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* @version 1.0 |
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*/ |
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#include <iostream> |
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#include <sstream> |
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#include <string> |
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|
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#include "brains/MoleculeCreator.hpp" |
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#include "brains/SimCreator.hpp" |
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#include "brains/SimSnapshotManager.hpp" |
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#include "io/DumpReader.hpp" |
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#include "io/parse_me.h" |
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#include "UseTheForce/ForceFieldFactory.hpp" |
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#include "utils/simError.h" |
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#include "utils/StringUtils.hpp" |
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#include "math/SeqRandNumGen.hpp" |
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#include "mdParser/MDLexer.hpp" |
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#include "mdParser/MDParser.hpp" |
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#include "mdParser/MDTreeParser.hpp" |
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#include "mdParser/SimplePreprocessor.hpp" |
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#ifdef IS_MPI |
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#include "io/mpiBASS.h" |
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#include "math/ParallelRandNumGen.hpp" |
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#endif |
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namespace oopse { |
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void SimCreator::parseFile(const std::string mdFileName, MakeStamps* stamps, |
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Globals* simParams){ |
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Globals* SimCreator::parseFile(const std::string mdFileName){ |
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Globals* simParams = NULL; |
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try { |
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// Create a preprocessor that preprocesses md file into an ostringstream |
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std::stringstream ppStream; |
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#ifdef IS_MPI |
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int streamSize; |
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const int masterNode = 0; |
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int commStatus; |
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if (worldRank == masterNode) { |
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#endif |
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SimplePreprocessor preprocessor; |
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preprocessor.preprocess(mdFileName, ppStream); |
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#ifdef IS_MPI |
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//brocasting the stream size |
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streamSize = ppStream.str().size() +1; |
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commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); |
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commStatus = MPI_Bcast(ppStream.str().c_str(), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
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} else { |
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//get stream size |
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commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); |
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char* buf = new char[streamSize]; |
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assert(buf); |
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//receive file content |
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commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
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ppStream.str(buf); |
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delete buf; |
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} |
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#endif |
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// Create a scanner that reads from the input stream |
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MDLexer lexer(ppStream); |
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lexer.setFilename(mdFileName); |
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lexer.initDeferredLineCount(); |
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#ifdef IS_MPI |
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// Create a parser that reads from the scanner |
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MDParser parser(lexer); |
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parser.setFilename(mdFileName); |
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// Create an observer that synchorizes file name change |
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FilenameObserver observer; |
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observer.setLexer(&lexer); |
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observer.setParser(&parser); |
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lexer.setObserver(&observer); |
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if (worldRank == 0) { |
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#endif // is_mpi |
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set_interface_stamps(stamps, simParams); |
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#ifdef IS_MPI |
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mpiEventInit(); |
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#endif |
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yacc_BASS(mdFileName.c_str()); |
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#ifdef IS_MPI |
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throwMPIEvent(NULL); |
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} else { |
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set_interface_stamps(stamps, simParams); |
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mpiEventInit(); |
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MPIcheckPoint(); |
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mpiEventLoop(); |
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} |
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#endif |
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antlr::ASTFactory factory; |
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parser.initializeASTFactory(factory); |
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parser.setASTFactory(&factory); |
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parser.mdfile(); |
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// Create a tree parser that reads information into Globals |
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MDTreeParser treeParser; |
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treeParser.initializeASTFactory(factory); |
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treeParser.setASTFactory(&factory); |
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simParams = treeParser.walkTree(parser.getAST()); |
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} |
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catch (exception& e) { |
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cerr << "parser exception: " << e.what() << endl; |
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} |
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return simParams; |
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} |
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SimInfo* SimCreator::createSim(const std::string & mdFileName, |
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bool loadInitCoords) { |
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MakeStamps * stamps = new MakeStamps(); |
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Globals * simParams = new Globals(); |
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//parse meta-data file |
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parseFile(mdFileName, stamps, simParams); |
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Globals* simParams = parseFile(mdFileName); |
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//create the force field |
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ForceField * ff = ForceFieldFactory::getInstance() |
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} |
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ff->parse(forcefieldFileName); |
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//extract the molecule stamps |
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std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs; |
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compList(stamps, simParams, moleculeStampPairs); |
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//create SimInfo |
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SimInfo * info = new SimInfo(stamps, moleculeStampPairs, ff, simParams); |
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SimInfo * info = new SimInfo(ff, simParams); |
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//gather parameters (SimCreator only retrieves part of the parameters) |
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gatherParameters(info, mdFileName); |
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void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) { |
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//figure out the ouput file names |
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//figure out the output file names |
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std::string prefix; |
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#ifdef IS_MPI |
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} //end for(int i=0) |
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} |
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void SimCreator::compList(MakeStamps *stamps, Globals* simParams, |
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std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) { |
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int i; |
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char * id; |
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MoleculeStamp * currentStamp; |
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Component** the_components = simParams->getComponents(); |
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int n_components = simParams->getNComponents(); |
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|
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if (!simParams->haveNMol()) { |
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// we don't have the total number of molecules, so we assume it is |
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// given in each component |
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for(i = 0; i < n_components; i++) { |
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if (!the_components[i]->haveNMol()) { |
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// we have a problem |
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sprintf(painCave.errMsg, |
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"SimCreator 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(); |
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} |
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id = the_components[i]->getType(); |
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currentStamp = stamps->getMolStamp(id); |
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if (currentStamp == NULL) { |
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sprintf(painCave.errMsg, |
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"SimCreator error: Component \"%s\" was not found in the " |
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"list of declared molecules\n", id); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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moleculeStampPairs.push_back( |
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std::make_pair(currentStamp, the_components[i]->getNMol())); |
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} //end for (i = 0; i < n_components; i++) |
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} else { |
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sprintf(painCave.errMsg, "SimSetup error.\n" |
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"\tSorry, the ability to specify total" |
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" nMols and then give molfractions in the components\n" |
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"\tis not currently supported." |
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" Please give nMol in the components.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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#ifdef IS_MPI |
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strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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} |
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void SimCreator::setGlobalIndex(SimInfo *info) { |
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SimInfo::MoleculeIterator mi; |
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Molecule::AtomIterator ai; |
