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 <sprng.h>

#include "brains/MoleculeCreator.hpp"
#include "brains/SimCreator.hpp"
#include "brains/SimSnapshotManager.hpp"
#include "io/DumpReader.hpp"
#include "io/parse_me.h"
#include "UseTheForce/ForceFieldFactory.hpp"
#include "utils/simError.h"
#include "utils/StringUtils.hpp"
#ifdef IS_MPI
#include "io/mpiBASS.h"
#include "math/randomSPRNG.hpp"
#endif

namespace oopse {

void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps, Globals* simParams){

#ifdef IS_MPI

    if (worldRank == 0) {
#endif // is_mpi

        simParams->initalize();
        set_interface_stamps(stamps, simParams);

#ifdef IS_MPI

        mpiEventInit();

#endif

        yacc_BASS(mdFileName.c_str());

#ifdef IS_MPI

        throwMPIEvent(NULL);
    } else {
        set_interface_stamps(stamps, simParams);
        mpiEventInit();
        MPIcheckPoint();
        mpiEventLoop();
    }

#endif

}

SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
    
    MakeStamps * stamps = new MakeStamps();

    Globals * simParams = new Globals();

    //parse meta-data file
    parseFile(mdFileName, stamps, simParams);

    //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());
        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);
    
    //extract the molecule stamps
    std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
    compList(stamps, simParams, moleculeStampPairs);

    //create SimInfo
    SimInfo * info = new SimInfo(moleculeStampPairs, 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);
    }
    

    //load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
    //eta, chi for NPT integrator)
    if (loadInitCoords)
        loadCoordinates(info);    
    
    return info;
}

void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {

    //setup seed for random number generator
    int seedValue;
    Globals * simParams = info->getSimParams();

    if (simParams->haveSeed()) {
        seedValue = simParams->getSeed();

        if (seedValue < 100000000 ) {
            sprintf(painCave.errMsg,
                    "Seed for sprng library should contain at least 9 digits\n"
                        "OOPSE will generate a seed for user\n");

            painCave.isFatal = 0;
            simError();

            //using seed generated by system instead of invalid seed set by user 

#ifndef IS_MPI

            seedValue = make_sprng_seed();

#else

            if (worldRank == 0) {
                seedValue = make_sprng_seed();
            }

            MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);

#endif

        } //end if (seedValue /1000000000 == 0)
    } else {

#ifndef IS_MPI

        seedValue = make_sprng_seed();

#else

        if (worldRank == 0) {
            seedValue = make_sprng_seed();
        }

        MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);

#endif

    } //end of simParams->haveSeed()

    info->setSeed(seedValue);


    //figure out the ouput file names
    std::string prefix;

#ifdef IS_MPI

    if (worldRank == 0) {
#endif // is_mpi

        if (simParams->haveFinalConfig()) {
            prefix = getPrefix(simParams->getFinalConfig());
        } else {
            prefix = getPrefix(mdfile);
        }

        info->setFinalConfigFileName(prefix + ".eor");
        info->setDumpFileName(prefix + ".dump");
        info->setStatFileName(prefix + ".stat");

#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;
    randomSPRNG myRandom(info->getSeed());
    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();
    }

    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.getRandom() * 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.getRandom();

                if (y < exp(- a * x)) {
                    molToProcMap[i] = which_proc;
                    atomsPerProc[which_proc] += add_atoms;

                    done = 1;
                    continue;
                } else {
                    continue;
                }
            }
        }

        // 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::compList(MakeStamps *stamps, Globals* simParams,
                        std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
    int i;
    char * id;
    MoleculeStamp * currentStamp;
    Component** the_components = simParams->getComponents();
    int n_components = simParams->getNComponents();

    if (!simParams->haveNMol()) {
        // we don't have the total number of molecules, so we assume it is
        // given in each component

        for(i = 0; i < n_components; i++) {
            if (!the_components[i]->haveNMol()) {
                // we have a problem
                sprintf(painCave.errMsg,
                        "SimCreator Error. No global NMol or component NMol given.\n"
                            "\tCannot calculate the number of atoms.\n");

                painCave.isFatal = 1;
                simError();
            }

            id = the_components[i]->getType();
            currentStamp = (stamps->extractMolStamp(id))->getStamp();

            if (currentStamp == NULL) {
                sprintf(painCave.errMsg,
                        "SimCreator error: Component \"%s\" was not found in the "
                            "list of declared molecules\n", id);

                painCave.isFatal = 1;
                simError();
            }

            moleculeStampPairs.push_back(
                std::make_pair(currentStamp, the_components[i]->getNMol()));
        } //end for (i = 0; i < n_components; i++)
    } else {
        sprintf(painCave.errMsg, "SimSetup error.\n"
                                     "\tSorry, the ability to specify total"
                                     " nMols and then give molfractions in the components\n"
                                     "\tis not currently supported."
                                     " Please give nMol in the components.\n");

        painCave.isFatal = 1;
        simError();
    }

#ifdef IS_MPI

    strcpy(checkPointMsg, "Component stamps successfully extracted\n");
    MPIcheckPoint();

#endif // is_mpi

}

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

    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());
        painCave.isFatal = 1;
        simError();
    }

    //copy the current snapshot to previous snapshot
    info->getSnapshotManager()->advance();
}

} //end namespace oopse


Revision:	1957
Committed:	Tue Jan 25 17:45:23 2005 UTC (20 years, 9 months ago) by tim
File size:	20788 byte(s)
Log Message:	(1) complete section parser's error message (2) add GhostTorsion (3) accumulate inertial tensor from the directional atoms before calculate rigidbody's inertial tensor
#	User	Rev	Content
1	gezelter	1930	/*
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 <sprng.h>
51
52			#include "brains/MoleculeCreator.hpp"
53			#include "brains/SimCreator.hpp"
54			#include "brains/SimSnapshotManager.hpp"
55			#include "io/DumpReader.hpp"
56			#include "io/parse_me.h"
57			#include "UseTheForce/ForceFieldFactory.hpp"
58			#include "utils/simError.h"
59			#include "utils/StringUtils.hpp"
60			#ifdef IS_MPI
61			#include "io/mpiBASS.h"
62			#include "math/randomSPRNG.hpp"
63			#endif
64
65			namespace oopse {
66
67			void SimCreator::parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* simParams){
68
69			#ifdef IS_MPI
70
71			if (worldRank == 0) {
72			#endif // is_mpi
73
74			simParams->initalize();
75			set_interface_stamps(stamps, simParams);
76
77			#ifdef IS_MPI
78
79			mpiEventInit();
80
81			#endif
82
83			yacc_BASS(mdFileName.c_str());
84
85			#ifdef IS_MPI
86
87			throwMPIEvent(NULL);
88			} else {
89			set_interface_stamps(stamps, simParams);
90			mpiEventInit();
91			MPIcheckPoint();
92			mpiEventLoop();
93			}
94
95			#endif
96
97			}
98
99			SimInfo* SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
100
101			MakeStamps * stamps = new MakeStamps();
102
103			Globals * simParams = new Globals();
104
105			//parse meta-data file
106			parseFile(mdFileName, stamps, simParams);
107
108			//create the force field
109			ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
110			simParams->getForceField());
111
112			if (ff == NULL) {
113			sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
114			simParams->getForceField());
115			painCave.isFatal = 1;
116			simError();
117			}
118
119	tim	1957	if (simParams->haveForceFieldFileName()) {
120			ff->setForceFieldFileName(simParams->getForceFieldFileName());
121			}
122
123	gezelter	1930	std::string forcefieldFileName;
124			forcefieldFileName = ff->getForceFieldFileName();
125
126			if (simParams->haveForceFieldVariant()) {
127			//If the force field has variant, the variant force field name will be
128			//Base.variant.frc. For exampel EAM.u6.frc
129
130			std::string variant = simParams->getForceFieldVariant();
131
132			std::string::size_type pos = forcefieldFileName.rfind(".frc");
133			variant = "." + variant;
134			if (pos != std::string::npos) {
135			forcefieldFileName.insert(pos, variant);
136			} else {
137			//If the default force field file name does not containt .frc suffix, just append the .variant
138			forcefieldFileName.append(variant);
139			}
140			}
141
142			ff->parse(forcefieldFileName);
143
144			//extract the molecule stamps
145			std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146			compList(stamps, simParams, moleculeStampPairs);
147
148			//create SimInfo
149			SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
150
151			//gather parameters (SimCreator only retrieves part of the parameters)
152			gatherParameters(info, mdFileName);
153
154			//divide the molecules and determine the global index of molecules
155			#ifdef IS_MPI
156			divideMolecules(info);
157			#endif
158
159			//create the molecules
160			createMolecules(info);
161
162
163			//allocate memory for DataStorage(circular reference, need to break it)
164			info->setSnapshotManager(new SimSnapshotManager(info));
165
166			//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
167			//global index will never change again). Local indices of atoms and rigidbodies are already set by
168			//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
169			setGlobalIndex(info);
170
171			//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
172			//atoms don't have the global index yet (their global index are all initialized to -1).
173			//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
174			//we can determine the beginning global indices of atoms before they get created.
175			SimInfo::MoleculeIterator mi;
176			Molecule* mol;
177			for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
178			info->addExcludePairs(mol);
179			}
180
181
182			//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
183			//eta, chi for NPT integrator)
184			if (loadInitCoords)
185			loadCoordinates(info);
186
187			return info;
188			}
189
190			void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
191
192			//setup seed for random number generator
193			int seedValue;
194			Globals * simParams = info->getSimParams();
195
196			if (simParams->haveSeed()) {
197			seedValue = simParams->getSeed();
198
199			if (seedValue < 100000000 ) {
200			sprintf(painCave.errMsg,
201			"Seed for sprng library should contain at least 9 digits\n"
202			"OOPSE will generate a seed for user\n");
203
204			painCave.isFatal = 0;
205			simError();
206
207			//using seed generated by system instead of invalid seed set by user
208
209			#ifndef IS_MPI
210
211			seedValue = make_sprng_seed();
212
213			#else
214
215			if (worldRank == 0) {
216			seedValue = make_sprng_seed();
217			}
218
219			MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
220
221			#endif
222
223			} //end if (seedValue /1000000000 == 0)
224			} else {
225
226			#ifndef IS_MPI
227
228			seedValue = make_sprng_seed();
229
230			#else
231
232			if (worldRank == 0) {
233			seedValue = make_sprng_seed();
234			}
235
236			MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
237
238			#endif
239
240			} //end of simParams->haveSeed()
241
242			info->setSeed(seedValue);
243
244
245			//figure out the ouput file names
246			std::string prefix;
247
248			#ifdef IS_MPI
249
250			if (worldRank == 0) {
251			#endif // is_mpi
252
253			if (simParams->haveFinalConfig()) {
254			prefix = getPrefix(simParams->getFinalConfig());
255			} else {
256			prefix = getPrefix(mdfile);
257			}
258
259			info->setFinalConfigFileName(prefix + ".eor");
260			info->setDumpFileName(prefix + ".dump");
261			info->setStatFileName(prefix + ".stat");
262
263			#ifdef IS_MPI
264
265			}
266
267			#endif
268
269			}
270
271			#ifdef IS_MPI
272			void SimCreator::divideMolecules(SimInfo *info) {
273			double numerator;
274			double denominator;
275			double precast;
276			double x;
277			double y;
278			double a;
279			int old_atoms;
280			int add_atoms;
281			int new_atoms;
282			int nTarget;
283			int done;
284			int i;
285			int j;
286			int loops;
287			int which_proc;
288			int nProcessors;
289			std::vector<int> atomsPerProc;
290			randomSPRNG myRandom(info->getSeed());
291			int nGlobalMols = info->getNGlobalMolecules();
292			std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
293
294			MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
295
296			if (nProcessors > nGlobalMols) {
297			sprintf(painCave.errMsg,
298			"nProcessors (%d) > nMol (%d)\n"
299			"\tThe number of processors is larger than\n"
300			"\tthe number of molecules. This will not result in a \n"
301			"\tusable division of atoms for force decomposition.\n"
302			"\tEither try a smaller number of processors, or run the\n"
303			"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
304
305			painCave.isFatal = 1;
306			simError();
307			}
308
309			a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
310
311			//initialize atomsPerProc
312			atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
313
314			if (worldRank == 0) {
315			numerator = info->getNGlobalAtoms();
316			denominator = nProcessors;
317			precast = numerator / denominator;
318			nTarget = (int)(precast + 0.5);
319
320			for(i = 0; i < nGlobalMols; i++) {
321			done = 0;
322			loops = 0;
323
324			while (!done) {
325			loops++;
326
327			// Pick a processor at random
328
329			which_proc = (int) (myRandom.getRandom() * nProcessors);
330
331			//get the molecule stamp first
332			int stampId = info->getMoleculeStampId(i);
333			MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
334
335			// How many atoms does this processor have so far?
336			old_atoms = atomsPerProc[which_proc];
337			add_atoms = moleculeStamp->getNAtoms();
338			new_atoms = old_atoms + add_atoms;
339
340			// If we've been through this loop too many times, we need
341			// to just give up and assign the molecule to this processor
342			// and be done with it.
343
344			if (loops > 100) {
345			sprintf(painCave.errMsg,
346			"I've tried 100 times to assign molecule %d to a "
347			" processor, but can't find a good spot.\n"
348			"I'm assigning it at random to processor %d.\n",
349			i, which_proc);
350
351			painCave.isFatal = 0;
352			simError();
353
354			molToProcMap[i] = which_proc;
355			atomsPerProc[which_proc] += add_atoms;
356
357			done = 1;
358			continue;
359			}
360
361			// If we can add this molecule to this processor without sending
362			// it above nTarget, then go ahead and do it:
363
364			if (new_atoms <= nTarget) {
365			molToProcMap[i] = which_proc;
366			atomsPerProc[which_proc] += add_atoms;
367
368			done = 1;
369			continue;
370			}
371
372			// The only situation left is when new_atoms > nTarget. We
373			// want to accept this with some probability that dies off the
374			// farther we are from nTarget
375
376			// roughly: x = new_atoms - nTarget
377			// Pacc(x) = exp(- a * x)
378			// where a = penalty / (average atoms per molecule)
379
380			x = (double)(new_atoms - nTarget);
381			y = myRandom.getRandom();
382
383			if (y < exp(- a * x)) {
384			molToProcMap[i] = which_proc;
385			atomsPerProc[which_proc] += add_atoms;
386
387			done = 1;
388			continue;
389			} else {
390			continue;
391			}
392			}
393			}
394
395			// Spray out this nonsense to all other processors:
396
397			MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
398			} else {
399
400			// Listen to your marching orders from processor 0:
401
402			MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
403			}
404
405			info->setMolToProcMap(molToProcMap);
406			sprintf(checkPointMsg,
407			"Successfully divided the molecules among the processors.\n");
408			MPIcheckPoint();
409			}
410
411			#endif
412
413			void SimCreator::createMolecules(SimInfo *info) {
414			MoleculeCreator molCreator;
415			int stampId;
416
417			for(int i = 0; i < info->getNGlobalMolecules(); i++) {
418
419			#ifdef IS_MPI
420
421			if (info->getMolToProc(i) == worldRank) {
422			#endif
423
424			stampId = info->getMoleculeStampId(i);
425			Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
426			stampId, i, info->getLocalIndexManager());
427
428			info->addMolecule(mol);
429
430			#ifdef IS_MPI
431
432			}
433
434			#endif
435
436			} //end for(int i=0)
437			}
438
439			void SimCreator::compList(MakeStamps stamps, Globals simParams,
440			std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
441			int i;
442			char * id;
443			MoleculeStamp * currentStamp;
444			Component** the_components = simParams->getComponents();
445			int n_components = simParams->getNComponents();
446
447			if (!simParams->haveNMol()) {
448			// we don't have the total number of molecules, so we assume it is
449			// given in each component
450
451			for(i = 0; i < n_components; i++) {
452			if (!the_components[i]->haveNMol()) {
453			// we have a problem
454			sprintf(painCave.errMsg,
455			"SimCreator Error. No global NMol or component NMol given.\n"
456			"\tCannot calculate the number of atoms.\n");
457
458			painCave.isFatal = 1;
459			simError();
460			}
461
462			id = the_components[i]->getType();
463			currentStamp = (stamps->extractMolStamp(id))->getStamp();
464
465			if (currentStamp == NULL) {
466			sprintf(painCave.errMsg,
467			"SimCreator error: Component \"%s\" was not found in the "
468			"list of declared molecules\n", id);
469
470			painCave.isFatal = 1;
471			simError();
472			}
473
474			moleculeStampPairs.push_back(
475			std::make_pair(currentStamp, the_components[i]->getNMol()));
476			} //end for (i = 0; i < n_components; i++)
477			} else {
478			sprintf(painCave.errMsg, "SimSetup error.\n"
479			"\tSorry, the ability to specify total"
480			" nMols and then give molfractions in the components\n"
481			"\tis not currently supported."
482			" Please give nMol in the components.\n");
483
484			painCave.isFatal = 1;
485			simError();
486			}
487
488			#ifdef IS_MPI
489
490			strcpy(checkPointMsg, "Component stamps successfully extracted\n");
491			MPIcheckPoint();
492
493			#endif // is_mpi
494
495			}
496
497			void SimCreator::setGlobalIndex(SimInfo *info) {
498			SimInfo::MoleculeIterator mi;
499			Molecule::AtomIterator ai;
500			Molecule::RigidBodyIterator ri;
501			Molecule::CutoffGroupIterator ci;
502			Molecule * mol;
503			Atom * atom;
504			RigidBody * rb;
505			CutoffGroup * cg;
506			int beginAtomIndex;
507			int beginRigidBodyIndex;
508			int beginCutoffGroupIndex;
509			int nGlobalAtoms = info->getNGlobalAtoms();
510
511			#ifndef IS_MPI
512
513			beginAtomIndex = 0;
514			beginRigidBodyIndex = 0;
515			beginCutoffGroupIndex = 0;
516
517			#else
518
519			int nproc;
520			int myNode;
521
522			myNode = worldRank;
523			MPI_Comm_size(MPI_COMM_WORLD, &nproc);
524
525			std::vector < int > tmpAtomsInProc(nproc, 0);
526			std::vector < int > tmpRigidBodiesInProc(nproc, 0);
527			std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
528			std::vector < int > NumAtomsInProc(nproc, 0);
529			std::vector < int > NumRigidBodiesInProc(nproc, 0);
530			std::vector < int > NumCutoffGroupsInProc(nproc, 0);
531
532			tmpAtomsInProc[myNode] = info->getNAtoms();
533			tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
534			tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
535
536			//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
537			MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
538			MPI_SUM, MPI_COMM_WORLD);
539			MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
540			MPI_INT, MPI_SUM, MPI_COMM_WORLD);
541			MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
542			MPI_INT, MPI_SUM, MPI_COMM_WORLD);
543
544			beginAtomIndex = 0;
545			beginRigidBodyIndex = 0;
546			beginCutoffGroupIndex = 0;
547
548			for(int i = 0; i < myNode; i++) {
549			beginAtomIndex += NumAtomsInProc[i];
550			beginRigidBodyIndex += NumRigidBodiesInProc[i];
551			beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
552			}
553
554			#endif
555
556			for(mol = info->beginMolecule(mi); mol != NULL;
557			mol = info->nextMolecule(mi)) {
558
559			//local index(index in DataStorge) of atom is important
560			for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
561			atom->setGlobalIndex(beginAtomIndex++);
562			}
563
564			for(rb = mol->beginRigidBody(ri); rb != NULL;
565			rb = mol->nextRigidBody(ri)) {
566			rb->setGlobalIndex(beginRigidBodyIndex++);
567			}
568
569			//local index of cutoff group is trivial, it only depends on the order of travesing
570			for(cg = mol->beginCutoffGroup(ci); cg != NULL;
571			cg = mol->nextCutoffGroup(ci)) {
572			cg->setGlobalIndex(beginCutoffGroupIndex++);
573			}
574			}
575
576			//fill globalGroupMembership
577			std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
578			for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
579			for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
580
581			for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
582			globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
583			}
584
585			}
586			}
587
588			#ifdef IS_MPI
589			// Since the globalGroupMembership has been zero filled and we've only
590			// poked values into the atoms we know, we can do an Allreduce
591			// to get the full globalGroupMembership array (We think).
592			// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
593			// docs said we could.
594			std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
595			MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
596			MPI_INT, MPI_SUM, MPI_COMM_WORLD);
597			info->setGlobalGroupMembership(tmpGroupMembership);
598			#else
599			info->setGlobalGroupMembership(globalGroupMembership);
600			#endif
601
602			//fill molMembership
603			std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
604
605			for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
606
607			for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
608			globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
609			}
610			}
611
612			#ifdef IS_MPI
613			std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
614
615			MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
616			MPI_INT, MPI_SUM, MPI_COMM_WORLD);
617
618			info->setGlobalMolMembership(tmpMolMembership);
619			#else
620			info->setGlobalMolMembership(globalMolMembership);
621			#endif
622
623			}
624
625			void SimCreator::loadCoordinates(SimInfo* info) {
626			Globals* simParams;
627			simParams = info->getSimParams();
628
629			if (!simParams->haveInitialConfig()) {
630			sprintf(painCave.errMsg,
631			"Cannot intialize a simulation without an initial configuration file.\n");
632			painCave.isFatal = 1;;
633			simError();
634			}
635
636			DumpReader reader(info, simParams->getInitialConfig());
637			int nframes = reader.getNFrames();
638
639			if (nframes > 0) {
640			reader.readFrame(nframes - 1);
641			} else {
642			//invalid initial coordinate file
643			sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
644			simParams->getInitialConfig());
645			painCave.isFatal = 1;
646			simError();
647			}
648
649			//copy the current snapshot to previous snapshot
650			info->getSnapshotManager()->advance();
651			}
652
653			} //end namespace oopse
654
655