src/brains/SimModel.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 SimModel.cpp
 * @author    tlin
 * @date  11/02/2004
 * @version 1.0
 */

#include <algorithm>

#include "brains/SimModel.hpp"
#include "utils/MemoryUtils.hpp"

namespace oopse {

SimModel::SimModel() : nAtom_(0), nBond_(0), nBend_(0), nTorsion_(0), nRigidBody_(0), 
        nIntegrableObjects_(0), nCutoffGroup_(0), nConstraints_(0), sman_(NULL){

}

SimModel::~SimModel() {
    MemoryUtils::deleteVectorOfPointer(molecules_);
    delete sman_;

}


bool SimModel::addMolecule(Molecule* mol) {
    std::vector<Molecule*>::iterator i;
    i = std::find(molecules_.begin(), molecules_.end(), mol);
    if (i != molecules_.end() ) {
        molecules_.push_back(mol);

        nAtoms_ += mol->getNAtoms();
        nBonds_ += mol->getNBonds();
        nBends_ += mol->getNBends();
        nTorsions_ += mol->getNTorsions();
        nRigidBodies_ += mol->getNRigidBodies();
        nIntegrableObjects_ += mol->getNIntegrableObjects();
        nCutoffGroups_ += mol->getNCutoffGroups();
        nConstraints_ += mol->getNConstraints();

        return true;
    } else {
        return false;
    }
}

bool SimModel::removeMolecule(Molecule* mol) {
    std::vector<Molecule*>::iterator i;
    i = std::find(molecules_.begin(), molecules_.end(), mol);

    if (i != molecules_.end() ) {
        molecules_.push_back(mol);
        nAtoms_ -= mol->getNAtoms();
        nBonds_ -= mol->getNBonds();
        nBends_ -= mol->getNBends();
        nTorsions_ -= mol->getNTorsions();
        nRigidBodies_ -= mol->getNRigidBodies();
        nIntegrableObjects_ -= mol->getNIntegrableObjects();
        nCutoffGroups_ -= mol->getNCutoffGroups();
        nConstraints_ -= mol->getNConstraints();

        return true;
    } else {
        return false;
    }


}    

        
Molecule* SimModel::beginMolecule(std::vector<Molecule*>::iterator& i) {
    i = molecules_.begin();
    return i == molecules_.end() ? NULL : *i;
}    

Molecule* SimModel::nextMolecule(std::vector<Molecule*>::iterator& i) {
    ++i;
    return i == molecules_.end() ? NULL : *i;    
}


void SimModel::calcNDF() {
    int ndf_local;
    std::vector<Molecule*>::iterator i;
    std::vector<StuntDouble*>::iterator j;
    Molecule* mol;
    StuntDouble* integrableObject;

    ndf_local = 0;
    
    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; 
               integrableObject = mol->nextIntegrableObject(j)) {

            ndf_local += 3;

            if (integrableObject->isDirectional()) {
                if (integrableObject->isLinear()) {
                    ndf_local += 2;
                } else {
                    ndf_local += 3;
                }
            }
            
        }
    }
    
    // n_constraints is local, so subtract them on each processor:

    ndf_local -= nConstraints_;

#ifdef IS_MPI
    MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
#else
    ndf_ = ndf_local;
#endif

    // nZconstraints is global, as are the 3 COM translations for the 
    // entire system:

    ndf_ = ndf_ - 3 - nZconstraints;

}

void SimModel::calcNDFRaw() {
    int ndfRaw_local;

    std::vector<Molecule*>::iterator i;
    std::vector<StuntDouble*>::iterator j;
    Molecule* mol;
    StuntDouble* integrableObject;

    // Raw degrees of freedom that we have to set
    ndfRaw_local = 0;
    
    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
               integrableObject = mol->nextIntegrableObject(j)) {

            ndfRaw_local += 3;

            if (integrableObject->isDirectional()) {
                if (integrableObject->isLinear()) {
                    ndfRaw_local += 2;
                } else {
                    ndfRaw_local += 3;
                }
            }
            
        }
    }
    
#ifdef IS_MPI
    MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
#else
    ndfRaw_ = ndfRaw_local;
#endif
}

void SimModel::calcNDFTrans() {
    int ndfTrans_local;

    ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;


#ifdef IS_MPI
    MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
#else
    ndfTrans_ = ndfTrans_local;
#endif

    ndfTrans_ = ndfTrans_ - 3 - nZconstraints;
 
}


}//end namespace oopse
Revision:	1699
Committed:	Tue Nov 2 17:00:12 2004 UTC (19 years, 7 months ago) by tim
File size:	5574 byte(s)
Log Message:	SimModel in progress
#	User	Rev	Content
1	tim	1699	/*
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 SimModel.cpp
28			* @author tlin
29			* @date 11/02/2004
30			* @version 1.0
31			*/
32
33			#include <algorithm>
34
35			#include "brains/SimModel.hpp"
36			#include "utils/MemoryUtils.hpp"
37
38			namespace oopse {
39
40			SimModel::SimModel() : nAtom_(0), nBond_(0), nBend_(0), nTorsion_(0), nRigidBody_(0),
41			nIntegrableObjects_(0), nCutoffGroup_(0), nConstraints_(0), sman_(NULL){
42
43			}
44
45			SimModel::~SimModel() {
46			MemoryUtils::deleteVectorOfPointer(molecules_);
47			delete sman_;
48
49			}
50
51
52			bool SimModel::addMolecule(Molecule* mol) {
53			std::vector<Molecule*>::iterator i;
54			i = std::find(molecules_.begin(), molecules_.end(), mol);
55			if (i != molecules_.end() ) {
56			molecules_.push_back(mol);
57
58			nAtoms_ += mol->getNAtoms();
59			nBonds_ += mol->getNBonds();
60			nBends_ += mol->getNBends();
61			nTorsions_ += mol->getNTorsions();
62			nRigidBodies_ += mol->getNRigidBodies();
63			nIntegrableObjects_ += mol->getNIntegrableObjects();
64			nCutoffGroups_ += mol->getNCutoffGroups();
65			nConstraints_ += mol->getNConstraints();
66
67			return true;
68			} else {
69			return false;
70			}
71			}
72
73			bool SimModel::removeMolecule(Molecule* mol) {
74			std::vector<Molecule*>::iterator i;
75			i = std::find(molecules_.begin(), molecules_.end(), mol);
76
77			if (i != molecules_.end() ) {
78			molecules_.push_back(mol);
79			nAtoms_ -= mol->getNAtoms();
80			nBonds_ -= mol->getNBonds();
81			nBends_ -= mol->getNBends();
82			nTorsions_ -= mol->getNTorsions();
83			nRigidBodies_ -= mol->getNRigidBodies();
84			nIntegrableObjects_ -= mol->getNIntegrableObjects();
85			nCutoffGroups_ -= mol->getNCutoffGroups();
86			nConstraints_ -= mol->getNConstraints();
87
88			return true;
89			} else {
90			return false;
91			}
92
93
94			}
95
96
97			Molecule* SimModel::beginMolecule(std::vector<Molecule*>::iterator& i) {
98			i = molecules_.begin();
99			return i == molecules_.end() ? NULL : *i;
100			}
101
102			Molecule* SimModel::nextMolecule(std::vector<Molecule*>::iterator& i) {
103			++i;
104			return i == molecules_.end() ? NULL : *i;
105			}
106
107
108			void SimModel::calcNDF() {
109			int ndf_local;
110			std::vector<Molecule*>::iterator i;
111			std::vector<StuntDouble*>::iterator j;
112			Molecule* mol;
113			StuntDouble* integrableObject;
114
115			ndf_local = 0;
116
117			for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
118			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
119			integrableObject = mol->nextIntegrableObject(j)) {
120
121			ndf_local += 3;
122
123			if (integrableObject->isDirectional()) {
124			if (integrableObject->isLinear()) {
125			ndf_local += 2;
126			} else {
127			ndf_local += 3;
128			}
129			}
130
131			}
132			}
133
134			// n_constraints is local, so subtract them on each processor:
135
136			ndf_local -= nConstraints_;
137
138			#ifdef IS_MPI
139			MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
140			#else
141			ndf_ = ndf_local;
142			#endif
143
144			// nZconstraints is global, as are the 3 COM translations for the
145			// entire system:
146
147			ndf_ = ndf_ - 3 - nZconstraints;
148
149			}
150
151			void SimModel::calcNDFRaw() {
152			int ndfRaw_local;
153
154			std::vector<Molecule*>::iterator i;
155			std::vector<StuntDouble*>::iterator j;
156			Molecule* mol;
157			StuntDouble* integrableObject;
158
159			// Raw degrees of freedom that we have to set
160			ndfRaw_local = 0;
161
162			for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
163			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
164			integrableObject = mol->nextIntegrableObject(j)) {
165
166			ndfRaw_local += 3;
167
168			if (integrableObject->isDirectional()) {
169			if (integrableObject->isLinear()) {
170			ndfRaw_local += 2;
171			} else {
172			ndfRaw_local += 3;
173			}
174			}
175
176			}
177			}
178
179			#ifdef IS_MPI
180			MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
181			#else
182			ndfRaw_ = ndfRaw_local;
183			#endif
184			}
185
186			void SimModel::calcNDFTrans() {
187			int ndfTrans_local;
188
189			ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
190
191
192			#ifdef IS_MPI
193			MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
194			#else
195			ndfTrans_ = ndfTrans_local;
196			#endif
197
198			ndfTrans_ = ndfTrans_ - 3 - nZconstraints;
199
200			}
201
202
203			}//end namespace oopse