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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
Revision 834 by chuckv, Fri Dec 30 23:15:59 2005 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 "UseTheForce/fCutoffPolicy.h"
57	+	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
58	+	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
59	+	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
60		#include "UseTheForce/doForces_interface.h"
61	<	#include "UseTheForce/notifyCutoffs_interface.h"
61	>	#include "UseTheForce/DarkSide/electrostatic_interface.h"
62	>	#include "UseTheForce/DarkSide/switcheroo_interface.h"
63		#include "utils/MemoryUtils.hpp"
64		#include "utils/simError.h"
65		#include "selection/SelectionManager.hpp"
66	+	#include "io/ForceFieldOptions.hpp"
67	+	#include "UseTheForce/ForceField.hpp"
68
69		#ifdef IS_MPI
70		#include "UseTheForce/mpiComponentPlan.h"
#	Line 64 | Line 72 | namespace oopse {
72		#endif
73
74		namespace oopse {
75	+	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
76	+	std::map<int, std::set<int> >::iterator i = container.find(index);
77	+	std::set<int> result;
78	+	if (i != container.end()) {
79	+	result = i->second;
80	+	}
81
82	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
83	<	ForceField* ff, Globals* simParams) :
84	<	forceField_(ff), simParams_(simParams),
85	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
86	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
87	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
88	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
89	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
90	<	sman_(NULL), fortranInitialized_(false) {
82	>	return result;
83	>	}
84	>
85	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
86	>	forceField_(ff), simParams_(simParams),
87	>	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
88	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
89	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
90	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
91	>	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
92	>	sman_(NULL), fortranInitialized_(false) {
93
94	<
95	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
96	<	MoleculeStamp* molStamp;
97	<	int nMolWithSameStamp;
98	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
99	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
100	<	CutoffGroupStamp* cgStamp;
101	<	RigidBodyStamp* rbStamp;
102	<	int nRigidAtoms = 0;
103	<
104	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
105	<	molStamp = i->first;
90	<	nMolWithSameStamp = i->second;
94	>	MoleculeStamp* molStamp;
95	>	int nMolWithSameStamp;
96	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
97	>	int nGroups = 0;      //total cutoff groups defined in meta-data file
98	>	CutoffGroupStamp* cgStamp;
99	>	RigidBodyStamp* rbStamp;
100	>	int nRigidAtoms = 0;
101	>	std::vector<Component*> components = simParams->getComponents();
102	>
103	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
104	>	molStamp = (*i)->getMoleculeStamp();
105	>	nMolWithSameStamp = (*i)->getNMol();
106
107		addMoleculeStamp(molStamp, nMolWithSameStamp);
108
109		//calculate atoms in molecules
110		nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
111
97	–
112		//calculate atoms in cutoff groups
113		int nAtomsInGroups = 0;
114		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
115
116		for (int j=0; j < nCutoffGroupsInStamp; j++) {
117	<	cgStamp = molStamp->getCutoffGroup(j);
118	<	nAtomsInGroups += cgStamp->getNMembers();
117	>	cgStamp = molStamp->getCutoffGroupStamp(j);
118	>	nAtomsInGroups += cgStamp->getNMembers();
119		}
120
121		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
122	+
123		nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
124
125		//calculate atoms in rigid bodies
#	Line 112 | Line 127 | SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*,
127		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
128
129		for (int j=0; j < nRigidBodiesInStamp; j++) {
130	<	rbStamp = molStamp->getRigidBody(j);
131	<	nAtomsInRigidBodies += rbStamp->getNMembers();
130	>	rbStamp = molStamp->getRigidBodyStamp(j);
131	>	nAtomsInRigidBodies += rbStamp->getNMembers();
132		}
133
134		nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
135		nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
136
137	<	}
137	>	}
138
139	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
140	<	//therefore the total number of cutoff groups in the system is equal to
141	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
142	<	//file plus the number of cutoff groups defined in meta-data file
143	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
139	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
140	>	//group therefore the total number of cutoff groups in the system is
141	>	//equal to the total number of atoms minus number of atoms belong to
142	>	//cutoff group defined in meta-data file plus the number of cutoff
143	>	//groups defined in meta-data file
144	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
145
146	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
147	<	//therefore the total number of  integrable objects in the system is equal to
148	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
149	<	//file plus the number of  rigid bodies defined in meta-data file
150	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
146	>	//every free atom (atom does not belong to rigid bodies) is an
147	>	//integrable object therefore the total number of integrable objects
148	>	//in the system is equal to the total number of atoms minus number of
149	>	//atoms belong to rigid body defined in meta-data file plus the number
150	>	//of rigid bodies defined in meta-data file
151	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
152	>	+ nGlobalRigidBodies_;
153	>
154	>	nGlobalMols_ = molStampIds_.size();
155
136	–	nGlobalMols_ = molStampIds_.size();
137	–
156		#ifdef IS_MPI
157	<	molToProcMap_.resize(nGlobalMols_);
157	>	molToProcMap_.resize(nGlobalMols_);
158		#endif
159
160	<	}
160	>	}
161
162	<	SimInfo::~SimInfo() {
162	>	SimInfo::~SimInfo() {
163		std::map<int, Molecule*>::iterator i;
164		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
165	<	delete i->second;
165	>	delete i->second;
166		}
167		molecules_.clear();
168	<
151	<	MemoryUtils::deletePointers(moleculeStamps_);
152	<
168	>
169		delete sman_;
170		delete simParams_;
171		delete forceField_;
172	<	}
172	>	}
173
174	<	int SimInfo::getNGlobalConstraints() {
174	>	int SimInfo::getNGlobalConstraints() {
175		int nGlobalConstraints;
176		#ifdef IS_MPI
177		MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
#	Line 164 | Line 180 | int SimInfo::getNGlobalConstraints() {
180		nGlobalConstraints =  nConstraints_;
181		#endif
182		return nGlobalConstraints;
183	<	}
183	>	}
184
185	<	bool SimInfo::addMolecule(Molecule* mol) {
185	>	bool SimInfo::addMolecule(Molecule* mol) {
186		MoleculeIterator i;
187
188		i = molecules_.find(mol->getGlobalIndex());
189		if (i == molecules_.end() ) {
190
191	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
191	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
192
193	<	nAtoms_ += mol->getNAtoms();
194	<	nBonds_ += mol->getNBonds();
195	<	nBends_ += mol->getNBends();
196	<	nTorsions_ += mol->getNTorsions();
197	<	nRigidBodies_ += mol->getNRigidBodies();
198	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
199	<	nCutoffGroups_ += mol->getNCutoffGroups();
200	<	nConstraints_ += mol->getNConstraintPairs();
193	>	nAtoms_ += mol->getNAtoms();
194	>	nBonds_ += mol->getNBonds();
195	>	nBends_ += mol->getNBends();
196	>	nTorsions_ += mol->getNTorsions();
197	>	nRigidBodies_ += mol->getNRigidBodies();
198	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
199	>	nCutoffGroups_ += mol->getNCutoffGroups();
200	>	nConstraints_ += mol->getNConstraintPairs();
201
202	<	addExcludePairs(mol);
202	>	addExcludePairs(mol);
203
204	<	return true;
204	>	return true;
205		} else {
206	<	return false;
206	>	return false;
207		}
208	<	}
208	>	}
209
210	<	bool SimInfo::removeMolecule(Molecule* mol) {
210	>	bool SimInfo::removeMolecule(Molecule* mol) {
211		MoleculeIterator i;
212		i = molecules_.find(mol->getGlobalIndex());
213
214		if (i != molecules_.end() ) {
215
216	<	assert(mol == i->second);
216	>	assert(mol == i->second);
217
218	<	nAtoms_ -= mol->getNAtoms();
219	<	nBonds_ -= mol->getNBonds();
220	<	nBends_ -= mol->getNBends();
221	<	nTorsions_ -= mol->getNTorsions();
222	<	nRigidBodies_ -= mol->getNRigidBodies();
223	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
224	<	nCutoffGroups_ -= mol->getNCutoffGroups();
225	<	nConstraints_ -= mol->getNConstraintPairs();
218	>	nAtoms_ -= mol->getNAtoms();
219	>	nBonds_ -= mol->getNBonds();
220	>	nBends_ -= mol->getNBends();
221	>	nTorsions_ -= mol->getNTorsions();
222	>	nRigidBodies_ -= mol->getNRigidBodies();
223	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
224	>	nCutoffGroups_ -= mol->getNCutoffGroups();
225	>	nConstraints_ -= mol->getNConstraintPairs();
226
227	<	removeExcludePairs(mol);
228	<	molecules_.erase(mol->getGlobalIndex());
229	<
230	<	delete mol;
227	>	removeExcludePairs(mol);
228	>	molecules_.erase(mol->getGlobalIndex());
229	>
230	>	delete mol;
231
232	<	return true;
232	>	return true;
233		} else {
234	<	return false;
234	>	return false;
235		}
236
237
238	<	}
238	>	}
239
240
241	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
241	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
242		i = molecules_.begin();
243		return i == molecules_.end() ? NULL : i->second;
244	<	}
244	>	}
245
246	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
246	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
247		++i;
248		return i == molecules_.end() ? NULL : i->second;
249	<	}
249	>	}
250
251
252	<	void SimInfo::calcNdf() {
252	>	void SimInfo::calcNdf() {
253		int ndf_local;
254		MoleculeIterator i;
255		std::vector<StuntDouble*>::iterator j;
#	Line 243 | Line 259 | void SimInfo::calcNdf() {
259		ndf_local = 0;
260
261		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
262	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
263	<	integrableObject = mol->nextIntegrableObject(j)) {
262	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
263	>	integrableObject = mol->nextIntegrableObject(j)) {
264
265	<	ndf_local += 3;
265	>	ndf_local += 3;
266
267	<	if (integrableObject->isDirectional()) {
268	<	if (integrableObject->isLinear()) {
269	<	ndf_local += 2;
270	<	} else {
271	<	ndf_local += 3;
272	<	}
273	<	}
267	>	if (integrableObject->isDirectional()) {
268	>	if (integrableObject->isLinear()) {
269	>	ndf_local += 2;
270	>	} else {
271	>	ndf_local += 3;
272	>	}
273	>	}
274
275	<	}//end for (integrableObject)
276	<	}// end for (mol)
275	>	}
276	>	}
277
278		// n_constraints is local, so subtract them on each processor
279		ndf_local -= nConstraints_;
#	Line 272 | Line 288 | void SimInfo::calcNdf() {
288		// entire system:
289		ndf_ = ndf_ - 3 - nZconstraint_;
290
291	<	}
291	>	}
292
293	<	void SimInfo::calcNdfRaw() {
293	>	void SimInfo::calcNdfRaw() {
294		int ndfRaw_local;
295
296		MoleculeIterator i;
#	Line 286 | Line 302 | void SimInfo::calcNdfRaw() {
302		ndfRaw_local = 0;
303
304		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
305	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
306	<	integrableObject = mol->nextIntegrableObject(j)) {
305	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
306	>	integrableObject = mol->nextIntegrableObject(j)) {
307
308	<	ndfRaw_local += 3;
308	>	ndfRaw_local += 3;
309
310	<	if (integrableObject->isDirectional()) {
311	<	if (integrableObject->isLinear()) {
312	<	ndfRaw_local += 2;
313	<	} else {
314	<	ndfRaw_local += 3;
315	<	}
316	<	}
310	>	if (integrableObject->isDirectional()) {
311	>	if (integrableObject->isLinear()) {
312	>	ndfRaw_local += 2;
313	>	} else {
314	>	ndfRaw_local += 3;
315	>	}
316	>	}
317
318	<	}
318	>	}
319		}
320
321		#ifdef IS_MPI
#	Line 307 | Line 323 | void SimInfo::calcNdfRaw() {
323		#else
324		ndfRaw_ = ndfRaw_local;
325		#endif
326	<	}
326	>	}
327
328	<	void SimInfo::calcNdfTrans() {
328	>	void SimInfo::calcNdfTrans() {
329		int ndfTrans_local;
330
331		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 323 | Line 339 | void SimInfo::calcNdfTrans() {
339
340		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
341
342	<	}
342	>	}
343
344	<	void SimInfo::addExcludePairs(Molecule* mol) {
344	>	void SimInfo::addExcludePairs(Molecule* mol) {
345		std::vector<Bond*>::iterator bondIter;
346		std::vector<Bend*>::iterator bendIter;
347		std::vector<Torsion*>::iterator torsionIter;
#	Line 336 | Line 352 | void SimInfo::addExcludePairs(Molecule* mol) {
352		int b;
353		int c;
354		int d;
355	+
356	+	std::map<int, std::set<int> > atomGroups;
357	+
358	+	Molecule::RigidBodyIterator rbIter;
359	+	RigidBody* rb;
360	+	Molecule::IntegrableObjectIterator ii;
361	+	StuntDouble* integrableObject;
362
363	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
364	+	integrableObject = mol->nextIntegrableObject(ii)) {
365	+
366	+	if (integrableObject->isRigidBody()) {
367	+	rb = static_cast<RigidBody*>(integrableObject);
368	+	std::vector<Atom*> atoms = rb->getAtoms();
369	+	std::set<int> rigidAtoms;
370	+	for (int i = 0; i < atoms.size(); ++i) {
371	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
372	+	}
373	+	for (int i = 0; i < atoms.size(); ++i) {
374	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
375	+	}
376	+	} else {
377	+	std::set<int> oneAtomSet;
378	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
379	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
380	+	}
381	+	}
382	+
383	+
384	+
385		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
386	<	a = bond->getAtomA()->getGlobalIndex();
387	<	b = bond->getAtomB()->getGlobalIndex();
388	<	exclude_.addPair(a, b);
386	>	a = bond->getAtomA()->getGlobalIndex();
387	>	b = bond->getAtomB()->getGlobalIndex();
388	>	exclude_.addPair(a, b);
389		}
390
391		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
392	<	a = bend->getAtomA()->getGlobalIndex();
393	<	b = bend->getAtomB()->getGlobalIndex();
394	<	c = bend->getAtomC()->getGlobalIndex();
392	>	a = bend->getAtomA()->getGlobalIndex();
393	>	b = bend->getAtomB()->getGlobalIndex();
394	>	c = bend->getAtomC()->getGlobalIndex();
395	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
396	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
397	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
398
399	<	exclude_.addPair(a, b);
400	<	exclude_.addPair(a, c);
401	<	exclude_.addPair(b, c);
399	>	exclude_.addPairs(rigidSetA, rigidSetB);
400	>	exclude_.addPairs(rigidSetA, rigidSetC);
401	>	exclude_.addPairs(rigidSetB, rigidSetC);
402	>
403	>	//exclude_.addPair(a, b);
404	>	//exclude_.addPair(a, c);
405	>	//exclude_.addPair(b, c);
406		}
407
408		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
409	<	a = torsion->getAtomA()->getGlobalIndex();
410	<	b = torsion->getAtomB()->getGlobalIndex();
411	<	c = torsion->getAtomC()->getGlobalIndex();
412	<	d = torsion->getAtomD()->getGlobalIndex();
409	>	a = torsion->getAtomA()->getGlobalIndex();
410	>	b = torsion->getAtomB()->getGlobalIndex();
411	>	c = torsion->getAtomC()->getGlobalIndex();
412	>	d = torsion->getAtomD()->getGlobalIndex();
413	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
414	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
415	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
416	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
417
418	<	exclude_.addPair(a, b);
419	<	exclude_.addPair(a, c);
420	<	exclude_.addPair(a, d);
421	<	exclude_.addPair(b, c);
422	<	exclude_.addPair(b, d);
423	<	exclude_.addPair(c, d);
418	>	exclude_.addPairs(rigidSetA, rigidSetB);
419	>	exclude_.addPairs(rigidSetA, rigidSetC);
420	>	exclude_.addPairs(rigidSetA, rigidSetD);
421	>	exclude_.addPairs(rigidSetB, rigidSetC);
422	>	exclude_.addPairs(rigidSetB, rigidSetD);
423	>	exclude_.addPairs(rigidSetC, rigidSetD);
424	>
425	>	/*
426	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
427	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
428	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
429	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
430	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
431	>	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
432	>
433	>
434	>	exclude_.addPair(a, b);
435	>	exclude_.addPair(a, c);
436	>	exclude_.addPair(a, d);
437	>	exclude_.addPair(b, c);
438	>	exclude_.addPair(b, d);
439	>	exclude_.addPair(c, d);
440	>	*/
441		}
442
443	<
444	<	}
443	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
444	>	std::vector<Atom*> atoms = rb->getAtoms();
445	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
446	>	for (int j = i + 1; j < atoms.size(); ++j) {
447	>	a = atoms[i]->getGlobalIndex();
448	>	b = atoms[j]->getGlobalIndex();
449	>	exclude_.addPair(a, b);
450	>	}
451	>	}
452	>	}
453
454	<	void SimInfo::removeExcludePairs(Molecule* mol) {
454	>	}
455	>
456	>	void SimInfo::removeExcludePairs(Molecule* mol) {
457		std::vector<Bond*>::iterator bondIter;
458		std::vector<Bend*>::iterator bendIter;
459		std::vector<Torsion*>::iterator torsionIter;
#	Line 381 | Line 464 | void SimInfo::removeExcludePairs(Molecule* mol) {
464		int b;
465		int c;
466		int d;
467	+
468	+	std::map<int, std::set<int> > atomGroups;
469	+
470	+	Molecule::RigidBodyIterator rbIter;
471	+	RigidBody* rb;
472	+	Molecule::IntegrableObjectIterator ii;
473	+	StuntDouble* integrableObject;
474
475	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
476	+	integrableObject = mol->nextIntegrableObject(ii)) {
477	+
478	+	if (integrableObject->isRigidBody()) {
479	+	rb = static_cast<RigidBody*>(integrableObject);
480	+	std::vector<Atom*> atoms = rb->getAtoms();
481	+	std::set<int> rigidAtoms;
482	+	for (int i = 0; i < atoms.size(); ++i) {
483	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
484	+	}
485	+	for (int i = 0; i < atoms.size(); ++i) {
486	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
487	+	}
488	+	} else {
489	+	std::set<int> oneAtomSet;
490	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
491	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
492	+	}
493	+	}
494	+
495	+
496		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
497	<	a = bond->getAtomA()->getGlobalIndex();
498	<	b = bond->getAtomB()->getGlobalIndex();
499	<	exclude_.removePair(a, b);
497	>	a = bond->getAtomA()->getGlobalIndex();
498	>	b = bond->getAtomB()->getGlobalIndex();
499	>	exclude_.removePair(a, b);
500		}
501
502		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
503	<	a = bend->getAtomA()->getGlobalIndex();
504	<	b = bend->getAtomB()->getGlobalIndex();
505	<	c = bend->getAtomC()->getGlobalIndex();
503	>	a = bend->getAtomA()->getGlobalIndex();
504	>	b = bend->getAtomB()->getGlobalIndex();
505	>	c = bend->getAtomC()->getGlobalIndex();
506
507	<	exclude_.removePair(a, b);
508	<	exclude_.removePair(a, c);
509	<	exclude_.removePair(b, c);
507	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
508	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
509	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
510	>
511	>	exclude_.removePairs(rigidSetA, rigidSetB);
512	>	exclude_.removePairs(rigidSetA, rigidSetC);
513	>	exclude_.removePairs(rigidSetB, rigidSetC);
514	>
515	>	//exclude_.removePair(a, b);
516	>	//exclude_.removePair(a, c);
517	>	//exclude_.removePair(b, c);
518		}
519
520		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
521	<	a = torsion->getAtomA()->getGlobalIndex();
522	<	b = torsion->getAtomB()->getGlobalIndex();
523	<	c = torsion->getAtomC()->getGlobalIndex();
524	<	d = torsion->getAtomD()->getGlobalIndex();
521	>	a = torsion->getAtomA()->getGlobalIndex();
522	>	b = torsion->getAtomB()->getGlobalIndex();
523	>	c = torsion->getAtomC()->getGlobalIndex();
524	>	d = torsion->getAtomD()->getGlobalIndex();
525
526	<	exclude_.removePair(a, b);
527	<	exclude_.removePair(a, c);
528	<	exclude_.removePair(a, d);
529	<	exclude_.removePair(b, c);
530	<	exclude_.removePair(b, d);
531	<	exclude_.removePair(c, d);
526	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
527	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
528	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
529	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
530	>
531	>	exclude_.removePairs(rigidSetA, rigidSetB);
532	>	exclude_.removePairs(rigidSetA, rigidSetC);
533	>	exclude_.removePairs(rigidSetA, rigidSetD);
534	>	exclude_.removePairs(rigidSetB, rigidSetC);
535	>	exclude_.removePairs(rigidSetB, rigidSetD);
536	>	exclude_.removePairs(rigidSetC, rigidSetD);
537	>
538	>	/*
539	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
540	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
541	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
542	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
543	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
544	>	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
545	>
546	>
547	>	exclude_.removePair(a, b);
548	>	exclude_.removePair(a, c);
549	>	exclude_.removePair(a, d);
550	>	exclude_.removePair(b, c);
551	>	exclude_.removePair(b, d);
552	>	exclude_.removePair(c, d);
553	>	*/
554		}
555
556	<	}
556	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
557	>	std::vector<Atom*> atoms = rb->getAtoms();
558	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
559	>	for (int j = i + 1; j < atoms.size(); ++j) {
560	>	a = atoms[i]->getGlobalIndex();
561	>	b = atoms[j]->getGlobalIndex();
562	>	exclude_.removePair(a, b);
563	>	}
564	>	}
565	>	}
566
567	+	}
568
569	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
569	>
570	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
571		int curStampId;
572
573		//index from 0
#	Line 423 | Line 575 | void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp
575
576		moleculeStamps_.push_back(molStamp);
577		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
578	<	}
578	>	}
579
580	<	void SimInfo::update() {
580	>	void SimInfo::update() {
581
582		setupSimType();
583
#	Line 438 | Line 590 | void SimInfo::update() {
590		//setup fortran force field
591		/** @deprecate */
592		int isError = 0;
593	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
593	>
594	>	setupElectrostaticSummationMethod( isError );
595	>	setupSwitchingFunction();
596	>
597		if(isError){
598	<	sprintf( painCave.errMsg,
599	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
600	<	painCave.isFatal = 1;
601	<	simError();
598	>	sprintf( painCave.errMsg,
599	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
600	>	painCave.isFatal = 1;
601	>	simError();
602		}
603
604
#	Line 454 | Line 609 | void SimInfo::update() {
609		calcNdfTrans();
610
611		fortranInitialized_ = true;
612	<	}
612	>	}
613
614	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
614	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
615		SimInfo::MoleculeIterator mi;
616		Molecule* mol;
617		Molecule::AtomIterator ai;
#	Line 465 | Line 620 | std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
620
621		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
622
623	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
624	<	atomTypes.insert(atom->getAtomType());
625	<	}
623	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
624	>	atomTypes.insert(atom->getAtomType());
625	>	}
626
627		}
628
629		return atomTypes;
630	<	}
630	>	}
631
632	<	void SimInfo::setupSimType() {
632	>	void SimInfo::setupSimType() {
633		std::set<AtomType*>::iterator i;
634		std::set<AtomType*> atomTypes;
635		atomTypes = getUniqueAtomTypes();
#	Line 482 | Line 637 | void SimInfo::setupSimType() {
637		int useLennardJones = 0;
638		int useElectrostatic = 0;
639		int useEAM = 0;
640	+	int useSC = 0;
641		int useCharge = 0;
642		int useDirectional = 0;
643		int useDipole = 0;
644		int useGayBerne = 0;
645		int useSticky = 0;
646	+	int useStickyPower = 0;
647		int useShape = 0;
648		int useFLARB = 0; //it is not in AtomType yet
649		int useDirectionalAtom = 0;
650		int useElectrostatics = 0;
651		//usePBC and useRF are from simParams
652	<	int usePBC = simParams_->getPBC();
653	<	int useRF = simParams_->getUseRF();
652	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
653	>	int useRF;
654	>	int useSF;
655	>	std::string myMethod;
656
657	+	// set the useRF logical
658	+	useRF = 0;
659	+	useSF = 0;
660	+
661	+
662	+	if (simParams_->haveElectrostaticSummationMethod()) {
663	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
664	+	toUpper(myMethod);
665	+	if (myMethod == "REACTION_FIELD") {
666	+	useRF=1;
667	+	} else {
668	+	if (myMethod == "SHIFTED_FORCE") {
669	+	useSF = 1;
670	+	}
671	+	}
672	+	}
673	+
674		//loop over all of the atom types
675		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
676	<	useLennardJones |= (*i)->isLennardJones();
677	<	useElectrostatic |= (*i)->isElectrostatic();
678	<	useEAM |= (*i)->isEAM();
679	<	useCharge |= (*i)->isCharge();
680	<	useDirectional |= (*i)->isDirectional();
681	<	useDipole |= (*i)->isDipole();
682	<	useGayBerne |= (*i)->isGayBerne();
683	<	useSticky |= (*i)->isSticky();
684	<	useShape |= (*i)->isShape();
676	>	useLennardJones |= (*i)->isLennardJones();
677	>	useElectrostatic |= (*i)->isElectrostatic();
678	>	useEAM |= (*i)->isEAM();
679	>	useSC |= (*i)->isSC();
680	>	useCharge |= (*i)->isCharge();
681	>	useDirectional |= (*i)->isDirectional();
682	>	useDipole |= (*i)->isDipole();
683	>	useGayBerne |= (*i)->isGayBerne();
684	>	useSticky |= (*i)->isSticky();
685	>	useStickyPower |= (*i)->isStickyPower();
686	>	useShape |= (*i)->isShape();
687		}
688
689	<	if (useSticky || useDipole || useGayBerne || useShape) {
690	<	useDirectionalAtom = 1;
689	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
690	>	useDirectionalAtom = 1;
691		}
692
693		if (useCharge || useDipole) {
694	<	useElectrostatics = 1;
694	>	useElectrostatics = 1;
695		}
696
697		#ifdef IS_MPI
#	Line 540 | Line 718 | void SimInfo::setupSimType() {
718		temp = useSticky;
719		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
720
721	+	temp = useStickyPower;
722	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
723	+
724		temp = useGayBerne;
725		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
726
727		temp = useEAM;
728		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
729
730	+	temp = useSC;
731	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
732	+
733		temp = useShape;
734		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
735
#	Line 554 | Line 738 | void SimInfo::setupSimType() {
738
739		temp = useRF;
740		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
741	<
741	>
742	>	temp = useSF;
743	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
744	>
745		#endif
746
747		fInfo_.SIM_uses_PBC = usePBC;
#	Line 564 | Line 751 | void SimInfo::setupSimType() {
751		fInfo_.SIM_uses_Charges = useCharge;
752		fInfo_.SIM_uses_Dipoles = useDipole;
753		fInfo_.SIM_uses_Sticky = useSticky;
754	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
755		fInfo_.SIM_uses_GayBerne = useGayBerne;
756		fInfo_.SIM_uses_EAM = useEAM;
757	+	fInfo_.SIM_uses_SC = useSC;
758		fInfo_.SIM_uses_Shapes = useShape;
759		fInfo_.SIM_uses_FLARB = useFLARB;
760		fInfo_.SIM_uses_RF = useRF;
761	+	fInfo_.SIM_uses_SF = useSF;
762
763	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
764	<
765	<	if (simParams_->haveDielectric()) {
766	<	fInfo_.dielect = simParams_->getDielectric();
767	<	} else {
768	<	sprintf(painCave.errMsg,
769	<	"SimSetup Error: No Dielectric constant was set.\n"
770	<	"\tYou are trying to use Reaction Field without"
771	<	"\tsetting a dielectric constant!\n");
772	<	painCave.isFatal = 1;
773	<	simError();
774	<	}
585	<
586	<	} else {
587	<	fInfo_.dielect = 0.0;
763	>	if( myMethod == "REACTION_FIELD") {
764	>
765	>	if (simParams_->haveDielectric()) {
766	>	fInfo_.dielect = simParams_->getDielectric();
767	>	} else {
768	>	sprintf(painCave.errMsg,
769	>	"SimSetup Error: No Dielectric constant was set.\n"
770	>	"\tYou are trying to use Reaction Field without"
771	>	"\tsetting a dielectric constant!\n");
772	>	painCave.isFatal = 1;
773	>	simError();
774	>	}
775		}
776
777	<	}
777	>	}
778
779	<	void SimInfo::setupFortranSim() {
779	>	void SimInfo::setupFortranSim() {
780		int isError;
781		int nExclude;
782		std::vector<int> fortranGlobalGroupMembership;
#	Line 599 | Line 786 | void SimInfo::setupFortranSim() {
786
787		//globalGroupMembership_ is filled by SimCreator
788		for (int i = 0; i < nGlobalAtoms_; i++) {
789	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
789	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
790		}
791
792		//calculate mass ratio of cutoff group
#	Line 616 | Line 803 | void SimInfo::setupFortranSim() {
803		mfact.reserve(getNCutoffGroups());
804
805		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
806	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
806	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
807
808	<	totalMass = cg->getMass();
809	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
810	<	mfact.push_back(atom->getMass()/totalMass);
811	<	}
808	>	totalMass = cg->getMass();
809	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
810	>	// Check for massless groups - set mfact to 1 if true
811	>	if (totalMass != 0)
812	>	mfact.push_back(atom->getMass()/totalMass);
813	>	else
814	>	mfact.push_back( 1.0 );
815	>	}
816
817	<	}
817	>	}
818		}
819
820		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
#	Line 633 | Line 824 | void SimInfo::setupFortranSim() {
824		identArray.reserve(getNAtoms());
825
826		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
827	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
828	<	identArray.push_back(atom->getIdent());
829	<	}
827	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
828	>	identArray.push_back(atom->getIdent());
829	>	}
830		}
831
832		//fill molMembershipArray
833		//molMembershipArray is filled by SimCreator
834		std::vector<int> molMembershipArray(nGlobalAtoms_);
835		for (int i = 0; i < nGlobalAtoms_; i++) {
836	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
836	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
837		}
838
839		//setup fortran simulation
649	–	//gloalExcludes and molMembershipArray should go away (They are never used)
650	–	//why the hell fortran need to know molecule?
651	–	//OOPSE = Object-Obfuscated Parallel Simulation Engine
840		int nGlobalExcludes = 0;
841		int* globalExcludes = NULL;
842		int* excludeList = exclude_.getExcludeList();
843		setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
844	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
845	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
844	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
845	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
846
847		if( isError ){
848
849	<	sprintf( painCave.errMsg,
850	<	"There was an error setting the simulation information in fortran.\n" );
851	<	painCave.isFatal = 1;
852	<	painCave.severity = OOPSE_ERROR;
853	<	simError();
849	>	sprintf( painCave.errMsg,
850	>	"There was an error setting the simulation information in fortran.\n" );
851	>	painCave.isFatal = 1;
852	>	painCave.severity = OOPSE_ERROR;
853	>	simError();
854		}
855
856		#ifdef IS_MPI
857		sprintf( checkPointMsg,
858	<	"succesfully sent the simulation information to fortran.\n");
858	>	"succesfully sent the simulation information to fortran.\n");
859		MPIcheckPoint();
860		#endif // is_mpi
861	<	}
861	>	}
862
863
864		#ifdef IS_MPI
865	<	void SimInfo::setupFortranParallel() {
865	>	void SimInfo::setupFortranParallel() {
866
867		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
868		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
#	Line 690 | Line 878 | void SimInfo::setupFortranParallel() {
878
879		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
880
881	<	//local index(index in DataStorge) of atom is important
882	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
883	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
884	<	}
881	>	//local index(index in DataStorge) of atom is important
882	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
883	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
884	>	}
885
886	<	//local index of cutoff group is trivial, it only depends on the order of travesing
887	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
888	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
889	<	}
886	>	//local index of cutoff group is trivial, it only depends on the order of travesing
887	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
888	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
889	>	}
890
891		}
892
#	Line 718 | Line 906 | void SimInfo::setupFortranParallel() {
906		&localToGlobalCutoffGroupIndex[0], &isError);
907
908		if (isError) {
909	<	sprintf(painCave.errMsg,
910	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
911	<	painCave.isFatal = 1;
912	<	simError();
909	>	sprintf(painCave.errMsg,
910	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
911	>	painCave.isFatal = 1;
912	>	simError();
913		}
914
915		sprintf(checkPointMsg, " mpiRefresh successful.\n");
916		MPIcheckPoint();
917
918
919	<	}
919	>	}
920
921		#endif
922
923	<	double SimInfo::calcMaxCutoffRadius() {
923	>	void SimInfo::setupCutoff() {
924	>
925	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
926
927	+	// Check the cutoff policy
928	+	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
929
930	<	std::set<AtomType*> atomTypes;
931	<	std::set<AtomType*>::iterator i;
932	<	std::vector<double> cutoffRadius;
933	<
934	<	//get the unique atom types
743	<	atomTypes = getUniqueAtomTypes();
744	<
745	<	//query the max cutoff radius among these atom types
746	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
747	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
930	>	std::string myPolicy;
931	>	if (forceFieldOptions_.haveCutoffPolicy()){
932	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
933	>	}else if (simParams_->haveCutoffPolicy()) {
934	>	myPolicy = simParams_->getCutoffPolicy();
935		}
936
937	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
938	<	#ifdef IS_MPI
939	<	//pick the max cutoff radius among the processors
940	<	#endif
937	>	if (!myPolicy.empty()){
938	>	toUpper(myPolicy);
939	>	if (myPolicy == "MIX") {
940	>	cp = MIX_CUTOFF_POLICY;
941	>	} else {
942	>	if (myPolicy == "MAX") {
943	>	cp = MAX_CUTOFF_POLICY;
944	>	} else {
945	>	if (myPolicy == "TRADITIONAL") {
946	>	cp = TRADITIONAL_CUTOFF_POLICY;
947	>	} else {
948	>	// throw error
949	>	sprintf( painCave.errMsg,
950	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
951	>	painCave.isFatal = 1;
952	>	simError();
953	>	}
954	>	}
955	>	}
956	>	}
957	>	notifyFortranCutoffPolicy(&cp);
958
959	<	return maxCutoffRadius;
960	<	}
961	<
962	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
963	<
964	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
959	>	// Check the Skin Thickness for neighborlists
960	>	double skin;
961	>	if (simParams_->haveSkinThickness()) {
962	>	skin = simParams_->getSkinThickness();
963	>	notifyFortranSkinThickness(&skin);
964	>	}
965
966	<	if (!simParams_->haveRcut()){
967	<	sprintf(painCave.errMsg,
966	>	// Check if the cutoff was set explicitly:
967	>	if (simParams_->haveCutoffRadius()) {
968	>	rcut_ = simParams_->getCutoffRadius();
969	>	if (simParams_->haveSwitchingRadius()) {
970	>	rsw_  = simParams_->getSwitchingRadius();
971	>	} else {
972	>	rsw_ = rcut_;
973	>	}
974	>	notifyFortranCutoffs(&rcut_, &rsw_);
975	>
976	>	} else {
977	>
978	>	// For electrostatic atoms, we'll assume a large safe value:
979	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
980	>	sprintf(painCave.errMsg,
981		"SimCreator Warning: No value was set for the cutoffRadius.\n"
982		"\tOOPSE will use a default value of 15.0 angstroms"
983		"\tfor the cutoffRadius.\n");
984	<	painCave.isFatal = 0;
985	<	simError();
986	<	rcut = 15.0;
987	<	} else{
988	<	rcut = simParams_->getRcut();
984	>	painCave.isFatal = 0;
985	>	simError();
986	>	rcut_ = 15.0;
987	>
988	>	if (simParams_->haveElectrostaticSummationMethod()) {
989	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
990	>	toUpper(myMethod);
991	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
992	>	if (simParams_->haveSwitchingRadius()){
993	>	sprintf(painCave.errMsg,
994	>	"SimInfo Warning: A value was set for the switchingRadius\n"
995	>	"\teven though the electrostaticSummationMethod was\n"
996	>	"\tset to %s\n", myMethod.c_str());
997	>	painCave.isFatal = 1;
998	>	simError();
999	>	}
1000	>	}
1001		}
1002	<
1003	<	if (!simParams_->haveRsw()){
1004	<	sprintf(painCave.errMsg,
1005	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1006	<	"\tOOPSE will use a default value of\n"
1007	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
1008	<	painCave.isFatal = 0;
1009	<	simError();
1010	<	rsw = 0.95 * rcut;
1011	<	} else{
1012	<	rsw = simParams_->getRsw();
1002	>
1003	>	if (simParams_->haveSwitchingRadius()){
1004	>	rsw_ = simParams_->getSwitchingRadius();
1005	>	} else {
1006	>	sprintf(painCave.errMsg,
1007	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1008	>	"\tOOPSE will use a default value of\n"
1009	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1010	>	painCave.isFatal = 0;
1011	>	simError();
1012	>	rsw_ = 0.85 * rcut_;
1013		}
1014	<
1015	<	} else {
1016	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
1017	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
1014	>	notifyFortranCutoffs(&rcut_, &rsw_);
1015	>	} else {
1016	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1017	>	// We'll punt and let fortran figure out the cutoffs later.
1018
1019	<	if (simParams_->haveRcut()) {
791	<	rcut = simParams_->getRcut();
792	<	} else {
793	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
794	<	rcut = calcMaxCutoffRadius();
795	<	}
1019	>	notifyFortranYouAreOnYourOwn();
1020
1021	<	if (simParams_->haveRsw()) {
798	<	rsw  = simParams_->getRsw();
799	<	} else {
800	<	rsw = rcut;
801	<	}
802	<
1021	>	}
1022		}
1023	<	}
1023	>	}
1024
1025	<	void SimInfo::setupCutoff() {
1026	<	getCutoff(rcut_, rsw_);
1027	<	double rnblist = rcut_ + 1; // skin of neighbor list
1025	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1026	>
1027	>	int errorOut;
1028	>	int esm =  NONE;
1029	>	int sm = UNDAMPED;
1030	>	double alphaVal;
1031	>	double dielectric;
1032
1033	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1034	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
1035	<	}
1033	>	errorOut = isError;
1034	>	alphaVal = simParams_->getDampingAlpha();
1035	>	dielectric = simParams_->getDielectric();
1036
1037	<	void SimInfo::addProperty(GenericData* genData) {
1038	<	properties_.addProperty(genData);
1039	<	}
1040	<
1041	<	void SimInfo::removeProperty(const std::string& propName) {
1042	<	properties_.removeProperty(propName);
1043	<	}
1044	<
1045	<	void SimInfo::clearProperties() {
1046	<	properties_.clearProperties();
1047	<	}
1048	<
1049	<	std::vector<std::string> SimInfo::getPropertyNames() {
1050	<	return properties_.getPropertyNames();
1051	<	}
1052	<
1053	<	std::vector<GenericData*> SimInfo::getProperties() {
1054	<	return properties_.getProperties();
1055	<	}
1056	<
1057	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1058	<	return properties_.getPropertyByName(propName);
1059	<	}
1060	<
1061	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1062	<	//if (sman_ == sman_) {
1063	<	//    return;
1064	<	//}
1037	>	if (simParams_->haveElectrostaticSummationMethod()) {
1038	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1039	>	toUpper(myMethod);
1040	>	if (myMethod == "NONE") {
1041	>	esm = NONE;
1042	>	} else {
1043	>	if (myMethod == "SWITCHING_FUNCTION") {
1044	>	esm = SWITCHING_FUNCTION;
1045	>	} else {
1046	>	if (myMethod == "SHIFTED_POTENTIAL") {
1047	>	esm = SHIFTED_POTENTIAL;
1048	>	} else {
1049	>	if (myMethod == "SHIFTED_FORCE") {
1050	>	esm = SHIFTED_FORCE;
1051	>	} else {
1052	>	if (myMethod == "REACTION_FIELD") {
1053	>	esm = REACTION_FIELD;
1054	>	} else {
1055	>	// throw error
1056	>	sprintf( painCave.errMsg,
1057	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1058	>	"\t(Input file specified %s .)\n"
1059	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1060	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1061	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1062	>	painCave.isFatal = 1;
1063	>	simError();
1064	>	}
1065	>	}
1066	>	}
1067	>	}
1068	>	}
1069	>	}
1070	>
1071	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1072	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1073	>	toUpper(myScreen);
1074	>	if (myScreen == "UNDAMPED") {
1075	>	sm = UNDAMPED;
1076	>	} else {
1077	>	if (myScreen == "DAMPED") {
1078	>	sm = DAMPED;
1079	>	if (!simParams_->haveDampingAlpha()) {
1080	>	//throw error
1081	>	sprintf( painCave.errMsg,
1082	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1083	>	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1084	>	painCave.isFatal = 0;
1085	>	simError();
1086	>	}
1087	>	} else {
1088	>	// throw error
1089	>	sprintf( painCave.errMsg,
1090	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1091	>	"\t(Input file specified %s .)\n"
1092	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1093	>	"or \"damped\".\n", myScreen.c_str() );
1094	>	painCave.isFatal = 1;
1095	>	simError();
1096	>	}
1097	>	}
1098	>	}
1099
1100	<	//delete sman_;
1100	>	// let's pass some summation method variables to fortran
1101	>	setElectrostaticSumMethod( &esm );
1102	>	setFortranElectrostaticMethod( &esm );
1103	>	setScreeningMethod( &sm );
1104	>	setDampingAlpha( &alphaVal );
1105	>	setReactionFieldDielectric( &dielectric );
1106	>	initFortranFF( &errorOut );
1107	>	}
1108	>
1109	>	void SimInfo::setupSwitchingFunction() {
1110	>	int ft = CUBIC;
1111	>
1112	>	if (simParams_->haveSwitchingFunctionType()) {
1113	>	std::string funcType = simParams_->getSwitchingFunctionType();
1114	>	toUpper(funcType);
1115	>	if (funcType == "CUBIC") {
1116	>	ft = CUBIC;
1117	>	} else {
1118	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1119	>	ft = FIFTH_ORDER_POLY;
1120	>	} else {
1121	>	// throw error
1122	>	sprintf( painCave.errMsg,
1123	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1124	>	painCave.isFatal = 1;
1125	>	simError();
1126	>	}
1127	>	}
1128	>	}
1129	>
1130	>	// send switching function notification to switcheroo
1131	>	setFunctionType(&ft);
1132	>
1133	>	}
1134	>
1135	>	void SimInfo::addProperty(GenericData* genData) {
1136	>	properties_.addProperty(genData);
1137	>	}
1138	>
1139	>	void SimInfo::removeProperty(const std::string& propName) {
1140	>	properties_.removeProperty(propName);
1141	>	}
1142	>
1143	>	void SimInfo::clearProperties() {
1144	>	properties_.clearProperties();
1145	>	}
1146	>
1147	>	std::vector<std::string> SimInfo::getPropertyNames() {
1148	>	return properties_.getPropertyNames();
1149	>	}
1150	>
1151	>	std::vector<GenericData*> SimInfo::getProperties() {
1152	>	return properties_.getProperties();
1153	>	}
1154	>
1155	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1156	>	return properties_.getPropertyByName(propName);
1157	>	}
1158	>
1159	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1160	>	if (sman_ == sman) {
1161	>	return;
1162	>	}
1163	>	delete sman_;
1164		sman_ = sman;
1165
1166		Molecule* mol;
#	Line 852 | Line 1172 | void SimInfo::setSnapshotManager(SnapshotManager* sman
1172
1173		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1174
1175	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1176	<	atom->setSnapshotManager(sman_);
1177	<	}
1175	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1176	>	atom->setSnapshotManager(sman_);
1177	>	}
1178
1179	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1180	<	rb->setSnapshotManager(sman_);
1181	<	}
1179	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1180	>	rb->setSnapshotManager(sman_);
1181	>	}
1182		}
1183
1184	<	}
1184	>	}
1185
1186	<	Vector3d SimInfo::getComVel(){
1186	>	Vector3d SimInfo::getComVel(){
1187		SimInfo::MoleculeIterator i;
1188		Molecule* mol;
1189
#	Line 872 | Line 1192 | Vector3d SimInfo::getComVel(){
1192
1193
1194		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1195	<	double mass = mol->getMass();
1196	<	totalMass += mass;
1197	<	comVel += mass * mol->getComVel();
1195	>	double mass = mol->getMass();
1196	>	totalMass += mass;
1197	>	comVel += mass * mol->getComVel();
1198		}
1199
1200		#ifdef IS_MPI
#	Line 887 | Line 1207 | Vector3d SimInfo::getComVel(){
1207		comVel /= totalMass;
1208
1209		return comVel;
1210	<	}
1210	>	}
1211
1212	<	Vector3d SimInfo::getCom(){
1212	>	Vector3d SimInfo::getCom(){
1213		SimInfo::MoleculeIterator i;
1214		Molecule* mol;
1215
#	Line 897 | Line 1217 | Vector3d SimInfo::getCom(){
1217		double totalMass = 0.0;
1218
1219		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1220	<	double mass = mol->getMass();
1221	<	totalMass += mass;
1222	<	com += mass * mol->getCom();
1220	>	double mass = mol->getMass();
1221	>	totalMass += mass;
1222	>	com += mass * mol->getCom();
1223		}
1224
1225		#ifdef IS_MPI
#	Line 913 | Line 1233 | Vector3d SimInfo::getCom(){
1233
1234		return com;
1235
1236	<	}
1236	>	}
1237
1238	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1238	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1239
1240		return o;
1241	<	}
1241	>	}
1242	>
1243	>
1244	>	/*
1245	>	Returns center of mass and center of mass velocity in one function call.
1246	>	*/
1247	>
1248	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1249	>	SimInfo::MoleculeIterator i;
1250	>	Molecule* mol;
1251	>
1252	>
1253	>	double totalMass = 0.0;
1254	>
1255
1256	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1257	+	double mass = mol->getMass();
1258	+	totalMass += mass;
1259	+	com += mass * mol->getCom();
1260	+	comVel += mass * mol->getComVel();
1261	+	}
1262	+
1263	+	#ifdef IS_MPI
1264	+	double tmpMass = totalMass;
1265	+	Vector3d tmpCom(com);
1266	+	Vector3d tmpComVel(comVel);
1267	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1268	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1269	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1270	+	#endif
1271	+
1272	+	com /= totalMass;
1273	+	comVel /= totalMass;
1274	+	}
1275	+
1276	+	/*
1277	+	Return intertia tensor for entire system and angular momentum Vector.
1278	+
1279	+
1280	+	[  Ixx -Ixy  -Ixz ]
1281	+	J =| -Iyx  Iyy  -Iyz |
1282	+	[ -Izx -Iyz   Izz ]
1283	+	*/
1284	+
1285	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1286	+
1287	+
1288	+	double xx = 0.0;
1289	+	double yy = 0.0;
1290	+	double zz = 0.0;
1291	+	double xy = 0.0;
1292	+	double xz = 0.0;
1293	+	double yz = 0.0;
1294	+	Vector3d com(0.0);
1295	+	Vector3d comVel(0.0);
1296	+
1297	+	getComAll(com, comVel);
1298	+
1299	+	SimInfo::MoleculeIterator i;
1300	+	Molecule* mol;
1301	+
1302	+	Vector3d thisq(0.0);
1303	+	Vector3d thisv(0.0);
1304	+
1305	+	double thisMass = 0.0;
1306	+
1307	+
1308	+
1309	+
1310	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1311	+
1312	+	thisq = mol->getCom()-com;
1313	+	thisv = mol->getComVel()-comVel;
1314	+	thisMass = mol->getMass();
1315	+	// Compute moment of intertia coefficients.
1316	+	xx += thisq[0]*thisq[0]*thisMass;
1317	+	yy += thisq[1]*thisq[1]*thisMass;
1318	+	zz += thisq[2]*thisq[2]*thisMass;
1319	+
1320	+	// compute products of intertia
1321	+	xy += thisq[0]*thisq[1]*thisMass;
1322	+	xz += thisq[0]*thisq[2]*thisMass;
1323	+	yz += thisq[1]*thisq[2]*thisMass;
1324	+
1325	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1326	+
1327	+	}
1328	+
1329	+
1330	+	inertiaTensor(0,0) = yy + zz;
1331	+	inertiaTensor(0,1) = -xy;
1332	+	inertiaTensor(0,2) = -xz;
1333	+	inertiaTensor(1,0) = -xy;
1334	+	inertiaTensor(1,1) = xx + zz;
1335	+	inertiaTensor(1,2) = -yz;
1336	+	inertiaTensor(2,0) = -xz;
1337	+	inertiaTensor(2,1) = -yz;
1338	+	inertiaTensor(2,2) = xx + yy;
1339	+
1340	+	#ifdef IS_MPI
1341	+	Mat3x3d tmpI(inertiaTensor);
1342	+	Vector3d tmpAngMom;
1343	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1344	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1345	+	#endif
1346	+
1347	+	return;
1348	+	}
1349	+
1350	+	//Returns the angular momentum of the system
1351	+	Vector3d SimInfo::getAngularMomentum(){
1352	+
1353	+	Vector3d com(0.0);
1354	+	Vector3d comVel(0.0);
1355	+	Vector3d angularMomentum(0.0);
1356	+
1357	+	getComAll(com,comVel);
1358	+
1359	+	SimInfo::MoleculeIterator i;
1360	+	Molecule* mol;
1361	+
1362	+	Vector3d thisr(0.0);
1363	+	Vector3d thisp(0.0);
1364	+
1365	+	double thisMass;
1366	+
1367	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1368	+	thisMass = mol->getMass();
1369	+	thisr = mol->getCom()-com;
1370	+	thisp = (mol->getComVel()-comVel)*thisMass;
1371	+
1372	+	angularMomentum += cross( thisr, thisp );
1373	+
1374	+	}
1375	+
1376	+	#ifdef IS_MPI
1377	+	Vector3d tmpAngMom;
1378	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1379	+	#endif
1380	+
1381	+	return angularMomentum;
1382	+	}
1383	+
1384	+
1385		}//end namespace oopse
1386

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