namd 2.8 tentative patch

patches/namd-2.8.config

+
+
+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
+}

patches/namd-2.8.diff

+patch -u -l -b -F 5 --suffix=.preplumed "./Makefile" << \EOF_EOF
+--- ./Makefile.preplumed
++++ ./Makefile
+@@ -347,10 +347,12 @@
+ 	cat $(BUILDINFO).C; \
+ 	$(CXX) $(CXXFLAGS) $(COPTO)$(BUILDINFO).o $(COPTC) $(BUILDINFO).C
+ 
+ all:	$(BINARIES) $(LIBCUDARTSO)
+ 
++include .rootdir/Plumed.inc
++
+ namd2:	$(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
+ 	$(MAKEBUILDINFO)
+ 	$(CHARMC) -verbose -ld++-option \
+ 	"$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \
+ 	-module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -language charm++ \
+@@ -360,10 +362,11 @@
+ 	$(CUDALIB) \
+ 	$(DPMTALIB) \
+ 	$(DPMELIB) \
+ 	$(TCLLIB) \
+ 	$(FFTLIB) \
++        $(PLUMED_LOAD) \
+ 	$(PLUGINLIB) \
+ 	$(CHARMOPTS) \
+ 	-lm -o namd2
+ 
+ charmrun: $(CHARM)/bin/charmrun # XXX
+EOF_EOF
+patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.C" << \EOF_EOF
+--- ./src/SimParameters.C.preplumed
++++ ./src/SimParameters.C
+@@ -1231,10 +1231,17 @@
+       &colvarsOn, FALSE);
+     opts.require("colvars", "colvarsConfig",
+       "configuration for the collective variables", PARSE_STRING);
+     opts.optional("colvars", "colvarsInput",
+       "input restart file for the collective variables", PARSE_STRING);
++
++     // PLUMED
++     //// plumed
++     opts.optionalB("main", "plumed", "Is PLUMED active?",&plumedOn,FALSE);
++     opts.require("plumed", "plumedfile","PLUMED script",PARSE_STRING);
++     // END PLUMED
++
+ }
+ 
+ 
+ /* BEGIN gf */
+ void SimParameters::config_parser_mgridforce(ParseOptions &opts) {
+@@ -3511,11 +3518,11 @@
+    }
+    
+    // Global forces configuration
+ 
+    globalForcesOn = ( tclForcesOn || freeEnergyOn || miscForcesOn ||
+-                       (IMDon) || SMDOn || TMDOn || colvarsOn || symmetryOn );
++                       (IMDon) || SMDOn || TMDOn || colvarsOn || symmetryOn || plumedOn );
+ 
+ 
+    if (tclForcesOn)
+    {
+      iout << iINFO << "TCL GLOBAL FORCES ACTIVE\n";
+@@ -3596,10 +3603,25 @@
+      }
+ 
+      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/ComputeMgr.C" << \EOF_EOF
+--- ./src/ComputeMgr.C.preplumed
++++ ./src/ComputeMgr.C
+@@ -73,13 +73,134 @@
+ #include "GlobalMasterTcl.h"
+ #include "GlobalMasterSMD.h"
+ #include "GlobalMasterTMD.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("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);
++      modifyRequestedAtoms().resize(0);
++      for(int i=0;i<n;i++){
++        requestAtom(p[i]);
++        index[i]=p[i];
++      };
++      positions.resize(3*n);
++      forces.resize(3*n);
++      charges.resize(n);
++      masses.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("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;
+     computeDPMEObject = 0;
+@@ -656,10 +777,16 @@
+             );
+         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.h" << \EOF_EOF
+--- ./src/SimParameters.h.preplumed
++++ ./src/SimParameters.h
+@@ -351,10 +351,13 @@
+ 	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