void SingleDomainRMSD::readReference( const PDB& pdb ){
readAtomsFromPDB( pdb );
double wa=0, wd=0;
for(unsigned i=0;i<pdb.size();++i){ wa+=align[i]; wd+=displace[i]; }
Vector center;
for(unsigned i=0;i<pdb.size();++i){
align[i]=align[i] / wa; displace[i]=displace[i] / wd;
center+=reference_atoms[i]*align[i];
}
for(unsigned i=0;i<pdb.size();++i) reference_atoms[i]-=center;
}
void ReferenceAtoms::readAtomsFromPDB( const PDB& pdb, const bool allowblocks ){
if( !allowblocks && pdb.getNumberOfAtomBlocks()!=1 ) error("found multi-atom-block pdb format but expecting only one block of atoms");
for(unsigned i=0;i<pdb.size();++i){
indices.push_back( pdb.getAtomNumbers()[i] ); reference_atoms.push_back( pdb.getPositions()[i] );
align.push_back( pdb.getOccupancy()[i] ); displace.push_back( pdb.getBeta()[i] );
}
atom_der_index.resize( reference_atoms.size() );
}
void ActionAtomistic::readAtomsFromPDB( const PDB& pdb ){
Colvar*cc=dynamic_cast<Colvar*>(this);
if(cc && cc->checkIsEnergy()) error("can't read energies from pdb files");
for(unsigned j=0;j<indexes.size();j++){
if( indexes[j].index()>pdb.size() ) error("there are not enough atoms in the input pdb file");
if( pdb.getAtomNumbers()[j].index()!=indexes[j].index() ) error("there are atoms missing in the pdb file");
positions[j]=pdb.getPositions()[indexes[j].index()];
}
for(unsigned j=0;j<indexes.size();j++) charges[j]=pdb.getBeta()[indexes[j].index()];
for(unsigned j=0;j<indexes.size();j++) masses[j]=pdb.getOccupancy()[indexes[j].index()];
}
void MultiDomainRMSD::read( const PDB& pdb ) {
unsigned nblocks = pdb.getNumberOfAtomBlocks();
if( nblocks<2 ) error("multidomain RMSD only has one block of atoms");
std::vector<Vector> positions; std::vector<double> align, displace;
std::string num; blocks.resize( nblocks+1 ); blocks[0]=0;
for(unsigned i=0; i<nblocks; ++i) blocks[i+1]=pdb.getAtomBlockEnds()[i];
double tmp, lower=0.0, upper=std::numeric_limits<double>::max( );
if( pdb.getArgumentValue("LOWER_CUTOFF",tmp) ) lower=tmp;
if( pdb.getArgumentValue("UPPER_CUTOFF",tmp) ) upper=tmp;
bool nopbc=pdb.hasFlag("NOPBC");
domains.resize(0); weights.resize(0);
for(unsigned i=1; i<=nblocks; ++i) {
Tools::convert(i,num);
if( ftype=="RMSD" ) {
// parse("TYPE"+num, ftype );
lower=0.0; upper=std::numeric_limits<double>::max( );
if( pdb.getArgumentValue("LOWER_CUTOFF"+num,tmp) ) lower=tmp;
if( pdb.getArgumentValue("UPPER_CUTOFF"+num,tmp) ) upper=tmp;
nopbc=pdb.hasFlag("NOPBC");
}
domains.emplace_back( metricRegister().create<SingleDomainRMSD>( ftype ) );
positions.resize( blocks[i] - blocks[i-1] );
align.resize( blocks[i] - blocks[i-1] );
displace.resize( blocks[i] - blocks[i-1] );
unsigned n=0;
for(unsigned j=blocks[i-1]; j<blocks[i]; ++j) {
positions[n]=pdb.getPositions()[j];
align[n]=pdb.getOccupancy()[j];
displace[n]=pdb.getBeta()[j];
n++;
}
domains[i-1]->setBoundsOnDistances( !nopbc, lower, upper );
domains[i-1]->setReferenceAtoms( positions, align, displace );
domains[i-1]->setupRMSDObject();
double ww=0;
if( !pdb.getArgumentValue("WEIGHT"+num,ww) ) weights.push_back( 1.0 );
else weights.push_back( ww );
}
// And set the atom numbers for this object
indices.resize(0); atom_der_index.resize(0);
for(unsigned i=0; i<pdb.size(); ++i) { indices.push_back( pdb.getAtomNumbers()[i] ); atom_der_index.push_back(i); }
// setAtomNumbers( pdb.getAtomNumbers() );
}
int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
Units units;
PDB pdb;
// Parse everything
bool printhelpdebug; parseFlag("--help-debug",printhelpdebug);
if( printhelpdebug ){
fprintf(out,"%s",
"Additional options for debug (only to be used in regtest):\n"
" [--debug-float] : turns on the single precision version (to check float interface)\n"
" [--debug-dd] : use a fake domain decomposition\n"
" [--debug-pd] : use a fake particle decomposition\n"
);
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)){
CLTool* cl=cltoolRegister().create(CLToolOptions("driver-float")); //new Driver<float>(*this);
cl->setInputData(this->getInputData());
int ret=cl->main(in,out,pc);
delete cl;
return ret;
}
bool debug_pd=parse("--debug-pd",fakein);
bool debug_dd=parse("--debug-dd",fakein);
if( debug_pd || debug_dd ){
if(noatoms) error("cannot debug without atoms");
}
// set up for multi replica driver:
int multi=0;
parse("--multi",multi);
Communicator intracomm;
Communicator intercomm;
if(multi){
int ntot=pc.Get_size();
int nintra=ntot/multi;
if(multi*nintra!=ntot) error("invalid number of processes for multi environment");
pc.Split(pc.Get_rank()/nintra,pc.Get_rank(),intracomm);
pc.Split(pc.Get_rank()%nintra,pc.Get_rank(),intercomm);
} else {
intracomm.Set_comm(pc.Get_comm());
}
// set up for debug replica exchange:
bool debug_grex=parse("--debug-grex",fakein);
int grex_stride=0;
FILE*grex_log=NULL;
if(debug_grex){
if(noatoms) error("must have atoms to debug_grex");
if(multi<2) error("--debug_grex needs --multi with at least two replicas");
Tools::convert(fakein,grex_stride);
string n; Tools::convert(intercomm.Get_rank(),n);
string file;
parse("--debug-grex-log",file);
if(file.length()>0){
file+="."+n;
grex_log=fopen(file.c_str(),"w");
}
}
// Read the plumed input file name
string plumedFile; parse("--plumed",plumedFile);
// the timestep
double t; parse("--timestep",t);
real timestep=real(t);
// the stride
unsigned stride; parse("--trajectory-stride",stride);
// are we writing forces
string dumpforces(""), dumpforcesFmt("%f");;
if(!noatoms) parse("--dump-forces",dumpforces);
if(dumpforces!="") parse("--dump-forces-fmt",dumpforcesFmt);
string trajectory_fmt;
// Read in an xyz 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);
std::string traj_gro; parse("--igro",traj_gro);
if(traj_xyz.length()>0 && traj_gro.length()>0){
fprintf(stderr,"ERROR: cannot provide more than one trajectory file\n");
if(grex_log)fclose(grex_log);
return 1;
}
if(traj_xyz.length()>0 && trajectoryFile.length()==0){
trajectoryFile=traj_xyz;
trajectory_fmt="xyz";
}
if(traj_gro.length()>0 && trajectoryFile.length()==0){
trajectoryFile=traj_gro;
trajectory_fmt="gro";
}
if(trajectoryFile.length()==0){
fprintf(stderr,"ERROR: missing trajectory data\n");
if(grex_log)fclose(grex_log);
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);
if(!check) error("error reading pdb file");
}
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(),"%100lf",&(pbc_cli_box[4*i]));
} else if(words.size()==9) {
for(int i=0;i<9;i++) sscanf(words[i].c_str(),"%100lf",&(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;
}
}
}
if( debug_dd && debug_pd ) error("cannot use debug-dd and debug-pd at the same time");
if(debug_pd || debug_dd){
if( !Communicator::initialized() ) error("needs mpi for debug-pd");
}
Plumed p;
int rr=sizeof(real);
p.cmd("setRealPrecision",&rr);
int checknatoms=-1;
int step=0;
if(Communicator::initialized()){
if(multi){
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(multi){
string n;
Tools::convert(intercomm.Get_rank(),n);
trajectoryFile+="."+n;
}
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(Communicator::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;
std::vector<real> masses;
std::vector<real> charges;
std::vector<real> cell;
std::vector<real> virial;
// variables to test particle decomposition
int pd_nlocal;
int pd_start;
// variables to test random decomposition (=domain decomposition)
std::vector<int> dd_gatindex;
std::vector<int> dd_g2l;
std::vector<real> dd_masses;
std::vector<real> dd_charges;
std::vector<real> dd_forces;
std::vector<real> dd_coordinates;
int dd_nlocal;
// random stream to choose decompositions
Random rnd;
while(true){
if(!noatoms){
if(!Tools::getline(fp,line)) break;
}
int natoms;
bool first_step=false;
if(!noatoms){
if(trajectory_fmt=="gro") if(!Tools::getline(fp,line)) error("premature end of trajectory file");
sscanf(line.c_str(),"%100d",&natoms);
}
if(checknatoms<0 && !noatoms){
pd_nlocal=natoms;
pd_start=0;
first_step=true;
masses.assign(natoms,real(1.0));
charges.assign(natoms,real(0.0));
if(pdbfile.length()>0){
for(unsigned i=0;i<pdb.size();++i){
AtomNumber an=pdb.getAtomNumbers()[i];
unsigned index=an.index();
if( index>=unsigned(natoms) ) error("atom index in pdb exceeds the number of atoms in trajectory");
masses[index]=pdb.getOccupancy()[i];
charges[index]=pdb.getBeta()[i];
}
}
} else if( checknatoms<0 && noatoms ){
natoms=0;
}
if( checknatoms<0 ){
checknatoms=natoms;
p.cmd("setNatoms",&natoms);
p.cmd("init");
}
if(checknatoms!=natoms){
std::string stepstr; Tools::convert(step,stepstr);
error("number of atoms in frame " + stepstr + " does not match number of atoms in first frame");
}
coordinates.assign(3*natoms,real(0.0));
forces.assign(3*natoms,real(0.0));
cell.assign(9,real(0.0));
virial.assign(9,real(0.0));
if( first_step || rnd.U01()>0.5){
if(debug_pd){
int npe=intracomm.Get_size();
vector<int> loc(npe,0);
vector<int> start(npe,0);
for(int i=0;i<npe-1;i++){
int cc=(natoms*2*rnd.U01())/npe;
if(start[i]+cc>natoms) cc=natoms-start[i];
loc[i]=cc;
start[i+1]=start[i]+loc[i];
}
loc[npe-1]=natoms-start[npe-1];
intracomm.Bcast(loc,0);
intracomm.Bcast(start,0);
pd_nlocal=loc[intracomm.Get_rank()];
pd_start=start[intracomm.Get_rank()];
if(intracomm.Get_rank()==0){
fprintf(out,"\nDRIVER: Reassigning particle decomposition\n");
fprintf(out,"DRIVER: "); for(int i=0;i<npe;i++) fprintf(out,"%d ",loc[i]); printf("\n");
fprintf(out,"DRIVER: "); for(int i=0;i<npe;i++) fprintf(out,"%d ",start[i]); printf("\n");
}
p.cmd("setAtomsNlocal",&pd_nlocal);
p.cmd("setAtomsContiguous",&pd_start);
} else if(debug_dd){
int npe=intracomm.Get_size();
int rank=intracomm.Get_rank();
dd_charges.assign(natoms,0.0);
dd_masses.assign(natoms,0.0);
dd_gatindex.assign(natoms,-1);
dd_g2l.assign(natoms,-1);
dd_coordinates.assign(3*natoms,0.0);
dd_forces.assign(3*natoms,0.0);
dd_nlocal=0;
for(int i=0;i<natoms;++i){
double r=rnd.U01()*npe;
int n; for(n=0;n<npe;n++) if(n+1>r)break;
plumed_assert(n<npe);
if(n==rank){
dd_gatindex[dd_nlocal]=i;
dd_g2l[i]=dd_nlocal;
dd_charges[dd_nlocal]=charges[i];
dd_masses[dd_nlocal]=masses[i];
dd_nlocal++;
}
}
if(intracomm.Get_rank()==0){
fprintf(out,"\nDRIVER: Reassigning particle decomposition\n");
}
p.cmd("setAtomsNlocal",&dd_nlocal);
p.cmd("setAtomsGatindex",&dd_gatindex[0]);
}
}
int plumedStopCondition=0;
p.cmd("setStep",&step);
p.cmd("setStopFlag",&plumedStopCondition);
if(!noatoms){
if(trajectory_fmt=="xyz"){
if(!Tools::getline(fp,line)) error("premature end of trajectory 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(),"%100lf %100lf %100lf",&celld[0],&celld[4],&celld[8]);
} else if(words.size()==9){
sscanf(line.c_str(),"%100lf %100lf %100lf %100lf %100lf %100lf %100lf %100lf %100lf",
&celld[0], &celld[1], &celld[2],
&celld[3], &celld[4], &celld[5],
&celld[6], &celld[7], &celld[8]);
} else error("needed box in second line of xyz file");
} else { // from command line
celld=pbc_cli_box;
}
for(unsigned i=0;i<9;i++)cell[i]=real(celld[i]);
}
int ddist=0;
// Read coordinates
for(int i=0;i<natoms;i++){
bool ok=Tools::getline(fp,line);
if(!ok) error("premature end of trajectory file");
double cc[3];
if(trajectory_fmt=="xyz"){
char dummy[1000];
std::sscanf(line.c_str(),"%999s %100lf %100lf %100lf",dummy,&cc[0],&cc[1],&cc[2]);
} else if(trajectory_fmt=="gro"){
// do the gromacs way
if(!i){
//
// calculate the distance between dots (as in gromacs gmxlib/confio.c, routine get_w_conf )
//
const char *p1, *p2, *p3;
p1 = strchr(line.c_str(), '.');
if (p1 == NULL) error("seems there are no coordinates in the gro file");
p2 = strchr(&p1[1], '.');
if (p2 == NULL) error("seems there is only one coordinates in the gro file");
ddist = p2 - p1;
p3 = strchr(&p2[1], '.');
if (p3 == NULL)error("seems there are only two coordinates in the gro file");
if (p3 - p2 != ddist)error("not uniform spacing in fields in the gro file");
}
Tools::convert(line.substr(20,ddist),cc[0]);
Tools::convert(line.substr(20+ddist,ddist),cc[1]);
Tools::convert(line.substr(20+ddist+ddist,ddist),cc[2]);
} else plumed_error();
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(trajectory_fmt=="gro"){
if(!Tools::getline(fp,line)) error("premature end of trajectory file");
std::vector<string> words=Tools::getWords(line);
if(words.size()<3) error("cannot understand box format");
Tools::convert(words[0],cell[0]);
Tools::convert(words[1],cell[4]);
Tools::convert(words[2],cell[8]);
if(words.size()>3) Tools::convert(words[3],cell[1]);
if(words.size()>4) Tools::convert(words[4],cell[2]);
if(words.size()>5) Tools::convert(words[5],cell[3]);
if(words.size()>6) Tools::convert(words[6],cell[5]);
if(words.size()>7) Tools::convert(words[7],cell[6]);
if(words.size()>8) Tools::convert(words[8],cell[7]);
}
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];
}
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("calc");
// this is necessary as only processor zero is adding to the virial:
intracomm.Bcast(virial,0);
if(debug_pd) intracomm.Sum(forces);
if(debug_dd){
for(int i=0;i<dd_nlocal;i++){
forces[3*dd_gatindex[i]+0]=dd_forces[3*i+0];
forces[3*dd_gatindex[i]+1]=dd_forces[3*i+1];
forces[3*dd_gatindex[i]+2]=dd_forces[3*i+2];
}
dd_forces.assign(3*natoms,0.0);
intracomm.Sum(forces);
}
if(debug_grex &&step%grex_stride==0){
p.cmd("GREX savePositions");
if(intracomm.Get_rank()>0){
p.cmd("GREX prepare");
} else {
int r=intercomm.Get_rank();
int n=intercomm.Get_size();
int partner=r+(2*((r+step/grex_stride)%2))-1;
if(partner<0)partner=0;
if(partner>=n) partner=n-1;
p.cmd("GREX setPartner",&partner);
p.cmd("GREX calculate");
p.cmd("GREX shareAllDeltaBias");
for(int i=0;i<n;i++){
string s; Tools::convert(i,s);
real a; s="GREX getDeltaBias "+s; p.cmd(s.c_str(),&a);
if(grex_log) fprintf(grex_log," %f",a);
}
if(grex_log) fprintf(grex_log,"\n");
}
}
if(fp_forces){
fprintf(fp_forces,"%d\n",natoms);
string fmt=dumpforcesFmt+" "+dumpforcesFmt+" "+dumpforcesFmt+"\n";
fprintf(fp_forces,fmt.c_str(),virial[0],virial[4],virial[8]);
fmt="X "+fmt;
for(int i=0;i<natoms;i++)
fprintf(fp_forces,fmt.c_str(),forces[3*i],forces[3*i+1],forces[3*i+2]);
}
if(noatoms && plumedStopCondition) break;
step+=stride;
}
p.cmd("runFinalJobs");
if(fp_forces) fclose(fp_forces);
if(fp && fp!=in)fclose(fp);
if(grex_log) fclose(grex_log);
return 0;
}