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root/OpenMD/branches/development/src/brains/SimInfo.cpp

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trunk/src/brains/SimInfo.cpp (file contents), Revision 331 by tim, Sun Feb 13 21:18:27 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 48 | Line 48
48
49		#include <algorithm>
50		#include <set>
51	+	#include <map>
52
53		#include "brains/SimInfo.hpp"
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56	<	#include "UseTheForce/doForces_interface.h"
56	<	#include "UseTheForce/notifyCutoffs_interface.h"
56	>	#include "primitives/StuntDouble.hpp"
57		#include "utils/MemoryUtils.hpp"
58		#include "utils/simError.h"
59		#include "selection/SelectionManager.hpp"
60	+	#include "io/ForceFieldOptions.hpp"
61	+	#include "UseTheForce/ForceField.hpp"
62	+	#include "nonbonded/SwitchingFunction.hpp"
63
64	<	#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
67	<	#endif
68	<
69	<	namespace oopse {
70	<
71	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
72	<	ForceField* ff, Globals* simParams) :
73	<	forceField_(ff), simParams_(simParams),
74	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
75	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
76	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
74	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
75	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
76	<	sman_(NULL), fortranInitialized_(false), selectMan_(NULL) {
77	<
78	<
79	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
64	>	using namespace std;
65	>	namespace OpenMD {
66	>
67	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
68	>	forceField_(ff), simParams_(simParams),
69	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
70	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
71	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
72	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
73	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
74	>	nConstraints_(0), sman_(NULL), topologyDone_(false),
75	>	calcBoxDipole_(false), useAtomicVirial_(true) {
76	>
77		MoleculeStamp* molStamp;
78		int nMolWithSameStamp;
79		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
80	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
80	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
81		CutoffGroupStamp* cgStamp;
82		RigidBodyStamp* rbStamp;
83		int nRigidAtoms = 0;
84
85	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
86	<	molStamp = i->first;
87	<	nMolWithSameStamp = i->second;
88	<
89	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
90	<
91	<	//calculate atoms in molecules
92	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
93	<
94	<
95	<	//calculate atoms in cutoff groups
96	<	int nAtomsInGroups = 0;
97	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
98	<
99	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
100	<	cgStamp = molStamp->getCutoffGroup(j);
101	<	nAtomsInGroups += cgStamp->getNMembers();
102	<	}
103	<
104	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
105	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
106	<
107	<	//calculate atoms in rigid bodies
108	<	int nAtomsInRigidBodies = 0;
109	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
110	<
111	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
112	<	rbStamp = molStamp->getRigidBody(j);
113	<	nAtomsInRigidBodies += rbStamp->getNMembers();
114	<	}
115	<
116	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
117	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
118	<
85	>	vector<Component*> components = simParams->getComponents();
86	>
87	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
88	>	molStamp = (*i)->getMoleculeStamp();
89	>	nMolWithSameStamp = (*i)->getNMol();
90	>
91	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
92	>
93	>	//calculate atoms in molecules
94	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
95	>
96	>	//calculate atoms in cutoff groups
97	>	int nAtomsInGroups = 0;
98	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
99	>
100	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
101	>	cgStamp = molStamp->getCutoffGroupStamp(j);
102	>	nAtomsInGroups += cgStamp->getNMembers();
103	>	}
104	>
105	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
106	>
107	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
108	>
109	>	//calculate atoms in rigid bodies
110	>	int nAtomsInRigidBodies = 0;
111	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
112	>
113	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
114	>	rbStamp = molStamp->getRigidBodyStamp(j);
115	>	nAtomsInRigidBodies += rbStamp->getNMembers();
116	>	}
117	>
118	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
119	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
120	>
121		}
122	+
123	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
124	+	//group therefore the total number of cutoff groups in the system is
125	+	//equal to the total number of atoms minus number of atoms belong to
126	+	//cutoff group defined in meta-data file plus the number of cutoff
127	+	//groups defined in meta-data file
128	+	std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
129	+	std::cerr << "nCA = " << nCutoffAtoms << "\n";
130	+	std::cerr << "nG = " << nGroups << "\n";
131
124	–	//every free atom (atom does not belong to cutoff groups) is a cutoff group
125	–	//therefore the total number of cutoff groups in the system is equal to
126	–	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
127	–	//file plus the number of cutoff groups defined in meta-data file
132		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
133
134	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
135	<	//therefore the total number of  integrable objects in the system is equal to
136	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
137	<	//file plus the number of  rigid bodies defined in meta-data file
138	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
139	<
134	>	std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
135	>
136	>	//every free atom (atom does not belong to rigid bodies) is an
137	>	//integrable object therefore the total number of integrable objects
138	>	//in the system is equal to the total number of atoms minus number of
139	>	//atoms belong to rigid body defined in meta-data file plus the number
140	>	//of rigid bodies defined in meta-data file
141	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
142	>	+ nGlobalRigidBodies_;
143	>
144		nGlobalMols_ = molStampIds_.size();
137	–
138	–	#ifdef IS_MPI
145		molToProcMap_.resize(nGlobalMols_);
146	<	#endif
147	<
148	<	selectMan_ = new SelectionManager(this);
149	<	selectMan_->selectAll();
150	<	}
151	<
152	<	SimInfo::~SimInfo() {
153	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
154	<
149	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
150	<
146	>	}
147	>
148	>	SimInfo::~SimInfo() {
149	>	map<int, Molecule*>::iterator i;
150	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
151	>	delete i->second;
152	>	}
153	>	molecules_.clear();
154	>
155		delete sman_;
156		delete simParams_;
157		delete forceField_;
158	<	delete selectMan_;
155	<	}
158	>	}
159
157	–	int SimInfo::getNGlobalConstraints() {
158	–	int nGlobalConstraints;
159	–	#ifdef IS_MPI
160	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
161	–	MPI_COMM_WORLD);
162	–	#else
163	–	nGlobalConstraints =  nConstraints_;
164	–	#endif
165	–	return nGlobalConstraints;
166	–	}
160
161	<	bool SimInfo::addMolecule(Molecule* mol) {
161	>	bool SimInfo::addMolecule(Molecule* mol) {
162		MoleculeIterator i;
163	<
163	>
164		i = molecules_.find(mol->getGlobalIndex());
165		if (i == molecules_.end() ) {
166	<
167	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
168	<
169	<	nAtoms_ += mol->getNAtoms();
170	<	nBonds_ += mol->getNBonds();
171	<	nBends_ += mol->getNBends();
172	<	nTorsions_ += mol->getNTorsions();
173	<	nRigidBodies_ += mol->getNRigidBodies();
174	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
175	<	nCutoffGroups_ += mol->getNCutoffGroups();
176	<	nConstraints_ += mol->getNConstraintPairs();
177	<
178	<	addExcludePairs(mol);
179	<
180	<	return true;
181	<	} else {
182	<	return false;
166	>
167	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
168	>
169	>	nAtoms_ += mol->getNAtoms();
170	>	nBonds_ += mol->getNBonds();
171	>	nBends_ += mol->getNBends();
172	>	nTorsions_ += mol->getNTorsions();
173	>	nInversions_ += mol->getNInversions();
174	>	nRigidBodies_ += mol->getNRigidBodies();
175	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
176	>	nCutoffGroups_ += mol->getNCutoffGroups();
177	>	nConstraints_ += mol->getNConstraintPairs();
178	>
179	>	addInteractionPairs(mol);
180	>
181	>	return true;
182	>	} else {
183	>	return false;
184		}
185	<	}
186	<
187	<	bool SimInfo::removeMolecule(Molecule* mol) {
185	>	}
186	>
187	>	bool SimInfo::removeMolecule(Molecule* mol) {
188		MoleculeIterator i;
189		i = molecules_.find(mol->getGlobalIndex());
190
191		if (i != molecules_.end() ) {
192
193	<	assert(mol == i->second);
193	>	assert(mol == i->second);
194
195	<	nAtoms_ -= mol->getNAtoms();
196	<	nBonds_ -= mol->getNBonds();
197	<	nBends_ -= mol->getNBends();
198	<	nTorsions_ -= mol->getNTorsions();
199	<	nRigidBodies_ -= mol->getNRigidBodies();
200	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
201	<	nCutoffGroups_ -= mol->getNCutoffGroups();
202	<	nConstraints_ -= mol->getNConstraintPairs();
195	>	nAtoms_ -= mol->getNAtoms();
196	>	nBonds_ -= mol->getNBonds();
197	>	nBends_ -= mol->getNBends();
198	>	nTorsions_ -= mol->getNTorsions();
199	>	nInversions_ -= mol->getNInversions();
200	>	nRigidBodies_ -= mol->getNRigidBodies();
201	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
202	>	nCutoffGroups_ -= mol->getNCutoffGroups();
203	>	nConstraints_ -= mol->getNConstraintPairs();
204
205	<	removeExcludePairs(mol);
206	<	molecules_.erase(mol->getGlobalIndex());
205	>	removeInteractionPairs(mol);
206	>	molecules_.erase(mol->getGlobalIndex());
207
208	<	delete mol;
208	>	delete mol;
209
210	<	return true;
210	>	return true;
211		} else {
212	<	return false;
212	>	return false;
213		}
214	+	}
215
220	–
221	–	}
222	–
216
217	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
217	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
218		i = molecules_.begin();
219		return i == molecules_.end() ? NULL : i->second;
220	<	}
220	>	}
221
222	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
222	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
223		++i;
224		return i == molecules_.end() ? NULL : i->second;
225	<	}
225	>	}
226
227
228	<	void SimInfo::calcNdf() {
228	>	void SimInfo::calcNdf() {
229		int ndf_local;
230		MoleculeIterator i;
231	<	std::vector<StuntDouble*>::iterator j;
231	>	vector<StuntDouble*>::iterator j;
232		Molecule* mol;
233		StuntDouble* integrableObject;
234
235		ndf_local = 0;
236
237		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
238	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
239	<	integrableObject = mol->nextIntegrableObject(j)) {
238	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
239	>	integrableObject = mol->nextIntegrableObject(j)) {
240
241	<	ndf_local += 3;
241	>	ndf_local += 3;
242
243	<	if (integrableObject->isDirectional()) {
244	<	if (integrableObject->isLinear()) {
245	<	ndf_local += 2;
246	<	} else {
247	<	ndf_local += 3;
248	<	}
249	<	}
243	>	if (integrableObject->isDirectional()) {
244	>	if (integrableObject->isLinear()) {
245	>	ndf_local += 2;
246	>	} else {
247	>	ndf_local += 3;
248	>	}
249	>	}
250
251	<	}//end for (integrableObject)
252	<	}// end for (mol)
251	>	}
252	>	}
253
254		// n_constraints is local, so subtract them on each processor
255		ndf_local -= nConstraints_;
#	Line 271 | Line 264 | void SimInfo::calcNdf() {
264		// entire system:
265		ndf_ = ndf_ - 3 - nZconstraint_;
266
267	<	}
267	>	}
268
269	<	void SimInfo::calcNdfRaw() {
269	>	int SimInfo::getFdf() {
270	>	#ifdef IS_MPI
271	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
272	>	#else
273	>	fdf_ = fdf_local;
274	>	#endif
275	>	return fdf_;
276	>	}
277	>
278	>	void SimInfo::calcNdfRaw() {
279		int ndfRaw_local;
280
281		MoleculeIterator i;
282	<	std::vector<StuntDouble*>::iterator j;
282	>	vector<StuntDouble*>::iterator j;
283		Molecule* mol;
284		StuntDouble* integrableObject;
285
#	Line 285 | Line 287 | void SimInfo::calcNdfRaw() {
287		ndfRaw_local = 0;
288
289		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
290	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291	<	integrableObject = mol->nextIntegrableObject(j)) {
290	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291	>	integrableObject = mol->nextIntegrableObject(j)) {
292
293	<	ndfRaw_local += 3;
293	>	ndfRaw_local += 3;
294
295	<	if (integrableObject->isDirectional()) {
296	<	if (integrableObject->isLinear()) {
297	<	ndfRaw_local += 2;
298	<	} else {
299	<	ndfRaw_local += 3;
300	<	}
301	<	}
295	>	if (integrableObject->isDirectional()) {
296	>	if (integrableObject->isLinear()) {
297	>	ndfRaw_local += 2;
298	>	} else {
299	>	ndfRaw_local += 3;
300	>	}
301	>	}
302
303	<	}
303	>	}
304		}
305
306		#ifdef IS_MPI
#	Line 306 | Line 308 | void SimInfo::calcNdfRaw() {
308		#else
309		ndfRaw_ = ndfRaw_local;
310		#endif
311	<	}
311	>	}
312
313	<	void SimInfo::calcNdfTrans() {
313	>	void SimInfo::calcNdfTrans() {
314		int ndfTrans_local;
315
316		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 322 | Line 324 | void SimInfo::calcNdfTrans() {
324
325		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
326
327	<	}
327	>	}
328
329	<	void SimInfo::addExcludePairs(Molecule* mol) {
330	<	std::vector<Bond*>::iterator bondIter;
331	<	std::vector<Bend*>::iterator bendIter;
332	<	std::vector<Torsion*>::iterator torsionIter;
329	>	void SimInfo::addInteractionPairs(Molecule* mol) {
330	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
331	>	vector<Bond*>::iterator bondIter;
332	>	vector<Bend*>::iterator bendIter;
333	>	vector<Torsion*>::iterator torsionIter;
334	>	vector<Inversion*>::iterator inversionIter;
335		Bond* bond;
336		Bend* bend;
337		Torsion* torsion;
338	+	Inversion* inversion;
339		int a;
340		int b;
341		int c;
342		int d;
338	–
339	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
340	–	a = bond->getAtomA()->getGlobalIndex();
341	–	b = bond->getAtomB()->getGlobalIndex();
342	–	exclude_.addPair(a, b);
343	–	}
343
344	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
345	<	a = bend->getAtomA()->getGlobalIndex();
346	<	b = bend->getAtomB()->getGlobalIndex();
347	<	c = bend->getAtomC()->getGlobalIndex();
344	>	// atomGroups can be used to add special interaction maps between
345	>	// groups of atoms that are in two separate rigid bodies.
346	>	// However, most site-site interactions between two rigid bodies
347	>	// are probably not special, just the ones between the physically
348	>	// bonded atoms.  Interactions *within* a single rigid body should
349	>	// always be excluded.  These are done at the bottom of this
350	>	// function.
351
352	<	exclude_.addPair(a, b);
353	<	exclude_.addPair(a, c);
354	<	exclude_.addPair(b, c);
355	<	}
356	<
357	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
358	<	a = torsion->getAtomA()->getGlobalIndex();
359	<	b = torsion->getAtomB()->getGlobalIndex();
360	<	c = torsion->getAtomC()->getGlobalIndex();
361	<	d = torsion->getAtomD()->getGlobalIndex();
352	>	map<int, set<int> > atomGroups;
353	>	Molecule::RigidBodyIterator rbIter;
354	>	RigidBody* rb;
355	>	Molecule::IntegrableObjectIterator ii;
356	>	StuntDouble* integrableObject;
357	>
358	>	for (integrableObject = mol->beginIntegrableObject(ii);
359	>	integrableObject != NULL;
360	>	integrableObject = mol->nextIntegrableObject(ii)) {
361	>
362	>	if (integrableObject->isRigidBody()) {
363	>	rb = static_cast<RigidBody*>(integrableObject);
364	>	vector<Atom*> atoms = rb->getAtoms();
365	>	set<int> rigidAtoms;
366	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
367	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
368	>	}
369	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
370	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
371	>	}
372	>	} else {
373	>	set<int> oneAtomSet;
374	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
375	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
376	>	}
377	>	}
378	>
379	>	for (bond= mol->beginBond(bondIter); bond != NULL;
380	>	bond = mol->nextBond(bondIter)) {
381
382	<	exclude_.addPair(a, b);
383	<	exclude_.addPair(a, c);
384	<	exclude_.addPair(a, d);
385	<	exclude_.addPair(b, c);
386	<	exclude_.addPair(b, d);
387	<	exclude_.addPair(c, d);
382	>	a = bond->getAtomA()->getGlobalIndex();
383	>	b = bond->getAtomB()->getGlobalIndex();
384	>
385	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
386	>	oneTwoInteractions_.addPair(a, b);
387	>	} else {
388	>	excludedInteractions_.addPair(a, b);
389	>	}
390		}
391
392	<
393	<	}
392	>	for (bend= mol->beginBend(bendIter); bend != NULL;
393	>	bend = mol->nextBend(bendIter)) {
394
395	<	void SimInfo::removeExcludePairs(Molecule* mol) {
396	<	std::vector<Bond*>::iterator bondIter;
397	<	std::vector<Bend*>::iterator bendIter;
398	<	std::vector<Torsion*>::iterator torsionIter;
395	>	a = bend->getAtomA()->getGlobalIndex();
396	>	b = bend->getAtomB()->getGlobalIndex();
397	>	c = bend->getAtomC()->getGlobalIndex();
398	>
399	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
400	>	oneTwoInteractions_.addPair(a, b);
401	>	oneTwoInteractions_.addPair(b, c);
402	>	} else {
403	>	excludedInteractions_.addPair(a, b);
404	>	excludedInteractions_.addPair(b, c);
405	>	}
406	>
407	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
408	>	oneThreeInteractions_.addPair(a, c);
409	>	} else {
410	>	excludedInteractions_.addPair(a, c);
411	>	}
412	>	}
413	>
414	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
415	>	torsion = mol->nextTorsion(torsionIter)) {
416	>
417	>	a = torsion->getAtomA()->getGlobalIndex();
418	>	b = torsion->getAtomB()->getGlobalIndex();
419	>	c = torsion->getAtomC()->getGlobalIndex();
420	>	d = torsion->getAtomD()->getGlobalIndex();
421	>
422	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
423	>	oneTwoInteractions_.addPair(a, b);
424	>	oneTwoInteractions_.addPair(b, c);
425	>	oneTwoInteractions_.addPair(c, d);
426	>	} else {
427	>	excludedInteractions_.addPair(a, b);
428	>	excludedInteractions_.addPair(b, c);
429	>	excludedInteractions_.addPair(c, d);
430	>	}
431	>
432	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
433	>	oneThreeInteractions_.addPair(a, c);
434	>	oneThreeInteractions_.addPair(b, d);
435	>	} else {
436	>	excludedInteractions_.addPair(a, c);
437	>	excludedInteractions_.addPair(b, d);
438	>	}
439	>
440	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
441	>	oneFourInteractions_.addPair(a, d);
442	>	} else {
443	>	excludedInteractions_.addPair(a, d);
444	>	}
445	>	}
446	>
447	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
448	>	inversion = mol->nextInversion(inversionIter)) {
449	>
450	>	a = inversion->getAtomA()->getGlobalIndex();
451	>	b = inversion->getAtomB()->getGlobalIndex();
452	>	c = inversion->getAtomC()->getGlobalIndex();
453	>	d = inversion->getAtomD()->getGlobalIndex();
454	>
455	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
456	>	oneTwoInteractions_.addPair(a, b);
457	>	oneTwoInteractions_.addPair(a, c);
458	>	oneTwoInteractions_.addPair(a, d);
459	>	} else {
460	>	excludedInteractions_.addPair(a, b);
461	>	excludedInteractions_.addPair(a, c);
462	>	excludedInteractions_.addPair(a, d);
463	>	}
464	>
465	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
466	>	oneThreeInteractions_.addPair(b, c);
467	>	oneThreeInteractions_.addPair(b, d);
468	>	oneThreeInteractions_.addPair(c, d);
469	>	} else {
470	>	excludedInteractions_.addPair(b, c);
471	>	excludedInteractions_.addPair(b, d);
472	>	excludedInteractions_.addPair(c, d);
473	>	}
474	>	}
475	>
476	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
477	>	rb = mol->nextRigidBody(rbIter)) {
478	>	vector<Atom*> atoms = rb->getAtoms();
479	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
480	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
481	>	a = atoms[i]->getGlobalIndex();
482	>	b = atoms[j]->getGlobalIndex();
483	>	excludedInteractions_.addPair(a, b);
484	>	}
485	>	}
486	>	}
487	>
488	>	}
489	>
490	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
491	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
492	>	vector<Bond*>::iterator bondIter;
493	>	vector<Bend*>::iterator bendIter;
494	>	vector<Torsion*>::iterator torsionIter;
495	>	vector<Inversion*>::iterator inversionIter;
496		Bond* bond;
497		Bend* bend;
498		Torsion* torsion;
499	+	Inversion* inversion;
500		int a;
501		int b;
502		int c;
503		int d;
504	+
505	+	map<int, set<int> > atomGroups;
506	+	Molecule::RigidBodyIterator rbIter;
507	+	RigidBody* rb;
508	+	Molecule::IntegrableObjectIterator ii;
509	+	StuntDouble* integrableObject;
510
511	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
512	<	a = bond->getAtomA()->getGlobalIndex();
513	<	b = bond->getAtomB()->getGlobalIndex();
514	<	exclude_.removePair(a, b);
511	>	for (integrableObject = mol->beginIntegrableObject(ii);
512	>	integrableObject != NULL;
513	>	integrableObject = mol->nextIntegrableObject(ii)) {
514	>
515	>	if (integrableObject->isRigidBody()) {
516	>	rb = static_cast<RigidBody*>(integrableObject);
517	>	vector<Atom*> atoms = rb->getAtoms();
518	>	set<int> rigidAtoms;
519	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
520	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
521	>	}
522	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
523	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
524	>	}
525	>	} else {
526	>	set<int> oneAtomSet;
527	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
528	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
529	>	}
530	>	}
531	>
532	>	for (bond= mol->beginBond(bondIter); bond != NULL;
533	>	bond = mol->nextBond(bondIter)) {
534	>
535	>	a = bond->getAtomA()->getGlobalIndex();
536	>	b = bond->getAtomB()->getGlobalIndex();
537	>
538	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
539	>	oneTwoInteractions_.removePair(a, b);
540	>	} else {
541	>	excludedInteractions_.removePair(a, b);
542	>	}
543		}
544
545	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
546	<	a = bend->getAtomA()->getGlobalIndex();
392	<	b = bend->getAtomB()->getGlobalIndex();
393	<	c = bend->getAtomC()->getGlobalIndex();
545	>	for (bend= mol->beginBend(bendIter); bend != NULL;
546	>	bend = mol->nextBend(bendIter)) {
547
548	<	exclude_.removePair(a, b);
549	<	exclude_.removePair(a, c);
550	<	exclude_.removePair(b, c);
548	>	a = bend->getAtomA()->getGlobalIndex();
549	>	b = bend->getAtomB()->getGlobalIndex();
550	>	c = bend->getAtomC()->getGlobalIndex();
551	>
552	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
553	>	oneTwoInteractions_.removePair(a, b);
554	>	oneTwoInteractions_.removePair(b, c);
555	>	} else {
556	>	excludedInteractions_.removePair(a, b);
557	>	excludedInteractions_.removePair(b, c);
558	>	}
559	>
560	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
561	>	oneThreeInteractions_.removePair(a, c);
562	>	} else {
563	>	excludedInteractions_.removePair(a, c);
564	>	}
565		}
566
567	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
568	<	a = torsion->getAtomA()->getGlobalIndex();
402	<	b = torsion->getAtomB()->getGlobalIndex();
403	<	c = torsion->getAtomC()->getGlobalIndex();
404	<	d = torsion->getAtomD()->getGlobalIndex();
567	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
568	>	torsion = mol->nextTorsion(torsionIter)) {
569
570	<	exclude_.removePair(a, b);
571	<	exclude_.removePair(a, c);
572	<	exclude_.removePair(a, d);
573	<	exclude_.removePair(b, c);
574	<	exclude_.removePair(b, d);
575	<	exclude_.removePair(c, d);
570	>	a = torsion->getAtomA()->getGlobalIndex();
571	>	b = torsion->getAtomB()->getGlobalIndex();
572	>	c = torsion->getAtomC()->getGlobalIndex();
573	>	d = torsion->getAtomD()->getGlobalIndex();
574	>
575	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
576	>	oneTwoInteractions_.removePair(a, b);
577	>	oneTwoInteractions_.removePair(b, c);
578	>	oneTwoInteractions_.removePair(c, d);
579	>	} else {
580	>	excludedInteractions_.removePair(a, b);
581	>	excludedInteractions_.removePair(b, c);
582	>	excludedInteractions_.removePair(c, d);
583	>	}
584	>
585	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
586	>	oneThreeInteractions_.removePair(a, c);
587	>	oneThreeInteractions_.removePair(b, d);
588	>	} else {
589	>	excludedInteractions_.removePair(a, c);
590	>	excludedInteractions_.removePair(b, d);
591	>	}
592	>
593	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
594	>	oneFourInteractions_.removePair(a, d);
595	>	} else {
596	>	excludedInteractions_.removePair(a, d);
597	>	}
598		}
599
600	<	}
600	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
601	>	inversion = mol->nextInversion(inversionIter)) {
602
603	+	a = inversion->getAtomA()->getGlobalIndex();
604	+	b = inversion->getAtomB()->getGlobalIndex();
605	+	c = inversion->getAtomC()->getGlobalIndex();
606	+	d = inversion->getAtomD()->getGlobalIndex();
607
608	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
609	<	int curStampId;
608	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
609	>	oneTwoInteractions_.removePair(a, b);
610	>	oneTwoInteractions_.removePair(a, c);
611	>	oneTwoInteractions_.removePair(a, d);
612	>	} else {
613	>	excludedInteractions_.removePair(a, b);
614	>	excludedInteractions_.removePair(a, c);
615	>	excludedInteractions_.removePair(a, d);
616	>	}
617
618	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
619	+	oneThreeInteractions_.removePair(b, c);
620	+	oneThreeInteractions_.removePair(b, d);
621	+	oneThreeInteractions_.removePair(c, d);
622	+	} else {
623	+	excludedInteractions_.removePair(b, c);
624	+	excludedInteractions_.removePair(b, d);
625	+	excludedInteractions_.removePair(c, d);
626	+	}
627	+	}
628	+
629	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
630	+	rb = mol->nextRigidBody(rbIter)) {
631	+	vector<Atom*> atoms = rb->getAtoms();
632	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
633	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
634	+	a = atoms[i]->getGlobalIndex();
635	+	b = atoms[j]->getGlobalIndex();
636	+	excludedInteractions_.removePair(a, b);
637	+	}
638	+	}
639	+	}
640	+
641	+	}
642	+
643	+
644	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
645	+	int curStampId;
646	+
647		//index from 0
648		curStampId = moleculeStamps_.size();
649
650		moleculeStamps_.push_back(molStamp);
651		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
652	<	}
652	>	}
653
427	–	void SimInfo::update() {
654
655	<	setupSimType();
656	<
657	<	#ifdef IS_MPI
658	<	setupFortranParallel();
659	<	#endif
660	<
661	<	setupFortranSim();
662	<
663	<	//setup fortran force field
438	<	/** @deprecate */
439	<	int isError = 0;
440	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
441	<	if(isError){
442	<	sprintf( painCave.errMsg,
443	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
444	<	painCave.isFatal = 1;
445	<	simError();
446	<	}
447	<
448	<
449	<	setupCutoff();
450	<
655	>	/**
656	>	* update
657	>	*
658	>	*  Performs the global checks and variable settings after the
659	>	*  objects have been created.
660	>	*
661	>	*/
662	>	void SimInfo::update() {
663	>	setupSimVariables();
664		calcNdf();
665		calcNdfRaw();
666		calcNdfTrans();
667	<
668	<	fortranInitialized_ = true;
669	<	}
670	<
671	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
667	>	}
668	>
669	>	/**
670	>	* getSimulatedAtomTypes
671	>	*
672	>	* Returns an STL set of AtomType* that are actually present in this
673	>	* simulation.  Must query all processors to assemble this information.
674	>	*
675	>	*/
676	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
677		SimInfo::MoleculeIterator mi;
678		Molecule* mol;
679		Molecule::AtomIterator ai;
680		Atom* atom;
681	<	std::set<AtomType*> atomTypes;
681	>	set<AtomType*> atomTypes;
682	>
683	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
684	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
685	>	atomTypes.insert(atom->getAtomType());
686	>	}
687	>	}
688
689	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
689	>	#ifdef IS_MPI
690
691	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
692	<	atomTypes.insert(atom->getAtomType());
469	<	}
470	<
471	<	}
691	>	// loop over the found atom types on this processor, and add their
692	>	// numerical idents to a vector:
693
694	<	return atomTypes;
695	<	}
694	>	vector<int> foundTypes;
695	>	set<AtomType*>::iterator i;
696	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
697	>	foundTypes.push_back( (*i)->getIdent() );
698
699	<	void SimInfo::setupSimType() {
700	<	std::set<AtomType*>::iterator i;
478	<	std::set<AtomType*> atomTypes;
479	<	atomTypes = getUniqueAtomTypes();
480	<
481	<	int useLennardJones = 0;
482	<	int useElectrostatic = 0;
483	<	int useEAM = 0;
484	<	int useCharge = 0;
485	<	int useDirectional = 0;
486	<	int useDipole = 0;
487	<	int useGayBerne = 0;
488	<	int useSticky = 0;
489	<	int useShape = 0;
490	<	int useFLARB = 0; //it is not in AtomType yet
491	<	int useDirectionalAtom = 0;
492	<	int useElectrostatics = 0;
493	<	//usePBC and useRF are from simParams
494	<	int usePBC = simParams_->getPBC();
495	<	int useRF = simParams_->getUseRF();
699	>	// count_local holds the number of found types on this processor
700	>	int count_local = foundTypes.size();
701
702	+	// count holds the total number of found types on all processors
703	+	// (some will be redundant with the ones found locally):
704	+	int count;
705	+	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
706	+
707	+	// create a vector to hold the globally found types, and resize it:
708	+	vector<int> ftGlobal;
709	+	ftGlobal.resize(count);
710	+	vector<int> counts;
711	+
712	+	int nproc = MPI::COMM_WORLD.Get_size();
713	+	counts.resize(nproc);
714	+	vector<int> disps;
715	+	disps.resize(nproc);
716	+
717	+	// now spray out the foundTypes to all the other processors:
718	+
719	+	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
720	+	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
721	+
722	+	// foundIdents is a stl set, so inserting an already found ident
723	+	// will have no effect.
724	+	set<int> foundIdents;
725	+	vector<int>::iterator j;
726	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
727	+	foundIdents.insert((*j));
728	+
729	+	// now iterate over the foundIdents and get the actual atom types
730	+	// that correspond to these:
731	+	set<int>::iterator it;
732	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
733	+	atomTypes.insert( forceField_->getAtomType((*it)) );
734	+
735	+	#endif
736	+
737	+	return atomTypes;
738	+	}
739	+
740	+	void SimInfo::setupSimVariables() {
741	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
742	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
743	+	calcBoxDipole_ = false;
744	+	if ( simParams_->haveAccumulateBoxDipole() )
745	+	if ( simParams_->getAccumulateBoxDipole() ) {
746	+	calcBoxDipole_ = true;
747	+	}
748	+
749	+	set<AtomType*>::iterator i;
750	+	set<AtomType*> atomTypes;
751	+	atomTypes = getSimulatedAtomTypes();
752	+	int usesElectrostatic = 0;
753	+	int usesMetallic = 0;
754	+	int usesDirectional = 0;
755		//loop over all of the atom types
756		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
757	<	useLennardJones |= (*i)->isLennardJones();
758	<	useElectrostatic |= (*i)->isElectrostatic();
759	<	useEAM |= (*i)->isEAM();
502	<	useCharge |= (*i)->isCharge();
503	<	useDirectional |= (*i)->isDirectional();
504	<	useDipole |= (*i)->isDipole();
505	<	useGayBerne |= (*i)->isGayBerne();
506	<	useSticky |= (*i)->isSticky();
507	<	useShape |= (*i)->isShape();
757	>	usesElectrostatic |= (*i)->isElectrostatic();
758	>	usesMetallic |= (*i)->isMetal();
759	>	usesDirectional |= (*i)->isDirectional();
760		}
761
510	–	if (useSticky || useDipole || useGayBerne || useShape) {
511	–	useDirectionalAtom = 1;
512	–	}
513	–
514	–	if (useCharge || useDipole) {
515	–	useElectrostatics = 1;
516	–	}
517	–
762		#ifdef IS_MPI
763		int temp;
764	+	temp = usesDirectional;
765	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766
767	<	temp = usePBC;
768	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767	>	temp = usesMetallic;
768	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769
770	<	temp = useDirectionalAtom;
771	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770	>	temp = usesElectrostatic;
771	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
772	>	#endif
773	>	}
774
527	–	temp = useLennardJones;
528	–	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
775
776	<	temp = useElectrostatics;
777	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776	>	vector<int> SimInfo::getGlobalAtomIndices() {
777	>	SimInfo::MoleculeIterator mi;
778	>	Molecule* mol;
779	>	Molecule::AtomIterator ai;
780	>	Atom* atom;
781
782	<	temp = useCharge;
534	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
535	<
536	<	temp = useDipole;
537	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
538	<
539	<	temp = useSticky;
540	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
541	<
542	<	temp = useGayBerne;
543	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
544	<
545	<	temp = useEAM;
546	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
547	<
548	<	temp = useShape;
549	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
550	<
551	<	temp = useFLARB;
552	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
553	<
554	<	temp = useRF;
555	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
782	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
783
784	<	#endif
784	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
785	>
786	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
787	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
788	>	}
789	>	}
790	>	return GlobalAtomIndices;
791	>	}
792
559	–	fInfo_.SIM_uses_PBC = usePBC;
560	–	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
561	–	fInfo_.SIM_uses_LennardJones = useLennardJones;
562	–	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
563	–	fInfo_.SIM_uses_Charges = useCharge;
564	–	fInfo_.SIM_uses_Dipoles = useDipole;
565	–	fInfo_.SIM_uses_Sticky = useSticky;
566	–	fInfo_.SIM_uses_GayBerne = useGayBerne;
567	–	fInfo_.SIM_uses_EAM = useEAM;
568	–	fInfo_.SIM_uses_Shapes = useShape;
569	–	fInfo_.SIM_uses_FLARB = useFLARB;
570	–	fInfo_.SIM_uses_RF = useRF;
793
794	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
794	>	vector<int> SimInfo::getGlobalGroupIndices() {
795	>	SimInfo::MoleculeIterator mi;
796	>	Molecule* mol;
797	>	Molecule::CutoffGroupIterator ci;
798	>	CutoffGroup* cg;
799
800	<	if (simParams_->haveDielectric()) {
801	<	fInfo_.dielect = simParams_->getDielectric();
802	<	} else {
803	<	sprintf(painCave.errMsg,
804	<	"SimSetup Error: No Dielectric constant was set.\n"
805	<	"\tYou are trying to use Reaction Field without"
806	<	"\tsetting a dielectric constant!\n");
807	<	painCave.isFatal = 1;
808	<	simError();
809	<	}
584	<
585	<	} else {
586	<	fInfo_.dielect = 0.0;
800	>	vector<int> GlobalGroupIndices;
801	>
802	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
803	>
804	>	//local index of cutoff group is trivial, it only depends on the
805	>	//order of travesing
806	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
807	>	cg = mol->nextCutoffGroup(ci)) {
808	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
809	>	}
810		}
811	+	return GlobalGroupIndices;
812	+	}
813
589	–	}
814
815	<	void SimInfo::setupFortranSim() {
816	<	int isError;
593	<	int nExclude;
594	<	std::vector<int> fortranGlobalGroupMembership;
595	<
596	<	nExclude = exclude_.getSize();
597	<	isError = 0;
815	>	void SimInfo::prepareTopology() {
816	>	int nExclude, nOneTwo, nOneThree, nOneFour;
817
599	–	//globalGroupMembership_ is filled by SimCreator
600	–	for (int i = 0; i < nGlobalAtoms_; i++) {
601	–	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
602	–	}
603	–
818		//calculate mass ratio of cutoff group
605	–	std::vector<double> mfact;
819		SimInfo::MoleculeIterator mi;
820		Molecule* mol;
821		Molecule::CutoffGroupIterator ci;
822		CutoffGroup* cg;
823		Molecule::AtomIterator ai;
824		Atom* atom;
825	<	double totalMass;
825	>	RealType totalMass;
826
827	<	//to avoid memory reallocation, reserve enough space for mfact
828	<	mfact.reserve(getNCutoffGroups());
827	>	//to avoid memory reallocation, reserve enough space for massFactors_
828	>	massFactors_.clear();
829	>	massFactors_.reserve(getNCutoffGroups());
830
831		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
832	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
832	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
833	>	cg = mol->nextCutoffGroup(ci)) {
834
835	<	totalMass = cg->getMass();
836	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
837	<	mfact.push_back(atom->getMass()/totalMass);
838	<	}
839	<
840	<	}
835	>	totalMass = cg->getMass();
836	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
837	>	// Check for massless groups - set mfact to 1 if true
838	>	if (totalMass != 0)
839	>	massFactors_.push_back(atom->getMass()/totalMass);
840	>	else
841	>	massFactors_.push_back( 1.0 );
842	>	}
843	>	}
844		}
845
846	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
629	<	std::vector<int> identArray;
846	>	// Build the identArray_
847
848	<	//to avoid memory reallocation, reserve enough space identArray
849	<	identArray.reserve(getNAtoms());
633	<
848	>	identArray_.clear();
849	>	identArray_.reserve(getNAtoms());
850		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
851	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
852	<	identArray.push_back(atom->getIdent());
853	<	}
851	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
852	>	identArray_.push_back(atom->getIdent());
853	>	}
854		}
639	–
640	–	//fill molMembershipArray
641	–	//molMembershipArray is filled by SimCreator
642	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
643	–	for (int i = 0; i < nGlobalAtoms_; i++) {
644	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
645	–	}
855
856	<	//setup fortran simulation
648	<	//gloalExcludes and molMembershipArray should go away (They are never used)
649	<	//why the hell fortran need to know molecule?
650	<	//OOPSE = Object-Obfuscated Parallel Simulation Engine
651	<	int nGlobalExcludes = 0;
652	<	int* globalExcludes = NULL;
653	<	int* excludeList = exclude_.getExcludeList();
654	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
655	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
656	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
856	>	//scan topology
857
858	<	if( isError ){
858	>	nExclude = excludedInteractions_.getSize();
859	>	nOneTwo = oneTwoInteractions_.getSize();
860	>	nOneThree = oneThreeInteractions_.getSize();
861	>	nOneFour = oneFourInteractions_.getSize();
862
863	<	sprintf( painCave.errMsg,
864	<	"There was an error setting the simulation information in fortran.\n" );
865	<	painCave.isFatal = 1;
866	<	painCave.severity = OOPSE_ERROR;
664	<	simError();
665	<	}
863	>	int* excludeList = excludedInteractions_.getPairList();
864	>	int* oneTwoList = oneTwoInteractions_.getPairList();
865	>	int* oneThreeList = oneThreeInteractions_.getPairList();
866	>	int* oneFourList = oneFourInteractions_.getPairList();
867
868	<	#ifdef IS_MPI
869	<	sprintf( checkPointMsg,
870	<	"succesfully sent the simulation information to fortran.\n");
871	<	MPIcheckPoint();
872	<	#endif // is_mpi
873	<	}
874	<
674	<
675	<	#ifdef IS_MPI
676	<	void SimInfo::setupFortranParallel() {
868	>	//setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0],
869	>	//               &nExclude, excludeList,
870	>	//               &nOneTwo, oneTwoList,
871	>	//               &nOneThree, oneThreeList,
872	>	//               &nOneFour, oneFourList,
873	>	//               &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
874	>	//               &fortranGlobalGroupMembership[0], &isError);
875
876	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
877	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
680	<	std::vector<int> localToGlobalCutoffGroupIndex;
681	<	SimInfo::MoleculeIterator mi;
682	<	Molecule::AtomIterator ai;
683	<	Molecule::CutoffGroupIterator ci;
684	<	Molecule* mol;
685	<	Atom* atom;
686	<	CutoffGroup* cg;
687	<	mpiSimData parallelData;
688	<	int isError;
876	>	topologyDone_ = true;
877	>	}
878
879	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
879	>	void SimInfo::addProperty(GenericData* genData) {
880	>	properties_.addProperty(genData);
881	>	}
882
883	<	//local index(index in DataStorge) of atom is important
884	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
885	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
695	<	}
883	>	void SimInfo::removeProperty(const string& propName) {
884	>	properties_.removeProperty(propName);
885	>	}
886
887	<	//local index of cutoff group is trivial, it only depends on the order of travesing
888	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
889	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
700	<	}
701	<
702	<	}
887	>	void SimInfo::clearProperties() {
888	>	properties_.clearProperties();
889	>	}
890
891	<	//fill up mpiSimData struct
892	<	parallelData.nMolGlobal = getNGlobalMolecules();
893	<	parallelData.nMolLocal = getNMolecules();
894	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
895	<	parallelData.nAtomsLocal = getNAtoms();
896	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
897	<	parallelData.nGroupsLocal = getNCutoffGroups();
711	<	parallelData.myNode = worldRank;
712	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
891	>	vector<string> SimInfo::getPropertyNames() {
892	>	return properties_.getPropertyNames();
893	>	}
894	>
895	>	vector<GenericData*> SimInfo::getProperties() {
896	>	return properties_.getProperties();
897	>	}
898
899	<	//pass mpiSimData struct and index arrays to fortran
900	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
901	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
717	<	&localToGlobalCutoffGroupIndex[0], &isError);
899	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
900	>	return properties_.getPropertyByName(propName);
901	>	}
902
903	<	if (isError) {
904	<	sprintf(painCave.errMsg,
905	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
906	<	painCave.isFatal = 1;
723	<	simError();
724	<	}
725	<
726	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
727	<	MPIcheckPoint();
728	<
729	<
730	<	}
731	<
732	<	#endif
733	<
734	<	double SimInfo::calcMaxCutoffRadius() {
735	<
736	<
737	<	std::set<AtomType*> atomTypes;
738	<	std::set<AtomType*>::iterator i;
739	<	std::vector<double> cutoffRadius;
740	<
741	<	//get the unique atom types
742	<	atomTypes = getUniqueAtomTypes();
743	<
744	<	//query the max cutoff radius among these atom types
745	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
746	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
747	<	}
748	<
749	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
750	<	#ifdef IS_MPI
751	<	//pick the max cutoff radius among the processors
752	<	#endif
753	<
754	<	return maxCutoffRadius;
755	<	}
756	<
757	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
758	<
759	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
760	<
761	<	if (!simParams_->haveRcut()){
762	<	sprintf(painCave.errMsg,
763	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
764	<	"\tOOPSE will use a default value of 15.0 angstroms"
765	<	"\tfor the cutoffRadius.\n");
766	<	painCave.isFatal = 0;
767	<	simError();
768	<	rcut = 15.0;
769	<	} else{
770	<	rcut = simParams_->getRcut();
771	<	}
772	<
773	<	if (!simParams_->haveRsw()){
774	<	sprintf(painCave.errMsg,
775	<	"SimCreator Warning: No value was set for switchingRadius.\n"
776	<	"\tOOPSE will use a default value of\n"
777	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
778	<	painCave.isFatal = 0;
779	<	simError();
780	<	rsw = 0.95 * rcut;
781	<	} else{
782	<	rsw = simParams_->getRsw();
783	<	}
784	<
785	<	} else {
786	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
787	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
788	<
789	<	if (simParams_->haveRcut()) {
790	<	rcut = simParams_->getRcut();
791	<	} else {
792	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
793	<	rcut = calcMaxCutoffRadius();
794	<	}
795	<
796	<	if (simParams_->haveRsw()) {
797	<	rsw  = simParams_->getRsw();
798	<	} else {
799	<	rsw = rcut;
800	<	}
801	<
802	<	}
803	<	}
804	<
805	<	void SimInfo::setupCutoff() {
806	<	getCutoff(rcut_, rsw_);
807	<	double rnblist = rcut_ + 1; // skin of neighbor list
808	<
809	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
810	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
811	<	}
812	<
813	<	void SimInfo::addProperty(GenericData* genData) {
814	<	properties_.addProperty(genData);
815	<	}
816	<
817	<	void SimInfo::removeProperty(const std::string& propName) {
818	<	properties_.removeProperty(propName);
819	<	}
820	<
821	<	void SimInfo::clearProperties() {
822	<	properties_.clearProperties();
823	<	}
824	<
825	<	std::vector<std::string> SimInfo::getPropertyNames() {
826	<	return properties_.getPropertyNames();
827	<	}
828	<
829	<	std::vector<GenericData*> SimInfo::getProperties() {
830	<	return properties_.getProperties();
831	<	}
832	<
833	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
834	<	return properties_.getPropertyByName(propName);
835	<	}
836	<
837	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
838	<	if (sman_ == sman_) {
839	<	return;
840	<	}
841	<
903	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
904	>	if (sman_ == sman) {
905	>	return;
906	>	}
907		delete sman_;
908		sman_ = sman;
909
910		Molecule* mol;
911		RigidBody* rb;
912		Atom* atom;
913	+	CutoffGroup* cg;
914		SimInfo::MoleculeIterator mi;
915		Molecule::RigidBodyIterator rbIter;
916	<	Molecule::AtomIterator atomIter;;
916	>	Molecule::AtomIterator atomIter;
917	>	Molecule::CutoffGroupIterator cgIter;
918
919		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
920
921	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
922	<	atom->setSnapshotManager(sman_);
923	<	}
921	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
922	>	atom->setSnapshotManager(sman_);
923	>	}
924
925	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
926	<	rb->setSnapshotManager(sman_);
927	<	}
925	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
926	>	rb->setSnapshotManager(sman_);
927	>	}
928	>
929	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
930	>	cg->setSnapshotManager(sman_);
931	>	}
932		}
933
934	<	}
934	>	}
935
936	<	Vector3d SimInfo::getComVel(){
936	>	Vector3d SimInfo::getComVel(){
937		SimInfo::MoleculeIterator i;
938		Molecule* mol;
939
940		Vector3d comVel(0.0);
941	<	double totalMass = 0.0;
941	>	RealType totalMass = 0.0;
942
943
944		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
945	<	double mass = mol->getMass();
946	<	totalMass += mass;
947	<	comVel += mass * mol->getComVel();
945	>	RealType mass = mol->getMass();
946	>	totalMass += mass;
947	>	comVel += mass * mol->getComVel();
948		}
949
950		#ifdef IS_MPI
951	<	double tmpMass = totalMass;
951	>	RealType tmpMass = totalMass;
952		Vector3d tmpComVel(comVel);
953	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
954	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
953	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
954	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
955		#endif
956
957		comVel /= totalMass;
958
959		return comVel;
960	<	}
960	>	}
961
962	<	Vector3d SimInfo::getCom(){
962	>	Vector3d SimInfo::getCom(){
963		SimInfo::MoleculeIterator i;
964		Molecule* mol;
965
966		Vector3d com(0.0);
967	<	double totalMass = 0.0;
967	>	RealType totalMass = 0.0;
968
969		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
970	<	double mass = mol->getMass();
971	<	totalMass += mass;
972	<	com += mass * mol->getCom();
970	>	RealType mass = mol->getMass();
971	>	totalMass += mass;
972	>	com += mass * mol->getCom();
973		}
974
975		#ifdef IS_MPI
976	<	double tmpMass = totalMass;
976	>	RealType tmpMass = totalMass;
977		Vector3d tmpCom(com);
978	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
979	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
978	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
979	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
980		#endif
981
982		com /= totalMass;
983
984		return com;
985
986	<	}
986	>	}
987
988	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
988	>	ostream& operator <<(ostream& o, SimInfo& info) {
989
990		return o;
991	<	}
991	>	}
992	>
993	>
994	>	/*
995	>	Returns center of mass and center of mass velocity in one function call.
996	>	*/
997	>
998	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
999	>	SimInfo::MoleculeIterator i;
1000	>	Molecule* mol;
1001	>
1002	>
1003	>	RealType totalMass = 0.0;
1004	>
1005
1006	<	}//end namespace oopse
1006	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1007	>	RealType mass = mol->getMass();
1008	>	totalMass += mass;
1009	>	com += mass * mol->getCom();
1010	>	comVel += mass * mol->getComVel();
1011	>	}
1012	>
1013	>	#ifdef IS_MPI
1014	>	RealType tmpMass = totalMass;
1015	>	Vector3d tmpCom(com);
1016	>	Vector3d tmpComVel(comVel);
1017	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1018	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1019	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1020	>	#endif
1021	>
1022	>	com /= totalMass;
1023	>	comVel /= totalMass;
1024	>	}
1025	>
1026	>	/*
1027	>	Return intertia tensor for entire system and angular momentum Vector.
1028
1029	+
1030	+	[  Ixx -Ixy  -Ixz ]
1031	+	J =| -Iyx  Iyy  -Iyz |
1032	+	[ -Izx -Iyz   Izz ]
1033	+	*/
1034	+
1035	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1036	+
1037	+
1038	+	RealType xx = 0.0;
1039	+	RealType yy = 0.0;
1040	+	RealType zz = 0.0;
1041	+	RealType xy = 0.0;
1042	+	RealType xz = 0.0;
1043	+	RealType yz = 0.0;
1044	+	Vector3d com(0.0);
1045	+	Vector3d comVel(0.0);
1046	+
1047	+	getComAll(com, comVel);
1048	+
1049	+	SimInfo::MoleculeIterator i;
1050	+	Molecule* mol;
1051	+
1052	+	Vector3d thisq(0.0);
1053	+	Vector3d thisv(0.0);
1054	+
1055	+	RealType thisMass = 0.0;
1056	+
1057	+
1058	+
1059	+
1060	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1061	+
1062	+	thisq = mol->getCom()-com;
1063	+	thisv = mol->getComVel()-comVel;
1064	+	thisMass = mol->getMass();
1065	+	// Compute moment of intertia coefficients.
1066	+	xx += thisq[0]*thisq[0]*thisMass;
1067	+	yy += thisq[1]*thisq[1]*thisMass;
1068	+	zz += thisq[2]*thisq[2]*thisMass;
1069	+
1070	+	// compute products of intertia
1071	+	xy += thisq[0]*thisq[1]*thisMass;
1072	+	xz += thisq[0]*thisq[2]*thisMass;
1073	+	yz += thisq[1]*thisq[2]*thisMass;
1074	+
1075	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1076	+
1077	+	}
1078	+
1079	+
1080	+	inertiaTensor(0,0) = yy + zz;
1081	+	inertiaTensor(0,1) = -xy;
1082	+	inertiaTensor(0,2) = -xz;
1083	+	inertiaTensor(1,0) = -xy;
1084	+	inertiaTensor(1,1) = xx + zz;
1085	+	inertiaTensor(1,2) = -yz;
1086	+	inertiaTensor(2,0) = -xz;
1087	+	inertiaTensor(2,1) = -yz;
1088	+	inertiaTensor(2,2) = xx + yy;
1089	+
1090	+	#ifdef IS_MPI
1091	+	Mat3x3d tmpI(inertiaTensor);
1092	+	Vector3d tmpAngMom;
1093	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1094	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1095	+	#endif
1096	+
1097	+	return;
1098	+	}
1099	+
1100	+	//Returns the angular momentum of the system
1101	+	Vector3d SimInfo::getAngularMomentum(){
1102	+
1103	+	Vector3d com(0.0);
1104	+	Vector3d comVel(0.0);
1105	+	Vector3d angularMomentum(0.0);
1106	+
1107	+	getComAll(com,comVel);
1108	+
1109	+	SimInfo::MoleculeIterator i;
1110	+	Molecule* mol;
1111	+
1112	+	Vector3d thisr(0.0);
1113	+	Vector3d thisp(0.0);
1114	+
1115	+	RealType thisMass;
1116	+
1117	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1118	+	thisMass = mol->getMass();
1119	+	thisr = mol->getCom()-com;
1120	+	thisp = (mol->getComVel()-comVel)*thisMass;
1121	+
1122	+	angularMomentum += cross( thisr, thisp );
1123	+
1124	+	}
1125	+
1126	+	#ifdef IS_MPI
1127	+	Vector3d tmpAngMom;
1128	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1129	+	#endif
1130	+
1131	+	return angularMomentum;
1132	+	}
1133	+
1134	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1135	+	return IOIndexToIntegrableObject.at(index);
1136	+	}
1137	+
1138	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1139	+	IOIndexToIntegrableObject= v;
1140	+	}
1141	+
1142	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1143	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1144	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1145	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1146	+	*/
1147	+	void SimInfo::getGyrationalVolume(RealType &volume){
1148	+	Mat3x3d intTensor;
1149	+	RealType det;
1150	+	Vector3d dummyAngMom;
1151	+	RealType sysconstants;
1152	+	RealType geomCnst;
1153	+
1154	+	geomCnst = 3.0/2.0;
1155	+	/* Get the inertial tensor and angular momentum for free*/
1156	+	getInertiaTensor(intTensor,dummyAngMom);
1157	+
1158	+	det = intTensor.determinant();
1159	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1160	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1161	+	return;
1162	+	}
1163	+
1164	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1165	+	Mat3x3d intTensor;
1166	+	Vector3d dummyAngMom;
1167	+	RealType sysconstants;
1168	+	RealType geomCnst;
1169	+
1170	+	geomCnst = 3.0/2.0;
1171	+	/* Get the inertial tensor and angular momentum for free*/
1172	+	getInertiaTensor(intTensor,dummyAngMom);
1173	+
1174	+	detI = intTensor.determinant();
1175	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1176	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1177	+	return;
1178	+	}
1179	+	/*
1180	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1181	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1182	+	sdByGlobalIndex_ = v;
1183	+	}
1184	+
1185	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1186	+	//assert(index < nAtoms_ + nRigidBodies_);
1187	+	return sdByGlobalIndex_.at(index);
1188	+	}
1189	+	*/
1190	+	int SimInfo::getNGlobalConstraints() {
1191	+	int nGlobalConstraints;
1192	+	#ifdef IS_MPI
1193	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1194	+	MPI_COMM_WORLD);
1195	+	#else
1196	+	nGlobalConstraints =  nConstraints_;
1197	+	#endif
1198	+	return nGlobalConstraints;
1199	+	}
1200	+
1201	+	}//end namespace OpenMD
1202	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 331 by tim, Sun Feb 13 21:18:27 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC

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