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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 328 by tim, Sun Feb 13 20:36:24 2005 UTC vs.
Revision 945 by gezelter, Tue Apr 25 02:09:01 2006 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 48 | Line 48
48
49		#include <algorithm>
50		#include <set>
51	+	#include <map>
52
53		#include "brains/SimInfo.hpp"
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56	+	#include "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), selectMan_(NULL) {
82	>	return result;
83	>	}
84	>
85	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
86	>	forceField_(ff), simParams_(simParams),
87	>	ndf_(0), fdf_local(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	<	selectMan_ = new SelectionManager(this);
143	<	selectMan_->selectAll();
144	<	}
160	>	}
161
162	<	SimInfo::~SimInfo() {
163	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
164	<
165	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
166	<
162	>	SimInfo::~SimInfo() {
163	>	std::map<int, Molecule*>::iterator i;
164	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
165	>	delete i->second;
166	>	}
167	>	molecules_.clear();
168	>
169		delete sman_;
170		delete simParams_;
171		delete forceField_;
172	<	delete selectMan_;
155	<	}
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 163 | 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();
226	<
227	<	removeExcludePairs(mol);
228	<	molecules_.erase(mol->getGlobalIndex());
229	<
230	<	delete mol;
231	<
232	<	return true;
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;
231	>
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 242 | 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 271 | Line 288 | void SimInfo::calcNdf() {
288		// entire system:
289		ndf_ = ndf_ - 3 - nZconstraint_;
290
291	<	}
291	>	}
292
293	<	void SimInfo::calcNdfRaw() {
293	>	int SimInfo::getFdf() {
294	>	#ifdef IS_MPI
295	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
296	>	#else
297	>	fdf_ = fdf_local;
298	>	#endif
299	>	return fdf_;
300	>	}
301	>
302	>	void SimInfo::calcNdfRaw() {
303		int ndfRaw_local;
304
305		MoleculeIterator i;
#	Line 285 | Line 311 | void SimInfo::calcNdfRaw() {
311		ndfRaw_local = 0;
312
313		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
314	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
315	<	integrableObject = mol->nextIntegrableObject(j)) {
314	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
315	>	integrableObject = mol->nextIntegrableObject(j)) {
316
317	<	ndfRaw_local += 3;
317	>	ndfRaw_local += 3;
318
319	<	if (integrableObject->isDirectional()) {
320	<	if (integrableObject->isLinear()) {
321	<	ndfRaw_local += 2;
322	<	} else {
323	<	ndfRaw_local += 3;
324	<	}
325	<	}
319	>	if (integrableObject->isDirectional()) {
320	>	if (integrableObject->isLinear()) {
321	>	ndfRaw_local += 2;
322	>	} else {
323	>	ndfRaw_local += 3;
324	>	}
325	>	}
326
327	<	}
327	>	}
328		}
329
330		#ifdef IS_MPI
#	Line 306 | Line 332 | void SimInfo::calcNdfRaw() {
332		#else
333		ndfRaw_ = ndfRaw_local;
334		#endif
335	<	}
335	>	}
336
337	<	void SimInfo::calcNdfTrans() {
337	>	void SimInfo::calcNdfTrans() {
338		int ndfTrans_local;
339
340		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 322 | Line 348 | void SimInfo::calcNdfTrans() {
348
349		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
350
351	<	}
351	>	}
352
353	<	void SimInfo::addExcludePairs(Molecule* mol) {
353	>	void SimInfo::addExcludePairs(Molecule* mol) {
354		std::vector<Bond*>::iterator bondIter;
355		std::vector<Bend*>::iterator bendIter;
356		std::vector<Torsion*>::iterator torsionIter;
#	Line 335 | Line 361 | void SimInfo::addExcludePairs(Molecule* mol) {
361		int b;
362		int c;
363		int d;
364	+
365	+	std::map<int, std::set<int> > atomGroups;
366	+
367	+	Molecule::RigidBodyIterator rbIter;
368	+	RigidBody* rb;
369	+	Molecule::IntegrableObjectIterator ii;
370	+	StuntDouble* integrableObject;
371
372	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
373	+	integrableObject = mol->nextIntegrableObject(ii)) {
374	+
375	+	if (integrableObject->isRigidBody()) {
376	+	rb = static_cast<RigidBody*>(integrableObject);
377	+	std::vector<Atom*> atoms = rb->getAtoms();
378	+	std::set<int> rigidAtoms;
379	+	for (int i = 0; i < atoms.size(); ++i) {
380	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
381	+	}
382	+	for (int i = 0; i < atoms.size(); ++i) {
383	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
384	+	}
385	+	} else {
386	+	std::set<int> oneAtomSet;
387	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
388	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
389	+	}
390	+	}
391	+
392	+
393	+
394		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
395	<	a = bond->getAtomA()->getGlobalIndex();
396	<	b = bond->getAtomB()->getGlobalIndex();
397	<	exclude_.addPair(a, b);
395	>	a = bond->getAtomA()->getGlobalIndex();
396	>	b = bond->getAtomB()->getGlobalIndex();
397	>	exclude_.addPair(a, b);
398		}
399
400		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
401	<	a = bend->getAtomA()->getGlobalIndex();
402	<	b = bend->getAtomB()->getGlobalIndex();
403	<	c = bend->getAtomC()->getGlobalIndex();
401	>	a = bend->getAtomA()->getGlobalIndex();
402	>	b = bend->getAtomB()->getGlobalIndex();
403	>	c = bend->getAtomC()->getGlobalIndex();
404	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
405	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
406	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
407
408	<	exclude_.addPair(a, b);
409	<	exclude_.addPair(a, c);
410	<	exclude_.addPair(b, c);
408	>	exclude_.addPairs(rigidSetA, rigidSetB);
409	>	exclude_.addPairs(rigidSetA, rigidSetC);
410	>	exclude_.addPairs(rigidSetB, rigidSetC);
411	>
412	>	//exclude_.addPair(a, b);
413	>	//exclude_.addPair(a, c);
414	>	//exclude_.addPair(b, c);
415		}
416
417		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
418	<	a = torsion->getAtomA()->getGlobalIndex();
419	<	b = torsion->getAtomB()->getGlobalIndex();
420	<	c = torsion->getAtomC()->getGlobalIndex();
421	<	d = torsion->getAtomD()->getGlobalIndex();
418	>	a = torsion->getAtomA()->getGlobalIndex();
419	>	b = torsion->getAtomB()->getGlobalIndex();
420	>	c = torsion->getAtomC()->getGlobalIndex();
421	>	d = torsion->getAtomD()->getGlobalIndex();
422	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
423	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
424	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
425	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
426
427	<	exclude_.addPair(a, b);
428	<	exclude_.addPair(a, c);
429	<	exclude_.addPair(a, d);
430	<	exclude_.addPair(b, c);
431	<	exclude_.addPair(b, d);
432	<	exclude_.addPair(c, d);
427	>	exclude_.addPairs(rigidSetA, rigidSetB);
428	>	exclude_.addPairs(rigidSetA, rigidSetC);
429	>	exclude_.addPairs(rigidSetA, rigidSetD);
430	>	exclude_.addPairs(rigidSetB, rigidSetC);
431	>	exclude_.addPairs(rigidSetB, rigidSetD);
432	>	exclude_.addPairs(rigidSetC, rigidSetD);
433	>
434	>	/*
435	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
436	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
437	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
438	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
439	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
440	>	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
441	>
442	>
443	>	exclude_.addPair(a, b);
444	>	exclude_.addPair(a, c);
445	>	exclude_.addPair(a, d);
446	>	exclude_.addPair(b, c);
447	>	exclude_.addPair(b, d);
448	>	exclude_.addPair(c, d);
449	>	*/
450		}
451
452	<
453	<	}
452	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
453	>	std::vector<Atom*> atoms = rb->getAtoms();
454	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
455	>	for (int j = i + 1; j < atoms.size(); ++j) {
456	>	a = atoms[i]->getGlobalIndex();
457	>	b = atoms[j]->getGlobalIndex();
458	>	exclude_.addPair(a, b);
459	>	}
460	>	}
461	>	}
462
463	<	void SimInfo::removeExcludePairs(Molecule* mol) {
463	>	}
464	>
465	>	void SimInfo::removeExcludePairs(Molecule* mol) {
466		std::vector<Bond*>::iterator bondIter;
467		std::vector<Bend*>::iterator bendIter;
468		std::vector<Torsion*>::iterator torsionIter;
#	Line 380 | Line 473 | void SimInfo::removeExcludePairs(Molecule* mol) {
473		int b;
474		int c;
475		int d;
476	+
477	+	std::map<int, std::set<int> > atomGroups;
478	+
479	+	Molecule::RigidBodyIterator rbIter;
480	+	RigidBody* rb;
481	+	Molecule::IntegrableObjectIterator ii;
482	+	StuntDouble* integrableObject;
483
484	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
485	+	integrableObject = mol->nextIntegrableObject(ii)) {
486	+
487	+	if (integrableObject->isRigidBody()) {
488	+	rb = static_cast<RigidBody*>(integrableObject);
489	+	std::vector<Atom*> atoms = rb->getAtoms();
490	+	std::set<int> rigidAtoms;
491	+	for (int i = 0; i < atoms.size(); ++i) {
492	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
493	+	}
494	+	for (int i = 0; i < atoms.size(); ++i) {
495	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
496	+	}
497	+	} else {
498	+	std::set<int> oneAtomSet;
499	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
500	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
501	+	}
502	+	}
503	+
504	+
505		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
506	<	a = bond->getAtomA()->getGlobalIndex();
507	<	b = bond->getAtomB()->getGlobalIndex();
508	<	exclude_.removePair(a, b);
506	>	a = bond->getAtomA()->getGlobalIndex();
507	>	b = bond->getAtomB()->getGlobalIndex();
508	>	exclude_.removePair(a, b);
509		}
510
511		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
512	<	a = bend->getAtomA()->getGlobalIndex();
513	<	b = bend->getAtomB()->getGlobalIndex();
514	<	c = bend->getAtomC()->getGlobalIndex();
512	>	a = bend->getAtomA()->getGlobalIndex();
513	>	b = bend->getAtomB()->getGlobalIndex();
514	>	c = bend->getAtomC()->getGlobalIndex();
515
516	<	exclude_.removePair(a, b);
517	<	exclude_.removePair(a, c);
518	<	exclude_.removePair(b, c);
516	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
517	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
518	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
519	>
520	>	exclude_.removePairs(rigidSetA, rigidSetB);
521	>	exclude_.removePairs(rigidSetA, rigidSetC);
522	>	exclude_.removePairs(rigidSetB, rigidSetC);
523	>
524	>	//exclude_.removePair(a, b);
525	>	//exclude_.removePair(a, c);
526	>	//exclude_.removePair(b, c);
527		}
528
529		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
530	<	a = torsion->getAtomA()->getGlobalIndex();
531	<	b = torsion->getAtomB()->getGlobalIndex();
532	<	c = torsion->getAtomC()->getGlobalIndex();
533	<	d = torsion->getAtomD()->getGlobalIndex();
530	>	a = torsion->getAtomA()->getGlobalIndex();
531	>	b = torsion->getAtomB()->getGlobalIndex();
532	>	c = torsion->getAtomC()->getGlobalIndex();
533	>	d = torsion->getAtomD()->getGlobalIndex();
534
535	<	exclude_.removePair(a, b);
536	<	exclude_.removePair(a, c);
537	<	exclude_.removePair(a, d);
538	<	exclude_.removePair(b, c);
539	<	exclude_.removePair(b, d);
540	<	exclude_.removePair(c, d);
535	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
536	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
537	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
538	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
539	>
540	>	exclude_.removePairs(rigidSetA, rigidSetB);
541	>	exclude_.removePairs(rigidSetA, rigidSetC);
542	>	exclude_.removePairs(rigidSetA, rigidSetD);
543	>	exclude_.removePairs(rigidSetB, rigidSetC);
544	>	exclude_.removePairs(rigidSetB, rigidSetD);
545	>	exclude_.removePairs(rigidSetC, rigidSetD);
546	>
547	>	/*
548	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
549	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
550	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
551	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
552	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
553	>	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
554	>
555	>
556	>	exclude_.removePair(a, b);
557	>	exclude_.removePair(a, c);
558	>	exclude_.removePair(a, d);
559	>	exclude_.removePair(b, c);
560	>	exclude_.removePair(b, d);
561	>	exclude_.removePair(c, d);
562	>	*/
563		}
564
565	<	}
565	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
566	>	std::vector<Atom*> atoms = rb->getAtoms();
567	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
568	>	for (int j = i + 1; j < atoms.size(); ++j) {
569	>	a = atoms[i]->getGlobalIndex();
570	>	b = atoms[j]->getGlobalIndex();
571	>	exclude_.removePair(a, b);
572	>	}
573	>	}
574	>	}
575
576	+	}
577
578	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
578	>
579	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
580		int curStampId;
581
582		//index from 0
#	Line 422 | Line 584 | void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp
584
585		moleculeStamps_.push_back(molStamp);
586		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
587	<	}
587	>	}
588
589	<	void SimInfo::update() {
589	>	void SimInfo::update() {
590
591		setupSimType();
592
#	Line 437 | Line 599 | void SimInfo::update() {
599		//setup fortran force field
600		/** @deprecate */
601		int isError = 0;
602	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
602	>
603	>	setupElectrostaticSummationMethod( isError );
604	>	setupSwitchingFunction();
605	>
606		if(isError){
607	<	sprintf( painCave.errMsg,
608	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
609	<	painCave.isFatal = 1;
610	<	simError();
607	>	sprintf( painCave.errMsg,
608	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
609	>	painCave.isFatal = 1;
610	>	simError();
611		}
612
613
#	Line 453 | Line 618 | void SimInfo::update() {
618		calcNdfTrans();
619
620		fortranInitialized_ = true;
621	<	}
621	>	}
622
623	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
623	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
624		SimInfo::MoleculeIterator mi;
625		Molecule* mol;
626		Molecule::AtomIterator ai;
#	Line 464 | Line 629 | std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
629
630		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
631
632	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
633	<	atomTypes.insert(atom->getAtomType());
634	<	}
632	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
633	>	atomTypes.insert(atom->getAtomType());
634	>	}
635
636		}
637
638		return atomTypes;
639	<	}
639	>	}
640
641	<	void SimInfo::setupSimType() {
641	>	void SimInfo::setupSimType() {
642		std::set<AtomType*>::iterator i;
643		std::set<AtomType*> atomTypes;
644		atomTypes = getUniqueAtomTypes();
#	Line 481 | Line 646 | void SimInfo::setupSimType() {
646		int useLennardJones = 0;
647		int useElectrostatic = 0;
648		int useEAM = 0;
649	+	int useSC = 0;
650		int useCharge = 0;
651		int useDirectional = 0;
652		int useDipole = 0;
653		int useGayBerne = 0;
654		int useSticky = 0;
655	+	int useStickyPower = 0;
656		int useShape = 0;
657		int useFLARB = 0; //it is not in AtomType yet
658		int useDirectionalAtom = 0;
659		int useElectrostatics = 0;
660		//usePBC and useRF are from simParams
661	<	int usePBC = simParams_->getPBC();
662	<	int useRF = simParams_->getUseRF();
661	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
662	>	int useRF;
663	>	int useSF;
664	>	std::string myMethod;
665
666	+	// set the useRF logical
667	+	useRF = 0;
668	+	useSF = 0;
669	+
670	+
671	+	if (simParams_->haveElectrostaticSummationMethod()) {
672	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
673	+	toUpper(myMethod);
674	+	if (myMethod == "REACTION_FIELD") {
675	+	useRF=1;
676	+	} else {
677	+	if (myMethod == "SHIFTED_FORCE") {
678	+	useSF = 1;
679	+	}
680	+	}
681	+	}
682	+
683		//loop over all of the atom types
684		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
685	<	useLennardJones |= (*i)->isLennardJones();
686	<	useElectrostatic |= (*i)->isElectrostatic();
687	<	useEAM |= (*i)->isEAM();
688	<	useCharge |= (*i)->isCharge();
689	<	useDirectional |= (*i)->isDirectional();
690	<	useDipole |= (*i)->isDipole();
691	<	useGayBerne |= (*i)->isGayBerne();
692	<	useSticky |= (*i)->isSticky();
693	<	useShape |= (*i)->isShape();
685	>	useLennardJones |= (*i)->isLennardJones();
686	>	useElectrostatic |= (*i)->isElectrostatic();
687	>	useEAM |= (*i)->isEAM();
688	>	useSC |= (*i)->isSC();
689	>	useCharge |= (*i)->isCharge();
690	>	useDirectional |= (*i)->isDirectional();
691	>	useDipole |= (*i)->isDipole();
692	>	useGayBerne |= (*i)->isGayBerne();
693	>	useSticky |= (*i)->isSticky();
694	>	useStickyPower |= (*i)->isStickyPower();
695	>	useShape |= (*i)->isShape();
696		}
697
698	<	if (useSticky || useDipole || useGayBerne || useShape) {
699	<	useDirectionalAtom = 1;
698	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
699	>	useDirectionalAtom = 1;
700		}
701
702		if (useCharge || useDipole) {
703	<	useElectrostatics = 1;
703	>	useElectrostatics = 1;
704		}
705
706		#ifdef IS_MPI
#	Line 539 | Line 727 | void SimInfo::setupSimType() {
727		temp = useSticky;
728		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
729
730	+	temp = useStickyPower;
731	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
732	+
733		temp = useGayBerne;
734		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
735
736		temp = useEAM;
737		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
738
739	+	temp = useSC;
740	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
741	+
742		temp = useShape;
743		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
744
#	Line 553 | Line 747 | void SimInfo::setupSimType() {
747
748		temp = useRF;
749		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
750	<
750	>
751	>	temp = useSF;
752	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
753	>
754		#endif
755
756		fInfo_.SIM_uses_PBC = usePBC;
#	Line 563 | Line 760 | void SimInfo::setupSimType() {
760		fInfo_.SIM_uses_Charges = useCharge;
761		fInfo_.SIM_uses_Dipoles = useDipole;
762		fInfo_.SIM_uses_Sticky = useSticky;
763	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
764		fInfo_.SIM_uses_GayBerne = useGayBerne;
765		fInfo_.SIM_uses_EAM = useEAM;
766	+	fInfo_.SIM_uses_SC = useSC;
767		fInfo_.SIM_uses_Shapes = useShape;
768		fInfo_.SIM_uses_FLARB = useFLARB;
769		fInfo_.SIM_uses_RF = useRF;
770	+	fInfo_.SIM_uses_SF = useSF;
771
772	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
773	<
774	<	if (simParams_->haveDielectric()) {
775	<	fInfo_.dielect = simParams_->getDielectric();
776	<	} else {
777	<	sprintf(painCave.errMsg,
778	<	"SimSetup Error: No Dielectric constant was set.\n"
779	<	"\tYou are trying to use Reaction Field without"
780	<	"\tsetting a dielectric constant!\n");
781	<	painCave.isFatal = 1;
782	<	simError();
783	<	}
584	<
585	<	} else {
586	<	fInfo_.dielect = 0.0;
772	>	if( myMethod == "REACTION_FIELD") {
773	>
774	>	if (simParams_->haveDielectric()) {
775	>	fInfo_.dielect = simParams_->getDielectric();
776	>	} else {
777	>	sprintf(painCave.errMsg,
778	>	"SimSetup Error: No Dielectric constant was set.\n"
779	>	"\tYou are trying to use Reaction Field without"
780	>	"\tsetting a dielectric constant!\n");
781	>	painCave.isFatal = 1;
782	>	simError();
783	>	}
784		}
785
786	<	}
786	>	}
787
788	<	void SimInfo::setupFortranSim() {
788	>	void SimInfo::setupFortranSim() {
789		int isError;
790		int nExclude;
791		std::vector<int> fortranGlobalGroupMembership;
#	Line 598 | Line 795 | void SimInfo::setupFortranSim() {
795
796		//globalGroupMembership_ is filled by SimCreator
797		for (int i = 0; i < nGlobalAtoms_; i++) {
798	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
798	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
799		}
800
801		//calculate mass ratio of cutoff group
#	Line 615 | Line 812 | void SimInfo::setupFortranSim() {
812		mfact.reserve(getNCutoffGroups());
813
814		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
815	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
815	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
816
817	<	totalMass = cg->getMass();
818	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
819	<	mfact.push_back(atom->getMass()/totalMass);
820	<	}
817	>	totalMass = cg->getMass();
818	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
819	>	// Check for massless groups - set mfact to 1 if true
820	>	if (totalMass != 0)
821	>	mfact.push_back(atom->getMass()/totalMass);
822	>	else
823	>	mfact.push_back( 1.0 );
824	>	}
825
826	<	}
826	>	}
827		}
828
829		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
#	Line 632 | Line 833 | void SimInfo::setupFortranSim() {
833		identArray.reserve(getNAtoms());
834
835		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
836	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
837	<	identArray.push_back(atom->getIdent());
838	<	}
836	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
837	>	identArray.push_back(atom->getIdent());
838	>	}
839		}
840
841		//fill molMembershipArray
842		//molMembershipArray is filled by SimCreator
843		std::vector<int> molMembershipArray(nGlobalAtoms_);
844		for (int i = 0; i < nGlobalAtoms_; i++) {
845	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
845	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
846		}
847
848		//setup fortran simulation
648	–	//gloalExcludes and molMembershipArray should go away (They are never used)
649	–	//why the hell fortran need to know molecule?
650	–	//OOPSE = Object-Obfuscated Parallel Simulation Engine
849		int nGlobalExcludes = 0;
850		int* globalExcludes = NULL;
851		int* excludeList = exclude_.getExcludeList();
852		setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
853	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
854	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
853	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
854	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
855
856		if( isError ){
857
858	<	sprintf( painCave.errMsg,
859	<	"There was an error setting the simulation information in fortran.\n" );
860	<	painCave.isFatal = 1;
861	<	painCave.severity = OOPSE_ERROR;
862	<	simError();
858	>	sprintf( painCave.errMsg,
859	>	"There was an error setting the simulation information in fortran.\n" );
860	>	painCave.isFatal = 1;
861	>	painCave.severity = OOPSE_ERROR;
862	>	simError();
863		}
864
865		#ifdef IS_MPI
866		sprintf( checkPointMsg,
867	<	"succesfully sent the simulation information to fortran.\n");
867	>	"succesfully sent the simulation information to fortran.\n");
868		MPIcheckPoint();
869		#endif // is_mpi
870	<	}
870	>	}
871
872
873		#ifdef IS_MPI
874	<	void SimInfo::setupFortranParallel() {
874	>	void SimInfo::setupFortranParallel() {
875
876		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
877		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
#	Line 689 | Line 887 | void SimInfo::setupFortranParallel() {
887
888		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
889
890	<	//local index(index in DataStorge) of atom is important
891	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
892	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
893	<	}
890	>	//local index(index in DataStorge) of atom is important
891	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
892	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
893	>	}
894
895	<	//local index of cutoff group is trivial, it only depends on the order of travesing
896	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
897	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
898	<	}
895	>	//local index of cutoff group is trivial, it only depends on the order of travesing
896	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
897	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
898	>	}
899
900		}
901
#	Line 717 | Line 915 | void SimInfo::setupFortranParallel() {
915		&localToGlobalCutoffGroupIndex[0], &isError);
916
917		if (isError) {
918	<	sprintf(painCave.errMsg,
919	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
920	<	painCave.isFatal = 1;
921	<	simError();
918	>	sprintf(painCave.errMsg,
919	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
920	>	painCave.isFatal = 1;
921	>	simError();
922		}
923
924		sprintf(checkPointMsg, " mpiRefresh successful.\n");
925		MPIcheckPoint();
926
927
928	<	}
928	>	}
929
930		#endif
931
932	<	double SimInfo::calcMaxCutoffRadius() {
932	>	void SimInfo::setupCutoff() {
933	>
934	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
935
936	+	// Check the cutoff policy
937	+	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
938
939	<	std::set<AtomType*> atomTypes;
940	<	std::set<AtomType*>::iterator i;
941	<	std::vector<double> cutoffRadius;
942	<
943	<	//get the unique atom types
742	<	atomTypes = getUniqueAtomTypes();
743	<
744	<	//query the max cutoff radius among these atom types
745	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
746	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
939	>	std::string myPolicy;
940	>	if (forceFieldOptions_.haveCutoffPolicy()){
941	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
942	>	}else if (simParams_->haveCutoffPolicy()) {
943	>	myPolicy = simParams_->getCutoffPolicy();
944		}
945
946	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
947	<	#ifdef IS_MPI
948	<	//pick the max cutoff radius among the processors
949	<	#endif
946	>	if (!myPolicy.empty()){
947	>	toUpper(myPolicy);
948	>	if (myPolicy == "MIX") {
949	>	cp = MIX_CUTOFF_POLICY;
950	>	} else {
951	>	if (myPolicy == "MAX") {
952	>	cp = MAX_CUTOFF_POLICY;
953	>	} else {
954	>	if (myPolicy == "TRADITIONAL") {
955	>	cp = TRADITIONAL_CUTOFF_POLICY;
956	>	} else {
957	>	// throw error
958	>	sprintf( painCave.errMsg,
959	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
960	>	painCave.isFatal = 1;
961	>	simError();
962	>	}
963	>	}
964	>	}
965	>	}
966	>	notifyFortranCutoffPolicy(&cp);
967
968	<	return maxCutoffRadius;
969	<	}
970	<
971	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
972	<
973	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
968	>	// Check the Skin Thickness for neighborlists
969	>	double skin;
970	>	if (simParams_->haveSkinThickness()) {
971	>	skin = simParams_->getSkinThickness();
972	>	notifyFortranSkinThickness(&skin);
973	>	}
974
975	<	if (!simParams_->haveRcut()){
976	<	sprintf(painCave.errMsg,
975	>	// Check if the cutoff was set explicitly:
976	>	if (simParams_->haveCutoffRadius()) {
977	>	rcut_ = simParams_->getCutoffRadius();
978	>	if (simParams_->haveSwitchingRadius()) {
979	>	rsw_  = simParams_->getSwitchingRadius();
980	>	} else {
981	>	if (fInfo_.SIM_uses_Charges |
982	>	fInfo_.SIM_uses_Dipoles |
983	>	fInfo_.SIM_uses_RF) {
984	>
985	>	rsw_ = 0.85 * rcut_;
986	>	sprintf(painCave.errMsg,
987	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
988	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
989	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
990	>	painCave.isFatal = 0;
991	>	simError();
992	>	} else {
993	>	rsw_ = rcut_;
994	>	sprintf(painCave.errMsg,
995	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
996	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
997	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
998	>	painCave.isFatal = 0;
999	>	simError();
1000	>	}
1001	>	}
1002	>
1003	>	notifyFortranCutoffs(&rcut_, &rsw_);
1004	>
1005	>	} else {
1006	>
1007	>	// For electrostatic atoms, we'll assume a large safe value:
1008	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1009	>	sprintf(painCave.errMsg,
1010		"SimCreator Warning: No value was set for the cutoffRadius.\n"
1011		"\tOOPSE will use a default value of 15.0 angstroms"
1012		"\tfor the cutoffRadius.\n");
1013	<	painCave.isFatal = 0;
1014	<	simError();
1015	<	rcut = 15.0;
1016	<	} else{
1017	<	rcut = simParams_->getRcut();
1013	>	painCave.isFatal = 0;
1014	>	simError();
1015	>	rcut_ = 15.0;
1016	>
1017	>	if (simParams_->haveElectrostaticSummationMethod()) {
1018	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1019	>	toUpper(myMethod);
1020	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1021	>	if (simParams_->haveSwitchingRadius()){
1022	>	sprintf(painCave.errMsg,
1023	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1024	>	"\teven though the electrostaticSummationMethod was\n"
1025	>	"\tset to %s\n", myMethod.c_str());
1026	>	painCave.isFatal = 1;
1027	>	simError();
1028	>	}
1029	>	}
1030		}
1031	<
1032	<	if (!simParams_->haveRsw()){
1033	<	sprintf(painCave.errMsg,
1034	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1035	<	"\tOOPSE will use a default value of\n"
1036	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
1037	<	painCave.isFatal = 0;
1038	<	simError();
1039	<	rsw = 0.95 * rcut;
1040	<	} else{
1041	<	rsw = simParams_->getRsw();
1031	>
1032	>	if (simParams_->haveSwitchingRadius()){
1033	>	rsw_ = simParams_->getSwitchingRadius();
1034	>	} else {
1035	>	sprintf(painCave.errMsg,
1036	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1037	>	"\tOOPSE will use a default value of\n"
1038	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1039	>	painCave.isFatal = 0;
1040	>	simError();
1041	>	rsw_ = 0.85 * rcut_;
1042		}
1043	<
1044	<	} else {
1045	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
1046	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
1043	>	notifyFortranCutoffs(&rcut_, &rsw_);
1044	>	} else {
1045	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1046	>	// We'll punt and let fortran figure out the cutoffs later.
1047
1048	<	if (simParams_->haveRcut()) {
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	<	}
1048	>	notifyFortranYouAreOnYourOwn();
1049
1050	<	if (simParams_->haveRsw()) {
797	<	rsw  = simParams_->getRsw();
798	<	} else {
799	<	rsw = rcut;
800	<	}
801	<
1050	>	}
1051		}
1052	<	}
1052	>	}
1053
1054	<	void SimInfo::setupCutoff() {
1055	<	getCutoff(rcut_, rsw_);
1056	<	double rnblist = rcut_ + 1; // skin of neighbor list
1054	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1055	>
1056	>	int errorOut;
1057	>	int esm =  NONE;
1058	>	int sm = UNDAMPED;
1059	>	double alphaVal;
1060	>	double dielectric;
1061
1062	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1063	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
1064	<	}
1062	>	errorOut = isError;
1063	>	alphaVal = simParams_->getDampingAlpha();
1064	>	dielectric = simParams_->getDielectric();
1065
1066	<	void SimInfo::addProperty(GenericData* genData) {
1067	<	properties_.addProperty(genData);
1068	<	}
1069	<
1070	<	void SimInfo::removeProperty(const std::string& propName) {
1071	<	properties_.removeProperty(propName);
1072	<	}
1073	<
1074	<	void SimInfo::clearProperties() {
1075	<	properties_.clearProperties();
1076	<	}
1077	<
1078	<	std::vector<std::string> SimInfo::getPropertyNames() {
1079	<	return properties_.getPropertyNames();
1080	<	}
1081	<
1082	<	std::vector<GenericData*> SimInfo::getProperties() {
1083	<	return properties_.getProperties();
1084	<	}
1085	<
1086	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1087	<	return properties_.getPropertyByName(propName);
1088	<	}
1066	>	if (simParams_->haveElectrostaticSummationMethod()) {
1067	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1068	>	toUpper(myMethod);
1069	>	if (myMethod == "NONE") {
1070	>	esm = NONE;
1071	>	} else {
1072	>	if (myMethod == "SWITCHING_FUNCTION") {
1073	>	esm = SWITCHING_FUNCTION;
1074	>	} else {
1075	>	if (myMethod == "SHIFTED_POTENTIAL") {
1076	>	esm = SHIFTED_POTENTIAL;
1077	>	} else {
1078	>	if (myMethod == "SHIFTED_FORCE") {
1079	>	esm = SHIFTED_FORCE;
1080	>	} else {
1081	>	if (myMethod == "REACTION_FIELD") {
1082	>	esm = REACTION_FIELD;
1083	>	} else {
1084	>	// throw error
1085	>	sprintf( painCave.errMsg,
1086	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1087	>	"\t(Input file specified %s .)\n"
1088	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1089	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1090	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1091	>	painCave.isFatal = 1;
1092	>	simError();
1093	>	}
1094	>	}
1095	>	}
1096	>	}
1097	>	}
1098	>	}
1099	>
1100	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1101	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1102	>	toUpper(myScreen);
1103	>	if (myScreen == "UNDAMPED") {
1104	>	sm = UNDAMPED;
1105	>	} else {
1106	>	if (myScreen == "DAMPED") {
1107	>	sm = DAMPED;
1108	>	if (!simParams_->haveDampingAlpha()) {
1109	>	//throw error
1110	>	sprintf( painCave.errMsg,
1111	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1112	>	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1113	>	painCave.isFatal = 0;
1114	>	simError();
1115	>	}
1116	>	} else {
1117	>	// throw error
1118	>	sprintf( painCave.errMsg,
1119	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1120	>	"\t(Input file specified %s .)\n"
1121	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1122	>	"or \"damped\".\n", myScreen.c_str() );
1123	>	painCave.isFatal = 1;
1124	>	simError();
1125	>	}
1126	>	}
1127	>	}
1128	>
1129	>	// let's pass some summation method variables to fortran
1130	>	setElectrostaticSummationMethod( &esm );
1131	>	setFortranElectrostaticMethod( &esm );
1132	>	setScreeningMethod( &sm );
1133	>	setDampingAlpha( &alphaVal );
1134	>	setReactionFieldDielectric( &dielectric );
1135	>	initFortranFF( &errorOut );
1136	>	}
1137
1138	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1138	>	void SimInfo::setupSwitchingFunction() {
1139	>	int ft = CUBIC;
1140	>
1141	>	if (simParams_->haveSwitchingFunctionType()) {
1142	>	std::string funcType = simParams_->getSwitchingFunctionType();
1143	>	toUpper(funcType);
1144	>	if (funcType == "CUBIC") {
1145	>	ft = CUBIC;
1146	>	} else {
1147	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1148	>	ft = FIFTH_ORDER_POLY;
1149	>	} else {
1150	>	// throw error
1151	>	sprintf( painCave.errMsg,
1152	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1153	>	painCave.isFatal = 1;
1154	>	simError();
1155	>	}
1156	>	}
1157	>	}
1158	>
1159	>	// send switching function notification to switcheroo
1160	>	setFunctionType(&ft);
1161	>
1162	>	}
1163	>
1164	>	void SimInfo::addProperty(GenericData* genData) {
1165	>	properties_.addProperty(genData);
1166	>	}
1167	>
1168	>	void SimInfo::removeProperty(const std::string& propName) {
1169	>	properties_.removeProperty(propName);
1170	>	}
1171	>
1172	>	void SimInfo::clearProperties() {
1173	>	properties_.clearProperties();
1174	>	}
1175	>
1176	>	std::vector<std::string> SimInfo::getPropertyNames() {
1177	>	return properties_.getPropertyNames();
1178	>	}
1179	>
1180	>	std::vector<GenericData*> SimInfo::getProperties() {
1181	>	return properties_.getProperties();
1182	>	}
1183	>
1184	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1185	>	return properties_.getPropertyByName(propName);
1186	>	}
1187	>
1188	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1189	>	if (sman_ == sman) {
1190	>	return;
1191	>	}
1192	>	delete sman_;
1193		sman_ = sman;
1194
1195		Molecule* mol;
#	Line 846 | Line 1201 | void SimInfo::setSnapshotManager(SnapshotManager* sman
1201
1202		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1203
1204	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1205	<	atom->setSnapshotManager(sman_);
1206	<	}
1204	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1205	>	atom->setSnapshotManager(sman_);
1206	>	}
1207
1208	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1209	<	rb->setSnapshotManager(sman_);
1210	<	}
1208	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1209	>	rb->setSnapshotManager(sman_);
1210	>	}
1211		}
1212
1213	<	}
1213	>	}
1214
1215	<	Vector3d SimInfo::getComVel(){
1215	>	Vector3d SimInfo::getComVel(){
1216		SimInfo::MoleculeIterator i;
1217		Molecule* mol;
1218
#	Line 866 | Line 1221 | Vector3d SimInfo::getComVel(){
1221
1222
1223		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1224	<	double mass = mol->getMass();
1225	<	totalMass += mass;
1226	<	comVel += mass * mol->getComVel();
1224	>	double mass = mol->getMass();
1225	>	totalMass += mass;
1226	>	comVel += mass * mol->getComVel();
1227		}
1228
1229		#ifdef IS_MPI
#	Line 881 | Line 1236 | Vector3d SimInfo::getComVel(){
1236		comVel /= totalMass;
1237
1238		return comVel;
1239	<	}
1239	>	}
1240
1241	<	Vector3d SimInfo::getCom(){
1241	>	Vector3d SimInfo::getCom(){
1242		SimInfo::MoleculeIterator i;
1243		Molecule* mol;
1244
#	Line 891 | Line 1246 | Vector3d SimInfo::getCom(){
1246		double totalMass = 0.0;
1247
1248		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1249	<	double mass = mol->getMass();
1250	<	totalMass += mass;
1251	<	com += mass * mol->getCom();
1249	>	double mass = mol->getMass();
1250	>	totalMass += mass;
1251	>	com += mass * mol->getCom();
1252		}
1253
1254		#ifdef IS_MPI
#	Line 907 | Line 1262 | Vector3d SimInfo::getCom(){
1262
1263		return com;
1264
1265	<	}
1265	>	}
1266
1267	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1267	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1268
1269		return o;
1270	<	}
1270	>	}
1271	>
1272	>
1273	>	/*
1274	>	Returns center of mass and center of mass velocity in one function call.
1275	>	*/
1276	>
1277	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1278	>	SimInfo::MoleculeIterator i;
1279	>	Molecule* mol;
1280	>
1281	>
1282	>	double totalMass = 0.0;
1283	>
1284
1285	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1286	+	double mass = mol->getMass();
1287	+	totalMass += mass;
1288	+	com += mass * mol->getCom();
1289	+	comVel += mass * mol->getComVel();
1290	+	}
1291	+
1292	+	#ifdef IS_MPI
1293	+	double tmpMass = totalMass;
1294	+	Vector3d tmpCom(com);
1295	+	Vector3d tmpComVel(comVel);
1296	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1297	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1298	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1299	+	#endif
1300	+
1301	+	com /= totalMass;
1302	+	comVel /= totalMass;
1303	+	}
1304	+
1305	+	/*
1306	+	Return intertia tensor for entire system and angular momentum Vector.
1307	+
1308	+
1309	+	[  Ixx -Ixy  -Ixz ]
1310	+	J =| -Iyx  Iyy  -Iyz |
1311	+	[ -Izx -Iyz   Izz ]
1312	+	*/
1313	+
1314	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1315	+
1316	+
1317	+	double xx = 0.0;
1318	+	double yy = 0.0;
1319	+	double zz = 0.0;
1320	+	double xy = 0.0;
1321	+	double xz = 0.0;
1322	+	double yz = 0.0;
1323	+	Vector3d com(0.0);
1324	+	Vector3d comVel(0.0);
1325	+
1326	+	getComAll(com, comVel);
1327	+
1328	+	SimInfo::MoleculeIterator i;
1329	+	Molecule* mol;
1330	+
1331	+	Vector3d thisq(0.0);
1332	+	Vector3d thisv(0.0);
1333	+
1334	+	double thisMass = 0.0;
1335	+
1336	+
1337	+
1338	+
1339	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1340	+
1341	+	thisq = mol->getCom()-com;
1342	+	thisv = mol->getComVel()-comVel;
1343	+	thisMass = mol->getMass();
1344	+	// Compute moment of intertia coefficients.
1345	+	xx += thisq[0]*thisq[0]*thisMass;
1346	+	yy += thisq[1]*thisq[1]*thisMass;
1347	+	zz += thisq[2]*thisq[2]*thisMass;
1348	+
1349	+	// compute products of intertia
1350	+	xy += thisq[0]*thisq[1]*thisMass;
1351	+	xz += thisq[0]*thisq[2]*thisMass;
1352	+	yz += thisq[1]*thisq[2]*thisMass;
1353	+
1354	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1355	+
1356	+	}
1357	+
1358	+
1359	+	inertiaTensor(0,0) = yy + zz;
1360	+	inertiaTensor(0,1) = -xy;
1361	+	inertiaTensor(0,2) = -xz;
1362	+	inertiaTensor(1,0) = -xy;
1363	+	inertiaTensor(1,1) = xx + zz;
1364	+	inertiaTensor(1,2) = -yz;
1365	+	inertiaTensor(2,0) = -xz;
1366	+	inertiaTensor(2,1) = -yz;
1367	+	inertiaTensor(2,2) = xx + yy;
1368	+
1369	+	#ifdef IS_MPI
1370	+	Mat3x3d tmpI(inertiaTensor);
1371	+	Vector3d tmpAngMom;
1372	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1373	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1374	+	#endif
1375	+
1376	+	return;
1377	+	}
1378	+
1379	+	//Returns the angular momentum of the system
1380	+	Vector3d SimInfo::getAngularMomentum(){
1381	+
1382	+	Vector3d com(0.0);
1383	+	Vector3d comVel(0.0);
1384	+	Vector3d angularMomentum(0.0);
1385	+
1386	+	getComAll(com,comVel);
1387	+
1388	+	SimInfo::MoleculeIterator i;
1389	+	Molecule* mol;
1390	+
1391	+	Vector3d thisr(0.0);
1392	+	Vector3d thisp(0.0);
1393	+
1394	+	double thisMass;
1395	+
1396	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1397	+	thisMass = mol->getMass();
1398	+	thisr = mol->getCom()-com;
1399	+	thisp = (mol->getComVel()-comVel)*thisMass;
1400	+
1401	+	angularMomentum += cross( thisr, thisp );
1402	+
1403	+	}
1404	+
1405	+	#ifdef IS_MPI
1406	+	Vector3d tmpAngMom;
1407	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1408	+	#endif
1409	+
1410	+	return angularMomentum;
1411	+	}
1412	+
1413	+
1414		}//end namespace oopse
1415

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