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"
#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 < nproc; 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);
#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:	1856
Committed:	Mon Dec 6 04:49:53 2004 UTC (19 years, 7 months ago) by tim
File size:	19494 byte(s)
Log Message:	fix a bug in Exclude List
#	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	#endif
47
48	namespace oopse {
49
50	void SimCreator::parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* simParams){
51
52	#ifdef IS_MPI
53
54	if (worldRank == 0) {
55	#endif // is_mpi
56
57	simParams->initalize();
58	set_interface_stamps(stamps, simParams);
59
60	#ifdef IS_MPI
61
62	mpiEventInit();
63
64	#endif
65
66	yacc_BASS(mdFileName.c_str());
67
68	#ifdef IS_MPI
69
70	throwMPIEvent(NULL);
71	} else {
72	set_interface_stamps(stamps, simParams);
73	mpiEventInit();
74	MPIcheckPoint();
75	mpiEventLoop();
76	}
77
78	#endif
79
80	}
81
82	SimInfo* SimCreator::createSim(const std::string & mdFileName) {
83
84	MakeStamps * stamps = new MakeStamps();
85
86	Globals * simParams = new Globals();
87
88	//parse meta-data file
89	parseFile(mdFileName, stamps, simParams);
90
91	//create the force field
92	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
93	simParams->getForceField());
94
95	if (ff == NULL) {
96	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
97	simParams->getForceField());
98	painCave.isFatal = 1;
99	simError();
100	}
101
102	std::string forcefieldFileName;
103	forcefieldFileName = ff->getForceFieldFileName();
104
105	if (simParams->haveForceFieldVariant()) {
106	//If the force field has variant, the variant force field name will be
107	//Base.variant.frc. For exampel EAM.u6.frc
108
109	std::string variant = simParams->getForceFieldVariant();
110
111	std::string::size_type pos = forcefieldFileName.rfind(".frc");
112	variant = "." + variant;
113	if (pos != std::string::npos) {
114	forcefieldFileName.insert(pos, variant);
115	} else {
116	//If the default force field file name does not containt .frc suffix, just append the .variant
117	forcefieldFileName.append(variant);
118	}
119	}
120
121	ff->parse(forcefieldFileName);
122
123	//extract the molecule stamps
124	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
125	compList(stamps, simParams, moleculeStampPairs);
126
127	//create SimInfo
128	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
129
130	//gather parameters (SimCreator only retrieves part of the parameters)
131	gatherParameters(info, mdFileName);
132
133	//divide the molecules and determine the global index of molecules
134	#ifdef IS_MPI
135	divideMolecules(info);
136	#endif
137
138	//create the molecules
139	createMolecules(info);
140
141
142	//allocate memory for DataStorage(circular reference, need to break it)
143	info->setSnapshotManager(new SimSnapshotManager(info));
144
145	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
146	//global index will never change again). Local indices of atoms and rigidbodies are already set by
147	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
148	setGlobalIndex(info);
149
150	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
151	//atoms don't have the global index yet (their global index are all initialized to -1).
152	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
153	//we can determine the beginning global indices of atoms before they get created.
154	SimInfo::MoleculeIterator mi;
155	Molecule* mol;
156	for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
157	info->addExcludePairs(mol);
158	}
159
160
161	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
162	//eta, chi for NPT integrator)
163	loadCoordinates(info);
164	return info;
165	}
166
167	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
168
169	//setup seed for random number generator
170	int seedValue;
171	Globals * simParams = info->getSimParams();
172
173	if (simParams->haveSeed()) {
174	seedValue = simParams->getSeed();
175
176	if (seedValue / 1000000000 == 0) {
177	sprintf(painCave.errMsg,
178	"Seed for sprng library should contain at least 9 digits\n"
179	"OOPSE will generate a seed for user\n");
180
181	painCave.isFatal = 0;
182	simError();
183
184	//using seed generated by system instead of invalid seed set by user
185
186	#ifndef IS_MPI
187
188	seedValue = make_sprng_seed();
189
190	#else
191
192	if (worldRank == 0) {
193	seedValue = make_sprng_seed();
194	}
195
196	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
197
198	#endif
199
200	} //end if (seedValue /1000000000 == 0)
201	} else {
202
203	#ifndef IS_MPI
204
205	seedValue = make_sprng_seed();
206
207	#else
208
209	if (worldRank == 0) {
210	seedValue = make_sprng_seed();
211	}
212
213	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
214
215	#endif
216
217	} //end of simParams->haveSeed()
218
219	info->setSeed(seedValue);
220
221
222	//figure out the ouput file names
223	std::string prefix;
224
225	#ifdef IS_MPI
226
227	if (worldRank == 0) {
228	#endif // is_mpi
229
230	if (simParams->haveFinalConfig()) {
231	prefix = getPrefix(simParams->getFinalConfig());
232	} else {
233	prefix = getPrefix(mdfile);
234	}
235
236	info->setFinalConfigFileName(prefix + ".eor");
237	info->setDumpFileName(prefix + ".dump");
238	info->setStatFileName(prefix + ".stat");
239
240	#ifdef IS_MPI
241
242	}
243
244	#endif
245
246	}
247
248	#ifdef IS_MPI
249	void SimCreator::divideMolecules(SimInfo *info) {
250	double numerator;
251	double denominator;
252	double precast;
253	double x;
254	double y;
255	double a;
256	int old_atoms;
257	int add_atoms;
258	int new_atoms;
259	int nTarget;
260	int done;
261	int i;
262	int j;
263	int loops;
264	int which_proc;
265	int nProcessors;
266	std::vector<int> atomsPerProc;
267	randomSPRNG myRandom(info->getSeed());
268	int nGlobalMols = info->getNGlobalMolecules();
269	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
270
271	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
272
273	if (nProcessors > nGlobalMols) {
274	sprintf(painCave.errMsg,
275	"nProcessors (%d) > nMol (%d)\n"
276	"\tThe number of processors is larger than\n"
277	"\tthe number of molecules. This will not result in a \n"
278	"\tusable division of atoms for force decomposition.\n"
279	"\tEither try a smaller number of processors, or run the\n"
280	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
281
282	painCave.isFatal = 1;
283	simError();
284	}
285
286	a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
287
288	//initialize atomsPerProc
289	atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
290
291	if (worldRank == 0) {
292	numerator = info->getNGlobalAtoms();
293	denominator = nProcessors;
294	precast = numerator / denominator;
295	nTarget = (int)(precast + 0.5);
296
297	for(i = 0; i < nGlobalMols; i++) {
298	done = 0;
299	loops = 0;
300
301	while (!done) {
302	loops++;
303
304	// Pick a processor at random
305
306	which_proc = (int) (myRandom.getRandom() * nProcessors);
307
308	//get the molecule stamp first
309	int stampId = info->getMoleculeStampId(i);
310	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
311
312	// How many atoms does this processor have so far?
313	old_atoms = atomsPerProc[which_proc];
314	add_atoms = moleculeStamp->getNAtoms();
315	new_atoms = old_atoms + add_atoms;
316
317	// If we've been through this loop too many times, we need
318	// to just give up and assign the molecule to this processor
319	// and be done with it.
320
321	if (loops > 100) {
322	sprintf(painCave.errMsg,
323	"I've tried 100 times to assign molecule %d to a "
324	" processor, but can't find a good spot.\n"
325	"I'm assigning it at random to processor %d.\n",
326	i, which_proc);
327
328	painCave.isFatal = 0;
329	simError();
330
331	molToProcMap[i] = which_proc;
332	atomsPerProc[which_proc] += add_atoms;
333
334	done = 1;
335	continue;
336	}
337
338	// If we can add this molecule to this processor without sending
339	// it above nTarget, then go ahead and do it:
340
341	if (new_atoms <= nTarget) {
342	molToProcMap[i] = which_proc;
343	atomsPerProc[which_proc] += add_atoms;
344
345	done = 1;
346	continue;
347	}
348
349	// The only situation left is when new_atoms > nTarget. We
350	// want to accept this with some probability that dies off the
351	// farther we are from nTarget
352
353	// roughly: x = new_atoms - nTarget
354	// Pacc(x) = exp(- a * x)
355	// where a = penalty / (average atoms per molecule)
356
357	x = (double)(new_atoms - nTarget);
358	y = myRandom.getRandom();
359
360	if (y < exp(- a * x)) {
361	molToProcMap[i] = which_proc;
362	atomsPerProc[which_proc] += add_atoms;
363
364	done = 1;
365	continue;
366	} else {
367	continue;
368	}
369	}
370	}
371
372	// Spray out this nonsense to all other processors:
373
374	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
375	} else {
376
377	// Listen to your marching orders from processor 0:
378
379	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
380	}
381
382	info->setMolToProcMap(molToProcMap);
383	sprintf(checkPointMsg,
384	"Successfully divided the molecules among the processors.\n");
385	MPIcheckPoint();
386	}
387
388	#endif
389
390	void SimCreator::createMolecules(SimInfo *info) {
391	MoleculeCreator molCreator;
392	int stampId;
393
394	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
395
396	#ifdef IS_MPI
397
398	if (info->getMolToProc(i) == worldRank) {
399	#endif
400
401	stampId = info->getMoleculeStampId(i);
402	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
403	stampId, i, info->getLocalIndexManager());
404
405	info->addMolecule(mol);
406
407	#ifdef IS_MPI
408
409	}
410
411	#endif
412
413	} //end for(int i=0)
414	}
415
416	void SimCreator::compList(MakeStamps stamps, Globals simParams,
417	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
418	int i;
419	char * id;
420	MoleculeStamp * currentStamp;
421	Component** the_components = simParams->getComponents();
422	int n_components = simParams->getNComponents();
423
424	if (!simParams->haveNMol()) {
425	// we don't have the total number of molecules, so we assume it is
426	// given in each component
427
428	for(i = 0; i < n_components; i++) {
429	if (!the_components[i]->haveNMol()) {
430	// we have a problem
431	sprintf(painCave.errMsg,
432	"SimCreator Error. No global NMol or component NMol given.\n"
433	"\tCannot calculate the number of atoms.\n");
434
435	painCave.isFatal = 1;
436	simError();
437	}
438
439	id = the_components[i]->getType();
440	currentStamp = (stamps->extractMolStamp(id))->getStamp();
441
442	if (currentStamp == NULL) {
443	sprintf(painCave.errMsg,
444	"SimCreator error: Component \"%s\" was not found in the "
445	"list of declared molecules\n", id);
446
447	painCave.isFatal = 1;
448	simError();
449	}
450
451	moleculeStampPairs.push_back(
452	std::make_pair(currentStamp, the_components[i]->getNMol()));
453	} //end for (i = 0; i < n_components; i++)
454	} else {
455	sprintf(painCave.errMsg, "SimSetup error.\n"
456	"\tSorry, the ability to specify total"
457	" nMols and then give molfractions in the components\n"
458	"\tis not currently supported."
459	" Please give nMol in the components.\n");
460
461	painCave.isFatal = 1;
462	simError();
463	}
464
465	#ifdef IS_MPI
466
467	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
468	MPIcheckPoint();
469
470	#endif // is_mpi
471
472	}
473
474	void SimCreator::setGlobalIndex(SimInfo *info) {
475	SimInfo::MoleculeIterator mi;
476	Molecule::AtomIterator ai;
477	Molecule::RigidBodyIterator ri;
478	Molecule::CutoffGroupIterator ci;
479	Molecule * mol;
480	Atom * atom;
481	RigidBody * rb;
482	CutoffGroup * cg;
483	int beginAtomIndex;
484	int beginRigidBodyIndex;
485	int beginCutoffGroupIndex;
486	int nGlobalAtoms = info->getNGlobalAtoms();
487
488	#ifndef IS_MPI
489
490	beginAtomIndex = 0;
491	beginRigidBodyIndex = 0;
492	beginCutoffGroupIndex = 0;
493
494	#else
495
496	int nproc;
497	int myNode;
498
499	myNode = worldRank;
500	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
501
502	std::vector < int > tmpAtomsInProc(nproc, 0);
503	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
504	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
505	std::vector < int > NumAtomsInProc(nproc, 0);
506	std::vector < int > NumRigidBodiesInProc(nproc, 0);
507	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
508
509	tmpAtomsInProc[myNode] = info->getNAtoms();
510	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
511	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
512
513	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
514	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
515	MPI_SUM, MPI_COMM_WORLD);
516	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
517	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
518	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
519	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
520
521	beginAtomIndex = 0;
522	beginRigidBodyIndex = 0;
523	beginCutoffGroupIndex = 0;
524
525	for(int i = 0; i < nproc; i++) {
526	beginAtomIndex += NumAtomsInProc[i];
527	beginRigidBodyIndex += NumRigidBodiesInProc[i];
528	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
529	}
530
531	#endif
532
533	for(mol = info->beginMolecule(mi); mol != NULL;
534	mol = info->nextMolecule(mi)) {
535
536	//local index(index in DataStorge) of atom is important
537	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
538	atom->setGlobalIndex(beginAtomIndex++);
539	}
540
541	for(rb = mol->beginRigidBody(ri); rb != NULL;
542	rb = mol->nextRigidBody(ri)) {
543	rb->setGlobalIndex(beginRigidBodyIndex++);
544	}
545
546	//local index of cutoff group is trivial, it only depends on the order of travesing
547	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
548	cg = mol->nextCutoffGroup(ci)) {
549	cg->setGlobalIndex(beginCutoffGroupIndex++);
550	}
551	}
552
553	//fill globalGroupMembership
554	std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
555	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
556	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
557
558	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
559	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
560	}
561
562	}
563	}
564
565	#ifdef IS_MPI
566	// Since the globalGroupMembership has been zero filled and we've only
567	// poked values into the atoms we know, we can do an Allreduce
568	// to get the full globalGroupMembership array (We think).
569	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
570	// docs said we could.
571	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
572	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
573	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
574	#else
575	info->setGlobalGroupMembership(globalGroupMembership);
576	#endif
577
578	//fill molMembership
579	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
580
581	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
582
583	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
584	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
585	}
586
587	#ifdef IS_MPI
588	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
589
590	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
591	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
592
593	info->setGlobalMolMembership(tmpMolMembership);
594	#else
595	info->setGlobalMolMembership(globalMolMembership);
596	#endif
597
598	}
599	}
600
601	void SimCreator::loadCoordinates(SimInfo* info) {
602	Globals* simParams;
603	simParams = info->getSimParams();
604
605	if (!simParams->haveInitialConfig()) {
606	sprintf(painCave.errMsg,
607	"Cannot intialize a simulation without an initial configuration file.\n");
608	painCave.isFatal = 1;;
609	simError();
610	}
611
612	DumpReader reader(info, simParams->getInitialConfig());
613	int nframes = reader.getNFrames();
614
615	if (nframes > 0) {
616	reader.readFrame(nframes - 1);
617	} else {
618	//invalid initial coordinate file
619	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
620	simParams->getInitialConfig());
621	painCave.isFatal = 1;
622	simError();
623	}
624
625	}
626
627	} //end namespace oopse
628
629