src/brains/SimCreator.cpp

/*
 * Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
 * 
 * Contact: oopse@oopse.org
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */

/**
 * @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();
    }

    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();
    }

}

} //end namespace oopse


Revision:	1903
Committed:	Thu Jan 6 00:16:07 2005 UTC (19 years, 7 months ago) by tim
File size:	19633 byte(s)
Log Message:	simpleBuilder in progress
#	Content
1	/*
2	* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project
3	*
4	* Contact: oopse@oopse.org
5	*
6	* This program is free software; you can redistribute it and/or
7	* modify it under the terms of the GNU Lesser General Public License
8	* as published by the Free Software Foundation; either version 2.1
9	* of the License, or (at your option) any later version.
10	* All we ask is that proper credit is given for our work, which includes
11	* - but is not limited to - adding the above copyright notice to the beginning
12	* of your source code files, and to any copyright notice that you may distribute
13	* with programs based on this work.
14	*
15	* This program is distributed in the hope that it will be useful,
16	* but WITHOUT ANY WARRANTY; without even the implied warranty of
17	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18	* GNU Lesser General Public License for more details.
19	*
20	* You should have received a copy of the GNU Lesser General Public License
21	* along with this program; if not, write to the Free Software
22	* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
23	*
24	*/
25
26	/**
27	* @file SimCreator.cpp
28	* @author tlin
29	* @date 11/03/2004
30	* @time 13:51am
31	* @version 1.0
32	*/
33
34	#include <sprng.h>
35
36	#include "brains/MoleculeCreator.hpp"
37	#include "brains/SimCreator.hpp"
38	#include "brains/SimSnapshotManager.hpp"
39	#include "io/DumpReader.hpp"
40	#include "io/parse_me.h"
41	#include "UseTheForce/ForceFieldFactory.hpp"
42	#include "utils/simError.h"
43	#include "utils/StringUtils.hpp"
44	#ifdef IS_MPI
45	#include "io/mpiBASS.h"
46	#include "math/randomSPRNG.hpp"
47	#endif
48
49	namespace oopse {
50
51	void SimCreator::parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* simParams){
52
53	#ifdef IS_MPI
54
55	if (worldRank == 0) {
56	#endif // is_mpi
57
58	simParams->initalize();
59	set_interface_stamps(stamps, simParams);
60
61	#ifdef IS_MPI
62
63	mpiEventInit();
64
65	#endif
66
67	yacc_BASS(mdFileName.c_str());
68
69	#ifdef IS_MPI
70
71	throwMPIEvent(NULL);
72	} else {
73	set_interface_stamps(stamps, simParams);
74	mpiEventInit();
75	MPIcheckPoint();
76	mpiEventLoop();
77	}
78
79	#endif
80
81	}
82
83	SimInfo* SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
84
85	MakeStamps * stamps = new MakeStamps();
86
87	Globals * simParams = new Globals();
88
89	//parse meta-data file
90	parseFile(mdFileName, stamps, simParams);
91
92	//create the force field
93	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
94	simParams->getForceField());
95
96	if (ff == NULL) {
97	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
98	simParams->getForceField());
99	painCave.isFatal = 1;
100	simError();
101	}
102
103	std::string forcefieldFileName;
104	forcefieldFileName = ff->getForceFieldFileName();
105
106	if (simParams->haveForceFieldVariant()) {
107	//If the force field has variant, the variant force field name will be
108	//Base.variant.frc. For exampel EAM.u6.frc
109
110	std::string variant = simParams->getForceFieldVariant();
111
112	std::string::size_type pos = forcefieldFileName.rfind(".frc");
113	variant = "." + variant;
114	if (pos != std::string::npos) {
115	forcefieldFileName.insert(pos, variant);
116	} else {
117	//If the default force field file name does not containt .frc suffix, just append the .variant
118	forcefieldFileName.append(variant);
119	}
120	}
121
122	ff->parse(forcefieldFileName);
123
124	//extract the molecule stamps
125	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
126	compList(stamps, simParams, moleculeStampPairs);
127
128	//create SimInfo
129	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
130
131	//gather parameters (SimCreator only retrieves part of the parameters)
132	gatherParameters(info, mdFileName);
133
134	//divide the molecules and determine the global index of molecules
135	#ifdef IS_MPI
136	divideMolecules(info);
137	#endif
138
139	//create the molecules
140	createMolecules(info);
141
142
143	//allocate memory for DataStorage(circular reference, need to break it)
144	info->setSnapshotManager(new SimSnapshotManager(info));
145
146	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
147	//global index will never change again). Local indices of atoms and rigidbodies are already set by
148	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
149	setGlobalIndex(info);
150
151	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
152	//atoms don't have the global index yet (their global index are all initialized to -1).
153	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
154	//we can determine the beginning global indices of atoms before they get created.
155	SimInfo::MoleculeIterator mi;
156	Molecule* mol;
157	for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
158	info->addExcludePairs(mol);
159	}
160
161
162	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
163	//eta, chi for NPT integrator)
164	if (loadInitCoords)
165	loadCoordinates(info);
166
167	return info;
168	}
169
170	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
171
172	//setup seed for random number generator
173	int seedValue;
174	Globals * simParams = info->getSimParams();
175
176	if (simParams->haveSeed()) {
177	seedValue = simParams->getSeed();
178
179	if (seedValue < 100000000 ) {
180	sprintf(painCave.errMsg,
181	"Seed for sprng library should contain at least 9 digits\n"
182	"OOPSE will generate a seed for user\n");
183
184	painCave.isFatal = 0;
185	simError();
186
187	//using seed generated by system instead of invalid seed set by user
188
189	#ifndef IS_MPI
190
191	seedValue = make_sprng_seed();
192
193	#else
194
195	if (worldRank == 0) {
196	seedValue = make_sprng_seed();
197	}
198
199	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
200
201	#endif
202
203	} //end if (seedValue /1000000000 == 0)
204	} else {
205
206	#ifndef IS_MPI
207
208	seedValue = make_sprng_seed();
209
210	#else
211
212	if (worldRank == 0) {
213	seedValue = make_sprng_seed();
214	}
215
216	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
217
218	#endif
219
220	} //end of simParams->haveSeed()
221
222	info->setSeed(seedValue);
223
224
225	//figure out the ouput file names
226	std::string prefix;
227
228	#ifdef IS_MPI
229
230	if (worldRank == 0) {
231	#endif // is_mpi
232
233	if (simParams->haveFinalConfig()) {
234	prefix = getPrefix(simParams->getFinalConfig());
235	} else {
236	prefix = getPrefix(mdfile);
237	}
238
239	info->setFinalConfigFileName(prefix + ".eor");
240	info->setDumpFileName(prefix + ".dump");
241	info->setStatFileName(prefix + ".stat");
242
243	#ifdef IS_MPI
244
245	}
246
247	#endif
248
249	}
250
251	#ifdef IS_MPI
252	void SimCreator::divideMolecules(SimInfo *info) {
253	double numerator;
254	double denominator;
255	double precast;
256	double x;
257	double y;
258	double a;
259	int old_atoms;
260	int add_atoms;
261	int new_atoms;
262	int nTarget;
263	int done;
264	int i;
265	int j;
266	int loops;
267	int which_proc;
268	int nProcessors;
269	std::vector<int> atomsPerProc;
270	randomSPRNG myRandom(info->getSeed());
271	int nGlobalMols = info->getNGlobalMolecules();
272	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
273
274	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
275
276	if (nProcessors > nGlobalMols) {
277	sprintf(painCave.errMsg,
278	"nProcessors (%d) > nMol (%d)\n"
279	"\tThe number of processors is larger than\n"
280	"\tthe number of molecules. This will not result in a \n"
281	"\tusable division of atoms for force decomposition.\n"
282	"\tEither try a smaller number of processors, or run the\n"
283	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
284
285	painCave.isFatal = 1;
286	simError();
287	}
288
289	a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
290
291	//initialize atomsPerProc
292	atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
293
294	if (worldRank == 0) {
295	numerator = info->getNGlobalAtoms();
296	denominator = nProcessors;
297	precast = numerator / denominator;
298	nTarget = (int)(precast + 0.5);
299
300	for(i = 0; i < nGlobalMols; i++) {
301	done = 0;
302	loops = 0;
303
304	while (!done) {
305	loops++;
306
307	// Pick a processor at random
308
309	which_proc = (int) (myRandom.getRandom() * nProcessors);
310
311	//get the molecule stamp first
312	int stampId = info->getMoleculeStampId(i);
313	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
314
315	// How many atoms does this processor have so far?
316	old_atoms = atomsPerProc[which_proc];
317	add_atoms = moleculeStamp->getNAtoms();
318	new_atoms = old_atoms + add_atoms;
319
320	// If we've been through this loop too many times, we need
321	// to just give up and assign the molecule to this processor
322	// and be done with it.
323
324	if (loops > 100) {
325	sprintf(painCave.errMsg,
326	"I've tried 100 times to assign molecule %d to a "
327	" processor, but can't find a good spot.\n"
328	"I'm assigning it at random to processor %d.\n",
329	i, which_proc);
330
331	painCave.isFatal = 0;
332	simError();
333
334	molToProcMap[i] = which_proc;
335	atomsPerProc[which_proc] += add_atoms;
336
337	done = 1;
338	continue;
339	}
340
341	// If we can add this molecule to this processor without sending
342	// it above nTarget, then go ahead and do it:
343
344	if (new_atoms <= nTarget) {
345	molToProcMap[i] = which_proc;
346	atomsPerProc[which_proc] += add_atoms;
347
348	done = 1;
349	continue;
350	}
351
352	// The only situation left is when new_atoms > nTarget. We
353	// want to accept this with some probability that dies off the
354	// farther we are from nTarget
355
356	// roughly: x = new_atoms - nTarget
357	// Pacc(x) = exp(- a * x)
358	// where a = penalty / (average atoms per molecule)
359
360	x = (double)(new_atoms - nTarget);
361	y = myRandom.getRandom();
362
363	if (y < exp(- a * x)) {
364	molToProcMap[i] = which_proc;
365	atomsPerProc[which_proc] += add_atoms;
366
367	done = 1;
368	continue;
369	} else {
370	continue;
371	}
372	}
373	}
374
375	// Spray out this nonsense to all other processors:
376
377	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
378	} else {
379
380	// Listen to your marching orders from processor 0:
381
382	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
383	}
384
385	info->setMolToProcMap(molToProcMap);
386	sprintf(checkPointMsg,
387	"Successfully divided the molecules among the processors.\n");
388	MPIcheckPoint();
389	}
390
391	#endif
392
393	void SimCreator::createMolecules(SimInfo *info) {
394	MoleculeCreator molCreator;
395	int stampId;
396
397	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
398
399	#ifdef IS_MPI
400
401	if (info->getMolToProc(i) == worldRank) {
402	#endif
403
404	stampId = info->getMoleculeStampId(i);
405	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
406	stampId, i, info->getLocalIndexManager());
407
408	info->addMolecule(mol);
409
410	#ifdef IS_MPI
411
412	}
413
414	#endif
415
416	} //end for(int i=0)
417	}
418
419	void SimCreator::compList(MakeStamps stamps, Globals simParams,
420	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
421	int i;
422	char * id;
423	MoleculeStamp * currentStamp;
424	Component** the_components = simParams->getComponents();
425	int n_components = simParams->getNComponents();
426
427	if (!simParams->haveNMol()) {
428	// we don't have the total number of molecules, so we assume it is
429	// given in each component
430
431	for(i = 0; i < n_components; i++) {
432	if (!the_components[i]->haveNMol()) {
433	// we have a problem
434	sprintf(painCave.errMsg,
435	"SimCreator Error. No global NMol or component NMol given.\n"
436	"\tCannot calculate the number of atoms.\n");
437
438	painCave.isFatal = 1;
439	simError();
440	}
441
442	id = the_components[i]->getType();
443	currentStamp = (stamps->extractMolStamp(id))->getStamp();
444
445	if (currentStamp == NULL) {
446	sprintf(painCave.errMsg,
447	"SimCreator error: Component \"%s\" was not found in the "
448	"list of declared molecules\n", id);
449
450	painCave.isFatal = 1;
451	simError();
452	}
453
454	moleculeStampPairs.push_back(
455	std::make_pair(currentStamp, the_components[i]->getNMol()));
456	} //end for (i = 0; i < n_components; i++)
457	} else {
458	sprintf(painCave.errMsg, "SimSetup error.\n"
459	"\tSorry, the ability to specify total"
460	" nMols and then give molfractions in the components\n"
461	"\tis not currently supported."
462	" Please give nMol in the components.\n");
463
464	painCave.isFatal = 1;
465	simError();
466	}
467
468	#ifdef IS_MPI
469
470	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
471	MPIcheckPoint();
472
473	#endif // is_mpi
474
475	}
476
477	void SimCreator::setGlobalIndex(SimInfo *info) {
478	SimInfo::MoleculeIterator mi;
479	Molecule::AtomIterator ai;
480	Molecule::RigidBodyIterator ri;
481	Molecule::CutoffGroupIterator ci;
482	Molecule * mol;
483	Atom * atom;
484	RigidBody * rb;
485	CutoffGroup * cg;
486	int beginAtomIndex;
487	int beginRigidBodyIndex;
488	int beginCutoffGroupIndex;
489	int nGlobalAtoms = info->getNGlobalAtoms();
490
491	#ifndef IS_MPI
492
493	beginAtomIndex = 0;
494	beginRigidBodyIndex = 0;
495	beginCutoffGroupIndex = 0;
496
497	#else
498
499	int nproc;
500	int myNode;
501
502	myNode = worldRank;
503	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
504
505	std::vector < int > tmpAtomsInProc(nproc, 0);
506	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
507	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
508	std::vector < int > NumAtomsInProc(nproc, 0);
509	std::vector < int > NumRigidBodiesInProc(nproc, 0);
510	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
511
512	tmpAtomsInProc[myNode] = info->getNAtoms();
513	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
514	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
515
516	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
517	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
518	MPI_SUM, MPI_COMM_WORLD);
519	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
520	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
521	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
522	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
523
524	beginAtomIndex = 0;
525	beginRigidBodyIndex = 0;
526	beginCutoffGroupIndex = 0;
527
528	for(int i = 0; i < myNode; i++) {
529	beginAtomIndex += NumAtomsInProc[i];
530	beginRigidBodyIndex += NumRigidBodiesInProc[i];
531	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
532	}
533
534	#endif
535
536	for(mol = info->beginMolecule(mi); mol != NULL;
537	mol = info->nextMolecule(mi)) {
538
539	//local index(index in DataStorge) of atom is important
540	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
541	atom->setGlobalIndex(beginAtomIndex++);
542	}
543
544	for(rb = mol->beginRigidBody(ri); rb != NULL;
545	rb = mol->nextRigidBody(ri)) {
546	rb->setGlobalIndex(beginRigidBodyIndex++);
547	}
548
549	//local index of cutoff group is trivial, it only depends on the order of travesing
550	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
551	cg = mol->nextCutoffGroup(ci)) {
552	cg->setGlobalIndex(beginCutoffGroupIndex++);
553	}
554	}
555
556	//fill globalGroupMembership
557	std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
558	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
559	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
560
561	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
562	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
563	}
564
565	}
566	}
567
568	#ifdef IS_MPI
569	// Since the globalGroupMembership has been zero filled and we've only
570	// poked values into the atoms we know, we can do an Allreduce
571	// to get the full globalGroupMembership array (We think).
572	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
573	// docs said we could.
574	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
575	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
576	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
577	info->setGlobalGroupMembership(tmpGroupMembership);
578	#else
579	info->setGlobalGroupMembership(globalGroupMembership);
580	#endif
581
582	//fill molMembership
583	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
584
585	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
586
587	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
588	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
589	}
590	}
591
592	#ifdef IS_MPI
593	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
594
595	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
596	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
597
598	info->setGlobalMolMembership(tmpMolMembership);
599	#else
600	info->setGlobalMolMembership(globalMolMembership);
601	#endif
602
603	}
604
605	void SimCreator::loadCoordinates(SimInfo* info) {
606	Globals* simParams;
607	simParams = info->getSimParams();
608
609	if (!simParams->haveInitialConfig()) {
610	sprintf(painCave.errMsg,
611	"Cannot intialize a simulation without an initial configuration file.\n");
612	painCave.isFatal = 1;;
613	simError();
614	}
615
616	DumpReader reader(info, simParams->getInitialConfig());
617	int nframes = reader.getNFrames();
618
619	if (nframes > 0) {
620	reader.readFrame(nframes - 1);
621	} else {
622	//invalid initial coordinate file
623	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
624	simParams->getInitialConfig());
625	painCave.isFatal = 1;
626	simError();
627	}
628
629	}
630
631	} //end namespace oopse
632
633