src/primitives/Molecule.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 Molecule.cpp
 * @author    tlin
 * @date  10/28/2004
 * @version 1.0
 */ 

#include <algorithm>
#include <set>

#include "primitives/Molecule.hpp"
#include "utils/MemoryUtils.hpp"

namespace oopse {

Molecule::~Molecule() {

    MemoryUtils::deleteVectorOfPointer(atoms_);
    MemoryUtils::deleteVectorOfPointer(bonds_);
    MemoryUtils::deleteVectorOfPointer(bends_);
    MemoryUtils::deleteVectorOfPointer(torsions_);
    MemoryUtils::deleteVectorOfPointer(rigidBodies_);
    MemoryUtils::deleteVectorOfPointer(cutoffGroups_);

    //integrableObjects_ don't own the objects
    integrableObjects_.clear();
    
}

void Molecule::addAtom(Atom* atom) {
    if (std::find(atoms_.begin(), atoms_.end(), atom) == atoms_.end()) {
        atoms_.push_back(atom);
    }
}

void Molecule::addBond(Bond* bond) {
    if (std::find(bonds_.begin(), bonds_.end(), bond) == bonds_.end()) {
        bonds_.push_back(bond);
    }
}

void Molecule::addBend(Bend* bend) {
    if (std::find(bends_.begin(), bends_.end(), bend) == bends_.end()) {
        bends_.push_back(bend);
    }
}

void Molecule::addTorsion(Torsion* torsion) {
    if (std::find(torsions_.begin(), torsions_.end(), torsion) == torsions_.end()) {
        torsions_.push_back(torsion);
    }
}

void Molecule::addRigidBody(RigidBody *rb) {
    if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) == rigidBodies_.end()) {
        rigidBodies_.push_back(rb);
    }
}

void Molecule::addCutoffGroup(CutoffGroup* cp) {
    if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) == cutoffGroups_.end()) {
        cutoffGroups_.push_back(cp);
    }

}

void Molecule::complete() {
    
    std::set<Atom*> allAtoms;
    allAtoms.insert(atoms_.begin(), atoms_.end());

    std::set<Atom*> rigidAtoms;
    RigidBody* rb;
    std::vector<RigidBody*>::iterator rbIter;

    
    for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
        rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter());
    }

    //find all free atoms (which do not belong to rigid bodies)  
    //performs the "difference" operation from set theory,  the output range contains a copy of every
    //element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in 
    //[rigidAtoms.begin(), rigidAtoms.end()).
    std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(),
                            std::back_inserter(integrableObjects_));

    if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) {
        //Some atoms in rigidAtoms are not in allAtoms, something must be wrong
    }

    integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end());
}

Atom* Molecule::beginAtom(std::vector<Atom*>::iterator& i) {
    i = atoms_.begin();
    return (i == atoms_.end()) ? NULL : *i;
}

Atom* Molecule::nextAtom(std::vector<Atom*>::iterator& i) {
    ++i;
    return (i == atoms_.end()) ? NULL : *i;    
}

Bond* Molecule::beginBond(std::vector<Bond*>::iterator& i) {
    i = bonds_.begin();
    return (i == bonds_.end()) ? NULL : *i;
}

Bond* Molecule::nextBond(std::vector<Bond*>::iterator& i) {
    ++i;
    return (i == bonds_.end()) ? NULL : *i;    

}


Bend* Molecule::beginBend(std::vector<Bend*>::iterator& i) {
    i = bends_.begin();
    return (i == bends_.end()) ? NULL : *i;
}

Bend* Molecule::nextBend(std::vector<Bend*>::iterator& i) {
    ++i;
    return (i == bends_.end()) ? NULL : *i;    
}

Torsion* Molecule::beginTorsion(std::vector<Torsion*>::iterator& i) {
    i = torsions_.begin();
    return (i == torsions_.end()) ? NULL : *i;
}

Torsion* Molecule::nextTorsion(std::vector<Torsion*>::iterator& i) {
    ++i;
    return (i == torsions_.end()) ? NULL : *i;    
}    

RigidBody* Molecule::beginRigidBody(std::vector<RigidBody*>::iterator& i) {
    i = rigidBodies_.begin();
    return (i == rigidBodies_.end()) ? NULL : *i;
}

RigidBody* Molecule::nextRigidBody(std::vector<RigidBody*>::iterator& i) {
    ++i;
    return (i == rigidBodies_.end()) ? NULL : *i;    
}

StuntDouble* Molecule::beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
    i = integrableObjects_.begin();
    return (i == integrableObjects_.end()) ? NULL : *i;
}

StuntDouble* Molecule::nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
    ++i;
    return (i == integrableObjects_.end()) ? NULL : *i;    
}    

CutoffGroup* Molecule::beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
    i = cutoffGroups_.begin();
    return (i == cutoffGroups_.end()) ? NULL : *i;
}

CutoffGroup* Molecule::nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {            
    ++i;
    return (i == cutoffGroups_.end()) ? NULL : *i;    
} 

void Molecule::calcForces() {
    RigidBody* rb;
    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    std::vector<RigidBody*>::iterator rbIter;
    std::vector<Bond*>::iterator bondIter;;
    std::vector<Bend*>::iterator bendIter;
    std::vector<Torsion*>::iterator torsionIter;

    for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
        rb->updateAtoms();
    }

    for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
        bond->calc_forces();
    }

    for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
        bend->calc_forces();
    }

    for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) {
        torsion->calc_forces();
    }
    
}

double Molecule::getPotential() {
    //RigidBody* rb;
    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    //std::vector<RigidBody*> rbIter;
    std::vector<Bond*>::iterator bondIter;;
    std::vector<Bend*>::iterator bendIter;
    std::vector<Torsion*>::iterator torsionIter;

    double potential = 0;
    
    //for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
    //    rb->updateAtoms();
    //}

    for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
        potential += bond->get_potential();
    }

    for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
        potential += bend->get_potential();
    }

    for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) {
        potential += torsion->get_potential();
    }
    
    return potential;
}

Vector3d Molecule::getCom() {
    StuntDouble* sd;
    std::vector<StuntDouble*>::iterator i;
    Vector3d com;
    double totalMass = 0;
    double mass;
    
    for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
        mass = sd->getMass();
        totalMass += mass;
        com += sd->getPos() * mass;    
    }

    com /= totalMass;

    return com;
}

void Molecule::moveCom(const Vector3d& delta) {
    StuntDouble* sd;
    std::vector<StuntDouble*>::iterator i;
    
    for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
        sd->setPos(sd->getPos() + delta);
    }

}

Vector3d Molecule::getComVel() {
    StuntDouble* sd;
    std::vector<StuntDouble*>::iterator i;
    Vector3d velCom;
    double totalMass = 0;
    double mass;
    
    for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
        mass = sd->getMass();
        totalMass += mass;
        velCom += sd->getVel() * mass;    
    }

    velCom /= totalMass;

    return velCom;
}

std::ostream& operator <<(std::ostream& o, Molecule& mol) {
    o << std::endl;
    o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl;
    o << mol.getNAtoms() << " atoms" << std::endl;
    o << mol.getNBonds() << " bonds" << std::endl;
    o << mol.getNBends() << " bends" << std::endl;
    o << mol.getNTorsions() << " torsions" << std::endl;
    o << mol.getNRigidBodies() << " rigid bodies" << std::endl;
    o << mol.getNIntegrableObjects() << "integrable objects" << std::endl;
    o << mol.getNCutoffGroups() << "cutoff groups" << std::endl;

    return o;
}

}//end namespace oopse
Revision:	1701
Committed:	Wed Nov 3 16:08:43 2004 UTC (19 years, 8 months ago) by tim
File size:	9213 byte(s)
Log Message:	mess up ......
#	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 Molecule.cpp
28	* @author tlin
29	* @date 10/28/2004
30	* @version 1.0
31	*/
32
33	#include <algorithm>
34	#include <set>
35
36	#include "primitives/Molecule.hpp"
37	#include "utils/MemoryUtils.hpp"
38
39	namespace oopse {
40
41	Molecule::~Molecule() {
42
43	MemoryUtils::deleteVectorOfPointer(atoms_);
44	MemoryUtils::deleteVectorOfPointer(bonds_);
45	MemoryUtils::deleteVectorOfPointer(bends_);
46	MemoryUtils::deleteVectorOfPointer(torsions_);
47	MemoryUtils::deleteVectorOfPointer(rigidBodies_);
48	MemoryUtils::deleteVectorOfPointer(cutoffGroups_);
49
50	//integrableObjects_ don't own the objects
51	integrableObjects_.clear();
52
53	}
54
55	void Molecule::addAtom(Atom* atom) {
56	if (std::find(atoms_.begin(), atoms_.end(), atom) == atoms_.end()) {
57	atoms_.push_back(atom);
58	}
59	}
60
61	void Molecule::addBond(Bond* bond) {
62	if (std::find(bonds_.begin(), bonds_.end(), bond) == bonds_.end()) {
63	bonds_.push_back(bond);
64	}
65	}
66
67	void Molecule::addBend(Bend* bend) {
68	if (std::find(bends_.begin(), bends_.end(), bend) == bends_.end()) {
69	bends_.push_back(bend);
70	}
71	}
72
73	void Molecule::addTorsion(Torsion* torsion) {
74	if (std::find(torsions_.begin(), torsions_.end(), torsion) == torsions_.end()) {
75	torsions_.push_back(torsion);
76	}
77	}
78
79	void Molecule::addRigidBody(RigidBody *rb) {
80	if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) == rigidBodies_.end()) {
81	rigidBodies_.push_back(rb);
82	}
83	}
84
85	void Molecule::addCutoffGroup(CutoffGroup* cp) {
86	if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) == cutoffGroups_.end()) {
87	cutoffGroups_.push_back(cp);
88	}
89
90	}
91
92	void Molecule::complete() {
93
94	std::set<Atom*> allAtoms;
95	allAtoms.insert(atoms_.begin(), atoms_.end());
96
97	std::set<Atom*> rigidAtoms;
98	RigidBody* rb;
99	std::vector<RigidBody*>::iterator rbIter;
100
101
102	for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
103	rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter());
104	}
105
106	//find all free atoms (which do not belong to rigid bodies)
107	//performs the "difference" operation from set theory, the output range contains a copy of every
108	//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in
109	//[rigidAtoms.begin(), rigidAtoms.end()).
110	std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(),
111	std::back_inserter(integrableObjects_));
112
113	if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) {
114	//Some atoms in rigidAtoms are not in allAtoms, something must be wrong
115	}
116
117	integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end());
118	}
119
120	Atom* Molecule::beginAtom(std::vector<Atom*>::iterator& i) {
121	i = atoms_.begin();
122	return (i == atoms_.end()) ? NULL : *i;
123	}
124
125	Atom* Molecule::nextAtom(std::vector<Atom*>::iterator& i) {
126	++i;
127	return (i == atoms_.end()) ? NULL : *i;
128	}
129
130	Bond* Molecule::beginBond(std::vector<Bond*>::iterator& i) {
131	i = bonds_.begin();
132	return (i == bonds_.end()) ? NULL : *i;
133	}
134
135	Bond* Molecule::nextBond(std::vector<Bond*>::iterator& i) {
136	++i;
137	return (i == bonds_.end()) ? NULL : *i;
138
139	}
140
141
142	Bend* Molecule::beginBend(std::vector<Bend*>::iterator& i) {
143	i = bends_.begin();
144	return (i == bends_.end()) ? NULL : *i;
145	}
146
147	Bend* Molecule::nextBend(std::vector<Bend*>::iterator& i) {
148	++i;
149	return (i == bends_.end()) ? NULL : *i;
150	}
151
152	Torsion* Molecule::beginTorsion(std::vector<Torsion*>::iterator& i) {
153	i = torsions_.begin();
154	return (i == torsions_.end()) ? NULL : *i;
155	}
156
157	Torsion* Molecule::nextTorsion(std::vector<Torsion*>::iterator& i) {
158	++i;
159	return (i == torsions_.end()) ? NULL : *i;
160	}
161
162	RigidBody* Molecule::beginRigidBody(std::vector<RigidBody*>::iterator& i) {
163	i = rigidBodies_.begin();
164	return (i == rigidBodies_.end()) ? NULL : *i;
165	}
166
167	RigidBody* Molecule::nextRigidBody(std::vector<RigidBody*>::iterator& i) {
168	++i;
169	return (i == rigidBodies_.end()) ? NULL : *i;
170	}
171
172	StuntDouble* Molecule::beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
173	i = integrableObjects_.begin();
174	return (i == integrableObjects_.end()) ? NULL : *i;
175	}
176
177	StuntDouble* Molecule::nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
178	++i;
179	return (i == integrableObjects_.end()) ? NULL : *i;
180	}
181
182	CutoffGroup* Molecule::beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
183	i = cutoffGroups_.begin();
184	return (i == cutoffGroups_.end()) ? NULL : *i;
185	}
186
187	CutoffGroup* Molecule::nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
188	++i;
189	return (i == cutoffGroups_.end()) ? NULL : *i;
190	}
191
192	void Molecule::calcForces() {
193	RigidBody* rb;
194	Bond* bond;
195	Bend* bend;
196	Torsion* torsion;
197	std::vector<RigidBody*>::iterator rbIter;
198	std::vector<Bond*>::iterator bondIter;;
199	std::vector<Bend*>::iterator bendIter;
200	std::vector<Torsion*>::iterator torsionIter;
201
202	for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
203	rb->updateAtoms();
204	}
205
206	for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
207	bond->calc_forces();
208	}
209
210	for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
211	bend->calc_forces();
212	}
213
214	for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) {
215	torsion->calc_forces();
216	}
217
218	}
219
220	double Molecule::getPotential() {
221	//RigidBody* rb;
222	Bond* bond;
223	Bend* bend;
224	Torsion* torsion;
225	//std::vector<RigidBody*> rbIter;
226	std::vector<Bond*>::iterator bondIter;;
227	std::vector<Bend*>::iterator bendIter;
228	std::vector<Torsion*>::iterator torsionIter;
229
230	double potential = 0;
231
232	//for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
233	// rb->updateAtoms();
234	//}
235
236	for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
237	potential += bond->get_potential();
238	}
239
240	for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
241	potential += bend->get_potential();
242	}
243
244	for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) {
245	potential += torsion->get_potential();
246	}
247
248	return potential;
249	}
250
251	Vector3d Molecule::getCom() {
252	StuntDouble* sd;
253	std::vector<StuntDouble*>::iterator i;
254	Vector3d com;
255	double totalMass = 0;
256	double mass;
257
258	for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
259	mass = sd->getMass();
260	totalMass += mass;
261	com += sd->getPos() * mass;
262	}
263
264	com /= totalMass;
265
266	return com;
267	}
268
269	void Molecule::moveCom(const Vector3d& delta) {
270	StuntDouble* sd;
271	std::vector<StuntDouble*>::iterator i;
272
273	for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
274	sd->setPos(sd->getPos() + delta);
275	}
276
277	}
278
279	Vector3d Molecule::getComVel() {
280	StuntDouble* sd;
281	std::vector<StuntDouble*>::iterator i;
282	Vector3d velCom;
283	double totalMass = 0;
284	double mass;
285
286	for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
287	mass = sd->getMass();
288	totalMass += mass;
289	velCom += sd->getVel() * mass;
290	}
291
292	velCom /= totalMass;
293
294	return velCom;
295	}
296
297	std::ostream& operator <<(std::ostream& o, Molecule& mol) {
298	o << std::endl;
299	o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl;
300	o << mol.getNAtoms() << " atoms" << std::endl;
301	o << mol.getNBonds() << " bonds" << std::endl;
302	o << mol.getNBends() << " bends" << std::endl;
303	o << mol.getNTorsions() << " torsions" << std::endl;
304	o << mol.getNRigidBodies() << " rigid bodies" << std::endl;
305	o << mol.getNIntegrableObjects() << "integrable objects" << std::endl;
306	o << mol.getNCutoffGroups() << "cutoff groups" << std::endl;
307
308	return o;
309	}
310
311	}//end namespace oopse