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

}


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

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

    //create the force field
    ForceFiled* ff = ForceFieldFactory::getInstance()->createForceField(globals->getForceField());
    
    //create SimModel
    model = new SimInfo();
    
    //gather parameters 
    gatherParameters(model);
    
    //divide the molecules and determine the global index of molecules

    //create the molecules

    //create atoms, bonds, bend, torsions, rigidbodies 

    //allocate memory for DataStorage(circular reference, need to break it)
    model->setSnapshotManager(new SimSnapshotManager(model);
    
    //load initial coordinates
    DumpReader reader();
    reader.readFrame(model);
    
    //initialize fortran    
    return model;
}    

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::createMolecule() {
    Molecule* mol = new Molecule();


    //create atoms
    mol->addAtom();

    //create rigid bodies
    createRigidBody(mol);
    
    //create bonds

    
}

} //end namespace oopse
Revision:	1713
Committed:	Fri Nov 5 02:56:22 2004 UTC (19 years, 8 months ago) by tim
File size:	3286 byte(s)
Log Message:	Pain......
#	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			SimModel* SimCreator::createSim(const std::string& mdfile) {
67			MakeStamps* stamps;
68
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			//create SimModel
78			model = new SimInfo();
79
80			//gather parameters
81			gatherParameters(model);
82
83			//divide the molecules and determine the global index of molecules
84
85			//create the molecules
86
87			//create atoms, bonds, bend, torsions, rigidbodies
88
89			//allocate memory for DataStorage(circular reference, need to break it)
90			model->setSnapshotManager(new SimSnapshotManager(model);
91
92			//load initial coordinates
93			DumpReader reader();
94			reader.readFrame(model);
95
96			//initialize fortran
97			return model;
98			}
99
100			void SimCreator::gatherParameters(SimModel* model) {
101			model->addProperty(new StringGenericData("Ensemble", globals->getForceFiled()));
102			model->addProperty(new DoubleGenericData("dt"), globals->getDt());
103			}
104
105			#ifdef IS_MPI
106	tim	1713	void SimCreator::mpiMolDivide(){
107
108			mpiSim = new mpiSimulation(info);
109	tim	1712
110	tim	1713	mpiSim->divideLabor();
111	tim	1712
112	tim	1713	strcpy(checkPointMsg, "Passed nlocal consistency check.");
113			MPIcheckPoint();
114	tim	1712	}
115	tim	1713	#endif
116	tim	1712
117	tim	1713	Molecule* SimCreator::createMolecule() {
118			Molecule* mol = new Molecule();
119
120
121			//create atoms
122			mol->addAtom();
123
124			//create rigid bodies
125			createRigidBody(mol);
126
127			//create bonds
128
129
130
131			}
132
133	tim	1703	} //end namespace oopse