From f6f34a21af94550dd94e7455c4c1e61f2863c968 Mon Sep 17 00:00:00 2001
From: Drobot Viktor <linux776@gmail.com>
Date: Mon, 5 Nov 2018 19:22:37 +0300
Subject: [PATCH] Added patches for NAMD (versions 2.12 and git-latest 2.13b2)
---
patches/namd-2.12.config | 30 ++++
patches/namd-2.12.diff | 271 ++++++++++++++++++++++++++++++++++++
patches/namd-2.13b2.config | 30 ++++
patches/namd-2.13b2.diff | 276 +++++++++++++++++++++++++++++++++++++
4 files changed, 607 insertions(+)
create mode 100644 patches/namd-2.12.config
create mode 100644 patches/namd-2.12.diff
create mode 100644 patches/namd-2.13b2.config
create mode 100644 patches/namd-2.13b2.diff
diff --git a/patches/namd-2.12.config b/patches/namd-2.12.config
new file mode 100644
index 000000000..352a7ba8b
--- /dev/null
+++ b/patches/namd-2.12.config
@@ -0,0 +1,30 @@
+
+
+function plumed_preliminary_test(){
+# check if the README.txt contains the word NAMD
+ grep -q NAMD README.txt 1>/dev/null 2>/dev/null && test -f */Make.config
+}
+
+function plumed_patch_info(){
+cat << EOF
+
+To enable PLUMED in a NAMD simulation one should add the following lines in the NAMD configuration file
+(often named as xxx.namd or xxx.conf) and run the plumed-patched version of NAMD with it:
+
+\verbatim
+plumed on
+plumedfile plumed.dat
+\endverbatim
+
+The first line tells NAMD to run with PLUMED and the second line specifies the PLUMED input file.
+
+\bug NAMD does not currently take into account virial contributions
+from PLUMED. Please use constant volume simulations only.
+
+For more information on NAMD you should visit http://www.ks.uiuc.edu/Research/namd/
+
+EOF
+}
+
+plumed_ignore_mpi=yes
+
diff --git a/patches/namd-2.12.diff b/patches/namd-2.12.diff
new file mode 100644
index 000000000..f24360157
--- /dev/null
+++ b/patches/namd-2.12.diff
@@ -0,0 +1,271 @@
+patch -u -l -b -F 5 -N --suffix=.preplumed "./Makefile" << \EOF_EOF
+--- ./Makefile.preplumed
++++ ./Makefile
+@@ -359,13 +359,15 @@
+ CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(FMM) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN $(TCL) $(PYTHON) $(FFT) $(CUDA) $(MIC) $(MEMOPT) $(CCS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF) $(EXTRAINCS) $(MSA) $(CKLOOP)
+ CXXFLAGS = $(CXXBASEFLAGS) $(CXXOPTS)
+ CXXMICFLAGS = $(CXXBASEFLAGS) $(CXXOPTS) $(CXXMICOPTS)
+ CXXTHREADFLAGS = $(CXXBASEFLAGS) $(CXXTHREADOPTS)
+ CXXSIMPARAMFLAGS = $(CXXBASEFLAGS) $(CXXSIMPARAMOPTS)
+ CXXNOALIASFLAGS = $(CXXBASEFLAGS) $(CXXNOALIASOPTS)
++include .rootdir/Plumed.inc
++
+ CXXCOLVARFLAGS = $(CXXBASEFLAGS) $(CXXCOLVAROPTS)
+ GXXFLAGS = $(CXXBASEFLAGS) -DNO_STRSTREAM_H
+ CFLAGS = $(COPTI)$(SRCDIR) $(TCL) $(COPTS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF)
+ PLUGINGCCFLAGS = $(COPTI)$(PLUGINSRCDIR) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN
+ PLUGINCFLAGS = $(PLUGINGCCFLAGS) $(COPTS)
+ SBCFLAGS = $(COPTI)$(SBSRCDIR) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN -DPSFGEN_USEPLUGINS $(TCL) $(COPTS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF)
+ SBGCCFLAGS = $(COPTI)$(SBSRCDIR) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN -DPSFGEN_USEPLUGINS $(TCL) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF)
+@@ -394,13 +396,14 @@
+ $(CUDAOBJS) \
+ $(CUDALIB) \
+ $(DPMTALIB) \
+ $(DPMELIB) \
+ $(FMMLIB) \
+ $(TCLLIB) \
++ $(PLUMED_LOAD) \
+ $(PYTHONLIB) \
+ $(FFTLIB) \
+ $(PLUGINLIB) \
+ $(SBLIB) \
+ $(CHARMOPTS) \
+ $(EXTRALINKLIBS) \
+ -lm -o namd2
+EOF_EOF
+patch -u -l -b -F 5 --suffix=.preplumed "./src/ComputeMgr.C" << \EOF_EOF
+--- ./src/ComputeMgr.C.preplumed
++++ ./src/ComputeMgr.C
+@@ -80,12 +80,135 @@
+ #include "GlobalMasterSMD.h"
+ #include "GlobalMasterTMD.h"
+ #include "GlobalMasterSymmetry.h"
+ #include "GlobalMasterEasy.h"
+ #include "GlobalMasterMisc.h"
++// PLUMED
++#include "../Plumed.h"
++// END PLUMED
+ #include "GlobalMasterFreeEnergy.h"
+ #include "GlobalMasterColvars.h"
++class GlobalMasterPlumed:
++ public GlobalMasterEasy,
++ private PLMD::Plumed
++{
++ std::vector<int> index;
++ std::vector<double> positions;
++ std::vector<double> forces;
++ std::vector<double> masses;
++ std::vector<double> charges;
++ double box[3][3];
++ SimParameters *spar;
++public:
++ GlobalMasterPlumed():
++ GlobalMasterEasy("plumedScript")
++ {
++ easy_init(config);
++ }
++ void easy_init(const char* config)
++ {
++ int realPrecision=sizeof(double);
++ cmd("setRealPrecision",&realPrecision);
++ spar=Node::Object()->simParameters;
++
++ double energyUnits=4.184;
++ double lengthUnits=0.1;
++ double timeUnits=0.001;
++ cmd("setMDEnergyUnits",&energyUnits);
++ cmd("setMDLengthUnits",&lengthUnits);
++ cmd("setMDTimeUnits",&timeUnits);
++
++ cmd("setPlumedDat",spar->plumedFilename);
++
++ int natoms=Node::Object()->molecule->numAtoms;
++ cmd("setNatoms",&natoms);
++
++ cmd("setMDEngine","namd");
++
++ cmd("setLog",stdout);
++
++ double dt=spar->dt;
++ cmd("setTimestep",&dt);
++ cmd("setNoVirial");
++ cmd("init");
++
++ int s=step+1;
++ cmd("setStep",&s);
++ share();
++
++ }
++
++ void share(){
++ int* p;
++ int n;
++ bool redo=false;
++ cmd("prepareDependencies");
++ cmd("createFullList",&n);
++ cmd("getFullList",&p);
++ if(index.size()!=n)redo=true;
++ if(!redo) for(int i=0;i<n;i++) if(index[i]!=p[i]) { redo=true; break;};
++ if(redo){
++ index.resize(n);
++ masses.resize(n);
++ modifyRequestedAtoms().resize(0);
++ for(int i=0;i<n;i++){
++ requestAtom(p[i]);
++ masses[i]=getMass(p[i]);
++ index[i]=p[i];
++ };
++ positions.resize(3*n);
++ forces.resize(3*n);
++ charges.resize(n);
++
++ cmd("setAtomsNlocal",&n);
++ cmd("setAtomsGatindex",&index[0]);
++ }
++ cmd("clearFullList");
++ }
++
++ void easy_calc(){
++
++ for(int i=0;i<index.size();i++){
++ Vector coord;
++ getPosition(index[i],coord);
++ positions[3*i+0]=coord.x;
++ positions[3*i+1]=coord.y;
++ positions[3*i+2]=coord.z;
++ masses[i]=Node::Object()->molecule->atommass(index[i]);
++ charges[i]=Node::Object()->molecule->atomcharge(index[i]);
++ };
++
++ if(spar->lattice.volume()>0.0){
++ for(int i=0;i<3;i++) box[0][i]=spar->lattice.a()[i];
++ for(int i=0;i<3;i++) box[1][i]=spar->lattice.b()[i];
++ for(int i=0;i<3;i++) box[2][i]=spar->lattice.c()[i];
++ cmd("setBox",&box[0][0]);
++ }
++
++ for(int i=0;i<forces.size();i++) forces[i]=0.0;
++
++ cmd("setMasses",&masses[0]); cmd("setCharges",&charges[0]);
++ cmd("setPositions",&positions[0]);
++ cmd("setForces",&forces[0]);
++
++ cmd("shareData");
++ cmd("performCalc");
++
++ for(int i=0;i<index.size();i++){
++ Vector f;
++ f.x=forces[3*i+0];
++ f.y=forces[3*i+1];
++ f.z=forces[3*i+2];
++ int j=addForce(index[i],f);
++ };
++
++ int s=step+1;
++ cmd("setStep",&s);
++ share();
++
++ }
++};
+
+ ComputeMgr::ComputeMgr()
+ {
+ CkpvAccess(BOCclass_group).computeMgr = thisgroup;
+ computeGlobalObject = 0;
+@@ -785,10 +908,15 @@
+ masterServerObject->addClient(new GlobalMasterSymmetry());
+ if (simParams->TMDOn)
+ masterServerObject->addClient(new GlobalMasterTMD());
+ if (simParams->miscForcesOn)
+ masterServerObject->addClient(new GlobalMasterMisc());
++ // PLUMED
++ if (simParams->plumedOn){
++ masterServerObject->addClient(new GlobalMasterPlumed());
++ }
++ // END PLUMED
+ if ( simParams->freeEnergyOn )
+ masterServerObject->addClient(new GlobalMasterFreeEnergy());
+ if ( simParams->colvarsOn )
+ masterServerObject->addClient(new GlobalMasterColvars());
+
+EOF_EOF
+patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.C" << \EOF_EOF
+--- ./src/SimParameters.C.preplumed
++++ ./src/SimParameters.C
+@@ -1324,10 +1324,17 @@
+ opts.optionalB("main", "GBIS", "Use GB implicit solvent?",
+ &GBISOn, FALSE);
+ opts.optionalB("main", "GBISSer", "Use GB implicit solvent?",
+ &GBISserOn, FALSE);
+
++
++ // PLUMED
++ //// plumed
++ opts.optionalB("main", "plumed", "Is PLUMED active?",&plumedOn,FALSE);
++ opts.require("plumed", "plumedfile","PLUMED script",PARSE_STRING);
++ // END PLUMED
++
+ opts.optional("GBIS", "solventDielectric",
+ "Solvent Dielectric", &solvent_dielectric, 78.5);
+ opts.optional("GBIS", "intrinsicRadiusOffset",
+ "Coulomb Radius Offset", &coulomb_radius_offset, 0.09);
+ opts.optional("GBIS", "ionConcentration",
+@@ -4299,12 +4307,12 @@
+ }
+
+ // Global forces configuration
+
+ globalForcesOn = ( tclForcesOn || freeEnergyOn || miscForcesOn ||
+ (IMDon && ! IMDignore) || SMDOn || TMDOn ||
+- colvarsOn || symmetryOn || qmForcesOn );
++ colvarsOn || symmetryOn || qmForcesOn || plumedOn );
+
+
+ if (tclForcesOn)
+ {
+ iout << iINFO << "TCL GLOBAL FORCES ACTIVE\n";
+@@ -4384,10 +4391,25 @@
+ }
+
+ iout << endi;
+ }
+
++ // PLUMED
++ if (plumedOn)
++ {
++ iout << iINFO << "PLUMED ACTIVE\n";
++
++ current = config->find("plumedfile");
++ iout << iINFO << "PLUMED CONFIG FILE "<< current->data << "\n" << endi;
++ strcpy(plumedFilename,current->data);
++
++ ifstream plumedFile(current->data);
++ if ( ! plumedFile ) NAMD_die("Error reading PLUMED config file.\n");
++
++ }
++ // END PLUMED
++
+ if (IMDon)
+ {
+ iout << iINFO << "INTERACTIVE MD ACTIVE\n";
+ iout << iINFO << "INTERACTIVE MD PORT " << IMDport << "\n";
+ iout << iINFO << "INTERACTIVE MD FREQ " << IMDfreq << "\n";
+EOF_EOF
+patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.h" << \EOF_EOF
+--- ./src/SimParameters.h.preplumed
++++ ./src/SimParameters.h
+@@ -430,10 +430,13 @@
+ char tclBCArgs[128]; // Extra args for calcforces command
+ Bool freeEnergyOn; // Doing free energy perturbation?
+ Bool miscForcesOn; // Using misc forces?
+ Bool colvarsOn; // Using the colvars module?
+
++ Bool plumedOn; // Using Plumed?
++ char plumedFilename[1024]; // Plumed filename
++
+ Bool fixedAtomsOn; // Are there fixed atoms?
+ Bool fixedAtomsForces; // Calculate forces anyway?
+
+ Bool langevinOn; // Flag TRUE-> langevin dynamics active
+ BigReal langevinTemp; // Temperature for Langevin dynamics
+EOF_EOF
diff --git a/patches/namd-2.13b2.config b/patches/namd-2.13b2.config
new file mode 100644
index 000000000..352a7ba8b
--- /dev/null
+++ b/patches/namd-2.13b2.config
@@ -0,0 +1,30 @@
+
+
+function plumed_preliminary_test(){
+# check if the README.txt contains the word NAMD
+ grep -q NAMD README.txt 1>/dev/null 2>/dev/null && test -f */Make.config
+}
+
+function plumed_patch_info(){
+cat << EOF
+
+To enable PLUMED in a NAMD simulation one should add the following lines in the NAMD configuration file
+(often named as xxx.namd or xxx.conf) and run the plumed-patched version of NAMD with it:
+
+\verbatim
+plumed on
+plumedfile plumed.dat
+\endverbatim
+
+The first line tells NAMD to run with PLUMED and the second line specifies the PLUMED input file.
+
+\bug NAMD does not currently take into account virial contributions
+from PLUMED. Please use constant volume simulations only.
+
+For more information on NAMD you should visit http://www.ks.uiuc.edu/Research/namd/
+
+EOF
+}
+
+plumed_ignore_mpi=yes
+
diff --git a/patches/namd-2.13b2.diff b/patches/namd-2.13b2.diff
new file mode 100644
index 000000000..656bd2c9f
--- /dev/null
+++ b/patches/namd-2.13b2.diff
@@ -0,0 +1,276 @@
+patch -u -l -b -F 5 -N --suffix=.preplumed "./Makefile" << \EOF_EOF
+--- ./Makefile.preplumed
++++ ./Makefile
+@@ -359,16 +359,18 @@
+ CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(FMM) $(COPTI)$(PLUGININCDIR) $(COPTI)$(COLVARSINCDIR) $(COPTD)STATIC_PLUGIN $(TCL) $(PYTHON) $(FFT) $(CUDA) $(MIC) $(MEMOPT) $(CCS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF) $(EXTRAINCS) $(MSA) $(CKLOOP)
+ CXXFLAGS = $(CXXBASEFLAGS) $(CXXOPTS)
+ CXXMICFLAGS = $(CXXBASEFLAGS) $(CXXOPTS) $(CXXMICOPTS)
+ CXXTHREADFLAGS = $(CXXBASEFLAGS) $(CXXTHREADOPTS)
+ CXXSIMPARAMFLAGS = $(CXXBASEFLAGS) $(CXXSIMPARAMOPTS)
+ CXXNOALIASFLAGS = $(CXXBASEFLAGS) $(CXXNOALIASOPTS)
++include .rootdir/Plumed.inc
++
+ COLVARSCXXFLAGS = $(CXXBASEFLAGS) $(CXXCOLVAROPTS) $(COPTI)$(LEPTONINCDIR) -DLEPTON -DLEPTON_USE_STATIC_LIBRARIES
+ GXXFLAGS = $(CXXBASEFLAGS) -DNO_STRSTREAM_H
+ CFLAGS = $(COPTI)$(SRCDIR) $(TCL) $(COPTS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF)
+ PLUGINGCCFLAGS = $(COPTI)$(PLUGINSRCDIR) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN
+ PLUGINCFLAGS = $(PLUGINGCCFLAGS) $(COPTS)
+ SBCFLAGS = $(COPTI)$(SBSRCDIR) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN -DPSFGEN_USEPLUGINS $(TCL) $(COPTS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF)
+ SBGCCFLAGS = $(COPTI)$(SBSRCDIR) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN -DPSFGEN_USEPLUGINS $(TCL) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF)
+ COLVARSGXXFLAGS= $(GXXFLAGS)
+ LEPTONGCCFLAGS= $(COPTI)$(LEPTONINCDIR)
+ LEPTONCXXFLAGS=$(CXXBASEFLAGS) $(COPTI)$(LEPTONINCDIR) -DLEPTON_BUILDING_STATIC_LIBRARY
+@@ -394,15 +396,16 @@
+ $(CUDAOBJS) \
+ $(CUDALIB) \
+ $(DPMTALIB) \
+ $(DPMELIB) \
+ $(FMMLIB) \
+ $(TCLLIB) \
++ $(PLUMED_LOAD) \
+ $(PYTHONLIB) \
+ $(FFTLIB) \
+ $(PLUGINLIB) \
+ $(SBLIB) \
+ $(COLVARSLIB) \
+ $(LEPTONOBJS) \
+ $(CHARMOPTS) \
+ $(EXTRALINKLIBS) \
+ $(MATHLIBS) -o namd2
+EOF_EOF
+patch -u -l -b -F 5 --suffix=.preplumed "./src/ComputeMgr.C" << \EOF_EOF
+--- ./src/ComputeMgr.C.preplumed
++++ ./src/ComputeMgr.C
+@@ -80,12 +80,135 @@
+ #include "GlobalMasterSMD.h"
+ #include "GlobalMasterTMD.h"
+ #include "GlobalMasterSymmetry.h"
+ #include "GlobalMasterEasy.h"
+ #include "GlobalMasterMisc.h"
++// PLUMED
++#include "../Plumed.h"
++// END PLUMED
+ #include "GlobalMasterFreeEnergy.h"
+ #include "GlobalMasterColvars.h"
++class GlobalMasterPlumed:
++ public GlobalMasterEasy,
++ private PLMD::Plumed
++{
++ std::vector<int> index;
++ std::vector<double> positions;
++ std::vector<double> forces;
++ std::vector<double> masses;
++ std::vector<double> charges;
++ double box[3][3];
++ SimParameters *spar;
++public:
++ GlobalMasterPlumed():
++ GlobalMasterEasy("plumedScript")
++ {
++ easy_init(config);
++ }
++ void easy_init(const char* config)
++ {
++ int realPrecision=sizeof(double);
++ cmd("setRealPrecision",&realPrecision);
++ spar=Node::Object()->simParameters;
++
++ double energyUnits=4.184;
++ double lengthUnits=0.1;
++ double timeUnits=0.001;
++ cmd("setMDEnergyUnits",&energyUnits);
++ cmd("setMDLengthUnits",&lengthUnits);
++ cmd("setMDTimeUnits",&timeUnits);
++
++ cmd("setPlumedDat",spar->plumedFilename);
++
++ int natoms=Node::Object()->molecule->numAtoms;
++ cmd("setNatoms",&natoms);
++
++ cmd("setMDEngine","namd");
++
++ cmd("setLog",stdout);
++
++ double dt=spar->dt;
++ cmd("setTimestep",&dt);
++ cmd("setNoVirial");
++ cmd("init");
++
++ int s=step+1;
++ cmd("setStep",&s);
++ share();
++
++ }
++
++ void share(){
++ int* p;
++ int n;
++ bool redo=false;
++ cmd("prepareDependencies");
++ cmd("createFullList",&n);
++ cmd("getFullList",&p);
++ if(index.size()!=n)redo=true;
++ if(!redo) for(int i=0;i<n;i++) if(index[i]!=p[i]) { redo=true; break;};
++ if(redo){
++ index.resize(n);
++ masses.resize(n);
++ modifyRequestedAtoms().resize(0);
++ for(int i=0;i<n;i++){
++ requestAtom(p[i]);
++ masses[i]=getMass(p[i]);
++ index[i]=p[i];
++ };
++ positions.resize(3*n);
++ forces.resize(3*n);
++ charges.resize(n);
++
++ cmd("setAtomsNlocal",&n);
++ cmd("setAtomsGatindex",&index[0]);
++ }
++ cmd("clearFullList");
++ }
++
++ void easy_calc(){
++
++ for(int i=0;i<index.size();i++){
++ Vector coord;
++ getPosition(index[i],coord);
++ positions[3*i+0]=coord.x;
++ positions[3*i+1]=coord.y;
++ positions[3*i+2]=coord.z;
++ masses[i]=Node::Object()->molecule->atommass(index[i]);
++ charges[i]=Node::Object()->molecule->atomcharge(index[i]);
++ };
++
++ if(spar->lattice.volume()>0.0){
++ for(int i=0;i<3;i++) box[0][i]=spar->lattice.a()[i];
++ for(int i=0;i<3;i++) box[1][i]=spar->lattice.b()[i];
++ for(int i=0;i<3;i++) box[2][i]=spar->lattice.c()[i];
++ cmd("setBox",&box[0][0]);
++ }
++
++ for(int i=0;i<forces.size();i++) forces[i]=0.0;
++
++ cmd("setMasses",&masses[0]); cmd("setCharges",&charges[0]);
++ cmd("setPositions",&positions[0]);
++ cmd("setForces",&forces[0]);
++
++ cmd("shareData");
++ cmd("performCalc");
++
++ for(int i=0;i<index.size();i++){
++ Vector f;
++ f.x=forces[3*i+0];
++ f.y=forces[3*i+1];
++ f.z=forces[3*i+2];
++ int j=addForce(index[i],f);
++ };
++
++ int s=step+1;
++ cmd("setStep",&s);
++ share();
++
++ }
++};
+
+ ComputeMgr::ComputeMgr()
+ {
+ CkpvAccess(BOCclass_group).computeMgr = thisgroup;
+ computeGlobalObject = 0;
+@@ -785,10 +908,15 @@
+ masterServerObject->addClient(new GlobalMasterSymmetry());
+ if (simParams->TMDOn)
+ masterServerObject->addClient(new GlobalMasterTMD());
+ if (simParams->miscForcesOn)
+ masterServerObject->addClient(new GlobalMasterMisc());
++ // PLUMED
++ if (simParams->plumedOn){
++ masterServerObject->addClient(new GlobalMasterPlumed());
++ }
++ // END PLUMED
+ if ( simParams->freeEnergyOn )
+ masterServerObject->addClient(new GlobalMasterFreeEnergy());
+ if ( simParams->colvarsOn )
+ masterServerObject->addClient(new GlobalMasterColvars());
+
+EOF_EOF
+patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.C" << \EOF_EOF
+--- ./src/SimParameters.C.preplumed
++++ ./src/SimParameters.C
+@@ -1324,10 +1324,17 @@
+ opts.optionalB("main", "GBIS", "Use GB implicit solvent?",
+ &GBISOn, FALSE);
+ opts.optionalB("main", "GBISSer", "Use GB implicit solvent?",
+ &GBISserOn, FALSE);
+
++
++ // PLUMED
++ //// plumed
++ opts.optionalB("main", "plumed", "Is PLUMED active?",&plumedOn,FALSE);
++ opts.require("plumed", "plumedfile","PLUMED script",PARSE_STRING);
++ // END PLUMED
++
+ opts.optional("GBIS", "solventDielectric",
+ "Solvent Dielectric", &solvent_dielectric, 78.5);
+ opts.optional("GBIS", "intrinsicRadiusOffset",
+ "Coulomb Radius Offset", &coulomb_radius_offset, 0.09);
+ opts.optional("GBIS", "ionConcentration",
+@@ -4299,12 +4307,12 @@
+ }
+
+ // Global forces configuration
+
+ globalForcesOn = ( tclForcesOn || freeEnergyOn || miscForcesOn ||
+ (IMDon && ! (IMDignore || IMDignoreForces)) || SMDOn || TMDOn ||
+- colvarsOn || symmetryOn || qmForcesOn );
++ colvarsOn || symmetryOn || qmForcesOn || plumedOn );
+
+
+ if (tclForcesOn)
+ {
+ iout << iINFO << "TCL GLOBAL FORCES ACTIVE\n";
+@@ -4384,10 +4391,25 @@
+ }
+
+ iout << endi;
+ }
+
++ // PLUMED
++ if (plumedOn)
++ {
++ iout << iINFO << "PLUMED ACTIVE\n";
++
++ current = config->find("plumedfile");
++ iout << iINFO << "PLUMED CONFIG FILE "<< current->data << "\n" << endi;
++ strcpy(plumedFilename,current->data);
++
++ ifstream plumedFile(current->data);
++ if ( ! plumedFile ) NAMD_die("Error reading PLUMED config file.\n");
++
++ }
++ // END PLUMED
++
+ if (IMDon)
+ {
+ iout << iINFO << "INTERACTIVE MD ACTIVE\n";
+ iout << iINFO << "INTERACTIVE MD PORT " << IMDport << "\n";
+ iout << iINFO << "INTERACTIVE MD FREQ " << IMDfreq << "\n";
+EOF_EOF
+patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.h" << \EOF_EOF
+--- ./src/SimParameters.h.preplumed
++++ ./src/SimParameters.h
+@@ -430,10 +430,13 @@
+ char tclBCArgs[128]; // Extra args for calcforces command
+ Bool freeEnergyOn; // Doing free energy perturbation?
+ Bool miscForcesOn; // Using misc forces?
+ Bool colvarsOn; // Using the colvars module?
+
++ Bool plumedOn; // Using Plumed?
++ char plumedFilename[1024]; // Plumed filename
++
+ Bool fixedAtomsOn; // Are there fixed atoms?
+ Bool fixedAtomsForces; // Calculate forces anyway?
+
+ Bool langevinOn; // Flag TRUE-> langevin dynamics active
+ BigReal langevinTemp; // Temperature for Langevin dynamics
+EOF_EOF
--
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