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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 274 by tim, Tue Jan 25 21:59:18 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1750 by gezelter, Thu Jun 7 12:53:46 2012 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 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 48 | Line 49
49
50		#include <algorithm>
51		#include <set>
52	+	#include <map>
53
54		#include "brains/SimInfo.hpp"
55		#include "math/Vector3.hpp"
56		#include "primitives/Molecule.hpp"
57	<	#include "UseTheForce/doForces_interface.h"
56	<	#include "UseTheForce/notifyCutoffs_interface.h"
57	>	#include "primitives/StuntDouble.hpp"
58		#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60	<
60	>	#include "selection/SelectionManager.hpp"
61	>	#include "io/ForceFieldOptions.hpp"
62	>	#include "brains/ForceField.hpp"
63	>	#include "nonbonded/SwitchingFunction.hpp"
64		#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
63	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68	<	namespace oopse {
69	<
70	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
71	<	ForceField* ff, Globals* simParams) :
72	<	forceField_(ff), simParams_(simParams),
73	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
77	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
78	<	sman_(NULL), fortranInitialized_(false) {
79	<
80	<
78	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
68	>	using namespace std;
69	>	namespace OpenMD {
70	>
71	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72	>	forceField_(ff), simParams_(simParams),
73	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0),
76	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79	>	calcBoxDipole_(false), useAtomicVirial_(true) {
80	>
81		MoleculeStamp* molStamp;
82		int nMolWithSameStamp;
83		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
84	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
85		CutoffGroupStamp* cgStamp;
86		RigidBodyStamp* rbStamp;
87		int nRigidAtoms = 0;
88
89	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
90	<	molStamp = i->first;
91	<	nMolWithSameStamp = i->second;
92	<
93	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
94	<
95	<	//calculate atoms in molecules
96	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
97	<
98	<
99	<	//calculate atoms in cutoff groups
100	<	int nAtomsInGroups = 0;
101	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
102	<
103	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
104	<	cgStamp = molStamp->getCutoffGroup(j);
105	<	nAtomsInGroups += cgStamp->getNMembers();
106	<	}
107	<
108	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
109	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
110	<
111	<	//calculate atoms in rigid bodies
112	<	int nAtomsInRigidBodies = 0;
113	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
114	<
115	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
116	<	rbStamp = molStamp->getRigidBody(j);
117	<	nAtomsInRigidBodies += rbStamp->getNMembers();
118	<	}
119	<
120	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
121	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
122	<
89	>	vector<Component*> components = simParams->getComponents();
90	>
91	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
92	>	molStamp = (*i)->getMoleculeStamp();
93	>	nMolWithSameStamp = (*i)->getNMol();
94	>
95	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
96	>
97	>	//calculate atoms in molecules
98	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
99	>
100	>	//calculate atoms in cutoff groups
101	>	int nAtomsInGroups = 0;
102	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
103	>
104	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
105	>	cgStamp = molStamp->getCutoffGroupStamp(j);
106	>	nAtomsInGroups += cgStamp->getNMembers();
107	>	}
108	>
109	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
110	>
111	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
112	>
113	>	//calculate atoms in rigid bodies
114	>	int nAtomsInRigidBodies = 0;
115	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
116	>
117	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
118	>	rbStamp = molStamp->getRigidBodyStamp(j);
119	>	nAtomsInRigidBodies += rbStamp->getNMembers();
120	>	}
121	>
122	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
123	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
124	>
125		}
126	+
127	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
128	+	//group therefore the total number of cutoff groups in the system is
129	+	//equal to the total number of atoms minus number of atoms belong to
130	+	//cutoff group defined in meta-data file plus the number of cutoff
131	+	//groups defined in meta-data file
132
123	–	//every free atom (atom does not belong to cutoff groups) is a cutoff group
124	–	//therefore the total number of cutoff groups in the system is equal to
125	–	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
126	–	//file plus the number of cutoff groups defined in meta-data file
133		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
128	–
129	–	//every free atom (atom does not belong to rigid bodies) is an integrable object
130	–	//therefore the total number of  integrable objects in the system is equal to
131	–	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
132	–	//file plus the number of  rigid bodies defined in meta-data file
133	–	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
134	–
135	–	nGlobalMols_ = molStampIds_.size();
136	–
137	–	#ifdef IS_MPI
138	–	molToProcMap_.resize(nGlobalMols_);
139	–	#endif
134
135	<	}
136	<
137	<	SimInfo::~SimInfo() {
138	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
139	<
140	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
135	>	//every free atom (atom does not belong to rigid bodies) is an
136	>	//integrable object therefore the total number of integrable objects
137	>	//in the system is equal to the total number of atoms minus number of
138	>	//atoms belong to rigid body defined in meta-data file plus the number
139	>	//of rigid bodies defined in meta-data file
140	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
141	>	+ nGlobalRigidBodies_;
142
143	+	nGlobalMols_ = molStampIds_.size();
144	+	molToProcMap_.resize(nGlobalMols_);
145	+	}
146	+
147	+	SimInfo::~SimInfo() {
148	+	map<int, Molecule*>::iterator i;
149	+	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
150	+	delete i->second;
151	+	}
152	+	molecules_.clear();
153	+
154		delete sman_;
155		delete simParams_;
156		delete forceField_;
157	+	}
158
152	–	}
159
160	<	int SimInfo::getNGlobalConstraints() {
155	<	int nGlobalConstraints;
156	<	#ifdef IS_MPI
157	<	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
158	<	MPI_COMM_WORLD);
159	<	#else
160	<	nGlobalConstraints =  nConstraints_;
161	<	#endif
162	<	return nGlobalConstraints;
163	<	}
164	<
165	<	bool SimInfo::addMolecule(Molecule* mol) {
160	>	bool SimInfo::addMolecule(Molecule* mol) {
161		MoleculeIterator i;
162	<
162	>
163		i = molecules_.find(mol->getGlobalIndex());
164		if (i == molecules_.end() ) {
165	<
166	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
167	<
168	<	nAtoms_ += mol->getNAtoms();
169	<	nBonds_ += mol->getNBonds();
170	<	nBends_ += mol->getNBends();
171	<	nTorsions_ += mol->getNTorsions();
172	<	nRigidBodies_ += mol->getNRigidBodies();
173	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
174	<	nCutoffGroups_ += mol->getNCutoffGroups();
175	<	nConstraints_ += mol->getNConstraintPairs();
176	<
177	<	addExcludePairs(mol);
178	<
179	<	return true;
165	>
166	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
167	>
168	>	nAtoms_ += mol->getNAtoms();
169	>	nBonds_ += mol->getNBonds();
170	>	nBends_ += mol->getNBends();
171	>	nTorsions_ += mol->getNTorsions();
172	>	nInversions_ += mol->getNInversions();
173	>	nRigidBodies_ += mol->getNRigidBodies();
174	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
175	>	nCutoffGroups_ += mol->getNCutoffGroups();
176	>	nConstraints_ += mol->getNConstraintPairs();
177	>
178	>	addInteractionPairs(mol);
179	>
180	>	return true;
181		} else {
182	<	return false;
182	>	return false;
183		}
184	<	}
185	<
186	<	bool SimInfo::removeMolecule(Molecule* mol) {
184	>	}
185	>
186	>	bool SimInfo::removeMolecule(Molecule* mol) {
187		MoleculeIterator i;
188		i = molecules_.find(mol->getGlobalIndex());
189
190		if (i != molecules_.end() ) {
191
192	<	assert(mol == i->second);
192	>	assert(mol == i->second);
193
194	<	nAtoms_ -= mol->getNAtoms();
195	<	nBonds_ -= mol->getNBonds();
196	<	nBends_ -= mol->getNBends();
197	<	nTorsions_ -= mol->getNTorsions();
198	<	nRigidBodies_ -= mol->getNRigidBodies();
199	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
200	<	nCutoffGroups_ -= mol->getNCutoffGroups();
201	<	nConstraints_ -= mol->getNConstraintPairs();
194	>	nAtoms_ -= mol->getNAtoms();
195	>	nBonds_ -= mol->getNBonds();
196	>	nBends_ -= mol->getNBends();
197	>	nTorsions_ -= mol->getNTorsions();
198	>	nInversions_ -= mol->getNInversions();
199	>	nRigidBodies_ -= mol->getNRigidBodies();
200	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
201	>	nCutoffGroups_ -= mol->getNCutoffGroups();
202	>	nConstraints_ -= mol->getNConstraintPairs();
203
204	<	removeExcludePairs(mol);
205	<	molecules_.erase(mol->getGlobalIndex());
204	>	removeInteractionPairs(mol);
205	>	molecules_.erase(mol->getGlobalIndex());
206
207	<	delete mol;
207	>	delete mol;
208
209	<	return true;
209	>	return true;
210		} else {
211	<	return false;
211	>	return false;
212		}
213	+	}
214
217	–
218	–	}
219	–
215
216	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
216	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
217		i = molecules_.begin();
218		return i == molecules_.end() ? NULL : i->second;
219	<	}
219	>	}
220
221	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
221	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
222		++i;
223		return i == molecules_.end() ? NULL : i->second;
224	<	}
224	>	}
225
226
227	<	void SimInfo::calcNdf() {
228	<	int ndf_local;
227	>	void SimInfo::calcNdf() {
228	>	int ndf_local, nfq_local;
229		MoleculeIterator i;
230	<	std::vector<StuntDouble*>::iterator j;
230	>	vector<StuntDouble*>::iterator j;
231	>	vector<Atom*>::iterator k;
232	>
233		Molecule* mol;
234		StuntDouble* integrableObject;
235	+	Atom* atom;
236
237		ndf_local = 0;
238	+	nfq_local = 0;
239
240		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
241	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
242	<	integrableObject = mol->nextIntegrableObject(j)) {
241	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
242	>	integrableObject = mol->nextIntegrableObject(j)) {
243
244	<	ndf_local += 3;
244	>	ndf_local += 3;
245
246	<	if (integrableObject->isDirectional()) {
247	<	if (integrableObject->isLinear()) {
248	<	ndf_local += 2;
249	<	} else {
250	<	ndf_local += 3;
251	<	}
252	<	}
253	<
254	<	}//end for (integrableObject)
255	<	}// end for (mol)
246	>	if (integrableObject->isDirectional()) {
247	>	if (integrableObject->isLinear()) {
248	>	ndf_local += 2;
249	>	} else {
250	>	ndf_local += 3;
251	>	}
252	>	}
253	>	}
254	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
255	>	atom = mol->nextFluctuatingCharge(k)) {
256	>	if (atom->isFluctuatingCharge()) {
257	>	nfq_local++;
258	>	}
259	>	}
260	>	}
261
262	+	ndfLocal_ = ndf_local;
263	+
264		// n_constraints is local, so subtract them on each processor
265		ndf_local -= nConstraints_;
266
267		#ifdef IS_MPI
268		MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
269	+	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
270		#else
271		ndf_ = ndf_local;
272	+	nGlobalFluctuatingCharges_ = nfq_local;
273		#endif
274
275		// nZconstraints_ is global, as are the 3 COM translations for the
276		// entire system:
277		ndf_ = ndf_ - 3 - nZconstraint_;
278
279	<	}
279	>	}
280
281	<	void SimInfo::calcNdfRaw() {
281	>	int SimInfo::getFdf() {
282	>	#ifdef IS_MPI
283	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
284	>	#else
285	>	fdf_ = fdf_local;
286	>	#endif
287	>	return fdf_;
288	>	}
289	>
290	>	unsigned int SimInfo::getNLocalCutoffGroups(){
291	>	int nLocalCutoffAtoms = 0;
292	>	Molecule* mol;
293	>	MoleculeIterator mi;
294	>	CutoffGroup* cg;
295	>	Molecule::CutoffGroupIterator ci;
296	>
297	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
298	>
299	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
300	>	cg = mol->nextCutoffGroup(ci)) {
301	>	nLocalCutoffAtoms += cg->getNumAtom();
302	>
303	>	}
304	>	}
305	>
306	>	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
307	>	}
308	>
309	>	void SimInfo::calcNdfRaw() {
310		int ndfRaw_local;
311
312		MoleculeIterator i;
313	<	std::vector<StuntDouble*>::iterator j;
313	>	vector<StuntDouble*>::iterator j;
314		Molecule* mol;
315		StuntDouble* integrableObject;
316
#	Line 282 | Line 318 | void SimInfo::calcNdfRaw() {
318		ndfRaw_local = 0;
319
320		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
321	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
322	<	integrableObject = mol->nextIntegrableObject(j)) {
321	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
322	>	integrableObject = mol->nextIntegrableObject(j)) {
323
324	<	ndfRaw_local += 3;
324	>	ndfRaw_local += 3;
325
326	<	if (integrableObject->isDirectional()) {
327	<	if (integrableObject->isLinear()) {
328	<	ndfRaw_local += 2;
329	<	} else {
330	<	ndfRaw_local += 3;
331	<	}
332	<	}
326	>	if (integrableObject->isDirectional()) {
327	>	if (integrableObject->isLinear()) {
328	>	ndfRaw_local += 2;
329	>	} else {
330	>	ndfRaw_local += 3;
331	>	}
332	>	}
333
334	<	}
334	>	}
335		}
336
337		#ifdef IS_MPI
#	Line 303 | Line 339 | void SimInfo::calcNdfRaw() {
339		#else
340		ndfRaw_ = ndfRaw_local;
341		#endif
342	<	}
342	>	}
343
344	<	void SimInfo::calcNdfTrans() {
344	>	void SimInfo::calcNdfTrans() {
345		int ndfTrans_local;
346
347		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 319 | Line 355 | void SimInfo::calcNdfTrans() {
355
356		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
357
358	<	}
358	>	}
359
360	<	void SimInfo::addExcludePairs(Molecule* mol) {
361	<	std::vector<Bond*>::iterator bondIter;
362	<	std::vector<Bend*>::iterator bendIter;
363	<	std::vector<Torsion*>::iterator torsionIter;
360	>	void SimInfo::addInteractionPairs(Molecule* mol) {
361	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
362	>	vector<Bond*>::iterator bondIter;
363	>	vector<Bend*>::iterator bendIter;
364	>	vector<Torsion*>::iterator torsionIter;
365	>	vector<Inversion*>::iterator inversionIter;
366		Bond* bond;
367		Bend* bend;
368		Torsion* torsion;
369	+	Inversion* inversion;
370		int a;
371		int b;
372		int c;
373		int d;
335	–
336	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
337	–	a = bond->getAtomA()->getGlobalIndex();
338	–	b = bond->getAtomB()->getGlobalIndex();
339	–	exclude_.addPair(a, b);
340	–	}
374
375	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
376	<	a = bend->getAtomA()->getGlobalIndex();
377	<	b = bend->getAtomB()->getGlobalIndex();
378	<	c = bend->getAtomC()->getGlobalIndex();
375	>	// atomGroups can be used to add special interaction maps between
376	>	// groups of atoms that are in two separate rigid bodies.
377	>	// However, most site-site interactions between two rigid bodies
378	>	// are probably not special, just the ones between the physically
379	>	// bonded atoms.  Interactions *within* a single rigid body should
380	>	// always be excluded.  These are done at the bottom of this
381	>	// function.
382
383	<	exclude_.addPair(a, b);
384	<	exclude_.addPair(a, c);
385	<	exclude_.addPair(b, c);
386	<	}
387	<
388	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
389	<	a = torsion->getAtomA()->getGlobalIndex();
390	<	b = torsion->getAtomB()->getGlobalIndex();
391	<	c = torsion->getAtomC()->getGlobalIndex();
392	<	d = torsion->getAtomD()->getGlobalIndex();
383	>	map<int, set<int> > atomGroups;
384	>	Molecule::RigidBodyIterator rbIter;
385	>	RigidBody* rb;
386	>	Molecule::IntegrableObjectIterator ii;
387	>	StuntDouble* integrableObject;
388	>
389	>	for (integrableObject = mol->beginIntegrableObject(ii);
390	>	integrableObject != NULL;
391	>	integrableObject = mol->nextIntegrableObject(ii)) {
392	>
393	>	if (integrableObject->isRigidBody()) {
394	>	rb = static_cast<RigidBody*>(integrableObject);
395	>	vector<Atom*> atoms = rb->getAtoms();
396	>	set<int> rigidAtoms;
397	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
398	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
399	>	}
400	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
401	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
402	>	}
403	>	} else {
404	>	set<int> oneAtomSet;
405	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
406	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
407	>	}
408	>	}
409	>
410	>	for (bond= mol->beginBond(bondIter); bond != NULL;
411	>	bond = mol->nextBond(bondIter)) {
412
413	<	exclude_.addPair(a, b);
414	<	exclude_.addPair(a, c);
415	<	exclude_.addPair(a, d);
416	<	exclude_.addPair(b, c);
417	<	exclude_.addPair(b, d);
418	<	exclude_.addPair(c, d);
413	>	a = bond->getAtomA()->getGlobalIndex();
414	>	b = bond->getAtomB()->getGlobalIndex();
415	>
416	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
417	>	oneTwoInteractions_.addPair(a, b);
418	>	} else {
419	>	excludedInteractions_.addPair(a, b);
420	>	}
421		}
422
423	<
424	<	}
423	>	for (bend= mol->beginBend(bendIter); bend != NULL;
424	>	bend = mol->nextBend(bendIter)) {
425
426	<	void SimInfo::removeExcludePairs(Molecule* mol) {
427	<	std::vector<Bond*>::iterator bondIter;
428	<	std::vector<Bend*>::iterator bendIter;
429	<	std::vector<Torsion*>::iterator torsionIter;
426	>	a = bend->getAtomA()->getGlobalIndex();
427	>	b = bend->getAtomB()->getGlobalIndex();
428	>	c = bend->getAtomC()->getGlobalIndex();
429	>
430	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
431	>	oneTwoInteractions_.addPair(a, b);
432	>	oneTwoInteractions_.addPair(b, c);
433	>	} else {
434	>	excludedInteractions_.addPair(a, b);
435	>	excludedInteractions_.addPair(b, c);
436	>	}
437	>
438	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
439	>	oneThreeInteractions_.addPair(a, c);
440	>	} else {
441	>	excludedInteractions_.addPair(a, c);
442	>	}
443	>	}
444	>
445	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
446	>	torsion = mol->nextTorsion(torsionIter)) {
447	>
448	>	a = torsion->getAtomA()->getGlobalIndex();
449	>	b = torsion->getAtomB()->getGlobalIndex();
450	>	c = torsion->getAtomC()->getGlobalIndex();
451	>	d = torsion->getAtomD()->getGlobalIndex();
452	>
453	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
454	>	oneTwoInteractions_.addPair(a, b);
455	>	oneTwoInteractions_.addPair(b, c);
456	>	oneTwoInteractions_.addPair(c, d);
457	>	} else {
458	>	excludedInteractions_.addPair(a, b);
459	>	excludedInteractions_.addPair(b, c);
460	>	excludedInteractions_.addPair(c, d);
461	>	}
462	>
463	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
464	>	oneThreeInteractions_.addPair(a, c);
465	>	oneThreeInteractions_.addPair(b, d);
466	>	} else {
467	>	excludedInteractions_.addPair(a, c);
468	>	excludedInteractions_.addPair(b, d);
469	>	}
470	>
471	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
472	>	oneFourInteractions_.addPair(a, d);
473	>	} else {
474	>	excludedInteractions_.addPair(a, d);
475	>	}
476	>	}
477	>
478	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
479	>	inversion = mol->nextInversion(inversionIter)) {
480	>
481	>	a = inversion->getAtomA()->getGlobalIndex();
482	>	b = inversion->getAtomB()->getGlobalIndex();
483	>	c = inversion->getAtomC()->getGlobalIndex();
484	>	d = inversion->getAtomD()->getGlobalIndex();
485	>
486	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
487	>	oneTwoInteractions_.addPair(a, b);
488	>	oneTwoInteractions_.addPair(a, c);
489	>	oneTwoInteractions_.addPair(a, d);
490	>	} else {
491	>	excludedInteractions_.addPair(a, b);
492	>	excludedInteractions_.addPair(a, c);
493	>	excludedInteractions_.addPair(a, d);
494	>	}
495	>
496	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
497	>	oneThreeInteractions_.addPair(b, c);
498	>	oneThreeInteractions_.addPair(b, d);
499	>	oneThreeInteractions_.addPair(c, d);
500	>	} else {
501	>	excludedInteractions_.addPair(b, c);
502	>	excludedInteractions_.addPair(b, d);
503	>	excludedInteractions_.addPair(c, d);
504	>	}
505	>	}
506	>
507	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
508	>	rb = mol->nextRigidBody(rbIter)) {
509	>	vector<Atom*> atoms = rb->getAtoms();
510	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
511	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
512	>	a = atoms[i]->getGlobalIndex();
513	>	b = atoms[j]->getGlobalIndex();
514	>	excludedInteractions_.addPair(a, b);
515	>	}
516	>	}
517	>	}
518	>
519	>	}
520	>
521	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
522	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
523	>	vector<Bond*>::iterator bondIter;
524	>	vector<Bend*>::iterator bendIter;
525	>	vector<Torsion*>::iterator torsionIter;
526	>	vector<Inversion*>::iterator inversionIter;
527		Bond* bond;
528		Bend* bend;
529		Torsion* torsion;
530	+	Inversion* inversion;
531		int a;
532		int b;
533		int c;
534		int d;
535	+
536	+	map<int, set<int> > atomGroups;
537	+	Molecule::RigidBodyIterator rbIter;
538	+	RigidBody* rb;
539	+	Molecule::IntegrableObjectIterator ii;
540	+	StuntDouble* integrableObject;
541
542	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
543	<	a = bond->getAtomA()->getGlobalIndex();
544	<	b = bond->getAtomB()->getGlobalIndex();
545	<	exclude_.removePair(a, b);
542	>	for (integrableObject = mol->beginIntegrableObject(ii);
543	>	integrableObject != NULL;
544	>	integrableObject = mol->nextIntegrableObject(ii)) {
545	>
546	>	if (integrableObject->isRigidBody()) {
547	>	rb = static_cast<RigidBody*>(integrableObject);
548	>	vector<Atom*> atoms = rb->getAtoms();
549	>	set<int> rigidAtoms;
550	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
551	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
552	>	}
553	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
554	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
555	>	}
556	>	} else {
557	>	set<int> oneAtomSet;
558	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
559	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
560	>	}
561	>	}
562	>
563	>	for (bond= mol->beginBond(bondIter); bond != NULL;
564	>	bond = mol->nextBond(bondIter)) {
565	>
566	>	a = bond->getAtomA()->getGlobalIndex();
567	>	b = bond->getAtomB()->getGlobalIndex();
568	>
569	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
570	>	oneTwoInteractions_.removePair(a, b);
571	>	} else {
572	>	excludedInteractions_.removePair(a, b);
573	>	}
574		}
575
576	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
577	<	a = bend->getAtomA()->getGlobalIndex();
389	<	b = bend->getAtomB()->getGlobalIndex();
390	<	c = bend->getAtomC()->getGlobalIndex();
576	>	for (bend= mol->beginBend(bendIter); bend != NULL;
577	>	bend = mol->nextBend(bendIter)) {
578
579	<	exclude_.removePair(a, b);
580	<	exclude_.removePair(a, c);
581	<	exclude_.removePair(b, c);
579	>	a = bend->getAtomA()->getGlobalIndex();
580	>	b = bend->getAtomB()->getGlobalIndex();
581	>	c = bend->getAtomC()->getGlobalIndex();
582	>
583	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
584	>	oneTwoInteractions_.removePair(a, b);
585	>	oneTwoInteractions_.removePair(b, c);
586	>	} else {
587	>	excludedInteractions_.removePair(a, b);
588	>	excludedInteractions_.removePair(b, c);
589	>	}
590	>
591	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
592	>	oneThreeInteractions_.removePair(a, c);
593	>	} else {
594	>	excludedInteractions_.removePair(a, c);
595	>	}
596		}
597
598	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
599	<	a = torsion->getAtomA()->getGlobalIndex();
399	<	b = torsion->getAtomB()->getGlobalIndex();
400	<	c = torsion->getAtomC()->getGlobalIndex();
401	<	d = torsion->getAtomD()->getGlobalIndex();
598	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
599	>	torsion = mol->nextTorsion(torsionIter)) {
600
601	<	exclude_.removePair(a, b);
602	<	exclude_.removePair(a, c);
603	<	exclude_.removePair(a, d);
604	<	exclude_.removePair(b, c);
605	<	exclude_.removePair(b, d);
606	<	exclude_.removePair(c, d);
601	>	a = torsion->getAtomA()->getGlobalIndex();
602	>	b = torsion->getAtomB()->getGlobalIndex();
603	>	c = torsion->getAtomC()->getGlobalIndex();
604	>	d = torsion->getAtomD()->getGlobalIndex();
605	>
606	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
607	>	oneTwoInteractions_.removePair(a, b);
608	>	oneTwoInteractions_.removePair(b, c);
609	>	oneTwoInteractions_.removePair(c, d);
610	>	} else {
611	>	excludedInteractions_.removePair(a, b);
612	>	excludedInteractions_.removePair(b, c);
613	>	excludedInteractions_.removePair(c, d);
614	>	}
615	>
616	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
617	>	oneThreeInteractions_.removePair(a, c);
618	>	oneThreeInteractions_.removePair(b, d);
619	>	} else {
620	>	excludedInteractions_.removePair(a, c);
621	>	excludedInteractions_.removePair(b, d);
622	>	}
623	>
624	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
625	>	oneFourInteractions_.removePair(a, d);
626	>	} else {
627	>	excludedInteractions_.removePair(a, d);
628	>	}
629		}
630
631	<	}
631	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
632	>	inversion = mol->nextInversion(inversionIter)) {
633
634	+	a = inversion->getAtomA()->getGlobalIndex();
635	+	b = inversion->getAtomB()->getGlobalIndex();
636	+	c = inversion->getAtomC()->getGlobalIndex();
637	+	d = inversion->getAtomD()->getGlobalIndex();
638
639	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
640	<	int curStampId;
639	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
640	>	oneTwoInteractions_.removePair(a, b);
641	>	oneTwoInteractions_.removePair(a, c);
642	>	oneTwoInteractions_.removePair(a, d);
643	>	} else {
644	>	excludedInteractions_.removePair(a, b);
645	>	excludedInteractions_.removePair(a, c);
646	>	excludedInteractions_.removePair(a, d);
647	>	}
648
649	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
650	+	oneThreeInteractions_.removePair(b, c);
651	+	oneThreeInteractions_.removePair(b, d);
652	+	oneThreeInteractions_.removePair(c, d);
653	+	} else {
654	+	excludedInteractions_.removePair(b, c);
655	+	excludedInteractions_.removePair(b, d);
656	+	excludedInteractions_.removePair(c, d);
657	+	}
658	+	}
659	+
660	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
661	+	rb = mol->nextRigidBody(rbIter)) {
662	+	vector<Atom*> atoms = rb->getAtoms();
663	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
664	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
665	+	a = atoms[i]->getGlobalIndex();
666	+	b = atoms[j]->getGlobalIndex();
667	+	excludedInteractions_.removePair(a, b);
668	+	}
669	+	}
670	+	}
671	+
672	+	}
673	+
674	+
675	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
676	+	int curStampId;
677	+
678		//index from 0
679		curStampId = moleculeStamps_.size();
680
681		moleculeStamps_.push_back(molStamp);
682		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
683	<	}
683	>	}
684
424	–	void SimInfo::update() {
685
686	<	setupSimType();
687	<
688	<	#ifdef IS_MPI
689	<	setupFortranParallel();
690	<	#endif
691	<
692	<	setupFortranSim();
693	<
694	<	//setup fortran force field
435	<	/** @deprecate */
436	<	int isError = 0;
437	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
438	<	if(isError){
439	<	sprintf( painCave.errMsg,
440	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
441	<	painCave.isFatal = 1;
442	<	simError();
443	<	}
444	<
445	<
446	<	setupCutoff();
447	<
686	>	/**
687	>	* update
688	>	*
689	>	*  Performs the global checks and variable settings after the
690	>	*  objects have been created.
691	>	*
692	>	*/
693	>	void SimInfo::update() {
694	>	setupSimVariables();
695		calcNdf();
696		calcNdfRaw();
697		calcNdfTrans();
698	<
699	<	fortranInitialized_ = true;
700	<	}
701	<
702	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
698	>	}
699	>
700	>	/**
701	>	* getSimulatedAtomTypes
702	>	*
703	>	* Returns an STL set of AtomType* that are actually present in this
704	>	* simulation.  Must query all processors to assemble this information.
705	>	*
706	>	*/
707	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
708		SimInfo::MoleculeIterator mi;
709		Molecule* mol;
710		Molecule::AtomIterator ai;
711		Atom* atom;
712	<	std::set<AtomType*> atomTypes;
713	<
712	>	set<AtomType*> atomTypes;
713	>
714		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
715	+	for(atom = mol->beginAtom(ai); atom != NULL;
716	+	atom = mol->nextAtom(ai)) {
717	+	atomTypes.insert(atom->getAtomType());
718	+	}
719	+	}
720	+
721	+	#ifdef IS_MPI
722
723	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
724	<	atomTypes.insert(atom->getAtomType());
725	<	}
726	<
727	<	}
723	>	// loop over the found atom types on this processor, and add their
724	>	// numerical idents to a vector:
725	>
726	>	vector<int> foundTypes;
727	>	set<AtomType*>::iterator i;
728	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
729	>	foundTypes.push_back( (*i)->getIdent() );
730
731	<	return atomTypes;
732	<	}
731	>	// count_local holds the number of found types on this processor
732	>	int count_local = foundTypes.size();
733
734	<	void SimInfo::setupSimType() {
735	<	std::set<AtomType*>::iterator i;
736	<	std::set<AtomType*> atomTypes;
737	<	atomTypes = getUniqueAtomTypes();
738	<
739	<	int useLennardJones = 0;
479	<	int useElectrostatic = 0;
480	<	int useEAM = 0;
481	<	int useCharge = 0;
482	<	int useDirectional = 0;
483	<	int useDipole = 0;
484	<	int useGayBerne = 0;
485	<	int useSticky = 0;
486	<	int useShape = 0;
487	<	int useFLARB = 0; //it is not in AtomType yet
488	<	int useDirectionalAtom = 0;
489	<	int useElectrostatics = 0;
490	<	//usePBC and useRF are from simParams
491	<	int usePBC = simParams_->getPBC();
492	<	int useRF = simParams_->getUseRF();
734	>	int nproc = MPI::COMM_WORLD.Get_size();
735	>
736	>	// we need arrays to hold the counts and displacement vectors for
737	>	// all processors
738	>	vector<int> counts(nproc, 0);
739	>	vector<int> disps(nproc, 0);
740
741	<	//loop over all of the atom types
742	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
743	<	useLennardJones |= (*i)->isLennardJones();
744	<	useElectrostatic |= (*i)->isElectrostatic();
745	<	useEAM |= (*i)->isEAM();
746	<	useCharge |= (*i)->isCharge();
747	<	useDirectional |= (*i)->isDirectional();
748	<	useDipole |= (*i)->isDipole();
749	<	useGayBerne |= (*i)->isGayBerne();
750	<	useSticky |= (*i)->isSticky();
504	<	useShape |= (*i)->isShape();
741	>	// fill the counts array
742	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
743	>	1, MPI::INT);
744	>
745	>	// use the processor counts to compute the displacement array
746	>	disps[0] = 0;
747	>	int totalCount = counts[0];
748	>	for (int iproc = 1; iproc < nproc; iproc++) {
749	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
750	>	totalCount += counts[iproc];
751		}
752
753	<	if (useSticky || useDipole || useGayBerne || useShape) {
754	<	useDirectionalAtom = 1;
755	<	}
753	>	// we need a (possibly redundant) set of all found types:
754	>	vector<int> ftGlobal(totalCount);
755	>
756	>	// now spray out the foundTypes to all the other processors:
757	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
758	>	&ftGlobal[0], &counts[0], &disps[0],
759	>	MPI::INT);
760
761	<	if (useCharge || useDipole) {
512	<	useElectrostatics = 1;
513	<	}
761	>	vector<int>::iterator j;
762
763	<	#ifdef IS_MPI
764	<	int temp;
763	>	// foundIdents is a stl set, so inserting an already found ident
764	>	// will have no effect.
765	>	set<int> foundIdents;
766
767	<	temp = usePBC;
768	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
768	>	foundIdents.insert((*j));
769	>
770	>	// now iterate over the foundIdents and get the actual atom types
771	>	// that correspond to these:
772	>	set<int>::iterator it;
773	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
774	>	atomTypes.insert( forceField_->getAtomType((*it)) );
775	>
776	>	#endif
777
778	<	temp = useDirectionalAtom;
779	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
778	>	return atomTypes;
779	>	}
780
781	<	temp = useLennardJones;
782	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
781	>	void SimInfo::setupSimVariables() {
782	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
783	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
784	>	calcBoxDipole_ = false;
785	>	if ( simParams_->haveAccumulateBoxDipole() )
786	>	if ( simParams_->getAccumulateBoxDipole() ) {
787	>	calcBoxDipole_ = true;
788	>	}
789	>
790	>	set<AtomType*>::iterator i;
791	>	set<AtomType*> atomTypes;
792	>	atomTypes = getSimulatedAtomTypes();
793	>	int usesElectrostatic = 0;
794	>	int usesMetallic = 0;
795	>	int usesDirectional = 0;
796	>	int usesFluctuatingCharges =  0;
797	>	//loop over all of the atom types
798	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
799	>	usesElectrostatic |= (*i)->isElectrostatic();
800	>	usesMetallic |= (*i)->isMetal();
801	>	usesDirectional |= (*i)->isDirectional();
802	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
803	>	}
804	>
805	>	#ifdef IS_MPI
806	>	int temp;
807	>	temp = usesDirectional;
808	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
809	>
810	>	temp = usesMetallic;
811	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
812	>
813	>	temp = usesElectrostatic;
814	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
815
816	<	temp = useElectrostatics;
817	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816	>	temp = usesFluctuatingCharges;
817	>	MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
818	>	#else
819
820	<	temp = useCharge;
821	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
820	>	usesDirectionalAtoms_ = usesDirectional;
821	>	usesMetallicAtoms_ = usesMetallic;
822	>	usesElectrostaticAtoms_ = usesElectrostatic;
823	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
824
825	<	temp = useDipole;
826	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
825	>	#endif
826	>
827	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
828	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
829	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
830	>	}
831
536	–	temp = useSticky;
537	–	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
832
833	<	temp = useGayBerne;
834	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
833	>	vector<int> SimInfo::getGlobalAtomIndices() {
834	>	SimInfo::MoleculeIterator mi;
835	>	Molecule* mol;
836	>	Molecule::AtomIterator ai;
837	>	Atom* atom;
838
839	<	temp = useEAM;
543	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
544	<
545	<	temp = useShape;
546	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
547	<
548	<	temp = useFLARB;
549	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
550	<
551	<	temp = useRF;
552	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
839	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
840
841	<	#endif
841	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
842	>
843	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
844	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
845	>	}
846	>	}
847	>	return GlobalAtomIndices;
848	>	}
849
556	–	fInfo_.SIM_uses_PBC = usePBC;
557	–	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
558	–	fInfo_.SIM_uses_LennardJones = useLennardJones;
559	–	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
560	–	fInfo_.SIM_uses_Charges = useCharge;
561	–	fInfo_.SIM_uses_Dipoles = useDipole;
562	–	fInfo_.SIM_uses_Sticky = useSticky;
563	–	fInfo_.SIM_uses_GayBerne = useGayBerne;
564	–	fInfo_.SIM_uses_EAM = useEAM;
565	–	fInfo_.SIM_uses_Shapes = useShape;
566	–	fInfo_.SIM_uses_FLARB = useFLARB;
567	–	fInfo_.SIM_uses_RF = useRF;
850
851	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
851	>	vector<int> SimInfo::getGlobalGroupIndices() {
852	>	SimInfo::MoleculeIterator mi;
853	>	Molecule* mol;
854	>	Molecule::CutoffGroupIterator ci;
855	>	CutoffGroup* cg;
856
857	<	if (simParams_->haveDielectric()) {
858	<	fInfo_.dielect = simParams_->getDielectric();
859	<	} else {
860	<	sprintf(painCave.errMsg,
861	<	"SimSetup Error: No Dielectric constant was set.\n"
862	<	"\tYou are trying to use Reaction Field without"
863	<	"\tsetting a dielectric constant!\n");
864	<	painCave.isFatal = 1;
865	<	simError();
866	<	}
581	<
582	<	} else {
583	<	fInfo_.dielect = 0.0;
857	>	vector<int> GlobalGroupIndices;
858	>
859	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
860	>
861	>	//local index of cutoff group is trivial, it only depends on the
862	>	//order of travesing
863	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
864	>	cg = mol->nextCutoffGroup(ci)) {
865	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
866	>	}
867		}
868	+	return GlobalGroupIndices;
869	+	}
870
586	–	}
871
872	<	void SimInfo::setupFortranSim() {
873	<	int isError;
590	<	int nExclude;
591	<	std::vector<int> fortranGlobalGroupMembership;
592	<
593	<	nExclude = exclude_.getSize();
594	<	isError = 0;
872	>	void SimInfo::prepareTopology() {
873	>	int nExclude, nOneTwo, nOneThree, nOneFour;
874
596	–	//globalGroupMembership_ is filled by SimCreator
597	–	for (int i = 0; i < nGlobalAtoms_; i++) {
598	–	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
599	–	}
600	–
875		//calculate mass ratio of cutoff group
602	–	std::vector<double> mfact;
876		SimInfo::MoleculeIterator mi;
877		Molecule* mol;
878		Molecule::CutoffGroupIterator ci;
879		CutoffGroup* cg;
880		Molecule::AtomIterator ai;
881		Atom* atom;
882	<	double totalMass;
882	>	RealType totalMass;
883
884	<	//to avoid memory reallocation, reserve enough space for mfact
885	<	mfact.reserve(getNCutoffGroups());
884	>	/**
885	>	* The mass factor is the relative mass of an atom to the total
886	>	* mass of the cutoff group it belongs to.  By default, all atoms
887	>	* are their own cutoff groups, and therefore have mass factors of
888	>	* 1.  We need some special handling for massless atoms, which
889	>	* will be treated as carrying the entire mass of the cutoff
890	>	* group.
891	>	*/
892	>	massFactors_.clear();
893	>	massFactors_.resize(getNAtoms(), 1.0);
894
895		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
896	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
896	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
897	>	cg = mol->nextCutoffGroup(ci)) {
898
899	<	totalMass = cg->getMass();
900	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
901	<	mfact.push_back(atom->getMass()/totalMass);
902	<	}
903	<
904	<	}
899	>	totalMass = cg->getMass();
900	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
901	>	// Check for massless groups - set mfact to 1 if true
902	>	if (totalMass != 0)
903	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
904	>	else
905	>	massFactors_[atom->getLocalIndex()] = 1.0;
906	>	}
907	>	}
908		}
909
910	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
626	<	std::vector<int> identArray;
910	>	// Build the identArray_
911
912	<	//to avoid memory reallocation, reserve enough space identArray
913	<	identArray.reserve(getNAtoms());
630	<
912	>	identArray_.clear();
913	>	identArray_.reserve(getNAtoms());
914		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
915	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
916	<	identArray.push_back(atom->getIdent());
917	<	}
915	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
916	>	identArray_.push_back(atom->getIdent());
917	>	}
918		}
636	–
637	–	//fill molMembershipArray
638	–	//molMembershipArray is filled by SimCreator
639	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
640	–	for (int i = 0; i < nGlobalAtoms_; i++) {
641	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
642	–	}
919
920	<	//setup fortran simulation
645	<	//gloalExcludes and molMembershipArray should go away (They are never used)
646	<	//why the hell fortran need to know molecule?
647	<	//OOPSE = Object-Obfuscated Parallel Simulation Engine
648	<	int nGlobalExcludes = 0;
649	<	int* globalExcludes = NULL;
650	<	int* excludeList = exclude_.getExcludeList();
651	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
652	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
653	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
920	>	//scan topology
921
922	<	if( isError ){
922	>	nExclude = excludedInteractions_.getSize();
923	>	nOneTwo = oneTwoInteractions_.getSize();
924	>	nOneThree = oneThreeInteractions_.getSize();
925	>	nOneFour = oneFourInteractions_.getSize();
926
927	<	sprintf( painCave.errMsg,
928	<	"There was an error setting the simulation information in fortran.\n" );
929	<	painCave.isFatal = 1;
930	<	painCave.severity = OOPSE_ERROR;
661	<	simError();
662	<	}
927	>	int* excludeList = excludedInteractions_.getPairList();
928	>	int* oneTwoList = oneTwoInteractions_.getPairList();
929	>	int* oneThreeList = oneThreeInteractions_.getPairList();
930	>	int* oneFourList = oneFourInteractions_.getPairList();
931
932	<	#ifdef IS_MPI
933	<	sprintf( checkPointMsg,
666	<	"succesfully sent the simulation information to fortran.\n");
667	<	MPIcheckPoint();
668	<	#endif // is_mpi
669	<	}
932	>	topologyDone_ = true;
933	>	}
934
935	+	void SimInfo::addProperty(GenericData* genData) {
936	+	properties_.addProperty(genData);
937	+	}
938
939	<	#ifdef IS_MPI
940	<	void SimInfo::setupFortranParallel() {
941	<
675	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
676	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
677	<	std::vector<int> localToGlobalCutoffGroupIndex;
678	<	SimInfo::MoleculeIterator mi;
679	<	Molecule::AtomIterator ai;
680	<	Molecule::CutoffGroupIterator ci;
681	<	Molecule* mol;
682	<	Atom* atom;
683	<	CutoffGroup* cg;
684	<	mpiSimData parallelData;
685	<	int isError;
939	>	void SimInfo::removeProperty(const string& propName) {
940	>	properties_.removeProperty(propName);
941	>	}
942
943	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
943	>	void SimInfo::clearProperties() {
944	>	properties_.clearProperties();
945	>	}
946
947	<	//local index(index in DataStorge) of atom is important
948	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
949	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
950	<	}
947	>	vector<string> SimInfo::getPropertyNames() {
948	>	return properties_.getPropertyNames();
949	>	}
950	>
951	>	vector<GenericData*> SimInfo::getProperties() {
952	>	return properties_.getProperties();
953	>	}
954
955	<	//local index of cutoff group is trivial, it only depends on the order of travesing
695	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
696	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
697	<	}
698	<
699	<	}
700	<
701	<	//fill up mpiSimData struct
702	<	parallelData.nMolGlobal = getNGlobalMolecules();
703	<	parallelData.nMolLocal = getNMolecules();
704	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
705	<	parallelData.nAtomsLocal = getNAtoms();
706	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
707	<	parallelData.nGroupsLocal = getNCutoffGroups();
708	<	parallelData.myNode = worldRank;
709	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
710	<
711	<	//pass mpiSimData struct and index arrays to fortran
712	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
713	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
714	<	&localToGlobalCutoffGroupIndex[0], &isError);
715	<
716	<	if (isError) {
717	<	sprintf(painCave.errMsg,
718	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
719	<	painCave.isFatal = 1;
720	<	simError();
721	<	}
722	<
723	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
724	<	MPIcheckPoint();
725	<
726	<
727	<	}
728	<
729	<	#endif
730	<
731	<	double SimInfo::calcMaxCutoffRadius() {
732	<
733	<
734	<	std::set<AtomType*> atomTypes;
735	<	std::set<AtomType*>::iterator i;
736	<	std::vector<double> cutoffRadius;
737	<
738	<	//get the unique atom types
739	<	atomTypes = getUniqueAtomTypes();
740	<
741	<	//query the max cutoff radius among these atom types
742	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
743	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
744	<	}
745	<
746	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
747	<	#ifdef IS_MPI
748	<	//pick the max cutoff radius among the processors
749	<	#endif
750	<
751	<	return maxCutoffRadius;
752	<	}
753	<
754	<	void SimInfo::setupCutoff() {
755	<	double rcut_;  //cutoff radius
756	<	double rsw_; //switching radius
757	<
758	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
759	<
760	<	if (!simParams_->haveRcut()){
761	<	sprintf(painCave.errMsg,
762	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
763	<	"\tOOPSE will use a default value of 15.0 angstroms"
764	<	"\tfor the cutoffRadius.\n");
765	<	painCave.isFatal = 0;
766	<	simError();
767	<	rcut_ = 15.0;
768	<	} else{
769	<	rcut_ = simParams_->getRcut();
770	<	}
771	<
772	<	if (!simParams_->haveRsw()){
773	<	sprintf(painCave.errMsg,
774	<	"SimCreator Warning: No value was set for switchingRadius.\n"
775	<	"\tOOPSE will use a default value of\n"
776	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
777	<	painCave.isFatal = 0;
778	<	simError();
779	<	rsw_ = 0.95 * rcut_;
780	<	} else{
781	<	rsw_ = simParams_->getRsw();
782	<	}
783	<
784	<	} else {
785	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
786	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
787	<
788	<	if (simParams_->haveRcut()) {
789	<	rcut_ = simParams_->getRcut();
790	<	} else {
791	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
792	<	rcut_ = calcMaxCutoffRadius();
793	<	}
794	<
795	<	if (simParams_->haveRsw()) {
796	<	rsw_  = simParams_->getRsw();
797	<	} else {
798	<	rsw_ = rcut_;
799	<	}
800	<
801	<	}
802	<
803	<	double rnblist = rcut_ + 1; // skin of neighbor list
804	<
805	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
806	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
807	<	}
808	<
809	<	void SimInfo::addProperty(GenericData* genData) {
810	<	properties_.addProperty(genData);
811	<	}
812	<
813	<	void SimInfo::removeProperty(const std::string& propName) {
814	<	properties_.removeProperty(propName);
815	<	}
816	<
817	<	void SimInfo::clearProperties() {
818	<	properties_.clearProperties();
819	<	}
820	<
821	<	std::vector<std::string> SimInfo::getPropertyNames() {
822	<	return properties_.getPropertyNames();
823	<	}
824	<
825	<	std::vector<GenericData*> SimInfo::getProperties() {
826	<	return properties_.getProperties();
827	<	}
828	<
829	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
955	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
956		return properties_.getPropertyByName(propName);
957	<	}
957	>	}
958
959	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
959	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
960	>	if (sman_ == sman) {
961	>	return;
962	>	}
963	>	delete sman_;
964		sman_ = sman;
965
966		Molecule* mol;
967		RigidBody* rb;
968		Atom* atom;
969	+	CutoffGroup* cg;
970		SimInfo::MoleculeIterator mi;
971		Molecule::RigidBodyIterator rbIter;
972	<	Molecule::AtomIterator atomIter;;
972	>	Molecule::AtomIterator atomIter;
973	>	Molecule::CutoffGroupIterator cgIter;
974
975		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
976
977	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
978	<	atom->setSnapshotManager(sman_);
979	<	}
977	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
978	>	atom->setSnapshotManager(sman_);
979	>	}
980
981	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
982	<	rb->setSnapshotManager(sman_);
983	<	}
981	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
982	>	rb->setSnapshotManager(sman_);
983	>	}
984	>
985	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
986	>	cg->setSnapshotManager(sman_);
987	>	}
988		}
989
990	<	}
990	>	}
991
992	<	Vector3d SimInfo::getComVel(){
992	>	Vector3d SimInfo::getComVel(){
993		SimInfo::MoleculeIterator i;
994		Molecule* mol;
995
996		Vector3d comVel(0.0);
997	<	double totalMass = 0.0;
997	>	RealType totalMass = 0.0;
998
999
1000		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1001	<	double mass = mol->getMass();
1002	<	totalMass += mass;
1003	<	comVel += mass * mol->getComVel();
1001	>	RealType mass = mol->getMass();
1002	>	totalMass += mass;
1003	>	comVel += mass * mol->getComVel();
1004		}
1005
1006		#ifdef IS_MPI
1007	<	double tmpMass = totalMass;
1007	>	RealType tmpMass = totalMass;
1008		Vector3d tmpComVel(comVel);
1009	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1010	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1009	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1010	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1011		#endif
1012
1013		comVel /= totalMass;
1014
1015		return comVel;
1016	<	}
1016	>	}
1017
1018	<	Vector3d SimInfo::getCom(){
1018	>	Vector3d SimInfo::getCom(){
1019		SimInfo::MoleculeIterator i;
1020		Molecule* mol;
1021
1022		Vector3d com(0.0);
1023	<	double totalMass = 0.0;
1023	>	RealType totalMass = 0.0;
1024
1025		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1026	<	double mass = mol->getMass();
1027	<	totalMass += mass;
1028	<	com += mass * mol->getCom();
1026	>	RealType mass = mol->getMass();
1027	>	totalMass += mass;
1028	>	com += mass * mol->getCom();
1029		}
1030
1031		#ifdef IS_MPI
1032	<	double tmpMass = totalMass;
1032	>	RealType tmpMass = totalMass;
1033		Vector3d tmpCom(com);
1034	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1035	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1034	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1035	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1036		#endif
1037
1038		com /= totalMass;
1039
1040		return com;
1041
1042	<	}
1042	>	}
1043
1044	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1044	>	ostream& operator <<(ostream& o, SimInfo& info) {
1045
1046		return o;
1047	<	}
1047	>	}
1048	>
1049	>
1050	>	/*
1051	>	Returns center of mass and center of mass velocity in one function call.
1052	>	*/
1053	>
1054	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1055	>	SimInfo::MoleculeIterator i;
1056	>	Molecule* mol;
1057	>
1058	>
1059	>	RealType totalMass = 0.0;
1060	>
1061
1062	<	}//end namespace oopse
1062	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1063	>	RealType mass = mol->getMass();
1064	>	totalMass += mass;
1065	>	com += mass * mol->getCom();
1066	>	comVel += mass * mol->getComVel();
1067	>	}
1068	>
1069	>	#ifdef IS_MPI
1070	>	RealType tmpMass = totalMass;
1071	>	Vector3d tmpCom(com);
1072	>	Vector3d tmpComVel(comVel);
1073	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1074	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1075	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1076	>	#endif
1077	>
1078	>	com /= totalMass;
1079	>	comVel /= totalMass;
1080	>	}
1081	>
1082	>	/*
1083	>	Return intertia tensor for entire system and angular momentum Vector.
1084
1085	+
1086	+	[  Ixx -Ixy  -Ixz ]
1087	+	J =| -Iyx  Iyy  -Iyz |
1088	+	[ -Izx -Iyz   Izz ]
1089	+	*/
1090	+
1091	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1092	+
1093	+
1094	+	RealType xx = 0.0;
1095	+	RealType yy = 0.0;
1096	+	RealType zz = 0.0;
1097	+	RealType xy = 0.0;
1098	+	RealType xz = 0.0;
1099	+	RealType yz = 0.0;
1100	+	Vector3d com(0.0);
1101	+	Vector3d comVel(0.0);
1102	+
1103	+	getComAll(com, comVel);
1104	+
1105	+	SimInfo::MoleculeIterator i;
1106	+	Molecule* mol;
1107	+
1108	+	Vector3d thisq(0.0);
1109	+	Vector3d thisv(0.0);
1110	+
1111	+	RealType thisMass = 0.0;
1112	+
1113	+
1114	+
1115	+
1116	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1117	+
1118	+	thisq = mol->getCom()-com;
1119	+	thisv = mol->getComVel()-comVel;
1120	+	thisMass = mol->getMass();
1121	+	// Compute moment of intertia coefficients.
1122	+	xx += thisq[0]*thisq[0]*thisMass;
1123	+	yy += thisq[1]*thisq[1]*thisMass;
1124	+	zz += thisq[2]*thisq[2]*thisMass;
1125	+
1126	+	// compute products of intertia
1127	+	xy += thisq[0]*thisq[1]*thisMass;
1128	+	xz += thisq[0]*thisq[2]*thisMass;
1129	+	yz += thisq[1]*thisq[2]*thisMass;
1130	+
1131	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1132	+
1133	+	}
1134	+
1135	+
1136	+	inertiaTensor(0,0) = yy + zz;
1137	+	inertiaTensor(0,1) = -xy;
1138	+	inertiaTensor(0,2) = -xz;
1139	+	inertiaTensor(1,0) = -xy;
1140	+	inertiaTensor(1,1) = xx + zz;
1141	+	inertiaTensor(1,2) = -yz;
1142	+	inertiaTensor(2,0) = -xz;
1143	+	inertiaTensor(2,1) = -yz;
1144	+	inertiaTensor(2,2) = xx + yy;
1145	+
1146	+	#ifdef IS_MPI
1147	+	Mat3x3d tmpI(inertiaTensor);
1148	+	Vector3d tmpAngMom;
1149	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1150	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1151	+	#endif
1152	+
1153	+	return;
1154	+	}
1155	+
1156	+	//Returns the angular momentum of the system
1157	+	Vector3d SimInfo::getAngularMomentum(){
1158	+
1159	+	Vector3d com(0.0);
1160	+	Vector3d comVel(0.0);
1161	+	Vector3d angularMomentum(0.0);
1162	+
1163	+	getComAll(com,comVel);
1164	+
1165	+	SimInfo::MoleculeIterator i;
1166	+	Molecule* mol;
1167	+
1168	+	Vector3d thisr(0.0);
1169	+	Vector3d thisp(0.0);
1170	+
1171	+	RealType thisMass;
1172	+
1173	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1174	+	thisMass = mol->getMass();
1175	+	thisr = mol->getCom()-com;
1176	+	thisp = (mol->getComVel()-comVel)*thisMass;
1177	+
1178	+	angularMomentum += cross( thisr, thisp );
1179	+
1180	+	}
1181	+
1182	+	#ifdef IS_MPI
1183	+	Vector3d tmpAngMom;
1184	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1185	+	#endif
1186	+
1187	+	return angularMomentum;
1188	+	}
1189	+
1190	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1191	+	return IOIndexToIntegrableObject.at(index);
1192	+	}
1193	+
1194	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1195	+	IOIndexToIntegrableObject= v;
1196	+	}
1197	+
1198	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1199	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1200	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1201	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1202	+	*/
1203	+	void SimInfo::getGyrationalVolume(RealType &volume){
1204	+	Mat3x3d intTensor;
1205	+	RealType det;
1206	+	Vector3d dummyAngMom;
1207	+	RealType sysconstants;
1208	+	RealType geomCnst;
1209	+
1210	+	geomCnst = 3.0/2.0;
1211	+	/* Get the inertial tensor and angular momentum for free*/
1212	+	getInertiaTensor(intTensor,dummyAngMom);
1213	+
1214	+	det = intTensor.determinant();
1215	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1216	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1217	+	return;
1218	+	}
1219	+
1220	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1221	+	Mat3x3d intTensor;
1222	+	Vector3d dummyAngMom;
1223	+	RealType sysconstants;
1224	+	RealType geomCnst;
1225	+
1226	+	geomCnst = 3.0/2.0;
1227	+	/* Get the inertial tensor and angular momentum for free*/
1228	+	getInertiaTensor(intTensor,dummyAngMom);
1229	+
1230	+	detI = intTensor.determinant();
1231	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1232	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1233	+	return;
1234	+	}
1235	+	/*
1236	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1237	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1238	+	sdByGlobalIndex_ = v;
1239	+	}
1240	+
1241	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1242	+	//assert(index < nAtoms_ + nRigidBodies_);
1243	+	return sdByGlobalIndex_.at(index);
1244	+	}
1245	+	*/
1246	+	int SimInfo::getNGlobalConstraints() {
1247	+	int nGlobalConstraints;
1248	+	#ifdef IS_MPI
1249	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1250	+	MPI_COMM_WORLD);
1251	+	#else
1252	+	nGlobalConstraints =  nConstraints_;
1253	+	#endif
1254	+	return nGlobalConstraints;
1255	+	}
1256	+
1257	+	}//end namespace OpenMD
1258	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 274 by tim, Tue Jan 25 21:59:18 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1750 by gezelter, Thu Jun 7 12:53:46 2012 UTC

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