + +# Version info +SET(${REPOSITORY_NAME}_VERSION 0.0.1) +SET(${REPOSITORY_NAME}_MAJOR_VERSION 00) +SET(${REPOSITORY_NAME}_MAJOR_MINOR_VERSION 000000) +SET(${REPOSITORY_NAME}_VERSION_STRING "0.0.1 (Dev)") diff --git a/athena.pbs b/athena.pbs new file mode 100644 index 0000000..7136179 --- /dev/null +++ b/athena.pbs @@ -0,0 +1,21 @@ +##!/bin/bash +##This file was created on 12/12/2016 + +#this is a pbs script for Athena HPC, change accordingly +PBS -l nodes=1:ppn=4 -l walltime=18:00:00 +PBS -N test +PBS -o test.o +PBS -e test.e + +cd $PBS_O_WORKDIR +module load CMake +#module load Intel/13.x +pwd +echo $MKLROOT +echo $LD_LIBRARY_PATH +export OMP_NUM_THREADS=1 +#source /export/zimmerman/paulzim/qchem/qchemapr272016/paul.set.local +source /export/zimmerman/craldaz/bin/qchem.source +echo "working on ctest" +ctest -V + diff --git a/cmake/FindMKL.cmake b/cmake/FindMKL.cmake new file mode 100644 index 0000000..b9329ef --- /dev/null +++ b/cmake/FindMKL.cmake @@ -0,0 +1,340 @@ +# http://www.mail-archive.com/cmake@cmake.org/msg41869/FindMKL.cmake +# CMake script to detect Intel(R) Math Kernel Library (MKL) +# +# This will try to find Intel MKL libraries, and include path by automatic +# search through typical install locations and if failed it will +# examine MKLROOT environment variable. +# Note, MKLROOT is not set by IPP installer, it should be set manually. +# +# Usage example: +# set(MKL_USE_STATIC_LIBS ON) +# find_package(MKL) +# if (MKL_FOUND) +# include_directories(${MKL_INCLUDE_DIRS}) +# link_directories(${MKL_LIBRARY_DIRS}) +# add_executable(foo foo.cc) +# target_link_libraries(foo ${MKL_LIBRARIES}) +# endif() +# +# Variables used by this module, they can change the default behaviour and +# need to be set before calling find_package: +# +# MKL_ADDITIONAL_VERSIONS A list of version numbers to use for searching +# the MKL include directory. +# +# MKL_USE_STATIC_LIBS Can be set to ON to force the use of the static +# boost libraries. Defaults to OFF. +# +# MKL_FIND_DEBUG Set this to TRUE to enable debugging output +# of FindMKL.cmake if you are having problems. +# +# On return this will define: +# MKL_FOUND Indicates whether MKL was found (True/False) +# MKL_INCLUDE_DIRS MKL include folder +# MKL_LIBRARY_DIRS MKL libraries folder +# MKL_LIBRARIES MKL libraries names +# +# NOTE: this script has only been tested with Intel(R) Parallel Studio XE 2011 +# and may need changes for compatibility with older versions. +# +# Adapted from OpenCV IPP detection script +# https://code.ros.org/trac/opencv/browser/trunk/opencv/OpenCVFindIPP.cmake +# Many portions taken from FindBoost.cmake + +# TODO: +# - caller needs to link with libiomp5md.lib or /Qopenmp... +# - runtime DLLs: +# -> C:\Program Files\Intel\ComposerXE-2011 +# redist\ia32\mkl +# redist\intel64\mkl + +set(_MKL_IA32 FALSE) +set(_MKL_INTEL64 FALSE) +if (CMAKE_SIZEOF_VOID_P EQUAL 4) + set(_MKL_IA32 TRUE) +elseif (CMAKE_SIZEOF_VOID_P EQUAL 8) + set(_MKL_INTEL64 TRUE) +else() + message(FATAL_ERROR "Unsupported 'void *' size (${SIZEOF_VOID_P})") +endif() + +# Versions should be listed is decreasing order of preference +set(_MKL_TEST_VERSIONS ${MKL_ADDITIONAL_VERSIONS} + "2011" + # alternative form: "2011.xxx.y" + # (y is the release-update number and xxx is the package number) +) + +if (MKL_FIND_VERSION AND NOT MKL_FIND_QUIETLY) + message(WARNING "Requesting a specific version of Intel(R) MKL is not supported") +endif() + +# Use environment variables from Intel build scripts, if available +if (NOT MKL_ROOT AND NOT $ENV{MKLROOT} STREQUAL "") + set(MKL_ROOT $ENV{MKLROOT}) +endif() + +if (MKL_ROOT) + file(TO_CMAKE_PATH ${MKL_ROOT} MKL_ROOT) +endif() + +if (NOT INTEL_ROOT AND NOT $ENV{INTELROOT} STREQUAL "") + set(INTEL_ROOT $ENV{INTELROOT}) +endif() + +if (INTEL_ROOT) + file(TO_CMAKE_PATH ${INTEL_ROOT} INTEL_ROOT) +endif() + +if (MKL_FIND_DEBUG) + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "_MKL_TEST_VERSIONS = ${_MKL_TEST_VERSIONS}") + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "MKL_ADDITIONAL_VERSIONS = ${MKL_ADDITIONAL_VERSIONS}") + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "MKL_USE_STATIC_LIBS = ${MKL_USE_STATIC_LIBS}") + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "MKL_ROOT = ${MKL_ROOT}") + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "INTEL_ROOT = ${INTEL_ROOT}") +endif() + +# Find MKL include directory + +set(_MKL_ROOT_SEARCH_DIRS + ${MKL_ROOT} +) + +foreach (_MKL_VER ${_MKL_TEST_VERSIONS}) + if (WIN32) + list(APPEND _MKL_ROOT_SEARCH_DIRS "$ENV{ProgramFiles}/Intel/Composer XE/mkl") + else() + list(APPEND _MKL_ROOT_SEARCH_DIRS "/opt/intel/composerxe-${_MKL_VER}/mkl") + endif() +endforeach() + +if (MKL_FIND_DEBUG) + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "_MKL_ROOT_SEARCH_DIRS = ${_MKL_ROOT_SEARCH_DIRS}") +endif() + +find_path(MKL_INCLUDE_DIR + NAMES mkl.h + PATHS ${_MKL_ROOT_SEARCH_DIRS} + PATH_SUFFIXES include + DOC "The path to Intel(R) MKL header files" +) + +if (MKL_INCLUDE_DIR) + if (MKL_FIND_DEBUG) + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "location of mkl.h: ${MKL_INCLUDE_DIR}/mkl.h") + endif() +else() + if (MKL_FIND_DEBUG) + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "unable to find Intel(R) MKL header files. Please set MKLROOT" + " to the root directory containing MKL.") + endif() +endif() + +# Find MKL library directory + +set(_INTEL_LIBRARY_DIR_SUFFIXES "lib") +if (_MKL_IA32) + list(APPEND _INTEL_LIBRARY_DIR_SUFFIXES "lib/ia32") +elseif (_MKL_INTEL64) + list(APPEND _INTEL_LIBRARY_DIR_SUFFIXES "lib/intel64") +else() + message(FATAL_ERROR "unreachable") +endif() + +set(_MKL_LIBRARY_SEARCH_DIRS ${_MKL_ROOT_SEARCH_DIRS}) +if (MKL_INCLUDE_DIR) + list(APPEND _MKL_LIBRARY_SEARCH_DIRS "${MKL_INCLUDE_DIR}/..") +endif() + +if (MKL_FIND_DEBUG) + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "_INTEL_LIBRARY_DIR_SUFFIXES = ${_INTEL_LIBRARY_DIR_SUFFIXES}") + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "_MKL_LIBRARY_SEARCH_DIRS = ${_MKL_LIBRARY_SEARCH_DIRS}") +endif() + +set(MKL_LIB_PREFIX "mkl_") +if (MKL_USE_STATIC_LIBS) + if (_MKL_IA32) + if (WIN32) + set(_MKL_LIBRARIES intel_c) + else() + set(_MKL_LIBRARIES intel) + endif() + elseif (_MKL_INTEL64) + set(_MKL_LIBRARIES intel_lp64) + else() + message(FATAL_ERROR "unreachable") + endif() + + list(APPEND _MKL_LIBRARIES intel_thread) + list(APPEND _MKL_LIBRARIES core) +else() + set(_MKL_LIBRARIES rt) +endif() + +set(_MKL_MISSING_LIBRARIES "") +set(MKL_LIBRARIES "") +set(MKL_LIBRARY_DIRS "") +# Find MKL libraries +foreach (_MKL_LIB_RAW ${_MKL_LIBRARIES}) + set(_MKL_LIB ${MKL_LIB_PREFIX}${_MKL_LIB_RAW}) + string(TOUPPER ${_MKL_LIB} _MKL_LIB_UPPER) + + find_library(${_MKL_LIB_UPPER}_LIBRARY + NAMES ${_MKL_LIB} + PATHS ${_MKL_LIBRARY_SEARCH_DIRS} + PATH_SUFFIXES ${_INTEL_LIBRARY_DIR_SUFFIXES} + DOC "The path to Intel(R) MKL ${_MKL_LIB_RAW} library" + ) + mark_as_advanced(${_MKL_LIB_UPPER}_LIBRARY) + + if (NOT ${_MKL_LIB_UPPER}_LIBRARY) + list(APPEND _MKL_MISSING_LIBRARIES ${_MKL_LIB}) + else() + list(APPEND MKL_LIBRARIES ${${_MKL_LIB_UPPER}_LIBRARY}) + if (MKL_FIND_DEBUG) + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "Found ${_MKL_LIB}: ${${_MKL_LIB_UPPER}_LIBRARY}") + endif() + + get_filename_component(_MKL_LIB_PATH "${${_MKL_LIB_UPPER}_LIBRARY}" PATH) + list(APPEND MKL_LIBRARY_DIRS ${_MKL_LIB_PATH}) + endif() +endforeach() + +## Find OpenMP, pthread and math libraries + +set(_INTEL_LIBRARY_SEARCH_DIRS + ${INTEL_ROOT} + ${INTEL_ROOT}/compiler +) + +foreach(_MKL_DIR ${_MKL_ROOT_SEARCH_DIRS}) + list(APPEND _INTEL_LIBRARY_SEARCH_DIRS "${_MKL_DIR}/..") + list(APPEND _INTEL_LIBRARY_SEARCH_DIRS "${_MKL_DIR}/../compiler") +endforeach() + +if (MKL_FIND_DEBUG) + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "_INTEL_LIBRARY_SEARCH_DIRS = ${_INTEL_LIBRARY_SEARCH_DIRS}") +endif() + +if (NOT WIN32) + find_library(PTHREAD_LIBRARY pthread DOC "Path to POSIX threads library") +endif() + +set(_IOMP5_LIB iomp5) +if (WIN32) + if (MKL_USE_STATIC_LIBS) + list(APPEND _IOMP5_LIB libiomp5mt.lib) + else() + list(APPEND _IOMP5_LIB libiomp5md.lib) + endif() +endif() + +find_library(IOMP5_LIBRARY + NAMES ${_IOMP5_LIB} + PATHS ${_INTEL_LIBRARY_SEARCH_DIRS} + PATH_SUFFIXES ${_INTEL_LIBRARY_DIR_SUFFIXES} + DOC "Path to OpenMP runtime library" +) + +if (NOT IOMP5_LIBRARY) + # we could instead fallback to default library (via FindOpenMP.cmake) + list(APPEND _MKL_MISSING_LIBRARIES IOMP5) +else() + list(APPEND MKL_LIBRARIES ${IOMP5_LIBRARY}) + if (MKL_FIND_DEBUG) + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "Found IOMP5_LIBRARY: ${IOMP5_LIBRARY}") + endif() + + get_filename_component(_MKL_LIB_PATH "${IOMP5_LIBRARY}" PATH) + list(APPEND MKL_LIBRARY_DIRS ${_MKL_LIB_PATH}) +endif() + +# Optimized math library (optional) +set(_MATH_LIB imf) # linked by default with Intel compiler +if (WIN32) + if (MKL_USE_STATIC_LIBS) + list(APPEND _MATH_LIB libmmds.lib) # assumes (/MD) otherwise libmmt.lib (for /MT) + else() + list(APPEND _MATH_LIB libmmd.lib) + endif() +endif() + +find_library(MATH_LIBRARY + NAMES ${_MATH_LIB} + PATHS ${_INTEL_LIBRARY_SEARCH_DIRS} + PATH_SUFFIXES ${_INTEL_LIBRARY_DIR_SUFFIXES} + DOC "Path to optimized math library" +) + +if (NOT MATH_LIBRARY) + # we could instead fallback to default library (via FindOpenMP.cmake) + list(APPEND _MKL_MISSING_LIBRARIES MATH) +else() + list(APPEND MKL_LIBRARIES ${MATH_LIBRARY}) + if (MKL_FIND_DEBUG) + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "Found MATH_LIBRARY: ${MATH_LIBRARY}") + endif() + + get_filename_component(_MKL_LIB_PATH "${MATH_LIBRARY}" PATH) + list(APPEND MKL_LIBRARY_DIRS ${_MKL_LIB_PATH}) +endif() + +# Check all required libraries are available +list(REMOVE_DUPLICATES MKL_LIBRARY_DIRS) + +set(MKL_INCLUDE_DIRS + ${MKL_INCLUDE_DIR} +) + +set(MKL_FOUND TRUE) +if (NOT MKL_INCLUDE_DIR) + set(MKL_FOUND FALSE) + if (MKL_FIND_DEBUG) + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "MKL not found - MKL_INCLUDE_DIR was empty") + endif() +elseif (_MKL_MISSING_LIBRARIES) + set(MKL_FOUND FALSE) + if (MKL_FIND_DEBUG) + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "MKL not found - the following libraries are missing: " + "${_MKL_MISSING_LIBRARIES}") + endif() +endif() + +if (MKL_FOUND) + if (NOT MKL_FIND_QUIETLY OR MKL_FIND_DEBUG) + message(STATUS + "Intel(R) MKL was found:\n" + " MKL_INCLUDE_DIRS: ${MKL_INCLUDE_DIRS}\n" + " MKL_LIBRARY_DIRS: ${MKL_LIBRARY_DIRS}\n" + " MKL_LIBRARIES: ${MKL_LIBRARIES}" + ) + endif() +else() + if (MKL_FIND_REQUIRED) + message(SEND_ERROR "Intel(R) MKL could not be found.") + else() + message(STATUS "Intel(R) MKL could not be found.") + endif() +endif() + +mark_as_advanced( + MKL_INCLUDE_DIR + MKL_INCLUDE_DIRS + MKL_LIBRARY_DIRS +) diff --git a/cmake/TPLS/FindMKL.cmake b/cmake/TPLS/FindMKL.cmake new file mode 100644 index 0000000..b9329ef --- /dev/null +++ b/cmake/TPLS/FindMKL.cmake @@ -0,0 +1,340 @@ +# http://www.mail-archive.com/cmake@cmake.org/msg41869/FindMKL.cmake +# CMake script to detect Intel(R) Math Kernel Library (MKL) +# +# This will try to find Intel MKL libraries, and include path by automatic +# search through typical install locations and if failed it will +# examine MKLROOT environment variable. +# Note, MKLROOT is not set by IPP installer, it should be set manually. +# +# Usage example: +# set(MKL_USE_STATIC_LIBS ON) +# find_package(MKL) +# if (MKL_FOUND) +# include_directories(${MKL_INCLUDE_DIRS}) +# link_directories(${MKL_LIBRARY_DIRS}) +# add_executable(foo foo.cc) +# target_link_libraries(foo ${MKL_LIBRARIES}) +# endif() +# +# Variables used by this module, they can change the default behaviour and +# need to be set before calling find_package: +# +# MKL_ADDITIONAL_VERSIONS A list of version numbers to use for searching +# the MKL include directory. +# +# MKL_USE_STATIC_LIBS Can be set to ON to force the use of the static +# boost libraries. Defaults to OFF. +# +# MKL_FIND_DEBUG Set this to TRUE to enable debugging output +# of FindMKL.cmake if you are having problems. +# +# On return this will define: +# MKL_FOUND Indicates whether MKL was found (True/False) +# MKL_INCLUDE_DIRS MKL include folder +# MKL_LIBRARY_DIRS MKL libraries folder +# MKL_LIBRARIES MKL libraries names +# +# NOTE: this script has only been tested with Intel(R) Parallel Studio XE 2011 +# and may need changes for compatibility with older versions. +# +# Adapted from OpenCV IPP detection script +# https://code.ros.org/trac/opencv/browser/trunk/opencv/OpenCVFindIPP.cmake +# Many portions taken from FindBoost.cmake + +# TODO: +# - caller needs to link with libiomp5md.lib or /Qopenmp... +# - runtime DLLs: +# -> C:\Program Files\Intel\ComposerXE-2011 +# redist\ia32\mkl +# redist\intel64\mkl + +set(_MKL_IA32 FALSE) +set(_MKL_INTEL64 FALSE) +if (CMAKE_SIZEOF_VOID_P EQUAL 4) + set(_MKL_IA32 TRUE) +elseif (CMAKE_SIZEOF_VOID_P EQUAL 8) + set(_MKL_INTEL64 TRUE) +else() + message(FATAL_ERROR "Unsupported 'void *' size (${SIZEOF_VOID_P})") +endif() + +# Versions should be listed is decreasing order of preference +set(_MKL_TEST_VERSIONS ${MKL_ADDITIONAL_VERSIONS} + "2011" + # alternative form: "2011.xxx.y" + # (y is the release-update number and xxx is the package number) +) + +if (MKL_FIND_VERSION AND NOT MKL_FIND_QUIETLY) + message(WARNING "Requesting a specific version of Intel(R) MKL is not supported") +endif() + +# Use environment variables from Intel build scripts, if available +if (NOT MKL_ROOT AND NOT $ENV{MKLROOT} STREQUAL "") + set(MKL_ROOT $ENV{MKLROOT}) +endif() + +if (MKL_ROOT) + file(TO_CMAKE_PATH ${MKL_ROOT} MKL_ROOT) +endif() + +if (NOT INTEL_ROOT AND NOT $ENV{INTELROOT} STREQUAL "") + set(INTEL_ROOT $ENV{INTELROOT}) +endif() + +if (INTEL_ROOT) + file(TO_CMAKE_PATH ${INTEL_ROOT} INTEL_ROOT) +endif() + +if (MKL_FIND_DEBUG) + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "_MKL_TEST_VERSIONS = ${_MKL_TEST_VERSIONS}") + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "MKL_ADDITIONAL_VERSIONS = ${MKL_ADDITIONAL_VERSIONS}") + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "MKL_USE_STATIC_LIBS = ${MKL_USE_STATIC_LIBS}") + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "MKL_ROOT = ${MKL_ROOT}") + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "INTEL_ROOT = ${INTEL_ROOT}") +endif() + +# Find MKL include directory + +set(_MKL_ROOT_SEARCH_DIRS + ${MKL_ROOT} +) + +foreach (_MKL_VER ${_MKL_TEST_VERSIONS}) + if (WIN32) + list(APPEND _MKL_ROOT_SEARCH_DIRS "$ENV{ProgramFiles}/Intel/Composer XE/mkl") + else() + list(APPEND _MKL_ROOT_SEARCH_DIRS "/opt/intel/composerxe-${_MKL_VER}/mkl") + endif() +endforeach() + +if (MKL_FIND_DEBUG) + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "_MKL_ROOT_SEARCH_DIRS = ${_MKL_ROOT_SEARCH_DIRS}") +endif() + +find_path(MKL_INCLUDE_DIR + NAMES mkl.h + PATHS ${_MKL_ROOT_SEARCH_DIRS} + PATH_SUFFIXES include + DOC "The path to Intel(R) MKL header files" +) + +if (MKL_INCLUDE_DIR) + if (MKL_FIND_DEBUG) + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "location of mkl.h: ${MKL_INCLUDE_DIR}/mkl.h") + endif() +else() + if (MKL_FIND_DEBUG) + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "unable to find Intel(R) MKL header files. Please set MKLROOT" + " to the root directory containing MKL.") + endif() +endif() + +# Find MKL library directory + +set(_INTEL_LIBRARY_DIR_SUFFIXES "lib") +if (_MKL_IA32) + list(APPEND _INTEL_LIBRARY_DIR_SUFFIXES "lib/ia32") +elseif (_MKL_INTEL64) + list(APPEND _INTEL_LIBRARY_DIR_SUFFIXES "lib/intel64") +else() + message(FATAL_ERROR "unreachable") +endif() + +set(_MKL_LIBRARY_SEARCH_DIRS ${_MKL_ROOT_SEARCH_DIRS}) +if (MKL_INCLUDE_DIR) + list(APPEND _MKL_LIBRARY_SEARCH_DIRS "${MKL_INCLUDE_DIR}/..") +endif() + +if (MKL_FIND_DEBUG) + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "_INTEL_LIBRARY_DIR_SUFFIXES = ${_INTEL_LIBRARY_DIR_SUFFIXES}") + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "_MKL_LIBRARY_SEARCH_DIRS = ${_MKL_LIBRARY_SEARCH_DIRS}") +endif() + +set(MKL_LIB_PREFIX "mkl_") +if (MKL_USE_STATIC_LIBS) + if (_MKL_IA32) + if (WIN32) + set(_MKL_LIBRARIES intel_c) + else() + set(_MKL_LIBRARIES intel) + endif() + elseif (_MKL_INTEL64) + set(_MKL_LIBRARIES intel_lp64) + else() + message(FATAL_ERROR "unreachable") + endif() + + list(APPEND _MKL_LIBRARIES intel_thread) + list(APPEND _MKL_LIBRARIES core) +else() + set(_MKL_LIBRARIES rt) +endif() + +set(_MKL_MISSING_LIBRARIES "") +set(MKL_LIBRARIES "") +set(MKL_LIBRARY_DIRS "") +# Find MKL libraries +foreach (_MKL_LIB_RAW ${_MKL_LIBRARIES}) + set(_MKL_LIB ${MKL_LIB_PREFIX}${_MKL_LIB_RAW}) + string(TOUPPER ${_MKL_LIB} _MKL_LIB_UPPER) + + find_library(${_MKL_LIB_UPPER}_LIBRARY + NAMES ${_MKL_LIB} + PATHS ${_MKL_LIBRARY_SEARCH_DIRS} + PATH_SUFFIXES ${_INTEL_LIBRARY_DIR_SUFFIXES} + DOC "The path to Intel(R) MKL ${_MKL_LIB_RAW} library" + ) + mark_as_advanced(${_MKL_LIB_UPPER}_LIBRARY) + + if (NOT ${_MKL_LIB_UPPER}_LIBRARY) + list(APPEND _MKL_MISSING_LIBRARIES ${_MKL_LIB}) + else() + list(APPEND MKL_LIBRARIES ${${_MKL_LIB_UPPER}_LIBRARY}) + if (MKL_FIND_DEBUG) + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "Found ${_MKL_LIB}: ${${_MKL_LIB_UPPER}_LIBRARY}") + endif() + + get_filename_component(_MKL_LIB_PATH "${${_MKL_LIB_UPPER}_LIBRARY}" PATH) + list(APPEND MKL_LIBRARY_DIRS ${_MKL_LIB_PATH}) + endif() +endforeach() + +## Find OpenMP, pthread and math libraries + +set(_INTEL_LIBRARY_SEARCH_DIRS + ${INTEL_ROOT} + ${INTEL_ROOT}/compiler +) + +foreach(_MKL_DIR ${_MKL_ROOT_SEARCH_DIRS}) + list(APPEND _INTEL_LIBRARY_SEARCH_DIRS "${_MKL_DIR}/..") + list(APPEND _INTEL_LIBRARY_SEARCH_DIRS "${_MKL_DIR}/../compiler") +endforeach() + +if (MKL_FIND_DEBUG) + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "_INTEL_LIBRARY_SEARCH_DIRS = ${_INTEL_LIBRARY_SEARCH_DIRS}") +endif() + +if (NOT WIN32) + find_library(PTHREAD_LIBRARY pthread DOC "Path to POSIX threads library") +endif() + +set(_IOMP5_LIB iomp5) +if (WIN32) + if (MKL_USE_STATIC_LIBS) + list(APPEND _IOMP5_LIB libiomp5mt.lib) + else() + list(APPEND _IOMP5_LIB libiomp5md.lib) + endif() +endif() + +find_library(IOMP5_LIBRARY + NAMES ${_IOMP5_LIB} + PATHS ${_INTEL_LIBRARY_SEARCH_DIRS} + PATH_SUFFIXES ${_INTEL_LIBRARY_DIR_SUFFIXES} + DOC "Path to OpenMP runtime library" +) + +if (NOT IOMP5_LIBRARY) + # we could instead fallback to default library (via FindOpenMP.cmake) + list(APPEND _MKL_MISSING_LIBRARIES IOMP5) +else() + list(APPEND MKL_LIBRARIES ${IOMP5_LIBRARY}) + if (MKL_FIND_DEBUG) + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "Found IOMP5_LIBRARY: ${IOMP5_LIBRARY}") + endif() + + get_filename_component(_MKL_LIB_PATH "${IOMP5_LIBRARY}" PATH) + list(APPEND MKL_LIBRARY_DIRS ${_MKL_LIB_PATH}) +endif() + +# Optimized math library (optional) +set(_MATH_LIB imf) # linked by default with Intel compiler +if (WIN32) + if (MKL_USE_STATIC_LIBS) + list(APPEND _MATH_LIB libmmds.lib) # assumes (/MD) otherwise libmmt.lib (for /MT) + else() + list(APPEND _MATH_LIB libmmd.lib) + endif() +endif() + +find_library(MATH_LIBRARY + NAMES ${_MATH_LIB} + PATHS ${_INTEL_LIBRARY_SEARCH_DIRS} + PATH_SUFFIXES ${_INTEL_LIBRARY_DIR_SUFFIXES} + DOC "Path to optimized math library" +) + +if (NOT MATH_LIBRARY) + # we could instead fallback to default library (via FindOpenMP.cmake) + list(APPEND _MKL_MISSING_LIBRARIES MATH) +else() + list(APPEND MKL_LIBRARIES ${MATH_LIBRARY}) + if (MKL_FIND_DEBUG) + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "Found MATH_LIBRARY: ${MATH_LIBRARY}") + endif() + + get_filename_component(_MKL_LIB_PATH "${MATH_LIBRARY}" PATH) + list(APPEND MKL_LIBRARY_DIRS ${_MKL_LIB_PATH}) +endif() + +# Check all required libraries are available +list(REMOVE_DUPLICATES MKL_LIBRARY_DIRS) + +set(MKL_INCLUDE_DIRS + ${MKL_INCLUDE_DIR} +) + +set(MKL_FOUND TRUE) +if (NOT MKL_INCLUDE_DIR) + set(MKL_FOUND FALSE) + if (MKL_FIND_DEBUG) + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "MKL not found - MKL_INCLUDE_DIR was empty") + endif() +elseif (_MKL_MISSING_LIBRARIES) + set(MKL_FOUND FALSE) + if (MKL_FIND_DEBUG) + message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " + "MKL not found - the following libraries are missing: " + "${_MKL_MISSING_LIBRARIES}") + endif() +endif() + +if (MKL_FOUND) + if (NOT MKL_FIND_QUIETLY OR MKL_FIND_DEBUG) + message(STATUS + "Intel(R) MKL was found:\n" + " MKL_INCLUDE_DIRS: ${MKL_INCLUDE_DIRS}\n" + " MKL_LIBRARY_DIRS: ${MKL_LIBRARY_DIRS}\n" + " MKL_LIBRARIES: ${MKL_LIBRARIES}" + ) + endif() +else() + if (MKL_FIND_REQUIRED) + message(SEND_ERROR "Intel(R) MKL could not be found.") + else() + message(STATUS "Intel(R) MKL could not be found.") + endif() +endif() + +mark_as_advanced( + MKL_INCLUDE_DIR + MKL_INCLUDE_DIRS + MKL_LIBRARY_DIRS +) diff --git a/cmake/tribits b/cmake/tribits new file mode 120000 index 0000000..4c1134a --- /dev/null +++ b/cmake/tribits @@ -0,0 +1 @@ +../TriBITS/tribits \ No newline at end of file diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt new file mode 100644 index 0000000..8766975 --- /dev/null +++ b/docs/CMakeLists.txt @@ -0,0 +1,13 @@ +################################################################################ +# Documentation Generation +# +# Build documentation using Doxygen (www.doxygen.org) +# Builds the docs in the docs/ directory (HTML and LaTeX formats for a .pdf) +################################################################################ +find_package(Doxygen) +if(DOXYGEN_FOUND) + configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY) + add_custom_target(doc ALL ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMENT "Generating API documentation with Doxygen" VERBATIM +) +endif(DOXYGEN_FOUND) diff --git a/docs/Doxyfile.in b/docs/Doxyfile.in new file mode 100644 index 0000000..f23c65e --- /dev/null +++ b/docs/Doxyfile.in @@ -0,0 +1,1527 @@ +# Doxyfile 1.6.1 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project +# +# All text after a hash (#) is considered a comment and will be ignored +# The format is: +# TAG = value [value, ...] +# For lists items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (" ") + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all +# text before the first occurrence of this tag. Doxygen uses libiconv (or the +# iconv built into libc) for the transcoding. See +# http://www.gnu.org/software/libiconv for the list of possible encodings. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded +# by quotes) that should identify the project. + +PROJECT_NAME = #"@PROJECT_NAME@" + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. +# This could be handy for archiving the generated documentation or +# if some version control system is used. + +PROJECT_NUMBER = "@PROJECT_VERSION_MAJOR@.@PROJECT_VERSION_MINOR@" + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) +# base path where the generated documentation will be put. +# If a relative path is entered, it will be relative to the location +# where doxygen was started. If left blank the current directory will be used. + +OUTPUT_DIRECTORY = @CMAKE_CURRENT_BINARY_DIR@/doc + +# Project logo that appears on front page +PROJECT_LOGO = @CMAKE_CURRENT_SOURCE_DIR@/assets/project_logo.png + + +# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create +# 4096 sub-directories (in 2 levels) under the output directory of each output +# format and will distribute the generated files over these directories. +# Enabling this option can be useful when feeding doxygen a huge amount of +# source files, where putting all generated files in the same directory would +# otherwise cause performance problems for the file system. + +CREATE_SUBDIRS = NO + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# The default language is English, other supported languages are: +# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, +# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German, +# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English +# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, +# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrilic, Slovak, +# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese. + +OUTPUT_LANGUAGE = English + +# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will +# include brief member descriptions after the members that are listed in +# the file and class documentation (similar to JavaDoc). +# Set to NO to disable this. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend +# the brief description of a member or function before the detailed description. +# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator +# that is used to form the text in various listings. Each string +# in this list, if found as the leading text of the brief description, will be +# stripped from the text and the result after processing the whole list, is +# used as the annotated text. Otherwise, the brief description is used as-is. +# If left blank, the following values are used ("$name" is automatically +# replaced with the name of the entity): "The $name class" "The $name widget" +# "The $name file" "is" "provides" "specifies" "contains" +# "represents" "a" "an" "the" + +ABBREVIATE_BRIEF = + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# Doxygen will generate a detailed section even if there is only a brief +# description. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full +# path before files name in the file list and in the header files. If set +# to NO the shortest path that makes the file name unique will be used. + +FULL_PATH_NAMES = YES + +# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag +# can be used to strip a user-defined part of the path. Stripping is +# only done if one of the specified strings matches the left-hand part of +# the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the +# path to strip. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of +# the path mentioned in the documentation of a class, which tells +# the reader which header file to include in order to use a class. +# If left blank only the name of the header file containing the class +# definition is used. Otherwise one should specify the include paths that +# are normally passed to the compiler using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter +# (but less readable) file names. This can be useful is your file systems +# doesn't support long names like on DOS, Mac, or CD-ROM. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen +# will interpret the first line (until the first dot) of a JavaDoc-style +# comment as the brief description. If set to NO, the JavaDoc +# comments will behave just like regular Qt-style comments +# (thus requiring an explicit @brief command for a brief description.) + +JAVADOC_AUTOBRIEF = NO + +# If the QT_AUTOBRIEF tag is set to YES then Doxygen will +# interpret the first line (until the first dot) of a Qt-style +# comment as the brief description. If set to NO, the comments +# will behave just like regular Qt-style comments (thus requiring +# an explicit \brief command for a brief description.) + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen +# treat a multi-line C++ special comment block (i.e. a block of //! or /// +# comments) as a brief description. This used to be the default behaviour. +# The new default is to treat a multi-line C++ comment block as a detailed +# description. Set this tag to YES if you prefer the old behaviour instead. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented +# member inherits the documentation from any documented member that it +# re-implements. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce +# a new page for each member. If set to NO, the documentation of a member will +# be part of the file/class/namespace that contains it. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. +# Doxygen uses this value to replace tabs by spaces in code fragments. + +TAB_SIZE = 8 + +# This tag can be used to specify a number of aliases that acts +# as commands in the documentation. An alias has the form "name=value". +# For example adding "sideeffect=\par Side Effects:\n" will allow you to +# put the command \sideeffect (or @sideeffect) in the documentation, which +# will result in a user-defined paragraph with heading "Side Effects:". +# You can put \n's in the value part of an alias to insert newlines. + +ALIASES = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C +# sources only. Doxygen will then generate output that is more tailored for C. +# For instance, some of the names that are used will be different. The list +# of all members will be omitted, etc. + +OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java +# sources only. Doxygen will then generate output that is more tailored for +# Java. For instance, namespaces will be presented as packages, qualified +# scopes will look different, etc. + +OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources only. Doxygen will then generate output that is more tailored for +# Fortran. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for +# VHDL. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Doxygen selects the parser to use depending on the extension of the files it parses. +# With this tag you can assign which parser to use for a given extension. +# Doxygen has a built-in mapping, but you can override or extend it using this tag. +# The format is ext=language, where ext is a file extension, and language is one of +# the parsers supported by doxygen: IDL, Java, Javascript, C#, C, C++, D, PHP, +# Objective-C, Python, Fortran, VHDL, C, C++. For instance to make doxygen treat +# .inc files as Fortran files (default is PHP), and .f files as C (default is Fortran), +# use: inc=Fortran f=C. Note that for custom extensions you also need to set FILE_PATTERNS otherwise the files are not read by doxygen. + +EXTENSION_MAPPING = + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should +# set this tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. +# func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. + +BUILTIN_STL_SUPPORT = NO + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. +# Doxygen will parse them like normal C++ but will assume all classes use public +# instead of private inheritance when no explicit protection keyword is present. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate getter +# and setter methods for a property. Setting this option to YES (the default) +# will make doxygen to replace the get and set methods by a property in the +# documentation. This will only work if the methods are indeed getting or +# setting a simple type. If this is not the case, or you want to show the +# methods anyway, you should set this option to NO. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES, then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. + +DISTRIBUTE_GROUP_DOC = NO + +# Set the SUBGROUPING tag to YES (the default) to allow class member groups of +# the same type (for instance a group of public functions) to be put as a +# subgroup of that type (e.g. under the Public Functions section). Set it to +# NO to prevent subgrouping. Alternatively, this can be done per class using +# the \nosubgrouping command. + +SUBGROUPING = YES + +# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum +# is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically +# be useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. + +TYPEDEF_HIDES_STRUCT = NO + +# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to +# determine which symbols to keep in memory and which to flush to disk. +# When the cache is full, less often used symbols will be written to disk. +# For small to medium size projects (<1000 input files) the default value is +# probably good enough. For larger projects a too small cache size can cause +# doxygen to be busy swapping symbols to and from disk most of the time +# causing a significant performance penality. +# If the system has enough physical memory increasing the cache will improve the +# performance by keeping more symbols in memory. Note that the value works on +# a logarithmic scale so increasing the size by one will rougly double the +# memory usage. The cache size is given by this formula: +# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0, +# corresponding to a cache size of 2^16 = 65536 symbols + +SYMBOL_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in +# documentation are documented, even if no documentation was available. +# Private class members and static file members will be hidden unless +# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES + +EXTRACT_ALL = YES + +# If the EXTRACT_PRIVATE tag is set to YES all private members of a class +# will be included in the documentation. + +EXTRACT_PRIVATE = YES + +# If the EXTRACT_STATIC tag is set to YES all static members of a file +# will be included in the documentation. + +EXTRACT_STATIC = NO + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) +# defined locally in source files will be included in the documentation. +# If set to NO only classes defined in header files are included. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. When set to YES local +# methods, which are defined in the implementation section but not in +# the interface are included in the documentation. +# If set to NO (the default) only methods in the interface are included. + +EXTRACT_LOCAL_METHODS = NO + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base +# name of the file that contains the anonymous namespace. By default +# anonymous namespace are hidden. + +EXTRACT_ANON_NSPACES = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all +# undocumented members of documented classes, files or namespaces. +# If set to NO (the default) these members will be included in the +# various overviews, but no documentation section is generated. +# This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. +# If set to NO (the default) these classes will be included in the various +# overviews. This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all +# friend (class|struct|union) declarations. +# If set to NO (the default) these declarations will be included in the +# documentation. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any +# documentation blocks found inside the body of a function. +# If set to NO (the default) these blocks will be appended to the +# function's detailed documentation block. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation +# that is typed after a \internal command is included. If the tag is set +# to NO (the default) then the documentation will be excluded. +# Set it to YES to include the internal documentation. + +INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate +# file names in lower-case letters. If set to YES upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. + +CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen +# will show members with their full class and namespace scopes in the +# documentation. If set to YES the scope will be hidden. + +HIDE_SCOPE_NAMES = NO + +# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen +# will put a list of the files that are included by a file in the documentation +# of that file. + +SHOW_INCLUDE_FILES = YES + +# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] +# is inserted in the documentation for inline members. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen +# will sort the (detailed) documentation of file and class members +# alphabetically by member name. If set to NO the members will appear in +# declaration order. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the +# brief documentation of file, namespace and class members alphabetically +# by member name. If set to NO (the default) the members will appear in +# declaration order. + +SORT_BRIEF_DOCS = NO + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the (brief and detailed) documentation of class members so that constructors and destructors are listed first. If set to NO (the default) the constructors will appear in the respective orders defined by SORT_MEMBER_DOCS and SORT_BRIEF_DOCS. This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the +# hierarchy of group names into alphabetical order. If set to NO (the default) +# the group names will appear in their defined order. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be +# sorted by fully-qualified names, including namespaces. If set to +# NO (the default), the class list will be sorted only by class name, +# not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the +# alphabetical list. + +SORT_BY_SCOPE_NAME = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or +# disable (NO) the todo list. This list is created by putting \todo +# commands in the documentation. + +GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or +# disable (NO) the test list. This list is created by putting \test +# commands in the documentation. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or +# disable (NO) the bug list. This list is created by putting \bug +# commands in the documentation. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or +# disable (NO) the deprecated list. This list is created by putting +# \deprecated commands in the documentation. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional +# documentation sections, marked by \if sectionname ... \endif. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines +# the initial value of a variable or define consists of for it to appear in +# the documentation. If the initializer consists of more lines than specified +# here it will be hidden. Use a value of 0 to hide initializers completely. +# The appearance of the initializer of individual variables and defines in the +# documentation can be controlled using \showinitializer or \hideinitializer +# command in the documentation regardless of this setting. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated +# at the bottom of the documentation of classes and structs. If set to YES the +# list will mention the files that were used to generate the documentation. + +SHOW_USED_FILES = YES + +# If the sources in your project are distributed over multiple directories +# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy +# in the documentation. The default is NO. + +SHOW_DIRECTORIES = NO + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. +# This will remove the Files entry from the Quick Index and from the +# Folder Tree View (if specified). The default is YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the +# Namespaces page. +# This will remove the Namespaces entry from the Quick Index +# and from the Folder Tree View (if specified). The default is YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command , where is the value of +# the FILE_VERSION_FILTER tag, and is the name of an input file +# provided by doxygen. Whatever the program writes to standard output +# is used as the file version. See the manual for examples. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed by +# doxygen. The layout file controls the global structure of the generated output files +# in an output format independent way. The create the layout file that represents +# doxygen's defaults, run doxygen with the -l option. You can optionally specify a +# file name after the option, if omitted DoxygenLayout.xml will be used as the name +# of the layout file. + +LAYOUT_FILE = + +#--------------------------------------------------------------------------- +# configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated +# by doxygen. Possible values are YES and NO. If left blank NO is used. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated by doxygen. Possible values are YES and NO. If left blank +# NO is used. + +WARNINGS = YES + +# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings +# for undocumented members. If EXTRACT_ALL is set to YES then this flag will +# automatically be disabled. + +WARN_IF_UNDOCUMENTED = YES + +# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some +# parameters in a documented function, or documenting parameters that +# don't exist or using markup commands wrongly. + +WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be abled to get warnings for +# functions that are documented, but have no documentation for their parameters +# or return value. If set to NO (the default) doxygen will only warn about +# wrong or incomplete parameter documentation, but not about the absence of +# documentation. + +WARN_NO_PARAMDOC = NO + +# The WARN_FORMAT tag determines the format of the warning messages that +# doxygen can produce. The string should contain the $file, $line, and $text +# tags, which will be replaced by the file and line number from which the +# warning originated and the warning text. Optionally the format may contain +# $version, which will be replaced by the version of the file (if it could +# be obtained via FILE_VERSION_FILTER) + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning +# and error messages should be written. If left blank the output is written +# to stderr. + +WARN_LOGFILE = + +#--------------------------------------------------------------------------- +# configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag can be used to specify the files and/or directories that contain +# documented source files. You may enter file names like "myfile.cpp" or +# directories like "/usr/src/myproject". Separate the files or directories +# with spaces. + +INPUT = @CMAKE_CURRENT_SOURCE_DIR@/../GSM/ + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is +# also the default input encoding. Doxygen uses libiconv (or the iconv built +# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for +# the list of possible encodings. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank the following patterns are tested: +# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx +# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90 + +FILE_PATTERNS = *.cpp *.h *.h.in + +# The RECURSIVE tag can be used to turn specify whether or not subdirectories +# should be searched for input files as well. Possible values are YES and NO. +# If left blank NO is used. + +RECURSIVE = NO + +# The EXCLUDE tag can be used to specify files and/or directories that should +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. + +EXCLUDE = + +# The EXCLUDE_SYMLINKS tag can be used select whether or not files or +# directories that are symbolic links (a Unix filesystem feature) are excluded +# from the input. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. Note that the wildcards are matched +# against the file with absolute path, so to exclude all test directories +# for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or +# directories that contain example code fragments that are included (see +# the \include command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank all files are included. + +EXAMPLE_PATTERNS = + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude +# commands irrespective of the value of the RECURSIVE tag. +# Possible values are YES and NO. If left blank NO is used. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or +# directories that contain image that are included in the documentation (see +# the \image command). + +IMAGE_PATH = @CMAKE_CURRENT_SOURCE_DIR@/assets + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command , where +# is the value of the INPUT_FILTER tag, and is the name of an +# input file. Doxygen will then use the output that the filter program writes +# to standard output. +# If FILTER_PATTERNS is specified, this tag will be +# ignored. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. +# Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. +# The filters are a list of the form: +# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further +# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER +# is applied to all files. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will be used to filter the input files when producing source +# files to browse (i.e. when SOURCE_BROWSER is set to YES). + +FILTER_SOURCE_FILES = NO + +#--------------------------------------------------------------------------- +# configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will +# be generated. Documented entities will be cross-referenced with these sources. +# Note: To get rid of all source code in the generated output, make sure also +# VERBATIM_HEADERS is set to NO. + +SOURCE_BROWSER = NO + +# Setting the INLINE_SOURCES tag to YES will include the body +# of functions and classes directly in the documentation. + +INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct +# doxygen to hide any special comment blocks from generated source code +# fragments. Normal C and C++ comments will always remain visible. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES +# then for each documented function all documented +# functions referencing it will be listed. + +REFERENCED_BY_RELATION = NO + +# If the REFERENCES_RELATION tag is set to YES +# then for each documented function all documented entities +# called/used by that function will be listed. + +REFERENCES_RELATION = NO + +# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) +# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from +# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will +# link to the source code. +# Otherwise they will link to the documentation. + +REFERENCES_LINK_SOURCE = YES + +# If the USE_HTAGS tag is set to YES then the references to source code +# will point to the HTML generated by the htags(1) tool instead of doxygen +# built-in source browser. The htags tool is part of GNU's global source +# tagging system (see http://www.gnu.org/software/global/global.html). You +# will need version 4.8.6 or higher. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen +# will generate a verbatim copy of the header file for each class for +# which an include is specified. Set to NO to disable this. + +VERBATIM_HEADERS = YES + +#--------------------------------------------------------------------------- +# configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index +# of all compounds will be generated. Enable this if the project +# contains a lot of classes, structs, unions or interfaces. + +ALPHABETICAL_INDEX = NO + +# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then +# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns +# in which this list will be split (can be a number in the range [1..20]) + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all +# classes will be put under the same header in the alphabetical index. +# The IGNORE_PREFIX tag can be used to specify one or more prefixes that +# should be ignored while generating the index headers. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES (the default) Doxygen will +# generate HTML output. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `html' will be used as the default path. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for +# each generated HTML page (for example: .htm,.php,.asp). If it is left blank +# doxygen will generate files with .html extension. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a personal HTML header for +# each generated HTML page. If it is left blank doxygen will generate a +# standard header. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a personal HTML footer for +# each generated HTML page. If it is left blank doxygen will generate a +# standard footer. + +HTML_FOOTER = + +# If the HTML_TIMESTAMP tag is set to YES then the generated HTML +# documentation will contain the timesstamp. + +HTML_TIMESTAMP = NO + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading +# style sheet that is used by each HTML page. It can be used to +# fine-tune the look of the HTML output. If the tag is left blank doxygen +# will generate a default style sheet. Note that doxygen will try to copy +# the style sheet file to the HTML output directory, so don't put your own +# stylesheet in the HTML output directory as well, or it will be erased! + +HTML_STYLESHEET = + +# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, +# files or namespaces will be aligned in HTML using tables. If set to +# NO a bullet list will be used. + +HTML_ALIGN_MEMBERS = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. For this to work a browser that supports +# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox +# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari). + +HTML_DYNAMIC_SECTIONS = NO + +# If the GENERATE_DOCSET tag is set to YES, additional index files +# will be generated that can be used as input for Apple's Xcode 3 +# integrated development environment, introduced with OSX 10.5 (Leopard). +# To create a documentation set, doxygen will generate a Makefile in the +# HTML output directory. Running make will produce the docset in that +# directory and running "make install" will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find +# it at startup. +# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html for more information. + +GENERATE_DOCSET = NO + +# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the +# feed. A documentation feed provides an umbrella under which multiple +# documentation sets from a single provider (such as a company or product suite) +# can be grouped. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that +# should uniquely identify the documentation set bundle. This should be a +# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen +# will append .docset to the name. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# If the GENERATE_HTMLHELP tag is set to YES, additional index files +# will be generated that can be used as input for tools like the +# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) +# of the generated HTML documentation. + +GENERATE_HTMLHELP = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can +# be used to specify the file name of the resulting .chm file. You +# can add a path in front of the file if the result should not be +# written to the html output directory. + +CHM_FILE = + +# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can +# be used to specify the location (absolute path including file name) of +# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run +# the HTML help compiler on the generated index.hhp. + +HHC_LOCATION = + +# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag +# controls if a separate .chi index file is generated (YES) or that +# it should be included in the master .chm file (NO). + +GENERATE_CHI = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING +# is used to encode HtmlHelp index (hhk), content (hhc) and project file +# content. + +CHM_INDEX_ENCODING = + +# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag +# controls whether a binary table of contents is generated (YES) or a +# normal table of contents (NO) in the .chm file. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members +# to the contents of the HTML help documentation and to the tree view. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and QHP_VIRTUAL_FOLDER +# are set, an additional index file will be generated that can be used as input for +# Qt's qhelpgenerator to generate a Qt Compressed Help (.qch) of the generated +# HTML documentation. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can +# be used to specify the file name of the resulting .qch file. +# The path specified is relative to the HTML output folder. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#namespace + +QHP_NAMESPACE = + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#virtual-folders + +QHP_VIRTUAL_FOLDER = doc + +# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to add. +# For more information please see +# http://doc.trolltech.com/qthelpproject.html#custom-filters + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the custom filter to add.For more information please see +# Qt Help Project / Custom Filters. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this project's +# filter section matches. +# Qt Help Project / Filter Attributes. + +QHP_SECT_FILTER_ATTRS = + +# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can +# be used to specify the location of Qt's qhelpgenerator. +# If non-empty doxygen will try to run qhelpgenerator on the generated +# .qhp file. + +QHG_LOCATION = + +# The DISABLE_INDEX tag can be used to turn on/off the condensed index at +# top of each HTML page. The value NO (the default) enables the index and +# the value YES disables it. + +DISABLE_INDEX = NO + +# This tag can be used to set the number of enum values (range [1..20]) +# that doxygen will group on one line in the generated HTML documentation. + +ENUM_VALUES_PER_LINE = 4 + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. +# If the tag value is set to YES, a side panel will be generated +# containing a tree-like index structure (just like the one that +# is generated for HTML Help). For this to work a browser that supports +# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser). +# Windows users are probably better off using the HTML help feature. + +GENERATE_TREEVIEW = NO + +# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories, +# and Class Hierarchy pages using a tree view instead of an ordered list. + +USE_INLINE_TREES = NO + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be +# used to set the initial width (in pixels) of the frame in which the tree +# is shown. + +TREEVIEW_WIDTH = 250 + +# Use this tag to change the font size of Latex formulas included +# as images in the HTML documentation. The default is 10. Note that +# when you change the font size after a successful doxygen run you need +# to manually remove any form_*.png images from the HTML output directory +# to force them to be regenerated. + +FORMULA_FONTSIZE = 10 + +# When the SEARCHENGINE tag is enable doxygen will generate a search box for the HTML output. The underlying search engine uses javascript +# and DHTML and should work on any modern browser. Note that when using HTML help (GENERATE_HTMLHELP) or Qt help (GENERATE_QHP) +# there is already a search function so this one should typically +# be disabled. + +SEARCHENGINE = YES + +#--------------------------------------------------------------------------- +# configuration options related to the LaTeX output +#--------------------------------------------------------------------------- + +# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will +# generate Latex output. + +GENERATE_LATEX = NO + +# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `latex' will be used as the default path. + +LATEX_OUTPUT = latex + +# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be +# invoked. If left blank `latex' will be used as the default command name. + +LATEX_CMD_NAME = latex + +# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to +# generate index for LaTeX. If left blank `makeindex' will be used as the +# default command name. + +MAKEINDEX_CMD_NAME = makeindex + +# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact +# LaTeX documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_LATEX = NO + +# The PAPER_TYPE tag can be used to set the paper type that is used +# by the printer. Possible values are: a4, a4wide, letter, legal and +# executive. If left blank a4wide will be used. + +PAPER_TYPE = a4wide + +# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX +# packages that should be included in the LaTeX output. + +EXTRA_PACKAGES = + +# The LATEX_HEADER tag can be used to specify a personal LaTeX header for +# the generated latex document. The header should contain everything until +# the first chapter. If it is left blank doxygen will generate a +# standard header. Notice: only use this tag if you know what you are doing! + +LATEX_HEADER = + +# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated +# is prepared for conversion to pdf (using ps2pdf). The pdf file will +# contain links (just like the HTML output) instead of page references +# This makes the output suitable for online browsing using a pdf viewer. + +PDF_HYPERLINKS = YES + +# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of +# plain latex in the generated Makefile. Set this option to YES to get a +# higher quality PDF documentation. + +USE_PDFLATEX = YES + +# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. +# command to the generated LaTeX files. This will instruct LaTeX to keep +# running if errors occur, instead of asking the user for help. +# This option is also used when generating formulas in HTML. + +LATEX_BATCHMODE = NO + +# If LATEX_HIDE_INDICES is set to YES then doxygen will not +# include the index chapters (such as File Index, Compound Index, etc.) +# in the output. + +LATEX_HIDE_INDICES = NO + +# If LATEX_SOURCE_CODE is set to YES then doxygen will include source code with syntax highlighting in the LaTeX output. Note that which sources are shown also depends on other settings such as SOURCE_BROWSER. + +LATEX_SOURCE_CODE = NO + +#--------------------------------------------------------------------------- +# configuration options related to the RTF output +#--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output +# The RTF output is optimized for Word 97 and may not look very pretty with +# other RTF readers or editors. + +GENERATE_RTF = NO + +# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `rtf' will be used as the default path. + +RTF_OUTPUT = rtf + +# If the COMPACT_RTF tag is set to YES Doxygen generates more compact +# RTF documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_RTF = NO + +# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated +# will contain hyperlink fields. The RTF file will +# contain links (just like the HTML output) instead of page references. +# This makes the output suitable for online browsing using WORD or other +# programs which support those fields. +# Note: wordpad (write) and others do not support links. + +RTF_HYPERLINKS = NO + +# Load stylesheet definitions from file. Syntax is similar to doxygen's +# config file, i.e. a series of assignments. You only have to provide +# replacements, missing definitions are set to their default value. + +RTF_STYLESHEET_FILE = + +# Set optional variables used in the generation of an rtf document. +# Syntax is similar to doxygen's config file. + +RTF_EXTENSIONS_FILE = + +#--------------------------------------------------------------------------- +# configuration options related to the man page output +#--------------------------------------------------------------------------- + +# If the GENERATE_MAN tag is set to YES (the default) Doxygen will +# generate man pages + +GENERATE_MAN = NO + +# The MAN_OUTPUT tag is used to specify where the man pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `man' will be used as the default path. + +MAN_OUTPUT = man + +# The MAN_EXTENSION tag determines the extension that is added to +# the generated man pages (default is the subroutine's section .3) + +MAN_EXTENSION = .3 + +# If the MAN_LINKS tag is set to YES and Doxygen generates man output, +# then it will generate one additional man file for each entity +# documented in the real man page(s). These additional files +# only source the real man page, but without them the man command +# would be unable to find the correct page. The default is NO. + +MAN_LINKS = NO + +#--------------------------------------------------------------------------- +# configuration options related to the XML output +#--------------------------------------------------------------------------- + +# If the GENERATE_XML tag is set to YES Doxygen will +# generate an XML file that captures the structure of +# the code including all documentation. + +GENERATE_XML = NO + +# The XML_OUTPUT tag is used to specify where the XML pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `xml' will be used as the default path. + +XML_OUTPUT = xml + +# The XML_SCHEMA tag can be used to specify an XML schema, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_SCHEMA = + +# The XML_DTD tag can be used to specify an XML DTD, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_DTD = + +# If the XML_PROGRAMLISTING tag is set to YES Doxygen will +# dump the program listings (including syntax highlighting +# and cross-referencing information) to the XML output. Note that +# enabling this will significantly increase the size of the XML output. + +XML_PROGRAMLISTING = YES + +#--------------------------------------------------------------------------- +# configuration options for the AutoGen Definitions output +#--------------------------------------------------------------------------- + +# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will +# generate an AutoGen Definitions (see autogen.sf.net) file +# that captures the structure of the code including all +# documentation. Note that this feature is still experimental +# and incomplete at the moment. + +GENERATE_AUTOGEN_DEF = NO + +#--------------------------------------------------------------------------- +# configuration options related to the Perl module output +#--------------------------------------------------------------------------- + +# If the GENERATE_PERLMOD tag is set to YES Doxygen will +# generate a Perl module file that captures the structure of +# the code including all documentation. Note that this +# feature is still experimental and incomplete at the +# moment. + +GENERATE_PERLMOD = NO + +# If the PERLMOD_LATEX tag is set to YES Doxygen will generate +# the necessary Makefile rules, Perl scripts and LaTeX code to be able +# to generate PDF and DVI output from the Perl module output. + +PERLMOD_LATEX = NO + +# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be +# nicely formatted so it can be parsed by a human reader. +# This is useful +# if you want to understand what is going on. +# On the other hand, if this +# tag is set to NO the size of the Perl module output will be much smaller +# and Perl will parse it just the same. + +PERLMOD_PRETTY = YES + +# The names of the make variables in the generated doxyrules.make file +# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. +# This is useful so different doxyrules.make files included by the same +# Makefile don't overwrite each other's variables. + +PERLMOD_MAKEVAR_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the preprocessor +#--------------------------------------------------------------------------- + +# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will +# evaluate all C-preprocessor directives found in the sources and include +# files. + +ENABLE_PREPROCESSING = YES + +# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro +# names in the source code. If set to NO (the default) only conditional +# compilation will be performed. Macro expansion can be done in a controlled +# way by setting EXPAND_ONLY_PREDEF to YES. + +MACRO_EXPANSION = NO + +# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES +# then the macro expansion is limited to the macros specified with the +# PREDEFINED and EXPAND_AS_DEFINED tags. + +EXPAND_ONLY_PREDEF = NO + +# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files +# in the INCLUDE_PATH (see below) will be search if a #include is found. + +SEARCH_INCLUDES = YES + +# The INCLUDE_PATH tag can be used to specify one or more directories that +# contain include files that are not input files but should be processed by +# the preprocessor. + +INCLUDE_PATH = + +# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard +# patterns (like *.h and *.hpp) to filter out the header-files in the +# directories. If left blank, the patterns specified with FILE_PATTERNS will +# be used. + +INCLUDE_FILE_PATTERNS = + +# The PREDEFINED tag can be used to specify one or more macro names that +# are defined before the preprocessor is started (similar to the -D option of +# gcc). The argument of the tag is a list of macros of the form: name +# or name=definition (no spaces). If the definition and the = are +# omitted =1 is assumed. To prevent a macro definition from being +# undefined via #undef or recursively expanded use the := operator +# instead of the = operator. + +PREDEFINED = + +# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then +# this tag can be used to specify a list of macro names that should be expanded. +# The macro definition that is found in the sources will be used. +# Use the PREDEFINED tag if you want to use a different macro definition. + +EXPAND_AS_DEFINED = + +# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then +# doxygen's preprocessor will remove all function-like macros that are alone +# on a line, have an all uppercase name, and do not end with a semicolon. Such +# function macros are typically used for boiler-plate code, and will confuse +# the parser if not removed. + +SKIP_FUNCTION_MACROS = YES + +#--------------------------------------------------------------------------- +# Configuration::additions related to external references +#--------------------------------------------------------------------------- + +# The TAGFILES option can be used to specify one or more tagfiles. +# Optionally an initial location of the external documentation +# can be added for each tagfile. The format of a tag file without +# this location is as follows: +# +# TAGFILES = file1 file2 ... +# Adding location for the tag files is done as follows: +# +# TAGFILES = file1=loc1 "file2 = loc2" ... +# where "loc1" and "loc2" can be relative or absolute paths or +# URLs. If a location is present for each tag, the installdox tool +# does not have to be run to correct the links. +# Note that each tag file must have a unique name +# (where the name does NOT include the path) +# If a tag file is not located in the directory in which doxygen +# is run, you must also specify the path to the tagfile here. + +TAGFILES = + +# When a file name is specified after GENERATE_TAGFILE, doxygen will create +# a tag file that is based on the input files it reads. + +GENERATE_TAGFILE = + +# If the ALLEXTERNALS tag is set to YES all external classes will be listed +# in the class index. If set to NO only the inherited external classes +# will be listed. + +ALLEXTERNALS = NO + +# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed +# in the modules index. If set to NO, only the current project's groups will +# be listed. + +EXTERNAL_GROUPS = YES + +# The PERL_PATH should be the absolute path and name of the perl script +# interpreter (i.e. the result of `which perl'). + +PERL_PATH = /usr/bin/perl + +#--------------------------------------------------------------------------- +# Configuration options related to the dot tool +#--------------------------------------------------------------------------- + +# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will +# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base +# or super classes. Setting the tag to NO turns the diagrams off. Note that +# this option is superseded by the HAVE_DOT option below. This is only a +# fallback. It is recommended to install and use dot, since it yields more +# powerful graphs. + +CLASS_DIAGRAMS = YES + +# You can define message sequence charts within doxygen comments using the \msc +# command. Doxygen will then run the mscgen tool (see +# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the +# documentation. The MSCGEN_PATH tag allows you to specify the directory where +# the mscgen tool resides. If left empty the tool is assumed to be found in the +# default search path. + +MSCGEN_PATH = + +# If set to YES, the inheritance and collaboration graphs will hide +# inheritance and usage relations if the target is undocumented +# or is not a class. + +HIDE_UNDOC_RELATIONS = YES + +# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is +# available from the path. This tool is part of Graphviz, a graph visualization +# toolkit from AT&T and Lucent Bell Labs. The other options in this section +# have no effect if this option is set to NO (the default) +#This will automatically enable doxygen’s use of dot, if available. +#DOXYGEN_DOT_FOUND gets set (to YES, in my case) by the find_pacakge(Doxygen) command. + +HAVE_DOT = @DOXYGEN_DOT_FOUND@ + + + +# By default doxygen will write a font called FreeSans.ttf to the output +# directory and reference it in all dot files that doxygen generates. This +# font does not include all possible unicode characters however, so when you need +# these (or just want a differently looking font) you can specify the font name +# using DOT_FONTNAME. You need need to make sure dot is able to find the font, +# which can be done by putting it in a standard location or by setting the +# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory +# containing the font. + +DOT_FONTNAME = FreeSans + +# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. +# The default size is 10pt. + +DOT_FONTSIZE = 10 + +# By default doxygen will tell dot to use the output directory to look for the +# FreeSans.ttf font (which doxygen will put there itself). If you specify a +# different font using DOT_FONTNAME you can set the path where dot +# can find it using this tag. + +DOT_FONTPATH = + +# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect inheritance relations. Setting this tag to YES will force the +# the CLASS_DIAGRAMS tag to NO. + +CLASS_GRAPH = YES + +# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect implementation dependencies (inheritance, containment, and +# class references variables) of the class with other documented classes. + +COLLABORATION_GRAPH = YES + +# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for groups, showing the direct groups dependencies + +GROUP_GRAPHS = YES + +# If the UML_LOOK tag is set to YES doxygen will generate inheritance and +# collaboration diagrams in a style similar to the OMG's Unified Modeling +# Language. + +UML_LOOK = NO + +# If set to YES, the inheritance and collaboration graphs will show the +# relations between templates and their instances. + +TEMPLATE_RELATIONS = NO + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT +# tags are set to YES then doxygen will generate a graph for each documented +# file showing the direct and indirect include dependencies of the file with +# other documented files. + +INCLUDE_GRAPH = YES + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and +# HAVE_DOT tags are set to YES then doxygen will generate a graph for each +# documented header file showing the documented files that directly or +# indirectly include this file. + +INCLUDED_BY_GRAPH = YES + +# If the CALL_GRAPH and HAVE_DOT options are set to YES then +# doxygen will generate a call dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable call graphs +# for selected functions only using the \callgraph command. + +CALL_GRAPH = NO + +# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then +# doxygen will generate a caller dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable caller +# graphs for selected functions only using the \callergraph command. + +CALLER_GRAPH = NO + +# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen +# will graphical hierarchy of all classes instead of a textual one. + +GRAPHICAL_HIERARCHY = YES + +# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES +# then doxygen will show the dependencies a directory has on other directories +# in a graphical way. The dependency relations are determined by the #include +# relations between the files in the directories. + +DIRECTORY_GRAPH = YES + +# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images +# generated by dot. Possible values are png, jpg, or gif +# If left blank png will be used. + +DOT_IMAGE_FORMAT = png + +# The tag DOT_PATH can be used to specify the path where the dot tool can be +# found. If left blank, it is assumed the dot tool can be found in the path. + +DOT_PATH = + +# The DOTFILE_DIRS tag can be used to specify one or more directories that +# contain dot files that are included in the documentation (see the +# \dotfile command). + +DOTFILE_DIRS = + +# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of +# nodes that will be shown in the graph. If the number of nodes in a graph +# becomes larger than this value, doxygen will truncate the graph, which is +# visualized by representing a node as a red box. Note that doxygen if the +# number of direct children of the root node in a graph is already larger than +# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note +# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. + +DOT_GRAPH_MAX_NODES = 50 + +# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the +# graphs generated by dot. A depth value of 3 means that only nodes reachable +# from the root by following a path via at most 3 edges will be shown. Nodes +# that lay further from the root node will be omitted. Note that setting this +# option to 1 or 2 may greatly reduce the computation time needed for large +# code bases. Also note that the size of a graph can be further restricted by +# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. + +MAX_DOT_GRAPH_DEPTH = 0 + +# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent +# background. This is disabled by default, because dot on Windows does not +# seem to support this out of the box. Warning: Depending on the platform used, +# enabling this option may lead to badly anti-aliased labels on the edges of +# a graph (i.e. they become hard to read). + +DOT_TRANSPARENT = NO + +# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output +# files in one run (i.e. multiple -o and -T options on the command line). This +# makes dot run faster, but since only newer versions of dot (>1.8.10) +# support this, this feature is disabled by default. + +DOT_MULTI_TARGETS = NO + +# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will +# generate a legend page explaining the meaning of the various boxes and +# arrows in the dot generated graphs. + +GENERATE_LEGEND = YES + +# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will +# remove the intermediate dot files that are used to generate +# the various graphs. + +DOT_CLEANUP = YES diff --git a/docs/assets/project_logo.png b/docs/assets/project_logo.png new file mode 100644 index 0000000..b613b67 Binary files /dev/null and b/docs/assets/project_logo.png differ diff --git a/flux.pbs b/flux.pbs new file mode 100644 index 0000000..3089b2e --- /dev/null +++ b/flux.pbs @@ -0,0 +1,37 @@ +#!/bin/bash +##This file was created on 12/12/2016 +#this is a pbs script for the FLUX HPC, change accordingly + + +#### PBS preamble +#PBS -N test +#PBS -M craldaz@umich.edu +#PBS -m abe + +# Change the number of cores (ppn=1), amount of memory, and walltime: +#PBS -l nodes=1:ppn=1,mem=2000mb,walltime=00:30:20 +#PBS -j oe +#PBS -V + +# Change "example_flux" to the name of your Flux allocation: +#PBS -A ners590f16_fluxod +#PBS -q fluxod +#PBS -l qos=flux + +#### End PBS preamble + +# Show list of CPUs you ran on, if you're running under PBS +if [ -n "$PBS_NODEFILE" ]; then cat $PBS_NODEFILE; fi + +# Change to the directory you submitted from +if [ -n "$PBS_O_WORKDIR" ]; then cd $PBS_O_WORKDIR; fi + +# Put your job commands here: +echo "Hello, world" +module load intel/14.0.2 +#module load cmake +#alias mopac='~/opt/mopac/MOPAC2016.exe' +#export LD_LIBRARY_PATH=~/opt/mopac/ +#export MOPAC_LICENSE=~/opt/mopac/ +ctest -V + diff --git a/main.cpp b/main.cpp deleted file mode 100644 index 41aa614..0000000 --- a/main.cpp +++ /dev/null @@ -1,45 +0,0 @@ -#include -#include -#include - -#include "gstring.h" - - -using namespace std; - - -int main(int argc, char* argv[]){ - string inpfile; - string xyzfile; - string nprocs; - switch (argc){ - case 1: - inpfile="inpfileq"; - xyzfile="initial.xyz"; - nprocs="1"; - break; - case 2: - inpfile="inpfileq"; - xyzfile=argv[1]; - nprocs="1"; - break; - case 3: - inpfile="inpfileq"; - xyzfile=argv[1]; - nprocs=argv[2]; - break; - default: - cout << "Invalid command line options." << endl; - return -1; - } - - int nnprocs = atoi(nprocs.c_str()); - printf(" Number of QC processors: %i \n",nnprocs); - int name = atoi(xyzfile.c_str()); - GString gstr; - gstr.init(inpfile, name, nnprocs); - gstr.String_Method_Optimization(); - - - return 0; -} diff --git a/savefile.cpp b/savefile.cpp deleted file mode 100644 index 0278834..0000000 --- a/savefile.cpp +++ /dev/null @@ -1,42 +0,0 @@ -#if 0 - ofstream grad_file; - string grad_file_string = "grad_file.txt"; - grad_file.open(grad_file_string.c_str()); - grad_file.setf(ios::fixed); - grad_file.setf(ios::left); - grad_file << setprecision(6); - - ofstream tan_grad_file; - string tan_grad_file_string = "tan_grad_file.txt"; - tan_grad_file.open(tan_grad_file_string.c_str()); - tan_grad_file.setf(ios::fixed); - tan_grad_file.setf(ios::left); - tan_grad_file << setprecision(6); - - ofstream perp_grad_file; - string perp_grad_file_string = "perp_grad_file.txt"; - perp_grad_file.open(perp_grad_file_string.c_str()); - perp_grad_file.setf(ios::fixed); - perp_grad_file.setf(ios::left); - perp_grad_file << setprecision(6); - - ofstream Vfile; - string Vfile_string = "Vfile.txt"; - Vfile.open(Vfile_string.c_str()); - Vfile.setf(ios::fixed); - Vfile.setf(ios::left); - Vfile << setprecision(6); - - ofstream Vfile_kcal; - string Vfile_kcal_string = "Vfile_kcal.txt"; - Vfile_kcal.open(Vfile_kcal_string.c_str()); - Vfile_kcal.setf(ios::fixed); - Vfile_kcal.setf(ios::left); - Vfile_kcal << setprecision(6); -#endif - - ofstream SVfile; - string newSVfile; - SVfile.setf(ios::fixed); - SVfile.setf(ios::left); - SVfile << setprecision(6);