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namd-2.9.diff
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namd-2.9.diff
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patch -u -l -b -F 5 --suffix=.preplumed "./Makefile" << \EOF_EOF
--- ./Makefile.preplumed
+++ ./Makefile
@@ -359,10 +359,12 @@
CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN $(TCL) $(FFT) $(CUDA) $(MEMOPT) $(CCS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF) $(EXTRAINCS) $(MSA)
CXXFLAGS = $(CXXBASEFLAGS) $(CXXOPTS)
CXXTHREADFLAGS = $(CXXBASEFLAGS) $(CXXTHREADOPTS)
CXXSIMPARAMFLAGS = $(CXXBASEFLAGS) $(CXXSIMPARAMOPTS)
CXXNOALIASFLAGS = $(CXXBASEFLAGS) $(CXXNOALIASOPTS)
+include .rootdir/Plumed.inc
+
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)
@@ -394,10 +396,11 @@
$(CUDAOBJS) \
$(CUDALIB) \
$(DPMTALIB) \
$(DPMELIB) \
$(TCLLIB) \
+ $(PLUMED_LOAD) \
$(FFTLIB) \
$(PLUGINLIB) \
$(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(i);
+ charges[i]=Node::Object()->molecule->atommass(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("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",
@@ -4299,11 +4306,11 @@
}
// Global forces configuration
globalForcesOn = ( tclForcesOn || freeEnergyOn || miscForcesOn ||
- (IMDon && ! IMDignore) || SMDOn || TMDOn || colvarsOn || symmetryOn );
+ (IMDon && ! IMDignore) || SMDOn || TMDOn || colvarsOn || symmetryOn || 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