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"
#include "math/OOPSERandNumGen.hpp"
#ifdef IS_MPI
#include "io/mpiBASS.h"

#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) {

    //figure out the ouput 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");

#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();
    OOPSERandNumGen* myRandom;
    if (simParams->haveSeed()) {
        seedValue = simParams->getSeed();
        myRandom = new OOPSERandNumGen(seedValue);
    }else {
        myRandom = new OOPSERandNumGen();
    }   


    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::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

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

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

} //end namespace oopse


Revision:	2068
Committed:	Tue Mar 1 19:11:47 2005 UTC (19 years, 4 months ago) by tim
File size:	20696 byte(s)
Log Message:	adding OOPSERandNumGen
#	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 <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	#include "math/OOPSERandNumGen.hpp"
61	#ifdef IS_MPI
62	#include "io/mpiBASS.h"
63
64	#endif
65
66	namespace oopse {
67
68	void SimCreator::parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* simParams){
69
70	#ifdef IS_MPI
71
72	if (worldRank == 0) {
73	#endif // is_mpi
74
75	simParams->initalize();
76	set_interface_stamps(stamps, simParams);
77
78	#ifdef IS_MPI
79
80	mpiEventInit();
81
82	#endif
83
84	yacc_BASS(mdFileName.c_str());
85
86	#ifdef IS_MPI
87
88	throwMPIEvent(NULL);
89	} else {
90	set_interface_stamps(stamps, simParams);
91	mpiEventInit();
92	MPIcheckPoint();
93	mpiEventLoop();
94	}
95
96	#endif
97
98	}
99
100	SimInfo* SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
101
102	MakeStamps * stamps = new MakeStamps();
103
104	Globals * simParams = new Globals();
105
106	//parse meta-data file
107	parseFile(mdFileName, stamps, simParams);
108
109	//create the force field
110	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
111	simParams->getForceField());
112
113	if (ff == NULL) {
114	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
115	simParams->getForceField());
116	painCave.isFatal = 1;
117	simError();
118	}
119
120	if (simParams->haveForceFieldFileName()) {
121	ff->setForceFieldFileName(simParams->getForceFieldFileName());
122	}
123
124	std::string forcefieldFileName;
125	forcefieldFileName = ff->getForceFieldFileName();
126
127	if (simParams->haveForceFieldVariant()) {
128	//If the force field has variant, the variant force field name will be
129	//Base.variant.frc. For exampel EAM.u6.frc
130
131	std::string variant = simParams->getForceFieldVariant();
132
133	std::string::size_type pos = forcefieldFileName.rfind(".frc");
134	variant = "." + variant;
135	if (pos != std::string::npos) {
136	forcefieldFileName.insert(pos, variant);
137	} else {
138	//If the default force field file name does not containt .frc suffix, just append the .variant
139	forcefieldFileName.append(variant);
140	}
141	}
142
143	ff->parse(forcefieldFileName);
144
145	//extract the molecule stamps
146	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
147	compList(stamps, simParams, moleculeStampPairs);
148
149	//create SimInfo
150	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
151
152	//gather parameters (SimCreator only retrieves part of the parameters)
153	gatherParameters(info, mdFileName);
154
155	//divide the molecules and determine the global index of molecules
156	#ifdef IS_MPI
157	divideMolecules(info);
158	#endif
159
160	//create the molecules
161	createMolecules(info);
162
163
164	//allocate memory for DataStorage(circular reference, need to break it)
165	info->setSnapshotManager(new SimSnapshotManager(info));
166
167	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
168	//global index will never change again). Local indices of atoms and rigidbodies are already set by
169	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
170	setGlobalIndex(info);
171
172	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
173	//atoms don't have the global index yet (their global index are all initialized to -1).
174	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
175	//we can determine the beginning global indices of atoms before they get created.
176	SimInfo::MoleculeIterator mi;
177	Molecule* mol;
178	for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
179	info->addExcludePairs(mol);
180	}
181
182
183	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
184	//eta, chi for NPT integrator)
185	if (loadInitCoords)
186	loadCoordinates(info);
187
188	return info;
189	}
190
191	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
192
193	//figure out the ouput file names
194	std::string prefix;
195
196	#ifdef IS_MPI
197
198	if (worldRank == 0) {
199	#endif // is_mpi
200	Globals * simParams = info->getSimParams();
201	if (simParams->haveFinalConfig()) {
202	prefix = getPrefix(simParams->getFinalConfig());
203	} else {
204	prefix = getPrefix(mdfile);
205	}
206
207	info->setFinalConfigFileName(prefix + ".eor");
208	info->setDumpFileName(prefix + ".dump");
209	info->setStatFileName(prefix + ".stat");
210
211	#ifdef IS_MPI
212
213	}
214
215	#endif
216
217	}
218
219	#ifdef IS_MPI
220	void SimCreator::divideMolecules(SimInfo *info) {
221	double numerator;
222	double denominator;
223	double precast;
224	double x;
225	double y;
226	double a;
227	int old_atoms;
228	int add_atoms;
229	int new_atoms;
230	int nTarget;
231	int done;
232	int i;
233	int j;
234	int loops;
235	int which_proc;
236	int nProcessors;
237	std::vector<int> atomsPerProc;
238	int nGlobalMols = info->getNGlobalMolecules();
239	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
240
241	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
242
243	if (nProcessors > nGlobalMols) {
244	sprintf(painCave.errMsg,
245	"nProcessors (%d) > nMol (%d)\n"
246	"\tThe number of processors is larger than\n"
247	"\tthe number of molecules. This will not result in a \n"
248	"\tusable division of atoms for force decomposition.\n"
249	"\tEither try a smaller number of processors, or run the\n"
250	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
251
252	painCave.isFatal = 1;
253	simError();
254	}
255
256	int seedValue;
257	Globals * simParams = info->getSimParams();
258	OOPSERandNumGen* myRandom;
259	if (simParams->haveSeed()) {
260	seedValue = simParams->getSeed();
261	myRandom = new OOPSERandNumGen(seedValue);
262	}else {
263	myRandom = new OOPSERandNumGen();
264	}
265
266
267	a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
268
269	//initialize atomsPerProc
270	atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
271
272	if (worldRank == 0) {
273	numerator = info->getNGlobalAtoms();
274	denominator = nProcessors;
275	precast = numerator / denominator;
276	nTarget = (int)(precast + 0.5);
277
278	for(i = 0; i < nGlobalMols; i++) {
279	done = 0;
280	loops = 0;
281
282	while (!done) {
283	loops++;
284
285	// Pick a processor at random
286
287	which_proc = (int) (myRandom->rand() * nProcessors);
288
289	//get the molecule stamp first
290	int stampId = info->getMoleculeStampId(i);
291	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
292
293	// How many atoms does this processor have so far?
294	old_atoms = atomsPerProc[which_proc];
295	add_atoms = moleculeStamp->getNAtoms();
296	new_atoms = old_atoms + add_atoms;
297
298	// If we've been through this loop too many times, we need
299	// to just give up and assign the molecule to this processor
300	// and be done with it.
301
302	if (loops > 100) {
303	sprintf(painCave.errMsg,
304	"I've tried 100 times to assign molecule %d to a "
305	" processor, but can't find a good spot.\n"
306	"I'm assigning it at random to processor %d.\n",
307	i, which_proc);
308
309	painCave.isFatal = 0;
310	simError();
311
312	molToProcMap[i] = which_proc;
313	atomsPerProc[which_proc] += add_atoms;
314
315	done = 1;
316	continue;
317	}
318
319	// If we can add this molecule to this processor without sending
320	// it above nTarget, then go ahead and do it:
321
322	if (new_atoms <= nTarget) {
323	molToProcMap[i] = which_proc;
324	atomsPerProc[which_proc] += add_atoms;
325
326	done = 1;
327	continue;
328	}
329
330	// The only situation left is when new_atoms > nTarget. We
331	// want to accept this with some probability that dies off the
332	// farther we are from nTarget
333
334	// roughly: x = new_atoms - nTarget
335	// Pacc(x) = exp(- a * x)
336	// where a = penalty / (average atoms per molecule)
337
338	x = (double)(new_atoms - nTarget);
339	y = myRandom->rand();
340
341	if (y < exp(- a * x)) {
342	molToProcMap[i] = which_proc;
343	atomsPerProc[which_proc] += add_atoms;
344
345	done = 1;
346	continue;
347	} else {
348	continue;
349	}
350	}
351	}
352
353	delete myRandom;
354
355	// Spray out this nonsense to all other processors:
356
357	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
358	} else {
359
360	// Listen to your marching orders from processor 0:
361
362	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
363	}
364
365	info->setMolToProcMap(molToProcMap);
366	sprintf(checkPointMsg,
367	"Successfully divided the molecules among the processors.\n");
368	MPIcheckPoint();
369	}
370
371	#endif
372
373	void SimCreator::createMolecules(SimInfo *info) {
374	MoleculeCreator molCreator;
375	int stampId;
376
377	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
378
379	#ifdef IS_MPI
380
381	if (info->getMolToProc(i) == worldRank) {
382	#endif
383
384	stampId = info->getMoleculeStampId(i);
385	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
386	stampId, i, info->getLocalIndexManager());
387
388	info->addMolecule(mol);
389
390	#ifdef IS_MPI
391
392	}
393
394	#endif
395
396	} //end for(int i=0)
397	}
398
399	void SimCreator::compList(MakeStamps stamps, Globals simParams,
400	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
401	int i;
402	char * id;
403	MoleculeStamp * currentStamp;
404	Component** the_components = simParams->getComponents();
405	int n_components = simParams->getNComponents();
406
407	if (!simParams->haveNMol()) {
408	// we don't have the total number of molecules, so we assume it is
409	// given in each component
410
411	for(i = 0; i < n_components; i++) {
412	if (!the_components[i]->haveNMol()) {
413	// we have a problem
414	sprintf(painCave.errMsg,
415	"SimCreator Error. No global NMol or component NMol given.\n"
416	"\tCannot calculate the number of atoms.\n");
417
418	painCave.isFatal = 1;
419	simError();
420	}
421
422	id = the_components[i]->getType();
423	currentStamp = (stamps->extractMolStamp(id))->getStamp();
424
425	if (currentStamp == NULL) {
426	sprintf(painCave.errMsg,
427	"SimCreator error: Component \"%s\" was not found in the "
428	"list of declared molecules\n", id);
429
430	painCave.isFatal = 1;
431	simError();
432	}
433
434	moleculeStampPairs.push_back(
435	std::make_pair(currentStamp, the_components[i]->getNMol()));
436	} //end for (i = 0; i < n_components; i++)
437	} else {
438	sprintf(painCave.errMsg, "SimSetup error.\n"
439	"\tSorry, the ability to specify total"
440	" nMols and then give molfractions in the components\n"
441	"\tis not currently supported."
442	" Please give nMol in the components.\n");
443
444	painCave.isFatal = 1;
445	simError();
446	}
447
448	#ifdef IS_MPI
449
450	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
451	MPIcheckPoint();
452
453	#endif // is_mpi
454
455	}
456
457	void SimCreator::setGlobalIndex(SimInfo *info) {
458	SimInfo::MoleculeIterator mi;
459	Molecule::AtomIterator ai;
460	Molecule::RigidBodyIterator ri;
461	Molecule::CutoffGroupIterator ci;
462	Molecule * mol;
463	Atom * atom;
464	RigidBody * rb;
465	CutoffGroup * cg;
466	int beginAtomIndex;
467	int beginRigidBodyIndex;
468	int beginCutoffGroupIndex;
469	int nGlobalAtoms = info->getNGlobalAtoms();
470
471	#ifndef IS_MPI
472
473	beginAtomIndex = 0;
474	beginRigidBodyIndex = 0;
475	beginCutoffGroupIndex = 0;
476
477	#else
478
479	int nproc;
480	int myNode;
481
482	myNode = worldRank;
483	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
484
485	std::vector < int > tmpAtomsInProc(nproc, 0);
486	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
487	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
488	std::vector < int > NumAtomsInProc(nproc, 0);
489	std::vector < int > NumRigidBodiesInProc(nproc, 0);
490	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
491
492	tmpAtomsInProc[myNode] = info->getNAtoms();
493	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
494	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
495
496	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
497	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
498	MPI_SUM, MPI_COMM_WORLD);
499	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
500	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
501	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
502	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
503
504	beginAtomIndex = 0;
505	beginRigidBodyIndex = 0;
506	beginCutoffGroupIndex = 0;
507
508	for(int i = 0; i < myNode; i++) {
509	beginAtomIndex += NumAtomsInProc[i];
510	beginRigidBodyIndex += NumRigidBodiesInProc[i];
511	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
512	}
513
514	#endif
515
516	//rigidbody's index begins right after atom's
517	beginRigidBodyIndex += info->getNGlobalAtoms();
518
519	for(mol = info->beginMolecule(mi); mol != NULL;
520	mol = info->nextMolecule(mi)) {
521
522	//local index(index in DataStorge) of atom is important
523	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
524	atom->setGlobalIndex(beginAtomIndex++);
525	}
526
527	for(rb = mol->beginRigidBody(ri); rb != NULL;
528	rb = mol->nextRigidBody(ri)) {
529	rb->setGlobalIndex(beginRigidBodyIndex++);
530	}
531
532	//local index of cutoff group is trivial, it only depends on the order of travesing
533	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
534	cg = mol->nextCutoffGroup(ci)) {
535	cg->setGlobalIndex(beginCutoffGroupIndex++);
536	}
537	}
538
539	//fill globalGroupMembership
540	std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
541	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
542	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
543
544	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
545	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
546	}
547
548	}
549	}
550
551	#ifdef IS_MPI
552	// Since the globalGroupMembership has been zero filled and we've only
553	// poked values into the atoms we know, we can do an Allreduce
554	// to get the full globalGroupMembership array (We think).
555	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
556	// docs said we could.
557	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
558	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
559	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
560	info->setGlobalGroupMembership(tmpGroupMembership);
561	#else
562	info->setGlobalGroupMembership(globalGroupMembership);
563	#endif
564
565	//fill molMembership
566	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
567
568	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
569
570	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
571	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
572	}
573	}
574
575	#ifdef IS_MPI
576	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
577
578	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
579	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
580
581	info->setGlobalMolMembership(tmpMolMembership);
582	#else
583	info->setGlobalMolMembership(globalMolMembership);
584	#endif
585
586	}
587
588	void SimCreator::loadCoordinates(SimInfo* info) {
589	Globals* simParams;
590	simParams = info->getSimParams();
591
592	if (!simParams->haveInitialConfig()) {
593	sprintf(painCave.errMsg,
594	"Cannot intialize a simulation without an initial configuration file.\n");
595	painCave.isFatal = 1;;
596	simError();
597	}
598
599	DumpReader reader(info, simParams->getInitialConfig());
600	int nframes = reader.getNFrames();
601
602	if (nframes > 0) {
603	reader.readFrame(nframes - 1);
604	} else {
605	//invalid initial coordinate file
606	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
607	simParams->getInitialConfig());
608	painCave.isFatal = 1;
609	simError();
610	}
611
612	//copy the current snapshot to previous snapshot
613	info->getSnapshotManager()->advance();
614	}
615
616	} //end namespace oopse
617
618