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#include "UseTheForce/DUFF.hpp" |
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#include "UseTheForce/DarkSide/lj_interface.h" |
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#include "UseTheForce/DarkSide/charge_interface.h" |
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#include "UseTheForce/DarkSide/dipole_interface.h" |
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#include "UseTheForce/DarkSide/sticky_interface.h" |
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#include "UseTheForce/ForceFieldFactory.hpp" |
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#include "io/DirectionalAtomTypesSectionParser.hpp" |
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#include "io/AtomTypesSectionParser.hpp" |
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#include "io/LennardJonesAtomTypesSectionParser.hpp" |
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#include "io/ElectrostaticAtomTypesSectionParser.hpp" |
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#include "io/EAMAtomTypesSectionParser.hpp" |
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#include "io/StickyAtomTypesSectionParser.hpp" |
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#include "io/BondTypesSectionParser.hpp" |
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#include "io/BendTypesSectionParser.hpp" |
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#include "io/TorsionTypesSectionParser.hpp" |
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#include "UseTheForce/ForceFieldCreator.hpp" |
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namespace oopse { |
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|
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//definition of createDUFF |
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ForceField* createDUFF() { |
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return new DUFF(); |
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} |
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//static ForceFieldBuilder<DUFF>* DUFFCreator = new ForceFieldBuilder<DUFF>("DUFF"); |
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|
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DUFF::DUFF(){ |
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//register createDUFF to ForceFieldCreator |
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ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF); |
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//set default force field filename |
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setForceFieldFileName("DUFF.frc"); |
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|
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//the order of adding section parsers are important |
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//DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since |
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//These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create |
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//AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass |
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//of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the |
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//"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not |
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//important. AtomTypesSectionParser should be added before other atom type section parsers. |
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//Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser. |
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//The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are |
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//not important. |
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spMan_.push_back(new DirectionalAtomTypesSectionParser()); |
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spMan_.push_back(new AtomTypesSectionParser()); |
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spMan_.push_back(new LennardJonesAtomTypesSectionParser()); |
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spMan_.push_back(new ElectrostaticAtomTypesSectionParser()); |
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spMan_.push_back(new EAMAtomTypesSectionParser()); |
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spMan_.push_back(new StickyAtomTypesSectionParser()); |
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spMan_.push_back(new BondTypesSectionParser()); |
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spMan_.push_back(new BendTypesSectionParser()); |
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spMan_.push_back(new TorsionTypesSectionParser()); |
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|
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} |
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|
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void DUFF::parse(const std::string& filename) { |
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ifstrstream* ffStream; |
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ffStream = openForceFiledFile(filename); |
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const int bufferSize = 65535; |
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char line[bufferSize]; |
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AtomType* atomType; |
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std::string atomTypeName; |
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double mass; |
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double epsilon; |
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double sigma; |
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int status; |
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int ident = 1; //ident begins from 1 (fortran's index begins from 1) |
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int lineNo = 0; |
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> |
ffStream = openForceFieldFile(filename); |
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|
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< |
while(ffStream.getline(line, bufferSize)){ |
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++lineNo; |
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> |
spMan_.parse(*ffStream, *this); |
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|
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< |
//a line begins with '#' or '!' is comment which is skipped |
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if (line[0] != '#' ||line[0] != '!') { |
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StringTokenizer tokenizer(line); |
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|
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if (tokenizer.countTokens() >= 4) { |
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atomTypeName = tokenizer.nextToken(); |
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mass = tokenizer.nextTokenAsDouble(); |
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epsilon = tokenizer.nextTokenAsDouble(); |
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sigma = tokenizer.nextTokenAsDouble(); |
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> |
ForceField::AtomTypeContainer::MapTypeIterator i; |
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> |
AtomType* at; |
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< |
atomType = new AtomType(); |
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atomType->setName(atomTypeName); |
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< |
atomType->setMass(mass); |
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< |
|
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< |
//by default, all of the properties in AtomTypeProperties is set to 0 |
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< |
//In Lennard-Jones Force Field, we only need to set Lennard-Jones to true |
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atomType->setLennardJones(); |
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> |
for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) { |
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at->makeFortranAtomType(); |
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> |
} |
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|
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< |
atomType->setIdent(ident); |
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< |
atomType->addProperty(new DoubleGenericData("Epsilon", epsilon)); |
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< |
atomType->addProperty(new DoubleGenericData("Sigma", sigma)); |
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< |
atomType->complete(); |
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//notify a new LJtype atom type is created |
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< |
newLJtype(&ident, &sigma, &epsilon, &status); |
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|
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< |
//add atom type to AtomTypeContainer |
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< |
addAtomType(atomTypeName, atomType); |
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< |
++ident; |
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< |
|
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< |
} else { |
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< |
sprintf( painCave.errMsg, |
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< |
"Not enough tokens when parsing Lennard-Jones Force Field : %s\n" |
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< |
"in line %d : %s\n", |
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< |
filename.c_str(), lineNo, line); |
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< |
painCave.severity = OOPSE_ERROR; |
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< |
painCave.isFatal = 1; |
| 92 |
< |
simError(); |
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< |
} |
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< |
|
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< |
} |
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> |
for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) { |
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> |
at->complete(); |
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} |
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|
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delete ffStream; |
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} |
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|
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|
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void DUFF::parseAtomType(){ |
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} |
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|
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void DUFF::parseBondType(){ |
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} |
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|
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void DUFF::parseBendType(){ |
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} |
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|
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void DUFF::parseTorsionType(){ |
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|
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} |
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|
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} //end namespace oopse |
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