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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 331 by tim, Sun Feb 13 21:18:27 2005 UTC vs.
Revision 770 by tim, Fri Dec 2 15:38:03 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"
#	Line 64 | Line 70 | namespace oopse {
70		#endif
71
72		namespace oopse {
73	+	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
74	+	std::map<int, std::set<int> >::iterator i = container.find(index);
75	+	std::set<int> result;
76	+	if (i != container.end()) {
77	+	result = i->second;
78	+	}
79
80	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
81	<	ForceField* ff, Globals* simParams) :
82	<	forceField_(ff), simParams_(simParams),
83	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
84	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
85	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
86	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
87	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
88	<	sman_(NULL), fortranInitialized_(false), selectMan_(NULL) {
80	>	return result;
81	>	}
82	>
83	>	SimInfo::SimInfo(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) {
91
92	<
93	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
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	<
102	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
103	<	molStamp = i->first;
90	<	nMolWithSameStamp = i->second;
92	>	MoleculeStamp* molStamp;
93	>	int nMolWithSameStamp;
94	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
95	>	int nGroups = 0;      //total cutoff groups defined in meta-data file
96	>	CutoffGroupStamp* cgStamp;
97	>	RigidBodyStamp* rbStamp;
98	>	int nRigidAtoms = 0;
99	>	std::vector<Component*> components = simParams->getComponents();
100	>
101	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
102	>	molStamp = (*i)->getMoleculeStamp();
103	>	nMolWithSameStamp = (*i)->getNMol();
104
105		addMoleculeStamp(molStamp, nMolWithSameStamp);
106
107		//calculate atoms in molecules
108		nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
109
97	–
110		//calculate atoms in cutoff groups
111		int nAtomsInGroups = 0;
112		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
113
114		for (int j=0; j < nCutoffGroupsInStamp; j++) {
115	<	cgStamp = molStamp->getCutoffGroup(j);
116	<	nAtomsInGroups += cgStamp->getNMembers();
115	>	cgStamp = molStamp->getCutoffGroupStamp(j);
116	>	nAtomsInGroups += cgStamp->getNMembers();
117		}
118
119		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
120	+
121		nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
122
123		//calculate atoms in rigid bodies
#	Line 112 | Line 125 | SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*,
125		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
126
127		for (int j=0; j < nRigidBodiesInStamp; j++) {
128	<	rbStamp = molStamp->getRigidBody(j);
129	<	nAtomsInRigidBodies += rbStamp->getNMembers();
128	>	rbStamp = molStamp->getRigidBodyStamp(j);
129	>	nAtomsInRigidBodies += rbStamp->getNMembers();
130		}
131
132		nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
133		nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
134
135	<	}
135	>	}
136
137	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
138	<	//therefore the total number of cutoff groups in the system is equal to
139	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
140	<	//file plus the number of cutoff groups defined in meta-data file
141	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
137	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
138	>	//group therefore the total number of cutoff groups in the system is
139	>	//equal to the total number of atoms minus number of atoms belong to
140	>	//cutoff group defined in meta-data file plus the number of cutoff
141	>	//groups defined in meta-data file
142	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
143
144	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
145	<	//therefore the total number of  integrable objects in the system is equal to
146	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
147	<	//file plus the number of  rigid bodies defined in meta-data file
148	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
144	>	//every free atom (atom does not belong to rigid bodies) is an
145	>	//integrable object therefore the total number of integrable objects
146	>	//in the system is equal to the total number of atoms minus number of
147	>	//atoms belong to rigid body defined in meta-data file plus the number
148	>	//of rigid bodies defined in meta-data file
149	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
150	>	+ nGlobalRigidBodies_;
151	>
152	>	nGlobalMols_ = molStampIds_.size();
153
136	–	nGlobalMols_ = molStampIds_.size();
137	–
154		#ifdef IS_MPI
155	<	molToProcMap_.resize(nGlobalMols_);
155	>	molToProcMap_.resize(nGlobalMols_);
156		#endif
157
158	<	selectMan_ = new SelectionManager(this);
143	<	selectMan_->selectAll();
144	<	}
158	>	}
159
160	<	SimInfo::~SimInfo() {
161	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
162	<
163	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
164	<
160	>	SimInfo::~SimInfo() {
161	>	std::map<int, Molecule*>::iterator i;
162	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
163	>	delete i->second;
164	>	}
165	>	molecules_.clear();
166	>
167		delete sman_;
168		delete simParams_;
169		delete forceField_;
170	<	delete selectMan_;
155	<	}
170	>	}
171
172	<	int SimInfo::getNGlobalConstraints() {
172	>	int SimInfo::getNGlobalConstraints() {
173		int nGlobalConstraints;
174		#ifdef IS_MPI
175		MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
#	Line 163 | Line 178 | int SimInfo::getNGlobalConstraints() {
178		nGlobalConstraints =  nConstraints_;
179		#endif
180		return nGlobalConstraints;
181	<	}
181	>	}
182
183	<	bool SimInfo::addMolecule(Molecule* mol) {
183	>	bool SimInfo::addMolecule(Molecule* mol) {
184		MoleculeIterator i;
185
186		i = molecules_.find(mol->getGlobalIndex());
187		if (i == molecules_.end() ) {
188
189	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
189	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
190
191	<	nAtoms_ += mol->getNAtoms();
192	<	nBonds_ += mol->getNBonds();
193	<	nBends_ += mol->getNBends();
194	<	nTorsions_ += mol->getNTorsions();
195	<	nRigidBodies_ += mol->getNRigidBodies();
196	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
197	<	nCutoffGroups_ += mol->getNCutoffGroups();
198	<	nConstraints_ += mol->getNConstraintPairs();
191	>	nAtoms_ += mol->getNAtoms();
192	>	nBonds_ += mol->getNBonds();
193	>	nBends_ += mol->getNBends();
194	>	nTorsions_ += mol->getNTorsions();
195	>	nRigidBodies_ += mol->getNRigidBodies();
196	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
197	>	nCutoffGroups_ += mol->getNCutoffGroups();
198	>	nConstraints_ += mol->getNConstraintPairs();
199
200	<	addExcludePairs(mol);
200	>	addExcludePairs(mol);
201
202	<	return true;
202	>	return true;
203		} else {
204	<	return false;
204	>	return false;
205		}
206	<	}
206	>	}
207
208	<	bool SimInfo::removeMolecule(Molecule* mol) {
208	>	bool SimInfo::removeMolecule(Molecule* mol) {
209		MoleculeIterator i;
210		i = molecules_.find(mol->getGlobalIndex());
211
212		if (i != molecules_.end() ) {
213
214	<	assert(mol == i->second);
214	>	assert(mol == i->second);
215
216	<	nAtoms_ -= mol->getNAtoms();
217	<	nBonds_ -= mol->getNBonds();
218	<	nBends_ -= mol->getNBends();
219	<	nTorsions_ -= mol->getNTorsions();
220	<	nRigidBodies_ -= mol->getNRigidBodies();
221	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
222	<	nCutoffGroups_ -= mol->getNCutoffGroups();
223	<	nConstraints_ -= mol->getNConstraintPairs();
224	<
225	<	removeExcludePairs(mol);
226	<	molecules_.erase(mol->getGlobalIndex());
227	<
228	<	delete mol;
216	>	nAtoms_ -= mol->getNAtoms();
217	>	nBonds_ -= mol->getNBonds();
218	>	nBends_ -= mol->getNBends();
219	>	nTorsions_ -= mol->getNTorsions();
220	>	nRigidBodies_ -= mol->getNRigidBodies();
221	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
222	>	nCutoffGroups_ -= mol->getNCutoffGroups();
223	>	nConstraints_ -= mol->getNConstraintPairs();
224	>
225	>	removeExcludePairs(mol);
226	>	molecules_.erase(mol->getGlobalIndex());
227	>
228	>	delete mol;
229
230	<	return true;
230	>	return true;
231		} else {
232	<	return false;
232	>	return false;
233		}
234
235
236	<	}
236	>	}
237
238
239	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
239	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
240		i = molecules_.begin();
241		return i == molecules_.end() ? NULL : i->second;
242	<	}
242	>	}
243
244	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
244	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
245		++i;
246		return i == molecules_.end() ? NULL : i->second;
247	<	}
247	>	}
248
249
250	<	void SimInfo::calcNdf() {
250	>	void SimInfo::calcNdf() {
251		int ndf_local;
252		MoleculeIterator i;
253		std::vector<StuntDouble*>::iterator j;
#	Line 242 | Line 257 | void SimInfo::calcNdf() {
257		ndf_local = 0;
258
259		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
260	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
261	<	integrableObject = mol->nextIntegrableObject(j)) {
260	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
261	>	integrableObject = mol->nextIntegrableObject(j)) {
262
263	<	ndf_local += 3;
263	>	ndf_local += 3;
264
265	<	if (integrableObject->isDirectional()) {
266	<	if (integrableObject->isLinear()) {
267	<	ndf_local += 2;
268	<	} else {
269	<	ndf_local += 3;
270	<	}
271	<	}
265	>	if (integrableObject->isDirectional()) {
266	>	if (integrableObject->isLinear()) {
267	>	ndf_local += 2;
268	>	} else {
269	>	ndf_local += 3;
270	>	}
271	>	}
272
273	<	}//end for (integrableObject)
274	<	}// end for (mol)
273	>	}
274	>	}
275
276		// n_constraints is local, so subtract them on each processor
277		ndf_local -= nConstraints_;
#	Line 271 | Line 286 | void SimInfo::calcNdf() {
286		// entire system:
287		ndf_ = ndf_ - 3 - nZconstraint_;
288
289	<	}
289	>	}
290
291	<	void SimInfo::calcNdfRaw() {
291	>	void SimInfo::calcNdfRaw() {
292		int ndfRaw_local;
293
294		MoleculeIterator i;
#	Line 285 | Line 300 | void SimInfo::calcNdfRaw() {
300		ndfRaw_local = 0;
301
302		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
303	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
304	<	integrableObject = mol->nextIntegrableObject(j)) {
303	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
304	>	integrableObject = mol->nextIntegrableObject(j)) {
305
306	<	ndfRaw_local += 3;
306	>	ndfRaw_local += 3;
307
308	<	if (integrableObject->isDirectional()) {
309	<	if (integrableObject->isLinear()) {
310	<	ndfRaw_local += 2;
311	<	} else {
312	<	ndfRaw_local += 3;
313	<	}
314	<	}
308	>	if (integrableObject->isDirectional()) {
309	>	if (integrableObject->isLinear()) {
310	>	ndfRaw_local += 2;
311	>	} else {
312	>	ndfRaw_local += 3;
313	>	}
314	>	}
315
316	<	}
316	>	}
317		}
318
319		#ifdef IS_MPI
#	Line 306 | Line 321 | void SimInfo::calcNdfRaw() {
321		#else
322		ndfRaw_ = ndfRaw_local;
323		#endif
324	<	}
324	>	}
325
326	<	void SimInfo::calcNdfTrans() {
326	>	void SimInfo::calcNdfTrans() {
327		int ndfTrans_local;
328
329		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 322 | Line 337 | void SimInfo::calcNdfTrans() {
337
338		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
339
340	<	}
340	>	}
341
342	<	void SimInfo::addExcludePairs(Molecule* mol) {
342	>	void SimInfo::addExcludePairs(Molecule* mol) {
343		std::vector<Bond*>::iterator bondIter;
344		std::vector<Bend*>::iterator bendIter;
345		std::vector<Torsion*>::iterator torsionIter;
#	Line 335 | Line 350 | void SimInfo::addExcludePairs(Molecule* mol) {
350		int b;
351		int c;
352		int d;
353	+
354	+	std::map<int, std::set<int> > atomGroups;
355	+
356	+	Molecule::RigidBodyIterator rbIter;
357	+	RigidBody* rb;
358	+	Molecule::IntegrableObjectIterator ii;
359	+	StuntDouble* integrableObject;
360
361	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
362	+	integrableObject = mol->nextIntegrableObject(ii)) {
363	+
364	+	if (integrableObject->isRigidBody()) {
365	+	rb = static_cast<RigidBody*>(integrableObject);
366	+	std::vector<Atom*> atoms = rb->getAtoms();
367	+	std::set<int> rigidAtoms;
368	+	for (int i = 0; i < atoms.size(); ++i) {
369	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
370	+	}
371	+	for (int i = 0; i < atoms.size(); ++i) {
372	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
373	+	}
374	+	} else {
375	+	std::set<int> oneAtomSet;
376	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
377	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
378	+	}
379	+	}
380	+
381	+
382	+
383		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
384	<	a = bond->getAtomA()->getGlobalIndex();
385	<	b = bond->getAtomB()->getGlobalIndex();
386	<	exclude_.addPair(a, b);
384	>	a = bond->getAtomA()->getGlobalIndex();
385	>	b = bond->getAtomB()->getGlobalIndex();
386	>	exclude_.addPair(a, b);
387		}
388
389		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
390	<	a = bend->getAtomA()->getGlobalIndex();
391	<	b = bend->getAtomB()->getGlobalIndex();
392	<	c = bend->getAtomC()->getGlobalIndex();
390	>	a = bend->getAtomA()->getGlobalIndex();
391	>	b = bend->getAtomB()->getGlobalIndex();
392	>	c = bend->getAtomC()->getGlobalIndex();
393	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
394	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
395	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
396
397	<	exclude_.addPair(a, b);
398	<	exclude_.addPair(a, c);
399	<	exclude_.addPair(b, c);
397	>	exclude_.addPairs(rigidSetA, rigidSetB);
398	>	exclude_.addPairs(rigidSetA, rigidSetC);
399	>	exclude_.addPairs(rigidSetB, rigidSetC);
400	>
401	>	//exclude_.addPair(a, b);
402	>	//exclude_.addPair(a, c);
403	>	//exclude_.addPair(b, c);
404		}
405
406		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
407	<	a = torsion->getAtomA()->getGlobalIndex();
408	<	b = torsion->getAtomB()->getGlobalIndex();
409	<	c = torsion->getAtomC()->getGlobalIndex();
410	<	d = torsion->getAtomD()->getGlobalIndex();
407	>	a = torsion->getAtomA()->getGlobalIndex();
408	>	b = torsion->getAtomB()->getGlobalIndex();
409	>	c = torsion->getAtomC()->getGlobalIndex();
410	>	d = torsion->getAtomD()->getGlobalIndex();
411	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
412	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
413	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
414	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
415
416	<	exclude_.addPair(a, b);
417	<	exclude_.addPair(a, c);
418	<	exclude_.addPair(a, d);
419	<	exclude_.addPair(b, c);
420	<	exclude_.addPair(b, d);
421	<	exclude_.addPair(c, d);
416	>	exclude_.addPairs(rigidSetA, rigidSetB);
417	>	exclude_.addPairs(rigidSetA, rigidSetC);
418	>	exclude_.addPairs(rigidSetA, rigidSetD);
419	>	exclude_.addPairs(rigidSetB, rigidSetC);
420	>	exclude_.addPairs(rigidSetB, rigidSetD);
421	>	exclude_.addPairs(rigidSetC, rigidSetD);
422	>
423	>	/*
424	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
425	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
426	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
427	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
428	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
429	>	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
430	>
431	>
432	>	exclude_.addPair(a, b);
433	>	exclude_.addPair(a, c);
434	>	exclude_.addPair(a, d);
435	>	exclude_.addPair(b, c);
436	>	exclude_.addPair(b, d);
437	>	exclude_.addPair(c, d);
438	>	*/
439		}
440
441	<
442	<	}
441	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
442	>	std::vector<Atom*> atoms = rb->getAtoms();
443	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
444	>	for (int j = i + 1; j < atoms.size(); ++j) {
445	>	a = atoms[i]->getGlobalIndex();
446	>	b = atoms[j]->getGlobalIndex();
447	>	exclude_.addPair(a, b);
448	>	}
449	>	}
450	>	}
451
452	<	void SimInfo::removeExcludePairs(Molecule* mol) {
452	>	}
453	>
454	>	void SimInfo::removeExcludePairs(Molecule* mol) {
455		std::vector<Bond*>::iterator bondIter;
456		std::vector<Bend*>::iterator bendIter;
457		std::vector<Torsion*>::iterator torsionIter;
#	Line 380 | Line 462 | void SimInfo::removeExcludePairs(Molecule* mol) {
462		int b;
463		int c;
464		int d;
465	+
466	+	std::map<int, std::set<int> > atomGroups;
467	+
468	+	Molecule::RigidBodyIterator rbIter;
469	+	RigidBody* rb;
470	+	Molecule::IntegrableObjectIterator ii;
471	+	StuntDouble* integrableObject;
472
473	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
474	+	integrableObject = mol->nextIntegrableObject(ii)) {
475	+
476	+	if (integrableObject->isRigidBody()) {
477	+	rb = static_cast<RigidBody*>(integrableObject);
478	+	std::vector<Atom*> atoms = rb->getAtoms();
479	+	std::set<int> rigidAtoms;
480	+	for (int i = 0; i < atoms.size(); ++i) {
481	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
482	+	}
483	+	for (int i = 0; i < atoms.size(); ++i) {
484	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
485	+	}
486	+	} else {
487	+	std::set<int> oneAtomSet;
488	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
489	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
490	+	}
491	+	}
492	+
493	+
494		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
495	<	a = bond->getAtomA()->getGlobalIndex();
496	<	b = bond->getAtomB()->getGlobalIndex();
497	<	exclude_.removePair(a, b);
495	>	a = bond->getAtomA()->getGlobalIndex();
496	>	b = bond->getAtomB()->getGlobalIndex();
497	>	exclude_.removePair(a, b);
498		}
499
500		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
501	<	a = bend->getAtomA()->getGlobalIndex();
502	<	b = bend->getAtomB()->getGlobalIndex();
503	<	c = bend->getAtomC()->getGlobalIndex();
501	>	a = bend->getAtomA()->getGlobalIndex();
502	>	b = bend->getAtomB()->getGlobalIndex();
503	>	c = bend->getAtomC()->getGlobalIndex();
504
505	<	exclude_.removePair(a, b);
506	<	exclude_.removePair(a, c);
507	<	exclude_.removePair(b, c);
505	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
506	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
507	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
508	>
509	>	exclude_.removePairs(rigidSetA, rigidSetB);
510	>	exclude_.removePairs(rigidSetA, rigidSetC);
511	>	exclude_.removePairs(rigidSetB, rigidSetC);
512	>
513	>	//exclude_.removePair(a, b);
514	>	//exclude_.removePair(a, c);
515	>	//exclude_.removePair(b, c);
516		}
517
518		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
519	<	a = torsion->getAtomA()->getGlobalIndex();
520	<	b = torsion->getAtomB()->getGlobalIndex();
521	<	c = torsion->getAtomC()->getGlobalIndex();
522	<	d = torsion->getAtomD()->getGlobalIndex();
519	>	a = torsion->getAtomA()->getGlobalIndex();
520	>	b = torsion->getAtomB()->getGlobalIndex();
521	>	c = torsion->getAtomC()->getGlobalIndex();
522	>	d = torsion->getAtomD()->getGlobalIndex();
523
524	<	exclude_.removePair(a, b);
525	<	exclude_.removePair(a, c);
526	<	exclude_.removePair(a, d);
527	<	exclude_.removePair(b, c);
528	<	exclude_.removePair(b, d);
529	<	exclude_.removePair(c, d);
524	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
525	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
526	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
527	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
528	>
529	>	exclude_.removePairs(rigidSetA, rigidSetB);
530	>	exclude_.removePairs(rigidSetA, rigidSetC);
531	>	exclude_.removePairs(rigidSetA, rigidSetD);
532	>	exclude_.removePairs(rigidSetB, rigidSetC);
533	>	exclude_.removePairs(rigidSetB, rigidSetD);
534	>	exclude_.removePairs(rigidSetC, rigidSetD);
535	>
536	>	/*
537	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
538	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
539	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
540	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
541	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
542	>	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
543	>
544	>
545	>	exclude_.removePair(a, b);
546	>	exclude_.removePair(a, c);
547	>	exclude_.removePair(a, d);
548	>	exclude_.removePair(b, c);
549	>	exclude_.removePair(b, d);
550	>	exclude_.removePair(c, d);
551	>	*/
552		}
553
554	<	}
554	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
555	>	std::vector<Atom*> atoms = rb->getAtoms();
556	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
557	>	for (int j = i + 1; j < atoms.size(); ++j) {
558	>	a = atoms[i]->getGlobalIndex();
559	>	b = atoms[j]->getGlobalIndex();
560	>	exclude_.removePair(a, b);
561	>	}
562	>	}
563	>	}
564
565	+	}
566
567	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
567	>
568	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
569		int curStampId;
570
571		//index from 0
#	Line 422 | Line 573 | void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp
573
574		moleculeStamps_.push_back(molStamp);
575		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
576	<	}
576	>	}
577
578	<	void SimInfo::update() {
578	>	void SimInfo::update() {
579
580		setupSimType();
581
#	Line 437 | Line 588 | void SimInfo::update() {
588		//setup fortran force field
589		/** @deprecate */
590		int isError = 0;
591	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
591	>
592	>	setupElectrostaticSummationMethod( isError );
593	>	setupSwitchingFunction();
594	>
595		if(isError){
596	<	sprintf( painCave.errMsg,
597	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
598	<	painCave.isFatal = 1;
599	<	simError();
596	>	sprintf( painCave.errMsg,
597	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
598	>	painCave.isFatal = 1;
599	>	simError();
600		}
601
602
#	Line 453 | Line 607 | void SimInfo::update() {
607		calcNdfTrans();
608
609		fortranInitialized_ = true;
610	<	}
610	>	}
611
612	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
612	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
613		SimInfo::MoleculeIterator mi;
614		Molecule* mol;
615		Molecule::AtomIterator ai;
#	Line 464 | Line 618 | std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
618
619		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
620
621	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
622	<	atomTypes.insert(atom->getAtomType());
623	<	}
621	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
622	>	atomTypes.insert(atom->getAtomType());
623	>	}
624
625		}
626
627		return atomTypes;
628	<	}
628	>	}
629
630	<	void SimInfo::setupSimType() {
630	>	void SimInfo::setupSimType() {
631		std::set<AtomType*>::iterator i;
632		std::set<AtomType*> atomTypes;
633		atomTypes = getUniqueAtomTypes();
#	Line 481 | Line 635 | void SimInfo::setupSimType() {
635		int useLennardJones = 0;
636		int useElectrostatic = 0;
637		int useEAM = 0;
638	+	int useSC = 0;
639		int useCharge = 0;
640		int useDirectional = 0;
641		int useDipole = 0;
642		int useGayBerne = 0;
643		int useSticky = 0;
644	+	int useStickyPower = 0;
645		int useShape = 0;
646		int useFLARB = 0; //it is not in AtomType yet
647		int useDirectionalAtom = 0;
648		int useElectrostatics = 0;
649		//usePBC and useRF are from simParams
650	<	int usePBC = simParams_->getPBC();
651	<	int useRF = simParams_->getUseRF();
650	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
651	>	int useRF;
652	>	int useSF;
653	>	std::string myMethod;
654
655	+	// set the useRF logical
656	+	useRF = 0;
657	+	useSF = 0;
658	+
659	+
660	+	if (simParams_->haveElectrostaticSummationMethod()) {
661	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
662	+	toUpper(myMethod);
663	+	if (myMethod == "REACTION_FIELD") {
664	+	useRF=1;
665	+	} else {
666	+	if (myMethod == "SHIFTED_FORCE") {
667	+	useSF = 1;
668	+	}
669	+	}
670	+	}
671	+
672		//loop over all of the atom types
673		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
674	<	useLennardJones |= (*i)->isLennardJones();
675	<	useElectrostatic |= (*i)->isElectrostatic();
676	<	useEAM |= (*i)->isEAM();
677	<	useCharge |= (*i)->isCharge();
678	<	useDirectional |= (*i)->isDirectional();
679	<	useDipole |= (*i)->isDipole();
680	<	useGayBerne |= (*i)->isGayBerne();
681	<	useSticky |= (*i)->isSticky();
682	<	useShape |= (*i)->isShape();
674	>	useLennardJones |= (*i)->isLennardJones();
675	>	useElectrostatic |= (*i)->isElectrostatic();
676	>	useEAM |= (*i)->isEAM();
677	>	useSC |= (*i)->isSC();
678	>	useCharge |= (*i)->isCharge();
679	>	useDirectional |= (*i)->isDirectional();
680	>	useDipole |= (*i)->isDipole();
681	>	useGayBerne |= (*i)->isGayBerne();
682	>	useSticky |= (*i)->isSticky();
683	>	useStickyPower |= (*i)->isStickyPower();
684	>	useShape |= (*i)->isShape();
685		}
686
687	<	if (useSticky || useDipole || useGayBerne || useShape) {
688	<	useDirectionalAtom = 1;
687	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
688	>	useDirectionalAtom = 1;
689		}
690
691		if (useCharge || useDipole) {
692	<	useElectrostatics = 1;
692	>	useElectrostatics = 1;
693		}
694
695		#ifdef IS_MPI
#	Line 539 | Line 716 | void SimInfo::setupSimType() {
716		temp = useSticky;
717		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
718
719	+	temp = useStickyPower;
720	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
721	+
722		temp = useGayBerne;
723		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
724
725		temp = useEAM;
726		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
727
728	+	temp = useSC;
729	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
730	+
731		temp = useShape;
732		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
733
#	Line 553 | Line 736 | void SimInfo::setupSimType() {
736
737		temp = useRF;
738		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
739	<
739	>
740	>	temp = useSF;
741	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
742	>
743		#endif
744
745		fInfo_.SIM_uses_PBC = usePBC;
#	Line 563 | Line 749 | void SimInfo::setupSimType() {
749		fInfo_.SIM_uses_Charges = useCharge;
750		fInfo_.SIM_uses_Dipoles = useDipole;
751		fInfo_.SIM_uses_Sticky = useSticky;
752	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
753		fInfo_.SIM_uses_GayBerne = useGayBerne;
754		fInfo_.SIM_uses_EAM = useEAM;
755	+	fInfo_.SIM_uses_SC = useSC;
756		fInfo_.SIM_uses_Shapes = useShape;
757		fInfo_.SIM_uses_FLARB = useFLARB;
758		fInfo_.SIM_uses_RF = useRF;
759	+	fInfo_.SIM_uses_SF = useSF;
760
761	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
762	<
763	<	if (simParams_->haveDielectric()) {
764	<	fInfo_.dielect = simParams_->getDielectric();
765	<	} else {
766	<	sprintf(painCave.errMsg,
767	<	"SimSetup Error: No Dielectric constant was set.\n"
768	<	"\tYou are trying to use Reaction Field without"
769	<	"\tsetting a dielectric constant!\n");
770	<	painCave.isFatal = 1;
771	<	simError();
772	<	}
584	<
585	<	} else {
586	<	fInfo_.dielect = 0.0;
761	>	if( myMethod == "REACTION_FIELD") {
762	>
763	>	if (simParams_->haveDielectric()) {
764	>	fInfo_.dielect = simParams_->getDielectric();
765	>	} else {
766	>	sprintf(painCave.errMsg,
767	>	"SimSetup Error: No Dielectric constant was set.\n"
768	>	"\tYou are trying to use Reaction Field without"
769	>	"\tsetting a dielectric constant!\n");
770	>	painCave.isFatal = 1;
771	>	simError();
772	>	}
773		}
774
775	<	}
775	>	}
776
777	<	void SimInfo::setupFortranSim() {
777	>	void SimInfo::setupFortranSim() {
778		int isError;
779		int nExclude;
780		std::vector<int> fortranGlobalGroupMembership;
#	Line 598 | Line 784 | void SimInfo::setupFortranSim() {
784
785		//globalGroupMembership_ is filled by SimCreator
786		for (int i = 0; i < nGlobalAtoms_; i++) {
787	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
787	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
788		}
789
790		//calculate mass ratio of cutoff group
#	Line 615 | Line 801 | void SimInfo::setupFortranSim() {
801		mfact.reserve(getNCutoffGroups());
802
803		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
804	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
804	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
805
806	<	totalMass = cg->getMass();
807	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
808	<	mfact.push_back(atom->getMass()/totalMass);
809	<	}
806	>	totalMass = cg->getMass();
807	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
808	>	// Check for massless groups - set mfact to 1 if true
809	>	if (totalMass != 0)
810	>	mfact.push_back(atom->getMass()/totalMass);
811	>	else
812	>	mfact.push_back( 1.0 );
813	>	}
814
815	<	}
815	>	}
816		}
817
818		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
#	Line 632 | Line 822 | void SimInfo::setupFortranSim() {
822		identArray.reserve(getNAtoms());
823
824		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
825	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
826	<	identArray.push_back(atom->getIdent());
827	<	}
825	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
826	>	identArray.push_back(atom->getIdent());
827	>	}
828		}
829
830		//fill molMembershipArray
831		//molMembershipArray is filled by SimCreator
832		std::vector<int> molMembershipArray(nGlobalAtoms_);
833		for (int i = 0; i < nGlobalAtoms_; i++) {
834	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
834	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
835		}
836
837		//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
838		int nGlobalExcludes = 0;
839		int* globalExcludes = NULL;
840		int* excludeList = exclude_.getExcludeList();
841		setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
842	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
843	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
842	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
843	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
844
845		if( isError ){
846
847	<	sprintf( painCave.errMsg,
848	<	"There was an error setting the simulation information in fortran.\n" );
849	<	painCave.isFatal = 1;
850	<	painCave.severity = OOPSE_ERROR;
851	<	simError();
847	>	sprintf( painCave.errMsg,
848	>	"There was an error setting the simulation information in fortran.\n" );
849	>	painCave.isFatal = 1;
850	>	painCave.severity = OOPSE_ERROR;
851	>	simError();
852		}
853
854		#ifdef IS_MPI
855		sprintf( checkPointMsg,
856	<	"succesfully sent the simulation information to fortran.\n");
856	>	"succesfully sent the simulation information to fortran.\n");
857		MPIcheckPoint();
858		#endif // is_mpi
859	<	}
859	>	}
860
861
862		#ifdef IS_MPI
863	<	void SimInfo::setupFortranParallel() {
863	>	void SimInfo::setupFortranParallel() {
864
865		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
866		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
#	Line 689 | Line 876 | void SimInfo::setupFortranParallel() {
876
877		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
878
879	<	//local index(index in DataStorge) of atom is important
880	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
881	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
882	<	}
879	>	//local index(index in DataStorge) of atom is important
880	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
881	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
882	>	}
883
884	<	//local index of cutoff group is trivial, it only depends on the order of travesing
885	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
886	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
887	<	}
884	>	//local index of cutoff group is trivial, it only depends on the order of travesing
885	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
886	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
887	>	}
888
889		}
890
#	Line 717 | Line 904 | void SimInfo::setupFortranParallel() {
904		&localToGlobalCutoffGroupIndex[0], &isError);
905
906		if (isError) {
907	<	sprintf(painCave.errMsg,
908	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
909	<	painCave.isFatal = 1;
910	<	simError();
907	>	sprintf(painCave.errMsg,
908	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
909	>	painCave.isFatal = 1;
910	>	simError();
911		}
912
913		sprintf(checkPointMsg, " mpiRefresh successful.\n");
914		MPIcheckPoint();
915
916
917	<	}
917	>	}
918
919		#endif
920
921	<	double SimInfo::calcMaxCutoffRadius() {
735	<
736	<
737	<	std::set<AtomType*> atomTypes;
738	<	std::set<AtomType*>::iterator i;
739	<	std::vector<double> cutoffRadius;
740	<
741	<	//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));
747	<	}
748	<
749	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
750	<	#ifdef IS_MPI
751	<	//pick the max cutoff radius among the processors
752	<	#endif
753	<
754	<	return maxCutoffRadius;
755	<	}
756	<
757	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
921	>	void SimInfo::setupCutoff() {
922
923	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
923	>	// Check the cutoff policy
924	>	int cp =  TRADITIONAL_CUTOFF_POLICY;
925	>	if (simParams_->haveCutoffPolicy()) {
926	>	std::string myPolicy = simParams_->getCutoffPolicy();
927	>	toUpper(myPolicy);
928	>	if (myPolicy == "MIX") {
929	>	cp = MIX_CUTOFF_POLICY;
930	>	} else {
931	>	if (myPolicy == "MAX") {
932	>	cp = MAX_CUTOFF_POLICY;
933	>	} else {
934	>	if (myPolicy == "TRADITIONAL") {
935	>	cp = TRADITIONAL_CUTOFF_POLICY;
936	>	} else {
937	>	// throw error
938	>	sprintf( painCave.errMsg,
939	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
940	>	painCave.isFatal = 1;
941	>	simError();
942	>	}
943	>	}
944	>	}
945	>	}
946	>	notifyFortranCutoffPolicy(&cp);
947	>
948	>	// Check the Skin Thickness for neighborlists
949	>	double skin;
950	>	if (simParams_->haveSkinThickness()) {
951	>	skin = simParams_->getSkinThickness();
952	>	notifyFortranSkinThickness(&skin);
953	>	}
954
955	<	if (!simParams_->haveRcut()){
956	<	sprintf(painCave.errMsg,
955	>	// Check if the cutoff was set explicitly:
956	>	if (simParams_->haveCutoffRadius()) {
957	>	rcut_ = simParams_->getCutoffRadius();
958	>	if (simParams_->haveSwitchingRadius()) {
959	>	rsw_  = simParams_->getSwitchingRadius();
960	>	} else {
961	>	rsw_ = rcut_;
962	>	}
963	>	notifyFortranCutoffs(&rcut_, &rsw_);
964	>
965	>	} else {
966	>
967	>	// For electrostatic atoms, we'll assume a large safe value:
968	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
969	>	sprintf(painCave.errMsg,
970		"SimCreator Warning: No value was set for the cutoffRadius.\n"
971		"\tOOPSE will use a default value of 15.0 angstroms"
972		"\tfor the cutoffRadius.\n");
973	<	painCave.isFatal = 0;
974	<	simError();
975	<	rcut = 15.0;
976	<	} else{
977	<	rcut = simParams_->getRcut();
973	>	painCave.isFatal = 0;
974	>	simError();
975	>	rcut_ = 15.0;
976	>
977	>	if (simParams_->haveElectrostaticSummationMethod()) {
978	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
979	>	toUpper(myMethod);
980	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
981	>	if (simParams_->haveSwitchingRadius()){
982	>	sprintf(painCave.errMsg,
983	>	"SimInfo Warning: A value was set for the switchingRadius\n"
984	>	"\teven though the electrostaticSummationMethod was\n"
985	>	"\tset to %s\n", myMethod.c_str());
986	>	painCave.isFatal = 1;
987	>	simError();
988	>	}
989	>	}
990		}
991	<
992	<	if (!simParams_->haveRsw()){
993	<	sprintf(painCave.errMsg,
994	<	"SimCreator Warning: No value was set for switchingRadius.\n"
995	<	"\tOOPSE will use a default value of\n"
996	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
997	<	painCave.isFatal = 0;
998	<	simError();
999	<	rsw = 0.95 * rcut;
1000	<	} else{
1001	<	rsw = simParams_->getRsw();
991	>
992	>	if (simParams_->haveSwitchingRadius()){
993	>	rsw_ = simParams_->getSwitchingRadius();
994	>	} else {
995	>	sprintf(painCave.errMsg,
996	>	"SimCreator Warning: No value was set for switchingRadius.\n"
997	>	"\tOOPSE will use a default value of\n"
998	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
999	>	painCave.isFatal = 0;
1000	>	simError();
1001	>	rsw_ = 0.85 * rcut_;
1002		}
1003	<
1004	<	} else {
1005	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
1006	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
1003	>	notifyFortranCutoffs(&rcut_, &rsw_);
1004	>	} else {
1005	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1006	>	// We'll punt and let fortran figure out the cutoffs later.
1007
1008	<	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	<	}
1008	>	notifyFortranYouAreOnYourOwn();
1009
1010	<	if (simParams_->haveRsw()) {
797	<	rsw  = simParams_->getRsw();
798	<	} else {
799	<	rsw = rcut;
800	<	}
801	<
1010	>	}
1011		}
1012	<	}
1012	>	}
1013
1014	<	void SimInfo::setupCutoff() {
1015	<	getCutoff(rcut_, rsw_);
1016	<	double rnblist = rcut_ + 1; // skin of neighbor list
1014	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1015	>
1016	>	int errorOut;
1017	>	int esm =  NONE;
1018	>	int sm = UNDAMPED;
1019	>	double alphaVal;
1020	>	double dielectric;
1021
1022	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1023	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
1024	<	}
1022	>	errorOut = isError;
1023	>	alphaVal = simParams_->getDampingAlpha();
1024	>	dielectric = simParams_->getDielectric();
1025
1026	<	void SimInfo::addProperty(GenericData* genData) {
1027	<	properties_.addProperty(genData);
1028	<	}
1029	<
1030	<	void SimInfo::removeProperty(const std::string& propName) {
1031	<	properties_.removeProperty(propName);
1032	<	}
1033	<
1034	<	void SimInfo::clearProperties() {
1035	<	properties_.clearProperties();
1036	<	}
1037	<
1038	<	std::vector<std::string> SimInfo::getPropertyNames() {
1039	<	return properties_.getPropertyNames();
1040	<	}
1041	<
1042	<	std::vector<GenericData*> SimInfo::getProperties() {
1043	<	return properties_.getProperties();
1044	<	}
1045	<
1046	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1047	<	return properties_.getPropertyByName(propName);
1048	<	}
1049	<
1050	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1051	<	if (sman_ == sman_) {
1052	<	return;
1026	>	if (simParams_->haveElectrostaticSummationMethod()) {
1027	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1028	>	toUpper(myMethod);
1029	>	if (myMethod == "NONE") {
1030	>	esm = NONE;
1031	>	} else {
1032	>	if (myMethod == "SWITCHING_FUNCTION") {
1033	>	esm = SWITCHING_FUNCTION;
1034	>	} else {
1035	>	if (myMethod == "SHIFTED_POTENTIAL") {
1036	>	esm = SHIFTED_POTENTIAL;
1037	>	} else {
1038	>	if (myMethod == "SHIFTED_FORCE") {
1039	>	esm = SHIFTED_FORCE;
1040	>	} else {
1041	>	if (myMethod == "REACTION_FIELD") {
1042	>	esm = REACTION_FIELD;
1043	>	} else {
1044	>	// throw error
1045	>	sprintf( painCave.errMsg,
1046	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1047	>	"\t(Input file specified %s .)\n"
1048	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1049	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1050	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1051	>	painCave.isFatal = 1;
1052	>	simError();
1053	>	}
1054	>	}
1055	>	}
1056	>	}
1057	>	}
1058		}
1059
1060	+	if (simParams_->haveElectrostaticScreeningMethod()) {
1061	+	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1062	+	toUpper(myScreen);
1063	+	if (myScreen == "UNDAMPED") {
1064	+	sm = UNDAMPED;
1065	+	} else {
1066	+	if (myScreen == "DAMPED") {
1067	+	sm = DAMPED;
1068	+	if (!simParams_->haveDampingAlpha()) {
1069	+	//throw error
1070	+	sprintf( painCave.errMsg,
1071	+	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1072	+	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1073	+	painCave.isFatal = 0;
1074	+	simError();
1075	+	}
1076	+	} else {
1077	+	// throw error
1078	+	sprintf( painCave.errMsg,
1079	+	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1080	+	"\t(Input file specified %s .)\n"
1081	+	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1082	+	"or \"damped\".\n", myScreen.c_str() );
1083	+	painCave.isFatal = 1;
1084	+	simError();
1085	+	}
1086	+	}
1087	+	}
1088	+
1089	+	// let's pass some summation method variables to fortran
1090	+	setElectrostaticSummationMethod( &esm );
1091	+	notifyFortranElectrostaticMethod( &esm );
1092	+	setScreeningMethod( &sm );
1093	+	setDampingAlpha( &alphaVal );
1094	+	setReactionFieldDielectric( &dielectric );
1095	+	initFortranFF( &errorOut );
1096	+	}
1097	+
1098	+	void SimInfo::setupSwitchingFunction() {
1099	+	int ft = CUBIC;
1100	+
1101	+	if (simParams_->haveSwitchingFunctionType()) {
1102	+	std::string funcType = simParams_->getSwitchingFunctionType();
1103	+	toUpper(funcType);
1104	+	if (funcType == "CUBIC") {
1105	+	ft = CUBIC;
1106	+	} else {
1107	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1108	+	ft = FIFTH_ORDER_POLY;
1109	+	} else {
1110	+	// throw error
1111	+	sprintf( painCave.errMsg,
1112	+	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1113	+	painCave.isFatal = 1;
1114	+	simError();
1115	+	}
1116	+	}
1117	+	}
1118	+
1119	+	// send switching function notification to switcheroo
1120	+	setFunctionType(&ft);
1121	+
1122	+	}
1123	+
1124	+	void SimInfo::addProperty(GenericData* genData) {
1125	+	properties_.addProperty(genData);
1126	+	}
1127	+
1128	+	void SimInfo::removeProperty(const std::string& propName) {
1129	+	properties_.removeProperty(propName);
1130	+	}
1131	+
1132	+	void SimInfo::clearProperties() {
1133	+	properties_.clearProperties();
1134	+	}
1135	+
1136	+	std::vector<std::string> SimInfo::getPropertyNames() {
1137	+	return properties_.getPropertyNames();
1138	+	}
1139	+
1140	+	std::vector<GenericData*> SimInfo::getProperties() {
1141	+	return properties_.getProperties();
1142	+	}
1143	+
1144	+	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1145	+	return properties_.getPropertyByName(propName);
1146	+	}
1147	+
1148	+	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1149	+	if (sman_ == sman) {
1150	+	return;
1151	+	}
1152		delete sman_;
1153		sman_ = sman;
1154
#	Line 851 | Line 1161 | void SimInfo::setSnapshotManager(SnapshotManager* sman
1161
1162		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1163
1164	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1165	<	atom->setSnapshotManager(sman_);
1166	<	}
1164	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1165	>	atom->setSnapshotManager(sman_);
1166	>	}
1167
1168	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1169	<	rb->setSnapshotManager(sman_);
1170	<	}
1168	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1169	>	rb->setSnapshotManager(sman_);
1170	>	}
1171		}
1172
1173	<	}
1173	>	}
1174
1175	<	Vector3d SimInfo::getComVel(){
1175	>	Vector3d SimInfo::getComVel(){
1176		SimInfo::MoleculeIterator i;
1177		Molecule* mol;
1178
#	Line 871 | Line 1181 | Vector3d SimInfo::getComVel(){
1181
1182
1183		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1184	<	double mass = mol->getMass();
1185	<	totalMass += mass;
1186	<	comVel += mass * mol->getComVel();
1184	>	double mass = mol->getMass();
1185	>	totalMass += mass;
1186	>	comVel += mass * mol->getComVel();
1187		}
1188
1189		#ifdef IS_MPI
#	Line 886 | Line 1196 | Vector3d SimInfo::getComVel(){
1196		comVel /= totalMass;
1197
1198		return comVel;
1199	<	}
1199	>	}
1200
1201	<	Vector3d SimInfo::getCom(){
1201	>	Vector3d SimInfo::getCom(){
1202		SimInfo::MoleculeIterator i;
1203		Molecule* mol;
1204
#	Line 896 | Line 1206 | Vector3d SimInfo::getCom(){
1206		double totalMass = 0.0;
1207
1208		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1209	<	double mass = mol->getMass();
1210	<	totalMass += mass;
1211	<	com += mass * mol->getCom();
1209	>	double mass = mol->getMass();
1210	>	totalMass += mass;
1211	>	com += mass * mol->getCom();
1212		}
1213
1214		#ifdef IS_MPI
#	Line 912 | Line 1222 | Vector3d SimInfo::getCom(){
1222
1223		return com;
1224
1225	<	}
1225	>	}
1226
1227	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1227	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1228
1229		return o;
1230	<	}
1230	>	}
1231	>
1232	>
1233	>	/*
1234	>	Returns center of mass and center of mass velocity in one function call.
1235	>	*/
1236	>
1237	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1238	>	SimInfo::MoleculeIterator i;
1239	>	Molecule* mol;
1240	>
1241	>
1242	>	double totalMass = 0.0;
1243	>
1244
1245	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1246	+	double mass = mol->getMass();
1247	+	totalMass += mass;
1248	+	com += mass * mol->getCom();
1249	+	comVel += mass * mol->getComVel();
1250	+	}
1251	+
1252	+	#ifdef IS_MPI
1253	+	double tmpMass = totalMass;
1254	+	Vector3d tmpCom(com);
1255	+	Vector3d tmpComVel(comVel);
1256	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1257	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1258	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1259	+	#endif
1260	+
1261	+	com /= totalMass;
1262	+	comVel /= totalMass;
1263	+	}
1264	+
1265	+	/*
1266	+	Return intertia tensor for entire system and angular momentum Vector.
1267	+
1268	+
1269	+	[  Ixx -Ixy  -Ixz ]
1270	+	J =| -Iyx  Iyy  -Iyz |
1271	+	[ -Izx -Iyz   Izz ]
1272	+	*/
1273	+
1274	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1275	+
1276	+
1277	+	double xx = 0.0;
1278	+	double yy = 0.0;
1279	+	double zz = 0.0;
1280	+	double xy = 0.0;
1281	+	double xz = 0.0;
1282	+	double yz = 0.0;
1283	+	Vector3d com(0.0);
1284	+	Vector3d comVel(0.0);
1285	+
1286	+	getComAll(com, comVel);
1287	+
1288	+	SimInfo::MoleculeIterator i;
1289	+	Molecule* mol;
1290	+
1291	+	Vector3d thisq(0.0);
1292	+	Vector3d thisv(0.0);
1293	+
1294	+	double thisMass = 0.0;
1295	+
1296	+
1297	+
1298	+
1299	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1300	+
1301	+	thisq = mol->getCom()-com;
1302	+	thisv = mol->getComVel()-comVel;
1303	+	thisMass = mol->getMass();
1304	+	// Compute moment of intertia coefficients.
1305	+	xx += thisq[0]*thisq[0]*thisMass;
1306	+	yy += thisq[1]*thisq[1]*thisMass;
1307	+	zz += thisq[2]*thisq[2]*thisMass;
1308	+
1309	+	// compute products of intertia
1310	+	xy += thisq[0]*thisq[1]*thisMass;
1311	+	xz += thisq[0]*thisq[2]*thisMass;
1312	+	yz += thisq[1]*thisq[2]*thisMass;
1313	+
1314	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1315	+
1316	+	}
1317	+
1318	+
1319	+	inertiaTensor(0,0) = yy + zz;
1320	+	inertiaTensor(0,1) = -xy;
1321	+	inertiaTensor(0,2) = -xz;
1322	+	inertiaTensor(1,0) = -xy;
1323	+	inertiaTensor(1,1) = xx + zz;
1324	+	inertiaTensor(1,2) = -yz;
1325	+	inertiaTensor(2,0) = -xz;
1326	+	inertiaTensor(2,1) = -yz;
1327	+	inertiaTensor(2,2) = xx + yy;
1328	+
1329	+	#ifdef IS_MPI
1330	+	Mat3x3d tmpI(inertiaTensor);
1331	+	Vector3d tmpAngMom;
1332	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1333	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1334	+	#endif
1335	+
1336	+	return;
1337	+	}
1338	+
1339	+	//Returns the angular momentum of the system
1340	+	Vector3d SimInfo::getAngularMomentum(){
1341	+
1342	+	Vector3d com(0.0);
1343	+	Vector3d comVel(0.0);
1344	+	Vector3d angularMomentum(0.0);
1345	+
1346	+	getComAll(com,comVel);
1347	+
1348	+	SimInfo::MoleculeIterator i;
1349	+	Molecule* mol;
1350	+
1351	+	Vector3d thisr(0.0);
1352	+	Vector3d thisp(0.0);
1353	+
1354	+	double thisMass;
1355	+
1356	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1357	+	thisMass = mol->getMass();
1358	+	thisr = mol->getCom()-com;
1359	+	thisp = (mol->getComVel()-comVel)*thisMass;
1360	+
1361	+	angularMomentum += cross( thisr, thisp );
1362	+
1363	+	}
1364	+
1365	+	#ifdef IS_MPI
1366	+	Vector3d tmpAngMom;
1367	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1368	+	#endif
1369	+
1370	+	return angularMomentum;
1371	+	}
1372	+
1373	+
1374		}//end namespace oopse
1375

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