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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 432 by tim, Fri Mar 11 15:00:20 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1725 by gezelter, Sat May 26 18:13:43 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		#include "selection/SelectionManager.hpp"
61	<
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"
64	<	#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	<
79	<	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
124	–	//every free atom (atom does not belong to cutoff groups) is a cutoff group
125	–	//therefore the total number of cutoff groups in the system is equal to
126	–	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
127	–	//file plus the number of cutoff groups defined in meta-data file
133		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134	<
135	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
136	<	//therefore the total number of  integrable objects in the system is equal to
137	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
138	<	//file plus the number of  rigid bodies defined in meta-data file
139	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
140	<
134	>
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();
137	–
138	–	#ifdef IS_MPI
144		molToProcMap_.resize(nGlobalMols_);
145	<	#endif
146	<
147	<	}
148	<
144	<	SimInfo::~SimInfo() {
145	<	std::map<int, Molecule*>::iterator i;
145	>	}
146	>
147	>	SimInfo::~SimInfo() {
148	>	map<int, Molecule*>::iterator i;
149		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
150	<	delete i->second;
150	>	delete i->second;
151		}
152		molecules_.clear();
153	<
151	<	MemoryUtils::deletePointers(moleculeStamps_);
152	<
153	>
154		delete sman_;
155		delete simParams_;
156		delete forceField_;
157	<	}
157	>	}
158
158	–	int SimInfo::getNGlobalConstraints() {
159	–	int nGlobalConstraints;
160	–	#ifdef IS_MPI
161	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
162	–	MPI_COMM_WORLD);
163	–	#else
164	–	nGlobalConstraints =  nConstraints_;
165	–	#endif
166	–	return nGlobalConstraints;
167	–	}
159
160	<	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
221	–
222	–	}
223	–
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		// n_constraints is local, so subtract them on each processor
263		ndf_local -= nConstraints_;
264
265		#ifdef IS_MPI
266		MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
267	+	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
268		#else
269		ndf_ = ndf_local;
270	+	nGlobalFluctuatingCharges_ = nfq_local;
271		#endif
272
273		// nZconstraints_ is global, as are the 3 COM translations for the
274		// entire system:
275		ndf_ = ndf_ - 3 - nZconstraint_;
276
277	<	}
277	>	}
278
279	<	void SimInfo::calcNdfRaw() {
279	>	int SimInfo::getFdf() {
280	>	#ifdef IS_MPI
281	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
282	>	#else
283	>	fdf_ = fdf_local;
284	>	#endif
285	>	return fdf_;
286	>	}
287	>
288	>	unsigned int SimInfo::getNLocalCutoffGroups(){
289	>	int nLocalCutoffAtoms = 0;
290	>	Molecule* mol;
291	>	MoleculeIterator mi;
292	>	CutoffGroup* cg;
293	>	Molecule::CutoffGroupIterator ci;
294	>
295	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
296	>
297	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
298	>	cg = mol->nextCutoffGroup(ci)) {
299	>	nLocalCutoffAtoms += cg->getNumAtom();
300	>
301	>	}
302	>	}
303	>
304	>	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
305	>	}
306	>
307	>	void SimInfo::calcNdfRaw() {
308		int ndfRaw_local;
309
310		MoleculeIterator i;
311	<	std::vector<StuntDouble*>::iterator j;
311	>	vector<StuntDouble*>::iterator j;
312		Molecule* mol;
313		StuntDouble* integrableObject;
314
#	Line 286 | Line 316 | void SimInfo::calcNdfRaw() {
316		ndfRaw_local = 0;
317
318		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
319	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
320	<	integrableObject = mol->nextIntegrableObject(j)) {
319	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
320	>	integrableObject = mol->nextIntegrableObject(j)) {
321
322	<	ndfRaw_local += 3;
322	>	ndfRaw_local += 3;
323
324	<	if (integrableObject->isDirectional()) {
325	<	if (integrableObject->isLinear()) {
326	<	ndfRaw_local += 2;
327	<	} else {
328	<	ndfRaw_local += 3;
329	<	}
330	<	}
324	>	if (integrableObject->isDirectional()) {
325	>	if (integrableObject->isLinear()) {
326	>	ndfRaw_local += 2;
327	>	} else {
328	>	ndfRaw_local += 3;
329	>	}
330	>	}
331
332	<	}
332	>	}
333		}
334
335		#ifdef IS_MPI
#	Line 307 | Line 337 | void SimInfo::calcNdfRaw() {
337		#else
338		ndfRaw_ = ndfRaw_local;
339		#endif
340	<	}
340	>	}
341
342	<	void SimInfo::calcNdfTrans() {
342	>	void SimInfo::calcNdfTrans() {
343		int ndfTrans_local;
344
345		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 323 | Line 353 | void SimInfo::calcNdfTrans() {
353
354		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
355
356	<	}
356	>	}
357
358	<	void SimInfo::addExcludePairs(Molecule* mol) {
359	<	std::vector<Bond*>::iterator bondIter;
360	<	std::vector<Bend*>::iterator bendIter;
361	<	std::vector<Torsion*>::iterator torsionIter;
358	>	void SimInfo::addInteractionPairs(Molecule* mol) {
359	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
360	>	vector<Bond*>::iterator bondIter;
361	>	vector<Bend*>::iterator bendIter;
362	>	vector<Torsion*>::iterator torsionIter;
363	>	vector<Inversion*>::iterator inversionIter;
364		Bond* bond;
365		Bend* bend;
366		Torsion* torsion;
367	+	Inversion* inversion;
368		int a;
369		int b;
370		int c;
371		int d;
339	–
340	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
341	–	a = bond->getAtomA()->getGlobalIndex();
342	–	b = bond->getAtomB()->getGlobalIndex();
343	–	exclude_.addPair(a, b);
344	–	}
372
373	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
374	<	a = bend->getAtomA()->getGlobalIndex();
375	<	b = bend->getAtomB()->getGlobalIndex();
376	<	c = bend->getAtomC()->getGlobalIndex();
373	>	// atomGroups can be used to add special interaction maps between
374	>	// groups of atoms that are in two separate rigid bodies.
375	>	// However, most site-site interactions between two rigid bodies
376	>	// are probably not special, just the ones between the physically
377	>	// bonded atoms.  Interactions *within* a single rigid body should
378	>	// always be excluded.  These are done at the bottom of this
379	>	// function.
380
381	<	exclude_.addPair(a, b);
382	<	exclude_.addPair(a, c);
383	<	exclude_.addPair(b, c);
381	>	map<int, set<int> > atomGroups;
382	>	Molecule::RigidBodyIterator rbIter;
383	>	RigidBody* rb;
384	>	Molecule::IntegrableObjectIterator ii;
385	>	StuntDouble* integrableObject;
386	>
387	>	for (integrableObject = mol->beginIntegrableObject(ii);
388	>	integrableObject != NULL;
389	>	integrableObject = mol->nextIntegrableObject(ii)) {
390	>
391	>	if (integrableObject->isRigidBody()) {
392	>	rb = static_cast<RigidBody*>(integrableObject);
393	>	vector<Atom*> atoms = rb->getAtoms();
394	>	set<int> rigidAtoms;
395	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
396	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
397	>	}
398	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
399	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
400	>	}
401	>	} else {
402	>	set<int> oneAtomSet;
403	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
404	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
405	>	}
406	>	}
407	>
408	>	for (bond= mol->beginBond(bondIter); bond != NULL;
409	>	bond = mol->nextBond(bondIter)) {
410	>
411	>	a = bond->getAtomA()->getGlobalIndex();
412	>	b = bond->getAtomB()->getGlobalIndex();
413	>
414	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
415	>	oneTwoInteractions_.addPair(a, b);
416	>	} else {
417	>	excludedInteractions_.addPair(a, b);
418	>	}
419		}
420
421	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
422	<	a = torsion->getAtomA()->getGlobalIndex();
358	<	b = torsion->getAtomB()->getGlobalIndex();
359	<	c = torsion->getAtomC()->getGlobalIndex();
360	<	d = torsion->getAtomD()->getGlobalIndex();
421	>	for (bend= mol->beginBend(bendIter); bend != NULL;
422	>	bend = mol->nextBend(bendIter)) {
423
424	<	exclude_.addPair(a, b);
425	<	exclude_.addPair(a, c);
426	<	exclude_.addPair(a, d);
427	<	exclude_.addPair(b, c);
428	<	exclude_.addPair(b, d);
429	<	exclude_.addPair(c, d);
424	>	a = bend->getAtomA()->getGlobalIndex();
425	>	b = bend->getAtomB()->getGlobalIndex();
426	>	c = bend->getAtomC()->getGlobalIndex();
427	>
428	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
429	>	oneTwoInteractions_.addPair(a, b);
430	>	oneTwoInteractions_.addPair(b, c);
431	>	} else {
432	>	excludedInteractions_.addPair(a, b);
433	>	excludedInteractions_.addPair(b, c);
434	>	}
435	>
436	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
437	>	oneThreeInteractions_.addPair(a, c);
438	>	} else {
439	>	excludedInteractions_.addPair(a, c);
440	>	}
441		}
442
443	<	Molecule::RigidBodyIterator rbIter;
444	<	RigidBody* rb;
372	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
373	<	std::vector<Atom*> atoms = rb->getAtoms();
374	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
375	<	for (int j = i + 1; j < atoms.size(); ++j) {
376	<	a = atoms[i]->getGlobalIndex();
377	<	b = atoms[j]->getGlobalIndex();
378	<	exclude_.addPair(a, b);
379	<	}
380	<	}
381	<	}
443	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
444	>	torsion = mol->nextTorsion(torsionIter)) {
445
446	<	Molecule::CutoffGroupIterator cgIter;
447	<	CutoffGroup* cg;
448	<	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
449	<	std::vector<Atom*> atoms = cg->getAtoms();
387	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
388	<	for (int j = i + 1; j < atoms.size(); ++j) {
389	<	a = atoms[i]->getGlobalIndex();
390	<	b = atoms[j]->getGlobalIndex();
391	<	exclude_.addPair(a, b);
392	<	}
393	<	}
394	<	}
446	>	a = torsion->getAtomA()->getGlobalIndex();
447	>	b = torsion->getAtomB()->getGlobalIndex();
448	>	c = torsion->getAtomC()->getGlobalIndex();
449	>	d = torsion->getAtomD()->getGlobalIndex();
450
451	<	}
451	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
452	>	oneTwoInteractions_.addPair(a, b);
453	>	oneTwoInteractions_.addPair(b, c);
454	>	oneTwoInteractions_.addPair(c, d);
455	>	} else {
456	>	excludedInteractions_.addPair(a, b);
457	>	excludedInteractions_.addPair(b, c);
458	>	excludedInteractions_.addPair(c, d);
459	>	}
460
461	<	void SimInfo::removeExcludePairs(Molecule* mol) {
462	<	std::vector<Bond*>::iterator bondIter;
463	<	std::vector<Bend*>::iterator bendIter;
464	<	std::vector<Torsion*>::iterator torsionIter;
461	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
462	>	oneThreeInteractions_.addPair(a, c);
463	>	oneThreeInteractions_.addPair(b, d);
464	>	} else {
465	>	excludedInteractions_.addPair(a, c);
466	>	excludedInteractions_.addPair(b, d);
467	>	}
468	>
469	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
470	>	oneFourInteractions_.addPair(a, d);
471	>	} else {
472	>	excludedInteractions_.addPair(a, d);
473	>	}
474	>	}
475	>
476	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
477	>	inversion = mol->nextInversion(inversionIter)) {
478	>
479	>	a = inversion->getAtomA()->getGlobalIndex();
480	>	b = inversion->getAtomB()->getGlobalIndex();
481	>	c = inversion->getAtomC()->getGlobalIndex();
482	>	d = inversion->getAtomD()->getGlobalIndex();
483	>
484	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
485	>	oneTwoInteractions_.addPair(a, b);
486	>	oneTwoInteractions_.addPair(a, c);
487	>	oneTwoInteractions_.addPair(a, d);
488	>	} else {
489	>	excludedInteractions_.addPair(a, b);
490	>	excludedInteractions_.addPair(a, c);
491	>	excludedInteractions_.addPair(a, d);
492	>	}
493	>
494	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
495	>	oneThreeInteractions_.addPair(b, c);
496	>	oneThreeInteractions_.addPair(b, d);
497	>	oneThreeInteractions_.addPair(c, d);
498	>	} else {
499	>	excludedInteractions_.addPair(b, c);
500	>	excludedInteractions_.addPair(b, d);
501	>	excludedInteractions_.addPair(c, d);
502	>	}
503	>	}
504	>
505	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
506	>	rb = mol->nextRigidBody(rbIter)) {
507	>	vector<Atom*> atoms = rb->getAtoms();
508	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
509	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
510	>	a = atoms[i]->getGlobalIndex();
511	>	b = atoms[j]->getGlobalIndex();
512	>	excludedInteractions_.addPair(a, b);
513	>	}
514	>	}
515	>	}
516	>
517	>	}
518	>
519	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
520	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
521	>	vector<Bond*>::iterator bondIter;
522	>	vector<Bend*>::iterator bendIter;
523	>	vector<Torsion*>::iterator torsionIter;
524	>	vector<Inversion*>::iterator inversionIter;
525		Bond* bond;
526		Bend* bend;
527		Torsion* torsion;
528	+	Inversion* inversion;
529		int a;
530		int b;
531		int c;
532		int d;
533	+
534	+	map<int, set<int> > atomGroups;
535	+	Molecule::RigidBodyIterator rbIter;
536	+	RigidBody* rb;
537	+	Molecule::IntegrableObjectIterator ii;
538	+	StuntDouble* integrableObject;
539
540	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
541	<	a = bond->getAtomA()->getGlobalIndex();
542	<	b = bond->getAtomB()->getGlobalIndex();
543	<	exclude_.removePair(a, b);
540	>	for (integrableObject = mol->beginIntegrableObject(ii);
541	>	integrableObject != NULL;
542	>	integrableObject = mol->nextIntegrableObject(ii)) {
543	>
544	>	if (integrableObject->isRigidBody()) {
545	>	rb = static_cast<RigidBody*>(integrableObject);
546	>	vector<Atom*> atoms = rb->getAtoms();
547	>	set<int> rigidAtoms;
548	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
549	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
550	>	}
551	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
552	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
553	>	}
554	>	} else {
555	>	set<int> oneAtomSet;
556	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
557	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
558	>	}
559	>	}
560	>
561	>	for (bond= mol->beginBond(bondIter); bond != NULL;
562	>	bond = mol->nextBond(bondIter)) {
563	>
564	>	a = bond->getAtomA()->getGlobalIndex();
565	>	b = bond->getAtomB()->getGlobalIndex();
566	>
567	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
568	>	oneTwoInteractions_.removePair(a, b);
569	>	} else {
570	>	excludedInteractions_.removePair(a, b);
571	>	}
572		}
573
574	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
575	<	a = bend->getAtomA()->getGlobalIndex();
418	<	b = bend->getAtomB()->getGlobalIndex();
419	<	c = bend->getAtomC()->getGlobalIndex();
574	>	for (bend= mol->beginBend(bendIter); bend != NULL;
575	>	bend = mol->nextBend(bendIter)) {
576
577	<	exclude_.removePair(a, b);
578	<	exclude_.removePair(a, c);
579	<	exclude_.removePair(b, c);
577	>	a = bend->getAtomA()->getGlobalIndex();
578	>	b = bend->getAtomB()->getGlobalIndex();
579	>	c = bend->getAtomC()->getGlobalIndex();
580	>
581	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
582	>	oneTwoInteractions_.removePair(a, b);
583	>	oneTwoInteractions_.removePair(b, c);
584	>	} else {
585	>	excludedInteractions_.removePair(a, b);
586	>	excludedInteractions_.removePair(b, c);
587	>	}
588	>
589	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
590	>	oneThreeInteractions_.removePair(a, c);
591	>	} else {
592	>	excludedInteractions_.removePair(a, c);
593	>	}
594		}
595
596	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
597	<	a = torsion->getAtomA()->getGlobalIndex();
428	<	b = torsion->getAtomB()->getGlobalIndex();
429	<	c = torsion->getAtomC()->getGlobalIndex();
430	<	d = torsion->getAtomD()->getGlobalIndex();
596	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
597	>	torsion = mol->nextTorsion(torsionIter)) {
598
599	<	exclude_.removePair(a, b);
600	<	exclude_.removePair(a, c);
601	<	exclude_.removePair(a, d);
602	<	exclude_.removePair(b, c);
603	<	exclude_.removePair(b, d);
604	<	exclude_.removePair(c, d);
599	>	a = torsion->getAtomA()->getGlobalIndex();
600	>	b = torsion->getAtomB()->getGlobalIndex();
601	>	c = torsion->getAtomC()->getGlobalIndex();
602	>	d = torsion->getAtomD()->getGlobalIndex();
603	>
604	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
605	>	oneTwoInteractions_.removePair(a, b);
606	>	oneTwoInteractions_.removePair(b, c);
607	>	oneTwoInteractions_.removePair(c, d);
608	>	} else {
609	>	excludedInteractions_.removePair(a, b);
610	>	excludedInteractions_.removePair(b, c);
611	>	excludedInteractions_.removePair(c, d);
612	>	}
613	>
614	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
615	>	oneThreeInteractions_.removePair(a, c);
616	>	oneThreeInteractions_.removePair(b, d);
617	>	} else {
618	>	excludedInteractions_.removePair(a, c);
619	>	excludedInteractions_.removePair(b, d);
620	>	}
621	>
622	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
623	>	oneFourInteractions_.removePair(a, d);
624	>	} else {
625	>	excludedInteractions_.removePair(a, d);
626	>	}
627		}
628
629	<	Molecule::RigidBodyIterator rbIter;
630	<	RigidBody* rb;
442	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
443	<	std::vector<Atom*> atoms = rb->getAtoms();
444	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
445	<	for (int j = i + 1; j < atoms.size(); ++j) {
446	<	a = atoms[i]->getGlobalIndex();
447	<	b = atoms[j]->getGlobalIndex();
448	<	exclude_.removePair(a, b);
449	<	}
450	<	}
451	<	}
629	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
630	>	inversion = mol->nextInversion(inversionIter)) {
631
632	<	Molecule::CutoffGroupIterator cgIter;
633	<	CutoffGroup* cg;
634	<	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
635	<	std::vector<Atom*> atoms = cg->getAtoms();
457	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
458	<	for (int j = i + 1; j < atoms.size(); ++j) {
459	<	a = atoms[i]->getGlobalIndex();
460	<	b = atoms[j]->getGlobalIndex();
461	<	exclude_.removePair(a, b);
462	<	}
463	<	}
464	<	}
632	>	a = inversion->getAtomA()->getGlobalIndex();
633	>	b = inversion->getAtomB()->getGlobalIndex();
634	>	c = inversion->getAtomC()->getGlobalIndex();
635	>	d = inversion->getAtomD()->getGlobalIndex();
636
637	<	}
637	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
638	>	oneTwoInteractions_.removePair(a, b);
639	>	oneTwoInteractions_.removePair(a, c);
640	>	oneTwoInteractions_.removePair(a, d);
641	>	} else {
642	>	excludedInteractions_.removePair(a, b);
643	>	excludedInteractions_.removePair(a, c);
644	>	excludedInteractions_.removePair(a, d);
645	>	}
646
647	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
648	+	oneThreeInteractions_.removePair(b, c);
649	+	oneThreeInteractions_.removePair(b, d);
650	+	oneThreeInteractions_.removePair(c, d);
651	+	} else {
652	+	excludedInteractions_.removePair(b, c);
653	+	excludedInteractions_.removePair(b, d);
654	+	excludedInteractions_.removePair(c, d);
655	+	}
656	+	}
657
658	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
658	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
659	>	rb = mol->nextRigidBody(rbIter)) {
660	>	vector<Atom*> atoms = rb->getAtoms();
661	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
662	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
663	>	a = atoms[i]->getGlobalIndex();
664	>	b = atoms[j]->getGlobalIndex();
665	>	excludedInteractions_.removePair(a, b);
666	>	}
667	>	}
668	>	}
669	>
670	>	}
671	>
672	>
673	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
674		int curStampId;
675	<
675	>
676		//index from 0
677		curStampId = moleculeStamps_.size();
678
679		moleculeStamps_.push_back(molStamp);
680		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
681	<	}
681	>	}
682
479	–	void SimInfo::update() {
683
684	<	setupSimType();
685	<
686	<	#ifdef IS_MPI
687	<	setupFortranParallel();
688	<	#endif
689	<
690	<	setupFortranSim();
691	<
692	<	//setup fortran force field
490	<	/** @deprecate */
491	<	int isError = 0;
492	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
493	<	if(isError){
494	<	sprintf( painCave.errMsg,
495	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
496	<	painCave.isFatal = 1;
497	<	simError();
498	<	}
499	<
500	<
501	<	setupCutoff();
502	<
684	>	/**
685	>	* update
686	>	*
687	>	*  Performs the global checks and variable settings after the
688	>	*  objects have been created.
689	>	*
690	>	*/
691	>	void SimInfo::update() {
692	>	setupSimVariables();
693		calcNdf();
694		calcNdfRaw();
695		calcNdfTrans();
696	<
697	<	fortranInitialized_ = true;
698	<	}
699	<
700	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
696	>	}
697	>
698	>	/**
699	>	* getSimulatedAtomTypes
700	>	*
701	>	* Returns an STL set of AtomType* that are actually present in this
702	>	* simulation.  Must query all processors to assemble this information.
703	>	*
704	>	*/
705	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
706		SimInfo::MoleculeIterator mi;
707		Molecule* mol;
708		Molecule::AtomIterator ai;
709		Atom* atom;
710	<	std::set<AtomType*> atomTypes;
711	<
710	>	set<AtomType*> atomTypes;
711	>
712		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
713	+	for(atom = mol->beginAtom(ai); atom != NULL;
714	+	atom = mol->nextAtom(ai)) {
715	+	atomTypes.insert(atom->getAtomType());
716	+	}
717	+	}
718	+
719	+	#ifdef IS_MPI
720
721	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
722	<	atomTypes.insert(atom->getAtomType());
723	<	}
724	<
721	>	// loop over the found atom types on this processor, and add their
722	>	// numerical idents to a vector:
723	>
724	>	vector<int> foundTypes;
725	>	set<AtomType*>::iterator i;
726	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
727	>	foundTypes.push_back( (*i)->getIdent() );
728	>
729	>	// count_local holds the number of found types on this processor
730	>	int count_local = foundTypes.size();
731	>
732	>	int nproc = MPI::COMM_WORLD.Get_size();
733	>
734	>	// we need arrays to hold the counts and displacement vectors for
735	>	// all processors
736	>	vector<int> counts(nproc, 0);
737	>	vector<int> disps(nproc, 0);
738	>
739	>	// fill the counts array
740	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
741	>	1, MPI::INT);
742	>
743	>	// use the processor counts to compute the displacement array
744	>	disps[0] = 0;
745	>	int totalCount = counts[0];
746	>	for (int iproc = 1; iproc < nproc; iproc++) {
747	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
748	>	totalCount += counts[iproc];
749		}
750
751	<	return atomTypes;
752	<	}
751	>	// we need a (possibly redundant) set of all found types:
752	>	vector<int> ftGlobal(totalCount);
753	>
754	>	// now spray out the foundTypes to all the other processors:
755	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
756	>	&ftGlobal[0], &counts[0], &disps[0],
757	>	MPI::INT);
758
759	<	void SimInfo::setupSimType() {
760	<	std::set<AtomType*>::iterator i;
761	<	std::set<AtomType*> atomTypes;
762	<	atomTypes = getUniqueAtomTypes();
759	>	vector<int>::iterator j;
760	>
761	>	// foundIdents is a stl set, so inserting an already found ident
762	>	// will have no effect.
763	>	set<int> foundIdents;
764	>
765	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
766	>	foundIdents.insert((*j));
767
768	<	int useLennardJones = 0;
769	<	int useElectrostatic = 0;
770	<	int useEAM = 0;
771	<	int useCharge = 0;
772	<	int useDirectional = 0;
773	<	int useDipole = 0;
774	<	int useGayBerne = 0;
540	<	int useSticky = 0;
541	<	int useShape = 0;
542	<	int useFLARB = 0; //it is not in AtomType yet
543	<	int useDirectionalAtom = 0;
544	<	int useElectrostatics = 0;
545	<	//usePBC and useRF are from simParams
546	<	int usePBC = simParams_->getPBC();
547	<	int useRF = simParams_->getUseRF();
768	>	// now iterate over the foundIdents and get the actual atom types
769	>	// that correspond to these:
770	>	set<int>::iterator it;
771	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
772	>	atomTypes.insert( forceField_->getAtomType((*it)) );
773	>
774	>	#endif
775
776	+	return atomTypes;
777	+	}
778	+
779	+	void SimInfo::setupSimVariables() {
780	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
781	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
782	+	calcBoxDipole_ = false;
783	+	if ( simParams_->haveAccumulateBoxDipole() )
784	+	if ( simParams_->getAccumulateBoxDipole() ) {
785	+	calcBoxDipole_ = true;
786	+	}
787	+
788	+	set<AtomType*>::iterator i;
789	+	set<AtomType*> atomTypes;
790	+	atomTypes = getSimulatedAtomTypes();
791	+	int usesElectrostatic = 0;
792	+	int usesMetallic = 0;
793	+	int usesDirectional = 0;
794	+	int usesFluctuatingCharges =  0;
795		//loop over all of the atom types
796		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
797	<	useLennardJones |= (*i)->isLennardJones();
798	<	useElectrostatic |= (*i)->isElectrostatic();
799	<	useEAM |= (*i)->isEAM();
800	<	useCharge |= (*i)->isCharge();
555	<	useDirectional |= (*i)->isDirectional();
556	<	useDipole |= (*i)->isDipole();
557	<	useGayBerne |= (*i)->isGayBerne();
558	<	useSticky |= (*i)->isSticky();
559	<	useShape |= (*i)->isShape();
797	>	usesElectrostatic |= (*i)->isElectrostatic();
798	>	usesMetallic |= (*i)->isMetal();
799	>	usesDirectional |= (*i)->isDirectional();
800	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
801		}
802	<
562	<	if (useSticky || useDipole || useGayBerne || useShape) {
563	<	useDirectionalAtom = 1;
564	<	}
565	<
566	<	if (useCharge || useDipole) {
567	<	useElectrostatics = 1;
568	<	}
569	<
802	>
803		#ifdef IS_MPI
804		int temp;
805	+	temp = usesDirectional;
806	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
807	+
808	+	temp = usesMetallic;
809	+	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810	+
811	+	temp = usesElectrostatic;
812	+	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813
814	<	temp = usePBC;
815	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814	>	temp = usesFluctuatingCharges;
815	>	MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816	>	#else
817
818	<	temp = useDirectionalAtom;
819	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
818	>	usesDirectionalAtoms_ = usesDirectional;
819	>	usesMetallicAtoms_ = usesMetallic;
820	>	usesElectrostaticAtoms_ = usesElectrostatic;
821	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
822
823	<	temp = useLennardJones;
824	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
823	>	#endif
824	>
825	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
826	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
827	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
828	>	}
829
582	–	temp = useElectrostatics;
583	–	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
830
831	<	temp = useCharge;
832	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
831	>	vector<int> SimInfo::getGlobalAtomIndices() {
832	>	SimInfo::MoleculeIterator mi;
833	>	Molecule* mol;
834	>	Molecule::AtomIterator ai;
835	>	Atom* atom;
836
837	<	temp = useDipole;
589	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
590	<
591	<	temp = useSticky;
592	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
593	<
594	<	temp = useGayBerne;
595	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
596	<
597	<	temp = useEAM;
598	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
599	<
600	<	temp = useShape;
601	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
602	<
603	<	temp = useFLARB;
604	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
605	<
606	<	temp = useRF;
607	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
837	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
838
839	<	#endif
839	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
840	>
841	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
842	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
843	>	}
844	>	}
845	>	return GlobalAtomIndices;
846	>	}
847
611	–	fInfo_.SIM_uses_PBC = usePBC;
612	–	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
613	–	fInfo_.SIM_uses_LennardJones = useLennardJones;
614	–	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
615	–	fInfo_.SIM_uses_Charges = useCharge;
616	–	fInfo_.SIM_uses_Dipoles = useDipole;
617	–	fInfo_.SIM_uses_Sticky = useSticky;
618	–	fInfo_.SIM_uses_GayBerne = useGayBerne;
619	–	fInfo_.SIM_uses_EAM = useEAM;
620	–	fInfo_.SIM_uses_Shapes = useShape;
621	–	fInfo_.SIM_uses_FLARB = useFLARB;
622	–	fInfo_.SIM_uses_RF = useRF;
848
849	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
849	>	vector<int> SimInfo::getGlobalGroupIndices() {
850	>	SimInfo::MoleculeIterator mi;
851	>	Molecule* mol;
852	>	Molecule::CutoffGroupIterator ci;
853	>	CutoffGroup* cg;
854
855	<	if (simParams_->haveDielectric()) {
856	<	fInfo_.dielect = simParams_->getDielectric();
857	<	} else {
858	<	sprintf(painCave.errMsg,
859	<	"SimSetup Error: No Dielectric constant was set.\n"
860	<	"\tYou are trying to use Reaction Field without"
861	<	"\tsetting a dielectric constant!\n");
862	<	painCave.isFatal = 1;
863	<	simError();
864	<	}
636	<
637	<	} else {
638	<	fInfo_.dielect = 0.0;
855	>	vector<int> GlobalGroupIndices;
856	>
857	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
858	>
859	>	//local index of cutoff group is trivial, it only depends on the
860	>	//order of travesing
861	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
862	>	cg = mol->nextCutoffGroup(ci)) {
863	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
864	>	}
865		}
866	+	return GlobalGroupIndices;
867	+	}
868
641	–	}
869
870	<	void SimInfo::setupFortranSim() {
871	<	int isError;
645	<	int nExclude;
646	<	std::vector<int> fortranGlobalGroupMembership;
647	<
648	<	nExclude = exclude_.getSize();
649	<	isError = 0;
870	>	void SimInfo::prepareTopology() {
871	>	int nExclude, nOneTwo, nOneThree, nOneFour;
872
651	–	//globalGroupMembership_ is filled by SimCreator
652	–	for (int i = 0; i < nGlobalAtoms_; i++) {
653	–	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
654	–	}
655	–
873		//calculate mass ratio of cutoff group
657	–	std::vector<double> mfact;
874		SimInfo::MoleculeIterator mi;
875		Molecule* mol;
876		Molecule::CutoffGroupIterator ci;
877		CutoffGroup* cg;
878		Molecule::AtomIterator ai;
879		Atom* atom;
880	<	double totalMass;
880	>	RealType totalMass;
881
882	<	//to avoid memory reallocation, reserve enough space for mfact
883	<	mfact.reserve(getNCutoffGroups());
882	>	/**
883	>	* The mass factor is the relative mass of an atom to the total
884	>	* mass of the cutoff group it belongs to.  By default, all atoms
885	>	* are their own cutoff groups, and therefore have mass factors of
886	>	* 1.  We need some special handling for massless atoms, which
887	>	* will be treated as carrying the entire mass of the cutoff
888	>	* group.
889	>	*/
890	>	massFactors_.clear();
891	>	massFactors_.resize(getNAtoms(), 1.0);
892
893		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
894	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
894	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
895	>	cg = mol->nextCutoffGroup(ci)) {
896
897	<	totalMass = cg->getMass();
898	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
899	<	mfact.push_back(atom->getMass()/totalMass);
900	<	}
901	<
902	<	}
897	>	totalMass = cg->getMass();
898	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
899	>	// Check for massless groups - set mfact to 1 if true
900	>	if (totalMass != 0)
901	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
902	>	else
903	>	massFactors_[atom->getLocalIndex()] = 1.0;
904	>	}
905	>	}
906		}
907
908	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
681	<	std::vector<int> identArray;
908	>	// Build the identArray_
909
910	<	//to avoid memory reallocation, reserve enough space identArray
911	<	identArray.reserve(getNAtoms());
685	<
910	>	identArray_.clear();
911	>	identArray_.reserve(getNAtoms());
912		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
913	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
914	<	identArray.push_back(atom->getIdent());
915	<	}
913	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
914	>	identArray_.push_back(atom->getIdent());
915	>	}
916		}
691	–
692	–	//fill molMembershipArray
693	–	//molMembershipArray is filled by SimCreator
694	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
695	–	for (int i = 0; i < nGlobalAtoms_; i++) {
696	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
697	–	}
917
918	<	//setup fortran simulation
700	<	int nGlobalExcludes = 0;
701	<	int* globalExcludes = NULL;
702	<	int* excludeList = exclude_.getExcludeList();
703	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
704	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
705	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
918	>	//scan topology
919
920	<	if( isError ){
920	>	nExclude = excludedInteractions_.getSize();
921	>	nOneTwo = oneTwoInteractions_.getSize();
922	>	nOneThree = oneThreeInteractions_.getSize();
923	>	nOneFour = oneFourInteractions_.getSize();
924
925	<	sprintf( painCave.errMsg,
926	<	"There was an error setting the simulation information in fortran.\n" );
927	<	painCave.isFatal = 1;
928	<	painCave.severity = OOPSE_ERROR;
713	<	simError();
714	<	}
925	>	int* excludeList = excludedInteractions_.getPairList();
926	>	int* oneTwoList = oneTwoInteractions_.getPairList();
927	>	int* oneThreeList = oneThreeInteractions_.getPairList();
928	>	int* oneFourList = oneFourInteractions_.getPairList();
929
930	<	#ifdef IS_MPI
931	<	sprintf( checkPointMsg,
718	<	"succesfully sent the simulation information to fortran.\n");
719	<	MPIcheckPoint();
720	<	#endif // is_mpi
721	<	}
930	>	topologyDone_ = true;
931	>	}
932
933	+	void SimInfo::addProperty(GenericData* genData) {
934	+	properties_.addProperty(genData);
935	+	}
936
937	<	#ifdef IS_MPI
938	<	void SimInfo::setupFortranParallel() {
939	<
727	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
728	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
729	<	std::vector<int> localToGlobalCutoffGroupIndex;
730	<	SimInfo::MoleculeIterator mi;
731	<	Molecule::AtomIterator ai;
732	<	Molecule::CutoffGroupIterator ci;
733	<	Molecule* mol;
734	<	Atom* atom;
735	<	CutoffGroup* cg;
736	<	mpiSimData parallelData;
737	<	int isError;
937	>	void SimInfo::removeProperty(const string& propName) {
938	>	properties_.removeProperty(propName);
939	>	}
940
941	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
941	>	void SimInfo::clearProperties() {
942	>	properties_.clearProperties();
943	>	}
944
945	<	//local index(index in DataStorge) of atom is important
946	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
947	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
948	<	}
945	>	vector<string> SimInfo::getPropertyNames() {
946	>	return properties_.getPropertyNames();
947	>	}
948	>
949	>	vector<GenericData*> SimInfo::getProperties() {
950	>	return properties_.getProperties();
951	>	}
952
953	<	//local index of cutoff group is trivial, it only depends on the order of travesing
954	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
955	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
749	<	}
750	<
751	<	}
752	<
753	<	//fill up mpiSimData struct
754	<	parallelData.nMolGlobal = getNGlobalMolecules();
755	<	parallelData.nMolLocal = getNMolecules();
756	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
757	<	parallelData.nAtomsLocal = getNAtoms();
758	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
759	<	parallelData.nGroupsLocal = getNCutoffGroups();
760	<	parallelData.myNode = worldRank;
761	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
762	<
763	<	//pass mpiSimData struct and index arrays to fortran
764	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
765	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
766	<	&localToGlobalCutoffGroupIndex[0], &isError);
767	<
768	<	if (isError) {
769	<	sprintf(painCave.errMsg,
770	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
771	<	painCave.isFatal = 1;
772	<	simError();
773	<	}
774	<
775	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
776	<	MPIcheckPoint();
777	<
778	<
779	<	}
780	<
781	<	#endif
782	<
783	<	double SimInfo::calcMaxCutoffRadius() {
784	<
785	<
786	<	std::set<AtomType*> atomTypes;
787	<	std::set<AtomType*>::iterator i;
788	<	std::vector<double> cutoffRadius;
789	<
790	<	//get the unique atom types
791	<	atomTypes = getUniqueAtomTypes();
953	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
954	>	return properties_.getPropertyByName(propName);
955	>	}
956
957	<	//query the max cutoff radius among these atom types
794	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
795	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
796	<	}
797	<
798	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
799	<	#ifdef IS_MPI
800	<	//pick the max cutoff radius among the processors
801	<	#endif
802	<
803	<	return maxCutoffRadius;
804	<	}
805	<
806	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
807	<
808	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
809	<
810	<	if (!simParams_->haveRcut()){
811	<	sprintf(painCave.errMsg,
812	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
813	<	"\tOOPSE will use a default value of 15.0 angstroms"
814	<	"\tfor the cutoffRadius.\n");
815	<	painCave.isFatal = 0;
816	<	simError();
817	<	rcut = 15.0;
818	<	} else{
819	<	rcut = simParams_->getRcut();
820	<	}
821	<
822	<	if (!simParams_->haveRsw()){
823	<	sprintf(painCave.errMsg,
824	<	"SimCreator Warning: No value was set for switchingRadius.\n"
825	<	"\tOOPSE will use a default value of\n"
826	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
827	<	painCave.isFatal = 0;
828	<	simError();
829	<	rsw = 0.95 * rcut;
830	<	} else{
831	<	rsw = simParams_->getRsw();
832	<	}
833	<
834	<	} else {
835	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
836	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
837	<
838	<	if (simParams_->haveRcut()) {
839	<	rcut = simParams_->getRcut();
840	<	} else {
841	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
842	<	rcut = calcMaxCutoffRadius();
843	<	}
844	<
845	<	if (simParams_->haveRsw()) {
846	<	rsw  = simParams_->getRsw();
847	<	} else {
848	<	rsw = rcut;
849	<	}
850	<
851	<	}
852	<	}
853	<
854	<	void SimInfo::setupCutoff() {
855	<	getCutoff(rcut_, rsw_);
856	<	double rnblist = rcut_ + 1; // skin of neighbor list
857	<
858	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
859	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
860	<	}
861	<
862	<	void SimInfo::addProperty(GenericData* genData) {
863	<	properties_.addProperty(genData);
864	<	}
865	<
866	<	void SimInfo::removeProperty(const std::string& propName) {
867	<	properties_.removeProperty(propName);
868	<	}
869	<
870	<	void SimInfo::clearProperties() {
871	<	properties_.clearProperties();
872	<	}
873	<
874	<	std::vector<std::string> SimInfo::getPropertyNames() {
875	<	return properties_.getPropertyNames();
876	<	}
877	<
878	<	std::vector<GenericData*> SimInfo::getProperties() {
879	<	return properties_.getProperties();
880	<	}
881	<
882	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
883	<	return properties_.getPropertyByName(propName);
884	<	}
885	<
886	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
957	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
958		if (sman_ == sman) {
959	<	return;
959	>	return;
960		}
961		delete sman_;
962		sman_ = sman;
#	Line 893 | Line 964 | void SimInfo::setSnapshotManager(SnapshotManager* sman
964		Molecule* mol;
965		RigidBody* rb;
966		Atom* atom;
967	+	CutoffGroup* cg;
968		SimInfo::MoleculeIterator mi;
969		Molecule::RigidBodyIterator rbIter;
970	<	Molecule::AtomIterator atomIter;;
970	>	Molecule::AtomIterator atomIter;
971	>	Molecule::CutoffGroupIterator cgIter;
972
973		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
974
975	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
976	<	atom->setSnapshotManager(sman_);
977	<	}
975	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
976	>	atom->setSnapshotManager(sman_);
977	>	}
978
979	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
980	<	rb->setSnapshotManager(sman_);
981	<	}
979	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
980	>	rb->setSnapshotManager(sman_);
981	>	}
982	>
983	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
984	>	cg->setSnapshotManager(sman_);
985	>	}
986		}
987
988	<	}
988	>	}
989
990	<	Vector3d SimInfo::getComVel(){
990	>	Vector3d SimInfo::getComVel(){
991		SimInfo::MoleculeIterator i;
992		Molecule* mol;
993
994		Vector3d comVel(0.0);
995	<	double totalMass = 0.0;
995	>	RealType totalMass = 0.0;
996
997
998		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
999	<	double mass = mol->getMass();
1000	<	totalMass += mass;
1001	<	comVel += mass * mol->getComVel();
999	>	RealType mass = mol->getMass();
1000	>	totalMass += mass;
1001	>	comVel += mass * mol->getComVel();
1002		}
1003
1004		#ifdef IS_MPI
1005	<	double tmpMass = totalMass;
1005	>	RealType tmpMass = totalMass;
1006		Vector3d tmpComVel(comVel);
1007	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1008	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1007	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1008	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1009		#endif
1010
1011		comVel /= totalMass;
1012
1013		return comVel;
1014	<	}
1014	>	}
1015
1016	<	Vector3d SimInfo::getCom(){
1016	>	Vector3d SimInfo::getCom(){
1017		SimInfo::MoleculeIterator i;
1018		Molecule* mol;
1019
1020		Vector3d com(0.0);
1021	<	double totalMass = 0.0;
1021	>	RealType totalMass = 0.0;
1022
1023		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1024	<	double mass = mol->getMass();
1025	<	totalMass += mass;
1026	<	com += mass * mol->getCom();
1024	>	RealType mass = mol->getMass();
1025	>	totalMass += mass;
1026	>	com += mass * mol->getCom();
1027		}
1028
1029		#ifdef IS_MPI
1030	<	double tmpMass = totalMass;
1030	>	RealType tmpMass = totalMass;
1031		Vector3d tmpCom(com);
1032	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1033	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1032	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1033	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1034		#endif
1035
1036		com /= totalMass;
1037
1038		return com;
1039
1040	<	}
1040	>	}
1041
1042	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1042	>	ostream& operator <<(ostream& o, SimInfo& info) {
1043
1044		return o;
1045	<	}
1045	>	}
1046	>
1047	>
1048	>	/*
1049	>	Returns center of mass and center of mass velocity in one function call.
1050	>	*/
1051	>
1052	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1053	>	SimInfo::MoleculeIterator i;
1054	>	Molecule* mol;
1055	>
1056	>
1057	>	RealType totalMass = 0.0;
1058	>
1059
1060	<	}//end namespace oopse
1060	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1061	>	RealType mass = mol->getMass();
1062	>	totalMass += mass;
1063	>	com += mass * mol->getCom();
1064	>	comVel += mass * mol->getComVel();
1065	>	}
1066	>
1067	>	#ifdef IS_MPI
1068	>	RealType tmpMass = totalMass;
1069	>	Vector3d tmpCom(com);
1070	>	Vector3d tmpComVel(comVel);
1071	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1072	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1073	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1074	>	#endif
1075	>
1076	>	com /= totalMass;
1077	>	comVel /= totalMass;
1078	>	}
1079	>
1080	>	/*
1081	>	Return intertia tensor for entire system and angular momentum Vector.
1082
1083	+
1084	+	[  Ixx -Ixy  -Ixz ]
1085	+	J =| -Iyx  Iyy  -Iyz |
1086	+	[ -Izx -Iyz   Izz ]
1087	+	*/
1088	+
1089	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1090	+
1091	+
1092	+	RealType xx = 0.0;
1093	+	RealType yy = 0.0;
1094	+	RealType zz = 0.0;
1095	+	RealType xy = 0.0;
1096	+	RealType xz = 0.0;
1097	+	RealType yz = 0.0;
1098	+	Vector3d com(0.0);
1099	+	Vector3d comVel(0.0);
1100	+
1101	+	getComAll(com, comVel);
1102	+
1103	+	SimInfo::MoleculeIterator i;
1104	+	Molecule* mol;
1105	+
1106	+	Vector3d thisq(0.0);
1107	+	Vector3d thisv(0.0);
1108	+
1109	+	RealType thisMass = 0.0;
1110	+
1111	+
1112	+
1113	+
1114	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1115	+
1116	+	thisq = mol->getCom()-com;
1117	+	thisv = mol->getComVel()-comVel;
1118	+	thisMass = mol->getMass();
1119	+	// Compute moment of intertia coefficients.
1120	+	xx += thisq[0]*thisq[0]*thisMass;
1121	+	yy += thisq[1]*thisq[1]*thisMass;
1122	+	zz += thisq[2]*thisq[2]*thisMass;
1123	+
1124	+	// compute products of intertia
1125	+	xy += thisq[0]*thisq[1]*thisMass;
1126	+	xz += thisq[0]*thisq[2]*thisMass;
1127	+	yz += thisq[1]*thisq[2]*thisMass;
1128	+
1129	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1130	+
1131	+	}
1132	+
1133	+
1134	+	inertiaTensor(0,0) = yy + zz;
1135	+	inertiaTensor(0,1) = -xy;
1136	+	inertiaTensor(0,2) = -xz;
1137	+	inertiaTensor(1,0) = -xy;
1138	+	inertiaTensor(1,1) = xx + zz;
1139	+	inertiaTensor(1,2) = -yz;
1140	+	inertiaTensor(2,0) = -xz;
1141	+	inertiaTensor(2,1) = -yz;
1142	+	inertiaTensor(2,2) = xx + yy;
1143	+
1144	+	#ifdef IS_MPI
1145	+	Mat3x3d tmpI(inertiaTensor);
1146	+	Vector3d tmpAngMom;
1147	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1148	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1149	+	#endif
1150	+
1151	+	return;
1152	+	}
1153	+
1154	+	//Returns the angular momentum of the system
1155	+	Vector3d SimInfo::getAngularMomentum(){
1156	+
1157	+	Vector3d com(0.0);
1158	+	Vector3d comVel(0.0);
1159	+	Vector3d angularMomentum(0.0);
1160	+
1161	+	getComAll(com,comVel);
1162	+
1163	+	SimInfo::MoleculeIterator i;
1164	+	Molecule* mol;
1165	+
1166	+	Vector3d thisr(0.0);
1167	+	Vector3d thisp(0.0);
1168	+
1169	+	RealType thisMass;
1170	+
1171	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1172	+	thisMass = mol->getMass();
1173	+	thisr = mol->getCom()-com;
1174	+	thisp = (mol->getComVel()-comVel)*thisMass;
1175	+
1176	+	angularMomentum += cross( thisr, thisp );
1177	+
1178	+	}
1179	+
1180	+	#ifdef IS_MPI
1181	+	Vector3d tmpAngMom;
1182	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1183	+	#endif
1184	+
1185	+	return angularMomentum;
1186	+	}
1187	+
1188	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1189	+	return IOIndexToIntegrableObject.at(index);
1190	+	}
1191	+
1192	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1193	+	IOIndexToIntegrableObject= v;
1194	+	}
1195	+
1196	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1197	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1198	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1199	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1200	+	*/
1201	+	void SimInfo::getGyrationalVolume(RealType &volume){
1202	+	Mat3x3d intTensor;
1203	+	RealType det;
1204	+	Vector3d dummyAngMom;
1205	+	RealType sysconstants;
1206	+	RealType geomCnst;
1207	+
1208	+	geomCnst = 3.0/2.0;
1209	+	/* Get the inertial tensor and angular momentum for free*/
1210	+	getInertiaTensor(intTensor,dummyAngMom);
1211	+
1212	+	det = intTensor.determinant();
1213	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1214	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1215	+	return;
1216	+	}
1217	+
1218	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1219	+	Mat3x3d intTensor;
1220	+	Vector3d dummyAngMom;
1221	+	RealType sysconstants;
1222	+	RealType geomCnst;
1223	+
1224	+	geomCnst = 3.0/2.0;
1225	+	/* Get the inertial tensor and angular momentum for free*/
1226	+	getInertiaTensor(intTensor,dummyAngMom);
1227	+
1228	+	detI = intTensor.determinant();
1229	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1230	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1231	+	return;
1232	+	}
1233	+	/*
1234	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1235	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1236	+	sdByGlobalIndex_ = v;
1237	+	}
1238	+
1239	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1240	+	//assert(index < nAtoms_ + nRigidBodies_);
1241	+	return sdByGlobalIndex_.at(index);
1242	+	}
1243	+	*/
1244	+	int SimInfo::getNGlobalConstraints() {
1245	+	int nGlobalConstraints;
1246	+	#ifdef IS_MPI
1247	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1248	+	MPI_COMM_WORLD);
1249	+	#else
1250	+	nGlobalConstraints =  nConstraints_;
1251	+	#endif
1252	+	return nGlobalConstraints;
1253	+	}
1254	+
1255	+	}//end namespace OpenMD
1256	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 432 by tim, Fri Mar 11 15:00:20 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1725 by gezelter, Sat May 26 18:13:43 2012 UTC

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