ParseStatus Parser::parseCall() {
assert(lex[0].isIdentifier());
assert(lex[1].isDelimiter(DL_LPAREN));
Atom func = resolve(lex[0].text);
if (func.isNil()) {
// Couldn't resolve function call name.
return PARSE_ERROR;
}
lex++;
// Save the stack top.
Atom* args = stack.empty() ? NULL : &stack.back();
// Parse argument list, push arguments onto the stack.
ParseStatus error = parseAtomList();
if (error) return error;
if (args == NULL && !stack.empty()) args = &stack[0];
// Invoke function
if (func.isHook()) {
// Should emit code, but interpreting for now...
stack.push(Atom::nil);
func.getHook()(args);
}
// Done.
return PARSE_OK;
}
SetupMolInfo::SetupMolInfo( const ActionOptions&ao ):
Action(ao),
ActionSetup(ao),
ActionAtomistic(ao),
pdb(*new(PDB))
{
// Read what is contained in the pdb file
parse("MOLTYPE",mytype);
std::vector<SetupMolInfo*> moldat=plumed.getActionSet().select<SetupMolInfo*>();
if( moldat.size()!=0 ) error("cannot use more than one MOLINFO action in input");
std::vector<AtomNumber> backbone;
parseAtomList("CHAIN",backbone);
if( read_backbone.size()==0 ){
for(unsigned i=1;;++i){
parseAtomList("CHAIN",i,backbone);
if( backbone.size()==0 ) break;
read_backbone.push_back(backbone);
backbone.resize(0);
}
} else {
read_backbone.push_back(backbone);
}
if( read_backbone.size()==0 ){
std::string reference; parse("STRUCTURE",reference);
if( ! pdb.read(reference,plumed.getAtoms().usingNaturalUnits(),0.1/plumed.getAtoms().getUnits().getLength()))plumed_merror("missing input file " + reference );
std::vector<std::string> chains; pdb.getChainNames( chains );
log.printf(" pdb file named %s contains %u chains \n",reference.c_str(), static_cast<unsigned>(chains.size()));
for(unsigned i=0;i<chains.size();++i){
unsigned start,end; std::string errmsg;
pdb.getResidueRange( chains[i], start, end, errmsg );
if( errmsg.length()!=0 ) error( errmsg );
AtomNumber astart,aend;
pdb.getAtomRange( chains[i], astart, aend, errmsg );
if( errmsg.length()!=0 ) error( errmsg );
log.printf(" chain named %s contains residues %u to %u and atoms %u to %u \n",chains[i].c_str(),start,end,astart.serial(),aend.serial());
}
}
}
void ActionAtomistic::parseAtomList(const std::string&key, std::vector<AtomNumber> &t){
parseAtomList(key,-1,t);
}
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);
}
}
