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) {
    
    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)
    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 / 1000000000 == 0) {
            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:	1886
Committed:	Wed Dec 15 16:13:35 2004 UTC (19 years, 7 months ago) by tim
File size:	19584 byte(s)
Log Message:	MPI in NVE is working
#	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) {
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	loadCoordinates(info);
165	return info;
166	}
167
168	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
169
170	//setup seed for random number generator
171	int seedValue;
172	Globals * simParams = info->getSimParams();
173
174	if (simParams->haveSeed()) {
175	seedValue = simParams->getSeed();
176
177	if (seedValue / 1000000000 == 0) {
178	sprintf(painCave.errMsg,
179	"Seed for sprng library should contain at least 9 digits\n"
180	"OOPSE will generate a seed for user\n");
181
182	painCave.isFatal = 0;
183	simError();
184
185	//using seed generated by system instead of invalid seed set by user
186
187	#ifndef IS_MPI
188
189	seedValue = make_sprng_seed();
190
191	#else
192
193	if (worldRank == 0) {
194	seedValue = make_sprng_seed();
195	}
196
197	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
198
199	#endif
200
201	} //end if (seedValue /1000000000 == 0)
202	} else {
203
204	#ifndef IS_MPI
205
206	seedValue = make_sprng_seed();
207
208	#else
209
210	if (worldRank == 0) {
211	seedValue = make_sprng_seed();
212	}
213
214	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
215
216	#endif
217
218	} //end of simParams->haveSeed()
219
220	info->setSeed(seedValue);
221
222
223	//figure out the ouput file names
224	std::string prefix;
225
226	#ifdef IS_MPI
227
228	if (worldRank == 0) {
229	#endif // is_mpi
230
231	if (simParams->haveFinalConfig()) {
232	prefix = getPrefix(simParams->getFinalConfig());
233	} else {
234	prefix = getPrefix(mdfile);
235	}
236
237	info->setFinalConfigFileName(prefix + ".eor");
238	info->setDumpFileName(prefix + ".dump");
239	info->setStatFileName(prefix + ".stat");
240
241	#ifdef IS_MPI
242
243	}
244
245	#endif
246
247	}
248
249	#ifdef IS_MPI
250	void SimCreator::divideMolecules(SimInfo *info) {
251	double numerator;
252	double denominator;
253	double precast;
254	double x;
255	double y;
256	double a;
257	int old_atoms;
258	int add_atoms;
259	int new_atoms;
260	int nTarget;
261	int done;
262	int i;
263	int j;
264	int loops;
265	int which_proc;
266	int nProcessors;
267	std::vector<int> atomsPerProc;
268	randomSPRNG myRandom(info->getSeed());
269	int nGlobalMols = info->getNGlobalMolecules();
270	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
271
272	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
273
274	if (nProcessors > nGlobalMols) {
275	sprintf(painCave.errMsg,
276	"nProcessors (%d) > nMol (%d)\n"
277	"\tThe number of processors is larger than\n"
278	"\tthe number of molecules. This will not result in a \n"
279	"\tusable division of atoms for force decomposition.\n"
280	"\tEither try a smaller number of processors, or run the\n"
281	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
282
283	painCave.isFatal = 1;
284	simError();
285	}
286
287	a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
288
289	//initialize atomsPerProc
290	atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
291
292	if (worldRank == 0) {
293	numerator = info->getNGlobalAtoms();
294	denominator = nProcessors;
295	precast = numerator / denominator;
296	nTarget = (int)(precast + 0.5);
297
298	for(i = 0; i < nGlobalMols; i++) {
299	done = 0;
300	loops = 0;
301
302	while (!done) {
303	loops++;
304
305	// Pick a processor at random
306
307	which_proc = (int) (myRandom.getRandom() * nProcessors);
308
309	//get the molecule stamp first
310	int stampId = info->getMoleculeStampId(i);
311	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
312
313	// How many atoms does this processor have so far?
314	old_atoms = atomsPerProc[which_proc];
315	add_atoms = moleculeStamp->getNAtoms();
316	new_atoms = old_atoms + add_atoms;
317
318	// If we've been through this loop too many times, we need
319	// to just give up and assign the molecule to this processor
320	// and be done with it.
321
322	if (loops > 100) {
323	sprintf(painCave.errMsg,
324	"I've tried 100 times to assign molecule %d to a "
325	" processor, but can't find a good spot.\n"
326	"I'm assigning it at random to processor %d.\n",
327	i, which_proc);
328
329	painCave.isFatal = 0;
330	simError();
331
332	molToProcMap[i] = which_proc;
333	atomsPerProc[which_proc] += add_atoms;
334
335	done = 1;
336	continue;
337	}
338
339	// If we can add this molecule to this processor without sending
340	// it above nTarget, then go ahead and do it:
341
342	if (new_atoms <= nTarget) {
343	molToProcMap[i] = which_proc;
344	atomsPerProc[which_proc] += add_atoms;
345
346	done = 1;
347	continue;
348	}
349
350	// The only situation left is when new_atoms > nTarget. We
351	// want to accept this with some probability that dies off the
352	// farther we are from nTarget
353
354	// roughly: x = new_atoms - nTarget
355	// Pacc(x) = exp(- a * x)
356	// where a = penalty / (average atoms per molecule)
357
358	x = (double)(new_atoms - nTarget);
359	y = myRandom.getRandom();
360
361	if (y < exp(- a * x)) {
362	molToProcMap[i] = which_proc;
363	atomsPerProc[which_proc] += add_atoms;
364
365	done = 1;
366	continue;
367	} else {
368	continue;
369	}
370	}
371	}
372
373	// Spray out this nonsense to all other processors:
374
375	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
376	} else {
377
378	// Listen to your marching orders from processor 0:
379
380	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
381	}
382
383	info->setMolToProcMap(molToProcMap);
384	sprintf(checkPointMsg,
385	"Successfully divided the molecules among the processors.\n");
386	MPIcheckPoint();
387	}
388
389	#endif
390
391	void SimCreator::createMolecules(SimInfo *info) {
392	MoleculeCreator molCreator;
393	int stampId;
394
395	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
396
397	#ifdef IS_MPI
398
399	if (info->getMolToProc(i) == worldRank) {
400	#endif
401
402	stampId = info->getMoleculeStampId(i);
403	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
404	stampId, i, info->getLocalIndexManager());
405
406	info->addMolecule(mol);
407
408	#ifdef IS_MPI
409
410	}
411
412	#endif
413
414	} //end for(int i=0)
415	}
416
417	void SimCreator::compList(MakeStamps stamps, Globals simParams,
418	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
419	int i;
420	char * id;
421	MoleculeStamp * currentStamp;
422	Component** the_components = simParams->getComponents();
423	int n_components = simParams->getNComponents();
424
425	if (!simParams->haveNMol()) {
426	// we don't have the total number of molecules, so we assume it is
427	// given in each component
428
429	for(i = 0; i < n_components; i++) {
430	if (!the_components[i]->haveNMol()) {
431	// we have a problem
432	sprintf(painCave.errMsg,
433	"SimCreator Error. No global NMol or component NMol given.\n"
434	"\tCannot calculate the number of atoms.\n");
435
436	painCave.isFatal = 1;
437	simError();
438	}
439
440	id = the_components[i]->getType();
441	currentStamp = (stamps->extractMolStamp(id))->getStamp();
442
443	if (currentStamp == NULL) {
444	sprintf(painCave.errMsg,
445	"SimCreator error: Component \"%s\" was not found in the "
446	"list of declared molecules\n", id);
447
448	painCave.isFatal = 1;
449	simError();
450	}
451
452	moleculeStampPairs.push_back(
453	std::make_pair(currentStamp, the_components[i]->getNMol()));
454	} //end for (i = 0; i < n_components; i++)
455	} else {
456	sprintf(painCave.errMsg, "SimSetup error.\n"
457	"\tSorry, the ability to specify total"
458	" nMols and then give molfractions in the components\n"
459	"\tis not currently supported."
460	" Please give nMol in the components.\n");
461
462	painCave.isFatal = 1;
463	simError();
464	}
465
466	#ifdef IS_MPI
467
468	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
469	MPIcheckPoint();
470
471	#endif // is_mpi
472
473	}
474
475	void SimCreator::setGlobalIndex(SimInfo *info) {
476	SimInfo::MoleculeIterator mi;
477	Molecule::AtomIterator ai;
478	Molecule::RigidBodyIterator ri;
479	Molecule::CutoffGroupIterator ci;
480	Molecule * mol;
481	Atom * atom;
482	RigidBody * rb;
483	CutoffGroup * cg;
484	int beginAtomIndex;
485	int beginRigidBodyIndex;
486	int beginCutoffGroupIndex;
487	int nGlobalAtoms = info->getNGlobalAtoms();
488
489	#ifndef IS_MPI
490
491	beginAtomIndex = 0;
492	beginRigidBodyIndex = 0;
493	beginCutoffGroupIndex = 0;
494
495	#else
496
497	int nproc;
498	int myNode;
499
500	myNode = worldRank;
501	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
502
503	std::vector < int > tmpAtomsInProc(nproc, 0);
504	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
505	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
506	std::vector < int > NumAtomsInProc(nproc, 0);
507	std::vector < int > NumRigidBodiesInProc(nproc, 0);
508	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
509
510	tmpAtomsInProc[myNode] = info->getNAtoms();
511	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
512	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
513
514	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
515	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
516	MPI_SUM, MPI_COMM_WORLD);
517	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
518	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
519	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
520	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
521
522	beginAtomIndex = 0;
523	beginRigidBodyIndex = 0;
524	beginCutoffGroupIndex = 0;
525
526	for(int i = 0; i < myNode; i++) {
527	beginAtomIndex += NumAtomsInProc[i];
528	beginRigidBodyIndex += NumRigidBodiesInProc[i];
529	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
530	}
531
532	#endif
533
534	for(mol = info->beginMolecule(mi); mol != NULL;
535	mol = info->nextMolecule(mi)) {
536
537	//local index(index in DataStorge) of atom is important
538	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
539	atom->setGlobalIndex(beginAtomIndex++);
540	}
541
542	for(rb = mol->beginRigidBody(ri); rb != NULL;
543	rb = mol->nextRigidBody(ri)) {
544	rb->setGlobalIndex(beginRigidBodyIndex++);
545	}
546
547	//local index of cutoff group is trivial, it only depends on the order of travesing
548	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
549	cg = mol->nextCutoffGroup(ci)) {
550	cg->setGlobalIndex(beginCutoffGroupIndex++);
551	}
552	}
553
554	//fill globalGroupMembership
555	std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
556	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
557	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
558
559	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
560	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
561	}
562
563	}
564	}
565
566	#ifdef IS_MPI
567	// Since the globalGroupMembership has been zero filled and we've only
568	// poked values into the atoms we know, we can do an Allreduce
569	// to get the full globalGroupMembership array (We think).
570	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
571	// docs said we could.
572	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
573	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
574	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
575	info->setGlobalGroupMembership(tmpGroupMembership);
576	#else
577	info->setGlobalGroupMembership(globalGroupMembership);
578	#endif
579
580	//fill molMembership
581	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
582
583	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
584
585	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
586	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
587	}
588	}
589
590	#ifdef IS_MPI
591	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
592
593	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
594	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
595
596	info->setGlobalMolMembership(tmpMolMembership);
597	#else
598	info->setGlobalMolMembership(globalMolMembership);
599	#endif
600
601	}
602
603	void SimCreator::loadCoordinates(SimInfo* info) {
604	Globals* simParams;
605	simParams = info->getSimParams();
606
607	if (!simParams->haveInitialConfig()) {
608	sprintf(painCave.errMsg,
609	"Cannot intialize a simulation without an initial configuration file.\n");
610	painCave.isFatal = 1;;
611	simError();
612	}
613
614	DumpReader reader(info, simParams->getInitialConfig());
615	int nframes = reader.getNFrames();
616
617	if (nframes > 0) {
618	reader.readFrame(nframes - 1);
619	} else {
620	//invalid initial coordinate file
621	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
622	simParams->getInitialConfig());
623	painCave.isFatal = 1;
624	simError();
625	}
626
627	}
628
629	} //end namespace oopse
630
631