void CoordinationBase::prepare() {
if(nl->getStride()>0) {
if(firsttime || (getStep()%nl->getStride()==0)) {
requestAtoms(nl->getFullAtomList());
invalidateList=true;
firsttime=false;
} else {
requestAtoms(nl->getReducedAtomList());
invalidateList=false;
if(getExchangeStep()) error("Neighbor lists should be updated on exchange steps - choose a NL_STRIDE which divides the exchange stride!");
}
if(getExchangeStep()) firsttime=true;
}
}
IMD::IMD(const ActionOptions& ao):
Action(ao),
ActionAtomistic(ao),
ActionPilot(ao),
host("localhost"),
port(0),
wait(false),
wrap(false),
sock(NULL),
clientsock(NULL),
connected(false),
transferRate(100),
fscale(1.0)
{
natoms=plumed.getAtoms().getNatoms();
std::vector<AtomNumber> index(natoms);
for(int i=0;i<natoms;i++) index[i].setIndex(i);
requestAtoms(index);
coord.resize(natoms*3,float(0.0));
forces.resize(natoms*3,0.0);
parseFlag("WAIT",wait);
bool nowait=false;
parseFlag("NOWAIT",nowait);
if(nowait)wait=false;
parseFlag("WRAP",wrap);
parse("PORT",port);
parse("HOST",host);
parse("FSCALE",fscale);
checkRead();
log.printf(" with host %s\n",host.c_str());
log.printf(" with port %d\n",port);
if(wait) log.printf(" waiting for a connection\n");
else log.printf(" not waiting for a connection\n");
if(wrap) log.printf(" wrapping atoms\n");
else log.printf(" not wrapping atoms\n");
log.printf(" WMD forces will be scaled by %f\n",fscale);
if(comm.Get_rank()==0){
vmdsock_init();
sock = vmdsock_create();
vmdsock_bind(sock, port);
vmdsock_listen(sock);
}
connect();
}
void Mapping::prepare(){
if( mymap->mappingNeedsSetup() ){
// Get the arguments and atoms that are required
std::vector<AtomNumber> atoms; std::vector<std::string> args;
mymap->getAtomAndArgumentRequirements( atoms, args );
requestAtoms( atoms ); std::vector<Value*> req_args;
interpretArgumentList( args, req_args ); requestArguments( req_args );
// Duplicate all frames (duplicates are used by sketch-map)
mymap->duplicateFrameList();
// Get the number of frames in the path
unsigned nfram=getNumberOfReferencePoints();
fframes.resize( 2*nfram, 0.0 ); dfframes.resize( 2*nfram, 0.0 );
plumed_assert( !mymap->mappingNeedsSetup() );
// Resize all derivative arrays
mymap->setNumberOfAtomsAndArguments( atoms.size(), args.size() );
// Resize forces array
forcesToApply.resize( 3*getNumberOfAtoms() + 9 + getNumberOfArguments() );
}
}
CoordinationBase::CoordinationBase(const ActionOptions&ao):
PLUMED_COLVAR_INIT(ao),
pbc(true),
serial(false),
invalidateList(true),
firsttime(true)
{
parseFlag("SERIAL",serial);
vector<AtomNumber> ga_lista,gb_lista;
parseAtomList("GROUPA",ga_lista);
parseAtomList("GROUPB",gb_lista);
bool nopbc=!pbc;
parseFlag("NOPBC",nopbc);
pbc=!nopbc;
// pair stuff
bool dopair=false;
parseFlag("PAIR",dopair);
// neighbor list stuff
bool doneigh=false;
double nl_cut=0.0;
int nl_st=0;
parseFlag("NLIST",doneigh);
if(doneigh) {
parse("NL_CUTOFF",nl_cut);
if(nl_cut<=0.0) error("NL_CUTOFF should be explicitly specified and positive");
parse("NL_STRIDE",nl_st);
if(nl_st<=0) error("NL_STRIDE should be explicitly specified and positive");
}
addValueWithDerivatives(); setNotPeriodic();
if(gb_lista.size()>0) {
if(doneigh) nl= new NeighborList(ga_lista,gb_lista,dopair,pbc,getPbc(),nl_cut,nl_st);
else nl= new NeighborList(ga_lista,gb_lista,dopair,pbc,getPbc());
} else {
if(doneigh) nl= new NeighborList(ga_lista,pbc,getPbc(),nl_cut,nl_st);
else nl= new NeighborList(ga_lista,pbc,getPbc());
}
requestAtoms(nl->getFullAtomList());
log.printf(" between two groups of %u and %u atoms\n",static_cast<unsigned>(ga_lista.size()),static_cast<unsigned>(gb_lista.size()));
log.printf(" first group:\n");
for(unsigned int i=0; i<ga_lista.size(); ++i) {
if ( (i+1) % 25 == 0 ) log.printf(" \n");
log.printf(" %d", ga_lista[i].serial());
}
log.printf(" \n second group:\n");
for(unsigned int i=0; i<gb_lista.size(); ++i) {
if ( (i+1) % 25 == 0 ) log.printf(" \n");
log.printf(" %d", gb_lista[i].serial());
}
log.printf(" \n");
if(pbc) log.printf(" using periodic boundary conditions\n");
else log.printf(" without periodic boundary conditions\n");
if(dopair) log.printf(" with PAIR option\n");
if(doneigh) {
log.printf(" using neighbor lists with\n");
log.printf(" update every %d steps and cutoff %f\n",nl_st,nl_cut);
}
}
Mapping::Mapping(const ActionOptions&ao):
Action(ao),
ActionAtomistic(ao),
ActionWithArguments(ao),
ActionWithValue(ao),
ActionWithVessel(ao)
{
// Read the input
std::string mtype; parse("TYPE",mtype);
bool skipchecks; parseFlag("DISABLE_CHECKS",skipchecks);
// Setup the object that does the mapping
mymap = new PointWiseMapping( mtype, skipchecks );
// Read the properties we require
if( keywords.exists("PROPERTY") ){
std::vector<std::string> property;
parseVector("PROPERTY",property);
if(property.size()==0) error("no properties were specified");
mymap->setPropertyNames( property, false );
} else {
std::vector<std::string> property(1);
property[0]="sss";
mymap->setPropertyNames( property, true );
}
// Open reference file
std::string reference; parse("REFERENCE",reference);
FILE* fp=fopen(reference.c_str(),"r");
if(!fp) error("could not open reference file " + reference );
// Read all reference configurations
bool do_read=true; std::vector<double> weights;
unsigned nfram=0, wnorm=0., ww;
while (do_read){
PDB mypdb;
// Read the pdb file
do_read=mypdb.readFromFilepointer(fp,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength());
// Fix argument names
expandArgKeywordInPDB( mypdb );
if(do_read){
mymap->readFrame( mypdb ); ww=mymap->getWeight( nfram );
weights.push_back( ww );
wnorm+=ww; nfram++;
} else {
break;
}
}
fclose(fp);
if(nfram==0 ) error("no reference configurations were specified");
log.printf(" found %d configurations in file %s\n",nfram,reference.c_str() );
for(unsigned i=0;i<weights.size();++i) weights[i] /= wnorm;
mymap->setWeights( weights );
// Finish the setup of the mapping object
// Get the arguments and atoms that are required
std::vector<AtomNumber> atoms; std::vector<std::string> args;
mymap->getAtomAndArgumentRequirements( atoms, args );
requestAtoms( atoms ); std::vector<Value*> req_args;
interpretArgumentList( args, req_args ); requestArguments( req_args );
// Duplicate all frames (duplicates are used by sketch-map)
mymap->duplicateFrameList();
fframes.resize( 2*nfram, 0.0 ); dfframes.resize( 2*nfram, 0.0 );
plumed_assert( !mymap->mappingNeedsSetup() );
// Resize all derivative arrays
mymap->setNumberOfAtomsAndArguments( atoms.size(), args.size() );
// Resize forces array
if( getNumberOfAtoms()>0 ){
forcesToApply.resize( 3*getNumberOfAtoms() + 9 + getNumberOfArguments() );
} else {
forcesToApply.resize( getNumberOfArguments() );
}
}
