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root/OpenMD/trunk/src/brains/SimInfo.cpp

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 490 by tim, Wed Apr 13 18:41:17 2005 UTC vs.
Revision 1103 by chuckv, Fri Dec 29 20:21:53 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/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(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
86	<	ForceField* ff, Globals* simParams) :
87	<	stamps_(stamps), 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
97	<
98	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
99	<	MoleculeStamp* molStamp;
100	<	int nMolWithSameStamp;
101	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
102	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
103	<	CutoffGroupStamp* cgStamp;
104	<	RigidBodyStamp* rbStamp;
105	<	int nRigidAtoms = 0;
106	<
107	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
108	<	molStamp = i->first;
90	<	nMolWithSameStamp = i->second;
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	>	std::vector<Component*> components = simParams->getComponents();
105	>
106	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
107	>	molStamp = (*i)->getMoleculeStamp();
108	>	nMolWithSameStamp = (*i)->getNMol();
109
110		addMoleculeStamp(molStamp, nMolWithSameStamp);
111
112		//calculate atoms in molecules
113		nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
114
97	–
115		//calculate atoms in cutoff groups
116		int nAtomsInGroups = 0;
117		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
118
119		for (int j=0; j < nCutoffGroupsInStamp; j++) {
120	<	cgStamp = molStamp->getCutoffGroup(j);
121	<	nAtomsInGroups += cgStamp->getNMembers();
120	>	cgStamp = molStamp->getCutoffGroupStamp(j);
121	>	nAtomsInGroups += cgStamp->getNMembers();
122		}
123
124		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
125	+
126		nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
127
128		//calculate atoms in rigid bodies
#	Line 112 | Line 130 | SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::
130		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
131
132		for (int j=0; j < nRigidBodiesInStamp; j++) {
133	<	rbStamp = molStamp->getRigidBody(j);
134	<	nAtomsInRigidBodies += rbStamp->getNMembers();
133	>	rbStamp = molStamp->getRigidBodyStamp(j);
134	>	nAtomsInRigidBodies += rbStamp->getNMembers();
135		}
136
137		nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
138		nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
139
140	<	}
140	>	}
141
142	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
143	<	//therefore the total number of cutoff groups in the system is equal to
144	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
145	<	//file plus the number of cutoff groups defined in meta-data file
146	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
142	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
143	>	//group therefore the total number of cutoff groups in the system is
144	>	//equal to the total number of atoms minus number of atoms belong to
145	>	//cutoff group defined in meta-data file plus the number of cutoff
146	>	//groups defined in meta-data file
147	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
148
149	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
150	<	//therefore the total number of  integrable objects in the system is equal to
151	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
152	<	//file plus the number of  rigid bodies defined in meta-data file
153	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
149	>	//every free atom (atom does not belong to rigid bodies) is an
150	>	//integrable object therefore the total number of integrable objects
151	>	//in the system is equal to the total number of atoms minus number of
152	>	//atoms belong to rigid body defined in meta-data file plus the number
153	>	//of rigid bodies defined in meta-data file
154	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
155	>	+ nGlobalRigidBodies_;
156	>
157	>	nGlobalMols_ = molStampIds_.size();
158
136	–	nGlobalMols_ = molStampIds_.size();
137	–
159		#ifdef IS_MPI
160	<	molToProcMap_.resize(nGlobalMols_);
160	>	molToProcMap_.resize(nGlobalMols_);
161		#endif
162
163	<	}
163	>	}
164
165	<	SimInfo::~SimInfo() {
165	>	SimInfo::~SimInfo() {
166		std::map<int, Molecule*>::iterator i;
167		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
168	<	delete i->second;
168	>	delete i->second;
169		}
170		molecules_.clear();
171
151	–	delete stamps_;
172		delete sman_;
173		delete simParams_;
174		delete forceField_;
175	<	}
175	>	}
176
177	<	int SimInfo::getNGlobalConstraints() {
177	>	int SimInfo::getNGlobalConstraints() {
178		int nGlobalConstraints;
179		#ifdef IS_MPI
180		MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
#	Line 163 | Line 183 | int SimInfo::getNGlobalConstraints() {
183		nGlobalConstraints =  nConstraints_;
184		#endif
185		return nGlobalConstraints;
186	<	}
186	>	}
187
188	<	bool SimInfo::addMolecule(Molecule* mol) {
188	>	bool SimInfo::addMolecule(Molecule* mol) {
189		MoleculeIterator i;
190
191		i = molecules_.find(mol->getGlobalIndex());
192		if (i == molecules_.end() ) {
193
194	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
194	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
195
196	<	nAtoms_ += mol->getNAtoms();
197	<	nBonds_ += mol->getNBonds();
198	<	nBends_ += mol->getNBends();
199	<	nTorsions_ += mol->getNTorsions();
200	<	nRigidBodies_ += mol->getNRigidBodies();
201	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
202	<	nCutoffGroups_ += mol->getNCutoffGroups();
203	<	nConstraints_ += mol->getNConstraintPairs();
196	>	nAtoms_ += mol->getNAtoms();
197	>	nBonds_ += mol->getNBonds();
198	>	nBends_ += mol->getNBends();
199	>	nTorsions_ += mol->getNTorsions();
200	>	nRigidBodies_ += mol->getNRigidBodies();
201	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
202	>	nCutoffGroups_ += mol->getNCutoffGroups();
203	>	nConstraints_ += mol->getNConstraintPairs();
204
205	<	addExcludePairs(mol);
205	>	addExcludePairs(mol);
206
207	<	return true;
207	>	return true;
208		} else {
209	<	return false;
209	>	return false;
210		}
211	<	}
211	>	}
212
213	<	bool SimInfo::removeMolecule(Molecule* mol) {
213	>	bool SimInfo::removeMolecule(Molecule* mol) {
214		MoleculeIterator i;
215		i = molecules_.find(mol->getGlobalIndex());
216
217		if (i != molecules_.end() ) {
218
219	<	assert(mol == i->second);
219	>	assert(mol == i->second);
220
221	<	nAtoms_ -= mol->getNAtoms();
222	<	nBonds_ -= mol->getNBonds();
223	<	nBends_ -= mol->getNBends();
224	<	nTorsions_ -= mol->getNTorsions();
225	<	nRigidBodies_ -= mol->getNRigidBodies();
226	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
227	<	nCutoffGroups_ -= mol->getNCutoffGroups();
228	<	nConstraints_ -= mol->getNConstraintPairs();
221	>	nAtoms_ -= mol->getNAtoms();
222	>	nBonds_ -= mol->getNBonds();
223	>	nBends_ -= mol->getNBends();
224	>	nTorsions_ -= mol->getNTorsions();
225	>	nRigidBodies_ -= mol->getNRigidBodies();
226	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
227	>	nCutoffGroups_ -= mol->getNCutoffGroups();
228	>	nConstraints_ -= mol->getNConstraintPairs();
229
230	<	removeExcludePairs(mol);
231	<	molecules_.erase(mol->getGlobalIndex());
230	>	removeExcludePairs(mol);
231	>	molecules_.erase(mol->getGlobalIndex());
232
233	<	delete mol;
233	>	delete mol;
234
235	<	return true;
235	>	return true;
236		} else {
237	<	return false;
237	>	return false;
238		}
239
240
241	<	}
241	>	}
242
243
244	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
244	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
245		i = molecules_.begin();
246		return i == molecules_.end() ? NULL : i->second;
247	<	}
247	>	}
248
249	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
249	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
250		++i;
251		return i == molecules_.end() ? NULL : i->second;
252	<	}
252	>	}
253
254
255	<	void SimInfo::calcNdf() {
255	>	void SimInfo::calcNdf() {
256		int ndf_local;
257		MoleculeIterator i;
258		std::vector<StuntDouble*>::iterator j;
#	Line 242 | Line 262 | void SimInfo::calcNdf() {
262		ndf_local = 0;
263
264		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
265	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
266	<	integrableObject = mol->nextIntegrableObject(j)) {
265	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
266	>	integrableObject = mol->nextIntegrableObject(j)) {
267
268	<	ndf_local += 3;
268	>	ndf_local += 3;
269
270	<	if (integrableObject->isDirectional()) {
271	<	if (integrableObject->isLinear()) {
272	<	ndf_local += 2;
273	<	} else {
274	<	ndf_local += 3;
275	<	}
276	<	}
270	>	if (integrableObject->isDirectional()) {
271	>	if (integrableObject->isLinear()) {
272	>	ndf_local += 2;
273	>	} else {
274	>	ndf_local += 3;
275	>	}
276	>	}
277
278	<	}//end for (integrableObject)
279	<	}// end for (mol)
278	>	}
279	>	}
280
281		// n_constraints is local, so subtract them on each processor
282		ndf_local -= nConstraints_;
#	Line 271 | Line 291 | void SimInfo::calcNdf() {
291		// entire system:
292		ndf_ = ndf_ - 3 - nZconstraint_;
293
294	<	}
294	>	}
295
296	<	void SimInfo::calcNdfRaw() {
296	>	int SimInfo::getFdf() {
297	>	#ifdef IS_MPI
298	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
299	>	#else
300	>	fdf_ = fdf_local;
301	>	#endif
302	>	return fdf_;
303	>	}
304	>
305	>	void SimInfo::calcNdfRaw() {
306		int ndfRaw_local;
307
308		MoleculeIterator i;
#	Line 285 | Line 314 | void SimInfo::calcNdfRaw() {
314		ndfRaw_local = 0;
315
316		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
317	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
318	<	integrableObject = mol->nextIntegrableObject(j)) {
317	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
318	>	integrableObject = mol->nextIntegrableObject(j)) {
319
320	<	ndfRaw_local += 3;
320	>	ndfRaw_local += 3;
321
322	<	if (integrableObject->isDirectional()) {
323	<	if (integrableObject->isLinear()) {
324	<	ndfRaw_local += 2;
325	<	} else {
326	<	ndfRaw_local += 3;
327	<	}
328	<	}
322	>	if (integrableObject->isDirectional()) {
323	>	if (integrableObject->isLinear()) {
324	>	ndfRaw_local += 2;
325	>	} else {
326	>	ndfRaw_local += 3;
327	>	}
328	>	}
329
330	<	}
330	>	}
331		}
332
333		#ifdef IS_MPI
#	Line 306 | Line 335 | void SimInfo::calcNdfRaw() {
335		#else
336		ndfRaw_ = ndfRaw_local;
337		#endif
338	<	}
338	>	}
339
340	<	void SimInfo::calcNdfTrans() {
340	>	void SimInfo::calcNdfTrans() {
341		int ndfTrans_local;
342
343		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 322 | Line 351 | void SimInfo::calcNdfTrans() {
351
352		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
353
354	<	}
354	>	}
355
356	<	void SimInfo::addExcludePairs(Molecule* mol) {
356	>	void SimInfo::addExcludePairs(Molecule* mol) {
357		std::vector<Bond*>::iterator bondIter;
358		std::vector<Bend*>::iterator bendIter;
359		std::vector<Torsion*>::iterator torsionIter;
#	Line 335 | Line 364 | void SimInfo::addExcludePairs(Molecule* mol) {
364		int b;
365		int c;
366		int d;
367	+
368	+	std::map<int, std::set<int> > atomGroups;
369	+
370	+	Molecule::RigidBodyIterator rbIter;
371	+	RigidBody* rb;
372	+	Molecule::IntegrableObjectIterator ii;
373	+	StuntDouble* integrableObject;
374
375	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
376	+	integrableObject = mol->nextIntegrableObject(ii)) {
377	+
378	+	if (integrableObject->isRigidBody()) {
379	+	rb = static_cast<RigidBody*>(integrableObject);
380	+	std::vector<Atom*> atoms = rb->getAtoms();
381	+	std::set<int> rigidAtoms;
382	+	for (int i = 0; i < atoms.size(); ++i) {
383	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
384	+	}
385	+	for (int i = 0; i < atoms.size(); ++i) {
386	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
387	+	}
388	+	} else {
389	+	std::set<int> oneAtomSet;
390	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
391	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
392	+	}
393	+	}
394	+
395	+
396	+
397		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
398	<	a = bond->getAtomA()->getGlobalIndex();
399	<	b = bond->getAtomB()->getGlobalIndex();
400	<	exclude_.addPair(a, b);
398	>	a = bond->getAtomA()->getGlobalIndex();
399	>	b = bond->getAtomB()->getGlobalIndex();
400	>	exclude_.addPair(a, b);
401		}
402
403		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
404	<	a = bend->getAtomA()->getGlobalIndex();
405	<	b = bend->getAtomB()->getGlobalIndex();
406	<	c = bend->getAtomC()->getGlobalIndex();
404	>	a = bend->getAtomA()->getGlobalIndex();
405	>	b = bend->getAtomB()->getGlobalIndex();
406	>	c = bend->getAtomC()->getGlobalIndex();
407	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
408	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
409	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
410
411	<	exclude_.addPair(a, b);
412	<	exclude_.addPair(a, c);
413	<	exclude_.addPair(b, c);
411	>	exclude_.addPairs(rigidSetA, rigidSetB);
412	>	exclude_.addPairs(rigidSetA, rigidSetC);
413	>	exclude_.addPairs(rigidSetB, rigidSetC);
414	>
415	>	//exclude_.addPair(a, b);
416	>	//exclude_.addPair(a, c);
417	>	//exclude_.addPair(b, c);
418		}
419
420		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
421	<	a = torsion->getAtomA()->getGlobalIndex();
422	<	b = torsion->getAtomB()->getGlobalIndex();
423	<	c = torsion->getAtomC()->getGlobalIndex();
424	<	d = torsion->getAtomD()->getGlobalIndex();
421	>	a = torsion->getAtomA()->getGlobalIndex();
422	>	b = torsion->getAtomB()->getGlobalIndex();
423	>	c = torsion->getAtomC()->getGlobalIndex();
424	>	d = torsion->getAtomD()->getGlobalIndex();
425	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
426	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
427	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
428	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
429
430	<	exclude_.addPair(a, b);
431	<	exclude_.addPair(a, c);
432	<	exclude_.addPair(a, d);
433	<	exclude_.addPair(b, c);
434	<	exclude_.addPair(b, d);
435	<	exclude_.addPair(c, d);
367	<	}
430	>	exclude_.addPairs(rigidSetA, rigidSetB);
431	>	exclude_.addPairs(rigidSetA, rigidSetC);
432	>	exclude_.addPairs(rigidSetA, rigidSetD);
433	>	exclude_.addPairs(rigidSetB, rigidSetC);
434	>	exclude_.addPairs(rigidSetB, rigidSetD);
435	>	exclude_.addPairs(rigidSetC, rigidSetD);
436
437	<	Molecule::RigidBodyIterator rbIter;
438	<	RigidBody* rb;
437	>	/*
438	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
439	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
440	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
441	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
442	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
443	>	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
444	>
445	>
446	>	exclude_.addPair(a, b);
447	>	exclude_.addPair(a, c);
448	>	exclude_.addPair(a, d);
449	>	exclude_.addPair(b, c);
450	>	exclude_.addPair(b, d);
451	>	exclude_.addPair(c, d);
452	>	*/
453	>	}
454	>
455		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
456	<	std::vector<Atom*> atoms = rb->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_.addPair(a, b);
462	<	}
463	<	}
456	>	std::vector<Atom*> atoms = rb->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_.addPair(a, b);
462	>	}
463	>	}
464		}
465
466	<	}
466	>	}
467
468	<	void SimInfo::removeExcludePairs(Molecule* mol) {
468	>	void SimInfo::removeExcludePairs(Molecule* mol) {
469		std::vector<Bond*>::iterator bondIter;
470		std::vector<Bend*>::iterator bendIter;
471		std::vector<Torsion*>::iterator torsionIter;
#	Line 392 | Line 476 | void SimInfo::removeExcludePairs(Molecule* mol) {
476		int b;
477		int c;
478		int d;
479	+
480	+	std::map<int, std::set<int> > atomGroups;
481	+
482	+	Molecule::RigidBodyIterator rbIter;
483	+	RigidBody* rb;
484	+	Molecule::IntegrableObjectIterator ii;
485	+	StuntDouble* integrableObject;
486
487	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
488	+	integrableObject = mol->nextIntegrableObject(ii)) {
489	+
490	+	if (integrableObject->isRigidBody()) {
491	+	rb = static_cast<RigidBody*>(integrableObject);
492	+	std::vector<Atom*> atoms = rb->getAtoms();
493	+	std::set<int> rigidAtoms;
494	+	for (int i = 0; i < atoms.size(); ++i) {
495	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
496	+	}
497	+	for (int i = 0; i < atoms.size(); ++i) {
498	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
499	+	}
500	+	} else {
501	+	std::set<int> oneAtomSet;
502	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
503	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
504	+	}
505	+	}
506	+
507	+
508		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
509	<	a = bond->getAtomA()->getGlobalIndex();
510	<	b = bond->getAtomB()->getGlobalIndex();
511	<	exclude_.removePair(a, b);
509	>	a = bond->getAtomA()->getGlobalIndex();
510	>	b = bond->getAtomB()->getGlobalIndex();
511	>	exclude_.removePair(a, b);
512		}
513
514		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
515	<	a = bend->getAtomA()->getGlobalIndex();
516	<	b = bend->getAtomB()->getGlobalIndex();
517	<	c = bend->getAtomC()->getGlobalIndex();
515	>	a = bend->getAtomA()->getGlobalIndex();
516	>	b = bend->getAtomB()->getGlobalIndex();
517	>	c = bend->getAtomC()->getGlobalIndex();
518
519	<	exclude_.removePair(a, b);
520	<	exclude_.removePair(a, c);
521	<	exclude_.removePair(b, c);
519	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
520	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
521	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
522	>
523	>	exclude_.removePairs(rigidSetA, rigidSetB);
524	>	exclude_.removePairs(rigidSetA, rigidSetC);
525	>	exclude_.removePairs(rigidSetB, rigidSetC);
526	>
527	>	//exclude_.removePair(a, b);
528	>	//exclude_.removePair(a, c);
529	>	//exclude_.removePair(b, c);
530		}
531
532		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
533	<	a = torsion->getAtomA()->getGlobalIndex();
534	<	b = torsion->getAtomB()->getGlobalIndex();
535	<	c = torsion->getAtomC()->getGlobalIndex();
536	<	d = torsion->getAtomD()->getGlobalIndex();
533	>	a = torsion->getAtomA()->getGlobalIndex();
534	>	b = torsion->getAtomB()->getGlobalIndex();
535	>	c = torsion->getAtomC()->getGlobalIndex();
536	>	d = torsion->getAtomD()->getGlobalIndex();
537
538	<	exclude_.removePair(a, b);
539	<	exclude_.removePair(a, c);
540	<	exclude_.removePair(a, d);
541	<	exclude_.removePair(b, c);
542	<	exclude_.removePair(b, d);
543	<	exclude_.removePair(c, d);
538	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
539	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
540	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
541	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
542	>
543	>	exclude_.removePairs(rigidSetA, rigidSetB);
544	>	exclude_.removePairs(rigidSetA, rigidSetC);
545	>	exclude_.removePairs(rigidSetA, rigidSetD);
546	>	exclude_.removePairs(rigidSetB, rigidSetC);
547	>	exclude_.removePairs(rigidSetB, rigidSetD);
548	>	exclude_.removePairs(rigidSetC, rigidSetD);
549	>
550	>	/*
551	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
552	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
553	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
554	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
555	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
556	>	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
557	>
558	>
559	>	exclude_.removePair(a, b);
560	>	exclude_.removePair(a, c);
561	>	exclude_.removePair(a, d);
562	>	exclude_.removePair(b, c);
563	>	exclude_.removePair(b, d);
564	>	exclude_.removePair(c, d);
565	>	*/
566		}
567
426	–	Molecule::RigidBodyIterator rbIter;
427	–	RigidBody* rb;
568		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
569	<	std::vector<Atom*> atoms = rb->getAtoms();
570	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
571	<	for (int j = i + 1; j < atoms.size(); ++j) {
572	<	a = atoms[i]->getGlobalIndex();
573	<	b = atoms[j]->getGlobalIndex();
574	<	exclude_.removePair(a, b);
575	<	}
576	<	}
569	>	std::vector<Atom*> atoms = rb->getAtoms();
570	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
571	>	for (int j = i + 1; j < atoms.size(); ++j) {
572	>	a = atoms[i]->getGlobalIndex();
573	>	b = atoms[j]->getGlobalIndex();
574	>	exclude_.removePair(a, b);
575	>	}
576	>	}
577		}
578
579	<	}
579	>	}
580
581
582	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
582	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
583		int curStampId;
584
585		//index from 0
#	Line 447 | Line 587 | void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp
587
588		moleculeStamps_.push_back(molStamp);
589		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
590	<	}
590	>	}
591
592	<	void SimInfo::update() {
592	>	void SimInfo::update() {
593
594		setupSimType();
595
#	Line 462 | Line 602 | void SimInfo::update() {
602		//setup fortran force field
603		/** @deprecate */
604		int isError = 0;
465	–	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
466	–	if(isError){
467	–	sprintf( painCave.errMsg,
468	–	"ForceField error: There was an error initializing the forceField in fortran.\n" );
469	–	painCave.isFatal = 1;
470	–	simError();
471	–	}
472	–
605
606		setupCutoff();
607	+
608	+	setupElectrostaticSummationMethod( isError );
609	+	setupSwitchingFunction();
610	+	setupAccumulateBoxDipole();
611
612	+	if(isError){
613	+	sprintf( painCave.errMsg,
614	+	"ForceField error: There was an error initializing the forceField in fortran.\n" );
615	+	painCave.isFatal = 1;
616	+	simError();
617	+	}
618	+
619		calcNdf();
620		calcNdfRaw();
621		calcNdfTrans();
622
623		fortranInitialized_ = true;
624	<	}
624	>	}
625
626	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
626	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
627		SimInfo::MoleculeIterator mi;
628		Molecule* mol;
629		Molecule::AtomIterator ai;
#	Line 489 | Line 632 | std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
632
633		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
634
635	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
636	<	atomTypes.insert(atom->getAtomType());
637	<	}
635	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
636	>	atomTypes.insert(atom->getAtomType());
637	>	}
638
639		}
640
641		return atomTypes;
642	<	}
642	>	}
643
644	<	void SimInfo::setupSimType() {
644	>	void SimInfo::setupSimType() {
645		std::set<AtomType*>::iterator i;
646		std::set<AtomType*> atomTypes;
647		atomTypes = getUniqueAtomTypes();
#	Line 506 | Line 649 | void SimInfo::setupSimType() {
649		int useLennardJones = 0;
650		int useElectrostatic = 0;
651		int useEAM = 0;
652	+	int useSC = 0;
653		int useCharge = 0;
654		int useDirectional = 0;
655		int useDipole = 0;
656		int useGayBerne = 0;
657		int useSticky = 0;
658	+	int useStickyPower = 0;
659		int useShape = 0;
660		int useFLARB = 0; //it is not in AtomType yet
661		int useDirectionalAtom = 0;
662		int useElectrostatics = 0;
663		//usePBC and useRF are from simParams
664	<	int usePBC = simParams_->getPBC();
665	<	int useRF = simParams_->getUseRF();
664	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
665	>	int useRF;
666	>	int useSF;
667	>	int useSP;
668	>	int useBoxDipole;
669	>	std::string myMethod;
670
671	+	// set the useRF logical
672	+	useRF = 0;
673	+	useSF = 0;
674	+	useSP = 0;
675	+
676	+
677	+	if (simParams_->haveElectrostaticSummationMethod()) {
678	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
679	+	toUpper(myMethod);
680	+	if (myMethod == "REACTION_FIELD"){
681	+	useRF = 1;
682	+	} else if (myMethod == "SHIFTED_FORCE"){
683	+	useSF = 1;
684	+	} else if (myMethod == "SHIFTED_POTENTIAL"){
685	+	useSP = 1;
686	+	}
687	+	}
688	+
689	+	if (simParams_->haveAccumulateBoxDipole())
690	+	if (simParams_->getAccumulateBoxDipole())
691	+	useBoxDipole = 1;
692	+
693		//loop over all of the atom types
694		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
695	<	useLennardJones |= (*i)->isLennardJones();
696	<	useElectrostatic |= (*i)->isElectrostatic();
697	<	useEAM |= (*i)->isEAM();
698	<	useCharge |= (*i)->isCharge();
699	<	useDirectional |= (*i)->isDirectional();
700	<	useDipole |= (*i)->isDipole();
701	<	useGayBerne |= (*i)->isGayBerne();
702	<	useSticky |= (*i)->isSticky();
703	<	useShape |= (*i)->isShape();
695	>	useLennardJones |= (*i)->isLennardJones();
696	>	useElectrostatic |= (*i)->isElectrostatic();
697	>	useEAM |= (*i)->isEAM();
698	>	useSC |= (*i)->isSC();
699	>	useCharge |= (*i)->isCharge();
700	>	useDirectional |= (*i)->isDirectional();
701	>	useDipole |= (*i)->isDipole();
702	>	useGayBerne |= (*i)->isGayBerne();
703	>	useSticky |= (*i)->isSticky();
704	>	useStickyPower |= (*i)->isStickyPower();
705	>	useShape |= (*i)->isShape();
706		}
707
708	<	if (useSticky || useDipole || useGayBerne || useShape) {
709	<	useDirectionalAtom = 1;
708	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
709	>	useDirectionalAtom = 1;
710		}
711
712		if (useCharge || useDipole) {
713	<	useElectrostatics = 1;
713	>	useElectrostatics = 1;
714		}
715
716		#ifdef IS_MPI
#	Line 564 | Line 737 | void SimInfo::setupSimType() {
737		temp = useSticky;
738		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
739
740	+	temp = useStickyPower;
741	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
742	+
743		temp = useGayBerne;
744		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
745
746		temp = useEAM;
747		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
748
749	+	temp = useSC;
750	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
751	+
752		temp = useShape;
753		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
754
#	Line 578 | Line 757 | void SimInfo::setupSimType() {
757
758		temp = useRF;
759		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
760	<
760	>
761	>	temp = useSF;
762	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
763	>
764	>	temp = useSP;
765	>	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766	>
767	>	temp = useBoxDipole;
768	>	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769	>
770		#endif
771
772		fInfo_.SIM_uses_PBC = usePBC;
#	Line 588 | Line 776 | void SimInfo::setupSimType() {
776		fInfo_.SIM_uses_Charges = useCharge;
777		fInfo_.SIM_uses_Dipoles = useDipole;
778		fInfo_.SIM_uses_Sticky = useSticky;
779	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
780		fInfo_.SIM_uses_GayBerne = useGayBerne;
781		fInfo_.SIM_uses_EAM = useEAM;
782	+	fInfo_.SIM_uses_SC = useSC;
783		fInfo_.SIM_uses_Shapes = useShape;
784		fInfo_.SIM_uses_FLARB = useFLARB;
785		fInfo_.SIM_uses_RF = useRF;
786	+	fInfo_.SIM_uses_SF = useSF;
787	+	fInfo_.SIM_uses_SP = useSP;
788	+	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
789	+	}
790
791	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
598	<
599	<	if (simParams_->haveDielectric()) {
600	<	fInfo_.dielect = simParams_->getDielectric();
601	<	} else {
602	<	sprintf(painCave.errMsg,
603	<	"SimSetup Error: No Dielectric constant was set.\n"
604	<	"\tYou are trying to use Reaction Field without"
605	<	"\tsetting a dielectric constant!\n");
606	<	painCave.isFatal = 1;
607	<	simError();
608	<	}
609	<
610	<	} else {
611	<	fInfo_.dielect = 0.0;
612	<	}
613	<
614	<	}
615	<
616	<	void SimInfo::setupFortranSim() {
791	>	void SimInfo::setupFortranSim() {
792		int isError;
793		int nExclude;
794		std::vector<int> fortranGlobalGroupMembership;
#	Line 623 | Line 798 | void SimInfo::setupFortranSim() {
798
799		//globalGroupMembership_ is filled by SimCreator
800		for (int i = 0; i < nGlobalAtoms_; i++) {
801	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
801	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
802		}
803
804		//calculate mass ratio of cutoff group
805	<	std::vector<double> mfact;
805	>	std::vector<RealType> mfact;
806		SimInfo::MoleculeIterator mi;
807		Molecule* mol;
808		Molecule::CutoffGroupIterator ci;
809		CutoffGroup* cg;
810		Molecule::AtomIterator ai;
811		Atom* atom;
812	<	double totalMass;
812	>	RealType totalMass;
813
814		//to avoid memory reallocation, reserve enough space for mfact
815		mfact.reserve(getNCutoffGroups());
816
817		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
818	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
818	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
819
820	<	totalMass = cg->getMass();
821	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
822	<	mfact.push_back(atom->getMass()/totalMass);
823	<	}
820	>	totalMass = cg->getMass();
821	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
822	>	// Check for massless groups - set mfact to 1 if true
823	>	if (totalMass != 0)
824	>	mfact.push_back(atom->getMass()/totalMass);
825	>	else
826	>	mfact.push_back( 1.0 );
827	>	}
828
829	<	}
829	>	}
830		}
831
832		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
#	Line 657 | Line 836 | void SimInfo::setupFortranSim() {
836		identArray.reserve(getNAtoms());
837
838		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
839	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
840	<	identArray.push_back(atom->getIdent());
841	<	}
839	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
840	>	identArray.push_back(atom->getIdent());
841	>	}
842		}
843
844		//fill molMembershipArray
845		//molMembershipArray is filled by SimCreator
846		std::vector<int> molMembershipArray(nGlobalAtoms_);
847		for (int i = 0; i < nGlobalAtoms_; i++) {
848	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
848	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
849		}
850
851		//setup fortran simulation
#	Line 674 | Line 853 | void SimInfo::setupFortranSim() {
853		int* globalExcludes = NULL;
854		int* excludeList = exclude_.getExcludeList();
855		setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
856	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
857	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
856	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
857	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
858
859		if( isError ){
860
861	<	sprintf( painCave.errMsg,
862	<	"There was an error setting the simulation information in fortran.\n" );
863	<	painCave.isFatal = 1;
864	<	painCave.severity = OOPSE_ERROR;
865	<	simError();
861	>	sprintf( painCave.errMsg,
862	>	"There was an error setting the simulation information in fortran.\n" );
863	>	painCave.isFatal = 1;
864	>	painCave.severity = OOPSE_ERROR;
865	>	simError();
866		}
867
868		#ifdef IS_MPI
869		sprintf( checkPointMsg,
870	<	"succesfully sent the simulation information to fortran.\n");
870	>	"succesfully sent the simulation information to fortran.\n");
871		MPIcheckPoint();
872		#endif // is_mpi
694	–	}
873
874	+	// Setup number of neighbors in neighbor list if present
875	+	if (simParams_->haveNeighborListNeighbors()) {
876	+	setNeighbors(simParams_->getNeighborListNeighbors());
877	+	}
878	+
879
880	+	}
881	+
882	+
883		#ifdef IS_MPI
884	<	void SimInfo::setupFortranParallel() {
884	>	void SimInfo::setupFortranParallel() {
885
886		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
887		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
#	Line 711 | Line 897 | void SimInfo::setupFortranParallel() {
897
898		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
899
900	<	//local index(index in DataStorge) of atom is important
901	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
902	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
903	<	}
900	>	//local index(index in DataStorge) of atom is important
901	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
902	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
903	>	}
904
905	<	//local index of cutoff group is trivial, it only depends on the order of travesing
906	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
907	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
908	<	}
905	>	//local index of cutoff group is trivial, it only depends on the order of travesing
906	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
907	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
908	>	}
909
910		}
911
#	Line 739 | Line 925 | void SimInfo::setupFortranParallel() {
925		&localToGlobalCutoffGroupIndex[0], &isError);
926
927		if (isError) {
928	<	sprintf(painCave.errMsg,
929	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
930	<	painCave.isFatal = 1;
931	<	simError();
928	>	sprintf(painCave.errMsg,
929	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
930	>	painCave.isFatal = 1;
931	>	simError();
932		}
933
934		sprintf(checkPointMsg, " mpiRefresh successful.\n");
935		MPIcheckPoint();
936
937
938	<	}
938	>	}
939
940		#endif
941
942	<	double SimInfo::calcMaxCutoffRadius() {
942	>	void SimInfo::setupCutoff() {
943	>
944	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
945
946	+	// Check the cutoff policy
947	+	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
948
949	<	std::set<AtomType*> atomTypes;
950	<	std::set<AtomType*>::iterator i;
951	<	std::vector<double> cutoffRadius;
952	<
953	<	//get the unique atom types
764	<	atomTypes = getUniqueAtomTypes();
765	<
766	<	//query the max cutoff radius among these atom types
767	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
768	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
949	>	std::string myPolicy;
950	>	if (forceFieldOptions_.haveCutoffPolicy()){
951	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
952	>	}else if (simParams_->haveCutoffPolicy()) {
953	>	myPolicy = simParams_->getCutoffPolicy();
954		}
955
956	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
957	<	#ifdef IS_MPI
958	<	//pick the max cutoff radius among the processors
959	<	#endif
956	>	if (!myPolicy.empty()){
957	>	toUpper(myPolicy);
958	>	if (myPolicy == "MIX") {
959	>	cp = MIX_CUTOFF_POLICY;
960	>	} else {
961	>	if (myPolicy == "MAX") {
962	>	cp = MAX_CUTOFF_POLICY;
963	>	} else {
964	>	if (myPolicy == "TRADITIONAL") {
965	>	cp = TRADITIONAL_CUTOFF_POLICY;
966	>	} else {
967	>	// throw error
968	>	sprintf( painCave.errMsg,
969	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
970	>	painCave.isFatal = 1;
971	>	simError();
972	>	}
973	>	}
974	>	}
975	>	}
976	>	notifyFortranCutoffPolicy(&cp);
977
978	<	return maxCutoffRadius;
979	<	}
980	<
981	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
982	<
983	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
978	>	// Check the Skin Thickness for neighborlists
979	>	RealType skin;
980	>	if (simParams_->haveSkinThickness()) {
981	>	skin = simParams_->getSkinThickness();
982	>	notifyFortranSkinThickness(&skin);
983	>	}
984
985	<	if (!simParams_->haveRcut()){
986	<	sprintf(painCave.errMsg,
985	>	// Check if the cutoff was set explicitly:
986	>	if (simParams_->haveCutoffRadius()) {
987	>	rcut_ = simParams_->getCutoffRadius();
988	>	if (simParams_->haveSwitchingRadius()) {
989	>	rsw_  = simParams_->getSwitchingRadius();
990	>	} else {
991	>	if (fInfo_.SIM_uses_Charges |
992	>	fInfo_.SIM_uses_Dipoles |
993	>	fInfo_.SIM_uses_RF) {
994	>
995	>	rsw_ = 0.85 * rcut_;
996	>	sprintf(painCave.errMsg,
997	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
998	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
999	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1000	>	painCave.isFatal = 0;
1001	>	simError();
1002	>	} else {
1003	>	rsw_ = rcut_;
1004	>	sprintf(painCave.errMsg,
1005	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1006	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
1007	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1008	>	painCave.isFatal = 0;
1009	>	simError();
1010	>	}
1011	>	}
1012	>
1013	>	notifyFortranCutoffs(&rcut_, &rsw_);
1014	>
1015	>	} else {
1016	>
1017	>	// For electrostatic atoms, we'll assume a large safe value:
1018	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1019	>	sprintf(painCave.errMsg,
1020		"SimCreator Warning: No value was set for the cutoffRadius.\n"
1021		"\tOOPSE will use a default value of 15.0 angstroms"
1022		"\tfor the cutoffRadius.\n");
1023	<	painCave.isFatal = 0;
1024	<	simError();
1025	<	rcut = 15.0;
1026	<	} else{
1027	<	rcut = simParams_->getRcut();
1023	>	painCave.isFatal = 0;
1024	>	simError();
1025	>	rcut_ = 15.0;
1026	>
1027	>	if (simParams_->haveElectrostaticSummationMethod()) {
1028	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1029	>	toUpper(myMethod);
1030	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1031	>	if (simParams_->haveSwitchingRadius()){
1032	>	sprintf(painCave.errMsg,
1033	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1034	>	"\teven though the electrostaticSummationMethod was\n"
1035	>	"\tset to %s\n", myMethod.c_str());
1036	>	painCave.isFatal = 1;
1037	>	simError();
1038	>	}
1039	>	}
1040		}
1041	<
1042	<	if (!simParams_->haveRsw()){
1043	<	sprintf(painCave.errMsg,
1044	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1045	<	"\tOOPSE will use a default value of\n"
1046	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
1047	<	painCave.isFatal = 0;
1048	<	simError();
1049	<	rsw = 0.95 * rcut;
1050	<	} else{
1051	<	rsw = simParams_->getRsw();
1041	>
1042	>	if (simParams_->haveSwitchingRadius()){
1043	>	rsw_ = simParams_->getSwitchingRadius();
1044	>	} else {
1045	>	sprintf(painCave.errMsg,
1046	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1047	>	"\tOOPSE will use a default value of\n"
1048	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1049	>	painCave.isFatal = 0;
1050	>	simError();
1051	>	rsw_ = 0.85 * rcut_;
1052		}
1053	<
1054	<	} else {
1055	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
1056	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
1053	>	notifyFortranCutoffs(&rcut_, &rsw_);
1054	>	} else {
1055	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1056	>	// We'll punt and let fortran figure out the cutoffs later.
1057
1058	<	if (simParams_->haveRcut()) {
812	<	rcut = simParams_->getRcut();
813	<	} else {
814	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
815	<	rcut = calcMaxCutoffRadius();
816	<	}
1058	>	notifyFortranYouAreOnYourOwn();
1059
1060	<	if (simParams_->haveRsw()) {
1061	<	rsw  = simParams_->getRsw();
1060	>	}
1061	>	}
1062	>	}
1063	>
1064	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1065	>
1066	>	int errorOut;
1067	>	int esm =  NONE;
1068	>	int sm = UNDAMPED;
1069	>	RealType alphaVal;
1070	>	RealType dielectric;
1071	>
1072	>	errorOut = isError;
1073	>
1074	>	if (simParams_->haveElectrostaticSummationMethod()) {
1075	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1076	>	toUpper(myMethod);
1077	>	if (myMethod == "NONE") {
1078	>	esm = NONE;
1079	>	} else {
1080	>	if (myMethod == "SWITCHING_FUNCTION") {
1081	>	esm = SWITCHING_FUNCTION;
1082		} else {
1083	<	rsw = rcut;
1084	<	}
1083	>	if (myMethod == "SHIFTED_POTENTIAL") {
1084	>	esm = SHIFTED_POTENTIAL;
1085	>	} else {
1086	>	if (myMethod == "SHIFTED_FORCE") {
1087	>	esm = SHIFTED_FORCE;
1088	>	} else {
1089	>	if (myMethod == "REACTION_FIELD") {
1090	>	esm = REACTION_FIELD;
1091	>	dielectric = simParams_->getDielectric();
1092	>	if (!simParams_->haveDielectric()) {
1093	>	// throw warning
1094	>	sprintf( painCave.errMsg,
1095	>	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1096	>	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1097	>	painCave.isFatal = 0;
1098	>	simError();
1099	>	}
1100	>	} else {
1101	>	// throw error
1102	>	sprintf( painCave.errMsg,
1103	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1104	>	"\t(Input file specified %s .)\n"
1105	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1106	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1107	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1108	>	painCave.isFatal = 1;
1109	>	simError();
1110	>	}
1111	>	}
1112	>	}
1113	>	}
1114	>	}
1115	>	}
1116
1117	+	if (simParams_->haveElectrostaticScreeningMethod()) {
1118	+	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1119	+	toUpper(myScreen);
1120	+	if (myScreen == "UNDAMPED") {
1121	+	sm = UNDAMPED;
1122	+	} else {
1123	+	if (myScreen == "DAMPED") {
1124	+	sm = DAMPED;
1125	+	if (!simParams_->haveDampingAlpha()) {
1126	+	// first set a cutoff dependent alpha value
1127	+	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1128	+	alphaVal = 0.5125 - rcut_* 0.025;
1129	+	// for values rcut > 20.5, alpha is zero
1130	+	if (alphaVal < 0) alphaVal = 0;
1131	+
1132	+	// throw warning
1133	+	sprintf( painCave.errMsg,
1134	+	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1135	+	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1136	+	painCave.isFatal = 0;
1137	+	simError();
1138	+	} else {
1139	+	alphaVal = simParams_->getDampingAlpha();
1140	+	}
1141	+
1142	+	} else {
1143	+	// throw error
1144	+	sprintf( painCave.errMsg,
1145	+	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1146	+	"\t(Input file specified %s .)\n"
1147	+	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1148	+	"or \"damped\".\n", myScreen.c_str() );
1149	+	painCave.isFatal = 1;
1150	+	simError();
1151	+	}
1152	+	}
1153		}
1154	<	}
1154	>
1155	>	// let's pass some summation method variables to fortran
1156	>	setElectrostaticSummationMethod( &esm );
1157	>	setFortranElectrostaticMethod( &esm );
1158	>	setScreeningMethod( &sm );
1159	>	setDampingAlpha( &alphaVal );
1160	>	setReactionFieldDielectric( &dielectric );
1161	>	initFortranFF( &errorOut );
1162	>	}
1163
1164	<	void SimInfo::setupCutoff() {
1165	<	getCutoff(rcut_, rsw_);
829	<	double rnblist = rcut_ + 1; // skin of neighbor list
1164	>	void SimInfo::setupSwitchingFunction() {
1165	>	int ft = CUBIC;
1166
1167	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1168	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
1169	<	}
1167	>	if (simParams_->haveSwitchingFunctionType()) {
1168	>	std::string funcType = simParams_->getSwitchingFunctionType();
1169	>	toUpper(funcType);
1170	>	if (funcType == "CUBIC") {
1171	>	ft = CUBIC;
1172	>	} else {
1173	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1174	>	ft = FIFTH_ORDER_POLY;
1175	>	} else {
1176	>	// throw error
1177	>	sprintf( painCave.errMsg,
1178	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1179	>	painCave.isFatal = 1;
1180	>	simError();
1181	>	}
1182	>	}
1183	>	}
1184
1185	<	void SimInfo::addProperty(GenericData* genData) {
1186	<	properties_.addProperty(genData);
837	<	}
1185	>	// send switching function notification to switcheroo
1186	>	setFunctionType(&ft);
1187
1188	<	void SimInfo::removeProperty(const std::string& propName) {
1189	<	properties_.removeProperty(propName);
1190	<	}
1191	<
1192	<	void SimInfo::clearProperties() {
1188	>	}
1189	>
1190	>	void SimInfo::setupAccumulateBoxDipole() {
1191	>
1192	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1193	>	if ( simParams_->haveAccumulateBoxDipole() )
1194	>	if ( simParams_->getAccumulateBoxDipole() ) {
1195	>	setAccumulateBoxDipole();
1196	>	calcBoxDipole_ = true;
1197	>	}
1198	>
1199	>	}
1200	>
1201	>	void SimInfo::addProperty(GenericData* genData) {
1202	>	properties_.addProperty(genData);
1203	>	}
1204	>
1205	>	void SimInfo::removeProperty(const std::string& propName) {
1206	>	properties_.removeProperty(propName);
1207	>	}
1208	>
1209	>	void SimInfo::clearProperties() {
1210		properties_.clearProperties();
1211	<	}
1211	>	}
1212
1213	<	std::vector<std::string> SimInfo::getPropertyNames() {
1213	>	std::vector<std::string> SimInfo::getPropertyNames() {
1214		return properties_.getPropertyNames();
1215	<	}
1215	>	}
1216
1217	<	std::vector<GenericData*> SimInfo::getProperties() {
1217	>	std::vector<GenericData*> SimInfo::getProperties() {
1218		return properties_.getProperties();
1219	<	}
1219	>	}
1220
1221	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1221	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1222		return properties_.getPropertyByName(propName);
1223	<	}
1223	>	}
1224
1225	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1225	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1226		if (sman_ == sman) {
1227	<	return;
1227	>	return;
1228		}
1229		delete sman_;
1230		sman_ = sman;
#	Line 872 | Line 1238 | void SimInfo::setSnapshotManager(SnapshotManager* sman
1238
1239		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1240
1241	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1242	<	atom->setSnapshotManager(sman_);
1243	<	}
1241	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1242	>	atom->setSnapshotManager(sman_);
1243	>	}
1244
1245	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1246	<	rb->setSnapshotManager(sman_);
1247	<	}
1245	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1246	>	rb->setSnapshotManager(sman_);
1247	>	}
1248		}
1249
1250	<	}
1250	>	}
1251
1252	<	Vector3d SimInfo::getComVel(){
1252	>	Vector3d SimInfo::getComVel(){
1253		SimInfo::MoleculeIterator i;
1254		Molecule* mol;
1255
1256		Vector3d comVel(0.0);
1257	<	double totalMass = 0.0;
1257	>	RealType totalMass = 0.0;
1258
1259
1260		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1261	<	double mass = mol->getMass();
1262	<	totalMass += mass;
1263	<	comVel += mass * mol->getComVel();
1261	>	RealType mass = mol->getMass();
1262	>	totalMass += mass;
1263	>	comVel += mass * mol->getComVel();
1264		}
1265
1266		#ifdef IS_MPI
1267	<	double tmpMass = totalMass;
1267	>	RealType tmpMass = totalMass;
1268		Vector3d tmpComVel(comVel);
1269	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1270	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1269	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1270	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1271		#endif
1272
1273		comVel /= totalMass;
1274
1275		return comVel;
1276	<	}
1276	>	}
1277
1278	<	Vector3d SimInfo::getCom(){
1278	>	Vector3d SimInfo::getCom(){
1279		SimInfo::MoleculeIterator i;
1280		Molecule* mol;
1281
1282		Vector3d com(0.0);
1283	<	double totalMass = 0.0;
1283	>	RealType totalMass = 0.0;
1284
1285		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1286	<	double mass = mol->getMass();
1287	<	totalMass += mass;
1288	<	com += mass * mol->getCom();
1286	>	RealType mass = mol->getMass();
1287	>	totalMass += mass;
1288	>	com += mass * mol->getCom();
1289		}
1290
1291		#ifdef IS_MPI
1292	<	double tmpMass = totalMass;
1292	>	RealType tmpMass = totalMass;
1293		Vector3d tmpCom(com);
1294	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1295	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1294	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1295	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1296		#endif
1297
1298		com /= totalMass;
1299
1300		return com;
1301
1302	<	}
1302	>	}
1303
1304	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1304	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1305
1306		return o;
1307	<	}
1307	>	}
1308	>
1309	>
1310	>	/*
1311	>	Returns center of mass and center of mass velocity in one function call.
1312	>	*/
1313	>
1314	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1315	>	SimInfo::MoleculeIterator i;
1316	>	Molecule* mol;
1317	>
1318	>
1319	>	RealType totalMass = 0.0;
1320	>
1321
1322	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1323	+	RealType mass = mol->getMass();
1324	+	totalMass += mass;
1325	+	com += mass * mol->getCom();
1326	+	comVel += mass * mol->getComVel();
1327	+	}
1328	+
1329	+	#ifdef IS_MPI
1330	+	RealType tmpMass = totalMass;
1331	+	Vector3d tmpCom(com);
1332	+	Vector3d tmpComVel(comVel);
1333	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1334	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1335	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1336	+	#endif
1337	+
1338	+	com /= totalMass;
1339	+	comVel /= totalMass;
1340	+	}
1341	+
1342	+	/*
1343	+	Return intertia tensor for entire system and angular momentum Vector.
1344	+
1345	+
1346	+	[  Ixx -Ixy  -Ixz ]
1347	+	J =| -Iyx  Iyy  -Iyz |
1348	+	[ -Izx -Iyz   Izz ]
1349	+	*/
1350	+
1351	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1352	+
1353	+
1354	+	RealType xx = 0.0;
1355	+	RealType yy = 0.0;
1356	+	RealType zz = 0.0;
1357	+	RealType xy = 0.0;
1358	+	RealType xz = 0.0;
1359	+	RealType yz = 0.0;
1360	+	Vector3d com(0.0);
1361	+	Vector3d comVel(0.0);
1362	+
1363	+	getComAll(com, comVel);
1364	+
1365	+	SimInfo::MoleculeIterator i;
1366	+	Molecule* mol;
1367	+
1368	+	Vector3d thisq(0.0);
1369	+	Vector3d thisv(0.0);
1370	+
1371	+	RealType thisMass = 0.0;
1372	+
1373	+
1374	+
1375	+
1376	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1377	+
1378	+	thisq = mol->getCom()-com;
1379	+	thisv = mol->getComVel()-comVel;
1380	+	thisMass = mol->getMass();
1381	+	// Compute moment of intertia coefficients.
1382	+	xx += thisq[0]*thisq[0]*thisMass;
1383	+	yy += thisq[1]*thisq[1]*thisMass;
1384	+	zz += thisq[2]*thisq[2]*thisMass;
1385	+
1386	+	// compute products of intertia
1387	+	xy += thisq[0]*thisq[1]*thisMass;
1388	+	xz += thisq[0]*thisq[2]*thisMass;
1389	+	yz += thisq[1]*thisq[2]*thisMass;
1390	+
1391	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1392	+
1393	+	}
1394	+
1395	+
1396	+	inertiaTensor(0,0) = yy + zz;
1397	+	inertiaTensor(0,1) = -xy;
1398	+	inertiaTensor(0,2) = -xz;
1399	+	inertiaTensor(1,0) = -xy;
1400	+	inertiaTensor(1,1) = xx + zz;
1401	+	inertiaTensor(1,2) = -yz;
1402	+	inertiaTensor(2,0) = -xz;
1403	+	inertiaTensor(2,1) = -yz;
1404	+	inertiaTensor(2,2) = xx + yy;
1405	+
1406	+	#ifdef IS_MPI
1407	+	Mat3x3d tmpI(inertiaTensor);
1408	+	Vector3d tmpAngMom;
1409	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1410	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1411	+	#endif
1412	+
1413	+	return;
1414	+	}
1415	+
1416	+	//Returns the angular momentum of the system
1417	+	Vector3d SimInfo::getAngularMomentum(){
1418	+
1419	+	Vector3d com(0.0);
1420	+	Vector3d comVel(0.0);
1421	+	Vector3d angularMomentum(0.0);
1422	+
1423	+	getComAll(com,comVel);
1424	+
1425	+	SimInfo::MoleculeIterator i;
1426	+	Molecule* mol;
1427	+
1428	+	Vector3d thisr(0.0);
1429	+	Vector3d thisp(0.0);
1430	+
1431	+	RealType thisMass;
1432	+
1433	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1434	+	thisMass = mol->getMass();
1435	+	thisr = mol->getCom()-com;
1436	+	thisp = (mol->getComVel()-comVel)*thisMass;
1437	+
1438	+	angularMomentum += cross( thisr, thisp );
1439	+
1440	+	}
1441	+
1442	+	#ifdef IS_MPI
1443	+	Vector3d tmpAngMom;
1444	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1445	+	#endif
1446	+
1447	+	return angularMomentum;
1448	+	}
1449	+
1450	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1451	+	return IOIndexToIntegrableObject.at(index);
1452	+	}
1453	+
1454	+	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1455	+	IOIndexToIntegrableObject= v;
1456	+	}
1457	+
1458	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1459	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1460	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1461	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1462	+	*/
1463	+	void SimInfo::getGyrationalVolume(RealType &volume){
1464	+	Mat3x3d intTensor;
1465	+	RealType det;
1466	+	Vector3d dummyAngMom;
1467	+	RealType sysconstants;
1468	+	RealType geomCnst;
1469	+
1470	+	geomCnst = 3.0/2.0;
1471	+	/* Get the inertial tensor and angular momentum for free*/
1472	+	getInertiaTensor(intTensor,dummyAngMom);
1473	+
1474	+	det = intTensor.determinant();
1475	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1476	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1477	+	return;
1478	+	}
1479	+
1480	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1481	+	Mat3x3d intTensor;
1482	+	Vector3d dummyAngMom;
1483	+	RealType sysconstants;
1484	+	RealType geomCnst;
1485	+
1486	+	geomCnst = 3.0/2.0;
1487	+	/* Get the inertial tensor and angular momentum for free*/
1488	+	getInertiaTensor(intTensor,dummyAngMom);
1489	+
1490	+	detI = intTensor.determinant();
1491	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1492	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1493	+	return;
1494	+	}
1495	+	/*
1496	+	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1497	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1498	+	sdByGlobalIndex_ = v;
1499	+	}
1500	+
1501	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1502	+	//assert(index < nAtoms_ + nRigidBodies_);
1503	+	return sdByGlobalIndex_.at(index);
1504	+	}
1505	+	*/
1506		}//end namespace oopse
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