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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 274 by tim, Tue Jan 25 21:59:18 2005 UTC vs.
Revision 1129 by chrisfen, Fri Apr 20 18:15:48 2007 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/neighborLists_interface.h"
63	>	#include "UseTheForce/DarkSide/electrostatic_interface.h"
64	>	#include "UseTheForce/DarkSide/switcheroo_interface.h"
65		#include "utils/MemoryUtils.hpp"
66		#include "utils/simError.h"
67	+	#include "selection/SelectionManager.hpp"
68	+	#include "io/ForceFieldOptions.hpp"
69	+	#include "UseTheForce/ForceField.hpp"
70
71	+
72		#ifdef IS_MPI
73		#include "UseTheForce/mpiComponentPlan.h"
74		#include "UseTheForce/DarkSide/simParallel_interface.h"
75		#endif
76
77		namespace oopse {
78	+	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79	+	std::map<int, std::set<int> >::iterator i = container.find(index);
80	+	std::set<int> result;
81	+	if (i != container.end()) {
82	+	result = i->second;
83	+	}
84
85	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
86	<	ForceField* ff, Globals* simParams) :
87	<	forceField_(ff), simParams_(simParams),
88	<	ndf_(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) {
85	>	return result;
86	>	}
87	>
88	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
89	>	forceField_(ff), simParams_(simParams),
90	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
91	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
92	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
93	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
94	>	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
95	>	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false),
96	>	useAtomicVirial_(true) {
97
98	<
99	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
100	<	MoleculeStamp* molStamp;
101	<	int nMolWithSameStamp;
102	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
103	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
104	<	CutoffGroupStamp* cgStamp;
105	<	RigidBodyStamp* rbStamp;
106	<	int nRigidAtoms = 0;
107	<
108	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
109	<	molStamp = i->first;
89	<	nMolWithSameStamp = i->second;
98	>	MoleculeStamp* molStamp;
99	>	int nMolWithSameStamp;
100	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
101	>	int nGroups = 0;      //total cutoff groups defined in meta-data file
102	>	CutoffGroupStamp* cgStamp;
103	>	RigidBodyStamp* rbStamp;
104	>	int nRigidAtoms = 0;
105	>	std::vector<Component*> components = simParams->getComponents();
106	>
107	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
108	>	molStamp = (*i)->getMoleculeStamp();
109	>	nMolWithSameStamp = (*i)->getNMol();
110
111		addMoleculeStamp(molStamp, nMolWithSameStamp);
112
113		//calculate atoms in molecules
114		nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
115
96	–
116		//calculate atoms in cutoff groups
117		int nAtomsInGroups = 0;
118		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
119
120		for (int j=0; j < nCutoffGroupsInStamp; j++) {
121	<	cgStamp = molStamp->getCutoffGroup(j);
122	<	nAtomsInGroups += cgStamp->getNMembers();
121	>	cgStamp = molStamp->getCutoffGroupStamp(j);
122	>	nAtomsInGroups += cgStamp->getNMembers();
123		}
124
125		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
126	+
127		nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
128
129		//calculate atoms in rigid bodies
#	Line 111 | Line 131 | SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*,
131		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
132
133		for (int j=0; j < nRigidBodiesInStamp; j++) {
134	<	rbStamp = molStamp->getRigidBody(j);
135	<	nAtomsInRigidBodies += rbStamp->getNMembers();
134	>	rbStamp = molStamp->getRigidBodyStamp(j);
135	>	nAtomsInRigidBodies += rbStamp->getNMembers();
136		}
137
138		nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
139		nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
140
141	<	}
141	>	}
142
143	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
144	<	//therefore the total number of cutoff groups in the system is equal to
145	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
146	<	//file plus the number of cutoff groups defined in meta-data file
147	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
143	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
144	>	//group therefore the total number of cutoff groups in the system is
145	>	//equal to the total number of atoms minus number of atoms belong to
146	>	//cutoff group defined in meta-data file plus the number of cutoff
147	>	//groups defined in meta-data file
148	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
149
150	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
151	<	//therefore the total number of  integrable objects in the system is equal to
152	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
153	<	//file plus the number of  rigid bodies defined in meta-data file
154	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
150	>	//every free atom (atom does not belong to rigid bodies) is an
151	>	//integrable object therefore the total number of integrable objects
152	>	//in the system is equal to the total number of atoms minus number of
153	>	//atoms belong to rigid body defined in meta-data file plus the number
154	>	//of rigid bodies defined in meta-data file
155	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
156	>	+ nGlobalRigidBodies_;
157	>
158	>	nGlobalMols_ = molStampIds_.size();
159
135	–	nGlobalMols_ = molStampIds_.size();
136	–
160		#ifdef IS_MPI
161	<	molToProcMap_.resize(nGlobalMols_);
161	>	molToProcMap_.resize(nGlobalMols_);
162		#endif
140	–
141	–	}
163
164	<	SimInfo::~SimInfo() {
144	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
164	>	}
165
166	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
167	<
166	>	SimInfo::~SimInfo() {
167	>	std::map<int, Molecule*>::iterator i;
168	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
169	>	delete i->second;
170	>	}
171	>	molecules_.clear();
172	>
173		delete sman_;
174		delete simParams_;
175		delete forceField_;
176	+	}
177
178	<	}
153	<
154	<	int SimInfo::getNGlobalConstraints() {
178	>	int SimInfo::getNGlobalConstraints() {
179		int nGlobalConstraints;
180		#ifdef IS_MPI
181		MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
#	Line 160 | Line 184 | int SimInfo::getNGlobalConstraints() {
184		nGlobalConstraints =  nConstraints_;
185		#endif
186		return nGlobalConstraints;
187	<	}
187	>	}
188
189	<	bool SimInfo::addMolecule(Molecule* mol) {
189	>	bool SimInfo::addMolecule(Molecule* mol) {
190		MoleculeIterator i;
191
192		i = molecules_.find(mol->getGlobalIndex());
193		if (i == molecules_.end() ) {
194
195	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
195	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
196
197	<	nAtoms_ += mol->getNAtoms();
198	<	nBonds_ += mol->getNBonds();
199	<	nBends_ += mol->getNBends();
200	<	nTorsions_ += mol->getNTorsions();
201	<	nRigidBodies_ += mol->getNRigidBodies();
202	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
203	<	nCutoffGroups_ += mol->getNCutoffGroups();
204	<	nConstraints_ += mol->getNConstraintPairs();
197	>	nAtoms_ += mol->getNAtoms();
198	>	nBonds_ += mol->getNBonds();
199	>	nBends_ += mol->getNBends();
200	>	nTorsions_ += mol->getNTorsions();
201	>	nRigidBodies_ += mol->getNRigidBodies();
202	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
203	>	nCutoffGroups_ += mol->getNCutoffGroups();
204	>	nConstraints_ += mol->getNConstraintPairs();
205
206	<	addExcludePairs(mol);
206	>	addExcludePairs(mol);
207
208	<	return true;
208	>	return true;
209		} else {
210	<	return false;
210	>	return false;
211		}
212	<	}
212	>	}
213
214	<	bool SimInfo::removeMolecule(Molecule* mol) {
214	>	bool SimInfo::removeMolecule(Molecule* mol) {
215		MoleculeIterator i;
216		i = molecules_.find(mol->getGlobalIndex());
217
218		if (i != molecules_.end() ) {
219
220	<	assert(mol == i->second);
220	>	assert(mol == i->second);
221
222	<	nAtoms_ -= mol->getNAtoms();
223	<	nBonds_ -= mol->getNBonds();
224	<	nBends_ -= mol->getNBends();
225	<	nTorsions_ -= mol->getNTorsions();
226	<	nRigidBodies_ -= mol->getNRigidBodies();
227	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
228	<	nCutoffGroups_ -= mol->getNCutoffGroups();
229	<	nConstraints_ -= mol->getNConstraintPairs();
222	>	nAtoms_ -= mol->getNAtoms();
223	>	nBonds_ -= mol->getNBonds();
224	>	nBends_ -= mol->getNBends();
225	>	nTorsions_ -= mol->getNTorsions();
226	>	nRigidBodies_ -= mol->getNRigidBodies();
227	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
228	>	nCutoffGroups_ -= mol->getNCutoffGroups();
229	>	nConstraints_ -= mol->getNConstraintPairs();
230
231	<	removeExcludePairs(mol);
232	<	molecules_.erase(mol->getGlobalIndex());
231	>	removeExcludePairs(mol);
232	>	molecules_.erase(mol->getGlobalIndex());
233
234	<	delete mol;
234	>	delete mol;
235
236	<	return true;
236	>	return true;
237		} else {
238	<	return false;
238	>	return false;
239		}
240
241
242	<	}
242	>	}
243
244
245	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
245	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
246		i = molecules_.begin();
247		return i == molecules_.end() ? NULL : i->second;
248	<	}
248	>	}
249
250	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
250	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
251		++i;
252		return i == molecules_.end() ? NULL : i->second;
253	<	}
253	>	}
254
255
256	<	void SimInfo::calcNdf() {
256	>	void SimInfo::calcNdf() {
257		int ndf_local;
258		MoleculeIterator i;
259		std::vector<StuntDouble*>::iterator j;
#	Line 239 | Line 263 | void SimInfo::calcNdf() {
263		ndf_local = 0;
264
265		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
266	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
267	<	integrableObject = mol->nextIntegrableObject(j)) {
266	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
267	>	integrableObject = mol->nextIntegrableObject(j)) {
268
269	<	ndf_local += 3;
269	>	ndf_local += 3;
270
271	<	if (integrableObject->isDirectional()) {
272	<	if (integrableObject->isLinear()) {
273	<	ndf_local += 2;
274	<	} else {
275	<	ndf_local += 3;
276	<	}
277	<	}
271	>	if (integrableObject->isDirectional()) {
272	>	if (integrableObject->isLinear()) {
273	>	ndf_local += 2;
274	>	} else {
275	>	ndf_local += 3;
276	>	}
277	>	}
278
279	<	}//end for (integrableObject)
280	<	}// end for (mol)
279	>	}
280	>	}
281
282		// n_constraints is local, so subtract them on each processor
283		ndf_local -= nConstraints_;
#	Line 268 | Line 292 | void SimInfo::calcNdf() {
292		// entire system:
293		ndf_ = ndf_ - 3 - nZconstraint_;
294
295	<	}
295	>	}
296
297	<	void SimInfo::calcNdfRaw() {
297	>	int SimInfo::getFdf() {
298	>	#ifdef IS_MPI
299	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
300	>	#else
301	>	fdf_ = fdf_local;
302	>	#endif
303	>	return fdf_;
304	>	}
305	>
306	>	void SimInfo::calcNdfRaw() {
307		int ndfRaw_local;
308
309		MoleculeIterator i;
#	Line 282 | Line 315 | void SimInfo::calcNdfRaw() {
315		ndfRaw_local = 0;
316
317		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
318	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
319	<	integrableObject = mol->nextIntegrableObject(j)) {
318	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
319	>	integrableObject = mol->nextIntegrableObject(j)) {
320
321	<	ndfRaw_local += 3;
321	>	ndfRaw_local += 3;
322
323	<	if (integrableObject->isDirectional()) {
324	<	if (integrableObject->isLinear()) {
325	<	ndfRaw_local += 2;
326	<	} else {
327	<	ndfRaw_local += 3;
328	<	}
329	<	}
323	>	if (integrableObject->isDirectional()) {
324	>	if (integrableObject->isLinear()) {
325	>	ndfRaw_local += 2;
326	>	} else {
327	>	ndfRaw_local += 3;
328	>	}
329	>	}
330
331	<	}
331	>	}
332		}
333
334		#ifdef IS_MPI
#	Line 303 | Line 336 | void SimInfo::calcNdfRaw() {
336		#else
337		ndfRaw_ = ndfRaw_local;
338		#endif
339	<	}
339	>	}
340
341	<	void SimInfo::calcNdfTrans() {
341	>	void SimInfo::calcNdfTrans() {
342		int ndfTrans_local;
343
344		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 319 | Line 352 | void SimInfo::calcNdfTrans() {
352
353		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
354
355	<	}
355	>	}
356
357	<	void SimInfo::addExcludePairs(Molecule* mol) {
357	>	void SimInfo::addExcludePairs(Molecule* mol) {
358		std::vector<Bond*>::iterator bondIter;
359		std::vector<Bend*>::iterator bendIter;
360		std::vector<Torsion*>::iterator torsionIter;
#	Line 332 | Line 365 | void SimInfo::addExcludePairs(Molecule* mol) {
365		int b;
366		int c;
367		int d;
368	+
369	+	std::map<int, std::set<int> > atomGroups;
370	+
371	+	Molecule::RigidBodyIterator rbIter;
372	+	RigidBody* rb;
373	+	Molecule::IntegrableObjectIterator ii;
374	+	StuntDouble* integrableObject;
375
376	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
377	+	integrableObject = mol->nextIntegrableObject(ii)) {
378	+
379	+	if (integrableObject->isRigidBody()) {
380	+	rb = static_cast<RigidBody*>(integrableObject);
381	+	std::vector<Atom*> atoms = rb->getAtoms();
382	+	std::set<int> rigidAtoms;
383	+	for (int i = 0; i < atoms.size(); ++i) {
384	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
385	+	}
386	+	for (int i = 0; i < atoms.size(); ++i) {
387	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
388	+	}
389	+	} else {
390	+	std::set<int> oneAtomSet;
391	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
392	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
393	+	}
394	+	}
395	+
396	+
397	+
398		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
399	<	a = bond->getAtomA()->getGlobalIndex();
400	<	b = bond->getAtomB()->getGlobalIndex();
401	<	exclude_.addPair(a, b);
399	>	a = bond->getAtomA()->getGlobalIndex();
400	>	b = bond->getAtomB()->getGlobalIndex();
401	>	exclude_.addPair(a, b);
402		}
403
404		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
405	<	a = bend->getAtomA()->getGlobalIndex();
406	<	b = bend->getAtomB()->getGlobalIndex();
407	<	c = bend->getAtomC()->getGlobalIndex();
405	>	a = bend->getAtomA()->getGlobalIndex();
406	>	b = bend->getAtomB()->getGlobalIndex();
407	>	c = bend->getAtomC()->getGlobalIndex();
408	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
409	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
410	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
411
412	<	exclude_.addPair(a, b);
413	<	exclude_.addPair(a, c);
414	<	exclude_.addPair(b, c);
412	>	exclude_.addPairs(rigidSetA, rigidSetB);
413	>	exclude_.addPairs(rigidSetA, rigidSetC);
414	>	exclude_.addPairs(rigidSetB, rigidSetC);
415	>
416	>	//exclude_.addPair(a, b);
417	>	//exclude_.addPair(a, c);
418	>	//exclude_.addPair(b, c);
419		}
420
421		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
422	<	a = torsion->getAtomA()->getGlobalIndex();
423	<	b = torsion->getAtomB()->getGlobalIndex();
424	<	c = torsion->getAtomC()->getGlobalIndex();
425	<	d = torsion->getAtomD()->getGlobalIndex();
422	>	a = torsion->getAtomA()->getGlobalIndex();
423	>	b = torsion->getAtomB()->getGlobalIndex();
424	>	c = torsion->getAtomC()->getGlobalIndex();
425	>	d = torsion->getAtomD()->getGlobalIndex();
426	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
427	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
428	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
429	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
430
431	<	exclude_.addPair(a, b);
432	<	exclude_.addPair(a, c);
433	<	exclude_.addPair(a, d);
434	<	exclude_.addPair(b, c);
435	<	exclude_.addPair(b, d);
436	<	exclude_.addPair(c, d);
364	<	}
431	>	exclude_.addPairs(rigidSetA, rigidSetB);
432	>	exclude_.addPairs(rigidSetA, rigidSetC);
433	>	exclude_.addPairs(rigidSetA, rigidSetD);
434	>	exclude_.addPairs(rigidSetB, rigidSetC);
435	>	exclude_.addPairs(rigidSetB, rigidSetD);
436	>	exclude_.addPairs(rigidSetC, rigidSetD);
437
438	<
439	<	}
438	>	/*
439	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
440	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
441	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
442	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
443	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
444	>	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
445	>
446	>
447	>	exclude_.addPair(a, b);
448	>	exclude_.addPair(a, c);
449	>	exclude_.addPair(a, d);
450	>	exclude_.addPair(b, c);
451	>	exclude_.addPair(b, d);
452	>	exclude_.addPair(c, d);
453	>	*/
454	>	}
455
456	<	void SimInfo::removeExcludePairs(Molecule* mol) {
456	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
457	>	std::vector<Atom*> atoms = rb->getAtoms();
458	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
459	>	for (int j = i + 1; j < atoms.size(); ++j) {
460	>	a = atoms[i]->getGlobalIndex();
461	>	b = atoms[j]->getGlobalIndex();
462	>	exclude_.addPair(a, b);
463	>	}
464	>	}
465	>	}
466	>
467	>	}
468	>
469	>	void SimInfo::removeExcludePairs(Molecule* mol) {
470		std::vector<Bond*>::iterator bondIter;
471		std::vector<Bend*>::iterator bendIter;
472		std::vector<Torsion*>::iterator torsionIter;
#	Line 377 | Line 477 | void SimInfo::removeExcludePairs(Molecule* mol) {
477		int b;
478		int c;
479		int d;
480	+
481	+	std::map<int, std::set<int> > atomGroups;
482	+
483	+	Molecule::RigidBodyIterator rbIter;
484	+	RigidBody* rb;
485	+	Molecule::IntegrableObjectIterator ii;
486	+	StuntDouble* integrableObject;
487
488	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
489	+	integrableObject = mol->nextIntegrableObject(ii)) {
490	+
491	+	if (integrableObject->isRigidBody()) {
492	+	rb = static_cast<RigidBody*>(integrableObject);
493	+	std::vector<Atom*> atoms = rb->getAtoms();
494	+	std::set<int> rigidAtoms;
495	+	for (int i = 0; i < atoms.size(); ++i) {
496	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
497	+	}
498	+	for (int i = 0; i < atoms.size(); ++i) {
499	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
500	+	}
501	+	} else {
502	+	std::set<int> oneAtomSet;
503	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
504	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
505	+	}
506	+	}
507	+
508	+
509		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
510	<	a = bond->getAtomA()->getGlobalIndex();
511	<	b = bond->getAtomB()->getGlobalIndex();
512	<	exclude_.removePair(a, b);
510	>	a = bond->getAtomA()->getGlobalIndex();
511	>	b = bond->getAtomB()->getGlobalIndex();
512	>	exclude_.removePair(a, b);
513		}
514
515		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
516	<	a = bend->getAtomA()->getGlobalIndex();
517	<	b = bend->getAtomB()->getGlobalIndex();
518	<	c = bend->getAtomC()->getGlobalIndex();
516	>	a = bend->getAtomA()->getGlobalIndex();
517	>	b = bend->getAtomB()->getGlobalIndex();
518	>	c = bend->getAtomC()->getGlobalIndex();
519
520	<	exclude_.removePair(a, b);
521	<	exclude_.removePair(a, c);
522	<	exclude_.removePair(b, c);
520	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
521	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
522	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
523	>
524	>	exclude_.removePairs(rigidSetA, rigidSetB);
525	>	exclude_.removePairs(rigidSetA, rigidSetC);
526	>	exclude_.removePairs(rigidSetB, rigidSetC);
527	>
528	>	//exclude_.removePair(a, b);
529	>	//exclude_.removePair(a, c);
530	>	//exclude_.removePair(b, c);
531		}
532
533		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
534	<	a = torsion->getAtomA()->getGlobalIndex();
535	<	b = torsion->getAtomB()->getGlobalIndex();
536	<	c = torsion->getAtomC()->getGlobalIndex();
537	<	d = torsion->getAtomD()->getGlobalIndex();
534	>	a = torsion->getAtomA()->getGlobalIndex();
535	>	b = torsion->getAtomB()->getGlobalIndex();
536	>	c = torsion->getAtomC()->getGlobalIndex();
537	>	d = torsion->getAtomD()->getGlobalIndex();
538
539	<	exclude_.removePair(a, b);
540	<	exclude_.removePair(a, c);
541	<	exclude_.removePair(a, d);
542	<	exclude_.removePair(b, c);
543	<	exclude_.removePair(b, d);
544	<	exclude_.removePair(c, d);
539	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
540	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
541	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
542	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
543	>
544	>	exclude_.removePairs(rigidSetA, rigidSetB);
545	>	exclude_.removePairs(rigidSetA, rigidSetC);
546	>	exclude_.removePairs(rigidSetA, rigidSetD);
547	>	exclude_.removePairs(rigidSetB, rigidSetC);
548	>	exclude_.removePairs(rigidSetB, rigidSetD);
549	>	exclude_.removePairs(rigidSetC, rigidSetD);
550	>
551	>	/*
552	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
553	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
554	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
555	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
556	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
557	>	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
558	>
559	>
560	>	exclude_.removePair(a, b);
561	>	exclude_.removePair(a, c);
562	>	exclude_.removePair(a, d);
563	>	exclude_.removePair(b, c);
564	>	exclude_.removePair(b, d);
565	>	exclude_.removePair(c, d);
566	>	*/
567		}
568
569	<	}
569	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
570	>	std::vector<Atom*> atoms = rb->getAtoms();
571	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
572	>	for (int j = i + 1; j < atoms.size(); ++j) {
573	>	a = atoms[i]->getGlobalIndex();
574	>	b = atoms[j]->getGlobalIndex();
575	>	exclude_.removePair(a, b);
576	>	}
577	>	}
578	>	}
579
580	+	}
581
582	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
582	>
583	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
584		int curStampId;
585
586		//index from 0
#	Line 419 | Line 588 | void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp
588
589		moleculeStamps_.push_back(molStamp);
590		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
591	<	}
591	>	}
592
593	<	void SimInfo::update() {
593	>	void SimInfo::update() {
594
595		setupSimType();
596
#	Line 434 | Line 603 | void SimInfo::update() {
603		//setup fortran force field
604		/** @deprecate */
605		int isError = 0;
437	–	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
438	–	if(isError){
439	–	sprintf( painCave.errMsg,
440	–	"ForceField error: There was an error initializing the forceField in fortran.\n" );
441	–	painCave.isFatal = 1;
442	–	simError();
443	–	}
444	–
606
607		setupCutoff();
608	+
609	+	setupElectrostaticSummationMethod( isError );
610	+	setupSwitchingFunction();
611	+	setupAccumulateBoxDipole();
612
613	+	if(isError){
614	+	sprintf( painCave.errMsg,
615	+	"ForceField error: There was an error initializing the forceField in fortran.\n" );
616	+	painCave.isFatal = 1;
617	+	simError();
618	+	}
619	+
620		calcNdf();
621		calcNdfRaw();
622		calcNdfTrans();
623
624		fortranInitialized_ = true;
625	<	}
625	>	}
626
627	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
627	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
628		SimInfo::MoleculeIterator mi;
629		Molecule* mol;
630		Molecule::AtomIterator ai;
#	Line 461 | Line 633 | std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
633
634		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
635
636	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
637	<	atomTypes.insert(atom->getAtomType());
638	<	}
636	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
637	>	atomTypes.insert(atom->getAtomType());
638	>	}
639
640		}
641
642		return atomTypes;
643	<	}
643	>	}
644
645	<	void SimInfo::setupSimType() {
645	>	void SimInfo::setupSimType() {
646		std::set<AtomType*>::iterator i;
647		std::set<AtomType*> atomTypes;
648		atomTypes = getUniqueAtomTypes();
#	Line 478 | Line 650 | void SimInfo::setupSimType() {
650		int useLennardJones = 0;
651		int useElectrostatic = 0;
652		int useEAM = 0;
653	+	int useSC = 0;
654		int useCharge = 0;
655		int useDirectional = 0;
656		int useDipole = 0;
657		int useGayBerne = 0;
658		int useSticky = 0;
659	+	int useStickyPower = 0;
660		int useShape = 0;
661		int useFLARB = 0; //it is not in AtomType yet
662		int useDirectionalAtom = 0;
663		int useElectrostatics = 0;
664		//usePBC and useRF are from simParams
665	<	int usePBC = simParams_->getPBC();
666	<	int useRF = simParams_->getUseRF();
665	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
666	>	int useRF;
667	>	int useSF;
668	>	int useSP;
669	>	int useBoxDipole;
670
671	+	std::string myMethod;
672	+
673	+	// set the useRF logical
674	+	useRF = 0;
675	+	useSF = 0;
676	+	useSP = 0;
677	+
678	+
679	+	if (simParams_->haveElectrostaticSummationMethod()) {
680	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
681	+	toUpper(myMethod);
682	+	if (myMethod == "REACTION_FIELD"){
683	+	useRF = 1;
684	+	} else if (myMethod == "SHIFTED_FORCE"){
685	+	useSF = 1;
686	+	} else if (myMethod == "SHIFTED_POTENTIAL"){
687	+	useSP = 1;
688	+	}
689	+	}
690	+
691	+	if (simParams_->haveAccumulateBoxDipole())
692	+	if (simParams_->getAccumulateBoxDipole())
693	+	useBoxDipole = 1;
694	+
695	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
696	+
697		//loop over all of the atom types
698		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
699	<	useLennardJones |= (*i)->isLennardJones();
700	<	useElectrostatic |= (*i)->isElectrostatic();
701	<	useEAM |= (*i)->isEAM();
702	<	useCharge |= (*i)->isCharge();
703	<	useDirectional |= (*i)->isDirectional();
704	<	useDipole |= (*i)->isDipole();
705	<	useGayBerne |= (*i)->isGayBerne();
706	<	useSticky |= (*i)->isSticky();
707	<	useShape |= (*i)->isShape();
699	>	useLennardJones |= (*i)->isLennardJones();
700	>	useElectrostatic |= (*i)->isElectrostatic();
701	>	useEAM |= (*i)->isEAM();
702	>	useSC |= (*i)->isSC();
703	>	useCharge |= (*i)->isCharge();
704	>	useDirectional |= (*i)->isDirectional();
705	>	useDipole |= (*i)->isDipole();
706	>	useGayBerne |= (*i)->isGayBerne();
707	>	useSticky |= (*i)->isSticky();
708	>	useStickyPower |= (*i)->isStickyPower();
709	>	useShape |= (*i)->isShape();
710		}
711
712	<	if (useSticky || useDipole || useGayBerne || useShape) {
713	<	useDirectionalAtom = 1;
712	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
713	>	useDirectionalAtom = 1;
714		}
715
716		if (useCharge || useDipole) {
717	<	useElectrostatics = 1;
717	>	useElectrostatics = 1;
718		}
719
720		#ifdef IS_MPI
#	Line 536 | Line 741 | void SimInfo::setupSimType() {
741		temp = useSticky;
742		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
743
744	+	temp = useStickyPower;
745	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
746	+
747		temp = useGayBerne;
748		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
749
750		temp = useEAM;
751		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
752
753	+	temp = useSC;
754	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
755	+
756		temp = useShape;
757		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
758
#	Line 550 | Line 761 | void SimInfo::setupSimType() {
761
762		temp = useRF;
763		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
764	<
764	>
765	>	temp = useSF;
766	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767	>
768	>	temp = useSP;
769	>	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770	>
771	>	temp = useBoxDipole;
772	>	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
773	>
774	>	temp = useAtomicVirial_;
775	>	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776	>
777		#endif
778
779		fInfo_.SIM_uses_PBC = usePBC;
#	Line 560 | Line 783 | void SimInfo::setupSimType() {
783		fInfo_.SIM_uses_Charges = useCharge;
784		fInfo_.SIM_uses_Dipoles = useDipole;
785		fInfo_.SIM_uses_Sticky = useSticky;
786	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
787		fInfo_.SIM_uses_GayBerne = useGayBerne;
788		fInfo_.SIM_uses_EAM = useEAM;
789	+	fInfo_.SIM_uses_SC = useSC;
790		fInfo_.SIM_uses_Shapes = useShape;
791		fInfo_.SIM_uses_FLARB = useFLARB;
792		fInfo_.SIM_uses_RF = useRF;
793	+	fInfo_.SIM_uses_SF = useSF;
794	+	fInfo_.SIM_uses_SP = useSP;
795	+	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
796	+	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
797	+	}
798
799	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
570	<
571	<	if (simParams_->haveDielectric()) {
572	<	fInfo_.dielect = simParams_->getDielectric();
573	<	} else {
574	<	sprintf(painCave.errMsg,
575	<	"SimSetup Error: No Dielectric constant was set.\n"
576	<	"\tYou are trying to use Reaction Field without"
577	<	"\tsetting a dielectric constant!\n");
578	<	painCave.isFatal = 1;
579	<	simError();
580	<	}
581	<
582	<	} else {
583	<	fInfo_.dielect = 0.0;
584	<	}
585	<
586	<	}
587	<
588	<	void SimInfo::setupFortranSim() {
799	>	void SimInfo::setupFortranSim() {
800		int isError;
801		int nExclude;
802		std::vector<int> fortranGlobalGroupMembership;
#	Line 595 | Line 806 | void SimInfo::setupFortranSim() {
806
807		//globalGroupMembership_ is filled by SimCreator
808		for (int i = 0; i < nGlobalAtoms_; i++) {
809	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
809	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
810		}
811
812		//calculate mass ratio of cutoff group
813	<	std::vector<double> mfact;
813	>	std::vector<RealType> mfact;
814		SimInfo::MoleculeIterator mi;
815		Molecule* mol;
816		Molecule::CutoffGroupIterator ci;
817		CutoffGroup* cg;
818		Molecule::AtomIterator ai;
819		Atom* atom;
820	<	double totalMass;
820	>	RealType totalMass;
821
822		//to avoid memory reallocation, reserve enough space for mfact
823		mfact.reserve(getNCutoffGroups());
824
825		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
826	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
826	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
827
828	<	totalMass = cg->getMass();
829	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
830	<	mfact.push_back(atom->getMass()/totalMass);
831	<	}
828	>	totalMass = cg->getMass();
829	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
830	>	// Check for massless groups - set mfact to 1 if true
831	>	if (totalMass != 0)
832	>	mfact.push_back(atom->getMass()/totalMass);
833	>	else
834	>	mfact.push_back( 1.0 );
835	>	}
836
837	<	}
837	>	}
838		}
839
840		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
#	Line 629 | Line 844 | void SimInfo::setupFortranSim() {
844		identArray.reserve(getNAtoms());
845
846		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
847	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
848	<	identArray.push_back(atom->getIdent());
849	<	}
847	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
848	>	identArray.push_back(atom->getIdent());
849	>	}
850		}
851
852		//fill molMembershipArray
853		//molMembershipArray is filled by SimCreator
854		std::vector<int> molMembershipArray(nGlobalAtoms_);
855		for (int i = 0; i < nGlobalAtoms_; i++) {
856	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
856	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
857		}
858
859		//setup fortran simulation
645	–	//gloalExcludes and molMembershipArray should go away (They are never used)
646	–	//why the hell fortran need to know molecule?
647	–	//OOPSE = Object-Obfuscated Parallel Simulation Engine
860		int nGlobalExcludes = 0;
861		int* globalExcludes = NULL;
862		int* excludeList = exclude_.getExcludeList();
863		setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
864	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
865	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
864	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
865	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
866
867		if( isError ){
868
869	<	sprintf( painCave.errMsg,
870	<	"There was an error setting the simulation information in fortran.\n" );
871	<	painCave.isFatal = 1;
872	<	painCave.severity = OOPSE_ERROR;
873	<	simError();
869	>	sprintf( painCave.errMsg,
870	>	"There was an error setting the simulation information in fortran.\n" );
871	>	painCave.isFatal = 1;
872	>	painCave.severity = OOPSE_ERROR;
873	>	simError();
874		}
875
876		#ifdef IS_MPI
877		sprintf( checkPointMsg,
878	<	"succesfully sent the simulation information to fortran.\n");
878	>	"succesfully sent the simulation information to fortran.\n");
879		MPIcheckPoint();
880		#endif // is_mpi
669	–	}
881
882	+	// Setup number of neighbors in neighbor list if present
883	+	if (simParams_->haveNeighborListNeighbors()) {
884	+	int nlistNeighbors = simParams_->getNeighborListNeighbors();
885	+	setNeighbors(&nlistNeighbors);
886	+	}
887	+
888
889	+	}
890	+
891	+
892		#ifdef IS_MPI
893	<	void SimInfo::setupFortranParallel() {
893	>	void SimInfo::setupFortranParallel() {
894
895		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
896		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
#	Line 686 | Line 906 | void SimInfo::setupFortranParallel() {
906
907		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
908
909	<	//local index(index in DataStorge) of atom is important
910	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
911	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
912	<	}
909	>	//local index(index in DataStorge) of atom is important
910	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
911	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
912	>	}
913
914	<	//local index of cutoff group is trivial, it only depends on the order of travesing
915	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
916	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
917	<	}
914	>	//local index of cutoff group is trivial, it only depends on the order of travesing
915	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
916	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
917	>	}
918
919		}
920
#	Line 714 | Line 934 | void SimInfo::setupFortranParallel() {
934		&localToGlobalCutoffGroupIndex[0], &isError);
935
936		if (isError) {
937	<	sprintf(painCave.errMsg,
938	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
939	<	painCave.isFatal = 1;
940	<	simError();
937	>	sprintf(painCave.errMsg,
938	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
939	>	painCave.isFatal = 1;
940	>	simError();
941		}
942
943		sprintf(checkPointMsg, " mpiRefresh successful.\n");
944		MPIcheckPoint();
945
946
947	<	}
947	>	}
948
949		#endif
950
951	<	double SimInfo::calcMaxCutoffRadius() {
951	>	void SimInfo::setupCutoff() {
952	>
953	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
954
955	+	// Check the cutoff policy
956	+	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
957
958	<	std::set<AtomType*> atomTypes;
959	<	std::set<AtomType*>::iterator i;
960	<	std::vector<double> cutoffRadius;
958	>	// Set LJ shifting bools to false
959	>	ljsp_ = false;
960	>	ljsf_ = false;
961
962	<	//get the unique atom types
963	<	atomTypes = getUniqueAtomTypes();
964	<
965	<	//query the max cutoff radius among these atom types
966	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
743	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
962	>	std::string myPolicy;
963	>	if (forceFieldOptions_.haveCutoffPolicy()){
964	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
965	>	}else if (simParams_->haveCutoffPolicy()) {
966	>	myPolicy = simParams_->getCutoffPolicy();
967		}
968
969	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
970	<	#ifdef IS_MPI
971	<	//pick the max cutoff radius among the processors
972	<	#endif
969	>	if (!myPolicy.empty()){
970	>	toUpper(myPolicy);
971	>	if (myPolicy == "MIX") {
972	>	cp = MIX_CUTOFF_POLICY;
973	>	} else {
974	>	if (myPolicy == "MAX") {
975	>	cp = MAX_CUTOFF_POLICY;
976	>	} else {
977	>	if (myPolicy == "TRADITIONAL") {
978	>	cp = TRADITIONAL_CUTOFF_POLICY;
979	>	} else {
980	>	// throw error
981	>	sprintf( painCave.errMsg,
982	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
983	>	painCave.isFatal = 1;
984	>	simError();
985	>	}
986	>	}
987	>	}
988	>	}
989	>	notifyFortranCutoffPolicy(&cp);
990
991	<	return maxCutoffRadius;
992	<	}
991	>	// Check the Skin Thickness for neighborlists
992	>	RealType skin;
993	>	if (simParams_->haveSkinThickness()) {
994	>	skin = simParams_->getSkinThickness();
995	>	notifyFortranSkinThickness(&skin);
996	>	}
997	>
998	>	// Check if the cutoff was set explicitly:
999	>	if (simParams_->haveCutoffRadius()) {
1000	>	rcut_ = simParams_->getCutoffRadius();
1001	>	if (simParams_->haveSwitchingRadius()) {
1002	>	rsw_  = simParams_->getSwitchingRadius();
1003	>	} else {
1004	>	if (fInfo_.SIM_uses_Charges |
1005	>	fInfo_.SIM_uses_Dipoles |
1006	>	fInfo_.SIM_uses_RF) {
1007	>
1008	>	rsw_ = 0.85 * rcut_;
1009	>	sprintf(painCave.errMsg,
1010	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1011	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1012	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1013	>	painCave.isFatal = 0;
1014	>	simError();
1015	>	} else {
1016	>	rsw_ = rcut_;
1017	>	sprintf(painCave.errMsg,
1018	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1019	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
1020	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1021	>	painCave.isFatal = 0;
1022	>	simError();
1023	>	}
1024	>	}
1025
1026	<	void SimInfo::setupCutoff() {
1027	<	double rcut_;  //cutoff radius
1028	<	double rsw_; //switching radius
757	<
758	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1026	>	if (simParams_->haveElectrostaticSummationMethod()) {
1027	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1028	>	toUpper(myMethod);
1029
1030	<	if (!simParams_->haveRcut()){
1031	<	sprintf(painCave.errMsg,
1030	>	if (myMethod == "SHIFTED_POTENTIAL") {
1031	>	ljsp_ = true;
1032	>	} else if (myMethod == "SHIFTED_FORCE") {
1033	>	ljsf_ = true;
1034	>	}
1035	>	}
1036	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1037	>
1038	>	} else {
1039	>
1040	>	// For electrostatic atoms, we'll assume a large safe value:
1041	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1042	>	sprintf(painCave.errMsg,
1043		"SimCreator Warning: No value was set for the cutoffRadius.\n"
1044		"\tOOPSE will use a default value of 15.0 angstroms"
1045		"\tfor the cutoffRadius.\n");
1046	<	painCave.isFatal = 0;
1047	<	simError();
1048	<	rcut_ = 15.0;
1049	<	} else{
1050	<	rcut_ = simParams_->getRcut();
1046	>	painCave.isFatal = 0;
1047	>	simError();
1048	>	rcut_ = 15.0;
1049	>
1050	>	if (simParams_->haveElectrostaticSummationMethod()) {
1051	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1052	>	toUpper(myMethod);
1053	>
1054	>	// For the time being, we're tethering the LJ shifted behavior to the
1055	>	// electrostaticSummationMethod keyword options
1056	>	if (myMethod == "SHIFTED_POTENTIAL") {
1057	>	ljsp_ = true;
1058	>	} else if (myMethod == "SHIFTED_FORCE") {
1059	>	ljsf_ = true;
1060	>	}
1061	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1062	>	if (simParams_->haveSwitchingRadius()){
1063	>	sprintf(painCave.errMsg,
1064	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1065	>	"\teven though the electrostaticSummationMethod was\n"
1066	>	"\tset to %s\n", myMethod.c_str());
1067	>	painCave.isFatal = 1;
1068	>	simError();
1069	>	}
1070	>	}
1071		}
1072	<
1073	<	if (!simParams_->haveRsw()){
1074	<	sprintf(painCave.errMsg,
1075	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1076	<	"\tOOPSE will use a default value of\n"
1077	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
1078	<	painCave.isFatal = 0;
1079	<	simError();
1080	<	rsw_ = 0.95 * rcut_;
1081	<	} else{
1082	<	rsw_ = simParams_->getRsw();
1072	>
1073	>	if (simParams_->haveSwitchingRadius()){
1074	>	rsw_ = simParams_->getSwitchingRadius();
1075	>	} else {
1076	>	sprintf(painCave.errMsg,
1077	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1078	>	"\tOOPSE will use a default value of\n"
1079	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1080	>	painCave.isFatal = 0;
1081	>	simError();
1082	>	rsw_ = 0.85 * rcut_;
1083		}
1084
1085	<	} else {
1086	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
1087	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
1085	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1086	>
1087	>	} else {
1088	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1089	>	// We'll punt and let fortran figure out the cutoffs later.
1090
1091	<	if (simParams_->haveRcut()) {
789	<	rcut_ = simParams_->getRcut();
790	<	} else {
791	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
792	<	rcut_ = calcMaxCutoffRadius();
793	<	}
1091	>	notifyFortranYouAreOnYourOwn();
1092
1093	<	if (simParams_->haveRsw()) {
796	<	rsw_  = simParams_->getRsw();
797	<	} else {
798	<	rsw_ = rcut_;
799	<	}
800	<
1093	>	}
1094		}
1095	<
803	<	double rnblist = rcut_ + 1; // skin of neighbor list
1095	>	}
1096
1097	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1098	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
1099	<	}
1097	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1098	>
1099	>	int errorOut;
1100	>	int esm =  NONE;
1101	>	int sm = UNDAMPED;
1102	>	RealType alphaVal;
1103	>	RealType dielectric;
1104	>
1105	>	errorOut = isError;
1106
1107	<	void SimInfo::addProperty(GenericData* genData) {
1108	<	properties_.addProperty(genData);
1109	<	}
1107	>	if (simParams_->haveElectrostaticSummationMethod()) {
1108	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1109	>	toUpper(myMethod);
1110	>	if (myMethod == "NONE") {
1111	>	esm = NONE;
1112	>	} else {
1113	>	if (myMethod == "SWITCHING_FUNCTION") {
1114	>	esm = SWITCHING_FUNCTION;
1115	>	} else {
1116	>	if (myMethod == "SHIFTED_POTENTIAL") {
1117	>	esm = SHIFTED_POTENTIAL;
1118	>	} else {
1119	>	if (myMethod == "SHIFTED_FORCE") {
1120	>	esm = SHIFTED_FORCE;
1121	>	} else {
1122	>	if (myMethod == "REACTION_FIELD") {
1123	>	esm = REACTION_FIELD;
1124	>	dielectric = simParams_->getDielectric();
1125	>	if (!simParams_->haveDielectric()) {
1126	>	// throw warning
1127	>	sprintf( painCave.errMsg,
1128	>	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1129	>	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1130	>	painCave.isFatal = 0;
1131	>	simError();
1132	>	}
1133	>	} else {
1134	>	// throw error
1135	>	sprintf( painCave.errMsg,
1136	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1137	>	"\t(Input file specified %s .)\n"
1138	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1139	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1140	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1141	>	painCave.isFatal = 1;
1142	>	simError();
1143	>	}
1144	>	}
1145	>	}
1146	>	}
1147	>	}
1148	>	}
1149	>
1150	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1151	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1152	>	toUpper(myScreen);
1153	>	if (myScreen == "UNDAMPED") {
1154	>	sm = UNDAMPED;
1155	>	} else {
1156	>	if (myScreen == "DAMPED") {
1157	>	sm = DAMPED;
1158	>	if (!simParams_->haveDampingAlpha()) {
1159	>	// first set a cutoff dependent alpha value
1160	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1161	>	alphaVal = 0.5125 - rcut_* 0.025;
1162	>	// for values rcut > 20.5, alpha is zero
1163	>	if (alphaVal < 0) alphaVal = 0;
1164
1165	<	void SimInfo::removeProperty(const std::string& propName) {
1166	<	properties_.removeProperty(propName);
1167	<	}
1165	>	// throw warning
1166	>	sprintf( painCave.errMsg,
1167	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1168	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1169	>	painCave.isFatal = 0;
1170	>	simError();
1171	>	} else {
1172	>	alphaVal = simParams_->getDampingAlpha();
1173	>	}
1174	>
1175	>	} else {
1176	>	// throw error
1177	>	sprintf( painCave.errMsg,
1178	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1179	>	"\t(Input file specified %s .)\n"
1180	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1181	>	"or \"damped\".\n", myScreen.c_str() );
1182	>	painCave.isFatal = 1;
1183	>	simError();
1184	>	}
1185	>	}
1186	>	}
1187	>
1188	>	// let's pass some summation method variables to fortran
1189	>	setElectrostaticSummationMethod( &esm );
1190	>	setFortranElectrostaticMethod( &esm );
1191	>	setScreeningMethod( &sm );
1192	>	setDampingAlpha( &alphaVal );
1193	>	setReactionFieldDielectric( &dielectric );
1194	>	initFortranFF( &errorOut );
1195	>	}
1196
1197	<	void SimInfo::clearProperties() {
1198	<	properties_.clearProperties();
819	<	}
1197	>	void SimInfo::setupSwitchingFunction() {
1198	>	int ft = CUBIC;
1199
1200	<	std::vector<std::string> SimInfo::getPropertyNames() {
1201	<	return properties_.getPropertyNames();
1202	<	}
1203	<
1204	<	std::vector<GenericData*> SimInfo::getProperties() {
1205	<	return properties_.getProperties();
1206	<	}
1207	<
1208	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1209	<	return properties_.getPropertyByName(propName);
1210	<	}
1200	>	if (simParams_->haveSwitchingFunctionType()) {
1201	>	std::string funcType = simParams_->getSwitchingFunctionType();
1202	>	toUpper(funcType);
1203	>	if (funcType == "CUBIC") {
1204	>	ft = CUBIC;
1205	>	} else {
1206	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1207	>	ft = FIFTH_ORDER_POLY;
1208	>	} else {
1209	>	// throw error
1210	>	sprintf( painCave.errMsg,
1211	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1212	>	painCave.isFatal = 1;
1213	>	simError();
1214	>	}
1215	>	}
1216	>	}
1217
1218	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1218	>	// send switching function notification to switcheroo
1219	>	setFunctionType(&ft);
1220	>
1221	>	}
1222	>
1223	>	void SimInfo::setupAccumulateBoxDipole() {
1224	>
1225	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1226	>	if ( simParams_->haveAccumulateBoxDipole() )
1227	>	if ( simParams_->getAccumulateBoxDipole() ) {
1228	>	setAccumulateBoxDipole();
1229	>	calcBoxDipole_ = true;
1230	>	}
1231	>
1232	>	}
1233	>
1234	>	void SimInfo::addProperty(GenericData* genData) {
1235	>	properties_.addProperty(genData);
1236	>	}
1237	>
1238	>	void SimInfo::removeProperty(const std::string& propName) {
1239	>	properties_.removeProperty(propName);
1240	>	}
1241	>
1242	>	void SimInfo::clearProperties() {
1243	>	properties_.clearProperties();
1244	>	}
1245	>
1246	>	std::vector<std::string> SimInfo::getPropertyNames() {
1247	>	return properties_.getPropertyNames();
1248	>	}
1249	>
1250	>	std::vector<GenericData*> SimInfo::getProperties() {
1251	>	return properties_.getProperties();
1252	>	}
1253	>
1254	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1255	>	return properties_.getPropertyByName(propName);
1256	>	}
1257	>
1258	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1259	>	if (sman_ == sman) {
1260	>	return;
1261	>	}
1262	>	delete sman_;
1263		sman_ = sman;
1264
1265		Molecule* mol;
#	Line 842 | Line 1271 | void SimInfo::setSnapshotManager(SnapshotManager* sman
1271
1272		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1273
1274	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1275	<	atom->setSnapshotManager(sman_);
1276	<	}
1274	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1275	>	atom->setSnapshotManager(sman_);
1276	>	}
1277
1278	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1279	<	rb->setSnapshotManager(sman_);
1280	<	}
1278	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1279	>	rb->setSnapshotManager(sman_);
1280	>	}
1281		}
1282
1283	<	}
1283	>	}
1284
1285	<	Vector3d SimInfo::getComVel(){
1285	>	Vector3d SimInfo::getComVel(){
1286		SimInfo::MoleculeIterator i;
1287		Molecule* mol;
1288
1289		Vector3d comVel(0.0);
1290	<	double totalMass = 0.0;
1290	>	RealType totalMass = 0.0;
1291
1292
1293		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1294	<	double mass = mol->getMass();
1295	<	totalMass += mass;
1296	<	comVel += mass * mol->getComVel();
1294	>	RealType mass = mol->getMass();
1295	>	totalMass += mass;
1296	>	comVel += mass * mol->getComVel();
1297		}
1298
1299		#ifdef IS_MPI
1300	<	double tmpMass = totalMass;
1300	>	RealType tmpMass = totalMass;
1301		Vector3d tmpComVel(comVel);
1302	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1303	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1302	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1303	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1304		#endif
1305
1306		comVel /= totalMass;
1307
1308		return comVel;
1309	<	}
1309	>	}
1310
1311	<	Vector3d SimInfo::getCom(){
1311	>	Vector3d SimInfo::getCom(){
1312		SimInfo::MoleculeIterator i;
1313		Molecule* mol;
1314
1315		Vector3d com(0.0);
1316	<	double totalMass = 0.0;
1316	>	RealType totalMass = 0.0;
1317
1318		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1319	<	double mass = mol->getMass();
1320	<	totalMass += mass;
1321	<	com += mass * mol->getCom();
1319	>	RealType mass = mol->getMass();
1320	>	totalMass += mass;
1321	>	com += mass * mol->getCom();
1322		}
1323
1324		#ifdef IS_MPI
1325	<	double tmpMass = totalMass;
1325	>	RealType tmpMass = totalMass;
1326		Vector3d tmpCom(com);
1327	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1328	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1327	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1328	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1329		#endif
1330
1331		com /= totalMass;
1332
1333		return com;
1334
1335	<	}
1335	>	}
1336
1337	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1337	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1338
1339		return o;
1340	<	}
1340	>	}
1341	>
1342	>
1343	>	/*
1344	>	Returns center of mass and center of mass velocity in one function call.
1345	>	*/
1346	>
1347	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1348	>	SimInfo::MoleculeIterator i;
1349	>	Molecule* mol;
1350	>
1351	>
1352	>	RealType totalMass = 0.0;
1353	>
1354
1355	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1356	+	RealType mass = mol->getMass();
1357	+	totalMass += mass;
1358	+	com += mass * mol->getCom();
1359	+	comVel += mass * mol->getComVel();
1360	+	}
1361	+
1362	+	#ifdef IS_MPI
1363	+	RealType tmpMass = totalMass;
1364	+	Vector3d tmpCom(com);
1365	+	Vector3d tmpComVel(comVel);
1366	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1367	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1368	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1369	+	#endif
1370	+
1371	+	com /= totalMass;
1372	+	comVel /= totalMass;
1373	+	}
1374	+
1375	+	/*
1376	+	Return intertia tensor for entire system and angular momentum Vector.
1377	+
1378	+
1379	+	[  Ixx -Ixy  -Ixz ]
1380	+	J =| -Iyx  Iyy  -Iyz |
1381	+	[ -Izx -Iyz   Izz ]
1382	+	*/
1383	+
1384	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1385	+
1386	+
1387	+	RealType xx = 0.0;
1388	+	RealType yy = 0.0;
1389	+	RealType zz = 0.0;
1390	+	RealType xy = 0.0;
1391	+	RealType xz = 0.0;
1392	+	RealType yz = 0.0;
1393	+	Vector3d com(0.0);
1394	+	Vector3d comVel(0.0);
1395	+
1396	+	getComAll(com, comVel);
1397	+
1398	+	SimInfo::MoleculeIterator i;
1399	+	Molecule* mol;
1400	+
1401	+	Vector3d thisq(0.0);
1402	+	Vector3d thisv(0.0);
1403	+
1404	+	RealType thisMass = 0.0;
1405	+
1406	+
1407	+
1408	+
1409	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1410	+
1411	+	thisq = mol->getCom()-com;
1412	+	thisv = mol->getComVel()-comVel;
1413	+	thisMass = mol->getMass();
1414	+	// Compute moment of intertia coefficients.
1415	+	xx += thisq[0]*thisq[0]*thisMass;
1416	+	yy += thisq[1]*thisq[1]*thisMass;
1417	+	zz += thisq[2]*thisq[2]*thisMass;
1418	+
1419	+	// compute products of intertia
1420	+	xy += thisq[0]*thisq[1]*thisMass;
1421	+	xz += thisq[0]*thisq[2]*thisMass;
1422	+	yz += thisq[1]*thisq[2]*thisMass;
1423	+
1424	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1425	+
1426	+	}
1427	+
1428	+
1429	+	inertiaTensor(0,0) = yy + zz;
1430	+	inertiaTensor(0,1) = -xy;
1431	+	inertiaTensor(0,2) = -xz;
1432	+	inertiaTensor(1,0) = -xy;
1433	+	inertiaTensor(1,1) = xx + zz;
1434	+	inertiaTensor(1,2) = -yz;
1435	+	inertiaTensor(2,0) = -xz;
1436	+	inertiaTensor(2,1) = -yz;
1437	+	inertiaTensor(2,2) = xx + yy;
1438	+
1439	+	#ifdef IS_MPI
1440	+	Mat3x3d tmpI(inertiaTensor);
1441	+	Vector3d tmpAngMom;
1442	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1443	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1444	+	#endif
1445	+
1446	+	return;
1447	+	}
1448	+
1449	+	//Returns the angular momentum of the system
1450	+	Vector3d SimInfo::getAngularMomentum(){
1451	+
1452	+	Vector3d com(0.0);
1453	+	Vector3d comVel(0.0);
1454	+	Vector3d angularMomentum(0.0);
1455	+
1456	+	getComAll(com,comVel);
1457	+
1458	+	SimInfo::MoleculeIterator i;
1459	+	Molecule* mol;
1460	+
1461	+	Vector3d thisr(0.0);
1462	+	Vector3d thisp(0.0);
1463	+
1464	+	RealType thisMass;
1465	+
1466	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1467	+	thisMass = mol->getMass();
1468	+	thisr = mol->getCom()-com;
1469	+	thisp = (mol->getComVel()-comVel)*thisMass;
1470	+
1471	+	angularMomentum += cross( thisr, thisp );
1472	+
1473	+	}
1474	+
1475	+	#ifdef IS_MPI
1476	+	Vector3d tmpAngMom;
1477	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1478	+	#endif
1479	+
1480	+	return angularMomentum;
1481	+	}
1482	+
1483	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1484	+	return IOIndexToIntegrableObject.at(index);
1485	+	}
1486	+
1487	+	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1488	+	IOIndexToIntegrableObject= v;
1489	+	}
1490	+
1491	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1492	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1493	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1494	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1495	+	*/
1496	+	void SimInfo::getGyrationalVolume(RealType &volume){
1497	+	Mat3x3d intTensor;
1498	+	RealType det;
1499	+	Vector3d dummyAngMom;
1500	+	RealType sysconstants;
1501	+	RealType geomCnst;
1502	+
1503	+	geomCnst = 3.0/2.0;
1504	+	/* Get the inertial tensor and angular momentum for free*/
1505	+	getInertiaTensor(intTensor,dummyAngMom);
1506	+
1507	+	det = intTensor.determinant();
1508	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1509	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1510	+	return;
1511	+	}
1512	+
1513	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1514	+	Mat3x3d intTensor;
1515	+	Vector3d dummyAngMom;
1516	+	RealType sysconstants;
1517	+	RealType geomCnst;
1518	+
1519	+	geomCnst = 3.0/2.0;
1520	+	/* Get the inertial tensor and angular momentum for free*/
1521	+	getInertiaTensor(intTensor,dummyAngMom);
1522	+
1523	+	detI = intTensor.determinant();
1524	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1525	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1526	+	return;
1527	+	}
1528	+	/*
1529	+	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1530	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1531	+	sdByGlobalIndex_ = v;
1532	+	}
1533	+
1534	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1535	+	//assert(index < nAtoms_ + nRigidBodies_);
1536	+	return sdByGlobalIndex_.at(index);
1537	+	}
1538	+	*/
1539		}//end namespace oopse
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