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::mpiMolDivide(){
 
    mpiSim = new mpiSimulation(info);

    mpiSim->divideLabor();

}
#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:	1725
Committed:	Wed Nov 10 22:01:06 2004 UTC (19 years, 10 months ago) by tim
File size:	10375 byte(s)
Log Message:	another painful day (1) SimCreator, SimInfo, mpiSimulation (2) DumpReader, DumpWriter (InitializeFrom File will be removed) (3) ForceField (at least LJ) and BondType, BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors & Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint
#	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	1703	namespace oopse {
36
37	tim	1712	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	tim	1703	}
64
65	tim	1712
66	tim	1719	SimInfo* SimCreator::createSim(const std::string& mdfile) {
67			MakeStamps* stamps = new MakeStamps();
68	tim	1712
69			Globals* globals = new Globals();
70
71			//parse meta-data file
72			parseFile(mdfile, stamps, globals);
73
74			//create the force field
75	tim	1725	ForceFiled* ff = ForceFieldFactory::getInstance()->createObject(globals->getForceField());
76	tim	1712
77	tim	1719	//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	tim	1712
85	tim	1719	//gather parameters (SimCreator only retrieves the parameters which will be used to create
86			// the simulation)
87			gatherParameters(info);
88	tim	1712
89			//divide the molecules and determine the global index of molecules
90	tim	1719
91	tim	1712	//create the molecules
92	tim	1719	createMolecules(info);
93	tim	1712
94	tim	1725	//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	tim	1712	//allocate memory for DataStorage(circular reference, need to break it)
100	tim	1719	info->setSnapshotManager(new SimSnapshotManager(info);
101	tim	1712
102	tim	1725	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
103			//eta, chi for NPT integrator)
104	tim	1719	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	tim	1712
115			//initialize fortran
116	tim	1719
117			return info;
118	tim	1712	}
119
120	tim	1725	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	tim	1712	}
184
185			#ifdef IS_MPI
186	tim	1713	void SimCreator::mpiMolDivide(){
187
188			mpiSim = new mpiSimulation(info);
189	tim	1712
190	tim	1713	mpiSim->divideLabor();
191	tim	1712
192			}
193	tim	1713	#endif
194	tim	1712
195	tim	1719	Molecule* SimCreator::createMolecules(SimInfo* info) {
196	tim	1725	MoleculeCreator molCreator;
197			int stampId;
198	tim	1713
199
200	tim	1725	for (int i = 0; i < info->getNGlobalMolecules(); i++){
201			if (info->getMolToProc(i) == worldRank){
202	tim	1713
203	tim	1725	stampId = info->getMoleculeStampId(i);
204			Molecule* mol = molCreator.createMolecule(info->getForceField(),
205			info->getMoleculeStamp(stampId), stampId, i);
206	tim	1719
207			info->addMolecule(mol);
208			}
209			}
210
211	tim	1713	}
212
213	tim	1719
214			void SimSetup::compList(MakeStamps* stamps,SimInfo* info) {
215			int i;
216			char* id;
217			MoleculeStamp* currentStamp;
218			Component* the_components = info->getGlobals()->getComponents();
219			int n_components = info->getGlobals()->getNComponents();
220
221			if (!globals->haveNMol()){
222			// we don't have the total number of molecules, so we assume it is
223			// given in each component
224
225			for (i = 0; i < n_components; i++){
226			if (!the_components[i]->haveNMol()){
227			// we have a problem
228			sprintf(painCave.errMsg,
229			"SimSetup Error. No global NMol or component NMol given.\n"
230			"\tCannot calculate the number of atoms.\n");
231			painCave.isFatal = 1;
232			simError();
233			}
234
235			id = the_components[i]->getType();
236			currentStamp = stamps->extractMolStamp(id);
237			if (currentStamp == NULL){
238			sprintf(painCave.errMsg,
239			"SimSetup error: Component \"%s\" was not found in the "
240			"list of declared molecules\n",
241			id);
242			painCave.isFatal = 1;
243			simError();
244			}
245
246	tim	1725	info->addMoleculeStamp(currentStamp, the_components[i]->getNMol);
247	tim	1719
248			} //end for (i = 0; i < n_components; i++)
249
250			} else{
251			sprintf(painCave.errMsg,
252			"SimSetup error.\n"
253			"\tSorry, the ability to specify total"
254			" nMols and then give molfractions in the components\n"
255			"\tis not currently supported."
256			" Please give nMol in the components.\n");
257			painCave.isFatal = 1;
258			simError();
259			}
260
261			#ifdef IS_MPI
262			strcpy(checkPointMsg, "Component stamps successfully extracted\n");
263			MPIcheckPoint();
264			#endif // is_mpi
265			}
266
267	tim	1725	void SimCreator::setGlobalIndices(SimInfo* info) {
268			typename SimInfo::MoleculeIterator mi;
269			typename Molecule::AtomIterator ai;
270			typename Molecule::RigidBodyIterator ri;
271			typename Molecule::CutoffGroupIterator ci;
272			Molecule* mol;
273			Atom* atom;
274			RigidBody* rb;
275			CutoffGroup* cg;
276			int beginAtomIndex;
277			int beginRigidBodyIndex;
278			int beginCutoffGroupIndex;
279	tim	1719
280	tim	1725	#ifdef IS_MPI
281			beginAtomIndex = 0;
282			beginRigidBodyIndex = 0;
283			beginCutoffGroupIndex = 0;
284			#else
285			int nproc;
286			int myNode;
287
288			myNode = worldRank;
289			MPI_Comm_size(MPI_COMM_WORLD, &nproc);
290
291			std::vector<int> tmpAtomsInProc(nproc, 0);
292			std::vector<int> tmpRigidBodiesInProc(nproc, 0);
293			std::vector<int> tmpCutoffGroupsInProc(nproc, 0);
294			std::vector<int> NumAtomsInProc(nproc, 0);
295			std::vector<int> NumRigidBodiesInProc(nproc, 0);
296			std::vector<int> NumCutoffGroupsInProc(nproc, 0);
297
298			tmpAtomInProc[myNode] = info->getNAtoms();
299			tmpRigidBodiesInProc[myNode] = info->getNRigidBodiess();
300			tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroupss();
301
302			//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
303			MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
304			MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
305			MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
306
307			beginAtomIndex = 0;
308			beginRigidBodyIndex = 0;
309			beginCutoffGroupIndex = 0;
310
311			for (int i = 0; i < nproc; i++) {
312			beginAtomIndex += NumAtomsInProc[i];
313			beginRigidBodyIndex += NumRigidBodiesInProc[i];
314			beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
315			}
316
317			#endif
318
319			for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
320
321			//local index(index in DataStorge) of atom is important
322			for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
323			atom->setGlobalIndex(beginAtomIndex++);
324			}
325
326			for (rb = mol->beginRigidBody(ri); rb != NULL; rb = mol->nextRigidBody(ri)) {
327			rb->setGlobalIndex(beginRigidBodyIndex++);
328			}
329
330			//local index of cutoff group is trivial, it only depends on the order of travesing
331			for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
332			cg->setGlobalIndex(beginCutoffGroupIndex++);
333			}
334
335			}
336			}
337
338	tim	1703	} //end namespace oopse