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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
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* |
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*/ |
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|
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/** |
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* @file SimCreator.cpp |
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* @author tlin |
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* @date 11/03/2004 |
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* @time 13:51am |
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* @version 1.0 |
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*/ |
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|
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#include "brains/SimCreator.hpp" |
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/** |
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* @file SimCreator.cpp |
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* @author tlin |
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* @date 11/03/2004 |
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* @time 13:51am |
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* @version 1.0 |
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*/ |
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|
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#include "brains/SimCreator.hpp" |
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namespace oopse { |
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|
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void SimSetup::parseFile(char* mdfile, MakeStamps* stamps, Globals* globals){ |
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} |
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|
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|
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SimModel* SimCreator::createSim(const std::string& mdfile) { |
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MakeStamps* stamps; |
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SimInfo* SimCreator::createSim(const std::string& mdfile) { |
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MakeStamps* stamps = new MakeStamps(); |
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|
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Globals* globals = new Globals(); |
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parseFile(mdfile, stamps, globals); |
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|
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//create the force field |
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ForceFiled* ff = ForceFieldFactory::getInstance()->createForceField(globals->getForceField()); |
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ForceFiled* ff = ForceFieldFactory::getInstance()->createObject(globals->getForceField()); |
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|
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//create SimModel |
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model = new SimInfo(); |
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//create SimInfo |
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SimInfo* info = new SimInfo(); |
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info->setGlobals(globals); |
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info->setForceField(ff); |
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|
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//extract the molecule stamps and add them into SimInfo |
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compList(stamps, info); |
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|
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//gather parameters |
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gatherParameters(model); |
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//gather parameters (SimCreator only retrieves the parameters which will be used to create |
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// the simulation) |
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gatherParameters(info); |
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|
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//divide the molecules and determine the global index of molecules |
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|
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|
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//create the molecules |
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createMolecules(info); |
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|
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//create atoms, bonds, bend, torsions, rigidbodies |
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|
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//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the |
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//global index will never change again). Local indices of atoms and rigidbodies are already set by |
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//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager. |
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setGlobalIndices(info); |
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|
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//allocate memory for DataStorage(circular reference, need to break it) |
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model->setSnapshotManager(new SimSnapshotManager(model); |
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info->setSnapshotManager(new SimSnapshotManager(info); |
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|
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//load initial coordinates |
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DumpReader reader(); |
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reader.readFrame(model); |
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//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as |
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//eta, chi for NPT integrator) |
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DumpReader reader(info->getInitFilename()); |
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int nframes = reader->getNframes(); |
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|
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if (nframes > 0) { |
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reader.readFrame(info, nframes - 1); |
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} else { |
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//invalid initial coordinate file |
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|
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} |
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|
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|
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//initialize fortran |
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return model; |
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|
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return info; |
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} |
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|
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void SimCreator::gatherParameters(SimModel* model) { |
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model->addProperty(new StringGenericData("Ensemble", globals->getForceFiled())); |
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model->addProperty(new DoubleGenericData("dt"), globals->getDt()); |
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void SimCreator::gatherParameters(SimInfo* info) { |
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//model->addProperty(new StringGenericData("Ensemble", globals->getForceFiled())); |
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//model->addProperty(new DoubleGenericData("dt"), globals->getDt()); |
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|
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//setup seed for random number generator |
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int seedValue; |
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Globals* globals = info->getGlobals(); |
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|
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if (globals->haveSeed()){ |
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seedValue = globals->getSeed(); |
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|
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if(seedValue / 1000000000 == 0){ |
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sprintf(painCave.errMsg, |
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"Seed for sprng library should contain at least 9 digits\n" |
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"OOPSE will generate a seed for user\n"); |
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painCave.isFatal = 0; |
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simError(); |
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|
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//using seed generated by system instead of invalid seed set by user |
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#ifndef IS_MPI |
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seedValue = make_sprng_seed(); |
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#else |
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if (worldRank == 0){ |
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seedValue = make_sprng_seed(); |
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} |
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MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
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#endif |
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} //end if (seedValue /1000000000 == 0) |
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} else{ |
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|
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#ifndef IS_MPI |
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seedValue = make_sprng_seed(); |
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#else |
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if (worldRank == 0){ |
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seedValue = make_sprng_seed(); |
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} |
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MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
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#endif |
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}//end of globals->haveSeed() |
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info->setSeed(seedValue); |
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|
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// |
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std::string prefix; |
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#ifdef IS_MPI |
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if (worldRank == 0){ |
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#endif // is_mpi |
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|
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if(globals->haveFinalConfig()) { |
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prefix = getPrefix(globals->getFinalConfig()); |
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} else { |
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prefix = getPrefix(mdfile_); |
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} |
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|
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info->setFinalConfFileName(prefix + ".eor"); |
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info->setDumpFileName(prefix + ".dump"); |
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info->setStatFileName(prefix + ".stat"); |
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|
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#ifdef IS_MPI |
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} |
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#endif |
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|
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|
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|
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} |
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#ifdef IS_MPI |
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|
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mpiSim->divideLabor(); |
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|
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strcpy(checkPointMsg, "Passed nlocal consistency check."); |
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MPIcheckPoint(); |
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} |
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#endif |
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|
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Molecule* SimCreator::createMolecule() { |
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Molecule* mol = new Molecule(); |
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Molecule* SimCreator::createMolecules(SimInfo* info) { |
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MoleculeCreator molCreator; |
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int stampId; |
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|
|
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|
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for (int i = 0; i < info->getNGlobalMolecules(); i++){ |
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if (info->getMolToProc(i) == worldRank){ |
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|
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//create atoms |
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mol->addAtom(); |
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stampId = info->getMoleculeStampId(i); |
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Molecule* mol = molCreator.createMolecule(info->getForceField(), |
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info->getMoleculeStamp(stampId), stampId, i); |
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|
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info->addMolecule(mol); |
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} |
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} |
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|
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} |
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|
|
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//create rigid bodies |
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createRigidBody(mol); |
213 |
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|
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void SimSetup::compList(MakeStamps* stamps,SimInfo* info) { |
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> |
int i; |
216 |
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char* id; |
217 |
> |
MoleculeStamp* currentStamp; |
218 |
> |
Component* the_components = info->getGlobals()->getComponents(); |
219 |
> |
int n_components = info->getGlobals()->getNComponents(); |
220 |
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|
221 |
> |
if (!globals->haveNMol()){ |
222 |
> |
// we don't have the total number of molecules, so we assume it is |
223 |
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// given in each component |
224 |
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|
225 |
> |
for (i = 0; i < n_components; i++){ |
226 |
> |
if (!the_components[i]->haveNMol()){ |
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// we have a problem |
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> |
sprintf(painCave.errMsg, |
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> |
"SimSetup Error. No global NMol or component NMol given.\n" |
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"\tCannot calculate the number of atoms.\n"); |
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> |
painCave.isFatal = 1; |
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> |
simError(); |
233 |
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} |
234 |
> |
|
235 |
> |
id = the_components[i]->getType(); |
236 |
> |
currentStamp = stamps->extractMolStamp(id); |
237 |
> |
if (currentStamp == NULL){ |
238 |
> |
sprintf(painCave.errMsg, |
239 |
> |
"SimSetup error: Component \"%s\" was not found in the " |
240 |
> |
"list of declared molecules\n", |
241 |
> |
id); |
242 |
> |
painCave.isFatal = 1; |
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> |
simError(); |
244 |
> |
} |
245 |
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|
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> |
info->addMoleculeStamp(currentStamp, the_components[i]->getNMol); |
247 |
> |
|
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> |
} //end for (i = 0; i < n_components; i++) |
249 |
> |
|
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} else{ |
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> |
sprintf(painCave.errMsg, |
252 |
> |
"SimSetup error.\n" |
253 |
> |
"\tSorry, the ability to specify total" |
254 |
> |
" nMols and then give molfractions in the components\n" |
255 |
> |
"\tis not currently supported." |
256 |
> |
" Please give nMol in the components.\n"); |
257 |
> |
painCave.isFatal = 1; |
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> |
simError(); |
259 |
> |
} |
260 |
> |
|
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> |
#ifdef IS_MPI |
262 |
> |
strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
263 |
> |
MPIcheckPoint(); |
264 |
> |
#endif // is_mpi |
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> |
} |
266 |
> |
|
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> |
void SimCreator::setGlobalIndices(SimInfo* info) { |
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> |
typename SimInfo::MoleculeIterator mi; |
269 |
> |
typename Molecule::AtomIterator ai; |
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> |
typename Molecule::RigidBodyIterator ri; |
271 |
> |
typename Molecule::CutoffGroupIterator ci; |
272 |
> |
Molecule* mol; |
273 |
> |
Atom* atom; |
274 |
> |
RigidBody* rb; |
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> |
CutoffGroup* cg; |
276 |
> |
int beginAtomIndex; |
277 |
> |
int beginRigidBodyIndex; |
278 |
> |
int beginCutoffGroupIndex; |
279 |
> |
|
280 |
> |
#ifdef IS_MPI |
281 |
> |
beginAtomIndex = 0; |
282 |
> |
beginRigidBodyIndex = 0; |
283 |
> |
beginCutoffGroupIndex = 0; |
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> |
#else |
285 |
> |
int nproc; |
286 |
> |
int myNode; |
287 |
> |
|
288 |
> |
myNode = worldRank; |
289 |
> |
MPI_Comm_size(MPI_COMM_WORLD, &nproc); |
290 |
|
|
291 |
< |
//create bonds |
291 |
> |
std::vector<int> tmpAtomsInProc(nproc, 0); |
292 |
> |
std::vector<int> tmpRigidBodiesInProc(nproc, 0); |
293 |
> |
std::vector<int> tmpCutoffGroupsInProc(nproc, 0); |
294 |
> |
std::vector<int> NumAtomsInProc(nproc, 0); |
295 |
> |
std::vector<int> NumRigidBodiesInProc(nproc, 0); |
296 |
> |
std::vector<int> NumCutoffGroupsInProc(nproc, 0); |
297 |
|
|
298 |
+ |
tmpAtomInProc[myNode] = info->getNAtoms(); |
299 |
+ |
tmpRigidBodiesInProc[myNode] = info->getNRigidBodiess(); |
300 |
+ |
tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroupss(); |
301 |
|
|
302 |
+ |
//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups |
303 |
+ |
MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
304 |
+ |
MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
305 |
+ |
MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
306 |
+ |
|
307 |
+ |
beginAtomIndex = 0; |
308 |
+ |
beginRigidBodyIndex = 0; |
309 |
+ |
beginCutoffGroupIndex = 0; |
310 |
+ |
|
311 |
+ |
for (int i = 0; i < nproc; i++) { |
312 |
+ |
beginAtomIndex += NumAtomsInProc[i]; |
313 |
+ |
beginRigidBodyIndex += NumRigidBodiesInProc[i]; |
314 |
+ |
beginCutoffGroupIndex += NumCutoffGroupsInProc[i]; |
315 |
+ |
} |
316 |
|
|
317 |
+ |
#endif |
318 |
+ |
|
319 |
+ |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
320 |
+ |
|
321 |
+ |
//local index(index in DataStorge) of atom is important |
322 |
+ |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
323 |
+ |
atom->setGlobalIndex(beginAtomIndex++); |
324 |
+ |
} |
325 |
+ |
|
326 |
+ |
for (rb = mol->beginRigidBody(ri); rb != NULL; rb = mol->nextRigidBody(ri)) { |
327 |
+ |
rb->setGlobalIndex(beginRigidBodyIndex++); |
328 |
+ |
} |
329 |
+ |
|
330 |
+ |
//local index of cutoff group is trivial, it only depends on the order of travesing |
331 |
+ |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
332 |
+ |
cg->setGlobalIndex(beginCutoffGroupIndex++); |
333 |
+ |
} |
334 |
+ |
|
335 |
+ |
} |
336 |
|
} |
337 |
|
|
338 |
|
} //end namespace oopse |