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 SimSetup::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();
    }

    //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:	1738
Committed:	Sat Nov 13 05:08:12 2004 UTC (19 years, 8 months ago) by tim
File size:	17886 byte(s)
Log Message:	refactory, refactory, refactory
#	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 "brains/SimCreator.hpp"
35
36	namespace oopse {
37
38	void SimSetup::parseFile(const std::string& mdFileName, MakeStamps stamps, Globals globals) {
39
40	#ifdef IS_MPI
41
42	if (worldRank == 0) {
43	#endif // is_mpi
44
45	globals->initalize();
46	set_interface_stamps(stamps, globals);
47
48	#ifdef IS_MPI
49
50	mpiEventInit();
51
52	#endif
53
54	yacc_BASS(mdFileName.c_str());
55
56	#ifdef IS_MPI
57
58	throwMPIEvent(NULL);
59	} else {
60	set_interface_stamps(stamps, globals);
61	mpiEventInit();
62	MPIcheckPoint();
63	mpiEventLoop();
64	}
65
66	#endif
67
68	}
69
70	SimInfo* SimCreator::createSim(const std::string & mdFileName) {
71
72	mdFileName_ = mdFileName;
73
74	MakeStamps * stamps = new MakeStamps();
75
76	Globals * globals = new Globals();
77
78	//parse meta-data file
79	parseFile(mdFileName_, stamps, globals);
80
81	//create the force field
82	ForceFiled * ff = ForceFieldFactory::getInstance()->createObject(
83	globals->getForceField());
84
85	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
92	//extract the molecule stamps
93	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
94	compList(stamps, globals, moleculeStampPairs);
95
96	//create SimInfo
97	SimInfo * info = new SimInfo(moleculeStampPairs, ff, globals);
98
99	//gather parameters (SimCreator only retrieves part of the parameters)
100	gatherParameters(info);
101
102	//divide the molecules and determine the global index of molecules
103	divideMolecules(info);
104
105	//create the molecules
106	createMolecules(info);
107
108	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
109	//global index will never change again). Local indices of atoms and rigidbodies are already set by
110	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
111	setGlobalIndices(info);
112
113	//allocate memory for DataStorage(circular reference, need to break it)
114	info->setSnapshotManager(new SimSnapshotManager(info));
115
116	//initialize fortran -- setup the cutoff
117	initFortran(info);
118
119	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
120	//eta, chi for NPT integrator)
121	loadCoordinates(info);
122	return info;
123	}
124
125	void SimCreator::gatherParameters(SimInfo *info) {
126
127	//setup seed for random number generator
128	int seedValue;
129	Globals * globals = info->getGlobals();
130
131	if (globals->haveSeed()) {
132	seedValue = globals->getSeed();
133
134	if (seedValue / 1000000000 == 0) {
135	sprintf(painCave.errMsg,
136	"Seed for sprng library should contain at least 9 digits\n"
137	"OOPSE will generate a seed for user\n");
138
139	painCave.isFatal = 0;
140	simError();
141
142	//using seed generated by system instead of invalid seed set by user
143
144	#ifndef IS_MPI
145
146	seedValue = make_sprng_seed();
147
148	#else
149
150	if (worldRank == 0) {
151	seedValue = make_sprng_seed();
152	}
153
154	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
155
156	#endif
157
158	} //end if (seedValue /1000000000 == 0)
159	} else {
160
161	#ifndef IS_MPI
162
163	seedValue = make_sprng_seed();
164
165	#else
166
167	if (worldRank == 0) {
168	seedValue = make_sprng_seed();
169	}
170
171	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
172
173	#endif
174
175	} //end of globals->haveSeed()
176
177	info->setSeed(seedValue);
178
179
180	//figure out the ouput file names
181	std::string prefix;
182
183	#ifdef IS_MPI
184
185	if (worldRank == 0) {
186	#endif // is_mpi
187
188	if (globals->haveFinalConfig()) {
189	prefix = StringUtils::getPrefix(globals->getFinalConfig());
190	} else {
191	prefix = StringUtils::getPrefix(mdfile_);
192	}
193
194	info->setFinalConfigFileName(prefix + ".eor");
195	info->setDumpFileName(prefix + ".dump");
196	info->setStatFileName(prefix + ".stat");
197
198	#ifdef IS_MPI
199
200	}
201
202	#endif
203
204	}
205
206	#ifdef IS_MPI
207
208	void SimCreator::divideMolecules(SimInfo *info) {
209	double numerator;
210	double denominator;
211	double precast;
212	double x;
213	double y;
214	double a;
215	int old_atoms;
216	int add_atoms;
217	int new_atoms;
218	int nTarget;
219	int done;
220	int i;
221	int j;
222	int loops;
223	int which_proc;
224	int nProcessors;
225	int nGlobalMols;
226	std::vector < int > atomsPerProc;
227	randomSPRNG myRandom(info->getSeed());
228	int * molToProcMap = info->getMolToProcMapPointer();
229
230	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
231	nGlobalMols = info->getNGlobalMolecules();
232
233	if (nProcessors > nGlobalMols) {
234	sprintf(painCave.errMsg,
235	"nProcessors (%d) > nMol (%d)\n"
236	"\tThe number of processors is larger than\n"
237	"\tthe number of molecules. This will not result in a \n"
238	"\tusable division of atoms for force decomposition.\n"
239	"\tEither try a smaller number of processors, or run the\n"
240	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
241
242	painCave.isFatal = 1;
243	simError();
244	}
245
246	a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
247
248	//initialize atomsPerProc
249	atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
250
251	for(i = 0; i < nGlobalMols; i++) {
252	// default to an error condition:
253	molToProcMap[i] = -1;
254	}
255
256	if (worldRank == 0) {
257	numerator = info->getNGlobalAtoms();
258	denominator = nProcessors;
259	precast = numerator / denominator;
260	nTarget = (int)(precast + 0.5);
261
262	for(i = 0; i < nGlobalMols; i++) {
263	done = 0;
264	loops = 0;
265
266	while (!done) {
267	loops++;
268
269	// Pick a processor at random
270
271	which_proc = (int) (myRandom.getRandom() * nProcessors);
272
273	//get the molecule stamp first
274	int stampId = info->getMoleculeStampId(i);
275	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
276
277	// How many atoms does this processor have so far?
278	old_atoms = atomsPerProc[which_proc];
279	add_atoms = moleculeStamp->getNAtoms();
280	new_atoms = old_atoms + add_atoms;
281
282	// If we've been through this loop too many times, we need
283	// to just give up and assign the molecule to this processor
284	// and be done with it.
285
286	if (loops > 100) {
287	sprintf(painCave.errMsg,
288	"I've tried 100 times to assign molecule %d to a "
289	" processor, but can't find a good spot.\n"
290	"I'm assigning it at random to processor %d.\n",
291	i, which_proc);
292
293	painCave.isFatal = 0;
294	simError();
295
296	molToProcMap[i] = which_proc;
297	atomsPerProc[which_proc] += add_atoms;
298
299	done = 1;
300	continue;
301	}
302
303	// If we can add this molecule to this processor without sending
304	// it above nTarget, then go ahead and do it:
305
306	if (new_atoms <= nTarget) {
307	molToProcMap[i] = which_proc;
308	atomsPerProc[which_proc] += add_atoms;
309
310	done = 1;
311	continue;
312	}
313
314	// The only situation left is when new_atoms > nTarget. We
315	// want to accept this with some probability that dies off the
316	// farther we are from nTarget
317
318	// roughly: x = new_atoms - nTarget
319	// Pacc(x) = exp(- a * x)
320	// where a = penalty / (average atoms per molecule)
321
322	x = (double)(new_atoms - nTarget);
323	y = myRandom.getRandom();
324
325	if (y < exp(- a * x)) {
326	molToProcMap[i] = which_proc;
327	atomsPerProc[which_proc] += add_atoms;
328
329	done = 1;
330	continue;
331	} else {
332	continue;
333	}
334	}
335	}
336
337	// Spray out this nonsense to all other processors:
338
339	MPI_Bcast(molToProcMap, nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
340	} else {
341
342	// Listen to your marching orders from processor 0:
343
344	MPI_Bcast(molToProcMap, nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
345	}
346
347	sprintf(checkPointMsg,
348	"Successfully divided the molecules among the processors.\n");
349	MPIcheckPoint();
350	}
351
352	#endif
353
354	void SimCreator::createMolecules(SimInfo *info) {
355	MoleculeCreator molCreator;
356	int stampId;
357
358	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
359
360	#ifdef IS_MPI
361
362	if (info->getMolToProc(i) == worldRank) {
363	#endif
364
365	stampId = info->getMoleculeStampId(i);
366	Molecule * mol = molCreator.createMolecule(info->getForceField(),
367	info->getMoleculeStamp(stampId), stampId, i);
368
369	info->addMolecule(mol);
370
371	#ifdef IS_MPI
372
373	}
374
375	#endif
376
377	} //end for(int i=0)
378	}
379
380	void SimSetup::compList(MakeStamps stamps, Globals globals,
381	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
382	int i;
383	char * id;
384	MoleculeStamp * currentStamp;
385	Component * the_components = globals->getComponents();
386	int n_components = globals->getNComponents();
387
388	if (!globals->haveNMol()) {
389	// we don't have the total number of molecules, so we assume it is
390	// given in each component
391
392	for(i = 0; i < n_components; i++) {
393	if (!the_components[i]->haveNMol()) {
394	// we have a problem
395	sprintf(painCave.errMsg,
396	"SimSetup Error. No global NMol or component NMol given.\n"
397	"\tCannot calculate the number of atoms.\n");
398
399	painCave.isFatal = 1;
400	simError();
401	}
402
403	id = the_components[i]->getType();
404	currentStamp = stamps->extractMolStamp(id);
405
406	if (currentStamp == NULL) {
407	sprintf(painCave.errMsg,
408	"SimSetup error: Component \"%s\" was not found in the "
409	"list of declared molecules\n", id);
410
411	painCave.isFatal = 1;
412	simError();
413	}
414
415	moleculeStampPairs.push_back(
416	make_pair(currentStamp, the_components[i]->getNMol));
417	} //end for (i = 0; i < n_components; i++)
418	} else {
419	sprintf(painCave.errMsg, "SimSetup error.\n"
420	"\tSorry, the ability to specify total"
421	" nMols and then give molfractions in the components\n"
422	"\tis not currently supported."
423	" Please give nMol in the components.\n");
424
425	painCave.isFatal = 1;
426	simError();
427	}
428
429	#ifdef IS_MPI
430
431	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
432	MPIcheckPoint();
433
434	#endif // is_mpi
435
436	}
437
438	void SimCreator::setGlobalIndex(SimInfo *info) {
439	typename SimInfo::MoleculeIterator mi;
440	typename Molecule::AtomIterator ai;
441	typename Molecule::RigidBodyIterator ri;
442	typename Molecule::CutoffGroupIterator ci;
443	Molecule * mol;
444	Atom * atom;
445	RigidBody * rb;
446	CutoffGroup * cg;
447	int beginAtomIndex;
448	int beginRigidBodyIndex;
449	int beginCutoffGroupIndex;
450
451	#ifndef IS_MPI
452
453	beginAtomIndex = 0;
454	beginRigidBodyIndex = 0;
455	beginCutoffGroupIndex = 0;
456
457	#else
458
459	int nproc;
460	int myNode;
461
462	myNode = worldRank;
463	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
464
465	std::vector < int > tmpAtomsInProc(nproc, 0);
466	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
467	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
468	std::vector < int > NumAtomsInProc(nproc, 0);
469	std::vector < int > NumRigidBodiesInProc(nproc, 0);
470	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
471
472	tmpAtomsInProc[myNode] = info->getNAtoms();
473	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
474	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
475
476	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
477	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
478	MPI_SUM, MPI_COMM_WORLD);
479	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
480	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
481	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
482	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
483
484	beginAtomIndex = 0;
485	beginRigidBodyIndex = 0;
486	beginCutoffGroupIndex = 0;
487
488	for(int i = 0; i < nproc; i++) {
489	beginAtomIndex += NumAtomsInProc[i];
490	beginRigidBodyIndex += NumRigidBodiesInProc[i];
491	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
492	}
493
494	#endif
495
496	for(mol = info->beginMolecule(mi); mol != NULL;
497	mol = info->nextMolecule(mi)) {
498
499	//local index(index in DataStorge) of atom is important
500	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
501	atom->setGlobalIndex(beginAtomIndex++);
502	}
503
504	for(rb = mol->beginRigidBody(ri); rb != NULL;
505	rb = mol->nextRigidBody(ri)) {
506	rb->setGlobalIndex(beginRigidBodyIndex++);
507	}
508
509	//local index of cutoff group is trivial, it only depends on the order of travesing
510	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
511	cg = mol->nextCutoffGroup(ci)) {
512	cg->setGlobalIndex(beginCutoffGroupIndex++);
513	}
514	}
515
516	//fill globalGroupMembership
517	std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
518	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
519	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
520
521	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
522	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
523	}
524
525	}
526	}
527
528	#ifdef IS_MPI
529	// Since the globalGroupMembership has been zero filled and we've only
530	// poked values into the atoms we know, we can do an Allreduce
531	// to get the full globalGroupMembership array (We think).
532	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
533	// docs said we could.
534
535	MPI_Allreduce(&globalGroupMembership[0],
536	info->getGlobalGroupMembershipPointer(),
537	info->getNGlobalAtoms(),
538	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
539	#else
540	std::copy(globalGroupMembership.begin(), globalGroupMembership.end(),
541	info->getGlobalGroupMembershipPointer());
542	#endif
543
544	//fill molMembership
545	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
546
547	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
548
549	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
550	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
551	}
552
553	#ifdef IS_MPI
554	MPI_Allreduce(&globalMolMembership[0],
555	info->getGlobalMolMembershipPointer(),
556	info->getNGlobalAtoms(),
557	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
558	#else
559	std::copy(globalMolMembership.begin(), globalMolMembership.end(),
560	info->getGlobalMolMembershipPointer());
561	#endif
562
563	}
564
565	void SimCreator::loadCoordinates(SimInfo* info) {
566	Globals* globals;
567	globals = info->getGlobals();
568
569	if (!globals->haveInitialConfig()) {
570	sprintf(painCave.errMsg,
571	"Cannot intialize a simulation without an initial configuration file.\n");
572	painCave.isFatal = 1;;
573	simError();
574	}
575
576	DumpReader reader(globals->getInitialConfig());
577	int nframes = reader->getNframes();
578
579	if (nframes > 0) {
580	reader.readFrame(info, nframes - 1);
581	} else {
582	//invalid initial coordinate file
583	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
584	globals->getInitialConfig());
585	painCave.isFatal = 1;
586	simError();
587	}
588
589	}
590
591	} //end namespace oopse