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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 334 by tim, Mon Feb 14 17:57:01 2005 UTC vs.
Revision 764 by gezelter, Mon Nov 21 22:59:21 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(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
84	>	ForceField* ff, Globals* simParams) :
85	>	stamps_(stamps), forceField_(ff), simParams_(simParams),
86	>	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
87	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
88	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
89	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
90	>	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
91	>	sman_(NULL), fortranInitialized_(false) {
92
93
94	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
95	<	MoleculeStamp* molStamp;
96	<	int nMolWithSameStamp;
97	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
98	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
99	<	CutoffGroupStamp* cgStamp;
100	<	RigidBodyStamp* rbStamp;
101	<	int nRigidAtoms = 0;
94	>	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
95	>	MoleculeStamp* molStamp;
96	>	int nMolWithSameStamp;
97	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
98	>	int nGroups = 0;      //total cutoff groups defined in meta-data file
99	>	CutoffGroupStamp* cgStamp;
100	>	RigidBodyStamp* rbStamp;
101	>	int nRigidAtoms = 0;
102
103	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
103	>	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
104		molStamp = i->first;
105		nMolWithSameStamp = i->second;
106
#	Line 100 | Line 115 | SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*,
115		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
116
117		for (int j=0; j < nCutoffGroupsInStamp; j++) {
118	<	cgStamp = molStamp->getCutoffGroup(j);
119	<	nAtomsInGroups += cgStamp->getNMembers();
118	>	cgStamp = molStamp->getCutoffGroup(j);
119	>	nAtomsInGroups += cgStamp->getNMembers();
120		}
121
122		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
123	+
124		nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
125
126		//calculate atoms in rigid bodies
#	Line 112 | Line 128 | SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*,
128		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
129
130		for (int j=0; j < nRigidBodiesInStamp; j++) {
131	<	rbStamp = molStamp->getRigidBody(j);
132	<	nAtomsInRigidBodies += rbStamp->getNMembers();
131	>	rbStamp = molStamp->getRigidBody(j);
132	>	nAtomsInRigidBodies += rbStamp->getNMembers();
133		}
134
135		nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
136		nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
137
138	<	}
138	>	}
139
140	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
141	<	//therefore the total number of cutoff groups in the system is equal to
142	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
143	<	//file plus the number of cutoff groups defined in meta-data file
144	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
140	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
141	>	//group therefore the total number of cutoff groups in the system is
142	>	//equal to the total number of atoms minus number of atoms belong to
143	>	//cutoff group defined in meta-data file plus the number of cutoff
144	>	//groups defined in meta-data file
145	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
146
147	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
148	<	//therefore the total number of  integrable objects in the system is equal to
149	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
150	<	//file plus the number of  rigid bodies defined in meta-data file
151	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
147	>	//every free atom (atom does not belong to rigid bodies) is an
148	>	//integrable object therefore the total number of integrable objects
149	>	//in the system is equal to the total number of atoms minus number of
150	>	//atoms belong to rigid body defined in meta-data file plus the number
151	>	//of rigid bodies defined in meta-data file
152	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
153	>	+ nGlobalRigidBodies_;
154	>
155	>	nGlobalMols_ = molStampIds_.size();
156
136	–	nGlobalMols_ = molStampIds_.size();
137	–
157		#ifdef IS_MPI
158	<	molToProcMap_.resize(nGlobalMols_);
158	>	molToProcMap_.resize(nGlobalMols_);
159		#endif
160
161	<	selectMan_ = new SelectionManager(this);
143	<	selectMan_->selectAll();
144	<	}
161	>	}
162
163	<	SimInfo::~SimInfo() {
164	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
165	<
166	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
167	<
163	>	SimInfo::~SimInfo() {
164	>	std::map<int, Molecule*>::iterator i;
165	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
166	>	delete i->second;
167	>	}
168	>	molecules_.clear();
169	>
170	>	delete stamps_;
171		delete sman_;
172		delete simParams_;
173		delete forceField_;
174	<	delete selectMan_;
155	<	}
174	>	}
175
176	<	int SimInfo::getNGlobalConstraints() {
176	>	int SimInfo::getNGlobalConstraints() {
177		int nGlobalConstraints;
178		#ifdef IS_MPI
179		MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
#	Line 163 | Line 182 | int SimInfo::getNGlobalConstraints() {
182		nGlobalConstraints =  nConstraints_;
183		#endif
184		return nGlobalConstraints;
185	<	}
185	>	}
186
187	<	bool SimInfo::addMolecule(Molecule* mol) {
187	>	bool SimInfo::addMolecule(Molecule* mol) {
188		MoleculeIterator i;
189
190		i = molecules_.find(mol->getGlobalIndex());
191		if (i == molecules_.end() ) {
192
193	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
193	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
194
195	<	nAtoms_ += mol->getNAtoms();
196	<	nBonds_ += mol->getNBonds();
197	<	nBends_ += mol->getNBends();
198	<	nTorsions_ += mol->getNTorsions();
199	<	nRigidBodies_ += mol->getNRigidBodies();
200	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
201	<	nCutoffGroups_ += mol->getNCutoffGroups();
202	<	nConstraints_ += mol->getNConstraintPairs();
195	>	nAtoms_ += mol->getNAtoms();
196	>	nBonds_ += mol->getNBonds();
197	>	nBends_ += mol->getNBends();
198	>	nTorsions_ += mol->getNTorsions();
199	>	nRigidBodies_ += mol->getNRigidBodies();
200	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
201	>	nCutoffGroups_ += mol->getNCutoffGroups();
202	>	nConstraints_ += mol->getNConstraintPairs();
203
204	<	addExcludePairs(mol);
204	>	addExcludePairs(mol);
205
206	<	return true;
206	>	return true;
207		} else {
208	<	return false;
208	>	return false;
209		}
210	<	}
210	>	}
211
212	<	bool SimInfo::removeMolecule(Molecule* mol) {
212	>	bool SimInfo::removeMolecule(Molecule* mol) {
213		MoleculeIterator i;
214		i = molecules_.find(mol->getGlobalIndex());
215
216		if (i != molecules_.end() ) {
217
218	<	assert(mol == i->second);
218	>	assert(mol == i->second);
219
220	<	nAtoms_ -= mol->getNAtoms();
221	<	nBonds_ -= mol->getNBonds();
222	<	nBends_ -= mol->getNBends();
223	<	nTorsions_ -= mol->getNTorsions();
224	<	nRigidBodies_ -= mol->getNRigidBodies();
225	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
226	<	nCutoffGroups_ -= mol->getNCutoffGroups();
227	<	nConstraints_ -= mol->getNConstraintPairs();
220	>	nAtoms_ -= mol->getNAtoms();
221	>	nBonds_ -= mol->getNBonds();
222	>	nBends_ -= mol->getNBends();
223	>	nTorsions_ -= mol->getNTorsions();
224	>	nRigidBodies_ -= mol->getNRigidBodies();
225	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
226	>	nCutoffGroups_ -= mol->getNCutoffGroups();
227	>	nConstraints_ -= mol->getNConstraintPairs();
228
229	<	removeExcludePairs(mol);
230	<	molecules_.erase(mol->getGlobalIndex());
229	>	removeExcludePairs(mol);
230	>	molecules_.erase(mol->getGlobalIndex());
231
232	<	delete mol;
232	>	delete mol;
233
234	<	return true;
234	>	return true;
235		} else {
236	<	return false;
236	>	return false;
237		}
238
239
240	<	}
240	>	}
241
242
243	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
243	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
244		i = molecules_.begin();
245		return i == molecules_.end() ? NULL : i->second;
246	<	}
246	>	}
247
248	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
248	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
249		++i;
250		return i == molecules_.end() ? NULL : i->second;
251	<	}
251	>	}
252
253
254	<	void SimInfo::calcNdf() {
254	>	void SimInfo::calcNdf() {
255		int ndf_local;
256		MoleculeIterator i;
257		std::vector<StuntDouble*>::iterator j;
#	Line 242 | Line 261 | void SimInfo::calcNdf() {
261		ndf_local = 0;
262
263		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
264	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
265	<	integrableObject = mol->nextIntegrableObject(j)) {
264	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
265	>	integrableObject = mol->nextIntegrableObject(j)) {
266
267	<	ndf_local += 3;
267	>	ndf_local += 3;
268
269	<	if (integrableObject->isDirectional()) {
270	<	if (integrableObject->isLinear()) {
271	<	ndf_local += 2;
272	<	} else {
273	<	ndf_local += 3;
274	<	}
275	<	}
269	>	if (integrableObject->isDirectional()) {
270	>	if (integrableObject->isLinear()) {
271	>	ndf_local += 2;
272	>	} else {
273	>	ndf_local += 3;
274	>	}
275	>	}
276
277	<	}//end for (integrableObject)
277	>	}//end for (integrableObject)
278		}// end for (mol)
279
280		// n_constraints is local, so subtract them on each processor
#	Line 271 | Line 290 | void SimInfo::calcNdf() {
290		// entire system:
291		ndf_ = ndf_ - 3 - nZconstraint_;
292
293	<	}
293	>	}
294
295	<	void SimInfo::calcNdfRaw() {
295	>	void SimInfo::calcNdfRaw() {
296		int ndfRaw_local;
297
298		MoleculeIterator i;
#	Line 285 | Line 304 | void SimInfo::calcNdfRaw() {
304		ndfRaw_local = 0;
305
306		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
307	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
308	<	integrableObject = mol->nextIntegrableObject(j)) {
307	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
308	>	integrableObject = mol->nextIntegrableObject(j)) {
309
310	<	ndfRaw_local += 3;
310	>	ndfRaw_local += 3;
311
312	<	if (integrableObject->isDirectional()) {
313	<	if (integrableObject->isLinear()) {
314	<	ndfRaw_local += 2;
315	<	} else {
316	<	ndfRaw_local += 3;
317	<	}
318	<	}
312	>	if (integrableObject->isDirectional()) {
313	>	if (integrableObject->isLinear()) {
314	>	ndfRaw_local += 2;
315	>	} else {
316	>	ndfRaw_local += 3;
317	>	}
318	>	}
319
320	<	}
320	>	}
321		}
322
323		#ifdef IS_MPI
#	Line 306 | Line 325 | void SimInfo::calcNdfRaw() {
325		#else
326		ndfRaw_ = ndfRaw_local;
327		#endif
328	<	}
328	>	}
329
330	<	void SimInfo::calcNdfTrans() {
330	>	void SimInfo::calcNdfTrans() {
331		int ndfTrans_local;
332
333		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 322 | Line 341 | void SimInfo::calcNdfTrans() {
341
342		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
343
344	<	}
344	>	}
345
346	<	void SimInfo::addExcludePairs(Molecule* mol) {
346	>	void SimInfo::addExcludePairs(Molecule* mol) {
347		std::vector<Bond*>::iterator bondIter;
348		std::vector<Bend*>::iterator bendIter;
349		std::vector<Torsion*>::iterator torsionIter;
#	Line 335 | Line 354 | void SimInfo::addExcludePairs(Molecule* mol) {
354		int b;
355		int c;
356		int d;
357	+
358	+	std::map<int, std::set<int> > atomGroups;
359	+
360	+	Molecule::RigidBodyIterator rbIter;
361	+	RigidBody* rb;
362	+	Molecule::IntegrableObjectIterator ii;
363	+	StuntDouble* integrableObject;
364
365	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
366	+	integrableObject = mol->nextIntegrableObject(ii)) {
367	+
368	+	if (integrableObject->isRigidBody()) {
369	+	rb = static_cast<RigidBody*>(integrableObject);
370	+	std::vector<Atom*> atoms = rb->getAtoms();
371	+	std::set<int> rigidAtoms;
372	+	for (int i = 0; i < atoms.size(); ++i) {
373	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
374	+	}
375	+	for (int i = 0; i < atoms.size(); ++i) {
376	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
377	+	}
378	+	} else {
379	+	std::set<int> oneAtomSet;
380	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
381	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
382	+	}
383	+	}
384	+
385	+
386	+
387		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
388	<	a = bond->getAtomA()->getGlobalIndex();
389	<	b = bond->getAtomB()->getGlobalIndex();
390	<	exclude_.addPair(a, b);
388	>	a = bond->getAtomA()->getGlobalIndex();
389	>	b = bond->getAtomB()->getGlobalIndex();
390	>	exclude_.addPair(a, b);
391		}
392
393		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
394	<	a = bend->getAtomA()->getGlobalIndex();
395	<	b = bend->getAtomB()->getGlobalIndex();
396	<	c = bend->getAtomC()->getGlobalIndex();
394	>	a = bend->getAtomA()->getGlobalIndex();
395	>	b = bend->getAtomB()->getGlobalIndex();
396	>	c = bend->getAtomC()->getGlobalIndex();
397	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
398	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
399	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
400
401	<	exclude_.addPair(a, b);
402	<	exclude_.addPair(a, c);
403	<	exclude_.addPair(b, c);
401	>	exclude_.addPairs(rigidSetA, rigidSetB);
402	>	exclude_.addPairs(rigidSetA, rigidSetC);
403	>	exclude_.addPairs(rigidSetB, rigidSetC);
404	>
405	>	//exclude_.addPair(a, b);
406	>	//exclude_.addPair(a, c);
407	>	//exclude_.addPair(b, c);
408		}
409
410		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
411	<	a = torsion->getAtomA()->getGlobalIndex();
412	<	b = torsion->getAtomB()->getGlobalIndex();
413	<	c = torsion->getAtomC()->getGlobalIndex();
414	<	d = torsion->getAtomD()->getGlobalIndex();
411	>	a = torsion->getAtomA()->getGlobalIndex();
412	>	b = torsion->getAtomB()->getGlobalIndex();
413	>	c = torsion->getAtomC()->getGlobalIndex();
414	>	d = torsion->getAtomD()->getGlobalIndex();
415	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
416	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
417	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
418	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
419
420	<	exclude_.addPair(a, b);
421	<	exclude_.addPair(a, c);
422	<	exclude_.addPair(a, d);
423	<	exclude_.addPair(b, c);
424	<	exclude_.addPair(b, d);
425	<	exclude_.addPair(c, d);
420	>	exclude_.addPairs(rigidSetA, rigidSetB);
421	>	exclude_.addPairs(rigidSetA, rigidSetC);
422	>	exclude_.addPairs(rigidSetA, rigidSetD);
423	>	exclude_.addPairs(rigidSetB, rigidSetC);
424	>	exclude_.addPairs(rigidSetB, rigidSetD);
425	>	exclude_.addPairs(rigidSetC, rigidSetD);
426	>
427	>	/*
428	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
429	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
430	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
431	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
432	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
433	>	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
434	>
435	>
436	>	exclude_.addPair(a, b);
437	>	exclude_.addPair(a, c);
438	>	exclude_.addPair(a, d);
439	>	exclude_.addPair(b, c);
440	>	exclude_.addPair(b, d);
441	>	exclude_.addPair(c, d);
442	>	*/
443		}
444
445	<
446	<	}
445	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
446	>	std::vector<Atom*> atoms = rb->getAtoms();
447	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
448	>	for (int j = i + 1; j < atoms.size(); ++j) {
449	>	a = atoms[i]->getGlobalIndex();
450	>	b = atoms[j]->getGlobalIndex();
451	>	exclude_.addPair(a, b);
452	>	}
453	>	}
454	>	}
455
456	<	void SimInfo::removeExcludePairs(Molecule* mol) {
456	>	}
457	>
458	>	void SimInfo::removeExcludePairs(Molecule* mol) {
459		std::vector<Bond*>::iterator bondIter;
460		std::vector<Bend*>::iterator bendIter;
461		std::vector<Torsion*>::iterator torsionIter;
#	Line 380 | Line 466 | void SimInfo::removeExcludePairs(Molecule* mol) {
466		int b;
467		int c;
468		int d;
469	+
470	+	std::map<int, std::set<int> > atomGroups;
471	+
472	+	Molecule::RigidBodyIterator rbIter;
473	+	RigidBody* rb;
474	+	Molecule::IntegrableObjectIterator ii;
475	+	StuntDouble* integrableObject;
476
477	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
478	+	integrableObject = mol->nextIntegrableObject(ii)) {
479	+
480	+	if (integrableObject->isRigidBody()) {
481	+	rb = static_cast<RigidBody*>(integrableObject);
482	+	std::vector<Atom*> atoms = rb->getAtoms();
483	+	std::set<int> rigidAtoms;
484	+	for (int i = 0; i < atoms.size(); ++i) {
485	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
486	+	}
487	+	for (int i = 0; i < atoms.size(); ++i) {
488	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
489	+	}
490	+	} else {
491	+	std::set<int> oneAtomSet;
492	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
493	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
494	+	}
495	+	}
496	+
497	+
498		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
499	<	a = bond->getAtomA()->getGlobalIndex();
500	<	b = bond->getAtomB()->getGlobalIndex();
501	<	exclude_.removePair(a, b);
499	>	a = bond->getAtomA()->getGlobalIndex();
500	>	b = bond->getAtomB()->getGlobalIndex();
501	>	exclude_.removePair(a, b);
502		}
503
504		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
505	<	a = bend->getAtomA()->getGlobalIndex();
506	<	b = bend->getAtomB()->getGlobalIndex();
507	<	c = bend->getAtomC()->getGlobalIndex();
505	>	a = bend->getAtomA()->getGlobalIndex();
506	>	b = bend->getAtomB()->getGlobalIndex();
507	>	c = bend->getAtomC()->getGlobalIndex();
508
509	<	exclude_.removePair(a, b);
510	<	exclude_.removePair(a, c);
511	<	exclude_.removePair(b, c);
509	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
510	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
511	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
512	>
513	>	exclude_.removePairs(rigidSetA, rigidSetB);
514	>	exclude_.removePairs(rigidSetA, rigidSetC);
515	>	exclude_.removePairs(rigidSetB, rigidSetC);
516	>
517	>	//exclude_.removePair(a, b);
518	>	//exclude_.removePair(a, c);
519	>	//exclude_.removePair(b, c);
520		}
521
522		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
523	<	a = torsion->getAtomA()->getGlobalIndex();
524	<	b = torsion->getAtomB()->getGlobalIndex();
525	<	c = torsion->getAtomC()->getGlobalIndex();
526	<	d = torsion->getAtomD()->getGlobalIndex();
523	>	a = torsion->getAtomA()->getGlobalIndex();
524	>	b = torsion->getAtomB()->getGlobalIndex();
525	>	c = torsion->getAtomC()->getGlobalIndex();
526	>	d = torsion->getAtomD()->getGlobalIndex();
527
528	<	exclude_.removePair(a, b);
529	<	exclude_.removePair(a, c);
530	<	exclude_.removePair(a, d);
531	<	exclude_.removePair(b, c);
532	<	exclude_.removePair(b, d);
533	<	exclude_.removePair(c, d);
528	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
529	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
530	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
531	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
532	>
533	>	exclude_.removePairs(rigidSetA, rigidSetB);
534	>	exclude_.removePairs(rigidSetA, rigidSetC);
535	>	exclude_.removePairs(rigidSetA, rigidSetD);
536	>	exclude_.removePairs(rigidSetB, rigidSetC);
537	>	exclude_.removePairs(rigidSetB, rigidSetD);
538	>	exclude_.removePairs(rigidSetC, rigidSetD);
539	>
540	>	/*
541	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
542	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
543	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
544	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
545	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
546	>	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
547	>
548	>
549	>	exclude_.removePair(a, b);
550	>	exclude_.removePair(a, c);
551	>	exclude_.removePair(a, d);
552	>	exclude_.removePair(b, c);
553	>	exclude_.removePair(b, d);
554	>	exclude_.removePair(c, d);
555	>	*/
556		}
557
558	<	}
558	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
559	>	std::vector<Atom*> atoms = rb->getAtoms();
560	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
561	>	for (int j = i + 1; j < atoms.size(); ++j) {
562	>	a = atoms[i]->getGlobalIndex();
563	>	b = atoms[j]->getGlobalIndex();
564	>	exclude_.removePair(a, b);
565	>	}
566	>	}
567	>	}
568	>
569	>	}
570
571
572	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
572	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
573		int curStampId;
574
575		//index from 0
#	Line 422 | Line 577 | void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp
577
578		moleculeStamps_.push_back(molStamp);
579		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
580	<	}
580	>	}
581
582	<	void SimInfo::update() {
582	>	void SimInfo::update() {
583
584		setupSimType();
585
#	Line 437 | Line 592 | void SimInfo::update() {
592		//setup fortran force field
593		/** @deprecate */
594		int isError = 0;
595	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
595	>
596	>	setupElectrostaticSummationMethod( isError );
597	>	setupSwitchingFunction();
598	>
599		if(isError){
600	<	sprintf( painCave.errMsg,
601	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
602	<	painCave.isFatal = 1;
603	<	simError();
600	>	sprintf( painCave.errMsg,
601	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
602	>	painCave.isFatal = 1;
603	>	simError();
604		}
605
606
#	Line 453 | Line 611 | void SimInfo::update() {
611		calcNdfTrans();
612
613		fortranInitialized_ = true;
614	<	}
614	>	}
615
616	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
616	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
617		SimInfo::MoleculeIterator mi;
618		Molecule* mol;
619		Molecule::AtomIterator ai;
#	Line 464 | Line 622 | std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
622
623		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
624
625	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
626	<	atomTypes.insert(atom->getAtomType());
627	<	}
625	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
626	>	atomTypes.insert(atom->getAtomType());
627	>	}
628
629		}
630
631		return atomTypes;
632	<	}
632	>	}
633
634	<	void SimInfo::setupSimType() {
634	>	void SimInfo::setupSimType() {
635		std::set<AtomType*>::iterator i;
636		std::set<AtomType*> atomTypes;
637		atomTypes = getUniqueAtomTypes();
#	Line 481 | Line 639 | void SimInfo::setupSimType() {
639		int useLennardJones = 0;
640		int useElectrostatic = 0;
641		int useEAM = 0;
642	+	int useSC = 0;
643		int useCharge = 0;
644		int useDirectional = 0;
645		int useDipole = 0;
646		int useGayBerne = 0;
647		int useSticky = 0;
648	+	int useStickyPower = 0;
649		int useShape = 0;
650		int useFLARB = 0; //it is not in AtomType yet
651		int useDirectionalAtom = 0;
652		int useElectrostatics = 0;
653		//usePBC and useRF are from simParams
654	<	int usePBC = simParams_->getPBC();
655	<	int useRF = simParams_->getUseRF();
654	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
655	>	int useRF;
656	>	int useSF;
657	>	std::string myMethod;
658
659	+	// set the useRF logical
660	+	useRF = 0;
661	+	useSF = 0;
662	+
663	+
664	+	if (simParams_->haveElectrostaticSummationMethod()) {
665	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
666	+	toUpper(myMethod);
667	+	if (myMethod == "REACTION_FIELD") {
668	+	useRF=1;
669	+	} else {
670	+	if (myMethod == "SHIFTED_FORCE") {
671	+	useSF = 1;
672	+	}
673	+	}
674	+	}
675	+
676		//loop over all of the atom types
677		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
678	<	useLennardJones |= (*i)->isLennardJones();
679	<	useElectrostatic |= (*i)->isElectrostatic();
680	<	useEAM |= (*i)->isEAM();
681	<	useCharge |= (*i)->isCharge();
682	<	useDirectional |= (*i)->isDirectional();
683	<	useDipole |= (*i)->isDipole();
684	<	useGayBerne |= (*i)->isGayBerne();
685	<	useSticky |= (*i)->isSticky();
686	<	useShape |= (*i)->isShape();
678	>	useLennardJones |= (*i)->isLennardJones();
679	>	useElectrostatic |= (*i)->isElectrostatic();
680	>	useEAM |= (*i)->isEAM();
681	>	useSC |= (*i)->isSC();
682	>	useCharge |= (*i)->isCharge();
683	>	useDirectional |= (*i)->isDirectional();
684	>	useDipole |= (*i)->isDipole();
685	>	useGayBerne |= (*i)->isGayBerne();
686	>	useSticky |= (*i)->isSticky();
687	>	useStickyPower |= (*i)->isStickyPower();
688	>	useShape |= (*i)->isShape();
689		}
690
691	<	if (useSticky || useDipole || useGayBerne || useShape) {
692	<	useDirectionalAtom = 1;
691	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
692	>	useDirectionalAtom = 1;
693		}
694
695		if (useCharge || useDipole) {
696	<	useElectrostatics = 1;
696	>	useElectrostatics = 1;
697		}
698
699		#ifdef IS_MPI
#	Line 539 | Line 720 | void SimInfo::setupSimType() {
720		temp = useSticky;
721		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
722
723	+	temp = useStickyPower;
724	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
725	+
726		temp = useGayBerne;
727		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
728
729		temp = useEAM;
730		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
731
732	+	temp = useSC;
733	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
734	+
735		temp = useShape;
736		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
737
#	Line 553 | Line 740 | void SimInfo::setupSimType() {
740
741		temp = useRF;
742		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
743	<
743	>
744	>	temp = useSF;
745	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
746	>
747		#endif
748
749		fInfo_.SIM_uses_PBC = usePBC;
#	Line 563 | Line 753 | void SimInfo::setupSimType() {
753		fInfo_.SIM_uses_Charges = useCharge;
754		fInfo_.SIM_uses_Dipoles = useDipole;
755		fInfo_.SIM_uses_Sticky = useSticky;
756	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
757		fInfo_.SIM_uses_GayBerne = useGayBerne;
758		fInfo_.SIM_uses_EAM = useEAM;
759	+	fInfo_.SIM_uses_SC = useSC;
760		fInfo_.SIM_uses_Shapes = useShape;
761		fInfo_.SIM_uses_FLARB = useFLARB;
762		fInfo_.SIM_uses_RF = useRF;
763	+	fInfo_.SIM_uses_SF = useSF;
764
765	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
766	<
767	<	if (simParams_->haveDielectric()) {
768	<	fInfo_.dielect = simParams_->getDielectric();
769	<	} else {
770	<	sprintf(painCave.errMsg,
771	<	"SimSetup Error: No Dielectric constant was set.\n"
772	<	"\tYou are trying to use Reaction Field without"
773	<	"\tsetting a dielectric constant!\n");
774	<	painCave.isFatal = 1;
775	<	simError();
776	<	}
584	<
585	<	} else {
586	<	fInfo_.dielect = 0.0;
765	>	if( myMethod == "REACTION_FIELD") {
766	>
767	>	if (simParams_->haveDielectric()) {
768	>	fInfo_.dielect = simParams_->getDielectric();
769	>	} else {
770	>	sprintf(painCave.errMsg,
771	>	"SimSetup Error: No Dielectric constant was set.\n"
772	>	"\tYou are trying to use Reaction Field without"
773	>	"\tsetting a dielectric constant!\n");
774	>	painCave.isFatal = 1;
775	>	simError();
776	>	}
777		}
778
779	<	}
779	>	}
780
781	<	void SimInfo::setupFortranSim() {
781	>	void SimInfo::setupFortranSim() {
782		int isError;
783		int nExclude;
784		std::vector<int> fortranGlobalGroupMembership;
#	Line 598 | Line 788 | void SimInfo::setupFortranSim() {
788
789		//globalGroupMembership_ is filled by SimCreator
790		for (int i = 0; i < nGlobalAtoms_; i++) {
791	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
791	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
792		}
793
794		//calculate mass ratio of cutoff group
#	Line 615 | Line 805 | void SimInfo::setupFortranSim() {
805		mfact.reserve(getNCutoffGroups());
806
807		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
808	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
808	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
809
810	<	totalMass = cg->getMass();
811	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
812	<	mfact.push_back(atom->getMass()/totalMass);
813	<	}
810	>	totalMass = cg->getMass();
811	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
812	>	// Check for massless groups - set mfact to 1 if true
813	>	if (totalMass != 0)
814	>	mfact.push_back(atom->getMass()/totalMass);
815	>	else
816	>	mfact.push_back( 1.0 );
817	>	}
818
819	<	}
819	>	}
820		}
821
822		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
#	Line 632 | Line 826 | void SimInfo::setupFortranSim() {
826		identArray.reserve(getNAtoms());
827
828		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
829	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
830	<	identArray.push_back(atom->getIdent());
831	<	}
829	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
830	>	identArray.push_back(atom->getIdent());
831	>	}
832		}
833
834		//fill molMembershipArray
835		//molMembershipArray is filled by SimCreator
836		std::vector<int> molMembershipArray(nGlobalAtoms_);
837		for (int i = 0; i < nGlobalAtoms_; i++) {
838	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
838	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
839		}
840
841		//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
842		int nGlobalExcludes = 0;
843		int* globalExcludes = NULL;
844		int* excludeList = exclude_.getExcludeList();
845		setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
846	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
847	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
846	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
847	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
848
849		if( isError ){
850
851	<	sprintf( painCave.errMsg,
852	<	"There was an error setting the simulation information in fortran.\n" );
853	<	painCave.isFatal = 1;
854	<	painCave.severity = OOPSE_ERROR;
855	<	simError();
851	>	sprintf( painCave.errMsg,
852	>	"There was an error setting the simulation information in fortran.\n" );
853	>	painCave.isFatal = 1;
854	>	painCave.severity = OOPSE_ERROR;
855	>	simError();
856		}
857
858		#ifdef IS_MPI
859		sprintf( checkPointMsg,
860	<	"succesfully sent the simulation information to fortran.\n");
860	>	"succesfully sent the simulation information to fortran.\n");
861		MPIcheckPoint();
862		#endif // is_mpi
863	<	}
863	>	}
864
865
866		#ifdef IS_MPI
867	<	void SimInfo::setupFortranParallel() {
867	>	void SimInfo::setupFortranParallel() {
868
869		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
870		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
#	Line 689 | Line 880 | void SimInfo::setupFortranParallel() {
880
881		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
882
883	<	//local index(index in DataStorge) of atom is important
884	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
885	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
886	<	}
883	>	//local index(index in DataStorge) of atom is important
884	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
885	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
886	>	}
887
888	<	//local index of cutoff group is trivial, it only depends on the order of travesing
889	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
890	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
891	<	}
888	>	//local index of cutoff group is trivial, it only depends on the order of travesing
889	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
890	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
891	>	}
892
893		}
894
#	Line 717 | Line 908 | void SimInfo::setupFortranParallel() {
908		&localToGlobalCutoffGroupIndex[0], &isError);
909
910		if (isError) {
911	<	sprintf(painCave.errMsg,
912	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
913	<	painCave.isFatal = 1;
914	<	simError();
911	>	sprintf(painCave.errMsg,
912	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
913	>	painCave.isFatal = 1;
914	>	simError();
915		}
916
917		sprintf(checkPointMsg, " mpiRefresh successful.\n");
918		MPIcheckPoint();
919
920
921	<	}
921	>	}
922
923		#endif
924
925	<	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) {
925	>	void SimInfo::setupCutoff() {
926
927	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
927	>	// Check the cutoff policy
928	>	int cp =  TRADITIONAL_CUTOFF_POLICY;
929	>	if (simParams_->haveCutoffPolicy()) {
930	>	std::string myPolicy = simParams_->getCutoffPolicy();
931	>	toUpper(myPolicy);
932	>	if (myPolicy == "MIX") {
933	>	cp = MIX_CUTOFF_POLICY;
934	>	} else {
935	>	if (myPolicy == "MAX") {
936	>	cp = MAX_CUTOFF_POLICY;
937	>	} else {
938	>	if (myPolicy == "TRADITIONAL") {
939	>	cp = TRADITIONAL_CUTOFF_POLICY;
940	>	} else {
941	>	// throw error
942	>	sprintf( painCave.errMsg,
943	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
944	>	painCave.isFatal = 1;
945	>	simError();
946	>	}
947	>	}
948	>	}
949	>	}
950	>	notifyFortranCutoffPolicy(&cp);
951	>
952	>	// Check the Skin Thickness for neighborlists
953	>	double skin;
954	>	if (simParams_->haveSkinThickness()) {
955	>	skin = simParams_->getSkinThickness();
956	>	notifyFortranSkinThickness(&skin);
957	>	}
958
959	<	if (!simParams_->haveRcut()){
960	<	sprintf(painCave.errMsg,
959	>	// Check if the cutoff was set explicitly:
960	>	if (simParams_->haveCutoffRadius()) {
961	>	rcut_ = simParams_->getCutoffRadius();
962	>	if (simParams_->haveSwitchingRadius()) {
963	>	rsw_  = simParams_->getSwitchingRadius();
964	>	} else {
965	>	rsw_ = rcut_;
966	>	}
967	>	notifyFortranCutoffs(&rcut_, &rsw_);
968	>
969	>	} else {
970	>
971	>	// For electrostatic atoms, we'll assume a large safe value:
972	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
973	>	sprintf(painCave.errMsg,
974		"SimCreator Warning: No value was set for the cutoffRadius.\n"
975		"\tOOPSE will use a default value of 15.0 angstroms"
976		"\tfor the cutoffRadius.\n");
977	<	painCave.isFatal = 0;
978	<	simError();
979	<	rcut = 15.0;
980	<	} else{
981	<	rcut = simParams_->getRcut();
977	>	painCave.isFatal = 0;
978	>	simError();
979	>	rcut_ = 15.0;
980	>
981	>	if (simParams_->haveElectrostaticSummationMethod()) {
982	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
983	>	toUpper(myMethod);
984	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
985	>	if (simParams_->haveSwitchingRadius()){
986	>	sprintf(painCave.errMsg,
987	>	"SimInfo Warning: A value was set for the switchingRadius\n"
988	>	"\teven though the electrostaticSummationMethod was\n"
989	>	"\tset to %s\n", myMethod.c_str());
990	>	painCave.isFatal = 1;
991	>	simError();
992	>	}
993	>	}
994		}
995	<
996	<	if (!simParams_->haveRsw()){
997	<	sprintf(painCave.errMsg,
998	<	"SimCreator Warning: No value was set for switchingRadius.\n"
999	<	"\tOOPSE will use a default value of\n"
1000	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
1001	<	painCave.isFatal = 0;
1002	<	simError();
1003	<	rsw = 0.95 * rcut;
1004	<	} else{
1005	<	rsw = simParams_->getRsw();
995	>
996	>	if (simParams_->haveSwitchingRadius()){
997	>	rsw_ = simParams_->getSwitchingRadius();
998	>	} else {
999	>	sprintf(painCave.errMsg,
1000	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1001	>	"\tOOPSE will use a default value of\n"
1002	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1003	>	painCave.isFatal = 0;
1004	>	simError();
1005	>	rsw_ = 0.85 * rcut_;
1006		}
1007	<
1008	<	} else {
1009	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
1010	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
1007	>	notifyFortranCutoffs(&rcut_, &rsw_);
1008	>	} else {
1009	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1010	>	// We'll punt and let fortran figure out the cutoffs later.
1011
1012	<	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	<	}
1012	>	notifyFortranYouAreOnYourOwn();
1013
1014	<	if (simParams_->haveRsw()) {
797	<	rsw  = simParams_->getRsw();
798	<	} else {
799	<	rsw = rcut;
800	<	}
801	<
1014	>	}
1015		}
1016	<	}
1016	>	}
1017
1018	<	void SimInfo::setupCutoff() {
1019	<	getCutoff(rcut_, rsw_);
1020	<	double rnblist = rcut_ + 1; // skin of neighbor list
1018	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1019	>
1020	>	int errorOut;
1021	>	int esm =  NONE;
1022	>	int sm = UNDAMPED;
1023	>	double alphaVal;
1024	>	double dielectric;
1025
1026	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1027	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
1028	<	}
1026	>	errorOut = isError;
1027	>	alphaVal = simParams_->getDampingAlpha();
1028	>	dielectric = simParams_->getDielectric();
1029
1030	<	void SimInfo::addProperty(GenericData* genData) {
1031	<	properties_.addProperty(genData);
1032	<	}
1033	<
1034	<	void SimInfo::removeProperty(const std::string& propName) {
1035	<	properties_.removeProperty(propName);
1036	<	}
1037	<
1038	<	void SimInfo::clearProperties() {
1039	<	properties_.clearProperties();
1040	<	}
1041	<
1042	<	std::vector<std::string> SimInfo::getPropertyNames() {
1043	<	return properties_.getPropertyNames();
1044	<	}
1045	<
1046	<	std::vector<GenericData*> SimInfo::getProperties() {
1047	<	return properties_.getProperties();
1048	<	}
1049	<
1050	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1051	<	return properties_.getPropertyByName(propName);
1052	<	}
1053	<
1054	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1055	<	//if (sman_ == sman_) {
1056	<	//    return;
1057	<	//}
1030	>	if (simParams_->haveElectrostaticSummationMethod()) {
1031	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1032	>	toUpper(myMethod);
1033	>	if (myMethod == "NONE") {
1034	>	esm = NONE;
1035	>	} else {
1036	>	if (myMethod == "SWITCHING_FUNCTION") {
1037	>	esm = SWITCHING_FUNCTION;
1038	>	} else {
1039	>	if (myMethod == "SHIFTED_POTENTIAL") {
1040	>	esm = SHIFTED_POTENTIAL;
1041	>	} else {
1042	>	if (myMethod == "SHIFTED_FORCE") {
1043	>	esm = SHIFTED_FORCE;
1044	>	} else {
1045	>	if (myMethod == "REACTION_FIELD") {
1046	>	esm = REACTION_FIELD;
1047	>	} else {
1048	>	// throw error
1049	>	sprintf( painCave.errMsg,
1050	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1051	>	"\t(Input file specified %s .)\n"
1052	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1053	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1054	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1055	>	painCave.isFatal = 1;
1056	>	simError();
1057	>	}
1058	>	}
1059	>	}
1060	>	}
1061	>	}
1062	>	}
1063
1064	<	//delete sman_;
1064	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1065	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1066	>	toUpper(myScreen);
1067	>	if (myScreen == "UNDAMPED") {
1068	>	sm = UNDAMPED;
1069	>	} else {
1070	>	if (myScreen == "DAMPED") {
1071	>	sm = DAMPED;
1072	>	if (!simParams_->haveDampingAlpha()) {
1073	>	//throw error
1074	>	sprintf( painCave.errMsg,
1075	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1076	>	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1077	>	painCave.isFatal = 0;
1078	>	simError();
1079	>	}
1080	>	} else {
1081	>	// throw error
1082	>	sprintf( painCave.errMsg,
1083	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1084	>	"\t(Input file specified %s .)\n"
1085	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1086	>	"or \"damped\".\n", myScreen.c_str() );
1087	>	painCave.isFatal = 1;
1088	>	simError();
1089	>	}
1090	>	}
1091	>	}
1092	>
1093	>	// let's pass some summation method variables to fortran
1094	>	setElectrostaticSummationMethod( &esm );
1095	>	notifyFortranElectrostaticMethod( &esm );
1096	>	setScreeningMethod( &sm );
1097	>	setDampingAlpha( &alphaVal );
1098	>	setReactionFieldDielectric( &dielectric );
1099	>	initFortranFF( &errorOut );
1100	>	}
1101	>
1102	>	void SimInfo::setupSwitchingFunction() {
1103	>	int ft = CUBIC;
1104	>
1105	>	if (simParams_->haveSwitchingFunctionType()) {
1106	>	std::string funcType = simParams_->getSwitchingFunctionType();
1107	>	toUpper(funcType);
1108	>	if (funcType == "CUBIC") {
1109	>	ft = CUBIC;
1110	>	} else {
1111	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1112	>	ft = FIFTH_ORDER_POLY;
1113	>	} else {
1114	>	// throw error
1115	>	sprintf( painCave.errMsg,
1116	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1117	>	painCave.isFatal = 1;
1118	>	simError();
1119	>	}
1120	>	}
1121	>	}
1122	>
1123	>	// send switching function notification to switcheroo
1124	>	setFunctionType(&ft);
1125	>
1126	>	}
1127	>
1128	>	void SimInfo::addProperty(GenericData* genData) {
1129	>	properties_.addProperty(genData);
1130	>	}
1131	>
1132	>	void SimInfo::removeProperty(const std::string& propName) {
1133	>	properties_.removeProperty(propName);
1134	>	}
1135	>
1136	>	void SimInfo::clearProperties() {
1137	>	properties_.clearProperties();
1138	>	}
1139	>
1140	>	std::vector<std::string> SimInfo::getPropertyNames() {
1141	>	return properties_.getPropertyNames();
1142	>	}
1143	>
1144	>	std::vector<GenericData*> SimInfo::getProperties() {
1145	>	return properties_.getProperties();
1146	>	}
1147	>
1148	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1149	>	return properties_.getPropertyByName(propName);
1150	>	}
1151	>
1152	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1153	>	if (sman_ == sman) {
1154	>	return;
1155	>	}
1156	>	delete sman_;
1157		sman_ = sman;
1158
1159		Molecule* mol;
#	Line 851 | Line 1165 | void SimInfo::setSnapshotManager(SnapshotManager* sman
1165
1166		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1167
1168	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1169	<	atom->setSnapshotManager(sman_);
1170	<	}
1168	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1169	>	atom->setSnapshotManager(sman_);
1170	>	}
1171
1172	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1173	<	rb->setSnapshotManager(sman_);
1174	<	}
1172	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1173	>	rb->setSnapshotManager(sman_);
1174	>	}
1175		}
1176
1177	<	}
1177	>	}
1178
1179	<	Vector3d SimInfo::getComVel(){
1179	>	Vector3d SimInfo::getComVel(){
1180		SimInfo::MoleculeIterator i;
1181		Molecule* mol;
1182
#	Line 871 | Line 1185 | Vector3d SimInfo::getComVel(){
1185
1186
1187		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1188	<	double mass = mol->getMass();
1189	<	totalMass += mass;
1190	<	comVel += mass * mol->getComVel();
1188	>	double mass = mol->getMass();
1189	>	totalMass += mass;
1190	>	comVel += mass * mol->getComVel();
1191		}
1192
1193		#ifdef IS_MPI
#	Line 886 | Line 1200 | Vector3d SimInfo::getComVel(){
1200		comVel /= totalMass;
1201
1202		return comVel;
1203	<	}
1203	>	}
1204
1205	<	Vector3d SimInfo::getCom(){
1205	>	Vector3d SimInfo::getCom(){
1206		SimInfo::MoleculeIterator i;
1207		Molecule* mol;
1208
#	Line 896 | Line 1210 | Vector3d SimInfo::getCom(){
1210		double totalMass = 0.0;
1211
1212		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1213	<	double mass = mol->getMass();
1214	<	totalMass += mass;
1215	<	com += mass * mol->getCom();
1213	>	double mass = mol->getMass();
1214	>	totalMass += mass;
1215	>	com += mass * mol->getCom();
1216		}
1217
1218		#ifdef IS_MPI
#	Line 912 | Line 1226 | Vector3d SimInfo::getCom(){
1226
1227		return com;
1228
1229	<	}
1229	>	}
1230
1231	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1231	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1232
1233		return o;
1234	<	}
1234	>	}
1235	>
1236	>
1237	>	/*
1238	>	Returns center of mass and center of mass velocity in one function call.
1239	>	*/
1240	>
1241	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1242	>	SimInfo::MoleculeIterator i;
1243	>	Molecule* mol;
1244	>
1245	>
1246	>	double totalMass = 0.0;
1247	>
1248
1249	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1250	+	double mass = mol->getMass();
1251	+	totalMass += mass;
1252	+	com += mass * mol->getCom();
1253	+	comVel += mass * mol->getComVel();
1254	+	}
1255	+
1256	+	#ifdef IS_MPI
1257	+	double tmpMass = totalMass;
1258	+	Vector3d tmpCom(com);
1259	+	Vector3d tmpComVel(comVel);
1260	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1261	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1262	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1263	+	#endif
1264	+
1265	+	com /= totalMass;
1266	+	comVel /= totalMass;
1267	+	}
1268	+
1269	+	/*
1270	+	Return intertia tensor for entire system and angular momentum Vector.
1271	+
1272	+
1273	+	[  Ixx -Ixy  -Ixz ]
1274	+	J =| -Iyx  Iyy  -Iyz |
1275	+	[ -Izx -Iyz   Izz ]
1276	+	*/
1277	+
1278	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1279	+
1280	+
1281	+	double xx = 0.0;
1282	+	double yy = 0.0;
1283	+	double zz = 0.0;
1284	+	double xy = 0.0;
1285	+	double xz = 0.0;
1286	+	double yz = 0.0;
1287	+	Vector3d com(0.0);
1288	+	Vector3d comVel(0.0);
1289	+
1290	+	getComAll(com, comVel);
1291	+
1292	+	SimInfo::MoleculeIterator i;
1293	+	Molecule* mol;
1294	+
1295	+	Vector3d thisq(0.0);
1296	+	Vector3d thisv(0.0);
1297	+
1298	+	double thisMass = 0.0;
1299	+
1300	+
1301	+
1302	+
1303	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1304	+
1305	+	thisq = mol->getCom()-com;
1306	+	thisv = mol->getComVel()-comVel;
1307	+	thisMass = mol->getMass();
1308	+	// Compute moment of intertia coefficients.
1309	+	xx += thisq[0]*thisq[0]*thisMass;
1310	+	yy += thisq[1]*thisq[1]*thisMass;
1311	+	zz += thisq[2]*thisq[2]*thisMass;
1312	+
1313	+	// compute products of intertia
1314	+	xy += thisq[0]*thisq[1]*thisMass;
1315	+	xz += thisq[0]*thisq[2]*thisMass;
1316	+	yz += thisq[1]*thisq[2]*thisMass;
1317	+
1318	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1319	+
1320	+	}
1321	+
1322	+
1323	+	inertiaTensor(0,0) = yy + zz;
1324	+	inertiaTensor(0,1) = -xy;
1325	+	inertiaTensor(0,2) = -xz;
1326	+	inertiaTensor(1,0) = -xy;
1327	+	inertiaTensor(1,1) = xx + zz;
1328	+	inertiaTensor(1,2) = -yz;
1329	+	inertiaTensor(2,0) = -xz;
1330	+	inertiaTensor(2,1) = -yz;
1331	+	inertiaTensor(2,2) = xx + yy;
1332	+
1333	+	#ifdef IS_MPI
1334	+	Mat3x3d tmpI(inertiaTensor);
1335	+	Vector3d tmpAngMom;
1336	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1337	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1338	+	#endif
1339	+
1340	+	return;
1341	+	}
1342	+
1343	+	//Returns the angular momentum of the system
1344	+	Vector3d SimInfo::getAngularMomentum(){
1345	+
1346	+	Vector3d com(0.0);
1347	+	Vector3d comVel(0.0);
1348	+	Vector3d angularMomentum(0.0);
1349	+
1350	+	getComAll(com,comVel);
1351	+
1352	+	SimInfo::MoleculeIterator i;
1353	+	Molecule* mol;
1354	+
1355	+	Vector3d thisr(0.0);
1356	+	Vector3d thisp(0.0);
1357	+
1358	+	double thisMass;
1359	+
1360	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1361	+	thisMass = mol->getMass();
1362	+	thisr = mol->getCom()-com;
1363	+	thisp = (mol->getComVel()-comVel)*thisMass;
1364	+
1365	+	angularMomentum += cross( thisr, thisp );
1366	+
1367	+	}
1368	+
1369	+	#ifdef IS_MPI
1370	+	Vector3d tmpAngMom;
1371	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1372	+	#endif
1373	+
1374	+	return angularMomentum;
1375	+	}
1376	+
1377	+
1378		}//end namespace oopse
1379

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