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 "brains/SimCreator.hpp"

namespace oopse {

void SimCreator::parseFile(const std::string& mdFileName, MakeStamps *stamps, Globals *globals) {

#ifdef IS_MPI

    if (worldRank == 0) {
#endif // is_mpi

        globals->initalize();
        set_interface_stamps(stamps, globals);

#ifdef IS_MPI

        mpiEventInit();

#endif

        yacc_BASS(mdFileName.c_str());

#ifdef IS_MPI

        throwMPIEvent(NULL);
    } else {
        set_interface_stamps(stamps, globals);
        mpiEventInit();
        MPIcheckPoint();
        mpiEventLoop();
    }

#endif

}

SimInfo*  SimCreator::createSim(const std::string & mdFileName) {

    mdFileName_ = mdFileName;
    
    MakeStamps * stamps = new MakeStamps();

    Globals * globals = new Globals();

    //parse meta-data file
    parseFile(mdFileName_, stamps, globals);

    //create the force field
    ForceFiled * ff = ForceFieldFactory::getInstance()->createObject(
                          globals->getForceField());
    
    if (ff == NULL) {
        sprintf(painCave.errMsg, "ForceFiled Factory can not create %s force field\n",
                globals->getForceField());
        painCave.isFatal = 1;
        simError();
    }
    ff->parse();

    //extract the molecule stamps
    std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
    compList(stamps, globals, moleculeStampPairs);

    //create SimInfo
    SimInfo * info = new SimInfo(moleculeStampPairs, ff, globals);

    //gather parameters (SimCreator only retrieves part of the parameters)
    gatherParameters(info);

    //divide the molecules and determine the global index of molecules
    divideMolecules(info);

    //create the molecules
    createMolecules(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. 
    setGlobalIndices(info);

    //allocate memory for DataStorage(circular reference, need to break it)
    info->setSnapshotManager(new SimSnapshotManager(info));

    //initialize fortran -- setup the cutoff 
    initFortran(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) {

    //setup seed for random number generator
    int seedValue;
    Globals * globals = info->getGlobals();

    if (globals->haveSeed()) {
        seedValue = globals->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 globals->haveSeed()

    info->setSeed(seedValue);


    //figure out the ouput file names
    std::string prefix;

#ifdef IS_MPI

    if (worldRank == 0) {
#endif // is_mpi

        if (globals->haveFinalConfig()) {
            prefix = StringUtils::getPrefix(globals->getFinalConfig());
        } else {
            prefix = StringUtils::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->addMolecule(mol);

#ifdef IS_MPI

        }

#endif

    } //end for(int i=0)   
}

void SimSetup::compList(MakeStamps *stamps, Globals* globals,
                        std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
    int i;
    char * id;
    MoleculeStamp * currentStamp;
    Component * the_components = globals->getComponents();
    int n_components = globals->getNComponents();

    if (!globals->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,
                        "SimSetup 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);

            if (currentStamp == NULL) {
                sprintf(painCave.errMsg,
                        "SimSetup error: Component \"%s\" was not found in the "
                            "list of declared molecules\n", id);

                painCave.isFatal = 1;
                simError();
            }

            moleculeStampPairs.push_back(
                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) {
    typename SimInfo::MoleculeIterator mi;
    typename Molecule::AtomIterator ai;
    typename Molecule::RigidBodyIterator ri;
    typename 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 = beginMolecule(mi); mol != NULL; mol = 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* globals;
    globals = info->getGlobals();
    
    if (!globals->haveInitialConfig()) {
        sprintf(painCave.errMsg,
                "Cannot intialize a simulation without an initial configuration file.\n");
        painCave.isFatal = 1;;
        simError();
    }
        
    DumpReader reader(globals->getInitialConfig());
    int nframes = reader->getNframes();

    if (nframes > 0) {
        reader.readFrame(info, nframes - 1);
    } else {
        //invalid initial coordinate file
        sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
                globals->getInitialConfig());
        painCave.isFatal = 1;
        simError();
    }

}

} //end namespace oopse
Revision:	1740
Committed:	Mon Nov 15 23:00:32 2004 UTC (19 years, 8 months ago) by tim
File size:	17909 byte(s)
Log Message:	adding ForceFieldFactory and LJFF classes
#	User	Rev	Content
1	tim	1703	/*
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	tim	1725	/**
27			* @file SimCreator.cpp
28			* @author tlin
29			* @date 11/03/2004
30			* @time 13:51am
31			* @version 1.0
32			*/
33
34			#include "brains/SimCreator.hpp"
35	tim	1733
36	tim	1703	namespace oopse {
37
38	tim	1740	void SimCreator::parseFile(const std::string& mdFileName, MakeStamps stamps, Globals globals) {
39	tim	1733
40	tim	1712	#ifdef IS_MPI
41	tim	1733
42			if (worldRank == 0) {
43	tim	1712	#endif // is_mpi
44
45	tim	1733	globals->initalize();
46			set_interface_stamps(stamps, globals);
47	tim	1712
48	tim	1733	#ifdef IS_MPI
49	tim	1712
50	tim	1733	mpiEventInit();
51
52	tim	1712	#endif
53
54	tim	1733	yacc_BASS(mdFileName.c_str());
55	tim	1712
56			#ifdef IS_MPI
57	tim	1733
58			throwMPIEvent(NULL);
59			} else {
60			set_interface_stamps(stamps, globals);
61			mpiEventInit();
62			MPIcheckPoint();
63			mpiEventLoop();
64			}
65
66	tim	1712	#endif
67
68	tim	1703	}
69
70	tim	1733	SimInfo* SimCreator::createSim(const std::string & mdFileName) {
71	tim	1712
72	tim	1733	mdFileName_ = mdFileName;
73	tim	1712
74	tim	1733	MakeStamps * stamps = new MakeStamps();
75	tim	1712
76	tim	1733	Globals * globals = new Globals();
77
78	tim	1712	//parse meta-data file
79	tim	1733	parseFile(mdFileName_, stamps, globals);
80	tim	1712
81			//create the force field
82	tim	1733	ForceFiled * ff = ForceFieldFactory::getInstance()->createObject(
83			globals->getForceField());
84	tim	1740
85	tim	1733	if (ff == NULL) {
86			sprintf(painCave.errMsg, "ForceFiled Factory can not create %s force field\n",
87			globals->getForceField());
88			painCave.isFatal = 1;
89			simError();
90			}
91	tim	1740	ff->parse();
92	tim	1733
93			//extract the molecule stamps
94			std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
95			compList(stamps, globals, moleculeStampPairs);
96
97	tim	1719	//create SimInfo
98	tim	1733	SimInfo * info = new SimInfo(moleculeStampPairs, ff, globals);
99	tim	1719
100	tim	1733	//gather parameters (SimCreator only retrieves part of the parameters)
101	tim	1719	gatherParameters(info);
102	tim	1733
103	tim	1712	//divide the molecules and determine the global index of molecules
104	tim	1733	divideMolecules(info);
105
106	tim	1712	//create the molecules
107	tim	1719	createMolecules(info);
108	tim	1712
109	tim	1725	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
110			//global index will never change again). Local indices of atoms and rigidbodies are already set by
111	tim	1733	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
112	tim	1725	setGlobalIndices(info);
113	tim	1733
114	tim	1712	//allocate memory for DataStorage(circular reference, need to break it)
115	tim	1733	info->setSnapshotManager(new SimSnapshotManager(info));
116
117			//initialize fortran -- setup the cutoff
118			initFortran(info);
119
120	tim	1725	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
121			//eta, chi for NPT integrator)
122	tim	1733	loadCoordinates(info);
123	tim	1719	return info;
124	tim	1733	}
125	tim	1712
126	tim	1733	void SimCreator::gatherParameters(SimInfo *info) {
127	tim	1725
128			//setup seed for random number generator
129			int seedValue;
130	tim	1733	Globals * globals = info->getGlobals();
131
132			if (globals->haveSeed()) {
133	tim	1725	seedValue = globals->getSeed();
134
135	tim	1733	if (seedValue / 1000000000 == 0) {
136	tim	1725	sprintf(painCave.errMsg,
137	tim	1733	"Seed for sprng library should contain at least 9 digits\n"
138			"OOPSE will generate a seed for user\n");
139
140	tim	1725	painCave.isFatal = 0;
141			simError();
142
143	tim	1733	//using seed generated by system instead of invalid seed set by user
144
145	tim	1725	#ifndef IS_MPI
146	tim	1733
147	tim	1725	seedValue = make_sprng_seed();
148	tim	1733
149			#else
150
151			if (worldRank == 0) {
152	tim	1725	seedValue = make_sprng_seed();
153			}
154	tim	1733
155			MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
156
157			#endif
158
159	tim	1725	} //end if (seedValue /1000000000 == 0)
160	tim	1733	} else {
161
162	tim	1725	#ifndef IS_MPI
163	tim	1733
164	tim	1725	seedValue = make_sprng_seed();
165	tim	1733
166			#else
167
168			if (worldRank == 0) {
169	tim	1725	seedValue = make_sprng_seed();
170			}
171	tim	1733
172			MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
173
174	tim	1725	#endif
175	tim	1733
176			} //end of globals->haveSeed()
177
178	tim	1725	info->setSeed(seedValue);
179
180	tim	1733
181			//figure out the ouput file names
182	tim	1725	std::string prefix;
183	tim	1733
184	tim	1725	#ifdef IS_MPI
185	tim	1733
186			if (worldRank == 0) {
187	tim	1725	#endif // is_mpi
188	tim	1733
189			if (globals->haveFinalConfig()) {
190			prefix = StringUtils::getPrefix(globals->getFinalConfig());
191	tim	1725	} else {
192	tim	1733	prefix = StringUtils::getPrefix(mdfile_);
193	tim	1725	}
194	tim	1733
195			info->setFinalConfigFileName(prefix + ".eor");
196	tim	1725	info->setDumpFileName(prefix + ".dump");
197			info->setStatFileName(prefix + ".stat");
198
199			#ifdef IS_MPI
200	tim	1733
201	tim	1725	}
202
203	tim	1733	#endif
204	tim	1725
205	tim	1712	}
206
207			#ifdef IS_MPI
208
209	tim	1733	void SimCreator::divideMolecules(SimInfo *info) {
210	tim	1727	double numerator;
211			double denominator;
212			double precast;
213			double x;
214			double y;
215			double a;
216			int old_atoms;
217			int add_atoms;
218			int new_atoms;
219			int nTarget;
220			int done;
221			int i;
222			int j;
223			int loops;
224			int which_proc;
225	tim	1733	int nProcessors;
226			int nGlobalMols;
227			std::vector < int > atomsPerProc;
228			randomSPRNG myRandom(info->getSeed());
229			int * molToProcMap = info->getMolToProcMapPointer();
230	tim	1727
231	tim	1733	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
232			nGlobalMols = info->getNGlobalMolecules();
233	tim	1727
234	tim	1733	if (nProcessors > nGlobalMols) {
235	tim	1727	sprintf(painCave.errMsg,
236			"nProcessors (%d) > nMol (%d)\n"
237			"\tThe number of processors is larger than\n"
238			"\tthe number of molecules. This will not result in a \n"
239			"\tusable division of atoms for force decomposition.\n"
240			"\tEither try a smaller number of processors, or run the\n"
241	tim	1733	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
242	tim	1727
243			painCave.isFatal = 1;
244			simError();
245			}
246
247	tim	1733	a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
248	tim	1727
249	tim	1733	//initialize atomsPerProc
250			atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
251	tim	1727
252	tim	1733	for(i = 0; i < nGlobalMols; i++) {
253	tim	1727	// default to an error condition:
254	tim	1733	molToProcMap[i] = -1;
255	tim	1727	}
256
257	tim	1733	if (worldRank == 0) {
258			numerator = info->getNGlobalAtoms();
259			denominator = nProcessors;
260	tim	1727	precast = numerator / denominator;
261			nTarget = (int)(precast + 0.5);
262
263	tim	1733	for(i = 0; i < nGlobalMols; i++) {
264	tim	1727	done = 0;
265			loops = 0;
266
267			while (!done) {
268			loops++;
269
270			// Pick a processor at random
271
272	tim	1733	which_proc = (int) (myRandom.getRandom() * nProcessors);
273	tim	1727
274	tim	1733	//get the molecule stamp first
275			int stampId = info->getMoleculeStampId(i);
276			MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
277	tim	1727
278	tim	1733	// How many atoms does this processor have so far?
279			old_atoms = atomsPerProc[which_proc];
280			add_atoms = moleculeStamp->getNAtoms();
281	tim	1727	new_atoms = old_atoms + add_atoms;
282
283			// If we've been through this loop too many times, we need
284			// to just give up and assign the molecule to this processor
285			// and be done with it.
286
287			if (loops > 100) {
288	tim	1733	sprintf(painCave.errMsg,
289			"I've tried 100 times to assign molecule %d to a "
290			" processor, but can't find a good spot.\n"
291			"I'm assigning it at random to processor %d.\n",
292			i, which_proc);
293	tim	1727
294			painCave.isFatal = 0;
295			simError();
296
297	tim	1733	molToProcMap[i] = which_proc;
298			atomsPerProc[which_proc] += add_atoms;
299	tim	1727
300			done = 1;
301			continue;
302			}
303
304			// If we can add this molecule to this processor without sending
305			// it above nTarget, then go ahead and do it:
306
307			if (new_atoms <= nTarget) {
308	tim	1733	molToProcMap[i] = which_proc;
309			atomsPerProc[which_proc] += add_atoms;
310	tim	1727
311			done = 1;
312			continue;
313			}
314
315			// The only situation left is when new_atoms > nTarget. We
316			// want to accept this with some probability that dies off the
317			// farther we are from nTarget
318
319			// roughly: x = new_atoms - nTarget
320			// Pacc(x) = exp(- a * x)
321			// where a = penalty / (average atoms per molecule)
322
323			x = (double)(new_atoms - nTarget);
324	tim	1733	y = myRandom.getRandom();
325	tim	1727
326			if (y < exp(- a * x)) {
327	tim	1733	molToProcMap[i] = which_proc;
328			atomsPerProc[which_proc] += add_atoms;
329	tim	1727
330			done = 1;
331			continue;
332	tim	1733	} else {
333			continue;
334			}
335	tim	1727	}
336			}
337
338			// Spray out this nonsense to all other processors:
339
340	tim	1733	MPI_Bcast(molToProcMap, nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
341	tim	1727	} else {
342
343	tim	1733	// Listen to your marching orders from processor 0:
344	tim	1727
345	tim	1733	MPI_Bcast(molToProcMap, nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
346	tim	1727	}
347
348			sprintf(checkPointMsg,
349			"Successfully divided the molecules among the processors.\n");
350			MPIcheckPoint();
351	tim	1712	}
352	tim	1733
353	tim	1713	#endif
354	tim	1712
355	tim	1733	void SimCreator::createMolecules(SimInfo *info) {
356	tim	1725	MoleculeCreator molCreator;
357			int stampId;
358	tim	1713
359	tim	1733	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
360	tim	1713
361	tim	1733	#ifdef IS_MPI
362
363			if (info->getMolToProc(i) == worldRank) {
364			#endif
365
366	tim	1725	stampId = info->getMoleculeStampId(i);
367	tim	1733	Molecule * mol = molCreator.createMolecule(info->getForceField(),
368			info->getMoleculeStamp(stampId), stampId, i);
369
370	tim	1719	info->addMolecule(mol);
371	tim	1733
372			#ifdef IS_MPI
373
374	tim	1719	}
375	tim	1733
376			#endif
377
378			} //end for(int i=0)
379	tim	1713	}
380
381	tim	1733	void SimSetup::compList(MakeStamps stamps, Globals globals,
382			std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
383	tim	1719	int i;
384	tim	1733	char * id;
385			MoleculeStamp * currentStamp;
386			Component * the_components = globals->getComponents();
387			int n_components = globals->getNComponents();
388	tim	1719
389	tim	1733	if (!globals->haveNMol()) {
390	tim	1719	// we don't have the total number of molecules, so we assume it is
391			// given in each component
392
393	tim	1733	for(i = 0; i < n_components; i++) {
394			if (!the_components[i]->haveNMol()) {
395	tim	1719	// we have a problem
396			sprintf(painCave.errMsg,
397	tim	1733	"SimSetup Error. No global NMol or component NMol given.\n"
398			"\tCannot calculate the number of atoms.\n");
399
400	tim	1719	painCave.isFatal = 1;
401			simError();
402			}
403
404			id = the_components[i]->getType();
405			currentStamp = stamps->extractMolStamp(id);
406	tim	1733
407			if (currentStamp == NULL) {
408	tim	1719	sprintf(painCave.errMsg,
409	tim	1733	"SimSetup error: Component \"%s\" was not found in the "
410			"list of declared molecules\n", id);
411
412	tim	1719	painCave.isFatal = 1;
413			simError();
414	tim	1733	}
415	tim	1719
416	tim	1733	moleculeStampPairs.push_back(
417			make_pair(currentStamp, the_components[i]->getNMol));
418	tim	1719	} //end for (i = 0; i < n_components; i++)
419	tim	1733	} else {
420			sprintf(painCave.errMsg, "SimSetup error.\n"
421			"\tSorry, the ability to specify total"
422			" nMols and then give molfractions in the components\n"
423			"\tis not currently supported."
424			" Please give nMol in the components.\n");
425
426	tim	1719	painCave.isFatal = 1;
427			simError();
428			}
429	tim	1733
430	tim	1719	#ifdef IS_MPI
431	tim	1733
432			strcpy(checkPointMsg, "Component stamps successfully extracted\n");
433			MPIcheckPoint();
434
435	tim	1719	#endif // is_mpi
436	tim	1733
437	tim	1719	}
438
439	tim	1733	void SimCreator::setGlobalIndex(SimInfo *info) {
440	tim	1725	typename SimInfo::MoleculeIterator mi;
441			typename Molecule::AtomIterator ai;
442			typename Molecule::RigidBodyIterator ri;
443			typename Molecule::CutoffGroupIterator ci;
444	tim	1733	Molecule * mol;
445			Atom * atom;
446			RigidBody * rb;
447			CutoffGroup * cg;
448	tim	1725	int beginAtomIndex;
449			int beginRigidBodyIndex;
450			int beginCutoffGroupIndex;
451	tim	1719
452	tim	1733	#ifndef IS_MPI
453
454	tim	1725	beginAtomIndex = 0;
455			beginRigidBodyIndex = 0;
456			beginCutoffGroupIndex = 0;
457	tim	1733
458	tim	1725	#else
459	tim	1733
460	tim	1725	int nproc;
461			int myNode;
462
463			myNode = worldRank;
464			MPI_Comm_size(MPI_COMM_WORLD, &nproc);
465
466	tim	1733	std::vector < int > tmpAtomsInProc(nproc, 0);
467			std::vector < int > tmpRigidBodiesInProc(nproc, 0);
468			std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
469			std::vector < int > NumAtomsInProc(nproc, 0);
470			std::vector < int > NumRigidBodiesInProc(nproc, 0);
471			std::vector < int > NumCutoffGroupsInProc(nproc, 0);
472
473			tmpAtomsInProc[myNode] = info->getNAtoms();
474			tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
475			tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
476
477	tim	1725	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
478	tim	1733	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
479			MPI_SUM, MPI_COMM_WORLD);
480			MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
481			MPI_INT, MPI_SUM, MPI_COMM_WORLD);
482			MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
483			MPI_INT, MPI_SUM, MPI_COMM_WORLD);
484	tim	1725
485			beginAtomIndex = 0;
486			beginRigidBodyIndex = 0;
487			beginCutoffGroupIndex = 0;
488
489	tim	1733	for(int i = 0; i < nproc; i++) {
490	tim	1725	beginAtomIndex += NumAtomsInProc[i];
491			beginRigidBodyIndex += NumRigidBodiesInProc[i];
492	tim	1733	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
493	tim	1725	}
494	tim	1733
495	tim	1725	#endif
496
497	tim	1733	for(mol = info->beginMolecule(mi); mol != NULL;
498			mol = info->nextMolecule(mi)) {
499
500	tim	1725	//local index(index in DataStorge) of atom is important
501	tim	1733	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
502	tim	1725	atom->setGlobalIndex(beginAtomIndex++);
503			}
504
505	tim	1733	for(rb = mol->beginRigidBody(ri); rb != NULL;
506			rb = mol->nextRigidBody(ri)) {
507	tim	1725	rb->setGlobalIndex(beginRigidBodyIndex++);
508			}
509	tim	1733
510	tim	1725	//local index of cutoff group is trivial, it only depends on the order of travesing
511	tim	1733	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
512			cg = mol->nextCutoffGroup(ci)) {
513			cg->setGlobalIndex(beginCutoffGroupIndex++);
514			}
515			}
516
517	tim	1735	//fill globalGroupMembership
518	tim	1733	std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
519			for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
520	tim	1725	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
521	tim	1733
522			for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
523			globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
524			}
525
526			}
527			}
528	tim	1735
529			#ifdef IS_MPI
530	tim	1733	// Since the globalGroupMembership has been zero filled and we've only
531			// poked values into the atoms we know, we can do an Allreduce
532			// to get the full globalGroupMembership array (We think).
533			// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
534			// docs said we could.
535
536			MPI_Allreduce(&globalGroupMembership[0],
537			info->getGlobalGroupMembershipPointer(),
538			info->getNGlobalAtoms(),
539			MPI_INT, MPI_SUM, MPI_COMM_WORLD);
540	tim	1735	#else
541			std::copy(globalGroupMembership.begin(), globalGroupMembership.end(),
542			info->getGlobalGroupMembershipPointer());
543			#endif
544	tim	1733
545			//fill molMembership
546			std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
547
548			for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
549
550			for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
551			globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
552			}
553
554	tim	1735	#ifdef IS_MPI
555	tim	1733	MPI_Allreduce(&globalMolMembership[0],
556			info->getGlobalMolMembershipPointer(),
557			info->getNGlobalAtoms(),
558			MPI_INT, MPI_SUM, MPI_COMM_WORLD);
559	tim	1735	#else
560			std::copy(globalMolMembership.begin(), globalMolMembership.end(),
561			info->getGlobalMolMembershipPointer());
562			#endif
563
564	tim	1733	}
565
566			void SimCreator::loadCoordinates(SimInfo* info) {
567			Globals* globals;
568			globals = info->getGlobals();
569
570			if (!globals->haveInitialConfig()) {
571			sprintf(painCave.errMsg,
572			"Cannot intialize a simulation without an initial configuration file.\n");
573			painCave.isFatal = 1;;
574			simError();
575			}
576	tim	1725
577	tim	1733	DumpReader reader(globals->getInitialConfig());
578			int nframes = reader->getNframes();
579
580			if (nframes > 0) {
581			reader.readFrame(info, nframes - 1);
582			} else {
583	tim	1735	//invalid initial coordinate file
584	tim	1733	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
585			globals->getInitialConfig());
586			painCave.isFatal = 1;
587			simError();
588	tim	1725	}
589	tim	1733
590	tim	1725	}
591
592	tim	1703	} //end namespace oopse