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(char* mdfile,  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(mdfile);

#ifdef IS_MPI
    throwMPIEvent(NULL);
  }
  else{
  set_interface_stamps(stamps, globals);
  mpiEventInit();
  MPIcheckPoint();
  mpiEventLoop();
  }
#endif

}


SimInfo* SimCreator::createSim(const std::string& mdfile) {
    MakeStamps* stamps = new MakeStamps();
    
    Globals* globals = new Globals();

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

    //create the force field
    ForceFiled* ff = ForceFieldFactory::getInstance()->createObject(globals->getForceField());
    
    //create SimInfo
    SimInfo* info = new SimInfo();
    info->setGlobals(globals);
    info->setForceField(ff);

    //extract the molecule stamps and add them into SimInfo
    compList(stamps, info);
    
    //gather parameters (SimCreator only retrieves the parameters which will be used to create
    // the simulation)
    gatherParameters(info);
    
    //divide the molecules and determine the global index of molecules
    
    //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);
    
    //load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
    //eta, chi for NPT integrator)
    DumpReader reader(info->getInitFilename());
    int nframes = reader->getNframes();

    if (nframes > 0) {
        reader.readFrame(info, nframes - 1);
    } else {
        //invalid initial coordinate file
        
    }

    
    //initialize fortran    
    
    return info;
}    

void SimCreator::gatherParameters(SimInfo* info) {
    //model->addProperty(new StringGenericData("Ensemble", globals->getForceFiled()));
    //model->addProperty(new DoubleGenericData("dt"), globals->getDt());

    //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);

    //
    std::string prefix;
#ifdef IS_MPI
    if (worldRank == 0){
#endif // is_mpi
      
        if(globals->haveFinalConfig()) {
            prefix = getPrefix(globals->getFinalConfig());   
        } else {
            prefix = getPrefix(mdfile_);
        }
        
        info->setFinalConfFileName(prefix + ".eor");
        info->setDumpFileName(prefix + ".dump");
        info->setStatFileName(prefix + ".stat");

#ifdef IS_MPI
    }
#endif    


}

#ifdef IS_MPI
void SimCreator::divideMolecules(SimInfo* info){
    int nComponents;
    MoleculeStamp ** compStamps;
    randomSPRNG * myRandom;
    int * componentsNmol;
    int * AtomsPerProc;

    double numerator;
    double denominator;
    double precast;
    double x;
    double y;
    double a;
    int old_atoms;
    int add_atoms;
    int new_atoms;

    int nTarget;
    int molIndex;
    int atomIndex;
    int done;
    int i;
    int j;
    int loops;
    int which_proc;
    int nmol_global,
    nmol_local;
    int natoms_global,

    int baseSeed = info->getSeed();
    CutoffGroupStamp * cg;

    nComponents = info->nComponents;
    compStamps = info->compStamps;
    componentsNmol = info->componentsNmol;
    AtomsPerProc = new int[parallelData->nProcessors];

    parallelData->nMolGlobal = info->n_mol;

    if (parallelData->nProcessors > parallelData->nMolGlobal) {
        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",
                parallelData->nProcessors,
                parallelData->nMolGlobal);

        painCave.isFatal = 1;
        simError();
    }

    myRandom = new randomSPRNG(baseSeed);

    a = 3.0 * parallelData->nMolGlobal / parallelData->nAtomsGlobal;

    // Initialize things that we'll send out later:
    for( i = 0; i < parallelData->nProcessors; i++ ) {
        AtomsPerProc[i] = 0;
    }

    for( i = 0; i < parallelData->nMolGlobal; i++ ) {
        // default to an error condition:
        MolToProcMap[i] = -1;
    }

    if (parallelData->myNode == 0) {
        numerator = info->n_atoms;
        denominator = parallelData->nProcessors;
        precast = numerator / denominator;
        nTarget = (int)(precast + 0.5);

        // Build the array of molecule component types first
        molIndex = 0;

        for( i = 0; i < nComponents; i++ ) {
            for( j = 0; j < componentsNmol[i]; j++ ) {
                molIndex++;
            }
        }

        for( i = 0; i < molIndex; i++ ) {
            done = 0;
            loops = 0;

            while (!done) {
                loops++;

                // Pick a processor at random

                which_proc

                = (int) (myRandom->getRandom() * parallelData->nProcessors);

                // How many atoms does this processor have?

                old_atoms = AtomsPerProc[which_proc];
                add_atoms = compStamps[MolComponentType[i]]->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, parallelData->nMolGlobal, MPI_INT, 0,
                  MPI_COMM_WORLD);
    } else {

    // Listen to your marching orders from processor 0:

        MPI_Bcast(MolToProcMap, parallelData->nMolGlobal, MPI_INT, 0,
                  MPI_COMM_WORLD); }

    // Let's all check for sanity:

    nmol_local = 0;

    for( i = 0; i < parallelData->nMolGlobal; i++ ) {
        if (MolToProcMap[i] == parallelData->myNode) {
            nmol_local++;
        }
    }

    MPI_Allreduce(&nmol_local, &nmol_global, 1, MPI_INT, MPI_SUM,
                  MPI_COMM_WORLD);

    if (nmol_global != info->n_mol) {
        sprintf(painCave.errMsg,
                "The sum of all nmol_local, %d, did not equal the "
                    "total number of molecules, %d.\n",
                nmol_global,
                info->n_mol);

        painCave.isFatal = 1;
        simError();
    }

    sprintf(checkPointMsg,
            "Successfully divided the molecules among the processors.\n");
    MPIcheckPoint();
 
}
#endif

Molecule* SimCreator::createMolecules(SimInfo* info) {
    MoleculeCreator molCreator;
    int stampId;

    
    for (int i = 0; i < info->getNGlobalMolecules(); i++){
        if (info->getMolToProc(i) == worldRank){

            stampId = info->getMoleculeStampId(i);
            Molecule* mol = molCreator.createMolecule(info->getForceField(), 
                                                                                info->getMoleculeStamp(stampId), stampId, i);
                        
            info->addMolecule(mol);
        }
    }        
       
}

void SimSetup::compList(MakeStamps* stamps,SimInfo* info) {
    int i;
    char* id;
    MoleculeStamp* currentStamp;
    Component* the_components = info->getGlobals()->getComponents();
    int n_components = info->getGlobals()->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();
            }      

            info->addMoleculeStamp(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::setGlobalIndices(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;

#ifdef 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);

    tmpAtomInProc[myNode] = info->getNAtoms();
    tmpRigidBodiesInProc[myNode] = info->getNRigidBodiess();
    tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroupss();
    
    //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++);
        }        
        
    }
}

} //end namespace oopse
Revision:	1727
Committed:	Thu Nov 11 16:41:58 2004 UTC (19 years, 8 months ago) by tim
File size:	16172 byte(s)
Log Message:	add Snapshot.cpp, remove useless mpiSimulation
#	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	namespace oopse {
36
37	void SimSetup::parseFile(char* mdfile, MakeStamps* stamps, Globals* globals){
38	#ifdef IS_MPI
39	if (worldRank == 0){
40	#endif // is_mpi
41
42
43	globals->initalize();
44	set_interface_stamps(stamps, globals);
45
46	#ifdef IS_MPI
47	mpiEventInit();
48	#endif
49
50	yacc_BASS(mdfile);
51
52	#ifdef IS_MPI
53	throwMPIEvent(NULL);
54	}
55	else{
56	set_interface_stamps(stamps, globals);
57	mpiEventInit();
58	MPIcheckPoint();
59	mpiEventLoop();
60	}
61	#endif
62
63	}
64
65
66	SimInfo* SimCreator::createSim(const std::string& mdfile) {
67	MakeStamps* stamps = new MakeStamps();
68
69	Globals* globals = new Globals();
70
71	//parse meta-data file
72	parseFile(mdfile, stamps, globals);
73
74	//create the force field
75	ForceFiled* ff = ForceFieldFactory::getInstance()->createObject(globals->getForceField());
76
77	//create SimInfo
78	SimInfo* info = new SimInfo();
79	info->setGlobals(globals);
80	info->setForceField(ff);
81
82	//extract the molecule stamps and add them into SimInfo
83	compList(stamps, info);
84
85	//gather parameters (SimCreator only retrieves the parameters which will be used to create
86	// the simulation)
87	gatherParameters(info);
88
89	//divide the molecules and determine the global index of molecules
90
91	//create the molecules
92	createMolecules(info);
93
94	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
95	//global index will never change again). Local indices of atoms and rigidbodies are already set by
96	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
97	setGlobalIndices(info);
98
99	//allocate memory for DataStorage(circular reference, need to break it)
100	info->setSnapshotManager(new SimSnapshotManager(info);
101
102	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
103	//eta, chi for NPT integrator)
104	DumpReader reader(info->getInitFilename());
105	int nframes = reader->getNframes();
106
107	if (nframes > 0) {
108	reader.readFrame(info, nframes - 1);
109	} else {
110	//invalid initial coordinate file
111
112	}
113
114
115	//initialize fortran
116
117	return info;
118	}
119
120	void SimCreator::gatherParameters(SimInfo* info) {
121	//model->addProperty(new StringGenericData("Ensemble", globals->getForceFiled()));
122	//model->addProperty(new DoubleGenericData("dt"), globals->getDt());
123
124	//setup seed for random number generator
125	int seedValue;
126	Globals* globals = info->getGlobals();
127
128	if (globals->haveSeed()){
129	seedValue = globals->getSeed();
130
131	if(seedValue / 1000000000 == 0){
132	sprintf(painCave.errMsg,
133	"Seed for sprng library should contain at least 9 digits\n"
134	"OOPSE will generate a seed for user\n");
135	painCave.isFatal = 0;
136	simError();
137
138	//using seed generated by system instead of invalid seed set by user
139	#ifndef IS_MPI
140	seedValue = make_sprng_seed();
141	#else
142	if (worldRank == 0){
143	seedValue = make_sprng_seed();
144	}
145	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
146	#endif
147	} //end if (seedValue /1000000000 == 0)
148	} else{
149
150	#ifndef IS_MPI
151	seedValue = make_sprng_seed();
152	#else
153	if (worldRank == 0){
154	seedValue = make_sprng_seed();
155	}
156	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
157	#endif
158	}//end of globals->haveSeed()
159	info->setSeed(seedValue);
160
161	//
162	std::string prefix;
163	#ifdef IS_MPI
164	if (worldRank == 0){
165	#endif // is_mpi
166
167	if(globals->haveFinalConfig()) {
168	prefix = getPrefix(globals->getFinalConfig());
169	} else {
170	prefix = getPrefix(mdfile_);
171	}
172
173	info->setFinalConfFileName(prefix + ".eor");
174	info->setDumpFileName(prefix + ".dump");
175	info->setStatFileName(prefix + ".stat");
176
177	#ifdef IS_MPI
178	}
179	#endif
180
181
182
183	}
184
185	#ifdef IS_MPI
186	void SimCreator::divideMolecules(SimInfo* info){
187	int nComponents;
188	MoleculeStamp ** compStamps;
189	randomSPRNG * myRandom;
190	int * componentsNmol;
191	int * AtomsPerProc;
192
193	double numerator;
194	double denominator;
195	double precast;
196	double x;
197	double y;
198	double a;
199	int old_atoms;
200	int add_atoms;
201	int new_atoms;
202
203	int nTarget;
204	int molIndex;
205	int atomIndex;
206	int done;
207	int i;
208	int j;
209	int loops;
210	int which_proc;
211	int nmol_global,
212	nmol_local;
213	int natoms_global,
214
215	int baseSeed = info->getSeed();
216	CutoffGroupStamp * cg;
217
218	nComponents = info->nComponents;
219	compStamps = info->compStamps;
220	componentsNmol = info->componentsNmol;
221	AtomsPerProc = new int[parallelData->nProcessors];
222
223	parallelData->nMolGlobal = info->n_mol;
224
225	if (parallelData->nProcessors > parallelData->nMolGlobal) {
226	sprintf(painCave.errMsg,
227	"nProcessors (%d) > nMol (%d)\n"
228	"\tThe number of processors is larger than\n"
229	"\tthe number of molecules. This will not result in a \n"
230	"\tusable division of atoms for force decomposition.\n"
231	"\tEither try a smaller number of processors, or run the\n"
232	"\tsingle-processor version of OOPSE.\n",
233	parallelData->nProcessors,
234	parallelData->nMolGlobal);
235
236	painCave.isFatal = 1;
237	simError();
238	}
239
240	myRandom = new randomSPRNG(baseSeed);
241
242	a = 3.0 * parallelData->nMolGlobal / parallelData->nAtomsGlobal;
243
244	// Initialize things that we'll send out later:
245	for( i = 0; i < parallelData->nProcessors; i++ ) {
246	AtomsPerProc[i] = 0;
247	}
248
249	for( i = 0; i < parallelData->nMolGlobal; i++ ) {
250	// default to an error condition:
251	MolToProcMap[i] = -1;
252	}
253
254	if (parallelData->myNode == 0) {
255	numerator = info->n_atoms;
256	denominator = parallelData->nProcessors;
257	precast = numerator / denominator;
258	nTarget = (int)(precast + 0.5);
259
260	// Build the array of molecule component types first
261	molIndex = 0;
262
263	for( i = 0; i < nComponents; i++ ) {
264	for( j = 0; j < componentsNmol[i]; j++ ) {
265	molIndex++;
266	}
267	}
268
269	for( i = 0; i < molIndex; i++ ) {
270	done = 0;
271	loops = 0;
272
273	while (!done) {
274	loops++;
275
276	// Pick a processor at random
277
278	which_proc
279
280	= (int) (myRandom->getRandom() * parallelData->nProcessors);
281
282	// How many atoms does this processor have?
283
284	old_atoms = AtomsPerProc[which_proc];
285	add_atoms = compStamps[MolComponentType[i]]->getNAtoms();
286	new_atoms = old_atoms + add_atoms;
287
288	// If we've been through this loop too many times, we need
289	// to just give up and assign the molecule to this processor
290	// and be done with it.
291
292	if (loops > 100) {
293	sprintf(
294	painCave.errMsg,
295	"I've tried 100 times to assign molecule %d to a "
296	" processor, but can't find a good spot.\n"
297	"I'm assigning it at random to processor %d.\n",
298	i,
299	which_proc);
300
301	painCave.isFatal = 0;
302	simError();
303
304	MolToProcMap[i] = which_proc;
305	AtomsPerProc[which_proc] += add_atoms;
306
307	done = 1;
308	continue;
309	}
310
311	// If we can add this molecule to this processor without sending
312	// it above nTarget, then go ahead and do it:
313
314	if (new_atoms <= nTarget) {
315	MolToProcMap[i] = which_proc;
316	AtomsPerProc[which_proc] += add_atoms;
317
318	done = 1;
319	continue;
320	}
321
322	// The only situation left is when new_atoms > nTarget. We
323	// want to accept this with some probability that dies off the
324	// farther we are from nTarget
325
326	// roughly: x = new_atoms - nTarget
327	// Pacc(x) = exp(- a * x)
328	// where a = penalty / (average atoms per molecule)
329
330	x = (double)(new_atoms - nTarget);
331	y = myRandom->getRandom();
332
333	if (y < exp(- a * x)) {
334	MolToProcMap[i] = which_proc;
335	AtomsPerProc[which_proc] += add_atoms;
336
337	done = 1;
338	continue;
339	} else { continue; }
340	}
341	}
342
343	// Spray out this nonsense to all other processors:
344
345	MPI_Bcast(MolToProcMap, parallelData->nMolGlobal, MPI_INT, 0,
346	MPI_COMM_WORLD);
347	} else {
348
349	// Listen to your marching orders from processor 0:
350
351	MPI_Bcast(MolToProcMap, parallelData->nMolGlobal, MPI_INT, 0,
352	MPI_COMM_WORLD); }
353
354	// Let's all check for sanity:
355
356	nmol_local = 0;
357
358	for( i = 0; i < parallelData->nMolGlobal; i++ ) {
359	if (MolToProcMap[i] == parallelData->myNode) {
360	nmol_local++;
361	}
362	}
363
364	MPI_Allreduce(&nmol_local, &nmol_global, 1, MPI_INT, MPI_SUM,
365	MPI_COMM_WORLD);
366
367	if (nmol_global != info->n_mol) {
368	sprintf(painCave.errMsg,
369	"The sum of all nmol_local, %d, did not equal the "
370	"total number of molecules, %d.\n",
371	nmol_global,
372	info->n_mol);
373
374	painCave.isFatal = 1;
375	simError();
376	}
377
378	sprintf(checkPointMsg,
379	"Successfully divided the molecules among the processors.\n");
380	MPIcheckPoint();
381
382	}
383	#endif
384
385	Molecule* SimCreator::createMolecules(SimInfo* info) {
386	MoleculeCreator molCreator;
387	int stampId;
388
389
390	for (int i = 0; i < info->getNGlobalMolecules(); i++){
391	if (info->getMolToProc(i) == worldRank){
392
393	stampId = info->getMoleculeStampId(i);
394	Molecule* mol = molCreator.createMolecule(info->getForceField(),
395	info->getMoleculeStamp(stampId), stampId, i);
396
397	info->addMolecule(mol);
398	}
399	}
400
401	}
402
403	void SimSetup::compList(MakeStamps* stamps,SimInfo* info) {
404	int i;
405	char* id;
406	MoleculeStamp* currentStamp;
407	Component* the_components = info->getGlobals()->getComponents();
408	int n_components = info->getGlobals()->getNComponents();
409
410	if (!globals->haveNMol()){
411	// we don't have the total number of molecules, so we assume it is
412	// given in each component
413
414	for (i = 0; i < n_components; i++){
415	if (!the_components[i]->haveNMol()){
416	// we have a problem
417	sprintf(painCave.errMsg,
418	"SimSetup Error. No global NMol or component NMol given.\n"
419	"\tCannot calculate the number of atoms.\n");
420	painCave.isFatal = 1;
421	simError();
422	}
423
424	id = the_components[i]->getType();
425	currentStamp = stamps->extractMolStamp(id);
426	if (currentStamp == NULL){
427	sprintf(painCave.errMsg,
428	"SimSetup error: Component \"%s\" was not found in the "
429	"list of declared molecules\n",
430	id);
431	painCave.isFatal = 1;
432	simError();
433	}
434
435	info->addMoleculeStamp(currentStamp, the_components[i]->getNMol);
436
437	} //end for (i = 0; i < n_components; i++)
438
439	} else{
440	sprintf(painCave.errMsg,
441	"SimSetup error.\n"
442	"\tSorry, the ability to specify total"
443	" nMols and then give molfractions in the components\n"
444	"\tis not currently supported."
445	" Please give nMol in the components.\n");
446	painCave.isFatal = 1;
447	simError();
448	}
449
450	#ifdef IS_MPI
451	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
452	MPIcheckPoint();
453	#endif // is_mpi
454	}
455
456	void SimCreator::setGlobalIndices(SimInfo* info) {
457	typename SimInfo::MoleculeIterator mi;
458	typename Molecule::AtomIterator ai;
459	typename Molecule::RigidBodyIterator ri;
460	typename Molecule::CutoffGroupIterator ci;
461	Molecule* mol;
462	Atom* atom;
463	RigidBody* rb;
464	CutoffGroup* cg;
465	int beginAtomIndex;
466	int beginRigidBodyIndex;
467	int beginCutoffGroupIndex;
468
469	#ifdef IS_MPI
470	beginAtomIndex = 0;
471	beginRigidBodyIndex = 0;
472	beginCutoffGroupIndex = 0;
473	#else
474	int nproc;
475	int myNode;
476
477	myNode = worldRank;
478	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
479
480	std::vector<int> tmpAtomsInProc(nproc, 0);
481	std::vector<int> tmpRigidBodiesInProc(nproc, 0);
482	std::vector<int> tmpCutoffGroupsInProc(nproc, 0);
483	std::vector<int> NumAtomsInProc(nproc, 0);
484	std::vector<int> NumRigidBodiesInProc(nproc, 0);
485	std::vector<int> NumCutoffGroupsInProc(nproc, 0);
486
487	tmpAtomInProc[myNode] = info->getNAtoms();
488	tmpRigidBodiesInProc[myNode] = info->getNRigidBodiess();
489	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroupss();
490
491	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
492	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
493	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
494	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
495
496	beginAtomIndex = 0;
497	beginRigidBodyIndex = 0;
498	beginCutoffGroupIndex = 0;
499
500	for (int i = 0; i < nproc; i++) {
501	beginAtomIndex += NumAtomsInProc[i];
502	beginRigidBodyIndex += NumRigidBodiesInProc[i];
503	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
504	}
505
506	#endif
507
508	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
509
510	//local index(index in DataStorge) of atom is important
511	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
512	atom->setGlobalIndex(beginAtomIndex++);
513	}
514
515	for (rb = mol->beginRigidBody(ri); rb != NULL; rb = mol->nextRigidBody(ri)) {
516	rb->setGlobalIndex(beginRigidBodyIndex++);
517	}
518
519	//local index of cutoff group is trivial, it only depends on the order of travesing
520	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
521	cg->setGlobalIndex(beginCutoffGroupIndex++);
522	}
523
524	}
525	}
526
527	} //end namespace oopse