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();

        globalIndexToMol_.insert(make_pair(mol->getGlobalIndex(), mol));
        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();

        globalIndexToMol_.erase(mol->getGlobalIndex());
        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);        
    }

}


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:	1725
Committed:	Wed Nov 10 22:01:06 2004 UTC (19 years, 7 months ago) by tim
File size:	8934 byte(s)
Log Message:	another painful day (1) SimCreator, SimInfo, mpiSimulation (2) DumpReader, DumpWriter (InitializeFrom File will be removed) (3) ForceField (at least LJ) and BondType, BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors & Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint
#	Content
1	/*
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 SimInfo.cpp
28	* @author tlin
29	* @date 11/02/2004
30	* @version 1.0
31	*/
32
33	#include <algorithm>
34
35	#include "brains/SimInfo.hpp"
36	#include "utils/MemoryUtils.hpp"
37
38	namespace oopse {
39
40	SimInfo::SimInfo() : nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
41	nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), sman_(NULL){
42
43	}
44
45	SimInfo::~SimInfo() {
46	MemoryUtils::deleteVectorOfPointer(molecules_);
47	delete sman_;
48
49	}
50
51
52	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
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	globalIndexToMol_.insert(make_pair(mol->getGlobalIndex(), mol));
68	return true;
69	} else {
70	return false;
71	}
72	}
73
74	bool SimInfo::removeMolecule(Molecule* mol) {
75	std::vector<Molecule*>::iterator i;
76	i = std::find(molecules_.begin(), molecules_.end(), mol);
77
78	if (i != molecules_.end() ) {
79	molecules_.push_back(mol);
80	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
89	globalIndexToMol_.erase(mol->getGlobalIndex());
90	return true;
91	} else {
92	return false;
93	}
94
95
96	}
97
98
99	Molecule* SimInfo::beginMolecule(std::vector<Molecule*>::iterator& i) {
100	i = molecules_.begin();
101	return i == molecules_.end() ? NULL : *i;
102	}
103
104	Molecule* SimInfo::nextMolecule(std::vector<Molecule*>::iterator& i) {
105	++i;
106	return i == molecules_.end() ? NULL : *i;
107	}
108
109
110	void SimInfo::calcNdf() {
111	int ndf_local;
112	std::vector<Molecule*>::iterator i;
113	std::vector<StuntDouble*>::iterator j;
114	Molecule* mol;
115	StuntDouble* integrableObject;
116
117	ndf_local = 0;
118
119	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
120	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
121	integrableObject = mol->nextIntegrableObject(j)) {
122
123	ndf_local += 3;
124
125	if (integrableObject->isDirectional()) {
126	if (integrableObject->isLinear()) {
127	ndf_local += 2;
128	} else {
129	ndf_local += 3;
130	}
131	}
132
133	}//end for (integrableObject)
134	}// end for (mol)
135
136	// n_constraints is local, so subtract them on each processor
137	ndf_local -= nConstraints_;
138
139	#ifdef IS_MPI
140	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
141	#else
142	ndf_ = ndf_local;
143	#endif
144
145	// nZconstraints is global, as are the 3 COM translations for the
146	// entire system:
147	ndf_ = ndf_ - 3 - nZconstraints;
148
149	}
150
151	void SimInfo::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 SimInfo::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	void SimInfo::addExcludePairs(Molecule* mol) {
203	std::vector<Bond*>::iterator bondIter;
204	std::vector<Bend*>::iterator bendIter;
205	std::vector<Torsion*>::iterator torsionIter;
206	Bond* bond;
207	Bend* bend;
208	Torsion* torsion;
209	int a;
210	int b;
211	int c;
212	int d;
213
214	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
215	a = bond->getAtomA()->getGlobalIndex();
216	b = bond->getAtomB()->getGlobalIndex();
217	exclude_.addPair(a, b);
218	}
219
220	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
221	a = bend->getAtomA()->getGlobalIndex();
222	b = bend->getAtomB()->getGlobalIndex();
223	c = bend->getAtomC()->getGlobalIndex();
224
225	exclude_.addPair(a, b);
226	exclude_.addPair(a, c);
227	exclude_.addPair(b, c);
228	}
229
230	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) {
231	a = torsion->getAtomA()->getGlobalIndex();
232	b = torsion->getAtomB()->getGlobalIndex();
233	c = torsion->getAtomC()->getGlobalIndex();
234	d = torsion->getAtomD()->getGlobalIndex();
235
236	exclude_.addPair(a, b);
237	exclude_.addPair(a, c);
238	exclude_.addPair(a, d);
239	exclude_.addPair(b, c);
240	exclude_.addPair(b, d);
241	exclude_.addPair(c, d);
242	}
243
244
245	}
246
247	void SimInfo::removeExcludePairs(Molecule* mol) {
248	std::vector<Bond*>::iterator bondIter;
249	std::vector<Bend*>::iterator bendIter;
250	std::vector<Torsion*>::iterator torsionIter;
251	Bond* bond;
252	Bend* bend;
253	Torsion* torsion;
254	int a;
255	int b;
256	int c;
257	int d;
258
259	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
260	a = bond->getAtomA()->getGlobalIndex();
261	b = bond->getAtomB()->getGlobalIndex();
262	exclude_.removePair(a, b);
263	}
264
265	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
266	a = bend->getAtomA()->getGlobalIndex();
267	b = bend->getAtomB()->getGlobalIndex();
268	c = bend->getAtomC()->getGlobalIndex();
269
270	exclude_.removePair(a, b);
271	exclude_.removePair(a, c);
272	exclude_.removePair(b, c);
273	}
274
275	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) {
276	a = torsion->getAtomA()->getGlobalIndex();
277	b = torsion->getAtomB()->getGlobalIndex();
278	c = torsion->getAtomC()->getGlobalIndex();
279	d = torsion->getAtomD()->getGlobalIndex();
280
281	exclude_.removePair(a, b);
282	exclude_.removePair(a, c);
283	exclude_.removePair(a, d);
284	exclude_.removePair(b, c);
285	exclude_.removePair(b, d);
286	exclude_.removePair(c, d);
287	}
288
289	}
290
291
292	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
293	int curStampId;
294
295	//index from 0
296	curStampId = molStampIds_.size();
297
298	moleculeStamps_.push_back(molStamp);
299	molStampIds_.insert(molStampIds_.end(), nmol, curStampId)
300	}
301
302	std::ostream& operator <<(ostream& o, SimInfo& info) {
303
304	return o;
305	}
306
307	}//end namespace oopse