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

#include <algorithm>

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

namespace oopse {

SimInfo::SimInfo() : nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), 
        nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), sman_(NULL){

}

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

}


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

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


void SimInfo::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;
                }
            }
            
        }//end for (integrableObject)
    }// end for (mol)
    
    // 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 SimInfo::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 SimInfo::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;
 
}

void SimInfo::addExcludePairs(Molecule* mol) {
    std::vector<Bond*>::iterator bondIter;
    std::vector<Bend*>::iterator bendIter;
    std::vector<Torsion*>::iterator torsionIter;
    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    int a;
    int b;
    int c;
    int d;
    
    for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
        a = bond->getAtomA()->getGlobalIndex();
        b = bond->getAtomB()->getGlobalIndex();        
        exclude_.addPair(a, b);
    }

    for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
        a = bend->getAtomA()->getGlobalIndex();
        b = bend->getAtomB()->getGlobalIndex();        
        c = bend->getAtomC()->getGlobalIndex();

        exclude_.addPair(a, b);
        exclude_.addPair(a, c);
        exclude_.addPair(b, c);        
    }

    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) {
        a = torsion->getAtomA()->getGlobalIndex();
        b = torsion->getAtomB()->getGlobalIndex();        
        c = torsion->getAtomC()->getGlobalIndex();        
        d = torsion->getAtomD()->getGlobalIndex();        

        exclude_.addPair(a, b);
        exclude_.addPair(a, c);
        exclude_.addPair(a, d);
        exclude_.addPair(b, c);
        exclude_.addPair(b, d);
        exclude_.addPair(c, d);        
    }

    
}

void SimInfo::removeExcludePairs(Molecule* mol) {
    std::vector<Bond*>::iterator bondIter;
    std::vector<Bend*>::iterator bendIter;
    std::vector<Torsion*>::iterator torsionIter;
    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    int a;
    int b;
    int c;
    int d;
    
    for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
        a = bond->getAtomA()->getGlobalIndex();
        b = bond->getAtomB()->getGlobalIndex();        
        exclude_.removePair(a, b);
    }

    for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
        a = bend->getAtomA()->getGlobalIndex();
        b = bend->getAtomB()->getGlobalIndex();        
        c = bend->getAtomC()->getGlobalIndex();

        exclude_.removePair(a, b);
        exclude_.removePair(a, c);
        exclude_.removePair(b, c);        
    }

    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) {
        a = torsion->getAtomA()->getGlobalIndex();
        b = torsion->getAtomB()->getGlobalIndex();        
        c = torsion->getAtomC()->getGlobalIndex();        
        d = torsion->getAtomD()->getGlobalIndex();        

        exclude_.removePair(a, b);
        exclude_.removePair(a, c);
        exclude_.removePair(a, d);
        exclude_.removePair(b, c);
        exclude_.removePair(b, d);
        exclude_.removePair(c, d);        
    }

}


}//end namespace oopse
Revision:	1722
Committed:	Tue Nov 9 23:11:39 2004 UTC (19 years, 7 months ago) by tim
File size:	8479 byte(s)
Log Message:	adding ForceManager
#	User	Rev	Content
1	tim	1710	/*
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	gezelter	1490
26	tim	1710	/**
27			* @file SimInfo.cpp
28			* @author tlin
29			* @date 11/02/2004
30			* @version 1.0
31			*/
32	gezelter	1490
33	tim	1710	#include <algorithm>
34
35	tim	1492	#include "brains/SimInfo.hpp"
36	tim	1710	#include "utils/MemoryUtils.hpp"
37	gezelter	1490
38	tim	1710	namespace oopse {
39	gezelter	1490
40	tim	1710	SimInfo::SimInfo() : nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
41			nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), sman_(NULL){
42	gezelter	1490
43			}
44
45	tim	1710	SimInfo::~SimInfo() {
46			MemoryUtils::deleteVectorOfPointer(molecules_);
47			delete sman_;
48	gezelter	1490
49			}
50
51
52	tim	1710	bool SimInfo::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	gezelter	1490
58	tim	1710	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	gezelter	1490
67	tim	1710	return true;
68			} else {
69			return false;
70	gezelter	1490	}
71			}
72
73	tim	1710	bool SimInfo::removeMolecule(Molecule* mol) {
74			std::vector<Molecule*>::iterator i;
75			i = std::find(molecules_.begin(), molecules_.end(), mol);
76	gezelter	1490
77	tim	1710	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	gezelter	1490
88	tim	1710	return true;
89			} else {
90			return false;
91	gezelter	1490	}
92
93
94	tim	1710	}
95	gezelter	1490
96	tim	1710
97			Molecule* SimInfo::beginMolecule(std::vector<Molecule*>::iterator& i) {
98			i = molecules_.begin();
99			return i == molecules_.end() ? NULL : *i;
100			}
101	gezelter	1490
102	tim	1710	Molecule* SimInfo::nextMolecule(std::vector<Molecule*>::iterator& i) {
103			++i;
104			return i == molecules_.end() ? NULL : *i;
105	gezelter	1490	}
106
107
108	tim	1722	void SimInfo::calcNdf() {
109	tim	1710	int ndf_local;
110			std::vector<Molecule*>::iterator i;
111			std::vector<StuntDouble*>::iterator j;
112			Molecule* mol;
113			StuntDouble* integrableObject;
114	gezelter	1490
115	tim	1710	ndf_local = 0;
116	gezelter	1490
117	tim	1710	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
118			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
119			integrableObject = mol->nextIntegrableObject(j)) {
120	gezelter	1490
121	tim	1710	ndf_local += 3;
122	gezelter	1490
123	tim	1710	if (integrableObject->isDirectional()) {
124			if (integrableObject->isLinear()) {
125			ndf_local += 2;
126			} else {
127			ndf_local += 3;
128			}
129			}
130
131			}//end for (integrableObject)
132			}// end for (mol)
133	gezelter	1490
134	tim	1710	// n_constraints is local, so subtract them on each processor
135			ndf_local -= nConstraints_;
136	gezelter	1490
137			#ifdef IS_MPI
138	tim	1710	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
139	gezelter	1490	#else
140	tim	1710	ndf_ = ndf_local;
141	gezelter	1490	#endif
142
143	tim	1710	// nZconstraints is global, as are the 3 COM translations for the
144			// entire system:
145			ndf_ = ndf_ - 3 - nZconstraints;
146	gezelter	1490
147			}
148
149	tim	1722	void SimInfo::calcNdfRaw() {
150	tim	1710	int ndfRaw_local;
151	gezelter	1490
152	tim	1710	std::vector<Molecule*>::iterator i;
153			std::vector<StuntDouble*>::iterator j;
154			Molecule* mol;
155			StuntDouble* integrableObject;
156	gezelter	1490
157	tim	1710	// Raw degrees of freedom that we have to set
158			ndfRaw_local = 0;
159	gezelter	1490
160	tim	1710	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
161			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
162			integrableObject = mol->nextIntegrableObject(j)) {
163	gezelter	1490
164	tim	1710	ndfRaw_local += 3;
165	gezelter	1490
166	tim	1710	if (integrableObject->isDirectional()) {
167			if (integrableObject->isLinear()) {
168			ndfRaw_local += 2;
169			} else {
170			ndfRaw_local += 3;
171			}
172			}
173
174			}
175			}
176
177	gezelter	1490	#ifdef IS_MPI
178	tim	1710	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
179	gezelter	1490	#else
180	tim	1710	ndfRaw_ = ndfRaw_local;
181	gezelter	1490	#endif
182			}
183
184	tim	1722	void SimInfo::calcNdfTrans() {
185	tim	1710	int ndfTrans_local;
186	gezelter	1490
187	tim	1710	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
188	gezelter	1490
189
190			#ifdef IS_MPI
191	tim	1710	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
192	gezelter	1490	#else
193	tim	1710	ndfTrans_ = ndfTrans_local;
194	gezelter	1490	#endif
195
196	tim	1710	ndfTrans_ = ndfTrans_ - 3 - nZconstraints;
197	gezelter	1490
198			}
199
200	tim	1719	void SimInfo::addExcludePairs(Molecule* mol) {
201			std::vector<Bond*>::iterator bondIter;
202			std::vector<Bend*>::iterator bendIter;
203			std::vector<Torsion*>::iterator torsionIter;
204			Bond* bond;
205			Bend* bend;
206			Torsion* torsion;
207			int a;
208			int b;
209			int c;
210			int d;
211
212			for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
213			a = bond->getAtomA()->getGlobalIndex();
214			b = bond->getAtomB()->getGlobalIndex();
215			exclude_.addPair(a, b);
216			}
217	gezelter	1490
218	tim	1719	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
219			a = bend->getAtomA()->getGlobalIndex();
220			b = bend->getAtomB()->getGlobalIndex();
221			c = bend->getAtomC()->getGlobalIndex();
222
223			exclude_.addPair(a, b);
224			exclude_.addPair(a, c);
225			exclude_.addPair(b, c);
226			}
227
228			for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) {
229			a = torsion->getAtomA()->getGlobalIndex();
230			b = torsion->getAtomB()->getGlobalIndex();
231			c = torsion->getAtomC()->getGlobalIndex();
232			d = torsion->getAtomD()->getGlobalIndex();
233
234			exclude_.addPair(a, b);
235			exclude_.addPair(a, c);
236			exclude_.addPair(a, d);
237			exclude_.addPair(b, c);
238			exclude_.addPair(b, d);
239			exclude_.addPair(c, d);
240			}
241
242
243			}
244
245			void SimInfo::removeExcludePairs(Molecule* mol) {
246			std::vector<Bond*>::iterator bondIter;
247			std::vector<Bend*>::iterator bendIter;
248			std::vector<Torsion*>::iterator torsionIter;
249			Bond* bond;
250			Bend* bend;
251			Torsion* torsion;
252			int a;
253			int b;
254			int c;
255			int d;
256
257			for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
258			a = bond->getAtomA()->getGlobalIndex();
259			b = bond->getAtomB()->getGlobalIndex();
260			exclude_.removePair(a, b);
261			}
262
263			for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
264			a = bend->getAtomA()->getGlobalIndex();
265			b = bend->getAtomB()->getGlobalIndex();
266			c = bend->getAtomC()->getGlobalIndex();
267
268			exclude_.removePair(a, b);
269			exclude_.removePair(a, c);
270			exclude_.removePair(b, c);
271			}
272
273			for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) {
274			a = torsion->getAtomA()->getGlobalIndex();
275			b = torsion->getAtomB()->getGlobalIndex();
276			c = torsion->getAtomC()->getGlobalIndex();
277			d = torsion->getAtomD()->getGlobalIndex();
278
279			exclude_.removePair(a, b);
280			exclude_.removePair(a, c);
281			exclude_.removePair(a, d);
282			exclude_.removePair(b, c);
283			exclude_.removePair(b, d);
284			exclude_.removePair(c, d);
285			}
286
287			}
288
289
290	tim	1710	}//end namespace oopse