From 71dd89903f8e280cf62f0626dda7df2b9cfca02c Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Fri, 23 Nov 2012 14:36:11 +0100
Subject: [PATCH] Added functionality that allows you to run driver with no
atoms so that you can run on colvar files only
---
src/ActionAtomistic.cpp | 1 +
src/CLToolDriver.cpp | 279 +++++++++++++++++++++-------------------
2 files changed, 146 insertions(+), 134 deletions(-)
diff --git a/src/ActionAtomistic.cpp b/src/ActionAtomistic.cpp
index ae8a11a46..e77612e73 100644
--- a/src/ActionAtomistic.cpp
+++ b/src/ActionAtomistic.cpp
@@ -48,6 +48,7 @@ lockRequestAtoms(false),
atoms(plumed.getAtoms())
{
atoms.add(this);
+ if(atoms.getNatoms()==0) error("Cannot perform calculations involving atoms without atoms");
}
void ActionAtomistic::registerKeywords( Keywords& keys ){
diff --git a/src/CLToolDriver.cpp b/src/CLToolDriver.cpp
index 6199ed834..ecdbe0dc8 100644
--- a/src/CLToolDriver.cpp
+++ b/src/CLToolDriver.cpp
@@ -80,6 +80,7 @@ void CLToolDriver<real>::registerKeywords( Keywords& keys ){
keys.add("compulsory","--plumed","plumed.dat","specify the name of the plumed input file");
keys.add("compulsory","--timestep","1.0","the timestep that was used in the calculation that produced this trajectory in picoseconds");
keys.add("compulsory","--trajectory-stride","1","the frequency with which frames were output to this trajectory during the simulation");
+ keys.addFlag("--noatoms",false,"don't read in a trajectory. Just use colvar files as specified in plumed.dat");
keys.add("atoms","--ixyz","the trajectory in xyz format");
keys.add("optional","--length-units","units for length, either as a string or a number");
keys.add("optional","--dump-forces","dump the forces on a file");
@@ -124,6 +125,9 @@ int CLToolDriver<real>::main(FILE* in,FILE*out,PlumedCommunicator& pc){
);
return 0;
}
+ // Are we reading trajectory data
+ bool noatoms; parseFlag("--noatoms",noatoms);
+
std::string fakein;
bool debugfloat=parse("--debug-float",fakein);
if(debugfloat && sizeof(real)!=sizeof(float)){
@@ -136,12 +140,14 @@ int CLToolDriver<real>::main(FILE* in,FILE*out,PlumedCommunicator& pc){
bool debug_pd=parse("--debug-pd",fakein);
bool debug_dd=parse("--debug-dd",fakein);
+ if( debug_pd || debug_dd ) plumed_massert(!noatoms,"cannot debug without atoms");
int multi=1;
FILE*multi_log=NULL;
bool debug_grex=parse("--debug-grex",fakein);
PlumedCommunicator intracomm;
PlumedCommunicator intercomm;
if(debug_grex){
+ plumed_massert( !noatoms, "must have atoms to debug_grex");
Tools::convert(fakein,multi);
int ntot=pc.Get_size();
int nintra=ntot/multi;
@@ -168,58 +174,68 @@ int CLToolDriver<real>::main(FILE* in,FILE*out,PlumedCommunicator& pc){
unsigned stride; parse("--trajectory-stride",stride);
// are we writing forces
string dumpforces(""), dumpforcesFmt("%f");;
- parse("--dump-forces",dumpforces);
+ if(!noatoms) parse("--dump-forces",dumpforces);
if(dumpforces!="") parse("--dump-forces-fmt",dumpforcesFmt);
// Read in an xyz file
- string trajectoryFile("");
- std::string traj_xyz; parse("--ixyz",traj_xyz);
- if(traj_xyz.length()>0 && trajectoryFile.length()==0) trajectoryFile=traj_xyz;
- if(trajectoryFile.length()==0){
- fprintf(out,"ERROR: missing trajectory data\n");
- return 0;
- }
- string lengthUnits(""); parse("--length-units",lengthUnits);
- if(lengthUnits.length()>0) units.setLength(lengthUnits);
-
- string pdbfile; parse("--pdb",pdbfile);
- if(pdbfile.length()>0){
- bool check=pdb.read(pdbfile,false,1.0);
- plumed_massert(check,"error reading pdb file");
- }
+ string trajectoryFile(""), pdbfile("");
+ bool pbc_cli_given=false; vector<double> pbc_cli_box(9,0.0);
+ if(!noatoms){
+ std::string traj_xyz; parse("--ixyz",traj_xyz);
+ if(traj_xyz.length()>0 && trajectoryFile.length()==0) trajectoryFile=traj_xyz;
+ if(trajectoryFile.length()==0){
+ fprintf(stderr,"ERROR: missing trajectory data\n");
+ return 1;
+ }
+ string lengthUnits(""); parse("--length-units",lengthUnits);
+ if(lengthUnits.length()>0) units.setLength(lengthUnits);
+
+ parse("--pdb",pdbfile);
+ if(pdbfile.length()>0){
+ bool check=pdb.read(pdbfile,false,1.0);
+ plumed_massert(check,"error reading pdb file");
+ }
- string pbc_cli_list; parse("--box",pbc_cli_list);
- bool pbc_cli_given=false;
- vector<double> pbc_cli_box(9,0.0);
- if(pbc_cli_list.length()>0) {
- pbc_cli_given=true;
- vector<string> words=Tools::getWords(pbc_cli_list,",");
- if(words.size()==3){
- for(int i=0;i<3;i++) sscanf(words[i].c_str(),"%lf",&(pbc_cli_box[4*i]));
- } else if(words.size()==9) {
- for(int i=0;i<9;i++) sscanf(words[i].c_str(),"%lf",&(pbc_cli_box[i]));
- } else {
- string msg="ERROR: cannot parse command-line box "+pbc_cli_list;
- fprintf(stderr,"%s\n",msg.c_str());
- return 1;
- }
+ string pbc_cli_list; parse("--box",pbc_cli_list);
+ if(pbc_cli_list.length()>0) {
+ pbc_cli_given=true;
+ vector<string> words=Tools::getWords(pbc_cli_list,",");
+ if(words.size()==3){
+ for(int i=0;i<3;i++) sscanf(words[i].c_str(),"%lf",&(pbc_cli_box[4*i]));
+ } else if(words.size()==9) {
+ for(int i=0;i<9;i++) sscanf(words[i].c_str(),"%lf",&(pbc_cli_box[i]));
+ } else {
+ string msg="ERROR: cannot parse command-line box "+pbc_cli_list;
+ fprintf(stderr,"%s\n",msg.c_str());
+ return 1;
+ }
+ }
}
-
+
plumed_massert(!(debug_dd&debug_pd),"cannot use debug-dd and debug-pd at the same time");
if(debug_pd || debug_dd) plumed_massert(PlumedCommunicator::initialized(),"needs mpi for debug-pd");
- if(trajectoryFile.length()==0){
- string msg="ERROR: please specify a trajectory";
- fprintf(stderr,"%s\n",msg.c_str());
- return 1;
- }
-
Plumed p;
int rr=sizeof(real);
p.cmd("setRealPrecision",&rr);
- int checknatoms=0;
+ int checknatoms=-1;
+ int plumedStopCondition=0;
+ p.cmd("setStopFlag",&plumedStopCondition);
int step=0;
+ if(PlumedCommunicator::initialized()){
+ if(multi>1){
+ if(intracomm.Get_rank()==0) p.cmd("GREX setMPIIntercomm",&intercomm.Get_comm());
+ p.cmd("GREX setMPIIntracomm",&intracomm.Get_comm());
+ p.cmd("GREX init");
+ }
+ p.cmd("setMPIComm",&intracomm.Get_comm());
+ }
+ p.cmd("setMDLengthUnits",&units.getLength());
+ p.cmd("setMDEngine","driver");
+ p.cmd("setTimestep",×tep);
+ p.cmd("setPlumedDat",plumedFile.c_str());
+ p.cmd("setLog",out);
if(debug_grex){
string n;
@@ -227,29 +243,29 @@ int CLToolDriver<real>::main(FILE* in,FILE*out,PlumedCommunicator& pc){
trajectoryFile+="."+n;
}
- FILE* fp;
- if (trajectoryFile=="-")
- fp=in;
- else {
- fp=fopen(trajectoryFile.c_str(),"r");
- if(!fp){
- string msg="ERROR: Error opening XYZ file "+trajectoryFile;
- fprintf(stderr,"%s\n",msg.c_str());
- return 1;
- }
- }
-
-
- FILE* fp_forces=NULL;
- if(dumpforces.length()>0){
- if(PlumedCommunicator::initialized() && pc.Get_size()>1){
- string n;
- Tools::convert(pc.Get_rank(),n);
- dumpforces+="."+n;
- }
- fp_forces=fopen(dumpforces.c_str(),"w");
+ FILE* fp=NULL; FILE* fp_forces=NULL;
+ if(!noatoms){
+ if (trajectoryFile=="-")
+ fp=in;
+ else {
+ fp=fopen(trajectoryFile.c_str(),"r");
+ if(!fp){
+ string msg="ERROR: Error opening XYZ file "+trajectoryFile;
+ fprintf(stderr,"%s\n",msg.c_str());
+ return 1;
+ }
+ }
+
+ if(dumpforces.length()>0){
+ if(PlumedCommunicator::initialized() && pc.Get_size()>1){
+ string n;
+ Tools::convert(pc.Get_rank(),n);
+ dumpforces+="."+n;
+ }
+ fp_forces=fopen(dumpforces.c_str(),"w");
+ }
}
-
+
std::string line;
std::vector<real> coordinates;
std::vector<real> forces;
@@ -272,29 +288,16 @@ int CLToolDriver<real>::main(FILE* in,FILE*out,PlumedCommunicator& pc){
// random stream to choose decompositions
Random rnd;
- while(Tools::getline(fp,line)){
+ while(true){
+ if(!noatoms){
+ if(!Tools::getline(fp,line)) break;
+ } else if ( plumedStopCondition ) break;
int natoms;
bool ok;
bool first_step=false;
- sscanf(line.c_str(),"%d",&natoms);
- if(checknatoms==0){
- checknatoms=natoms;
- if(PlumedCommunicator::initialized()){
- if(multi>1){
- if(intracomm.Get_rank()==0) p.cmd("GREX setMPIIntercomm",&intercomm.Get_comm());
- p.cmd("GREX setMPIIntracomm",&intracomm.Get_comm());
- p.cmd("GREX init");
- }
- p.cmd("setMPIComm",&intracomm.Get_comm());
- }
- p.cmd("setMDLengthUnits",&units.getLength());
- p.cmd("setNatoms",&natoms);
- p.cmd("setMDEngine","driver");
- p.cmd("setTimestep",×tep);
- p.cmd("setPlumedDat",plumedFile.c_str());
- p.cmd("setLog",out);
- p.cmd("init");
+ if(!noatoms) sscanf(line.c_str(),"%d",&natoms);
+ if(checknatoms<0 && !noatoms){
pd_nlocal=natoms;
pd_start=0;
first_step=true;
@@ -309,7 +312,13 @@ int CLToolDriver<real>::main(FILE* in,FILE*out,PlumedCommunicator& pc){
charges[index]=pdb.getBeta()[i];
}
}
-
+ } else if( checknatoms<0 && noatoms ){
+ natoms=0;
+ }
+ if( checknatoms<0 ){
+ checknatoms=natoms;
+ p.cmd("setNatoms",&natoms);
+ p.cmd("init");
}
plumed_massert(checknatoms==natoms,"number of atom changed");
@@ -371,61 +380,63 @@ int CLToolDriver<real>::main(FILE* in,FILE*out,PlumedCommunicator& pc){
}
}
- ok=Tools::getline(fp,line);
- plumed_massert(ok,"premature end of file");
-
- std::vector<double> celld(9,0.0);
- if(pbc_cli_given==false) {
- std::vector<std::string> words;
- words=Tools::getWords(line);
- if(words.size()==3){
- sscanf(line.c_str(),"%lf %lf %lf",&celld[0],&celld[4],&celld[8]);
- } else if(words.size()==9){
- sscanf(line.c_str(),"%lf %lf %lf %lf %lf %lf %lf %lf %lf",
- &celld[0], &celld[1], &celld[2],
- &celld[3], &celld[4], &celld[5],
- &celld[6], &celld[7], &celld[8]);
- } else plumed_merror("needed box in second line");
- } else { // from command line
- celld=pbc_cli_box;
- }
- for(unsigned i=0;i<9;i++)cell[i]=real(celld[i]);
-
- // Read coordinates
- for(int i=0;i<natoms;i++){
- ok=Tools::getline(fp,line);
- plumed_massert(ok,"premature end of file");
- char dummy[1000];
- double cc[3];
- std::sscanf(line.c_str(),"%s %lf %lf %lf",dummy,&cc[0],&cc[1],&cc[2]);
- if(!debug_pd || ( i>=pd_start && i<pd_start+pd_nlocal) ){
- coordinates[3*i]=real(cc[0]);
- coordinates[3*i+1]=real(cc[1]);
- coordinates[3*i+2]=real(cc[2]);
- }
- if(debug_dd){
- for(int i=0;i<dd_nlocal;++i){
- int kk=dd_gatindex[i];
- dd_coordinates[3*i+0]=coordinates[3*kk+0];
- dd_coordinates[3*i+1]=coordinates[3*kk+1];
- dd_coordinates[3*i+2]=coordinates[3*kk+2];
- }
- }
- }
+ if(!noatoms){
+ ok=Tools::getline(fp,line);
+ plumed_massert(ok,"premature end of file");
+
+ std::vector<double> celld(9,0.0);
+ if(pbc_cli_given==false) {
+ std::vector<std::string> words;
+ words=Tools::getWords(line);
+ if(words.size()==3){
+ sscanf(line.c_str(),"%lf %lf %lf",&celld[0],&celld[4],&celld[8]);
+ } else if(words.size()==9){
+ sscanf(line.c_str(),"%lf %lf %lf %lf %lf %lf %lf %lf %lf",
+ &celld[0], &celld[1], &celld[2],
+ &celld[3], &celld[4], &celld[5],
+ &celld[6], &celld[7], &celld[8]);
+ } else plumed_merror("needed box in second line");
+ } else { // from command line
+ celld=pbc_cli_box;
+ }
+ for(unsigned i=0;i<9;i++)cell[i]=real(celld[i]);
+
+ // Read coordinates
+ for(int i=0;i<natoms;i++){
+ ok=Tools::getline(fp,line);
+ plumed_massert(ok,"premature end of file");
+ char dummy[1000];
+ double cc[3];
+ std::sscanf(line.c_str(),"%s %lf %lf %lf",dummy,&cc[0],&cc[1],&cc[2]);
+ if(!debug_pd || ( i>=pd_start && i<pd_start+pd_nlocal) ){
+ coordinates[3*i]=real(cc[0]);
+ coordinates[3*i+1]=real(cc[1]);
+ coordinates[3*i+2]=real(cc[2]);
+ }
+ if(debug_dd){
+ for(int i=0;i<dd_nlocal;++i){
+ int kk=dd_gatindex[i];
+ dd_coordinates[3*i+0]=coordinates[3*kk+0];
+ dd_coordinates[3*i+1]=coordinates[3*kk+1];
+ dd_coordinates[3*i+2]=coordinates[3*kk+2];
+ }
+ }
+ }
- if(debug_dd){
- p.cmd("setForces",&dd_forces[0]);
- p.cmd("setPositions",&dd_coordinates[0]);
- p.cmd("setMasses",&dd_masses[0]);
- p.cmd("setCharges",&dd_charges[0]);
- } else {
- p.cmd("setForces",&forces[3*pd_start]);
- p.cmd("setPositions",&coordinates[3*pd_start]);
- p.cmd("setMasses",&masses[pd_start]);
- p.cmd("setCharges",&charges[pd_start]);
+ if(debug_dd){
+ p.cmd("setForces",&dd_forces[0]);
+ p.cmd("setPositions",&dd_coordinates[0]);
+ p.cmd("setMasses",&dd_masses[0]);
+ p.cmd("setCharges",&dd_charges[0]);
+ } else {
+ p.cmd("setForces",&forces[3*pd_start]);
+ p.cmd("setPositions",&coordinates[3*pd_start]);
+ p.cmd("setMasses",&masses[pd_start]);
+ p.cmd("setCharges",&charges[pd_start]);
+ }
+ p.cmd("setBox",&cell[0]);
+ p.cmd("setVirial",&virial[0]);
}
- p.cmd("setBox",&cell[0]);
- p.cmd("setVirial",&virial[0]);
p.cmd("setStep",&step);
p.cmd("calc");
--
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