diff --git a/hadron_PDF/.gitignore b/hadron_PDF/.gitignore
deleted file mode 100644
index 874c63c..0000000
--- a/hadron_PDF/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-*.o
-
diff --git a/hadron_PDF/.vscode/launch.json b/hadron_PDF/.vscode/launch.json
deleted file mode 100644
index a4b89c3..0000000
--- a/hadron_PDF/.vscode/launch.json
+++ /dev/null
@@ -1,17 +0,0 @@
-{
- "version": "0.2.0",
- "configurations": [
- {
- "name": "(lldb) Launch",
- "type": "cppdbg",
- "request": "launch",
- "program": "enter program name, for example ${workspaceRoot}/a.out",
- "args": [],
- "stopAtEntry": false,
- "cwd": "${workspaceRoot}",
- "environment": [],
- "externalConsole": true,
- "MIMode": "lldb"
- }
- ]
- }
\ No newline at end of file
diff --git a/hadron_PDF/.vscode/settings.json b/hadron_PDF/.vscode/settings.json
deleted file mode 100644
index 8f7c85e..0000000
--- a/hadron_PDF/.vscode/settings.json
+++ /dev/null
@@ -1,20 +0,0 @@
-// Place your settings in this file to overwrite default and user settings.
-{
- "files.associations": {
- "*.cu": "cpp",
- "string": "cpp",
- "__config": "cpp",
- "cstddef": "cpp",
- "exception": "cpp",
- "initializer_list": "cpp",
- "new": "cpp",
- "stdexcept": "cpp",
- "typeinfo": "cpp",
- "iosfwd": "cpp",
- "__functional_base": "cpp",
- "memory": "cpp",
- "tuple": "cpp",
- "utility": "cpp"
- },
- "python.linting.pylintEnabled": false
-}
\ No newline at end of file
diff --git a/hadron_PDF/Makefile b/hadron_PDF/Makefile
deleted file mode 100644
index 12a7148..0000000
--- a/hadron_PDF/Makefile
+++ /dev/null
@@ -1,25 +0,0 @@
-CHROMA=/Users/tomluu/Research/lqcd/code/usqcd/install/chroma/bin
-CONFIG=$(CHROMA)/chroma-config
-CXX=$(shell $(CONFIG) --cxx) -g
-CXXFLAGS=$(shell $(CONFIG) --cxxflags) -I. -fsanitize=address -fno-omit-frame-pointer
-LDFLAGS=$(shell $(CONFIG) --ldflags) -fsanitize=address
-LIBS=$(shell $(CONFIG) --libs)
-
-HDRS=
-
-OBJS1= hadron_PDF.o permutations.o mom_project.o readwrite.o nucleon.o
-OBJS2= gauge_link.o
-
-hadron_PDF: $(OBJS1)
- $(CXX) -o $@ $(CXXFLAGS) $(OBJS1) $(LDFLAGS) $(LIBS)
-
-gauge_link: $(OBJS2)
- $(CXX) -o $@ $(CXXFLAGS) $(OBJS3) $(LDFLAGS) $(LIBS)
-
-%.o: %.cc $(HDRS)
- $(CXX) $(CXXFLAGS) -c $<
-
-clean:
- rm -rf hadron_PDF $(OBJS1) *~
- rm -rf gauge_link $(OBJS2) *~
- rm -rf multi_shift_test $(OBJS3) *~
diff --git a/hadron_PDF/cfgs/weak_field_4448.cfg b/hadron_PDF/cfgs/weak_field_4448.cfg
deleted file mode 100644
index ea6a93e..0000000
Binary files a/hadron_PDF/cfgs/weak_field_4448.cfg and /dev/null differ
diff --git a/hadron_PDF/cfgs/wilson_k0.1665_b5.32144_4by32_cfg_4000.lime b/hadron_PDF/cfgs/wilson_k0.1665_b5.32144_4by32_cfg_4000.lime
deleted file mode 100644
index a2b8f7b..0000000
Binary files a/hadron_PDF/cfgs/wilson_k0.1665_b5.32144_4by32_cfg_4000.lime and /dev/null differ
diff --git a/hadron_PDF/fh_xmldat b/hadron_PDF/fh_xmldat
deleted file mode 100644
index 76371e4..0000000
--- a/hadron_PDF/fh_xmldat
+++ /dev/null
@@ -1,79 +0,0 @@
-
-
-
-
-
-
- 0
- 0
- 32
- 1.1230098805263e-09
-
-
- 0
- 1
- 32
- 9.70590150780222e-10
-
-
- 0
- 2
- 32
- 9.2952511287283e-10
-
-
- 0
- 3
- 32
- 1.1842424313418e-09
-
-
- 1
- 0
- 32
- 1.21961091450593e-09
-
-
- 1
- 1
- 32
- 1.00454536660392e-09
-
-
- 1
- 2
- 32
- 1.00520623092845e-09
-
-
- 1
- 3
- 32
- 1.20294193992068e-09
-
-
- 2
- 0
- 32
- 9.29982124322602e-10
-
-
- 2
- 1
- 32
- 9.94554686836298e-10
-
-
- 2
- 2
- 32
- 1.12985175592534e-09
-
-
- 2
- 3
- 32
- 1.07050993347606e-09
-
-
-
\ No newline at end of file
diff --git a/hadron_PDF/gauge_link.cc b/hadron_PDF/gauge_link.cc
deleted file mode 100644
index 48cf2af..0000000
--- a/hadron_PDF/gauge_link.cc
+++ /dev/null
@@ -1,159 +0,0 @@
-#include
-#include "chroma.h"
-#include "actions/ferm/invert/syssolver_linop_cg.h"
-
-using namespace std;
-using namespace QDP;
-using namespace Chroma;
-
-Real one = 1.0;
-Real zero = 0.0;
-
-LatticeColorMatrix gauge_shift(const multi1d &U,
- const LatticeColorMatrix &v,
- const int sign, const int dir)
-{
- if (sign == 0)
- return v;
- return sign > 0 ? shift(adj(U[dir]) * v, -1, dir)
- : U[dir] * shift(v, +1, dir);
-}
-
-LatticeColorMatrix gauge_link(const multi1d &U, const int dir, const int displacement)
-{
- LatticeColorMatrix gaugelink = one;
-
- if (displacement == 0)
- {
- gaugelink = one;
- }
-
- else if (displacement > 0)
- {
- for (int stp = 1; stp <= displacement; stp++)
- {
- gaugelink = gauge_shift(U, gaugelink, 1, dir);
- }
- }
-
- else
- {
- for (int stp = -1; stp >= displacement; stp--)
- {
- gaugelink = gauge_shift(U, gaugelink, -1, dir);
- }
- }
- return gaugelink;
-}
-
-int main(int argc, char **argv)
-{
- initialize(&argc, &argv);
- START_CODE();
-
-
- XMLReader xml_in;
-
- try
- {
- xml_in.open(getXMLInputFileName());
- }
- catch (...)
- {
- cerr << "Error in Reading input XML:" << endl;
- QDP_abort(1);
- }
-
- multi1d nrow;
- Cfg_t cfg;
- int ncg_had = 0;
- int j_decay = 0;
- multi1d t_srce;
-
- int dir;
- int steps;
-
- //read in
- try
- {
- read(xml_in, "/chroma/Param/nrow", nrow);
- // cout<<"read nrow done"< u(Nd);
-
- //HotSt(u);
-
- gaugeStartup(gauge_file_xml, gauge_xml, u, cfg);
-
- unitarityCheck(u);
-
- LatticeColorMatrix gauge_link_orgnl = one;
- LatticeColorMatrix gauge_link_trnsfrmd = one;
- LatticeColorMatrix gauge_link_dffrnc = zero;
-
- LatticeColorMatrix g1 = one;
- LatticeColorMatrix g2 = one;
- LatticeColorMatrix g0 = one;
-
- gauge_link_orgnl = gauge_link(u, dir, steps);
-
- rgauge(u, g1);
-
- g0 = g1;
-
- if (steps == 0)
- {
- g2 = shift(g0, -1, dir);
- }
- else if (steps > 0)
- {
- for (int i = 1; i <= steps; i++)
- {
- g2 = shift(g0, -1, dir);
- g0 = g2;
- }
- }
- else
- {
- for (int i = -1; i >= steps; i--)
- {
- g2 = shift(g0, +1, dir);
- g0 = g2;
- }
- }
-
- gauge_link_trnsfrmd = gauge_link(u, +1, dir, steps);
-
- gauge_link_dffrnc = adj(g1) * gauge_link_trnsfrmd * g2 -
- gauge_link_orgnl;
-
- XMLFileWriter xml_out("gauge_link_difference");
- push(xml_out, "difference");
-
- write(xml_out, "delta", gauge_link_dffrnc);
-
- xml_out.flush();
- pop(xml_out);
-
- END_CODE();
- finalize();
- exit(0);
-}
\ No newline at end of file
diff --git a/hadron_PDF/gauge_link.h b/hadron_PDF/gauge_link.h
deleted file mode 100644
index 12d9e09..0000000
--- a/hadron_PDF/gauge_link.h
+++ /dev/null
@@ -1,43 +0,0 @@
-#ifndef GAUGE_LINK_H
-#define GAUGE_LINK_H
-
-LatticeColorMatrix gauge_shift(const multi1d &U, const LatticeColorMatrix &v, const int sign, const int dir)
-{
- if (sign == 0)
- return v;
- return sign > 0 ? shift(U[dir] * v, +1, dir)
- : shift(adj(U[dir]) * v, -1, dir);
-}
-// create a gauge link in \bar psi(n)L(n,n+\Delta\hat \mu)psi(n+\Delta \hat \mu)
-// L(n,n+\Delta\hat\mu)=U_\mu(n)*U_\mu(n+\hat\mu)*...*U_\mu(n+(\Delta-1)\hat\mu)
-LatticeColorMatrix gauge_link(const multi1d &U, const int sign, const int dir, const int displacement)
-{
- Real one = 1.0;
-
- LatticeColorMatrix gaugelink = one;
-
- if (displacement == 0)
- {
- return one;
- }
- else if (displacement > 0)
- {
- for (int stp = 1; stp < displacement; stp++)
- {
- gaugelink = gauge_shift(U, gaugelink, 1, dir);
- }
- return U[dir] * gaugelink;
- // return gaugelink;
- }
- else
- {
- for (int stp = -1; stp >= displacement; stp--)
- {
- gaugelink = gauge_shift(U, gaugelink, -1, dir);
- }
- return gaugelink;
- }
-}
-
-
-#endif
\ No newline at end of file
diff --git a/hadron_PDF/hadron.ini.xml b/hadron_PDF/hadron.ini.xml
deleted file mode 100644
index df812d9..0000000
--- a/hadron_PDF/hadron.ini.xml
+++ /dev/null
@@ -1,156 +0,0 @@
-
-
-
-
-
- MAKE_SOURCE
- 1
-
- 6
-
-
- 1
- POINT_SOURCE
- 3
- 0 0 0 0
-
- GAUGE_INV_GAUSSIAN
- 2.8284
- 20
- 3
-
-
-
- STOUT_SMEAR
- 0.0
- 0
- 3
-
-
-
-
- 1
- POINT_SINK
- 3
- 0 0 0 0
-
- GAUGE_INV_GAUSSIAN
- 2.8284
- 20
- 3
-
-
-
-
-
- default_gauge_field
- t160z0y0x0
-
-
-
-
- 3
- 3
-
-
-
-
- PROPAGATOR
- 1
-
- 10
- FULL
- false
- 1
-
- CLOVER
- -0.0743
- 1.58932722549812
- 0.902783591772098
-
- true
- 3
- 4.3
- 1.265
-
-
- STOUT_FERM_STATE
- 0.14
- 2
- 3
-
- SIMPLE_FERMBC
- 1 1 1 -1
-
-
-
-
- CG_INVERTER
- 1e-9
- 100
-
- -0.0743
- 1.58932722549812
- 0.902783591772098
-
- true
- 3
- 4.3
- 1.265
-
-
- 1.0e-8
- 0.1
- 10000000
- true
- BICGSTAB
- false
- false
- RECONS_12
- HALF
- RECONS_12
- false
-
-
-
- default_gauge_field
- t160z0y0x0
- t160z0y0x0_pt_pt
-
-
-
-
-
- Save the prop
- QIO_WRITE_NAMED_OBJECT
- 1
-
- t160z0y0x0_sh_pt
- LatticePropagatorF
-
-
- ./props/testProp
- SINGLEFILE
-
-
-
-
-
- Pion (meson) PDF
- 15
-
-
- Nucleon PDF
- Avg
- 0 0 0 0
- ./data/
-
-
-
- 4 4 4 32
-
-
- SZINQIO
- ./cfgs/wilson_k0.1665_b5.32144_4by32_cfg_4000.lime
-
-
diff --git a/hadron_PDF/hadron_PDF b/hadron_PDF/hadron_PDF
deleted file mode 100755
index b1eda28..0000000
Binary files a/hadron_PDF/hadron_PDF and /dev/null differ
diff --git a/hadron_PDF/hadron_PDF.cc b/hadron_PDF/hadron_PDF.cc
deleted file mode 100644
index 677e0b2..0000000
--- a/hadron_PDF/hadron_PDF.cc
+++ /dev/null
@@ -1,337 +0,0 @@
-#include
-#include "chroma.h"
-#include "actions/ferm/invert/syssolver_linop_cg.h"
-#include "gauge_link.h"
-#include "multi_shift.h"
-#include "nucleon.h"
-
-using namespace std;
-using namespace QDP;
-using namespace Chroma;
-
-#define PASS(ln) cout << "====== PASS " << ln << " ======" << endl
-
-typedef OLattice, Nc>, Ns>> LatticePropagatorReImPrt;
-
-typedef OLattice, Nc>>> LatticeColorMatrixReImPrt;
-
-LatticePropagator getPointSource(const multi1d &pos, const int &time_dir)
-{
- START_CODE();
-
- //result vector:
- LatticePropagator result = zero;
- for (unsigned int c = 0; c < Nc; c++)
- {
- //fill lattice color vector with a one at pos:
- LatticeColorVector tmpcolorvec = zero;
- srcfil(tmpcolorvec, pos, c);
-
- //inject in larger source:
- for (unsigned int s = 0; s < Ns; s++)
- {
- LatticeFermion tmpferm = zero;
- CvToFerm(tmpcolorvec, tmpferm, s);
- FermToProp(tmpferm, result, c, s);
- }
- }
- END_CODE();
-
- return result;
-}
-
-bool linkageHack(void)
-{
- bool foo = true;
- // Inline Measurements
- foo &= InlineAggregateEnv::registerAll();
- foo &= GaugeInitEnv::registerAll();
-
- return foo;
-}
-
-int main(int argc, char **argv)
-{
-
- initialize(&argc, &argv);
- START_CODE();
-
- linkageHack();
-
- Real one = 1.0;
- Real zero = 0.0;
-
- XMLReader xml_in;
-
- try
- {
- xml_in.open(getXMLInputFileName());
- }
- catch (...)
- {
- cerr << "Error in Reading input XML:" << endl;
- QDP_abort(1);
- }
-
- multi1d nrow;
- Cfg_t cfg;
- Real mass = 0.0;
- string prpgtr_fl;
- multi1d bndry_cndtns;
- int ncg_had = 0;
- int j_decay = 0;
- multi1d t_srce;
-
- int dir;
- int steps;
-
- Real wvf_param;
- int wvfIntPar;
-
- /*
- * Meson parameters. . .
- */
- int gamma;
- bool meson;
-
- /*
- * Nucleon parameters. . .
- */
- Nucleon_system nucleon;
- string file_dir;
- string spin;
- multi1d pN(4);
- bool baryon;
-
- //================= set parameters =====================
-
- try
- {
- read(xml_in, "/chroma/Param/nrow", nrow);
- read(xml_in, "/chroma/Cfg", cfg);
- read(xml_in, "/chroma/Param/InlineMeasurements/elem/propagator/Param/FermionAction/Mass", mass);
- read(xml_in, "/chroma/Param/InlineMeasurements/elem/propagator/Param/FermionAction/FermState/FermionBC/boundary", bndry_cndtns);
- read(xml_in, "/chroma/Param/InlineMeasurements/elem/Param/Source/Source_Smearing/j_decay", j_decay);
- read(xml_in, "/chroma/Param/InlineMeasurements/elem/Param/Source/Source_Smearing/t_srce", t_srce);
- read(xml_in, "/chroma/Param/InlineMeasurements/elem/displacement/dir", dir);
- read(xml_in, "/chroma/Param/InlineMeasurements/elem/displacement/steps", steps);
- }
- catch (const string &e)
- {
- QDPIO::cerr << "Parsing XML: " << e << endl;
- QDP_abort(1);
- }
- try
- {
- read(xml_in, "/chroma/Param/InlineMeasurements/elem/meson/gamma", gamma);
- QDPIO::cout << "Performing meson measurement(s)" << endl;
- meson = true;
- }
- catch (const string &e)
- {
- meson = false;
- }
- try
- {
- read(xml_in, "/chroma/Param/InlineMeasurements/elem/nucleon/spin", spin);
- read(xml_in, "/chroma/Param/InlineMeasurements/elem/nucleon/pmom", pN);
- read(xml_in, "/chroma/Param/InlineMeasurements/elem/nucleon/file_dir", file_dir);
- QDPIO::cout << "Performing nucleon measurement(s)" << endl;
- baryon = true;
- }
- catch (const string &e)
- {
- baryon = false;
- }
-
- Layout::setLattSize(nrow);
- Layout::create();
-
- LatticePropagator quark_prpgtr = zero;
- LatticePropagator quark_src = zero;
- quark_src = getPointSource(t_srce, j_decay);
-
- XMLReader rd(xml_in, "/chroma/Param/InlineMeasurements/elem/propagator/Param");
-
- SimpleFermBCParams bc_prmtrs;
-
- GroupXML_t InvertParam = readXMLGroup(rd, "InvertParam", "invType");
-
- //boundary conditions
- bc_prmtrs.boundary.resize(Nd);
- for (int i = 0; i < Nd - 1; i++)
- {
- bc_prmtrs.boundary[i] = bndry_cndtns[i]; //BC_TYPE_PERIODIC;
- }
- bc_prmtrs.boundary[Nd - 1] = bndry_cndtns[Nd - 1]; //BC_TYPE_ANTIPERIODIC;
-
- //calculate propagator
-
- typedef LatticeFermion T;
- typedef multi1d P;
- Handle> fbc_handle(new SimpleFermBC(bc_prmtrs));
- Handle> cfs(new CreateSimpleFermState(fbc_handle));
-
- EvenOddPrecWilsonFermAct S(cfs, mass);
-
- //============= create gauge configurations ===================
-
- XMLReader gauge_file_xml, gauge_xml;
- multi1d u(Nd);
- //HotSt(u);
-
- gaugeStartup(gauge_file_xml, gauge_xml, u, cfg);
- unitarityCheck(u);
-
- //======================================================
- //
- // BEFORE rgauge
- //
- //======================================================
-
- //=================== 1st inversion =====================
-
- Handle> state(S.createState(u));
- LinOpSysSolverCGEnv::registerAll();
- QuarkSpinType quarkSpinType = QUARK_SPIN_TYPE_FULL;
-
- try
- {
- XMLFileWriter xml_out("1st_propagator");
- push(xml_out, "meson_crrltr");
-
- S.quarkProp(quark_prpgtr, xml_out,
- quark_src, state, InvertParam,
- quarkSpinType, ncg_had);
-
- xml_out.flush();
- pop(xml_out);
- }
- catch (const string &e)
- {
- QDPIO::cout << "Error trying to perform the inversion:" << e << endl;
- QDP_abort(1);
- }
-
- //============== 1st propagator sink smearing (not applied here)!!!!================
- /* try
- {
- // Get the name of the smearing
- string smearing_name;
- read(xml_in, "/chroma/Param/InlineMeasurements/elem/Param/Sink/Sink_Smearing/SinkType", smearing_name);
-
- QDPIO::cout << "sink smearing:" << smearing_name << endl;
-
- Handle>
- sinkSmearing(ThePropSinkSmearingFactory::Instance().createObject(smearing_name, xml_in, "/chroma/Param/InlineMeasurements/elem/Param/Sink/Sink_Smearing", u));
-
- (*sinkSmearing)(quark_prpgtr);
- }
- catch (const string &e)
- {
- QDPIO::cerr << ": Caught Exception : " << e << endl;
- QDP_abort(1);
- }
-*/
- //======================Feynman-Hellman Source=========================
-
- //Src^{H}(Delta)=gaugelink(z,z+\Delta \hat \mu)*quark_prpatr(z+Delta), Needs to shift quark_prpatr(z) to quark_prpatr quark_prpatr(z+Delta)
-
- //calculate propagator with FH source
- LatticePropagator quark_prpgtr_Delta = zero;
- LatticePropagator FH_src = zero;
- LatticePropagator FH_quark_prpgtr = zero;
- LatticeColorMatrix gaugelink = zero;
-
- try
- {
- gaugelink = gauge_link(u, +1, dir, steps);
-
- quark_prpgtr_Delta = multi_shift(quark_prpgtr, steps, dir, nrow[dir], bndry_cndtns[dir]);
-
- //Gamma(8)=gamma^3 comes from the definition of quasi-PDF
-
- // LatticePropagator FH_src = Gamma(8)* gaugelink * quark_prpgtr_Delta; Wrong!, QDP does not support Gamma multiply with ColorMatrix
-
- FH_src = gaugelink * (Gamma(8) * quark_prpgtr_Delta);
-
- //======================Feynman-Hellman Source=========================
-
- Handle> state(S.createState(u));
-
- LinOpSysSolverCGEnv::registerAll();
-
- QuarkSpinType quarkSpinType = QUARK_SPIN_TYPE_FULL;
-
- //===============2nd inversion Feynman-Hellman propagator==================
-
- XMLFileWriter xml_out("fh_xmldat");
- push(xml_out, "FH_meson_crrltr");
- S.quarkProp(FH_quark_prpgtr, xml_out,
- FH_src, state, InvertParam,
- quarkSpinType, ncg_had);
- xml_out.flush();
- pop(xml_out);
- }
- catch (const string &e)
- {
- QDPIO::cout << "Error trying to perform the inversion:" << e << endl;
- QDP_abort(1);
- }
-
- if(meson) {
- //=========================meson-correlation function========================
-
- LatticePropagator anti_quark_prpgtr = Gamma(gamma) * quark_prpgtr * Gamma(gamma);
- LatticeComplex tr_prpgtrs = trace(Gamma(gamma) * adj(anti_quark_prpgtr) * Gamma(gamma) * FH_quark_prpgtr);
-
- //=========================HDF5 Output========================
-
- LatticePropagatorReImPrt quark_prpgtr_Re = real(quark_prpgtr);
- LatticePropagatorReImPrt quark_prpgtr_Im = imag(quark_prpgtr);
-
- LatticePropagatorReImPrt quark_prpgtr_shftd_Re = real(quark_prpgtr_Delta);
- LatticePropagatorReImPrt quark_prpgtr_shftd_Im = imag(quark_prpgtr_Delta);
-
- LatticeColorMatrixReImPrt gaugelink_Re = real(gaugelink);
- LatticeColorMatrixReImPrt gaugelink_Im = imag(gaugelink);
-
- LatticePropagatorReImPrt FH_src_Re = real(FH_src);
- LatticePropagatorReImPrt FH_src_Im = imag(FH_src);
-
- LatticePropagatorReImPrt FH_quark_prpgtrRe = real(FH_quark_prpgtr);
- LatticePropagatorReImPrt FH_quark_prpgtrIm = imag(FH_quark_prpgtr);
-
- LatticeDouble tr_prpgtrs_Re = real(tr_prpgtrs);
- LatticeDouble tr_prpgtrs_Im = imag(tr_prpgtrs);
-
- string pi_mtrx_elmnt = "";
- string meson_interp = "ubar Gamma(" + to_string(gamma)+") u";
-
-
-
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diff --git a/hadron_PDF/misc/get_point_source.h b/hadron_PDF/misc/get_point_source.h
deleted file mode 100644
index 8594cfe..0000000
--- a/hadron_PDF/misc/get_point_source.h
+++ /dev/null
@@ -1,29 +0,0 @@
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-{
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\ No newline at end of file
diff --git a/hadron_PDF/misc/pion_PDF_Data_Analysis.nb b/hadron_PDF/misc/pion_PDF_Data_Analysis.nb
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-
diff --git a/hadron_PDF/misc/xml_path.py b/hadron_PDF/misc/xml_path.py
deleted file mode 100755
index 696dd1b..0000000
--- a/hadron_PDF/misc/xml_path.py
+++ /dev/null
@@ -1,8 +0,0 @@
-from lxml import etree
-with open('try_in.xml', 'r') as xml_file:
- xml_string=xml_file.read().replace('\n', '')
-root = etree.fromstring(xml_string)
-tree = etree.ElementTree(root)
-for e in root.iter():
- if (e.tag=='SinkType'):
- print tree.getpath(e)
\ No newline at end of file
diff --git a/hadron_PDF/mom_project.cc b/hadron_PDF/mom_project.cc
deleted file mode 100644
index 73d3584..0000000
--- a/hadron_PDF/mom_project.cc
+++ /dev/null
@@ -1,90 +0,0 @@
-// -*- C++ -*-
-// $Id$
-/*! \file
- * \brief Momentum projection routines definitions
- */
-
-#include "chromabase.h"
-#include
-#include
-#include
-#include
-#include "chroma.h"
-#include "mom_project.h"
-using namespace QDP;
-
-int mom_project::initialize( const multi1d& momentum, const multi1d& source_pts )
-{
- int i;
-
- for(i=0;i mom(Nd);
- multi1d my_coord(Nd);
- int mu;
- LatticeReal p_dot_x = zero;
- LatticeColorMatrix fwd;
-
- std::cout << "here I am!" << std::endl;
-
- std::cout << "Layout::lattSize()[0]= " << Layout::lattSize()[0]<< std::endl;
- std::cout << "Layout::lattSize()[1]= " << Layout::lattSize()[1]<< std::endl;
- std::cout << "Layout::lattSize()[2]= " << Layout::lattSize()[2]<< std::endl;
- std::cout << "Layout::lattSize()[3]= " << Layout::lattSize()[3]<< std::endl;
-
- std::cout << "Getting coordinates ..." << std::endl;
-
- for(mu=0; mu mom_project::project_momentum( const LatticePropagator& S )
-{
- multi1d CC;
-
- CC=sumMulti(phase * S,TimeSliceFunc(Nd-1));
-
- return CC;
-}
-
-multi1d mom_project::project_momentum( const LatticeColorMatrix& S )
-{
- multi1d CC;
-
- CC=sumMulti(phase * S,TimeSliceFunc(Nd-1));
-
- return CC;
-}
-
-multi1d mom_project::project_momentum( const LatticeComplex& S )
-{
- multi1d CC;
-
- CC=sumMulti(phase * S,TimeSliceFunc(Nd-1));
-
- return CC;
-}
diff --git a/hadron_PDF/mom_project.h b/hadron_PDF/mom_project.h
deleted file mode 100644
index bd49036..0000000
--- a/hadron_PDF/mom_project.h
+++ /dev/null
@@ -1,50 +0,0 @@
-// -*- C++ -*-
-// $Id$
-/*! \file
- * \brief Momentum projection routines definitions
- */
-
-#include "chromabase.h"
-#include
-#include
-#include
-#include
-using namespace QDP;
-
-#ifndef __mom_project_h__
-#define __mom_project_h__
-
-class mom_project
-{
- public:
-
- mom_project() {
- p.resize(Nd);
- src.resize(Nd);
- };
-
- mom_project( const multi1d& momentum, const multi1d& source_pts ) {
- p.resize(Nd);
- src.resize(Nd);
- initialize( momentum, source_pts );
- };
-
- multi1d project_momentum( const LatticeComplex& S);
- multi1d project_momentum( const LatticeColorMatrix& S );
- multi1d project_momentum( const LatticePropagator& S );
- /* Propagator project_momentum( const LatticePropagator& S ); */
-
- int initialize( const multi1d& momentum, const multi1d& source_pts );
-
- private:
-
- multi1d p;
- multi1d src;
- LatticeComplex phase;
-
- int calcPhase(void);
-
-};
-
-
-#endif
diff --git a/hadron_PDF/multi_shift.h b/hadron_PDF/multi_shift.h
deleted file mode 100644
index 2cfb3bb..0000000
--- a/hadron_PDF/multi_shift.h
+++ /dev/null
@@ -1,95 +0,0 @@
-/*==========================================
-Multiple shift with boundary condition imposed.
-multi_shit(typ objct, int steps , int dir, int N, int bndry_cndtn)
-returns the shifted objct.
-
-steps : number of steps in unit of lattice spacing.
-dir : direction index
-N : number of total lattice spacing in direction dir
-bndry_cndtn: +1: periodic boundary condition f(x+N) = f(x)
- -1: anti-periodic boundary condition f(x+N) = -f(x)
-==========================================*/
-#ifndef MULTI_SHIFT
-#define MULTI_SHIFT
-
-#include "chroma.h"
-
-using namespace std;
-
-
-template
-Typ multi_shift(Typ objct, int steps, int dir, int N, int bndry_cndtn)
-{
- Typ objct_tmp1 = objct;
- Typ objct_tmp2 = objct;
- Real one = 1.0;
- Real zero = 0.0;
- if (bndry_cndtn == 1)//periodic boundary condition
- {
- if (steps > 0)
- {
- for (int stp = 1; stp <= steps; stp++)
- {
- objct_tmp2 = shift(objct_tmp1, +1, dir);
- objct_tmp1 = objct_tmp2;
- }
- }
-
- else if (steps < 0)
- {
- for (int stp = -1; stp >= steps; stp--)
- {
- objct_tmp2 = shift(objct_tmp1, -1, dir);
- objct_tmp1 = objct_tmp2;
- }
- }
-
- else
- {
- objct_tmp1 = objct;
- }
-
- return objct_tmp1;
- }
- else if (bndry_cndtn == -1)//anti-periodic boundary condition
- {
- LatticeInt coord_in_dir = Layout::latticeCoordinate(dir);//cretaed indcies of each lattice site in diraction dir;
- LatticeInt shftd_coord_in_dir = multi_shift(coord_in_dir, steps, dir, N, +1);
- //shifting indcies (steps) steps in diraction dir;
-
- LatticeDouble shft_phs_in_dir = one;//shft_phs_in_dir: the phase factor on each site
-
- if (steps > 0)
- {
- shft_phs_in_dir = LatticeRealD(pow(-1, LatticeInt(shftd_coord_in_dir < steps))); //those sites acrossing the bondary in direction dir, receives a -1 factor
- //e.g before shifting W = 0 1 2 3...27 28 29 30 31
- // after shifting(steps=3,dir =3) W'= 3 4 5 6...30 31 0 1 2
- //QDP shift: W'=shift(W,+1,dir) gives W'[n] = W[n+1]
- //W'[29;;31] = 0 1 2, have accrossed boundary dues receives a -1 factor, (-1)^(W'[n]= N + steps)));
- //e.g before shifting W = 0 1 2 3...27 28 29 30 31
- // after shifting(steps= -3,dir=3) W'= 29 30 31 0...30 31 0 27 28
- //QDP shift: W'=shift(W,-1,dir) gives W'[n] = W[n-1]
- //W'[0;;3] = 29 30 31 have accrossed boundary dues receives a -1 factor, (-1)^(W'[n]>= N + steps)
- // where N=32 in the example, W dennotes coord_in_dir and W' denotes shftd_coord_in_dir in the code
- }
- else
- {
- ;
- }
-
- return shft_phs_in_dir * (multi_shift(objct, steps, dir, N, +1));
- }
-
- else
- {
- QDPIO::cerr << "Invalid boundary condition for multi_shift " << endl;
- QDP_abort(1);
- }
-}
-
-#endif
\ No newline at end of file
diff --git a/hadron_PDF/myMultiD.h b/hadron_PDF/myMultiD.h
deleted file mode 100644
index b49905c..0000000
--- a/hadron_PDF/myMultiD.h
+++ /dev/null
@@ -1,76 +0,0 @@
-#ifndef __multiD_h__
-#define __multiD_h__
-
-#include "qdp.h"
-using namespace std;
-using namespace QDP;
-
-
-template class multi6d
-{
- public:
- // Basic constructor
- multi6d() {F=0;n1=n2=n3=n4=n5=n6=sz=0;copymem=false;}
- multi6d(T *f,int ns6, int ns5, int ns4, int ns3, int ns2, int ns1) {F=f; n1=ns1; n2=ns2; n3=ns3; n4=ns4; n5=ns5; n6=ns6; sz=n1*n2*n3*n4*n5*n6; copymem=true;}
- explicit multi6d(int ns6, int ns5, int ns4, int ns3, int ns2, int ns1) {copymem=false;F=0;resize(ns6,ns5,ns4,ns3,ns2,ns1);}
- ~multi6d() {if (! copymem) {delete[] F;}}
-
- //! Copy constructor
- multi6d(const multi6d& s): copymem(false), n1(s.n1), n2(s.n2), n3(s.n3), n4(s.n4), n5(s.n5),n6(s.n6), sz(s.sz), F(0)
- {
- resize(n6,n5,n4,n3,n2,n1);
-
- for(int i=0; i < sz; ++i)
- F[i] = s.F[i];
- }
-
- //! Allocate mem for the array
- void resize(int ns6, int ns5, int ns4, int ns3, int ns2, int ns1)
- {
- if(copymem) {
- QDPIO::cerr <<"multi6d block: invalid resize of a copy of memory" << endl;
- exit(1);
- }
-
- // Only delete if the array is not NULL. If it is NULL
- // deleting may be bad
- if ( F != 0x0 ) {
- delete[] F;
- }
-
- n1=ns1; n2=ns2; n3=ns3; n4=ns4; n5=ns5; n6=ns6; sz=n1*n2*n3*n4*n5*n6; F = new(nothrow) T[sz];
- if( F == 0x0 ) {
- QDP_error_exit("Unable to new memory in multi6d block::resize(%d,%d,%d,%d,%d,%d)\n",ns6,ns5,ns4,ns3,ns2,ns1);
- }
- }
-
- //! Size of array
- int size1() const {return n1;}
- int size2() const {return n2;}
- int size3() const {return n3;}
- int size4() const {return n4;}
- int size5() const {return n5;}
- int size6() const {return n6;}
-
- // Return reference to an element
- T& operator()(int n, int m, int l, int k, int j, int i) {return F[i+n1*(j+n2*(k+n3*(l+n4*(m+n5*(n)))))];}
- const T& operator()(int n, int m, int l, int k, int j, int i) const {return F[i+n1*(j+n2*(k+n3*(l+n4*(m+n5*(n)))))];}
-
- // Return multi4d reference
- multi5d operator[](int n) {return multi5d(F+n1*n2*n3*n4*n5*n,n5,n4,n3,n2,n1);}
- const multi5d operator[](int n) const {return multi5d(F+n1*n2*n3*n4*n5*n,n5,n4,n3,n2,n1);}
-
-private:
- bool copymem;
- int n1;
- int n2;
- int n3;
- int n4;
- int n5;
- int n6;
- int sz;
- T *F;
-};
-
-
-#endif
diff --git a/hadron_PDF/notes/FH_drgrm.png b/hadron_PDF/notes/FH_drgrm.png
deleted file mode 100644
index 0cd7e57..0000000
Binary files a/hadron_PDF/notes/FH_drgrm.png and /dev/null differ
diff --git a/hadron_PDF/notes/Note_on_Feyman_Hellman_Method.md b/hadron_PDF/notes/Note_on_Feyman_Hellman_Method.md
deleted file mode 100644
index 9b1a571..0000000
--- a/hadron_PDF/notes/Note_on_Feyman_Hellman_Method.md
+++ /dev/null
@@ -1,28 +0,0 @@
-# Quark Propagator
-
-The quark propagator $S_{x',x}$ is a $4\times4$ matrix with each element is a SU(3) color matrix. $S_{x',x}$ represents a quark propagating from source $x$ to site $x'$, in which $x'$ is the row index and x is the column index (for both Dirac spinor and color indices).
-
-
-
-# Feynman-Hellman Method
-
-Feynman-Hellman Method
-
-
-
-
- $$
- Src^{\mathrm{FH}}_{z,x} \left(\Delta\right)= \mathcal{L}\left(z,z+\Delta\right)\gamma^z S_{z+\Delta,x}
- $$
-where $\mathcal{L}\left(z,z+\Delta\right)$ is the gauge link from $z$ to $z+\Delta$
-
- $$
- S^{\mathrm{FH}}_{y,x}\left(\Delta\right) = \sum_z \left(D\!\!\!\!/^{-1}\right)_{y,z} Src^{\mathrm{FH}}_{z,x}\left(\Delta\right)
- $$
- where $D\!\!\!\!/$denotes the Dirac operator hence $D\!\!\!\!/^{-1}$denotes the inversion.
-
- The correlation function is given by
-
- $$
-C_{y,x}\left(\Delta\right)=\mathrm{tr}\left[\gamma^5\left(S^\dagger\right)_{y,x}\gamma^5 S^{\mathrm{FH}}_{y,x}\left(\Delta\right)\right]
- $$
\ No newline at end of file
diff --git a/hadron_PDF/notes/note_on_QDP_Chroma.md b/hadron_PDF/notes/note_on_QDP_Chroma.md
deleted file mode 100644
index 0e7fc68..0000000
--- a/hadron_PDF/notes/note_on_QDP_Chroma.md
+++ /dev/null
@@ -1,71 +0,0 @@
-
-# Link Variables
-
-The relations between link variables stored in Chroma ( $\mathcal{U}$ ) and in text books ( $U$ ) are
-
- $$
- U_\mu(n) = \mathcal{U}_{\mu}(n)
- $$
-
-
-
-# QDP++ Shift
-
- The QDP++ shift acts as
-
- $$
- G'=\text{shift}(G,\pm1,\mu)
- \Rightarrow G'[\mu][n]= G[\mu][n\pm\hat \mu]
- $$
-
-# Fermion Propagator $S[n]_{\alpha\beta}^{ab}$
-
-The fermion propagator takes the form
-
-$$S[n]_{\alpha_{n}\beta_{src}}^{a_{n}b_{src}}$$
-where $\alpha,\,\beta$ are Dirac Spinor indices and $a,\,b$ are color indices. $S[n]_{\alpha\beta}^{ab}$ represents the propagator from a lattice site $n$ propagating ***from*** source site (an input parameter in inverter function)
-
-
-The gauge transformation of a fermion propagator is
-
-$$S[n]_{\alpha_{n}\beta_{src}}^{a_{n}b_{src}}\rightarrow \sum_{a'=0,b'=0}^{3}g(n)^{a,a'} S[n]_{\alpha_{n}\beta_{src}}^{a'_{n} b'_{src}} g^{\dagger}(src)^{b'b}$$
-
-where $g$ is the SU(3) transformation matrix.
-
-S[n] is stored in memory as
-
-$$
-S(\{n_x,n_y,n_z,n_t\})\rightarrow\left(
-\begin{array}{cc}
-\left(
-\begin{array}{cc}
-T_{00}
-\end{array}
-\right)^{a_{n} b_{src}} & \cdots & \cdots & \left(
-\begin{array}{cc}
-T_{03}
-\end{array}
-\right)^{a_{n} b_{src}} \\
-\cdots&\cdots&\cdots&\cdots\\
-\cdots&\cdots&\cdots&\cdots\\
-\left(
-\begin{array}{cc}
-T_{30}
-\end{array}
-\right)^{a_{n} b_{src}} &\cdots & \cdots &\left(
-\begin{array}{cc}
-T_{33}
-\end{array}
-\right)^{a_{n} b_{src}}
-\end{array}
-\right)_{\alpha_n\beta_{src}}
-$$
-
-where $T_{\alpha_n \beta_{src}}$ is a $3\times 3$ color matrix.
-
-# F-H Source
-
-$$
-\left(S(n)_{\alpha'_n \beta'_{src}}^{a'_n b'_{src}}\right)^\dagger \mathcal{L}_{\mu}[n,n+\Delta\hat\mu]_{\alpha_n,\alpha'_{n+\Delta\hat\mu}}^{a_n b_{n+\Delta\hat\mu}}
-$$
-
diff --git a/hadron_PDF/nucleon.cc b/hadron_PDF/nucleon.cc
deleted file mode 100644
index 150e840..0000000
--- a/hadron_PDF/nucleon.cc
+++ /dev/null
@@ -1,807 +0,0 @@
-#include "chroma.h"
-#include "permutations.h"
-#include