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);

    
    //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;
    int nGlobalMols;
    std::vector < int > atomsPerProc;
    randomSPRNG myRandom(info->getSeed());
    int * molToProcMap = info->getMolToProcMapPointer();

    MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
    nGlobalMols = info->getNGlobalMolecules();

    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);

    for(i = 0; i < nGlobalMols; i++) {
        // default to an error condition:
        molToProcMap[i] = -1;
    }

    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, nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
    } else {

        // Listen to your marching orders from processor 0:

        MPI_Bcast(molToProcMap, nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
    }

    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;

#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.

    MPI_Allreduce(&globalGroupMembership[0],
                  info->getGlobalGroupMembershipPointer(),
                  info->getNGlobalAtoms(),
                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
#else
    std::copy(globalGroupMembership.begin(), globalGroupMembership.end(), 
        info->getGlobalGroupMembershipPointer());
#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
    MPI_Allreduce(&globalMolMembership[0],
                  info->getGlobalMolMembershipPointer(),
                  info->getNGlobalAtoms(),
                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
#else
    std::copy(globalMolMembership.begin(), globalMolMembership.end(), 
        info->getGlobalMolMembershipPointer());
#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:	1841
Committed:	Fri Dec 3 17:59:45 2004 UTC (19 years, 7 months ago) by tim
File size:	19040 byte(s)
Log Message:	begin to fix bugs
#	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
151
152	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
153	//eta, chi for NPT integrator)
154	loadCoordinates(info);
155	return info;
156	}
157
158	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
159
160	//setup seed for random number generator
161	int seedValue;
162	Globals * simParams = info->getSimParams();
163
164	if (simParams->haveSeed()) {
165	seedValue = simParams->getSeed();
166
167	if (seedValue / 1000000000 == 0) {
168	sprintf(painCave.errMsg,
169	"Seed for sprng library should contain at least 9 digits\n"
170	"OOPSE will generate a seed for user\n");
171
172	painCave.isFatal = 0;
173	simError();
174
175	//using seed generated by system instead of invalid seed set by user
176
177	#ifndef IS_MPI
178
179	seedValue = make_sprng_seed();
180
181	#else
182
183	if (worldRank == 0) {
184	seedValue = make_sprng_seed();
185	}
186
187	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
188
189	#endif
190
191	} //end if (seedValue /1000000000 == 0)
192	} else {
193
194	#ifndef IS_MPI
195
196	seedValue = make_sprng_seed();
197
198	#else
199
200	if (worldRank == 0) {
201	seedValue = make_sprng_seed();
202	}
203
204	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
205
206	#endif
207
208	} //end of simParams->haveSeed()
209
210	info->setSeed(seedValue);
211
212
213	//figure out the ouput file names
214	std::string prefix;
215
216	#ifdef IS_MPI
217
218	if (worldRank == 0) {
219	#endif // is_mpi
220
221	if (simParams->haveFinalConfig()) {
222	prefix = getPrefix(simParams->getFinalConfig());
223	} else {
224	prefix = getPrefix(mdfile);
225	}
226
227	info->setFinalConfigFileName(prefix + ".eor");
228	info->setDumpFileName(prefix + ".dump");
229	info->setStatFileName(prefix + ".stat");
230
231	#ifdef IS_MPI
232
233	}
234
235	#endif
236
237	}
238
239	#ifdef IS_MPI
240	void SimCreator::divideMolecules(SimInfo *info) {
241	double numerator;
242	double denominator;
243	double precast;
244	double x;
245	double y;
246	double a;
247	int old_atoms;
248	int add_atoms;
249	int new_atoms;
250	int nTarget;
251	int done;
252	int i;
253	int j;
254	int loops;
255	int which_proc;
256	int nProcessors;
257	int nGlobalMols;
258	std::vector < int > atomsPerProc;
259	randomSPRNG myRandom(info->getSeed());
260	int * molToProcMap = info->getMolToProcMapPointer();
261
262	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
263	nGlobalMols = info->getNGlobalMolecules();
264
265	if (nProcessors > nGlobalMols) {
266	sprintf(painCave.errMsg,
267	"nProcessors (%d) > nMol (%d)\n"
268	"\tThe number of processors is larger than\n"
269	"\tthe number of molecules. This will not result in a \n"
270	"\tusable division of atoms for force decomposition.\n"
271	"\tEither try a smaller number of processors, or run the\n"
272	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
273
274	painCave.isFatal = 1;
275	simError();
276	}
277
278	a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
279
280	//initialize atomsPerProc
281	atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
282
283	for(i = 0; i < nGlobalMols; i++) {
284	// default to an error condition:
285	molToProcMap[i] = -1;
286	}
287
288	if (worldRank == 0) {
289	numerator = info->getNGlobalAtoms();
290	denominator = nProcessors;
291	precast = numerator / denominator;
292	nTarget = (int)(precast + 0.5);
293
294	for(i = 0; i < nGlobalMols; i++) {
295	done = 0;
296	loops = 0;
297
298	while (!done) {
299	loops++;
300
301	// Pick a processor at random
302
303	which_proc = (int) (myRandom.getRandom() * nProcessors);
304
305	//get the molecule stamp first
306	int stampId = info->getMoleculeStampId(i);
307	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
308
309	// How many atoms does this processor have so far?
310	old_atoms = atomsPerProc[which_proc];
311	add_atoms = moleculeStamp->getNAtoms();
312	new_atoms = old_atoms + add_atoms;
313
314	// If we've been through this loop too many times, we need
315	// to just give up and assign the molecule to this processor
316	// and be done with it.
317
318	if (loops > 100) {
319	sprintf(painCave.errMsg,
320	"I've tried 100 times to assign molecule %d to a "
321	" processor, but can't find a good spot.\n"
322	"I'm assigning it at random to processor %d.\n",
323	i, which_proc);
324
325	painCave.isFatal = 0;
326	simError();
327
328	molToProcMap[i] = which_proc;
329	atomsPerProc[which_proc] += add_atoms;
330
331	done = 1;
332	continue;
333	}
334
335	// If we can add this molecule to this processor without sending
336	// it above nTarget, then go ahead and do it:
337
338	if (new_atoms <= nTarget) {
339	molToProcMap[i] = which_proc;
340	atomsPerProc[which_proc] += add_atoms;
341
342	done = 1;
343	continue;
344	}
345
346	// The only situation left is when new_atoms > nTarget. We
347	// want to accept this with some probability that dies off the
348	// farther we are from nTarget
349
350	// roughly: x = new_atoms - nTarget
351	// Pacc(x) = exp(- a * x)
352	// where a = penalty / (average atoms per molecule)
353
354	x = (double)(new_atoms - nTarget);
355	y = myRandom.getRandom();
356
357	if (y < exp(- a * x)) {
358	molToProcMap[i] = which_proc;
359	atomsPerProc[which_proc] += add_atoms;
360
361	done = 1;
362	continue;
363	} else {
364	continue;
365	}
366	}
367	}
368
369	// Spray out this nonsense to all other processors:
370
371	MPI_Bcast(molToProcMap, nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
372	} else {
373
374	// Listen to your marching orders from processor 0:
375
376	MPI_Bcast(molToProcMap, nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
377	}
378
379	sprintf(checkPointMsg,
380	"Successfully divided the molecules among the processors.\n");
381	MPIcheckPoint();
382	}
383
384	#endif
385
386	void SimCreator::createMolecules(SimInfo *info) {
387	MoleculeCreator molCreator;
388	int stampId;
389
390	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
391
392	#ifdef IS_MPI
393
394	if (info->getMolToProc(i) == worldRank) {
395	#endif
396
397	stampId = info->getMoleculeStampId(i);
398	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
399	stampId, i, info->getLocalIndexManager());
400
401	info->addMolecule(mol);
402
403	#ifdef IS_MPI
404
405	}
406
407	#endif
408
409	} //end for(int i=0)
410	}
411
412	void SimCreator::compList(MakeStamps stamps, Globals simParams,
413	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
414	int i;
415	char * id;
416	MoleculeStamp * currentStamp;
417	Component** the_components = simParams->getComponents();
418	int n_components = simParams->getNComponents();
419
420	if (!simParams->haveNMol()) {
421	// we don't have the total number of molecules, so we assume it is
422	// given in each component
423
424	for(i = 0; i < n_components; i++) {
425	if (!the_components[i]->haveNMol()) {
426	// we have a problem
427	sprintf(painCave.errMsg,
428	"SimCreator Error. No global NMol or component NMol given.\n"
429	"\tCannot calculate the number of atoms.\n");
430
431	painCave.isFatal = 1;
432	simError();
433	}
434
435	id = the_components[i]->getType();
436	currentStamp = (stamps->extractMolStamp(id))->getStamp();
437
438	if (currentStamp == NULL) {
439	sprintf(painCave.errMsg,
440	"SimCreator error: Component \"%s\" was not found in the "
441	"list of declared molecules\n", id);
442
443	painCave.isFatal = 1;
444	simError();
445	}
446
447	moleculeStampPairs.push_back(
448	std::make_pair(currentStamp, the_components[i]->getNMol()));
449	} //end for (i = 0; i < n_components; i++)
450	} else {
451	sprintf(painCave.errMsg, "SimSetup error.\n"
452	"\tSorry, the ability to specify total"
453	" nMols and then give molfractions in the components\n"
454	"\tis not currently supported."
455	" Please give nMol in the components.\n");
456
457	painCave.isFatal = 1;
458	simError();
459	}
460
461	#ifdef IS_MPI
462
463	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
464	MPIcheckPoint();
465
466	#endif // is_mpi
467
468	}
469
470	void SimCreator::setGlobalIndex(SimInfo *info) {
471	SimInfo::MoleculeIterator mi;
472	Molecule::AtomIterator ai;
473	Molecule::RigidBodyIterator ri;
474	Molecule::CutoffGroupIterator ci;
475	Molecule * mol;
476	Atom * atom;
477	RigidBody * rb;
478	CutoffGroup * cg;
479	int beginAtomIndex;
480	int beginRigidBodyIndex;
481	int beginCutoffGroupIndex;
482
483	#ifndef IS_MPI
484
485	beginAtomIndex = 0;
486	beginRigidBodyIndex = 0;
487	beginCutoffGroupIndex = 0;
488
489	#else
490
491	int nproc;
492	int myNode;
493
494	myNode = worldRank;
495	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
496
497	std::vector < int > tmpAtomsInProc(nproc, 0);
498	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
499	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
500	std::vector < int > NumAtomsInProc(nproc, 0);
501	std::vector < int > NumRigidBodiesInProc(nproc, 0);
502	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
503
504	tmpAtomsInProc[myNode] = info->getNAtoms();
505	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
506	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
507
508	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
509	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
510	MPI_SUM, MPI_COMM_WORLD);
511	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
512	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
513	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
514	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
515
516	beginAtomIndex = 0;
517	beginRigidBodyIndex = 0;
518	beginCutoffGroupIndex = 0;
519
520	for(int i = 0; i < nproc; i++) {
521	beginAtomIndex += NumAtomsInProc[i];
522	beginRigidBodyIndex += NumRigidBodiesInProc[i];
523	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
524	}
525
526	#endif
527
528	for(mol = info->beginMolecule(mi); mol != NULL;
529	mol = info->nextMolecule(mi)) {
530
531	//local index(index in DataStorge) of atom is important
532	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
533	atom->setGlobalIndex(beginAtomIndex++);
534	}
535
536	for(rb = mol->beginRigidBody(ri); rb != NULL;
537	rb = mol->nextRigidBody(ri)) {
538	rb->setGlobalIndex(beginRigidBodyIndex++);
539	}
540
541	//local index of cutoff group is trivial, it only depends on the order of travesing
542	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
543	cg = mol->nextCutoffGroup(ci)) {
544	cg->setGlobalIndex(beginCutoffGroupIndex++);
545	}
546	}
547
548	//fill globalGroupMembership
549	std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
550	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
551	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
552
553	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
554	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
555	}
556
557	}
558	}
559
560	#ifdef IS_MPI
561	// Since the globalGroupMembership has been zero filled and we've only
562	// poked values into the atoms we know, we can do an Allreduce
563	// to get the full globalGroupMembership array (We think).
564	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
565	// docs said we could.
566
567	MPI_Allreduce(&globalGroupMembership[0],
568	info->getGlobalGroupMembershipPointer(),
569	info->getNGlobalAtoms(),
570	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
571	#else
572	std::copy(globalGroupMembership.begin(), globalGroupMembership.end(),
573	info->getGlobalGroupMembershipPointer());
574	#endif
575
576	//fill molMembership
577	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
578
579	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
580
581	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
582	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
583	}
584
585	#ifdef IS_MPI
586	MPI_Allreduce(&globalMolMembership[0],
587	info->getGlobalMolMembershipPointer(),
588	info->getNGlobalAtoms(),
589	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
590	#else
591	std::copy(globalMolMembership.begin(), globalMolMembership.end(),
592	info->getGlobalMolMembershipPointer());
593	#endif
594
595	}
596	}
597
598	void SimCreator::loadCoordinates(SimInfo* info) {
599	Globals* simParams;
600	simParams = info->getSimParams();
601
602	if (!simParams->haveInitialConfig()) {
603	sprintf(painCave.errMsg,
604	"Cannot intialize a simulation without an initial configuration file.\n");
605	painCave.isFatal = 1;;
606	simError();
607	}
608
609	DumpReader reader(info, simParams->getInitialConfig());
610	int nframes = reader.getNFrames();
611
612	if (nframes > 0) {
613	reader.readFrame(nframes - 1);
614	} else {
615	//invalid initial coordinate file
616	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
617	simParams->getInitialConfig());
618	painCave.isFatal = 1;
619	simError();
620	}
621
622	}
623
624	} //end namespace oopse