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) {
    MoleculeIterator i;
    i = std::find(molecules_.begin(), molecules_.end(), mol);
    if (i != molecules_.end() ) {

        molecules_.insert(make_pair(mol->getGlobalIndex(), 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) {
    MoleculeIterator i;
    i = std::find(molecules_.begin(), molecules_.end(), mol);

    if (i != molecules_.end() ) {

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

        molecules_.erase(mol->getGlobalIndex());

        delete mol;
        
        return true;
    } else {
        return false;
    }


}    

        
Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
    i = molecules_.begin();
    return i == molecules_.end() ? NULL : *i;
}    

Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
    ++i;
    return i == molecules_.end() ? NULL : *i;    
}


void SimInfo::calcNdf() {
    int ndf_local;
    MoleculeIterator 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;

    MoleculeIterator 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);        
    }

}


void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
    int curStampId;

    //index from 0
    curStampId = molStampIds_.size();

    moleculeStamps_.push_back(molStamp);
    molStampIds_.insert(molStampIds_.end(), nmol, curStampId)
}

std::ostream& operator <<(ostream& o, SimInfo& info) {

    return o;
}

}//end namespace oopse
Revision:	1726
Committed:	Wed Nov 10 22:50:03 2004 UTC (20 years, 11 months ago) by tim
File size:	8796 byte(s)
Log Message:	more work on SimInfo
#	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	tim	1726	//MemoryUtils::deleteVectorOfPointer(molecules_);
47	tim	1710	delete sman_;
48	gezelter	1490
49			}
50
51
52	tim	1710	bool SimInfo::addMolecule(Molecule* mol) {
53	tim	1726	MoleculeIterator i;
54	tim	1710	i = std::find(molecules_.begin(), molecules_.end(), mol);
55			if (i != molecules_.end() ) {
56	gezelter	1490
57	tim	1726	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
58
59	tim	1710	nAtoms_ += mol->getNAtoms();
60			nBonds_ += mol->getNBonds();
61			nBends_ += mol->getNBends();
62			nTorsions_ += mol->getNTorsions();
63			nRigidBodies_ += mol->getNRigidBodies();
64			nIntegrableObjects_ += mol->getNIntegrableObjects();
65			nCutoffGroups_ += mol->getNCutoffGroups();
66			nConstraints_ += mol->getNConstraints();
67	gezelter	1490
68	tim	1710	return true;
69			} else {
70			return false;
71	gezelter	1490	}
72			}
73
74	tim	1710	bool SimInfo::removeMolecule(Molecule* mol) {
75	tim	1726	MoleculeIterator i;
76	tim	1710	i = std::find(molecules_.begin(), molecules_.end(), mol);
77	gezelter	1490
78	tim	1710	if (i != molecules_.end() ) {
79	tim	1726
80	tim	1710	nAtoms_ -= mol->getNAtoms();
81			nBonds_ -= mol->getNBonds();
82			nBends_ -= mol->getNBends();
83			nTorsions_ -= mol->getNTorsions();
84			nRigidBodies_ -= mol->getNRigidBodies();
85			nIntegrableObjects_ -= mol->getNIntegrableObjects();
86			nCutoffGroups_ -= mol->getNCutoffGroups();
87			nConstraints_ -= mol->getNConstraints();
88	gezelter	1490
89	tim	1726	molecules_.erase(mol->getGlobalIndex());
90
91			delete mol;
92
93	tim	1710	return true;
94			} else {
95			return false;
96	gezelter	1490	}
97
98
99	tim	1710	}
100	gezelter	1490
101	tim	1710
102	tim	1726	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
103	tim	1710	i = molecules_.begin();
104			return i == molecules_.end() ? NULL : *i;
105			}
106	gezelter	1490
107	tim	1726	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
108	tim	1710	++i;
109			return i == molecules_.end() ? NULL : *i;
110	gezelter	1490	}
111
112
113	tim	1722	void SimInfo::calcNdf() {
114	tim	1710	int ndf_local;
115	tim	1726	MoleculeIterator i;
116	tim	1710	std::vector<StuntDouble*>::iterator j;
117			Molecule* mol;
118			StuntDouble* integrableObject;
119	gezelter	1490
120	tim	1710	ndf_local = 0;
121	gezelter	1490
122	tim	1710	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
123			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
124			integrableObject = mol->nextIntegrableObject(j)) {
125	gezelter	1490
126	tim	1710	ndf_local += 3;
127	gezelter	1490
128	tim	1710	if (integrableObject->isDirectional()) {
129			if (integrableObject->isLinear()) {
130			ndf_local += 2;
131			} else {
132			ndf_local += 3;
133			}
134			}
135
136			}//end for (integrableObject)
137			}// end for (mol)
138	gezelter	1490
139	tim	1710	// n_constraints is local, so subtract them on each processor
140			ndf_local -= nConstraints_;
141	gezelter	1490
142			#ifdef IS_MPI
143	tim	1710	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
144	gezelter	1490	#else
145	tim	1710	ndf_ = ndf_local;
146	gezelter	1490	#endif
147
148	tim	1710	// nZconstraints is global, as are the 3 COM translations for the
149			// entire system:
150			ndf_ = ndf_ - 3 - nZconstraints;
151	gezelter	1490
152			}
153
154	tim	1722	void SimInfo::calcNdfRaw() {
155	tim	1710	int ndfRaw_local;
156	gezelter	1490
157	tim	1726	MoleculeIterator i;
158	tim	1710	std::vector<StuntDouble*>::iterator j;
159			Molecule* mol;
160			StuntDouble* integrableObject;
161	gezelter	1490
162	tim	1710	// Raw degrees of freedom that we have to set
163			ndfRaw_local = 0;
164	gezelter	1490
165	tim	1710	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
166			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
167			integrableObject = mol->nextIntegrableObject(j)) {
168	gezelter	1490
169	tim	1710	ndfRaw_local += 3;
170	gezelter	1490
171	tim	1710	if (integrableObject->isDirectional()) {
172			if (integrableObject->isLinear()) {
173			ndfRaw_local += 2;
174			} else {
175			ndfRaw_local += 3;
176			}
177			}
178
179			}
180			}
181
182	gezelter	1490	#ifdef IS_MPI
183	tim	1710	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
184	gezelter	1490	#else
185	tim	1710	ndfRaw_ = ndfRaw_local;
186	gezelter	1490	#endif
187			}
188
189	tim	1722	void SimInfo::calcNdfTrans() {
190	tim	1710	int ndfTrans_local;
191	gezelter	1490
192	tim	1710	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
193	gezelter	1490
194
195			#ifdef IS_MPI
196	tim	1710	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
197	gezelter	1490	#else
198	tim	1710	ndfTrans_ = ndfTrans_local;
199	gezelter	1490	#endif
200
201	tim	1710	ndfTrans_ = ndfTrans_ - 3 - nZconstraints;
202	gezelter	1490
203			}
204
205	tim	1719	void SimInfo::addExcludePairs(Molecule* mol) {
206			std::vector<Bond*>::iterator bondIter;
207			std::vector<Bend*>::iterator bendIter;
208			std::vector<Torsion*>::iterator torsionIter;
209			Bond* bond;
210			Bend* bend;
211			Torsion* torsion;
212			int a;
213			int b;
214			int c;
215			int d;
216
217			for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
218			a = bond->getAtomA()->getGlobalIndex();
219			b = bond->getAtomB()->getGlobalIndex();
220			exclude_.addPair(a, b);
221			}
222	gezelter	1490
223	tim	1719	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
224			a = bend->getAtomA()->getGlobalIndex();
225			b = bend->getAtomB()->getGlobalIndex();
226			c = bend->getAtomC()->getGlobalIndex();
227
228			exclude_.addPair(a, b);
229			exclude_.addPair(a, c);
230			exclude_.addPair(b, c);
231			}
232
233			for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) {
234			a = torsion->getAtomA()->getGlobalIndex();
235			b = torsion->getAtomB()->getGlobalIndex();
236			c = torsion->getAtomC()->getGlobalIndex();
237			d = torsion->getAtomD()->getGlobalIndex();
238
239			exclude_.addPair(a, b);
240			exclude_.addPair(a, c);
241			exclude_.addPair(a, d);
242			exclude_.addPair(b, c);
243			exclude_.addPair(b, d);
244			exclude_.addPair(c, d);
245			}
246
247
248			}
249
250			void SimInfo::removeExcludePairs(Molecule* mol) {
251			std::vector<Bond*>::iterator bondIter;
252			std::vector<Bend*>::iterator bendIter;
253			std::vector<Torsion*>::iterator torsionIter;
254			Bond* bond;
255			Bend* bend;
256			Torsion* torsion;
257			int a;
258			int b;
259			int c;
260			int d;
261
262			for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
263			a = bond->getAtomA()->getGlobalIndex();
264			b = bond->getAtomB()->getGlobalIndex();
265			exclude_.removePair(a, b);
266			}
267
268			for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
269			a = bend->getAtomA()->getGlobalIndex();
270			b = bend->getAtomB()->getGlobalIndex();
271			c = bend->getAtomC()->getGlobalIndex();
272
273			exclude_.removePair(a, b);
274			exclude_.removePair(a, c);
275			exclude_.removePair(b, c);
276			}
277
278			for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) {
279			a = torsion->getAtomA()->getGlobalIndex();
280			b = torsion->getAtomB()->getGlobalIndex();
281			c = torsion->getAtomC()->getGlobalIndex();
282			d = torsion->getAtomD()->getGlobalIndex();
283
284			exclude_.removePair(a, b);
285			exclude_.removePair(a, c);
286			exclude_.removePair(a, d);
287			exclude_.removePair(b, c);
288			exclude_.removePair(b, d);
289			exclude_.removePair(c, d);
290			}
291
292			}
293
294
295	tim	1725	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
296			int curStampId;
297
298			//index from 0
299			curStampId = molStampIds_.size();
300
301			moleculeStamps_.push_back(molStamp);
302			molStampIds_.insert(molStampIds_.end(), nmol, curStampId)
303			}
304
305			std::ostream& operator <<(ostream& o, SimInfo& info) {
306
307			return o;
308			}
309
310	tim	1710	}//end namespace oopse