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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 331 by tim, Sun Feb 13 21:18:27 2005 UTC vs.
Revision 1290 by cli2, Wed Sep 10 19:51:45 2008 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), selectMan_(NULL) {
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), nInversions_(0),
94	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
95	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
96	>	calcBoxDipole_(false), 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;
110	<	nMolWithSameStamp = i->second;
98	>
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	>	std::vector<Component*> components = simParams->getComponents();
108	>
109	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
110	>	molStamp = (*i)->getMoleculeStamp();
111	>	nMolWithSameStamp = (*i)->getNMol();
112
113		addMoleculeStamp(molStamp, nMolWithSameStamp);
114
115		//calculate atoms in molecules
116		nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
117
97	–
118		//calculate atoms in cutoff groups
119		int nAtomsInGroups = 0;
120		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
121
122		for (int j=0; j < nCutoffGroupsInStamp; j++) {
123	<	cgStamp = molStamp->getCutoffGroup(j);
124	<	nAtomsInGroups += cgStamp->getNMembers();
123	>	cgStamp = molStamp->getCutoffGroupStamp(j);
124	>	nAtomsInGroups += cgStamp->getNMembers();
125		}
126
127		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
128	+
129		nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
130
131		//calculate atoms in rigid bodies
#	Line 112 | Line 133 | SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*,
133		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
134
135		for (int j=0; j < nRigidBodiesInStamp; j++) {
136	<	rbStamp = molStamp->getRigidBody(j);
137	<	nAtomsInRigidBodies += rbStamp->getNMembers();
136	>	rbStamp = molStamp->getRigidBodyStamp(j);
137	>	nAtomsInRigidBodies += rbStamp->getNMembers();
138		}
139
140		nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
141		nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
142
143	<	}
143	>	}
144
145	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
146	<	//therefore the total number of cutoff groups in the system is equal to
147	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
148	<	//file plus the number of cutoff groups defined in meta-data file
149	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
145	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
146	>	//group therefore the total number of cutoff groups in the system is
147	>	//equal to the total number of atoms minus number of atoms belong to
148	>	//cutoff group defined in meta-data file plus the number of cutoff
149	>	//groups defined in meta-data file
150	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
151
152	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
153	<	//therefore the total number of  integrable objects in the system is equal to
154	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
155	<	//file plus the number of  rigid bodies defined in meta-data file
156	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
152	>	//every free atom (atom does not belong to rigid bodies) is an
153	>	//integrable object therefore the total number of integrable objects
154	>	//in the system is equal to the total number of atoms minus number of
155	>	//atoms belong to rigid body defined in meta-data file plus the number
156	>	//of rigid bodies defined in meta-data file
157	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
158	>	+ nGlobalRigidBodies_;
159	>
160	>	nGlobalMols_ = molStampIds_.size();
161	>	molToProcMap_.resize(nGlobalMols_);
162	>	}
163
164	<	nGlobalMols_ = molStampIds_.size();
165	<
166	<	#ifdef IS_MPI
167	<	molToProcMap_.resize(nGlobalMols_);
168	<	#endif
169	<
170	<	selectMan_ = new SelectionManager(this);
143	<	selectMan_->selectAll();
144	<	}
145	<
146	<	SimInfo::~SimInfo() {
147	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
148	<
149	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
150	<
164	>	SimInfo::~SimInfo() {
165	>	std::map<int, Molecule*>::iterator i;
166	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
167	>	delete i->second;
168	>	}
169	>	molecules_.clear();
170	>
171		delete sman_;
172		delete simParams_;
173		delete forceField_;
174	<	delete selectMan_;
155	<	}
174	>	}
175
176	<	int SimInfo::getNGlobalConstraints() {
176	>	int SimInfo::getNGlobalConstraints() {
177		int nGlobalConstraints;
178		#ifdef IS_MPI
179		MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
#	Line 163 | Line 182 | int SimInfo::getNGlobalConstraints() {
182		nGlobalConstraints =  nConstraints_;
183		#endif
184		return nGlobalConstraints;
185	<	}
185	>	}
186
187	<	bool SimInfo::addMolecule(Molecule* mol) {
187	>	bool SimInfo::addMolecule(Molecule* mol) {
188		MoleculeIterator i;
189
190		i = molecules_.find(mol->getGlobalIndex());
191		if (i == molecules_.end() ) {
192
193	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
193	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
194
195	<	nAtoms_ += mol->getNAtoms();
196	<	nBonds_ += mol->getNBonds();
197	<	nBends_ += mol->getNBends();
198	<	nTorsions_ += mol->getNTorsions();
199	<	nRigidBodies_ += mol->getNRigidBodies();
200	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
201	<	nCutoffGroups_ += mol->getNCutoffGroups();
202	<	nConstraints_ += mol->getNConstraintPairs();
195	>	nAtoms_ += mol->getNAtoms();
196	>	nBonds_ += mol->getNBonds();
197	>	nBends_ += mol->getNBends();
198	>	nTorsions_ += mol->getNTorsions();
199	>	nInversions_ += mol->getNInversions();
200	>	nRigidBodies_ += mol->getNRigidBodies();
201	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
202	>	nCutoffGroups_ += mol->getNCutoffGroups();
203	>	nConstraints_ += mol->getNConstraintPairs();
204
205	<	addExcludePairs(mol);
206	<
207	<	return true;
205	>	addInteractionPairs(mol);
206	>
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	>	nInversions_ -= mol->getNInversions();
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	>	removeInteractionPairs(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 242 | 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 271 | 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 285 | 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 306 | 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 322 | Line 352 | void SimInfo::calcNdfTrans() {
352
353		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
354
355	<	}
355	>	}
356
357	<	void SimInfo::addExcludePairs(Molecule* mol) {
357	>	void SimInfo::addInteractionPairs(Molecule* mol) {
358	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
359		std::vector<Bond*>::iterator bondIter;
360		std::vector<Bend*>::iterator bendIter;
361		std::vector<Torsion*>::iterator torsionIter;
362	+	std::vector<Inversion*>::iterator inversionIter;
363		Bond* bond;
364		Bend* bend;
365		Torsion* torsion;
366	+	Inversion* inversion;
367		int a;
368		int b;
369		int c;
370		int d;
371	+
372	+	// atomGroups can be used to add special interaction maps between
373	+	// groups of atoms that are in two separate rigid bodies.
374	+	// However, most site-site interactions between two rigid bodies
375	+	// are probably not special, just the ones between the physically
376	+	// bonded atoms.  Interactions *within* a single rigid body should
377	+	// always be excluded.  These are done at the bottom of this
378	+	// function.
379	+
380	+	std::map<int, std::set<int> > atomGroups;
381	+	Molecule::RigidBodyIterator rbIter;
382	+	RigidBody* rb;
383	+	Molecule::IntegrableObjectIterator ii;
384	+	StuntDouble* integrableObject;
385
386	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
387	<	a = bond->getAtomA()->getGlobalIndex();
388	<	b = bond->getAtomB()->getGlobalIndex();
389	<	exclude_.addPair(a, b);
386	>	for (integrableObject = mol->beginIntegrableObject(ii);
387	>	integrableObject != NULL;
388	>	integrableObject = mol->nextIntegrableObject(ii)) {
389	>
390	>	if (integrableObject->isRigidBody()) {
391	>	rb = static_cast<RigidBody*>(integrableObject);
392	>	std::vector<Atom*> atoms = rb->getAtoms();
393	>	std::set<int> rigidAtoms;
394	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
395	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
396	>	}
397	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
398	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
399	>	}
400	>	} else {
401	>	std::set<int> oneAtomSet;
402	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
403	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
404	>	}
405	>	}
406	>
407	>	for (bond= mol->beginBond(bondIter); bond != NULL;
408	>	bond = mol->nextBond(bondIter)) {
409	>
410	>	a = bond->getAtomA()->getGlobalIndex();
411	>	b = bond->getAtomB()->getGlobalIndex();
412	>
413	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
414	>	oneTwoInteractions_.addPair(a, b);
415	>	} else {
416	>	excludedInteractions_.addPair(a, b);
417	>	}
418		}
419
420	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
421	<	a = bend->getAtomA()->getGlobalIndex();
347	<	b = bend->getAtomB()->getGlobalIndex();
348	<	c = bend->getAtomC()->getGlobalIndex();
420	>	for (bend= mol->beginBend(bendIter); bend != NULL;
421	>	bend = mol->nextBend(bendIter)) {
422
423	<	exclude_.addPair(a, b);
424	<	exclude_.addPair(a, c);
425	<	exclude_.addPair(b, c);
423	>	a = bend->getAtomA()->getGlobalIndex();
424	>	b = bend->getAtomB()->getGlobalIndex();
425	>	c = bend->getAtomC()->getGlobalIndex();
426	>
427	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
428	>	oneTwoInteractions_.addPair(a, b);
429	>	oneTwoInteractions_.addPair(b, c);
430	>	} else {
431	>	excludedInteractions_.addPair(a, b);
432	>	excludedInteractions_.addPair(b, c);
433	>	}
434	>
435	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
436	>	oneThreeInteractions_.addPair(a, c);
437	>	} else {
438	>	excludedInteractions_.addPair(a, c);
439	>	}
440		}
441
442	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
443	<	a = torsion->getAtomA()->getGlobalIndex();
357	<	b = torsion->getAtomB()->getGlobalIndex();
358	<	c = torsion->getAtomC()->getGlobalIndex();
359	<	d = torsion->getAtomD()->getGlobalIndex();
442	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
443	>	torsion = mol->nextTorsion(torsionIter)) {
444
445	<	exclude_.addPair(a, b);
446	<	exclude_.addPair(a, c);
447	<	exclude_.addPair(a, d);
448	<	exclude_.addPair(b, c);
449	<	exclude_.addPair(b, d);
450	<	exclude_.addPair(c, d);
445	>	a = torsion->getAtomA()->getGlobalIndex();
446	>	b = torsion->getAtomB()->getGlobalIndex();
447	>	c = torsion->getAtomC()->getGlobalIndex();
448	>	d = torsion->getAtomD()->getGlobalIndex();
449	>
450	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
451	>	oneTwoInteractions_.addPair(a, b);
452	>	oneTwoInteractions_.addPair(b, c);
453	>	oneTwoInteractions_.addPair(c, d);
454	>	} else {
455	>	excludedInteractions_.addPair(a, b);
456	>	excludedInteractions_.addPair(b, c);
457	>	excludedInteractions_.addPair(c, d);
458	>	}
459	>
460	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
461	>	oneThreeInteractions_.addPair(a, c);
462	>	oneThreeInteractions_.addPair(b, d);
463	>	} else {
464	>	excludedInteractions_.addPair(a, c);
465	>	excludedInteractions_.addPair(b, d);
466	>	}
467	>
468	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
469	>	oneFourInteractions_.addPair(a, d);
470	>	} else {
471	>	excludedInteractions_.addPair(a, d);
472	>	}
473		}
474
475	<
476	<	}
475	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
476	>	inversion = mol->nextInversion(inversionIter)) {
477
478	<	void SimInfo::removeExcludePairs(Molecule* mol) {
478	>	a = inversion->getAtomA()->getGlobalIndex();
479	>	b = inversion->getAtomB()->getGlobalIndex();
480	>	c = inversion->getAtomC()->getGlobalIndex();
481	>	d = inversion->getAtomD()->getGlobalIndex();
482	>
483	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
484	>	oneTwoInteractions_.addPair(a, b);
485	>	oneTwoInteractions_.addPair(a, c);
486	>	oneTwoInteractions_.addPair(a, d);
487	>	} else {
488	>	excludedInteractions_.addPair(a, b);
489	>	excludedInteractions_.addPair(a, c);
490	>	excludedInteractions_.addPair(a, d);
491	>	}
492	>
493	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
494	>	oneThreeInteractions_.addPair(b, c);
495	>	oneThreeInteractions_.addPair(b, d);
496	>	oneThreeInteractions_.addPair(c, d);
497	>	} else {
498	>	excludedInteractions_.addPair(b, c);
499	>	excludedInteractions_.addPair(b, d);
500	>	excludedInteractions_.addPair(c, d);
501	>	}
502	>	}
503	>
504	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
505	>	rb = mol->nextRigidBody(rbIter)) {
506	>	std::vector<Atom*> atoms = rb->getAtoms();
507	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
508	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
509	>	a = atoms[i]->getGlobalIndex();
510	>	b = atoms[j]->getGlobalIndex();
511	>	excludedInteractions_.addPair(a, b);
512	>	}
513	>	}
514	>	}
515	>
516	>	}
517	>
518	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
519	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
520		std::vector<Bond*>::iterator bondIter;
521		std::vector<Bend*>::iterator bendIter;
522		std::vector<Torsion*>::iterator torsionIter;
523	+	std::vector<Inversion*>::iterator inversionIter;
524		Bond* bond;
525		Bend* bend;
526		Torsion* torsion;
527	+	Inversion* inversion;
528		int a;
529		int b;
530		int c;
531		int d;
532	+
533	+	std::map<int, std::set<int> > atomGroups;
534	+	Molecule::RigidBodyIterator rbIter;
535	+	RigidBody* rb;
536	+	Molecule::IntegrableObjectIterator ii;
537	+	StuntDouble* integrableObject;
538
539	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
540	<	a = bond->getAtomA()->getGlobalIndex();
541	<	b = bond->getAtomB()->getGlobalIndex();
542	<	exclude_.removePair(a, b);
539	>	for (integrableObject = mol->beginIntegrableObject(ii);
540	>	integrableObject != NULL;
541	>	integrableObject = mol->nextIntegrableObject(ii)) {
542	>
543	>	if (integrableObject->isRigidBody()) {
544	>	rb = static_cast<RigidBody*>(integrableObject);
545	>	std::vector<Atom*> atoms = rb->getAtoms();
546	>	std::set<int> rigidAtoms;
547	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
548	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
549	>	}
550	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
551	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
552	>	}
553	>	} else {
554	>	std::set<int> oneAtomSet;
555	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
556	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
557	>	}
558	>	}
559	>
560	>	for (bond= mol->beginBond(bondIter); bond != NULL;
561	>	bond = mol->nextBond(bondIter)) {
562	>
563	>	a = bond->getAtomA()->getGlobalIndex();
564	>	b = bond->getAtomB()->getGlobalIndex();
565	>
566	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
567	>	oneTwoInteractions_.removePair(a, b);
568	>	} else {
569	>	excludedInteractions_.removePair(a, b);
570	>	}
571		}
572
573	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
574	<	a = bend->getAtomA()->getGlobalIndex();
392	<	b = bend->getAtomB()->getGlobalIndex();
393	<	c = bend->getAtomC()->getGlobalIndex();
573	>	for (bend= mol->beginBend(bendIter); bend != NULL;
574	>	bend = mol->nextBend(bendIter)) {
575
576	<	exclude_.removePair(a, b);
577	<	exclude_.removePair(a, c);
578	<	exclude_.removePair(b, c);
576	>	a = bend->getAtomA()->getGlobalIndex();
577	>	b = bend->getAtomB()->getGlobalIndex();
578	>	c = bend->getAtomC()->getGlobalIndex();
579	>
580	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
581	>	oneTwoInteractions_.removePair(a, b);
582	>	oneTwoInteractions_.removePair(b, c);
583	>	} else {
584	>	excludedInteractions_.removePair(a, b);
585	>	excludedInteractions_.removePair(b, c);
586	>	}
587	>
588	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
589	>	oneThreeInteractions_.removePair(a, c);
590	>	} else {
591	>	excludedInteractions_.removePair(a, c);
592	>	}
593		}
594
595	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
596	<	a = torsion->getAtomA()->getGlobalIndex();
402	<	b = torsion->getAtomB()->getGlobalIndex();
403	<	c = torsion->getAtomC()->getGlobalIndex();
404	<	d = torsion->getAtomD()->getGlobalIndex();
595	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
596	>	torsion = mol->nextTorsion(torsionIter)) {
597
598	<	exclude_.removePair(a, b);
599	<	exclude_.removePair(a, c);
600	<	exclude_.removePair(a, d);
601	<	exclude_.removePair(b, c);
602	<	exclude_.removePair(b, d);
603	<	exclude_.removePair(c, d);
598	>	a = torsion->getAtomA()->getGlobalIndex();
599	>	b = torsion->getAtomB()->getGlobalIndex();
600	>	c = torsion->getAtomC()->getGlobalIndex();
601	>	d = torsion->getAtomD()->getGlobalIndex();
602	>
603	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
604	>	oneTwoInteractions_.removePair(a, b);
605	>	oneTwoInteractions_.removePair(b, c);
606	>	oneTwoInteractions_.removePair(c, d);
607	>	} else {
608	>	excludedInteractions_.removePair(a, b);
609	>	excludedInteractions_.removePair(b, c);
610	>	excludedInteractions_.removePair(c, d);
611	>	}
612	>
613	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
614	>	oneThreeInteractions_.removePair(a, c);
615	>	oneThreeInteractions_.removePair(b, d);
616	>	} else {
617	>	excludedInteractions_.removePair(a, c);
618	>	excludedInteractions_.removePair(b, d);
619	>	}
620	>
621	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
622	>	oneFourInteractions_.removePair(a, d);
623	>	} else {
624	>	excludedInteractions_.removePair(a, d);
625	>	}
626		}
627
628	<	}
628	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
629	>	inversion = mol->nextInversion(inversionIter)) {
630
631	+	a = inversion->getAtomA()->getGlobalIndex();
632	+	b = inversion->getAtomB()->getGlobalIndex();
633	+	c = inversion->getAtomC()->getGlobalIndex();
634	+	d = inversion->getAtomD()->getGlobalIndex();
635
636	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
637	<	int curStampId;
636	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
637	>	oneTwoInteractions_.removePair(a, b);
638	>	oneTwoInteractions_.removePair(a, c);
639	>	oneTwoInteractions_.removePair(a, d);
640	>	} else {
641	>	excludedInteractions_.removePair(a, b);
642	>	excludedInteractions_.removePair(a, c);
643	>	excludedInteractions_.removePair(a, d);
644	>	}
645
646	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
647	+	oneThreeInteractions_.removePair(b, c);
648	+	oneThreeInteractions_.removePair(b, d);
649	+	oneThreeInteractions_.removePair(c, d);
650	+	} else {
651	+	excludedInteractions_.removePair(b, c);
652	+	excludedInteractions_.removePair(b, d);
653	+	excludedInteractions_.removePair(c, d);
654	+	}
655	+	}
656	+
657	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
658	+	rb = mol->nextRigidBody(rbIter)) {
659	+	std::vector<Atom*> atoms = rb->getAtoms();
660	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
661	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
662	+	a = atoms[i]->getGlobalIndex();
663	+	b = atoms[j]->getGlobalIndex();
664	+	excludedInteractions_.removePair(a, b);
665	+	}
666	+	}
667	+	}
668	+
669	+	}
670	+
671	+
672	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
673	+	int curStampId;
674	+
675		//index from 0
676		curStampId = moleculeStamps_.size();
677
678		moleculeStamps_.push_back(molStamp);
679		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
680	<	}
680	>	}
681
682	<	void SimInfo::update() {
682	>	void SimInfo::update() {
683
684		setupSimType();
685
#	Line 437 | Line 692 | void SimInfo::update() {
692		//setup fortran force field
693		/** @deprecate */
694		int isError = 0;
440	–	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
441	–	if(isError){
442	–	sprintf( painCave.errMsg,
443	–	"ForceField error: There was an error initializing the forceField in fortran.\n" );
444	–	painCave.isFatal = 1;
445	–	simError();
446	–	}
447	–
695
696		setupCutoff();
697	+
698	+	setupElectrostaticSummationMethod( isError );
699	+	setupSwitchingFunction();
700	+	setupAccumulateBoxDipole();
701
702	+	if(isError){
703	+	sprintf( painCave.errMsg,
704	+	"ForceField error: There was an error initializing the forceField in fortran.\n" );
705	+	painCave.isFatal = 1;
706	+	simError();
707	+	}
708	+
709		calcNdf();
710		calcNdfRaw();
711		calcNdfTrans();
712
713		fortranInitialized_ = true;
714	<	}
714	>	}
715
716	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
716	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
717		SimInfo::MoleculeIterator mi;
718		Molecule* mol;
719		Molecule::AtomIterator ai;
#	Line 464 | Line 722 | std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
722
723		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
724
725	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
726	<	atomTypes.insert(atom->getAtomType());
727	<	}
725	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
726	>	atomTypes.insert(atom->getAtomType());
727	>	}
728
729		}
730
731		return atomTypes;
732	<	}
732	>	}
733
734	<	void SimInfo::setupSimType() {
734	>	void SimInfo::setupSimType() {
735		std::set<AtomType*>::iterator i;
736		std::set<AtomType*> atomTypes;
737		atomTypes = getUniqueAtomTypes();
#	Line 481 | Line 739 | void SimInfo::setupSimType() {
739		int useLennardJones = 0;
740		int useElectrostatic = 0;
741		int useEAM = 0;
742	+	int useSC = 0;
743		int useCharge = 0;
744		int useDirectional = 0;
745		int useDipole = 0;
746		int useGayBerne = 0;
747		int useSticky = 0;
748	+	int useStickyPower = 0;
749		int useShape = 0;
750		int useFLARB = 0; //it is not in AtomType yet
751		int useDirectionalAtom = 0;
752		int useElectrostatics = 0;
753		//usePBC and useRF are from simParams
754	<	int usePBC = simParams_->getPBC();
755	<	int useRF = simParams_->getUseRF();
754	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
755	>	int useRF;
756	>	int useSF;
757	>	int useSP;
758	>	int useBoxDipole;
759
760	+	std::string myMethod;
761	+
762	+	// set the useRF logical
763	+	useRF = 0;
764	+	useSF = 0;
765	+	useSP = 0;
766	+
767	+
768	+	if (simParams_->haveElectrostaticSummationMethod()) {
769	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
770	+	toUpper(myMethod);
771	+	if (myMethod == "REACTION_FIELD"){
772	+	useRF = 1;
773	+	} else if (myMethod == "SHIFTED_FORCE"){
774	+	useSF = 1;
775	+	} else if (myMethod == "SHIFTED_POTENTIAL"){
776	+	useSP = 1;
777	+	}
778	+	}
779	+
780	+	if (simParams_->haveAccumulateBoxDipole())
781	+	if (simParams_->getAccumulateBoxDipole())
782	+	useBoxDipole = 1;
783	+
784	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
785	+
786		//loop over all of the atom types
787		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
788	<	useLennardJones |= (*i)->isLennardJones();
789	<	useElectrostatic |= (*i)->isElectrostatic();
790	<	useEAM |= (*i)->isEAM();
791	<	useCharge |= (*i)->isCharge();
792	<	useDirectional |= (*i)->isDirectional();
793	<	useDipole |= (*i)->isDipole();
794	<	useGayBerne |= (*i)->isGayBerne();
795	<	useSticky |= (*i)->isSticky();
796	<	useShape |= (*i)->isShape();
788	>	useLennardJones |= (*i)->isLennardJones();
789	>	useElectrostatic |= (*i)->isElectrostatic();
790	>	useEAM |= (*i)->isEAM();
791	>	useSC |= (*i)->isSC();
792	>	useCharge |= (*i)->isCharge();
793	>	useDirectional |= (*i)->isDirectional();
794	>	useDipole |= (*i)->isDipole();
795	>	useGayBerne |= (*i)->isGayBerne();
796	>	useSticky |= (*i)->isSticky();
797	>	useStickyPower |= (*i)->isStickyPower();
798	>	useShape |= (*i)->isShape();
799		}
800
801	<	if (useSticky || useDipole || useGayBerne || useShape) {
802	<	useDirectionalAtom = 1;
801	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
802	>	useDirectionalAtom = 1;
803		}
804
805		if (useCharge || useDipole) {
806	<	useElectrostatics = 1;
806	>	useElectrostatics = 1;
807		}
808
809		#ifdef IS_MPI
#	Line 539 | Line 830 | void SimInfo::setupSimType() {
830		temp = useSticky;
831		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
832
833	+	temp = useStickyPower;
834	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
835	+
836		temp = useGayBerne;
837		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
838
839		temp = useEAM;
840		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
841
842	+	temp = useSC;
843	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
844	+
845		temp = useShape;
846		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
847
#	Line 553 | Line 850 | void SimInfo::setupSimType() {
850
851		temp = useRF;
852		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
853	<
853	>
854	>	temp = useSF;
855	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
856	>
857	>	temp = useSP;
858	>	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
859	>
860	>	temp = useBoxDipole;
861	>	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
862	>
863	>	temp = useAtomicVirial_;
864	>	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
865	>
866		#endif
867
868		fInfo_.SIM_uses_PBC = usePBC;
#	Line 563 | Line 872 | void SimInfo::setupSimType() {
872		fInfo_.SIM_uses_Charges = useCharge;
873		fInfo_.SIM_uses_Dipoles = useDipole;
874		fInfo_.SIM_uses_Sticky = useSticky;
875	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
876		fInfo_.SIM_uses_GayBerne = useGayBerne;
877		fInfo_.SIM_uses_EAM = useEAM;
878	+	fInfo_.SIM_uses_SC = useSC;
879		fInfo_.SIM_uses_Shapes = useShape;
880		fInfo_.SIM_uses_FLARB = useFLARB;
881		fInfo_.SIM_uses_RF = useRF;
882	+	fInfo_.SIM_uses_SF = useSF;
883	+	fInfo_.SIM_uses_SP = useSP;
884	+	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
885	+	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
886	+	}
887
888	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
573	<
574	<	if (simParams_->haveDielectric()) {
575	<	fInfo_.dielect = simParams_->getDielectric();
576	<	} else {
577	<	sprintf(painCave.errMsg,
578	<	"SimSetup Error: No Dielectric constant was set.\n"
579	<	"\tYou are trying to use Reaction Field without"
580	<	"\tsetting a dielectric constant!\n");
581	<	painCave.isFatal = 1;
582	<	simError();
583	<	}
584	<
585	<	} else {
586	<	fInfo_.dielect = 0.0;
587	<	}
588	<
589	<	}
590	<
591	<	void SimInfo::setupFortranSim() {
888	>	void SimInfo::setupFortranSim() {
889		int isError;
890	<	int nExclude;
890	>	int nExclude, nOneTwo, nOneThree, nOneFour;
891		std::vector<int> fortranGlobalGroupMembership;
892
596	–	nExclude = exclude_.getSize();
893		isError = 0;
894
895		//globalGroupMembership_ is filled by SimCreator
896		for (int i = 0; i < nGlobalAtoms_; i++) {
897	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
897	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
898		}
899
900		//calculate mass ratio of cutoff group
901	<	std::vector<double> mfact;
901	>	std::vector<RealType> mfact;
902		SimInfo::MoleculeIterator mi;
903		Molecule* mol;
904		Molecule::CutoffGroupIterator ci;
905		CutoffGroup* cg;
906		Molecule::AtomIterator ai;
907		Atom* atom;
908	<	double totalMass;
908	>	RealType totalMass;
909
910		//to avoid memory reallocation, reserve enough space for mfact
911		mfact.reserve(getNCutoffGroups());
912
913		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
914	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
914	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
915
916	<	totalMass = cg->getMass();
917	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
918	<	mfact.push_back(atom->getMass()/totalMass);
919	<	}
920	<
921	<	}
916	>	totalMass = cg->getMass();
917	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
918	>	// Check for massless groups - set mfact to 1 if true
919	>	if (totalMass != 0)
920	>	mfact.push_back(atom->getMass()/totalMass);
921	>	else
922	>	mfact.push_back( 1.0 );
923	>	}
924	>	}
925		}
926
927		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
#	Line 632 | Line 931 | void SimInfo::setupFortranSim() {
931		identArray.reserve(getNAtoms());
932
933		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
934	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
935	<	identArray.push_back(atom->getIdent());
936	<	}
934	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
935	>	identArray.push_back(atom->getIdent());
936	>	}
937		}
938
939		//fill molMembershipArray
940		//molMembershipArray is filled by SimCreator
941		std::vector<int> molMembershipArray(nGlobalAtoms_);
942		for (int i = 0; i < nGlobalAtoms_; i++) {
943	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
943	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
944		}
945
946		//setup fortran simulation
947	<	//gloalExcludes and molMembershipArray should go away (They are never used)
948	<	//why the hell fortran need to know molecule?
949	<	//OOPSE = Object-Obfuscated Parallel Simulation Engine
950	<	int nGlobalExcludes = 0;
951	<	int* globalExcludes = NULL;
653	<	int* excludeList = exclude_.getExcludeList();
654	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
655	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
656	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
947	>
948	>	nExclude = excludedInteractions_.getSize();
949	>	nOneTwo = oneTwoInteractions_.getSize();
950	>	nOneThree = oneThreeInteractions_.getSize();
951	>	nOneFour = oneFourInteractions_.getSize();
952
953	<	if( isError ){
953	>	std::cerr << "excludedInteractions contains: " << excludedInteractions_.getSize() << " pairs \n";
954	>	std::cerr << "oneTwoInteractions contains: " << oneTwoInteractions_.getSize() << " pairs \n";
955	>	std::cerr << "oneThreeInteractions contains: " << oneThreeInteractions_.getSize() << " pairs \n";
956	>	std::cerr << "oneFourInteractions contains: " << oneFourInteractions_.getSize() << " pairs \n";
957
958	<	sprintf( painCave.errMsg,
959	<	"There was an error setting the simulation information in fortran.\n" );
960	<	painCave.isFatal = 1;
961	<	painCave.severity = OOPSE_ERROR;
664	<	simError();
665	<	}
958	>	int* excludeList = excludedInteractions_.getPairList();
959	>	int* oneTwoList = oneTwoInteractions_.getPairList();
960	>	int* oneThreeList = oneThreeInteractions_.getPairList();
961	>	int* oneFourList = oneFourInteractions_.getPairList();
962
963	<	#ifdef IS_MPI
963	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
964	>	&nExclude, excludeList,
965	>	&nOneTwo, oneTwoList,
966	>	&nOneThree, oneThreeList,
967	>	&nOneFour, oneFourList,
968	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
969	>	&fortranGlobalGroupMembership[0], &isError);
970	>
971	>	if( isError ){
972	>
973	>	sprintf( painCave.errMsg,
974	>	"There was an error setting the simulation information in fortran.\n" );
975	>	painCave.isFatal = 1;
976	>	painCave.severity = OOPSE_ERROR;
977	>	simError();
978	>	}
979	>
980	>
981		sprintf( checkPointMsg,
982	<	"succesfully sent the simulation information to fortran.\n");
983	<	MPIcheckPoint();
984	<	#endif // is_mpi
985	<	}
982	>	"succesfully sent the simulation information to fortran.\n");
983	>
984	>	errorCheckPoint();
985	>
986	>	// Setup number of neighbors in neighbor list if present
987	>	if (simParams_->haveNeighborListNeighbors()) {
988	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
989	>	setNeighbors(&nlistNeighbors);
990	>	}
991	>
992
993	+	}
994
995	<	#ifdef IS_MPI
996	<	void SimInfo::setupFortranParallel() {
997	<
995	>
996	>	void SimInfo::setupFortranParallel() {
997	>	#ifdef IS_MPI
998		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
999		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1000		std::vector<int> localToGlobalCutoffGroupIndex;
#	Line 689 | Line 1009 | void SimInfo::setupFortranParallel() {
1009
1010		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1011
1012	<	//local index(index in DataStorge) of atom is important
1013	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1014	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1015	<	}
1012	>	//local index(index in DataStorge) of atom is important
1013	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1014	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1015	>	}
1016
1017	<	//local index of cutoff group is trivial, it only depends on the order of travesing
1018	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1019	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1020	<	}
1017	>	//local index of cutoff group is trivial, it only depends on the order of travesing
1018	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1019	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1020	>	}
1021
1022		}
1023
#	Line 717 | Line 1037 | void SimInfo::setupFortranParallel() {
1037		&localToGlobalCutoffGroupIndex[0], &isError);
1038
1039		if (isError) {
1040	<	sprintf(painCave.errMsg,
1041	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1042	<	painCave.isFatal = 1;
1043	<	simError();
1040	>	sprintf(painCave.errMsg,
1041	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1042	>	painCave.isFatal = 1;
1043	>	simError();
1044		}
1045
1046		sprintf(checkPointMsg, " mpiRefresh successful.\n");
1047	<	MPIcheckPoint();
1047	>	errorCheckPoint();
1048
729	–
730	–	}
731	–
1049		#endif
1050	+	}
1051
1052	<	double SimInfo::calcMaxCutoffRadius() {
1052	>	void SimInfo::setupCutoff() {
1053	>
1054	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1055
1056	+	// Check the cutoff policy
1057	+	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1058
1059	<	std::set<AtomType*> atomTypes;
1060	<	std::set<AtomType*>::iterator i;
1061	<	std::vector<double> cutoffRadius;
1059	>	// Set LJ shifting bools to false
1060	>	ljsp_ = false;
1061	>	ljsf_ = false;
1062
1063	<	//get the unique atom types
1064	<	atomTypes = getUniqueAtomTypes();
1065	<
1066	<	//query the max cutoff radius among these atom types
1067	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
746	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
1063	>	std::string myPolicy;
1064	>	if (forceFieldOptions_.haveCutoffPolicy()){
1065	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
1066	>	}else if (simParams_->haveCutoffPolicy()) {
1067	>	myPolicy = simParams_->getCutoffPolicy();
1068		}
1069
1070	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
1071	<	#ifdef IS_MPI
1072	<	//pick the max cutoff radius among the processors
1073	<	#endif
1070	>	if (!myPolicy.empty()){
1071	>	toUpper(myPolicy);
1072	>	if (myPolicy == "MIX") {
1073	>	cp = MIX_CUTOFF_POLICY;
1074	>	} else {
1075	>	if (myPolicy == "MAX") {
1076	>	cp = MAX_CUTOFF_POLICY;
1077	>	} else {
1078	>	if (myPolicy == "TRADITIONAL") {
1079	>	cp = TRADITIONAL_CUTOFF_POLICY;
1080	>	} else {
1081	>	// throw error
1082	>	sprintf( painCave.errMsg,
1083	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1084	>	painCave.isFatal = 1;
1085	>	simError();
1086	>	}
1087	>	}
1088	>	}
1089	>	}
1090	>	notifyFortranCutoffPolicy(&cp);
1091
1092	<	return maxCutoffRadius;
1093	<	}
1092	>	// Check the Skin Thickness for neighborlists
1093	>	RealType skin;
1094	>	if (simParams_->haveSkinThickness()) {
1095	>	skin = simParams_->getSkinThickness();
1096	>	notifyFortranSkinThickness(&skin);
1097	>	}
1098	>
1099	>	// Check if the cutoff was set explicitly:
1100	>	if (simParams_->haveCutoffRadius()) {
1101	>	rcut_ = simParams_->getCutoffRadius();
1102	>	if (simParams_->haveSwitchingRadius()) {
1103	>	rsw_  = simParams_->getSwitchingRadius();
1104	>	} else {
1105	>	if (fInfo_.SIM_uses_Charges |
1106	>	fInfo_.SIM_uses_Dipoles |
1107	>	fInfo_.SIM_uses_RF) {
1108	>
1109	>	rsw_ = 0.85 * rcut_;
1110	>	sprintf(painCave.errMsg,
1111	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1112	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1113	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1114	>	painCave.isFatal = 0;
1115	>	simError();
1116	>	} else {
1117	>	rsw_ = rcut_;
1118	>	sprintf(painCave.errMsg,
1119	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1120	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
1121	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1122	>	painCave.isFatal = 0;
1123	>	simError();
1124	>	}
1125	>	}
1126
1127	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
1128	<
1129	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1127	>	if (simParams_->haveElectrostaticSummationMethod()) {
1128	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1129	>	toUpper(myMethod);
1130
1131	<	if (!simParams_->haveRcut()){
1132	<	sprintf(painCave.errMsg,
1131	>	if (myMethod == "SHIFTED_POTENTIAL") {
1132	>	ljsp_ = true;
1133	>	} else if (myMethod == "SHIFTED_FORCE") {
1134	>	ljsf_ = true;
1135	>	}
1136	>	}
1137	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1138	>
1139	>	} else {
1140	>
1141	>	// For electrostatic atoms, we'll assume a large safe value:
1142	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1143	>	sprintf(painCave.errMsg,
1144		"SimCreator Warning: No value was set for the cutoffRadius.\n"
1145		"\tOOPSE will use a default value of 15.0 angstroms"
1146		"\tfor the cutoffRadius.\n");
1147	<	painCave.isFatal = 0;
1148	<	simError();
1149	<	rcut = 15.0;
1150	<	} else{
1151	<	rcut = simParams_->getRcut();
1147	>	painCave.isFatal = 0;
1148	>	simError();
1149	>	rcut_ = 15.0;
1150	>
1151	>	if (simParams_->haveElectrostaticSummationMethod()) {
1152	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1153	>	toUpper(myMethod);
1154	>
1155	>	// For the time being, we're tethering the LJ shifted behavior to the
1156	>	// electrostaticSummationMethod keyword options
1157	>	if (myMethod == "SHIFTED_POTENTIAL") {
1158	>	ljsp_ = true;
1159	>	} else if (myMethod == "SHIFTED_FORCE") {
1160	>	ljsf_ = true;
1161	>	}
1162	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1163	>	if (simParams_->haveSwitchingRadius()){
1164	>	sprintf(painCave.errMsg,
1165	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1166	>	"\teven though the electrostaticSummationMethod was\n"
1167	>	"\tset to %s\n", myMethod.c_str());
1168	>	painCave.isFatal = 1;
1169	>	simError();
1170	>	}
1171	>	}
1172		}
1173	<
1174	<	if (!simParams_->haveRsw()){
1175	<	sprintf(painCave.errMsg,
1176	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1177	<	"\tOOPSE will use a default value of\n"
1178	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
1179	<	painCave.isFatal = 0;
1180	<	simError();
1181	<	rsw = 0.95 * rcut;
1182	<	} else{
1183	<	rsw = simParams_->getRsw();
1173	>
1174	>	if (simParams_->haveSwitchingRadius()){
1175	>	rsw_ = simParams_->getSwitchingRadius();
1176	>	} else {
1177	>	sprintf(painCave.errMsg,
1178	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1179	>	"\tOOPSE will use a default value of\n"
1180	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1181	>	painCave.isFatal = 0;
1182	>	simError();
1183	>	rsw_ = 0.85 * rcut_;
1184		}
1185
1186	<	} else {
1187	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
1188	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
1186	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1187	>
1188	>	} else {
1189	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1190	>	// We'll punt and let fortran figure out the cutoffs later.
1191
1192	<	if (simParams_->haveRcut()) {
790	<	rcut = simParams_->getRcut();
791	<	} else {
792	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
793	<	rcut = calcMaxCutoffRadius();
794	<	}
1192	>	notifyFortranYouAreOnYourOwn();
1193
1194	<	if (simParams_->haveRsw()) {
797	<	rsw  = simParams_->getRsw();
798	<	} else {
799	<	rsw = rcut;
800	<	}
801	<
1194	>	}
1195		}
1196	<	}
1196	>	}
1197
1198	<	void SimInfo::setupCutoff() {
1199	<	getCutoff(rcut_, rsw_);
1200	<	double rnblist = rcut_ + 1; // skin of neighbor list
1198	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1199	>
1200	>	int errorOut;
1201	>	int esm =  NONE;
1202	>	int sm = UNDAMPED;
1203	>	RealType alphaVal;
1204	>	RealType dielectric;
1205	>
1206	>	errorOut = isError;
1207
1208	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1209	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
1210	<	}
1211	<
1212	<	void SimInfo::addProperty(GenericData* genData) {
1213	<	properties_.addProperty(genData);
1214	<	}
1215	<
1216	<	void SimInfo::removeProperty(const std::string& propName) {
1217	<	properties_.removeProperty(propName);
1218	<	}
1219	<
1220	<	void SimInfo::clearProperties() {
1221	<	properties_.clearProperties();
1222	<	}
1223	<
1224	<	std::vector<std::string> SimInfo::getPropertyNames() {
1225	<	return properties_.getPropertyNames();
1226	<	}
1227	<
1228	<	std::vector<GenericData*> SimInfo::getProperties() {
1229	<	return properties_.getProperties();
1230	<	}
1231	<
1232	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1233	<	return properties_.getPropertyByName(propName);
1234	<	}
1235	<
1236	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1237	<	if (sman_ == sman_) {
1238	<	return;
1208	>	if (simParams_->haveElectrostaticSummationMethod()) {
1209	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1210	>	toUpper(myMethod);
1211	>	if (myMethod == "NONE") {
1212	>	esm = NONE;
1213	>	} else {
1214	>	if (myMethod == "SWITCHING_FUNCTION") {
1215	>	esm = SWITCHING_FUNCTION;
1216	>	} else {
1217	>	if (myMethod == "SHIFTED_POTENTIAL") {
1218	>	esm = SHIFTED_POTENTIAL;
1219	>	} else {
1220	>	if (myMethod == "SHIFTED_FORCE") {
1221	>	esm = SHIFTED_FORCE;
1222	>	} else {
1223	>	if (myMethod == "REACTION_FIELD") {
1224	>	esm = REACTION_FIELD;
1225	>	dielectric = simParams_->getDielectric();
1226	>	if (!simParams_->haveDielectric()) {
1227	>	// throw warning
1228	>	sprintf( painCave.errMsg,
1229	>	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1230	>	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1231	>	painCave.isFatal = 0;
1232	>	simError();
1233	>	}
1234	>	} else {
1235	>	// throw error
1236	>	sprintf( painCave.errMsg,
1237	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1238	>	"\t(Input file specified %s .)\n"
1239	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1240	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1241	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1242	>	painCave.isFatal = 1;
1243	>	simError();
1244	>	}
1245	>	}
1246	>	}
1247	>	}
1248	>	}
1249		}
1250
1251	+	if (simParams_->haveElectrostaticScreeningMethod()) {
1252	+	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1253	+	toUpper(myScreen);
1254	+	if (myScreen == "UNDAMPED") {
1255	+	sm = UNDAMPED;
1256	+	} else {
1257	+	if (myScreen == "DAMPED") {
1258	+	sm = DAMPED;
1259	+	if (!simParams_->haveDampingAlpha()) {
1260	+	// first set a cutoff dependent alpha value
1261	+	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1262	+	alphaVal = 0.5125 - rcut_* 0.025;
1263	+	// for values rcut > 20.5, alpha is zero
1264	+	if (alphaVal < 0) alphaVal = 0;
1265	+
1266	+	// throw warning
1267	+	sprintf( painCave.errMsg,
1268	+	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1269	+	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1270	+	painCave.isFatal = 0;
1271	+	simError();
1272	+	} else {
1273	+	alphaVal = simParams_->getDampingAlpha();
1274	+	}
1275	+
1276	+	} else {
1277	+	// throw error
1278	+	sprintf( painCave.errMsg,
1279	+	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1280	+	"\t(Input file specified %s .)\n"
1281	+	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1282	+	"or \"damped\".\n", myScreen.c_str() );
1283	+	painCave.isFatal = 1;
1284	+	simError();
1285	+	}
1286	+	}
1287	+	}
1288	+
1289	+	// let's pass some summation method variables to fortran
1290	+	setElectrostaticSummationMethod( &esm );
1291	+	setFortranElectrostaticMethod( &esm );
1292	+	setScreeningMethod( &sm );
1293	+	setDampingAlpha( &alphaVal );
1294	+	setReactionFieldDielectric( &dielectric );
1295	+	initFortranFF( &errorOut );
1296	+	}
1297	+
1298	+	void SimInfo::setupSwitchingFunction() {
1299	+	int ft = CUBIC;
1300	+
1301	+	if (simParams_->haveSwitchingFunctionType()) {
1302	+	std::string funcType = simParams_->getSwitchingFunctionType();
1303	+	toUpper(funcType);
1304	+	if (funcType == "CUBIC") {
1305	+	ft = CUBIC;
1306	+	} else {
1307	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1308	+	ft = FIFTH_ORDER_POLY;
1309	+	} else {
1310	+	// throw error
1311	+	sprintf( painCave.errMsg,
1312	+	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1313	+	painCave.isFatal = 1;
1314	+	simError();
1315	+	}
1316	+	}
1317	+	}
1318	+
1319	+	// send switching function notification to switcheroo
1320	+	setFunctionType(&ft);
1321	+
1322	+	}
1323	+
1324	+	void SimInfo::setupAccumulateBoxDipole() {
1325	+
1326	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1327	+	if ( simParams_->haveAccumulateBoxDipole() )
1328	+	if ( simParams_->getAccumulateBoxDipole() ) {
1329	+	setAccumulateBoxDipole();
1330	+	calcBoxDipole_ = true;
1331	+	}
1332	+
1333	+	}
1334	+
1335	+	void SimInfo::addProperty(GenericData* genData) {
1336	+	properties_.addProperty(genData);
1337	+	}
1338	+
1339	+	void SimInfo::removeProperty(const std::string& propName) {
1340	+	properties_.removeProperty(propName);
1341	+	}
1342	+
1343	+	void SimInfo::clearProperties() {
1344	+	properties_.clearProperties();
1345	+	}
1346	+
1347	+	std::vector<std::string> SimInfo::getPropertyNames() {
1348	+	return properties_.getPropertyNames();
1349	+	}
1350	+
1351	+	std::vector<GenericData*> SimInfo::getProperties() {
1352	+	return properties_.getProperties();
1353	+	}
1354	+
1355	+	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1356	+	return properties_.getPropertyByName(propName);
1357	+	}
1358	+
1359	+	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1360	+	if (sman_ == sman) {
1361	+	return;
1362	+	}
1363		delete sman_;
1364		sman_ = sman;
1365
#	Line 851 | Line 1372 | void SimInfo::setSnapshotManager(SnapshotManager* sman
1372
1373		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1374
1375	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1376	<	atom->setSnapshotManager(sman_);
1377	<	}
1375	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1376	>	atom->setSnapshotManager(sman_);
1377	>	}
1378
1379	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1380	<	rb->setSnapshotManager(sman_);
1381	<	}
1379	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1380	>	rb->setSnapshotManager(sman_);
1381	>	}
1382		}
1383
1384	<	}
1384	>	}
1385
1386	<	Vector3d SimInfo::getComVel(){
1386	>	Vector3d SimInfo::getComVel(){
1387		SimInfo::MoleculeIterator i;
1388		Molecule* mol;
1389
1390		Vector3d comVel(0.0);
1391	<	double totalMass = 0.0;
1391	>	RealType totalMass = 0.0;
1392
1393
1394		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1395	<	double mass = mol->getMass();
1396	<	totalMass += mass;
1397	<	comVel += mass * mol->getComVel();
1395	>	RealType mass = mol->getMass();
1396	>	totalMass += mass;
1397	>	comVel += mass * mol->getComVel();
1398		}
1399
1400		#ifdef IS_MPI
1401	<	double tmpMass = totalMass;
1401	>	RealType tmpMass = totalMass;
1402		Vector3d tmpComVel(comVel);
1403	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1404	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1403	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1404	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1405		#endif
1406
1407		comVel /= totalMass;
1408
1409		return comVel;
1410	<	}
1410	>	}
1411
1412	<	Vector3d SimInfo::getCom(){
1412	>	Vector3d SimInfo::getCom(){
1413		SimInfo::MoleculeIterator i;
1414		Molecule* mol;
1415
1416		Vector3d com(0.0);
1417	<	double totalMass = 0.0;
1417	>	RealType totalMass = 0.0;
1418
1419		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1420	<	double mass = mol->getMass();
1421	<	totalMass += mass;
1422	<	com += mass * mol->getCom();
1420	>	RealType mass = mol->getMass();
1421	>	totalMass += mass;
1422	>	com += mass * mol->getCom();
1423		}
1424
1425		#ifdef IS_MPI
1426	<	double tmpMass = totalMass;
1426	>	RealType tmpMass = totalMass;
1427		Vector3d tmpCom(com);
1428	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1429	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1428	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1429	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1430		#endif
1431
1432		com /= totalMass;
1433
1434		return com;
1435
1436	<	}
1436	>	}
1437
1438	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1438	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1439
1440		return o;
1441	<	}
1441	>	}
1442	>
1443	>
1444	>	/*
1445	>	Returns center of mass and center of mass velocity in one function call.
1446	>	*/
1447	>
1448	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1449	>	SimInfo::MoleculeIterator i;
1450	>	Molecule* mol;
1451	>
1452	>
1453	>	RealType totalMass = 0.0;
1454	>
1455
1456	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1457	+	RealType mass = mol->getMass();
1458	+	totalMass += mass;
1459	+	com += mass * mol->getCom();
1460	+	comVel += mass * mol->getComVel();
1461	+	}
1462	+
1463	+	#ifdef IS_MPI
1464	+	RealType tmpMass = totalMass;
1465	+	Vector3d tmpCom(com);
1466	+	Vector3d tmpComVel(comVel);
1467	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1468	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1469	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1470	+	#endif
1471	+
1472	+	com /= totalMass;
1473	+	comVel /= totalMass;
1474	+	}
1475	+
1476	+	/*
1477	+	Return intertia tensor for entire system and angular momentum Vector.
1478	+
1479	+
1480	+	[  Ixx -Ixy  -Ixz ]
1481	+	J =| -Iyx  Iyy  -Iyz |
1482	+	[ -Izx -Iyz   Izz ]
1483	+	*/
1484	+
1485	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1486	+
1487	+
1488	+	RealType xx = 0.0;
1489	+	RealType yy = 0.0;
1490	+	RealType zz = 0.0;
1491	+	RealType xy = 0.0;
1492	+	RealType xz = 0.0;
1493	+	RealType yz = 0.0;
1494	+	Vector3d com(0.0);
1495	+	Vector3d comVel(0.0);
1496	+
1497	+	getComAll(com, comVel);
1498	+
1499	+	SimInfo::MoleculeIterator i;
1500	+	Molecule* mol;
1501	+
1502	+	Vector3d thisq(0.0);
1503	+	Vector3d thisv(0.0);
1504	+
1505	+	RealType thisMass = 0.0;
1506	+
1507	+
1508	+
1509	+
1510	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1511	+
1512	+	thisq = mol->getCom()-com;
1513	+	thisv = mol->getComVel()-comVel;
1514	+	thisMass = mol->getMass();
1515	+	// Compute moment of intertia coefficients.
1516	+	xx += thisq[0]*thisq[0]*thisMass;
1517	+	yy += thisq[1]*thisq[1]*thisMass;
1518	+	zz += thisq[2]*thisq[2]*thisMass;
1519	+
1520	+	// compute products of intertia
1521	+	xy += thisq[0]*thisq[1]*thisMass;
1522	+	xz += thisq[0]*thisq[2]*thisMass;
1523	+	yz += thisq[1]*thisq[2]*thisMass;
1524	+
1525	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1526	+
1527	+	}
1528	+
1529	+
1530	+	inertiaTensor(0,0) = yy + zz;
1531	+	inertiaTensor(0,1) = -xy;
1532	+	inertiaTensor(0,2) = -xz;
1533	+	inertiaTensor(1,0) = -xy;
1534	+	inertiaTensor(1,1) = xx + zz;
1535	+	inertiaTensor(1,2) = -yz;
1536	+	inertiaTensor(2,0) = -xz;
1537	+	inertiaTensor(2,1) = -yz;
1538	+	inertiaTensor(2,2) = xx + yy;
1539	+
1540	+	#ifdef IS_MPI
1541	+	Mat3x3d tmpI(inertiaTensor);
1542	+	Vector3d tmpAngMom;
1543	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1544	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1545	+	#endif
1546	+
1547	+	return;
1548	+	}
1549	+
1550	+	//Returns the angular momentum of the system
1551	+	Vector3d SimInfo::getAngularMomentum(){
1552	+
1553	+	Vector3d com(0.0);
1554	+	Vector3d comVel(0.0);
1555	+	Vector3d angularMomentum(0.0);
1556	+
1557	+	getComAll(com,comVel);
1558	+
1559	+	SimInfo::MoleculeIterator i;
1560	+	Molecule* mol;
1561	+
1562	+	Vector3d thisr(0.0);
1563	+	Vector3d thisp(0.0);
1564	+
1565	+	RealType thisMass;
1566	+
1567	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1568	+	thisMass = mol->getMass();
1569	+	thisr = mol->getCom()-com;
1570	+	thisp = (mol->getComVel()-comVel)*thisMass;
1571	+
1572	+	angularMomentum += cross( thisr, thisp );
1573	+
1574	+	}
1575	+
1576	+	#ifdef IS_MPI
1577	+	Vector3d tmpAngMom;
1578	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1579	+	#endif
1580	+
1581	+	return angularMomentum;
1582	+	}
1583	+
1584	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1585	+	return IOIndexToIntegrableObject.at(index);
1586	+	}
1587	+
1588	+	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1589	+	IOIndexToIntegrableObject= v;
1590	+	}
1591	+
1592	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1593	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1594	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1595	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1596	+	*/
1597	+	void SimInfo::getGyrationalVolume(RealType &volume){
1598	+	Mat3x3d intTensor;
1599	+	RealType det;
1600	+	Vector3d dummyAngMom;
1601	+	RealType sysconstants;
1602	+	RealType geomCnst;
1603	+
1604	+	geomCnst = 3.0/2.0;
1605	+	/* Get the inertial tensor and angular momentum for free*/
1606	+	getInertiaTensor(intTensor,dummyAngMom);
1607	+
1608	+	det = intTensor.determinant();
1609	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1610	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1611	+	return;
1612	+	}
1613	+
1614	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1615	+	Mat3x3d intTensor;
1616	+	Vector3d dummyAngMom;
1617	+	RealType sysconstants;
1618	+	RealType geomCnst;
1619	+
1620	+	geomCnst = 3.0/2.0;
1621	+	/* Get the inertial tensor and angular momentum for free*/
1622	+	getInertiaTensor(intTensor,dummyAngMom);
1623	+
1624	+	detI = intTensor.determinant();
1625	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1626	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1627	+	return;
1628	+	}
1629	+	/*
1630	+	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1631	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1632	+	sdByGlobalIndex_ = v;
1633	+	}
1634	+
1635	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1636	+	//assert(index < nAtoms_ + nRigidBodies_);
1637	+	return sdByGlobalIndex_.at(index);
1638	+	}
1639	+	*/
1640		}//end namespace oopse
1641

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