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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 430 by tim, Thu Mar 10 23:56:42 2005 UTC vs.
Revision 1050 by chrisfen, Fri Sep 22 22:19:59 2006 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 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 "primitives/StuntDouble.hpp"
57	+	#include "UseTheForce/fCutoffPolicy.h"
58	+	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	+	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60	+	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61		#include "UseTheForce/doForces_interface.h"
62	<	#include "UseTheForce/notifyCutoffs_interface.h"
62	>	#include "UseTheForce/DarkSide/electrostatic_interface.h"
63	>	#include "UseTheForce/DarkSide/switcheroo_interface.h"
64		#include "utils/MemoryUtils.hpp"
65		#include "utils/simError.h"
66		#include "selection/SelectionManager.hpp"
67	+	#include "io/ForceFieldOptions.hpp"
68	+	#include "UseTheForce/ForceField.hpp"
69
70		#ifdef IS_MPI
71		#include "UseTheForce/mpiComponentPlan.h"
#	Line 64 | Line 73 | namespace oopse {
73		#endif
74
75		namespace oopse {
76	+	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
77	+	std::map<int, std::set<int> >::iterator i = container.find(index);
78	+	std::set<int> result;
79	+	if (i != container.end()) {
80	+	result = i->second;
81	+	}
82
83	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
84	<	ForceField* ff, Globals* simParams) :
85	<	forceField_(ff), simParams_(simParams),
86	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
87	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
88	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
89	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
90	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
91	<	sman_(NULL), fortranInitialized_(false) {
83	>	return result;
84	>	}
85	>
86	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
87	>	forceField_(ff), simParams_(simParams),
88	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
89	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
90	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
91	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
92	>	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
93	>	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) {
94
95	<
96	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
97	<	MoleculeStamp* molStamp;
98	<	int nMolWithSameStamp;
99	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
100	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
101	<	CutoffGroupStamp* cgStamp;
102	<	RigidBodyStamp* rbStamp;
103	<	int nRigidAtoms = 0;
104	<
105	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
106	<	molStamp = i->first;
90	<	nMolWithSameStamp = i->second;
95	>	MoleculeStamp* molStamp;
96	>	int nMolWithSameStamp;
97	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
98	>	int nGroups = 0;      //total cutoff groups defined in meta-data file
99	>	CutoffGroupStamp* cgStamp;
100	>	RigidBodyStamp* rbStamp;
101	>	int nRigidAtoms = 0;
102	>	std::vector<Component*> components = simParams->getComponents();
103	>
104	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
105	>	molStamp = (*i)->getMoleculeStamp();
106	>	nMolWithSameStamp = (*i)->getNMol();
107
108		addMoleculeStamp(molStamp, nMolWithSameStamp);
109
110		//calculate atoms in molecules
111		nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
112
97	–
113		//calculate atoms in cutoff groups
114		int nAtomsInGroups = 0;
115		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
116
117		for (int j=0; j < nCutoffGroupsInStamp; j++) {
118	<	cgStamp = molStamp->getCutoffGroup(j);
119	<	nAtomsInGroups += cgStamp->getNMembers();
118	>	cgStamp = molStamp->getCutoffGroupStamp(j);
119	>	nAtomsInGroups += cgStamp->getNMembers();
120		}
121
122		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
123	+
124		nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
125
126		//calculate atoms in rigid bodies
#	Line 112 | Line 128 | SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*,
128		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
129
130		for (int j=0; j < nRigidBodiesInStamp; j++) {
131	<	rbStamp = molStamp->getRigidBody(j);
132	<	nAtomsInRigidBodies += rbStamp->getNMembers();
131	>	rbStamp = molStamp->getRigidBodyStamp(j);
132	>	nAtomsInRigidBodies += rbStamp->getNMembers();
133		}
134
135		nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
136		nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
137
138	<	}
138	>	}
139
140	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
141	<	//therefore the total number of cutoff groups in the system is equal to
142	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
143	<	//file plus the number of cutoff groups defined in meta-data file
144	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
140	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
141	>	//group therefore the total number of cutoff groups in the system is
142	>	//equal to the total number of atoms minus number of atoms belong to
143	>	//cutoff group defined in meta-data file plus the number of cutoff
144	>	//groups defined in meta-data file
145	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
146
147	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
148	<	//therefore the total number of  integrable objects in the system is equal to
149	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
150	<	//file plus the number of  rigid bodies defined in meta-data file
151	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
147	>	//every free atom (atom does not belong to rigid bodies) is an
148	>	//integrable object therefore the total number of integrable objects
149	>	//in the system is equal to the total number of atoms minus number of
150	>	//atoms belong to rigid body defined in meta-data file plus the number
151	>	//of rigid bodies defined in meta-data file
152	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
153	>	+ nGlobalRigidBodies_;
154	>
155	>	nGlobalMols_ = molStampIds_.size();
156
136	–	nGlobalMols_ = molStampIds_.size();
137	–
157		#ifdef IS_MPI
158	<	molToProcMap_.resize(nGlobalMols_);
158	>	molToProcMap_.resize(nGlobalMols_);
159		#endif
160
161	<	}
161	>	}
162
163	<	SimInfo::~SimInfo() {
163	>	SimInfo::~SimInfo() {
164		std::map<int, Molecule*>::iterator i;
165		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
166	<	delete i->second;
166	>	delete i->second;
167		}
168		molecules_.clear();
169	<
151	<	MemoryUtils::deletePointers(moleculeStamps_);
152	<
169	>
170		delete sman_;
171		delete simParams_;
172		delete forceField_;
173	<	}
173	>	}
174
175	<	int SimInfo::getNGlobalConstraints() {
175	>	int SimInfo::getNGlobalConstraints() {
176		int nGlobalConstraints;
177		#ifdef IS_MPI
178		MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
#	Line 164 | Line 181 | int SimInfo::getNGlobalConstraints() {
181		nGlobalConstraints =  nConstraints_;
182		#endif
183		return nGlobalConstraints;
184	<	}
184	>	}
185
186	<	bool SimInfo::addMolecule(Molecule* mol) {
186	>	bool SimInfo::addMolecule(Molecule* mol) {
187		MoleculeIterator i;
188
189		i = molecules_.find(mol->getGlobalIndex());
190		if (i == molecules_.end() ) {
191
192	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
192	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
193
194	<	nAtoms_ += mol->getNAtoms();
195	<	nBonds_ += mol->getNBonds();
196	<	nBends_ += mol->getNBends();
197	<	nTorsions_ += mol->getNTorsions();
198	<	nRigidBodies_ += mol->getNRigidBodies();
199	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
200	<	nCutoffGroups_ += mol->getNCutoffGroups();
201	<	nConstraints_ += mol->getNConstraintPairs();
194	>	nAtoms_ += mol->getNAtoms();
195	>	nBonds_ += mol->getNBonds();
196	>	nBends_ += mol->getNBends();
197	>	nTorsions_ += mol->getNTorsions();
198	>	nRigidBodies_ += mol->getNRigidBodies();
199	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
200	>	nCutoffGroups_ += mol->getNCutoffGroups();
201	>	nConstraints_ += mol->getNConstraintPairs();
202
203	<	addExcludePairs(mol);
203	>	addExcludePairs(mol);
204
205	<	return true;
205	>	return true;
206		} else {
207	<	return false;
207	>	return false;
208		}
209	<	}
209	>	}
210
211	<	bool SimInfo::removeMolecule(Molecule* mol) {
211	>	bool SimInfo::removeMolecule(Molecule* mol) {
212		MoleculeIterator i;
213		i = molecules_.find(mol->getGlobalIndex());
214
215		if (i != molecules_.end() ) {
216
217	<	assert(mol == i->second);
217	>	assert(mol == i->second);
218
219	<	nAtoms_ -= mol->getNAtoms();
220	<	nBonds_ -= mol->getNBonds();
221	<	nBends_ -= mol->getNBends();
222	<	nTorsions_ -= mol->getNTorsions();
223	<	nRigidBodies_ -= mol->getNRigidBodies();
224	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
225	<	nCutoffGroups_ -= mol->getNCutoffGroups();
226	<	nConstraints_ -= mol->getNConstraintPairs();
219	>	nAtoms_ -= mol->getNAtoms();
220	>	nBonds_ -= mol->getNBonds();
221	>	nBends_ -= mol->getNBends();
222	>	nTorsions_ -= mol->getNTorsions();
223	>	nRigidBodies_ -= mol->getNRigidBodies();
224	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
225	>	nCutoffGroups_ -= mol->getNCutoffGroups();
226	>	nConstraints_ -= mol->getNConstraintPairs();
227
228	<	removeExcludePairs(mol);
229	<	molecules_.erase(mol->getGlobalIndex());
228	>	removeExcludePairs(mol);
229	>	molecules_.erase(mol->getGlobalIndex());
230
231	<	delete mol;
231	>	delete mol;
232
233	<	return true;
233	>	return true;
234		} else {
235	<	return false;
235	>	return false;
236		}
237
238
239	<	}
239	>	}
240
241
242	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
242	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
243		i = molecules_.begin();
244		return i == molecules_.end() ? NULL : i->second;
245	<	}
245	>	}
246
247	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
247	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
248		++i;
249		return i == molecules_.end() ? NULL : i->second;
250	<	}
250	>	}
251
252
253	<	void SimInfo::calcNdf() {
253	>	void SimInfo::calcNdf() {
254		int ndf_local;
255		MoleculeIterator i;
256		std::vector<StuntDouble*>::iterator j;
#	Line 243 | Line 260 | void SimInfo::calcNdf() {
260		ndf_local = 0;
261
262		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
263	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
264	<	integrableObject = mol->nextIntegrableObject(j)) {
263	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
264	>	integrableObject = mol->nextIntegrableObject(j)) {
265
266	<	ndf_local += 3;
266	>	ndf_local += 3;
267
268	<	if (integrableObject->isDirectional()) {
269	<	if (integrableObject->isLinear()) {
270	<	ndf_local += 2;
271	<	} else {
272	<	ndf_local += 3;
273	<	}
274	<	}
268	>	if (integrableObject->isDirectional()) {
269	>	if (integrableObject->isLinear()) {
270	>	ndf_local += 2;
271	>	} else {
272	>	ndf_local += 3;
273	>	}
274	>	}
275
276	<	}//end for (integrableObject)
277	<	}// end for (mol)
276	>	}
277	>	}
278
279		// n_constraints is local, so subtract them on each processor
280		ndf_local -= nConstraints_;
#	Line 272 | Line 289 | void SimInfo::calcNdf() {
289		// entire system:
290		ndf_ = ndf_ - 3 - nZconstraint_;
291
292	<	}
292	>	}
293
294	<	void SimInfo::calcNdfRaw() {
294	>	int SimInfo::getFdf() {
295	>	#ifdef IS_MPI
296	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
297	>	#else
298	>	fdf_ = fdf_local;
299	>	#endif
300	>	return fdf_;
301	>	}
302	>
303	>	void SimInfo::calcNdfRaw() {
304		int ndfRaw_local;
305
306		MoleculeIterator i;
#	Line 286 | Line 312 | void SimInfo::calcNdfRaw() {
312		ndfRaw_local = 0;
313
314		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
315	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
316	<	integrableObject = mol->nextIntegrableObject(j)) {
315	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
316	>	integrableObject = mol->nextIntegrableObject(j)) {
317
318	<	ndfRaw_local += 3;
318	>	ndfRaw_local += 3;
319
320	<	if (integrableObject->isDirectional()) {
321	<	if (integrableObject->isLinear()) {
322	<	ndfRaw_local += 2;
323	<	} else {
324	<	ndfRaw_local += 3;
325	<	}
326	<	}
320	>	if (integrableObject->isDirectional()) {
321	>	if (integrableObject->isLinear()) {
322	>	ndfRaw_local += 2;
323	>	} else {
324	>	ndfRaw_local += 3;
325	>	}
326	>	}
327
328	<	}
328	>	}
329		}
330
331		#ifdef IS_MPI
#	Line 307 | Line 333 | void SimInfo::calcNdfRaw() {
333		#else
334		ndfRaw_ = ndfRaw_local;
335		#endif
336	<	}
336	>	}
337
338	<	void SimInfo::calcNdfTrans() {
338	>	void SimInfo::calcNdfTrans() {
339		int ndfTrans_local;
340
341		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 323 | Line 349 | void SimInfo::calcNdfTrans() {
349
350		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
351
352	<	}
352	>	}
353
354	<	void SimInfo::addExcludePairs(Molecule* mol) {
354	>	void SimInfo::addExcludePairs(Molecule* mol) {
355		std::vector<Bond*>::iterator bondIter;
356		std::vector<Bend*>::iterator bendIter;
357		std::vector<Torsion*>::iterator torsionIter;
#	Line 336 | Line 362 | void SimInfo::addExcludePairs(Molecule* mol) {
362		int b;
363		int c;
364		int d;
365	+
366	+	std::map<int, std::set<int> > atomGroups;
367	+
368	+	Molecule::RigidBodyIterator rbIter;
369	+	RigidBody* rb;
370	+	Molecule::IntegrableObjectIterator ii;
371	+	StuntDouble* integrableObject;
372
373	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
374	+	integrableObject = mol->nextIntegrableObject(ii)) {
375	+
376	+	if (integrableObject->isRigidBody()) {
377	+	rb = static_cast<RigidBody*>(integrableObject);
378	+	std::vector<Atom*> atoms = rb->getAtoms();
379	+	std::set<int> rigidAtoms;
380	+	for (int i = 0; i < atoms.size(); ++i) {
381	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
382	+	}
383	+	for (int i = 0; i < atoms.size(); ++i) {
384	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
385	+	}
386	+	} else {
387	+	std::set<int> oneAtomSet;
388	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
389	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
390	+	}
391	+	}
392	+
393	+
394	+
395		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
396	<	a = bond->getAtomA()->getGlobalIndex();
397	<	b = bond->getAtomB()->getGlobalIndex();
398	<	exclude_.addPair(a, b);
396	>	a = bond->getAtomA()->getGlobalIndex();
397	>	b = bond->getAtomB()->getGlobalIndex();
398	>	exclude_.addPair(a, b);
399		}
400
401		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
402	<	a = bend->getAtomA()->getGlobalIndex();
403	<	b = bend->getAtomB()->getGlobalIndex();
404	<	c = bend->getAtomC()->getGlobalIndex();
402	>	a = bend->getAtomA()->getGlobalIndex();
403	>	b = bend->getAtomB()->getGlobalIndex();
404	>	c = bend->getAtomC()->getGlobalIndex();
405	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
406	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
407	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
408
409	<	exclude_.addPair(a, b);
410	<	exclude_.addPair(a, c);
411	<	exclude_.addPair(b, c);
409	>	exclude_.addPairs(rigidSetA, rigidSetB);
410	>	exclude_.addPairs(rigidSetA, rigidSetC);
411	>	exclude_.addPairs(rigidSetB, rigidSetC);
412	>
413	>	//exclude_.addPair(a, b);
414	>	//exclude_.addPair(a, c);
415	>	//exclude_.addPair(b, c);
416		}
417
418		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
419	<	a = torsion->getAtomA()->getGlobalIndex();
420	<	b = torsion->getAtomB()->getGlobalIndex();
421	<	c = torsion->getAtomC()->getGlobalIndex();
422	<	d = torsion->getAtomD()->getGlobalIndex();
419	>	a = torsion->getAtomA()->getGlobalIndex();
420	>	b = torsion->getAtomB()->getGlobalIndex();
421	>	c = torsion->getAtomC()->getGlobalIndex();
422	>	d = torsion->getAtomD()->getGlobalIndex();
423	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
424	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
425	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
426	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
427
428	<	exclude_.addPair(a, b);
429	<	exclude_.addPair(a, c);
430	<	exclude_.addPair(a, d);
431	<	exclude_.addPair(b, c);
432	<	exclude_.addPair(b, d);
433	<	exclude_.addPair(c, d);
368	<	}
428	>	exclude_.addPairs(rigidSetA, rigidSetB);
429	>	exclude_.addPairs(rigidSetA, rigidSetC);
430	>	exclude_.addPairs(rigidSetA, rigidSetD);
431	>	exclude_.addPairs(rigidSetB, rigidSetC);
432	>	exclude_.addPairs(rigidSetB, rigidSetD);
433	>	exclude_.addPairs(rigidSetC, rigidSetD);
434
435	<	Molecule::RigidBodyIterator rbIter;
436	<	RigidBody* rb;
435	>	/*
436	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
437	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
438	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
439	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
440	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
441	>	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
442	>
443	>
444	>	exclude_.addPair(a, b);
445	>	exclude_.addPair(a, c);
446	>	exclude_.addPair(a, d);
447	>	exclude_.addPair(b, c);
448	>	exclude_.addPair(b, d);
449	>	exclude_.addPair(c, d);
450	>	*/
451	>	}
452	>
453		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
454	<	std::vector<Atom*> atoms = rb->getAtoms();
455	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
456	<	for (int j = i + 1; j < atoms.size(); ++j) {
457	<	a = atoms[i]->getGlobalIndex();
458	<	b = atoms[j]->getGlobalIndex();
459	<	exclude_.addPair(a, b);
460	<	}
461	<	}
454	>	std::vector<Atom*> atoms = rb->getAtoms();
455	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
456	>	for (int j = i + 1; j < atoms.size(); ++j) {
457	>	a = atoms[i]->getGlobalIndex();
458	>	b = atoms[j]->getGlobalIndex();
459	>	exclude_.addPair(a, b);
460	>	}
461	>	}
462		}
463
464	<	Molecule::CutoffGroupIterator cgIter;
384	<	CutoffGroup* cg;
385	<	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
386	<	std::vector<Atom*> atoms = cg->getAtoms();
387	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
388	<	for (int j = i + 1; j < atoms.size(); ++j) {
389	<	a = atoms[i]->getGlobalIndex();
390	<	b = atoms[j]->getGlobalIndex();
391	<	exclude_.addPair(a, b);
392	<	}
393	<	}
394	<	}
464	>	}
465
466	<	}
397	<
398	<	void SimInfo::removeExcludePairs(Molecule* mol) {
466	>	void SimInfo::removeExcludePairs(Molecule* mol) {
467		std::vector<Bond*>::iterator bondIter;
468		std::vector<Bend*>::iterator bendIter;
469		std::vector<Torsion*>::iterator torsionIter;
#	Line 406 | Line 474 | void SimInfo::removeExcludePairs(Molecule* mol) {
474		int b;
475		int c;
476		int d;
477	+
478	+	std::map<int, std::set<int> > atomGroups;
479	+
480	+	Molecule::RigidBodyIterator rbIter;
481	+	RigidBody* rb;
482	+	Molecule::IntegrableObjectIterator ii;
483	+	StuntDouble* integrableObject;
484
485	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
486	+	integrableObject = mol->nextIntegrableObject(ii)) {
487	+
488	+	if (integrableObject->isRigidBody()) {
489	+	rb = static_cast<RigidBody*>(integrableObject);
490	+	std::vector<Atom*> atoms = rb->getAtoms();
491	+	std::set<int> rigidAtoms;
492	+	for (int i = 0; i < atoms.size(); ++i) {
493	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
494	+	}
495	+	for (int i = 0; i < atoms.size(); ++i) {
496	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
497	+	}
498	+	} else {
499	+	std::set<int> oneAtomSet;
500	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
501	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
502	+	}
503	+	}
504	+
505	+
506		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
507	<	a = bond->getAtomA()->getGlobalIndex();
508	<	b = bond->getAtomB()->getGlobalIndex();
509	<	exclude_.removePair(a, b);
507	>	a = bond->getAtomA()->getGlobalIndex();
508	>	b = bond->getAtomB()->getGlobalIndex();
509	>	exclude_.removePair(a, b);
510		}
511
512		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
513	<	a = bend->getAtomA()->getGlobalIndex();
514	<	b = bend->getAtomB()->getGlobalIndex();
515	<	c = bend->getAtomC()->getGlobalIndex();
513	>	a = bend->getAtomA()->getGlobalIndex();
514	>	b = bend->getAtomB()->getGlobalIndex();
515	>	c = bend->getAtomC()->getGlobalIndex();
516
517	<	exclude_.removePair(a, b);
518	<	exclude_.removePair(a, c);
519	<	exclude_.removePair(b, c);
517	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
518	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
519	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
520	>
521	>	exclude_.removePairs(rigidSetA, rigidSetB);
522	>	exclude_.removePairs(rigidSetA, rigidSetC);
523	>	exclude_.removePairs(rigidSetB, rigidSetC);
524	>
525	>	//exclude_.removePair(a, b);
526	>	//exclude_.removePair(a, c);
527	>	//exclude_.removePair(b, c);
528		}
529
530		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
531	<	a = torsion->getAtomA()->getGlobalIndex();
532	<	b = torsion->getAtomB()->getGlobalIndex();
533	<	c = torsion->getAtomC()->getGlobalIndex();
534	<	d = torsion->getAtomD()->getGlobalIndex();
531	>	a = torsion->getAtomA()->getGlobalIndex();
532	>	b = torsion->getAtomB()->getGlobalIndex();
533	>	c = torsion->getAtomC()->getGlobalIndex();
534	>	d = torsion->getAtomD()->getGlobalIndex();
535
536	<	exclude_.removePair(a, b);
537	<	exclude_.removePair(a, c);
538	<	exclude_.removePair(a, d);
539	<	exclude_.removePair(b, c);
540	<	exclude_.removePair(b, d);
541	<	exclude_.removePair(c, d);
536	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
537	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
538	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
539	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
540	>
541	>	exclude_.removePairs(rigidSetA, rigidSetB);
542	>	exclude_.removePairs(rigidSetA, rigidSetC);
543	>	exclude_.removePairs(rigidSetA, rigidSetD);
544	>	exclude_.removePairs(rigidSetB, rigidSetC);
545	>	exclude_.removePairs(rigidSetB, rigidSetD);
546	>	exclude_.removePairs(rigidSetC, rigidSetD);
547	>
548	>	/*
549	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
550	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
551	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
552	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
553	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
554	>	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
555	>
556	>
557	>	exclude_.removePair(a, b);
558	>	exclude_.removePair(a, c);
559	>	exclude_.removePair(a, d);
560	>	exclude_.removePair(b, c);
561	>	exclude_.removePair(b, d);
562	>	exclude_.removePair(c, d);
563	>	*/
564		}
565
440	–	Molecule::RigidBodyIterator rbIter;
441	–	RigidBody* rb;
566		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
567	<	std::vector<Atom*> atoms = rb->getAtoms();
568	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
569	<	for (int j = i + 1; j < atoms.size(); ++j) {
570	<	a = atoms[i]->getGlobalIndex();
571	<	b = atoms[j]->getGlobalIndex();
572	<	exclude_.removePair(a, b);
573	<	}
574	<	}
567	>	std::vector<Atom*> atoms = rb->getAtoms();
568	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
569	>	for (int j = i + 1; j < atoms.size(); ++j) {
570	>	a = atoms[i]->getGlobalIndex();
571	>	b = atoms[j]->getGlobalIndex();
572	>	exclude_.removePair(a, b);
573	>	}
574	>	}
575		}
576
577	<	Molecule::CutoffGroupIterator cgIter;
454	<	CutoffGroup* cg;
455	<	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
456	<	std::vector<Atom*> atoms = cg->getAtoms();
457	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
458	<	for (int j = i + 1; j < atoms.size(); ++j) {
459	<	a = atoms[i]->getGlobalIndex();
460	<	b = atoms[j]->getGlobalIndex();
461	<	exclude_.removePair(a, b);
462	<	}
463	<	}
464	<	}
465	<
466	<	}
577	>	}
578
579
580	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
580	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
581		int curStampId;
582
583		//index from 0
#	Line 474 | Line 585 | void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp
585
586		moleculeStamps_.push_back(molStamp);
587		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
588	<	}
588	>	}
589
590	<	void SimInfo::update() {
590	>	void SimInfo::update() {
591
592		setupSimType();
593
#	Line 489 | Line 600 | void SimInfo::update() {
600		//setup fortran force field
601		/** @deprecate */
602		int isError = 0;
492	–	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
493	–	if(isError){
494	–	sprintf( painCave.errMsg,
495	–	"ForceField error: There was an error initializing the forceField in fortran.\n" );
496	–	painCave.isFatal = 1;
497	–	simError();
498	–	}
499	–
603
604		setupCutoff();
605	+
606	+	setupElectrostaticSummationMethod( isError );
607	+	setupSwitchingFunction();
608	+	setupAccumulateBoxDipole();
609
610	+	if(isError){
611	+	sprintf( painCave.errMsg,
612	+	"ForceField error: There was an error initializing the forceField in fortran.\n" );
613	+	painCave.isFatal = 1;
614	+	simError();
615	+	}
616	+
617		calcNdf();
618		calcNdfRaw();
619		calcNdfTrans();
620
621		fortranInitialized_ = true;
622	<	}
622	>	}
623
624	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
624	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
625		SimInfo::MoleculeIterator mi;
626		Molecule* mol;
627		Molecule::AtomIterator ai;
#	Line 516 | Line 630 | std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
630
631		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
632
633	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
634	<	atomTypes.insert(atom->getAtomType());
635	<	}
633	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
634	>	atomTypes.insert(atom->getAtomType());
635	>	}
636
637		}
638
639		return atomTypes;
640	<	}
640	>	}
641
642	<	void SimInfo::setupSimType() {
642	>	void SimInfo::setupSimType() {
643		std::set<AtomType*>::iterator i;
644		std::set<AtomType*> atomTypes;
645		atomTypes = getUniqueAtomTypes();
#	Line 533 | Line 647 | void SimInfo::setupSimType() {
647		int useLennardJones = 0;
648		int useElectrostatic = 0;
649		int useEAM = 0;
650	+	int useSC = 0;
651		int useCharge = 0;
652		int useDirectional = 0;
653		int useDipole = 0;
654		int useGayBerne = 0;
655		int useSticky = 0;
656	+	int useStickyPower = 0;
657		int useShape = 0;
658		int useFLARB = 0; //it is not in AtomType yet
659		int useDirectionalAtom = 0;
660		int useElectrostatics = 0;
661		//usePBC and useRF are from simParams
662	<	int usePBC = simParams_->getPBC();
663	<	int useRF = simParams_->getUseRF();
662	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
663	>	int useRF;
664	>	int useSF;
665	>	int useSP;
666	>	int useBoxDipole;
667	>	std::string myMethod;
668
669	+	// set the useRF logical
670	+	useRF = 0;
671	+	useSF = 0;
672	+
673	+
674	+	if (simParams_->haveElectrostaticSummationMethod()) {
675	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
676	+	toUpper(myMethod);
677	+	if (myMethod == "REACTION_FIELD"){
678	+	useRF=1;
679	+	} else if (myMethod == "SHIFTED_FORCE"){
680	+	useSF = 1;
681	+	} else if (myMethod == "SHIFTED_POTENTIAL"){
682	+	useSP = 1;
683	+	}
684	+	}
685	+
686	+	if (simParams_->haveAccumulateBoxDipole())
687	+	if (simParams_->getAccumulateBoxDipole())
688	+	useBoxDipole = 1;
689	+
690		//loop over all of the atom types
691		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
692	<	useLennardJones |= (*i)->isLennardJones();
693	<	useElectrostatic |= (*i)->isElectrostatic();
694	<	useEAM |= (*i)->isEAM();
695	<	useCharge |= (*i)->isCharge();
696	<	useDirectional |= (*i)->isDirectional();
697	<	useDipole |= (*i)->isDipole();
698	<	useGayBerne |= (*i)->isGayBerne();
699	<	useSticky |= (*i)->isSticky();
700	<	useShape |= (*i)->isShape();
692	>	useLennardJones |= (*i)->isLennardJones();
693	>	useElectrostatic |= (*i)->isElectrostatic();
694	>	useEAM |= (*i)->isEAM();
695	>	useSC |= (*i)->isSC();
696	>	useCharge |= (*i)->isCharge();
697	>	useDirectional |= (*i)->isDirectional();
698	>	useDipole |= (*i)->isDipole();
699	>	useGayBerne |= (*i)->isGayBerne();
700	>	useSticky |= (*i)->isSticky();
701	>	useStickyPower |= (*i)->isStickyPower();
702	>	useShape |= (*i)->isShape();
703		}
704
705	<	if (useSticky || useDipole || useGayBerne || useShape) {
706	<	useDirectionalAtom = 1;
705	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
706	>	useDirectionalAtom = 1;
707		}
708
709		if (useCharge || useDipole) {
710	<	useElectrostatics = 1;
710	>	useElectrostatics = 1;
711		}
712
713		#ifdef IS_MPI
#	Line 591 | Line 734 | void SimInfo::setupSimType() {
734		temp = useSticky;
735		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
736
737	+	temp = useStickyPower;
738	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
739	+
740		temp = useGayBerne;
741		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
742
743		temp = useEAM;
744		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
745
746	+	temp = useSC;
747	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
748	+
749		temp = useShape;
750		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
751
#	Line 605 | Line 754 | void SimInfo::setupSimType() {
754
755		temp = useRF;
756		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
757	<
757	>
758	>	temp = useSF;
759	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
760	>
761	>	temp = useSP;
762	>	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
763	>
764	>	temp = useBoxDipole;
765	>	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766	>
767		#endif
768
769		fInfo_.SIM_uses_PBC = usePBC;
#	Line 615 | Line 773 | void SimInfo::setupSimType() {
773		fInfo_.SIM_uses_Charges = useCharge;
774		fInfo_.SIM_uses_Dipoles = useDipole;
775		fInfo_.SIM_uses_Sticky = useSticky;
776	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
777		fInfo_.SIM_uses_GayBerne = useGayBerne;
778		fInfo_.SIM_uses_EAM = useEAM;
779	+	fInfo_.SIM_uses_SC = useSC;
780		fInfo_.SIM_uses_Shapes = useShape;
781		fInfo_.SIM_uses_FLARB = useFLARB;
782		fInfo_.SIM_uses_RF = useRF;
783	+	fInfo_.SIM_uses_SF = useSF;
784	+	fInfo_.SIM_uses_SP = useSP;
785	+	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
786	+	}
787
788	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
625	<
626	<	if (simParams_->haveDielectric()) {
627	<	fInfo_.dielect = simParams_->getDielectric();
628	<	} else {
629	<	sprintf(painCave.errMsg,
630	<	"SimSetup Error: No Dielectric constant was set.\n"
631	<	"\tYou are trying to use Reaction Field without"
632	<	"\tsetting a dielectric constant!\n");
633	<	painCave.isFatal = 1;
634	<	simError();
635	<	}
636	<
637	<	} else {
638	<	fInfo_.dielect = 0.0;
639	<	}
640	<
641	<	}
642	<
643	<	void SimInfo::setupFortranSim() {
788	>	void SimInfo::setupFortranSim() {
789		int isError;
790		int nExclude;
791		std::vector<int> fortranGlobalGroupMembership;
#	Line 650 | Line 795 | void SimInfo::setupFortranSim() {
795
796		//globalGroupMembership_ is filled by SimCreator
797		for (int i = 0; i < nGlobalAtoms_; i++) {
798	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
798	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
799		}
800
801		//calculate mass ratio of cutoff group
802	<	std::vector<double> mfact;
802	>	std::vector<RealType> mfact;
803		SimInfo::MoleculeIterator mi;
804		Molecule* mol;
805		Molecule::CutoffGroupIterator ci;
806		CutoffGroup* cg;
807		Molecule::AtomIterator ai;
808		Atom* atom;
809	<	double totalMass;
809	>	RealType totalMass;
810
811		//to avoid memory reallocation, reserve enough space for mfact
812		mfact.reserve(getNCutoffGroups());
813
814		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
815	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
815	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
816
817	<	totalMass = cg->getMass();
818	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
819	<	mfact.push_back(atom->getMass()/totalMass);
820	<	}
817	>	totalMass = cg->getMass();
818	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
819	>	// Check for massless groups - set mfact to 1 if true
820	>	if (totalMass != 0)
821	>	mfact.push_back(atom->getMass()/totalMass);
822	>	else
823	>	mfact.push_back( 1.0 );
824	>	}
825
826	<	}
826	>	}
827		}
828
829		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
#	Line 684 | Line 833 | void SimInfo::setupFortranSim() {
833		identArray.reserve(getNAtoms());
834
835		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
836	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
837	<	identArray.push_back(atom->getIdent());
838	<	}
836	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
837	>	identArray.push_back(atom->getIdent());
838	>	}
839		}
840
841		//fill molMembershipArray
842		//molMembershipArray is filled by SimCreator
843		std::vector<int> molMembershipArray(nGlobalAtoms_);
844		for (int i = 0; i < nGlobalAtoms_; i++) {
845	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
845	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
846		}
847
848		//setup fortran simulation
700	–	//gloalExcludes and molMembershipArray should go away (They are never used)
701	–	//why the hell fortran need to know molecule?
702	–	//OOPSE = Object-Obfuscated Parallel Simulation Engine
849		int nGlobalExcludes = 0;
850		int* globalExcludes = NULL;
851		int* excludeList = exclude_.getExcludeList();
852		setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
853	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
854	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
853	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
854	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
855
856		if( isError ){
857
858	<	sprintf( painCave.errMsg,
859	<	"There was an error setting the simulation information in fortran.\n" );
860	<	painCave.isFatal = 1;
861	<	painCave.severity = OOPSE_ERROR;
862	<	simError();
858	>	sprintf( painCave.errMsg,
859	>	"There was an error setting the simulation information in fortran.\n" );
860	>	painCave.isFatal = 1;
861	>	painCave.severity = OOPSE_ERROR;
862	>	simError();
863		}
864
865		#ifdef IS_MPI
866		sprintf( checkPointMsg,
867	<	"succesfully sent the simulation information to fortran.\n");
867	>	"succesfully sent the simulation information to fortran.\n");
868		MPIcheckPoint();
869		#endif // is_mpi
870	<	}
870	>	}
871
872
873		#ifdef IS_MPI
874	<	void SimInfo::setupFortranParallel() {
874	>	void SimInfo::setupFortranParallel() {
875
876		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
877		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
#	Line 741 | Line 887 | void SimInfo::setupFortranParallel() {
887
888		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
889
890	<	//local index(index in DataStorge) of atom is important
891	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
892	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
893	<	}
890	>	//local index(index in DataStorge) of atom is important
891	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
892	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
893	>	}
894
895	<	//local index of cutoff group is trivial, it only depends on the order of travesing
896	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
897	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
898	<	}
895	>	//local index of cutoff group is trivial, it only depends on the order of travesing
896	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
897	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
898	>	}
899
900		}
901
#	Line 769 | Line 915 | void SimInfo::setupFortranParallel() {
915		&localToGlobalCutoffGroupIndex[0], &isError);
916
917		if (isError) {
918	<	sprintf(painCave.errMsg,
919	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
920	<	painCave.isFatal = 1;
921	<	simError();
918	>	sprintf(painCave.errMsg,
919	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
920	>	painCave.isFatal = 1;
921	>	simError();
922		}
923
924		sprintf(checkPointMsg, " mpiRefresh successful.\n");
925		MPIcheckPoint();
926
927
928	<	}
928	>	}
929
930		#endif
931
932	<	double SimInfo::calcMaxCutoffRadius() {
932	>	void SimInfo::setupCutoff() {
933	>
934	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
935
936	+	// Check the cutoff policy
937	+	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
938
939	<	std::set<AtomType*> atomTypes;
940	<	std::set<AtomType*>::iterator i;
941	<	std::vector<double> cutoffRadius;
942	<
943	<	//get the unique atom types
794	<	atomTypes = getUniqueAtomTypes();
795	<
796	<	//query the max cutoff radius among these atom types
797	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
798	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
939	>	std::string myPolicy;
940	>	if (forceFieldOptions_.haveCutoffPolicy()){
941	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
942	>	}else if (simParams_->haveCutoffPolicy()) {
943	>	myPolicy = simParams_->getCutoffPolicy();
944		}
945
946	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
947	<	#ifdef IS_MPI
948	<	//pick the max cutoff radius among the processors
949	<	#endif
946	>	if (!myPolicy.empty()){
947	>	toUpper(myPolicy);
948	>	if (myPolicy == "MIX") {
949	>	cp = MIX_CUTOFF_POLICY;
950	>	} else {
951	>	if (myPolicy == "MAX") {
952	>	cp = MAX_CUTOFF_POLICY;
953	>	} else {
954	>	if (myPolicy == "TRADITIONAL") {
955	>	cp = TRADITIONAL_CUTOFF_POLICY;
956	>	} else {
957	>	// throw error
958	>	sprintf( painCave.errMsg,
959	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
960	>	painCave.isFatal = 1;
961	>	simError();
962	>	}
963	>	}
964	>	}
965	>	}
966	>	notifyFortranCutoffPolicy(&cp);
967
968	<	return maxCutoffRadius;
969	<	}
970	<
971	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
972	<
973	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
968	>	// Check the Skin Thickness for neighborlists
969	>	RealType skin;
970	>	if (simParams_->haveSkinThickness()) {
971	>	skin = simParams_->getSkinThickness();
972	>	notifyFortranSkinThickness(&skin);
973	>	}
974
975	<	if (!simParams_->haveRcut()){
976	<	sprintf(painCave.errMsg,
975	>	// Check if the cutoff was set explicitly:
976	>	if (simParams_->haveCutoffRadius()) {
977	>	rcut_ = simParams_->getCutoffRadius();
978	>	if (simParams_->haveSwitchingRadius()) {
979	>	rsw_  = simParams_->getSwitchingRadius();
980	>	} else {
981	>	if (fInfo_.SIM_uses_Charges |
982	>	fInfo_.SIM_uses_Dipoles |
983	>	fInfo_.SIM_uses_RF) {
984	>
985	>	rsw_ = 0.85 * rcut_;
986	>	sprintf(painCave.errMsg,
987	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
988	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
989	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
990	>	painCave.isFatal = 0;
991	>	simError();
992	>	} else {
993	>	rsw_ = rcut_;
994	>	sprintf(painCave.errMsg,
995	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
996	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
997	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
998	>	painCave.isFatal = 0;
999	>	simError();
1000	>	}
1001	>	}
1002	>
1003	>	notifyFortranCutoffs(&rcut_, &rsw_);
1004	>
1005	>	} else {
1006	>
1007	>	// For electrostatic atoms, we'll assume a large safe value:
1008	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1009	>	sprintf(painCave.errMsg,
1010		"SimCreator Warning: No value was set for the cutoffRadius.\n"
1011		"\tOOPSE will use a default value of 15.0 angstroms"
1012		"\tfor the cutoffRadius.\n");
1013	<	painCave.isFatal = 0;
1014	<	simError();
1015	<	rcut = 15.0;
1016	<	} else{
1017	<	rcut = simParams_->getRcut();
1013	>	painCave.isFatal = 0;
1014	>	simError();
1015	>	rcut_ = 15.0;
1016	>
1017	>	if (simParams_->haveElectrostaticSummationMethod()) {
1018	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1019	>	toUpper(myMethod);
1020	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1021	>	if (simParams_->haveSwitchingRadius()){
1022	>	sprintf(painCave.errMsg,
1023	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1024	>	"\teven though the electrostaticSummationMethod was\n"
1025	>	"\tset to %s\n", myMethod.c_str());
1026	>	painCave.isFatal = 1;
1027	>	simError();
1028	>	}
1029	>	}
1030		}
1031	<
1032	<	if (!simParams_->haveRsw()){
1033	<	sprintf(painCave.errMsg,
1034	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1035	<	"\tOOPSE will use a default value of\n"
1036	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
1037	<	painCave.isFatal = 0;
1038	<	simError();
1039	<	rsw = 0.95 * rcut;
1040	<	} else{
1041	<	rsw = simParams_->getRsw();
1031	>
1032	>	if (simParams_->haveSwitchingRadius()){
1033	>	rsw_ = simParams_->getSwitchingRadius();
1034	>	} else {
1035	>	sprintf(painCave.errMsg,
1036	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1037	>	"\tOOPSE will use a default value of\n"
1038	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1039	>	painCave.isFatal = 0;
1040	>	simError();
1041	>	rsw_ = 0.85 * rcut_;
1042		}
1043	<
1044	<	} else {
1045	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
1046	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
1043	>	notifyFortranCutoffs(&rcut_, &rsw_);
1044	>	} else {
1045	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1046	>	// We'll punt and let fortran figure out the cutoffs later.
1047
1048	<	if (simParams_->haveRcut()) {
842	<	rcut = simParams_->getRcut();
843	<	} else {
844	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
845	<	rcut = calcMaxCutoffRadius();
846	<	}
1048	>	notifyFortranYouAreOnYourOwn();
1049
1050	<	if (simParams_->haveRsw()) {
1051	<	rsw  = simParams_->getRsw();
1050	>	}
1051	>	}
1052	>	}
1053	>
1054	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1055	>
1056	>	int errorOut;
1057	>	int esm =  NONE;
1058	>	int sm = UNDAMPED;
1059	>	RealType alphaVal;
1060	>	RealType dielectric;
1061	>
1062	>	errorOut = isError;
1063	>
1064	>	if (simParams_->haveElectrostaticSummationMethod()) {
1065	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1066	>	toUpper(myMethod);
1067	>	if (myMethod == "NONE") {
1068	>	esm = NONE;
1069	>	} else {
1070	>	if (myMethod == "SWITCHING_FUNCTION") {
1071	>	esm = SWITCHING_FUNCTION;
1072		} else {
1073	<	rsw = rcut;
1074	<	}
1073	>	if (myMethod == "SHIFTED_POTENTIAL") {
1074	>	esm = SHIFTED_POTENTIAL;
1075	>	} else {
1076	>	if (myMethod == "SHIFTED_FORCE") {
1077	>	esm = SHIFTED_FORCE;
1078	>	} else {
1079	>	if (myMethod == "REACTION_FIELD") {
1080	>	esm = REACTION_FIELD;
1081	>	dielectric = simParams_->getDielectric();
1082	>	if (!simParams_->haveDielectric()) {
1083	>	// throw warning
1084	>	sprintf( painCave.errMsg,
1085	>	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1086	>	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1087	>	painCave.isFatal = 0;
1088	>	simError();
1089	>	}
1090	>	} else {
1091	>	// throw error
1092	>	sprintf( painCave.errMsg,
1093	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1094	>	"\t(Input file specified %s .)\n"
1095	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1096	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1097	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1098	>	painCave.isFatal = 1;
1099	>	simError();
1100	>	}
1101	>	}
1102	>	}
1103	>	}
1104	>	}
1105	>	}
1106
1107	+	if (simParams_->haveElectrostaticScreeningMethod()) {
1108	+	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1109	+	toUpper(myScreen);
1110	+	if (myScreen == "UNDAMPED") {
1111	+	sm = UNDAMPED;
1112	+	} else {
1113	+	if (myScreen == "DAMPED") {
1114	+	sm = DAMPED;
1115	+	if (!simParams_->haveDampingAlpha()) {
1116	+	// first set a cutoff dependent alpha value
1117	+	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1118	+	alphaVal = 0.5125 - rcut_* 0.025;
1119	+	// for values rcut > 20.5, alpha is zero
1120	+	if (alphaVal < 0) alphaVal = 0;
1121	+
1122	+	// throw warning
1123	+	sprintf( painCave.errMsg,
1124	+	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1125	+	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1126	+	painCave.isFatal = 0;
1127	+	simError();
1128	+	}
1129	+	} else {
1130	+	// throw error
1131	+	sprintf( painCave.errMsg,
1132	+	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1133	+	"\t(Input file specified %s .)\n"
1134	+	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1135	+	"or \"damped\".\n", myScreen.c_str() );
1136	+	painCave.isFatal = 1;
1137	+	simError();
1138	+	}
1139	+	}
1140		}
1141	<	}
1141	>
1142	>	// let's pass some summation method variables to fortran
1143	>	setElectrostaticSummationMethod( &esm );
1144	>	setFortranElectrostaticMethod( &esm );
1145	>	setScreeningMethod( &sm );
1146	>	setDampingAlpha( &alphaVal );
1147	>	setReactionFieldDielectric( &dielectric );
1148	>	initFortranFF( &errorOut );
1149	>	}
1150
1151	<	void SimInfo::setupCutoff() {
1152	<	getCutoff(rcut_, rsw_);
859	<	double rnblist = rcut_ + 1; // skin of neighbor list
1151	>	void SimInfo::setupSwitchingFunction() {
1152	>	int ft = CUBIC;
1153
1154	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1155	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
1156	<	}
1154	>	if (simParams_->haveSwitchingFunctionType()) {
1155	>	std::string funcType = simParams_->getSwitchingFunctionType();
1156	>	toUpper(funcType);
1157	>	if (funcType == "CUBIC") {
1158	>	ft = CUBIC;
1159	>	} else {
1160	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1161	>	ft = FIFTH_ORDER_POLY;
1162	>	} else {
1163	>	// throw error
1164	>	sprintf( painCave.errMsg,
1165	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1166	>	painCave.isFatal = 1;
1167	>	simError();
1168	>	}
1169	>	}
1170	>	}
1171
1172	<	void SimInfo::addProperty(GenericData* genData) {
1172	>	// send switching function notification to switcheroo
1173	>	setFunctionType(&ft);
1174	>
1175	>	}
1176	>
1177	>	void SimInfo::setupAccumulateBoxDipole() {
1178	>
1179	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1180	>	if ( simParams_->haveAccumulateBoxDipole() )
1181	>	if ( simParams_->getAccumulateBoxDipole() ) {
1182	>	setAccumulateBoxDipole();
1183	>	calcBoxDipole_ = true;
1184	>	}
1185	>
1186	>	}
1187	>
1188	>	void SimInfo::addProperty(GenericData* genData) {
1189		properties_.addProperty(genData);
1190	<	}
1190	>	}
1191
1192	<	void SimInfo::removeProperty(const std::string& propName) {
1192	>	void SimInfo::removeProperty(const std::string& propName) {
1193		properties_.removeProperty(propName);
1194	<	}
1194	>	}
1195
1196	<	void SimInfo::clearProperties() {
1196	>	void SimInfo::clearProperties() {
1197		properties_.clearProperties();
1198	<	}
1198	>	}
1199
1200	<	std::vector<std::string> SimInfo::getPropertyNames() {
1200	>	std::vector<std::string> SimInfo::getPropertyNames() {
1201		return properties_.getPropertyNames();
1202	<	}
1202	>	}
1203
1204	<	std::vector<GenericData*> SimInfo::getProperties() {
1204	>	std::vector<GenericData*> SimInfo::getProperties() {
1205		return properties_.getProperties();
1206	<	}
1206	>	}
1207
1208	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1208	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1209		return properties_.getPropertyByName(propName);
1210	<	}
1210	>	}
1211
1212	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1213	<	//if (sman_ == sman_) {
1214	<	//    return;
1215	<	//}
1216	<
894	<	//delete sman_;
1212	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1213	>	if (sman_ == sman) {
1214	>	return;
1215	>	}
1216	>	delete sman_;
1217		sman_ = sman;
1218
1219		Molecule* mol;
#	Line 903 | Line 1225 | void SimInfo::setSnapshotManager(SnapshotManager* sman
1225
1226		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1227
1228	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1229	<	atom->setSnapshotManager(sman_);
1230	<	}
1228	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1229	>	atom->setSnapshotManager(sman_);
1230	>	}
1231
1232	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1233	<	rb->setSnapshotManager(sman_);
1234	<	}
1232	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1233	>	rb->setSnapshotManager(sman_);
1234	>	}
1235		}
1236
1237	<	}
1237	>	}
1238
1239	<	Vector3d SimInfo::getComVel(){
1239	>	Vector3d SimInfo::getComVel(){
1240		SimInfo::MoleculeIterator i;
1241		Molecule* mol;
1242
1243		Vector3d comVel(0.0);
1244	<	double totalMass = 0.0;
1244	>	RealType totalMass = 0.0;
1245
1246
1247		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1248	<	double mass = mol->getMass();
1249	<	totalMass += mass;
1250	<	comVel += mass * mol->getComVel();
1248	>	RealType mass = mol->getMass();
1249	>	totalMass += mass;
1250	>	comVel += mass * mol->getComVel();
1251		}
1252
1253		#ifdef IS_MPI
1254	<	double tmpMass = totalMass;
1254	>	RealType tmpMass = totalMass;
1255		Vector3d tmpComVel(comVel);
1256	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1257	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1256	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1257	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1258		#endif
1259
1260		comVel /= totalMass;
1261
1262		return comVel;
1263	<	}
1263	>	}
1264
1265	<	Vector3d SimInfo::getCom(){
1265	>	Vector3d SimInfo::getCom(){
1266		SimInfo::MoleculeIterator i;
1267		Molecule* mol;
1268
1269		Vector3d com(0.0);
1270	<	double totalMass = 0.0;
1270	>	RealType totalMass = 0.0;
1271
1272		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1273	<	double mass = mol->getMass();
1274	<	totalMass += mass;
1275	<	com += mass * mol->getCom();
1273	>	RealType mass = mol->getMass();
1274	>	totalMass += mass;
1275	>	com += mass * mol->getCom();
1276		}
1277
1278		#ifdef IS_MPI
1279	<	double tmpMass = totalMass;
1279	>	RealType tmpMass = totalMass;
1280		Vector3d tmpCom(com);
1281	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1282	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1281	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1282	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1283		#endif
1284
1285		com /= totalMass;
1286
1287		return com;
1288
1289	<	}
1289	>	}
1290
1291	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1291	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1292
1293		return o;
1294	<	}
1294	>	}
1295	>
1296	>
1297	>	/*
1298	>	Returns center of mass and center of mass velocity in one function call.
1299	>	*/
1300	>
1301	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1302	>	SimInfo::MoleculeIterator i;
1303	>	Molecule* mol;
1304	>
1305	>
1306	>	RealType totalMass = 0.0;
1307	>
1308
1309	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1310	+	RealType mass = mol->getMass();
1311	+	totalMass += mass;
1312	+	com += mass * mol->getCom();
1313	+	comVel += mass * mol->getComVel();
1314	+	}
1315	+
1316	+	#ifdef IS_MPI
1317	+	RealType tmpMass = totalMass;
1318	+	Vector3d tmpCom(com);
1319	+	Vector3d tmpComVel(comVel);
1320	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1321	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1322	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1323	+	#endif
1324	+
1325	+	com /= totalMass;
1326	+	comVel /= totalMass;
1327	+	}
1328	+
1329	+	/*
1330	+	Return intertia tensor for entire system and angular momentum Vector.
1331	+
1332	+
1333	+	[  Ixx -Ixy  -Ixz ]
1334	+	J =| -Iyx  Iyy  -Iyz |
1335	+	[ -Izx -Iyz   Izz ]
1336	+	*/
1337	+
1338	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1339	+
1340	+
1341	+	RealType xx = 0.0;
1342	+	RealType yy = 0.0;
1343	+	RealType zz = 0.0;
1344	+	RealType xy = 0.0;
1345	+	RealType xz = 0.0;
1346	+	RealType yz = 0.0;
1347	+	Vector3d com(0.0);
1348	+	Vector3d comVel(0.0);
1349	+
1350	+	getComAll(com, comVel);
1351	+
1352	+	SimInfo::MoleculeIterator i;
1353	+	Molecule* mol;
1354	+
1355	+	Vector3d thisq(0.0);
1356	+	Vector3d thisv(0.0);
1357	+
1358	+	RealType thisMass = 0.0;
1359	+
1360	+
1361	+
1362	+
1363	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1364	+
1365	+	thisq = mol->getCom()-com;
1366	+	thisv = mol->getComVel()-comVel;
1367	+	thisMass = mol->getMass();
1368	+	// Compute moment of intertia coefficients.
1369	+	xx += thisq[0]*thisq[0]*thisMass;
1370	+	yy += thisq[1]*thisq[1]*thisMass;
1371	+	zz += thisq[2]*thisq[2]*thisMass;
1372	+
1373	+	// compute products of intertia
1374	+	xy += thisq[0]*thisq[1]*thisMass;
1375	+	xz += thisq[0]*thisq[2]*thisMass;
1376	+	yz += thisq[1]*thisq[2]*thisMass;
1377	+
1378	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1379	+
1380	+	}
1381	+
1382	+
1383	+	inertiaTensor(0,0) = yy + zz;
1384	+	inertiaTensor(0,1) = -xy;
1385	+	inertiaTensor(0,2) = -xz;
1386	+	inertiaTensor(1,0) = -xy;
1387	+	inertiaTensor(1,1) = xx + zz;
1388	+	inertiaTensor(1,2) = -yz;
1389	+	inertiaTensor(2,0) = -xz;
1390	+	inertiaTensor(2,1) = -yz;
1391	+	inertiaTensor(2,2) = xx + yy;
1392	+
1393	+	#ifdef IS_MPI
1394	+	Mat3x3d tmpI(inertiaTensor);
1395	+	Vector3d tmpAngMom;
1396	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1397	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1398	+	#endif
1399	+
1400	+	return;
1401	+	}
1402	+
1403	+	//Returns the angular momentum of the system
1404	+	Vector3d SimInfo::getAngularMomentum(){
1405	+
1406	+	Vector3d com(0.0);
1407	+	Vector3d comVel(0.0);
1408	+	Vector3d angularMomentum(0.0);
1409	+
1410	+	getComAll(com,comVel);
1411	+
1412	+	SimInfo::MoleculeIterator i;
1413	+	Molecule* mol;
1414	+
1415	+	Vector3d thisr(0.0);
1416	+	Vector3d thisp(0.0);
1417	+
1418	+	RealType thisMass;
1419	+
1420	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1421	+	thisMass = mol->getMass();
1422	+	thisr = mol->getCom()-com;
1423	+	thisp = (mol->getComVel()-comVel)*thisMass;
1424	+
1425	+	angularMomentum += cross( thisr, thisp );
1426	+
1427	+	}
1428	+
1429	+	#ifdef IS_MPI
1430	+	Vector3d tmpAngMom;
1431	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1432	+	#endif
1433	+
1434	+	return angularMomentum;
1435	+	}
1436	+
1437	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1438	+	return IOIndexToIntegrableObject.at(index);
1439	+	}
1440	+
1441	+	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1442	+	IOIndexToIntegrableObject= v;
1443	+	}
1444	+
1445	+	/*
1446	+	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1447	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1448	+	sdByGlobalIndex_ = v;
1449	+	}
1450	+
1451	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1452	+	//assert(index < nAtoms_ + nRigidBodies_);
1453	+	return sdByGlobalIndex_.at(index);
1454	+	}
1455	+	*/
1456		}//end namespace oopse
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