src/brains/SimCreator.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
/**
 * @file SimCreator.cpp
 * @author tlin
 * @date 11/03/2004
 * @time 13:51am
 * @version 1.0
 */

#include <iostream>
#include <sstream>
#include <string>

#include "brains/MoleculeCreator.hpp"
#include "brains/SimCreator.hpp"
#include "brains/SimSnapshotManager.hpp"
#include "io/DumpReader.hpp"
#include "UseTheForce/ForceFieldFactory.hpp"
#include "utils/simError.h"
#include "utils/StringUtils.hpp"
#include "math/SeqRandNumGen.hpp"
#include "mdParser/MDLexer.hpp"
#include "mdParser/MDParser.hpp"
#include "mdParser/MDTreeParser.hpp"
#include "mdParser/SimplePreprocessor.hpp"


#ifdef IS_MPI
#include "math/ParallelRandNumGen.hpp"
#endif

namespace oopse {
  
Globals* SimCreator::parseFile(const std::string mdFileName){
        Globals* simParams = NULL;
        try {

            // Create a preprocessor that preprocesses md file into an ostringstream
            std::stringstream ppStream;
#ifdef IS_MPI            
            int streamSize;
            const int masterNode = 0;
            int commStatus;
            if (worldRank == masterNode) {
#endif 
                
                SimplePreprocessor preprocessor;
                preprocessor.preprocess(mdFileName, ppStream);
                
#ifdef IS_MPI            
                //brocasting the stream size
                streamSize = ppStream.str().size() +1;
                commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);                   

                commStatus = MPI_Bcast(ppStream.str().c_str(), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); 
            
                
            } else {
                //get stream size
                commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);   
                
                  char* buf = new char[streamSize];
                  assert(buf);
                
                  //receive file content
                  commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); 
                
                  ppStream.str(buf);
                  delete buf;

            }
#endif            
            // Create a scanner that reads from the input stream
            MDLexer lexer(ppStream);
            lexer.setFilename(mdFileName);
            lexer.initDeferredLineCount();
    
            // Create a parser that reads from the scanner
            MDParser parser(lexer);
            parser.setFilename(mdFileName);

            // Create an observer that synchorizes file name change
            FilenameObserver observer;
            observer.setLexer(&lexer);
            observer.setParser(&parser);
            lexer.setObserver(&observer);
    
            antlr::ASTFactory factory;
            parser.initializeASTFactory(factory);
            parser.setASTFactory(&factory);
            parser.mdfile();

            // Create a tree parser that reads information into Globals
            MDTreeParser treeParser;
            treeParser.initializeASTFactory(factory);
            treeParser.setASTFactory(&factory);
             simParams = treeParser.walkTree(parser.getAST());

        }
        catch (exception& e) {
            cerr << "parser exception: " << e.what() << endl;
        }

        return simParams;
  }
  
  SimInfo*  SimCreator::createSim(const std::string & mdFileName, 
                                  bool loadInitCoords) {

    //parse meta-data file
    Globals* simParams = parseFile(mdFileName);
    
    //create the force field
    ForceField * ff = ForceFieldFactory::getInstance()
      ->createForceField(simParams->getForceField());
    
    if (ff == NULL) {
      sprintf(painCave.errMsg, 
              "ForceField Factory can not create %s force field\n",
              simParams->getForceField().c_str());
      painCave.isFatal = 1;
      simError();
    }
    
    if (simParams->haveForceFieldFileName()) {
      ff->setForceFieldFileName(simParams->getForceFieldFileName());
    }
    
    std::string forcefieldFileName;
    forcefieldFileName = ff->getForceFieldFileName();
    
    if (simParams->haveForceFieldVariant()) {
      //If the force field has variant, the variant force field name will be
      //Base.variant.frc. For exampel EAM.u6.frc
      
      std::string variant = simParams->getForceFieldVariant();
      
      std::string::size_type pos = forcefieldFileName.rfind(".frc");
      variant = "." + variant;
      if (pos != std::string::npos) {
        forcefieldFileName.insert(pos, variant);
      } else {
        //If the default force field file name does not containt .frc suffix, just append the .variant
        forcefieldFileName.append(variant);
      }
    } 
    
    ff->parse(forcefieldFileName);
        
    //create SimInfo
    SimInfo * info = new SimInfo(ff, simParams);
     
    //gather parameters (SimCreator only retrieves part of the parameters)
    gatherParameters(info, mdFileName);
    
    //divide the molecules and determine the global index of molecules
#ifdef IS_MPI
    divideMolecules(info);
#endif 
    
    //create the molecules
    createMolecules(info);
    
    
    //allocate memory for DataStorage(circular reference, need to break it)
    info->setSnapshotManager(new SimSnapshotManager(info));
    
    //set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
    //global index will never change again). Local indices of atoms and rigidbodies are already set by 
    //MoleculeCreator class which actually delegates the responsibility to LocalIndexManager. 
    setGlobalIndex(info);
    
    //Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
    //atoms don't have the global index yet  (their global index are all initialized to -1).
    //Therefore we have to call addExcludePairs explicitly here. A way to work around is that
    //we can determine the beginning global indices of atoms before they get created.
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
      info->addExcludePairs(mol);
    }
    
    if (loadInitCoords)
      loadCoordinates(info);    
    
    return info;
  }
  
  void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
    
    //figure out the output file names
    std::string prefix;
    
#ifdef IS_MPI
    
    if (worldRank == 0) {
#endif // is_mpi
      Globals * simParams = info->getSimParams();
      if (simParams->haveFinalConfig()) {
        prefix = getPrefix(simParams->getFinalConfig());
      } else {
        prefix = getPrefix(mdfile);
      }
      
      info->setFinalConfigFileName(prefix + ".eor");
      info->setDumpFileName(prefix + ".dump");
      info->setStatFileName(prefix + ".stat");
      info->setRestFileName(prefix + ".zang");
      
#ifdef IS_MPI
      
    }
    
#endif
    
  }
  
#ifdef IS_MPI
  void SimCreator::divideMolecules(SimInfo *info) {
    double numerator;
    double denominator;
    double precast;
    double x;
    double y;
    double a;
    int old_atoms;
    int add_atoms;
    int new_atoms;
    int nTarget;
    int done;
    int i;
    int j;
    int loops;
    int which_proc;
    int nProcessors;
    std::vector<int> atomsPerProc;
    int nGlobalMols = info->getNGlobalMolecules();
    std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
    
    MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
    
    if (nProcessors > nGlobalMols) {
      sprintf(painCave.errMsg,
              "nProcessors (%d) > nMol (%d)\n"
              "\tThe number of processors is larger than\n"
              "\tthe number of molecules.  This will not result in a \n"
              "\tusable division of atoms for force decomposition.\n"
              "\tEither try a smaller number of processors, or run the\n"
              "\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
      
      painCave.isFatal = 1;
      simError();
    }
    
    int seedValue;
    Globals * simParams = info->getSimParams();
    SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
    if (simParams->haveSeed()) {
      seedValue = simParams->getSeed();
      myRandom = new SeqRandNumGen(seedValue);
    }else {
      myRandom = new SeqRandNumGen();
    }   
    
    
    a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
    
    //initialize atomsPerProc
    atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
    
    if (worldRank == 0) {
      numerator = info->getNGlobalAtoms();
      denominator = nProcessors;
      precast = numerator / denominator;
      nTarget = (int)(precast + 0.5);
      
      for(i = 0; i < nGlobalMols; i++) {
        done = 0;
        loops = 0;
        
        while (!done) {
          loops++;
          
          // Pick a processor at random
          
          which_proc = (int) (myRandom->rand() * nProcessors);
          
          //get the molecule stamp first
          int stampId = info->getMoleculeStampId(i);
          MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
          
          // How many atoms does this processor have so far?
          old_atoms = atomsPerProc[which_proc];
          add_atoms = moleculeStamp->getNAtoms();
          new_atoms = old_atoms + add_atoms;
          
          // If we've been through this loop too many times, we need
          // to just give up and assign the molecule to this processor
          // and be done with it. 
          
          if (loops > 100) {
            sprintf(painCave.errMsg,
                    "I've tried 100 times to assign molecule %d to a "
                    " processor, but can't find a good spot.\n"
                    "I'm assigning it at random to processor %d.\n",
                    i, which_proc);
            
            painCave.isFatal = 0;
            simError();
            
            molToProcMap[i] = which_proc;
            atomsPerProc[which_proc] += add_atoms;
            
            done = 1;
            continue;
          }
          
          // If we can add this molecule to this processor without sending
          // it above nTarget, then go ahead and do it:
          
          if (new_atoms <= nTarget) {
            molToProcMap[i] = which_proc;
            atomsPerProc[which_proc] += add_atoms;
            
            done = 1;
            continue;
          }
          
          // The only situation left is when new_atoms > nTarget.  We
          // want to accept this with some probability that dies off the
          // farther we are from nTarget
          
          // roughly:  x = new_atoms - nTarget
          //           Pacc(x) = exp(- a * x)
          // where a = penalty / (average atoms per molecule)
          
          x = (double)(new_atoms - nTarget);
          y = myRandom->rand();
          
          if (y < exp(- a * x)) {
            molToProcMap[i] = which_proc;
            atomsPerProc[which_proc] += add_atoms;
            
            done = 1;
            continue;
          } else {
            continue;
          }
        }
      }
      
      delete myRandom;
      
      // Spray out this nonsense to all other processors:
      
      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
    } else {
      
      // Listen to your marching orders from processor 0:
      
      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
    }
    
    info->setMolToProcMap(molToProcMap);
    sprintf(checkPointMsg,
            "Successfully divided the molecules among the processors.\n");
    MPIcheckPoint();
  }
  
#endif
  
  void SimCreator::createMolecules(SimInfo *info) {
    MoleculeCreator molCreator;
    int stampId;
    
    for(int i = 0; i < info->getNGlobalMolecules(); i++) {
      
#ifdef IS_MPI
      
      if (info->getMolToProc(i) == worldRank) {
#endif
        
        stampId = info->getMoleculeStampId(i);
        Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
                                                   stampId, i, info->getLocalIndexManager());
        
        info->addMolecule(mol);
        
#ifdef IS_MPI
        
      }
      
#endif
      
    } //end for(int i=0)   
  }
    
  void SimCreator::setGlobalIndex(SimInfo *info) {
    SimInfo::MoleculeIterator mi;
    Molecule::AtomIterator ai;
    Molecule::RigidBodyIterator ri;
    Molecule::CutoffGroupIterator ci;
    Molecule * mol;
    Atom * atom;
    RigidBody * rb;
    CutoffGroup * cg;
    int beginAtomIndex;
    int beginRigidBodyIndex;
    int beginCutoffGroupIndex;
    int nGlobalAtoms = info->getNGlobalAtoms();
    
#ifndef IS_MPI
    
    beginAtomIndex = 0;
    beginRigidBodyIndex = 0;
    beginCutoffGroupIndex = 0;
    
#else
    
    int nproc;
    int myNode;
    
    myNode = worldRank;
    MPI_Comm_size(MPI_COMM_WORLD, &nproc);
    
    std::vector < int > tmpAtomsInProc(nproc, 0);
    std::vector < int > tmpRigidBodiesInProc(nproc, 0);
    std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
    std::vector < int > NumAtomsInProc(nproc, 0);
    std::vector < int > NumRigidBodiesInProc(nproc, 0);
    std::vector < int > NumCutoffGroupsInProc(nproc, 0);
    
    tmpAtomsInProc[myNode] = info->getNAtoms();
    tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
    tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
    
    //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
    MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
                  MPI_SUM, MPI_COMM_WORLD);
    MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
    MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
    
    beginAtomIndex = 0;
    beginRigidBodyIndex = 0;
    beginCutoffGroupIndex = 0;
    
    for(int i = 0; i < myNode; i++) {
      beginAtomIndex += NumAtomsInProc[i];
      beginRigidBodyIndex += NumRigidBodiesInProc[i];
      beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
    }
    
#endif
    
    //rigidbody's index begins right after atom's
    beginRigidBodyIndex += info->getNGlobalAtoms();
    
    for(mol = info->beginMolecule(mi); mol != NULL;
        mol = info->nextMolecule(mi)) {
      
      //local index(index in DataStorge) of atom is important
      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
        atom->setGlobalIndex(beginAtomIndex++);
      }
      
      for(rb = mol->beginRigidBody(ri); rb != NULL;
          rb = mol->nextRigidBody(ri)) {
        rb->setGlobalIndex(beginRigidBodyIndex++);
      }
      
      //local index of cutoff group is trivial, it only depends on the order of travesing
      for(cg = mol->beginCutoffGroup(ci); cg != NULL;
          cg = mol->nextCutoffGroup(ci)) {
        cg->setGlobalIndex(beginCutoffGroupIndex++);
      }
    }
    
    //fill globalGroupMembership
    std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
    for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {        
      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
        
        for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
          globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
        }
        
      }       
    }
    
#ifdef IS_MPI    
    // Since the globalGroupMembership has been zero filled and we've only
    // poked values into the atoms we know, we can do an Allreduce
    // to get the full globalGroupMembership array (We think).
    // This would be prettier if we could use MPI_IN_PLACE like the MPI-2
    // docs said we could.
    std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
    MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
    info->setGlobalGroupMembership(tmpGroupMembership);
#else
    info->setGlobalGroupMembership(globalGroupMembership);
#endif
    
    //fill molMembership
    std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
    
    for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
      
      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
        globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
      }
    }
    
#ifdef IS_MPI
    std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
    
    MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
    
    info->setGlobalMolMembership(tmpMolMembership);
#else
    info->setGlobalMolMembership(globalMolMembership);
#endif
    
  }
  
  void SimCreator::loadCoordinates(SimInfo* info) {
    Globals* simParams;
    simParams = info->getSimParams();
    
    if (!simParams->haveInitialConfig()) {
      sprintf(painCave.errMsg,
              "Cannot intialize a simulation without an initial configuration file.\n");
      painCave.isFatal = 1;;
      simError();
    }
    
    DumpReader reader(info, simParams->getInitialConfig());
    int nframes = reader.getNFrames();
    
    if (nframes > 0) {
      reader.readFrame(nframes - 1);
    } else {
      //invalid initial coordinate file
      sprintf(painCave.errMsg, 
              "Initial configuration file %s should at least contain one frame\n",
              simParams->getInitialConfig().c_str());
      painCave.isFatal = 1;
      simError();
    }
    
    //copy the current snapshot to previous snapshot
    info->getSnapshotManager()->advance();
  }
  
} //end namespace oopse


Revision:	2469
Committed:	Fri Dec 2 15:38:03 2005 UTC (18 years, 7 months ago) by tim
File size:	19946 byte(s)
Log Message:	End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Acknowledgement of the program authors must be made in any
10	* publication of scientific results based in part on use of the
11	* program. An acceptable form of acknowledgement is citation of
12	* the article in which the program was described (Matthew
13	* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	* Parallel Simulation Engine for Molecular Dynamics,"
16	* J. Comput. Chem. 26, pp. 252-271 (2005))
17	*
18	* 2. Redistributions of source code must retain the above copyright
19	* notice, this list of conditions and the following disclaimer.
20	*
21	* 3. Redistributions in binary form must reproduce the above copyright
22	* notice, this list of conditions and the following disclaimer in the
23	* documentation and/or other materials provided with the
24	* distribution.
25	*
26	* This software is provided "AS IS," without a warranty of any
27	* kind. All express or implied conditions, representations and
28	* warranties, including any implied warranty of merchantability,
29	* fitness for a particular purpose or non-infringement, are hereby
30	* excluded. The University of Notre Dame and its licensors shall not
31	* be liable for any damages suffered by licensee as a result of
32	* using, modifying or distributing the software or its
33	* derivatives. In no event will the University of Notre Dame or its
34	* licensors be liable for any lost revenue, profit or data, or for
35	* direct, indirect, special, consequential, incidental or punitive
36	* damages, however caused and regardless of the theory of liability,
37	* arising out of the use of or inability to use software, even if the
38	* University of Notre Dame has been advised of the possibility of
39	* such damages.
40	*/
41
42	/**
43	* @file SimCreator.cpp
44	* @author tlin
45	* @date 11/03/2004
46	* @time 13:51am
47	* @version 1.0
48	*/
49
50	#include <iostream>
51	#include <sstream>
52	#include <string>
53
54	#include "brains/MoleculeCreator.hpp"
55	#include "brains/SimCreator.hpp"
56	#include "brains/SimSnapshotManager.hpp"
57	#include "io/DumpReader.hpp"
58	#include "UseTheForce/ForceFieldFactory.hpp"
59	#include "utils/simError.h"
60	#include "utils/StringUtils.hpp"
61	#include "math/SeqRandNumGen.hpp"
62	#include "mdParser/MDLexer.hpp"
63	#include "mdParser/MDParser.hpp"
64	#include "mdParser/MDTreeParser.hpp"
65	#include "mdParser/SimplePreprocessor.hpp"
66
67
68	#ifdef IS_MPI
69	#include "math/ParallelRandNumGen.hpp"
70	#endif
71
72	namespace oopse {
73
74	Globals* SimCreator::parseFile(const std::string mdFileName){
75	Globals* simParams = NULL;
76	try {
77
78	// Create a preprocessor that preprocesses md file into an ostringstream
79	std::stringstream ppStream;
80	#ifdef IS_MPI
81	int streamSize;
82	const int masterNode = 0;
83	int commStatus;
84	if (worldRank == masterNode) {
85	#endif
86
87	SimplePreprocessor preprocessor;
88	preprocessor.preprocess(mdFileName, ppStream);
89
90	#ifdef IS_MPI
91	//brocasting the stream size
92	streamSize = ppStream.str().size() +1;
93	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
94
95	commStatus = MPI_Bcast(ppStream.str().c_str(), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
96
97
98	} else {
99	//get stream size
100	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
101
102	char* buf = new char[streamSize];
103	assert(buf);
104
105	//receive file content
106	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
107
108	ppStream.str(buf);
109	delete buf;
110
111	}
112	#endif
113	// Create a scanner that reads from the input stream
114	MDLexer lexer(ppStream);
115	lexer.setFilename(mdFileName);
116	lexer.initDeferredLineCount();
117
118	// Create a parser that reads from the scanner
119	MDParser parser(lexer);
120	parser.setFilename(mdFileName);
121
122	// Create an observer that synchorizes file name change
123	FilenameObserver observer;
124	observer.setLexer(&lexer);
125	observer.setParser(&parser);
126	lexer.setObserver(&observer);
127
128	antlr::ASTFactory factory;
129	parser.initializeASTFactory(factory);
130	parser.setASTFactory(&factory);
131	parser.mdfile();
132
133	// Create a tree parser that reads information into Globals
134	MDTreeParser treeParser;
135	treeParser.initializeASTFactory(factory);
136	treeParser.setASTFactory(&factory);
137	simParams = treeParser.walkTree(parser.getAST());
138
139	}
140	catch (exception& e) {
141	cerr << "parser exception: " << e.what() << endl;
142	}
143
144	return simParams;
145	}
146
147	SimInfo* SimCreator::createSim(const std::string & mdFileName,
148	bool loadInitCoords) {
149
150	//parse meta-data file
151	Globals* simParams = parseFile(mdFileName);
152
153	//create the force field
154	ForceField * ff = ForceFieldFactory::getInstance()
155	->createForceField(simParams->getForceField());
156
157	if (ff == NULL) {
158	sprintf(painCave.errMsg,
159	"ForceField Factory can not create %s force field\n",
160	simParams->getForceField().c_str());
161	painCave.isFatal = 1;
162	simError();
163	}
164
165	if (simParams->haveForceFieldFileName()) {
166	ff->setForceFieldFileName(simParams->getForceFieldFileName());
167	}
168
169	std::string forcefieldFileName;
170	forcefieldFileName = ff->getForceFieldFileName();
171
172	if (simParams->haveForceFieldVariant()) {
173	//If the force field has variant, the variant force field name will be
174	//Base.variant.frc. For exampel EAM.u6.frc
175
176	std::string variant = simParams->getForceFieldVariant();
177
178	std::string::size_type pos = forcefieldFileName.rfind(".frc");
179	variant = "." + variant;
180	if (pos != std::string::npos) {
181	forcefieldFileName.insert(pos, variant);
182	} else {
183	//If the default force field file name does not containt .frc suffix, just append the .variant
184	forcefieldFileName.append(variant);
185	}
186	}
187
188	ff->parse(forcefieldFileName);
189
190	//create SimInfo
191	SimInfo * info = new SimInfo(ff, simParams);
192
193	//gather parameters (SimCreator only retrieves part of the parameters)
194	gatherParameters(info, mdFileName);
195
196	//divide the molecules and determine the global index of molecules
197	#ifdef IS_MPI
198	divideMolecules(info);
199	#endif
200
201	//create the molecules
202	createMolecules(info);
203
204
205	//allocate memory for DataStorage(circular reference, need to break it)
206	info->setSnapshotManager(new SimSnapshotManager(info));
207
208	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
209	//global index will never change again). Local indices of atoms and rigidbodies are already set by
210	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
211	setGlobalIndex(info);
212
213	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
214	//atoms don't have the global index yet (their global index are all initialized to -1).
215	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
216	//we can determine the beginning global indices of atoms before they get created.
217	SimInfo::MoleculeIterator mi;
218	Molecule* mol;
219	for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
220	info->addExcludePairs(mol);
221	}
222
223	if (loadInitCoords)
224	loadCoordinates(info);
225
226	return info;
227	}
228
229	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
230
231	//figure out the output file names
232	std::string prefix;
233
234	#ifdef IS_MPI
235
236	if (worldRank == 0) {
237	#endif // is_mpi
238	Globals * simParams = info->getSimParams();
239	if (simParams->haveFinalConfig()) {
240	prefix = getPrefix(simParams->getFinalConfig());
241	} else {
242	prefix = getPrefix(mdfile);
243	}
244
245	info->setFinalConfigFileName(prefix + ".eor");
246	info->setDumpFileName(prefix + ".dump");
247	info->setStatFileName(prefix + ".stat");
248	info->setRestFileName(prefix + ".zang");
249
250	#ifdef IS_MPI
251
252	}
253
254	#endif
255
256	}
257
258	#ifdef IS_MPI
259	void SimCreator::divideMolecules(SimInfo *info) {
260	double numerator;
261	double denominator;
262	double precast;
263	double x;
264	double y;
265	double a;
266	int old_atoms;
267	int add_atoms;
268	int new_atoms;
269	int nTarget;
270	int done;
271	int i;
272	int j;
273	int loops;
274	int which_proc;
275	int nProcessors;
276	std::vector<int> atomsPerProc;
277	int nGlobalMols = info->getNGlobalMolecules();
278	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
279
280	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
281
282	if (nProcessors > nGlobalMols) {
283	sprintf(painCave.errMsg,
284	"nProcessors (%d) > nMol (%d)\n"
285	"\tThe number of processors is larger than\n"
286	"\tthe number of molecules. This will not result in a \n"
287	"\tusable division of atoms for force decomposition.\n"
288	"\tEither try a smaller number of processors, or run the\n"
289	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
290
291	painCave.isFatal = 1;
292	simError();
293	}
294
295	int seedValue;
296	Globals * simParams = info->getSimParams();
297	SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
298	if (simParams->haveSeed()) {
299	seedValue = simParams->getSeed();
300	myRandom = new SeqRandNumGen(seedValue);
301	}else {
302	myRandom = new SeqRandNumGen();
303	}
304
305
306	a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
307
308	//initialize atomsPerProc
309	atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
310
311	if (worldRank == 0) {
312	numerator = info->getNGlobalAtoms();
313	denominator = nProcessors;
314	precast = numerator / denominator;
315	nTarget = (int)(precast + 0.5);
316
317	for(i = 0; i < nGlobalMols; i++) {
318	done = 0;
319	loops = 0;
320
321	while (!done) {
322	loops++;
323
324	// Pick a processor at random
325
326	which_proc = (int) (myRandom->rand() * nProcessors);
327
328	//get the molecule stamp first
329	int stampId = info->getMoleculeStampId(i);
330	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
331
332	// How many atoms does this processor have so far?
333	old_atoms = atomsPerProc[which_proc];
334	add_atoms = moleculeStamp->getNAtoms();
335	new_atoms = old_atoms + add_atoms;
336
337	// If we've been through this loop too many times, we need
338	// to just give up and assign the molecule to this processor
339	// and be done with it.
340
341	if (loops > 100) {
342	sprintf(painCave.errMsg,
343	"I've tried 100 times to assign molecule %d to a "
344	" processor, but can't find a good spot.\n"
345	"I'm assigning it at random to processor %d.\n",
346	i, which_proc);
347
348	painCave.isFatal = 0;
349	simError();
350
351	molToProcMap[i] = which_proc;
352	atomsPerProc[which_proc] += add_atoms;
353
354	done = 1;
355	continue;
356	}
357
358	// If we can add this molecule to this processor without sending
359	// it above nTarget, then go ahead and do it:
360
361	if (new_atoms <= nTarget) {
362	molToProcMap[i] = which_proc;
363	atomsPerProc[which_proc] += add_atoms;
364
365	done = 1;
366	continue;
367	}
368
369	// The only situation left is when new_atoms > nTarget. We
370	// want to accept this with some probability that dies off the
371	// farther we are from nTarget
372
373	// roughly: x = new_atoms - nTarget
374	// Pacc(x) = exp(- a * x)
375	// where a = penalty / (average atoms per molecule)
376
377	x = (double)(new_atoms - nTarget);
378	y = myRandom->rand();
379
380	if (y < exp(- a * x)) {
381	molToProcMap[i] = which_proc;
382	atomsPerProc[which_proc] += add_atoms;
383
384	done = 1;
385	continue;
386	} else {
387	continue;
388	}
389	}
390	}
391
392	delete myRandom;
393
394	// Spray out this nonsense to all other processors:
395
396	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
397	} else {
398
399	// Listen to your marching orders from processor 0:
400
401	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
402	}
403
404	info->setMolToProcMap(molToProcMap);
405	sprintf(checkPointMsg,
406	"Successfully divided the molecules among the processors.\n");
407	MPIcheckPoint();
408	}
409
410	#endif
411
412	void SimCreator::createMolecules(SimInfo *info) {
413	MoleculeCreator molCreator;
414	int stampId;
415
416	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
417
418	#ifdef IS_MPI
419
420	if (info->getMolToProc(i) == worldRank) {
421	#endif
422
423	stampId = info->getMoleculeStampId(i);
424	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
425	stampId, i, info->getLocalIndexManager());
426
427	info->addMolecule(mol);
428
429	#ifdef IS_MPI
430
431	}
432
433	#endif
434
435	} //end for(int i=0)
436	}
437
438	void SimCreator::setGlobalIndex(SimInfo *info) {
439	SimInfo::MoleculeIterator mi;
440	Molecule::AtomIterator ai;
441	Molecule::RigidBodyIterator ri;
442	Molecule::CutoffGroupIterator ci;
443	Molecule * mol;
444	Atom * atom;
445	RigidBody * rb;
446	CutoffGroup * cg;
447	int beginAtomIndex;
448	int beginRigidBodyIndex;
449	int beginCutoffGroupIndex;
450	int nGlobalAtoms = info->getNGlobalAtoms();
451
452	#ifndef IS_MPI
453
454	beginAtomIndex = 0;
455	beginRigidBodyIndex = 0;
456	beginCutoffGroupIndex = 0;
457
458	#else
459
460	int nproc;
461	int myNode;
462
463	myNode = worldRank;
464	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
465
466	std::vector < int > tmpAtomsInProc(nproc, 0);
467	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
468	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
469	std::vector < int > NumAtomsInProc(nproc, 0);
470	std::vector < int > NumRigidBodiesInProc(nproc, 0);
471	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
472
473	tmpAtomsInProc[myNode] = info->getNAtoms();
474	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
475	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
476
477	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
478	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
479	MPI_SUM, MPI_COMM_WORLD);
480	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
481	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
482	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
483	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
484
485	beginAtomIndex = 0;
486	beginRigidBodyIndex = 0;
487	beginCutoffGroupIndex = 0;
488
489	for(int i = 0; i < myNode; i++) {
490	beginAtomIndex += NumAtomsInProc[i];
491	beginRigidBodyIndex += NumRigidBodiesInProc[i];
492	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
493	}
494
495	#endif
496
497	//rigidbody's index begins right after atom's
498	beginRigidBodyIndex += info->getNGlobalAtoms();
499
500	for(mol = info->beginMolecule(mi); mol != NULL;
501	mol = info->nextMolecule(mi)) {
502
503	//local index(index in DataStorge) of atom is important
504	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
505	atom->setGlobalIndex(beginAtomIndex++);
506	}
507
508	for(rb = mol->beginRigidBody(ri); rb != NULL;
509	rb = mol->nextRigidBody(ri)) {
510	rb->setGlobalIndex(beginRigidBodyIndex++);
511	}
512
513	//local index of cutoff group is trivial, it only depends on the order of travesing
514	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
515	cg = mol->nextCutoffGroup(ci)) {
516	cg->setGlobalIndex(beginCutoffGroupIndex++);
517	}
518	}
519
520	//fill globalGroupMembership
521	std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
522	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
523	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
524
525	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
526	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
527	}
528
529	}
530	}
531
532	#ifdef IS_MPI
533	// Since the globalGroupMembership has been zero filled and we've only
534	// poked values into the atoms we know, we can do an Allreduce
535	// to get the full globalGroupMembership array (We think).
536	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
537	// docs said we could.
538	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
539	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
540	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
541	info->setGlobalGroupMembership(tmpGroupMembership);
542	#else
543	info->setGlobalGroupMembership(globalGroupMembership);
544	#endif
545
546	//fill molMembership
547	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
548
549	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
550
551	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
552	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
553	}
554	}
555
556	#ifdef IS_MPI
557	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
558
559	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
560	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
561
562	info->setGlobalMolMembership(tmpMolMembership);
563	#else
564	info->setGlobalMolMembership(globalMolMembership);
565	#endif
566
567	}
568
569	void SimCreator::loadCoordinates(SimInfo* info) {
570	Globals* simParams;
571	simParams = info->getSimParams();
572
573	if (!simParams->haveInitialConfig()) {
574	sprintf(painCave.errMsg,
575	"Cannot intialize a simulation without an initial configuration file.\n");
576	painCave.isFatal = 1;;
577	simError();
578	}
579
580	DumpReader reader(info, simParams->getInitialConfig());
581	int nframes = reader.getNFrames();
582
583	if (nframes > 0) {
584	reader.readFrame(nframes - 1);
585	} else {
586	//invalid initial coordinate file
587	sprintf(painCave.errMsg,
588	"Initial configuration file %s should at least contain one frame\n",
589	simParams->getInitialConfig().c_str());
590	painCave.isFatal = 1;
591	simError();
592	}
593
594	//copy the current snapshot to previous snapshot
595	info->getSnapshotManager()->advance();
596	}
597
598	} //end namespace oopse
599
600