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()->createForceField(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);

    //allocate memory for DataStorage(circular reference, need to break it)
    info->setSnapshotManager(new SimSnapshotManager(info);
    
    //load initial coordinates
    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(SimModel* model) {
    model->addProperty(new StringGenericData("Ensemble", globals->getForceFiled()));
    model->addProperty(new DoubleGenericData("dt"), globals->getDt());
}

#ifdef IS_MPI
void SimCreator::mpiMolDivide(){
 
    mpiSim = new mpiSimulation(info);

    mpiSim->divideLabor();

    strcpy(checkPointMsg, "Passed nlocal consistency check.");
    MPIcheckPoint();
}
#endif

Molecule* SimCreator::createMolecules(SimInfo* info) {


    for (i = 0; i < mpiSim->getNMolGlobal(); i++){
        if (mol2proc[i] == worldRank){

            Molecule* mol = MoleculeCreator.createMolecule(molStamp, stampID, globalIndex);
                        
            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.moleculeStamps.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
}


} //end namespace oopse
Revision:	1719
Committed:	Fri Nov 5 23:38:27 2004 UTC (19 years, 10 months ago) by tim
File size:	5716 byte(s)
Log Message:	Fix Exclude class etc.
#	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			/**
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	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	1713	ForceFiled* ff = ForceFieldFactory::getInstance()->createForceField(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			//allocate memory for DataStorage(circular reference, need to break it)
95	tim	1719	info->setSnapshotManager(new SimSnapshotManager(info);
96	tim	1712
97			//load initial coordinates
98	tim	1719	DumpReader reader(info->getInitFilename());
99			int nframes = reader->getNframes();
100
101			if (nframes > 0) {
102			reader.readFrame(info, nframes - 1);
103			} else {
104			//invalid initial coordinate file
105
106			}
107
108	tim	1712
109			//initialize fortran
110	tim	1719
111			return info;
112	tim	1712	}
113
114			void SimCreator::gatherParameters(SimModel* model) {
115			model->addProperty(new StringGenericData("Ensemble", globals->getForceFiled()));
116			model->addProperty(new DoubleGenericData("dt"), globals->getDt());
117			}
118
119			#ifdef IS_MPI
120	tim	1713	void SimCreator::mpiMolDivide(){
121
122			mpiSim = new mpiSimulation(info);
123	tim	1712
124	tim	1713	mpiSim->divideLabor();
125	tim	1712
126	tim	1713	strcpy(checkPointMsg, "Passed nlocal consistency check.");
127			MPIcheckPoint();
128	tim	1712	}
129	tim	1713	#endif
130	tim	1712
131	tim	1719	Molecule* SimCreator::createMolecules(SimInfo* info) {
132	tim	1713
133
134
135	tim	1719	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
136			if (mol2proc[i] == worldRank){
137	tim	1713
138	tim	1719	Molecule* mol = MoleculeCreator.createMolecule(molStamp, stampID, globalIndex);
139
140			info->addMolecule(mol);
141			}
142			}
143
144	tim	1713	}
145
146	tim	1719
147			void SimSetup::compList(MakeStamps* stamps,SimInfo* info) {
148			int i;
149			char* id;
150			MoleculeStamp* currentStamp;
151			Component* the_components = info->getGlobals()->getComponents();
152			int n_components = info->getGlobals()->getNComponents();
153
154			if (!globals->haveNMol()){
155			// we don't have the total number of molecules, so we assume it is
156			// given in each component
157
158			for (i = 0; i < n_components; i++){
159			if (!the_components[i]->haveNMol()){
160			// we have a problem
161			sprintf(painCave.errMsg,
162			"SimSetup Error. No global NMol or component NMol given.\n"
163			"\tCannot calculate the number of atoms.\n");
164			painCave.isFatal = 1;
165			simError();
166			}
167
168			id = the_components[i]->getType();
169			currentStamp = stamps->extractMolStamp(id);
170			if (currentStamp == NULL){
171			sprintf(painCave.errMsg,
172			"SimSetup error: Component \"%s\" was not found in the "
173			"list of declared molecules\n",
174			id);
175			painCave.isFatal = 1;
176			simError();
177			}
178
179			info.moleculeStamps.push_back(make_pair(currentStamp, the_components[i]->getNMol()));
180
181			} //end for (i = 0; i < n_components; i++)
182
183			} else{
184			sprintf(painCave.errMsg,
185			"SimSetup error.\n"
186			"\tSorry, the ability to specify total"
187			" nMols and then give molfractions in the components\n"
188			"\tis not currently supported."
189			" Please give nMol in the components.\n");
190			painCave.isFatal = 1;
191			simError();
192			}
193
194			#ifdef IS_MPI
195			strcpy(checkPointMsg, "Component stamps successfully extracted\n");
196			MPIcheckPoint();
197			#endif // is_mpi
198			}
199
200
201	tim	1703	} //end namespace oopse