Backport several changes in GROMACS 2024

Colvars · Jan 11, 2024 · f714a1a · f714a1a
1 parent 5bb5611
commit f714a1a
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Showing 7 changed files with 15 additions and 10 deletions.
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp
@@ -40,10 +40,11 @@
  */
 
 #include "colvarproxygromacs.h"
-#include "colvarproxy_gromacs_version.h"
 
 #include <sstream>
 
+#include "colvarproxy_gromacs_version.h"
+
 
 namespace gmx
 {
@@ -59,7 +60,7 @@ ColvarProxyGromacs::ColvarProxyGromacs(const std::string& colvarsConfigString,
     gmxAtoms_(atoms), pbcType_(pbcType), logger_(logger), doParsing_(doParsing)
 {
     engine_name_ = "GROMACS";
-    version_int = get_version_from_string(COLVARPROXY_VERSION);
+    version_int  = get_version_from_string(COLVARPROXY_VERSION);
 
     //! From colvarproxy
     //! The 5 variables below are defined in the `colvarproxy` base class

diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.cpp
@@ -131,7 +131,10 @@ void ColvarsOptions::writeInternalParametersToKvt(KeyValueTreeObjectBuilder tree
 {
 
     // Copy the content of the colvars input file into a string for latter save in KVT
-    colvarsConfigString_ = TextReader::readFileToString(colvarsFileName_);
+    if (!colvarsFileName_.empty())
+    {
+        colvarsConfigString_ = TextReader::readFileToString(colvarsFileName_);
+    }
 
     // Write colvars input file as a string
     treeBuilder.addValue<std::string>(c_colvarsModuleName + "-" + c_configStringTag_, colvarsConfigString_);

diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.h b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.h
@@ -185,8 +185,8 @@ class ColvarsOptions final : public IMdpOptionProvider
 
     //! \}
 
-    //! Colvars config filename, default colvars.dat
-    std::string colvarsFileName_ = "colvars.dat";
+    //! Colvars config filename
+    std::string colvarsFileName_;
 
 
     //! Colvars seed for Langevin integrator

diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvars.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvars.cpp
@@ -77,7 +77,6 @@ class ColvarsTest : public ::testing::Test
     void addMdpOptionColvarsActive()
     {
         mdpValueBuilder_.rootObject().addValue("colvars-active", std::string("yes"));
-        mdpValueBuilder_.rootObject().addValue("colvars-filename", std::string("colvars.dat"));
     }
 
     //! build an mdp options tree that sets the options for the Colvars module

diff --git a/...applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputDefaultValuesWhenActive.xml b/...applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputDefaultValuesWhenActive.xml
@@ -5,7 +5,7 @@
 ; Colvars bias
 colvars-active           = true
 ; colvars config file
-colvars-configfile       = colvars.dat
+colvars-configfile       = 
 ; Colvars seed
 colvars-seed             = -1
 </String>

diff --git a/src/colvarmodule.h b/src/colvarmodule.h
@@ -10,6 +10,8 @@
 #ifndef COLVARMODULE_H
 #define COLVARMODULE_H
 
+#include <cstdint>
+
 #include "colvars_version.h"
 
 #ifndef COLVARS_DEBUG

diff --git a/src/colvarproxy.cpp b/src/colvarproxy.cpp
@@ -308,7 +308,7 @@ int colvarproxy_smp::smp_colvars_loop()
   colvarmodule *cv = cvm::main();
   colvarproxy *proxy = cv->proxy;
 #pragma omp parallel for
-  for (size_t i = 0; i < cv->variables_active_smp()->size(); i++) {
+  for (int i = 0; i < static_cast<int>(cv->variables_active_smp()->size()); i++) {
     colvar *x = (*(cv->variables_active_smp()))[i];
     int x_item = (*(cv->variables_active_smp_items()))[i];
     if (cvm::debug()) {
@@ -333,7 +333,7 @@ int colvarproxy_smp::smp_biases_loop()
 #pragma omp parallel
   {
 #pragma omp for
-    for (size_t i = 0; i < cv->biases_active()->size(); i++) {
+    for (int i = 0; i < static_cast<int>(cv->biases_active()->size()); i++) {
       colvarbias *b = (*(cv->biases_active()))[i];
       if (cvm::debug()) {
         cvm::log("Calculating bias \""+b->name+"\" on thread "+
@@ -360,7 +360,7 @@ int colvarproxy_smp::smp_biases_script_loop()
       cv->calc_scripted_forces();
     }
 #pragma omp for
-    for (size_t i = 0; i < cv->biases_active()->size(); i++) {
+    for (int i = 0; i < static_cast<int>(cv->biases_active()->size()); i++) {
       colvarbias *b = (*(cv->biases_active()))[i];
       if (cvm::debug()) {
         cvm::log("Calculating bias \""+b->name+"\" on thread "+