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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1744 by gezelter, Tue Jun 5 18:07:08 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->getNCutoffGroups();
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	+	cerr << "ndfLocal_ = " << ndfLocal_ << "\n";
264	+
265		// n_constraints is local, so subtract them on each processor
266		ndf_local -= nConstraints_;
267
268		#ifdef IS_MPI
269		MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
270	+	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
271		#else
272		ndf_ = ndf_local;
273	+	nGlobalFluctuatingCharges_ = nfq_local;
274		#endif
275
276		// nZconstraints_ is global, as are the 3 COM translations for the
277		// entire system:
278		ndf_ = ndf_ - 3 - nZconstraint_;
279
280	<	}
280	>	}
281
282	<	void SimInfo::calcNdfRaw() {
282	>	int SimInfo::getFdf() {
283	>	#ifdef IS_MPI
284	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
285	>	#else
286	>	fdf_ = fdf_local;
287	>	#endif
288	>	return fdf_;
289	>	}
290	>
291	>	unsigned int SimInfo::getNLocalCutoffGroups(){
292	>	int nLocalCutoffAtoms = 0;
293	>	Molecule* mol;
294	>	MoleculeIterator mi;
295	>	CutoffGroup* cg;
296	>	Molecule::CutoffGroupIterator ci;
297	>
298	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
299	>
300	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
301	>	cg = mol->nextCutoffGroup(ci)) {
302	>	nLocalCutoffAtoms += cg->getNumAtom();
303	>
304	>	}
305	>	}
306	>
307	>	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
308	>	}
309	>
310	>	void SimInfo::calcNdfRaw() {
311		int ndfRaw_local;
312
313		MoleculeIterator i;
314	<	std::vector<StuntDouble*>::iterator j;
314	>	vector<StuntDouble*>::iterator j;
315		Molecule* mol;
316		StuntDouble* integrableObject;
317
#	Line 282 | Line 319 | void SimInfo::calcNdfRaw() {
319		ndfRaw_local = 0;
320
321		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
322	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
323	<	integrableObject = mol->nextIntegrableObject(j)) {
322	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
323	>	integrableObject = mol->nextIntegrableObject(j)) {
324
325	<	ndfRaw_local += 3;
325	>	ndfRaw_local += 3;
326
327	<	if (integrableObject->isDirectional()) {
328	<	if (integrableObject->isLinear()) {
329	<	ndfRaw_local += 2;
330	<	} else {
331	<	ndfRaw_local += 3;
332	<	}
333	<	}
327	>	if (integrableObject->isDirectional()) {
328	>	if (integrableObject->isLinear()) {
329	>	ndfRaw_local += 2;
330	>	} else {
331	>	ndfRaw_local += 3;
332	>	}
333	>	}
334
335	<	}
335	>	}
336		}
337
338		#ifdef IS_MPI
#	Line 303 | Line 340 | void SimInfo::calcNdfRaw() {
340		#else
341		ndfRaw_ = ndfRaw_local;
342		#endif
343	<	}
343	>	}
344
345	<	void SimInfo::calcNdfTrans() {
345	>	void SimInfo::calcNdfTrans() {
346		int ndfTrans_local;
347
348		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 319 | Line 356 | void SimInfo::calcNdfTrans() {
356
357		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
358
359	<	}
359	>	}
360
361	<	void SimInfo::addExcludePairs(Molecule* mol) {
362	<	std::vector<Bond*>::iterator bondIter;
363	<	std::vector<Bend*>::iterator bendIter;
364	<	std::vector<Torsion*>::iterator torsionIter;
361	>	void SimInfo::addInteractionPairs(Molecule* mol) {
362	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
363	>	vector<Bond*>::iterator bondIter;
364	>	vector<Bend*>::iterator bendIter;
365	>	vector<Torsion*>::iterator torsionIter;
366	>	vector<Inversion*>::iterator inversionIter;
367		Bond* bond;
368		Bend* bend;
369		Torsion* torsion;
370	+	Inversion* inversion;
371		int a;
372		int b;
373		int c;
374		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	–	}
375
376	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
377	<	a = bend->getAtomA()->getGlobalIndex();
378	<	b = bend->getAtomB()->getGlobalIndex();
379	<	c = bend->getAtomC()->getGlobalIndex();
376	>	// atomGroups can be used to add special interaction maps between
377	>	// groups of atoms that are in two separate rigid bodies.
378	>	// However, most site-site interactions between two rigid bodies
379	>	// are probably not special, just the ones between the physically
380	>	// bonded atoms.  Interactions *within* a single rigid body should
381	>	// always be excluded.  These are done at the bottom of this
382	>	// function.
383
384	<	exclude_.addPair(a, b);
385	<	exclude_.addPair(a, c);
386	<	exclude_.addPair(b, c);
387	<	}
388	<
389	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
390	<	a = torsion->getAtomA()->getGlobalIndex();
391	<	b = torsion->getAtomB()->getGlobalIndex();
392	<	c = torsion->getAtomC()->getGlobalIndex();
393	<	d = torsion->getAtomD()->getGlobalIndex();
384	>	map<int, set<int> > atomGroups;
385	>	Molecule::RigidBodyIterator rbIter;
386	>	RigidBody* rb;
387	>	Molecule::IntegrableObjectIterator ii;
388	>	StuntDouble* integrableObject;
389	>
390	>	for (integrableObject = mol->beginIntegrableObject(ii);
391	>	integrableObject != NULL;
392	>	integrableObject = mol->nextIntegrableObject(ii)) {
393	>
394	>	if (integrableObject->isRigidBody()) {
395	>	rb = static_cast<RigidBody*>(integrableObject);
396	>	vector<Atom*> atoms = rb->getAtoms();
397	>	set<int> rigidAtoms;
398	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
399	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
400	>	}
401	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
402	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
403	>	}
404	>	} else {
405	>	set<int> oneAtomSet;
406	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
407	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
408	>	}
409	>	}
410	>
411	>	for (bond= mol->beginBond(bondIter); bond != NULL;
412	>	bond = mol->nextBond(bondIter)) {
413
414	<	exclude_.addPair(a, b);
415	<	exclude_.addPair(a, c);
416	<	exclude_.addPair(a, d);
417	<	exclude_.addPair(b, c);
418	<	exclude_.addPair(b, d);
419	<	exclude_.addPair(c, d);
414	>	a = bond->getAtomA()->getGlobalIndex();
415	>	b = bond->getAtomB()->getGlobalIndex();
416	>
417	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
418	>	oneTwoInteractions_.addPair(a, b);
419	>	} else {
420	>	excludedInteractions_.addPair(a, b);
421	>	}
422		}
423
424	<
425	<	}
424	>	for (bend= mol->beginBend(bendIter); bend != NULL;
425	>	bend = mol->nextBend(bendIter)) {
426
427	<	void SimInfo::removeExcludePairs(Molecule* mol) {
428	<	std::vector<Bond*>::iterator bondIter;
429	<	std::vector<Bend*>::iterator bendIter;
430	<	std::vector<Torsion*>::iterator torsionIter;
427	>	a = bend->getAtomA()->getGlobalIndex();
428	>	b = bend->getAtomB()->getGlobalIndex();
429	>	c = bend->getAtomC()->getGlobalIndex();
430	>
431	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
432	>	oneTwoInteractions_.addPair(a, b);
433	>	oneTwoInteractions_.addPair(b, c);
434	>	} else {
435	>	excludedInteractions_.addPair(a, b);
436	>	excludedInteractions_.addPair(b, c);
437	>	}
438	>
439	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
440	>	oneThreeInteractions_.addPair(a, c);
441	>	} else {
442	>	excludedInteractions_.addPair(a, c);
443	>	}
444	>	}
445	>
446	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
447	>	torsion = mol->nextTorsion(torsionIter)) {
448	>
449	>	a = torsion->getAtomA()->getGlobalIndex();
450	>	b = torsion->getAtomB()->getGlobalIndex();
451	>	c = torsion->getAtomC()->getGlobalIndex();
452	>	d = torsion->getAtomD()->getGlobalIndex();
453	>
454	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
455	>	oneTwoInteractions_.addPair(a, b);
456	>	oneTwoInteractions_.addPair(b, c);
457	>	oneTwoInteractions_.addPair(c, d);
458	>	} else {
459	>	excludedInteractions_.addPair(a, b);
460	>	excludedInteractions_.addPair(b, c);
461	>	excludedInteractions_.addPair(c, d);
462	>	}
463	>
464	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
465	>	oneThreeInteractions_.addPair(a, c);
466	>	oneThreeInteractions_.addPair(b, d);
467	>	} else {
468	>	excludedInteractions_.addPair(a, c);
469	>	excludedInteractions_.addPair(b, d);
470	>	}
471	>
472	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
473	>	oneFourInteractions_.addPair(a, d);
474	>	} else {
475	>	excludedInteractions_.addPair(a, d);
476	>	}
477	>	}
478	>
479	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
480	>	inversion = mol->nextInversion(inversionIter)) {
481	>
482	>	a = inversion->getAtomA()->getGlobalIndex();
483	>	b = inversion->getAtomB()->getGlobalIndex();
484	>	c = inversion->getAtomC()->getGlobalIndex();
485	>	d = inversion->getAtomD()->getGlobalIndex();
486	>
487	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
488	>	oneTwoInteractions_.addPair(a, b);
489	>	oneTwoInteractions_.addPair(a, c);
490	>	oneTwoInteractions_.addPair(a, d);
491	>	} else {
492	>	excludedInteractions_.addPair(a, b);
493	>	excludedInteractions_.addPair(a, c);
494	>	excludedInteractions_.addPair(a, d);
495	>	}
496	>
497	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
498	>	oneThreeInteractions_.addPair(b, c);
499	>	oneThreeInteractions_.addPair(b, d);
500	>	oneThreeInteractions_.addPair(c, d);
501	>	} else {
502	>	excludedInteractions_.addPair(b, c);
503	>	excludedInteractions_.addPair(b, d);
504	>	excludedInteractions_.addPair(c, d);
505	>	}
506	>	}
507	>
508	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
509	>	rb = mol->nextRigidBody(rbIter)) {
510	>	vector<Atom*> atoms = rb->getAtoms();
511	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
512	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
513	>	a = atoms[i]->getGlobalIndex();
514	>	b = atoms[j]->getGlobalIndex();
515	>	excludedInteractions_.addPair(a, b);
516	>	}
517	>	}
518	>	}
519	>
520	>	}
521	>
522	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
523	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
524	>	vector<Bond*>::iterator bondIter;
525	>	vector<Bend*>::iterator bendIter;
526	>	vector<Torsion*>::iterator torsionIter;
527	>	vector<Inversion*>::iterator inversionIter;
528		Bond* bond;
529		Bend* bend;
530		Torsion* torsion;
531	+	Inversion* inversion;
532		int a;
533		int b;
534		int c;
535		int d;
536	+
537	+	map<int, set<int> > atomGroups;
538	+	Molecule::RigidBodyIterator rbIter;
539	+	RigidBody* rb;
540	+	Molecule::IntegrableObjectIterator ii;
541	+	StuntDouble* integrableObject;
542
543	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
544	<	a = bond->getAtomA()->getGlobalIndex();
545	<	b = bond->getAtomB()->getGlobalIndex();
546	<	exclude_.removePair(a, b);
543	>	for (integrableObject = mol->beginIntegrableObject(ii);
544	>	integrableObject != NULL;
545	>	integrableObject = mol->nextIntegrableObject(ii)) {
546	>
547	>	if (integrableObject->isRigidBody()) {
548	>	rb = static_cast<RigidBody*>(integrableObject);
549	>	vector<Atom*> atoms = rb->getAtoms();
550	>	set<int> rigidAtoms;
551	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
552	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
553	>	}
554	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
555	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
556	>	}
557	>	} else {
558	>	set<int> oneAtomSet;
559	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
560	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
561	>	}
562	>	}
563	>
564	>	for (bond= mol->beginBond(bondIter); bond != NULL;
565	>	bond = mol->nextBond(bondIter)) {
566	>
567	>	a = bond->getAtomA()->getGlobalIndex();
568	>	b = bond->getAtomB()->getGlobalIndex();
569	>
570	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
571	>	oneTwoInteractions_.removePair(a, b);
572	>	} else {
573	>	excludedInteractions_.removePair(a, b);
574	>	}
575		}
576
577	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
578	<	a = bend->getAtomA()->getGlobalIndex();
389	<	b = bend->getAtomB()->getGlobalIndex();
390	<	c = bend->getAtomC()->getGlobalIndex();
577	>	for (bend= mol->beginBend(bendIter); bend != NULL;
578	>	bend = mol->nextBend(bendIter)) {
579
580	<	exclude_.removePair(a, b);
581	<	exclude_.removePair(a, c);
582	<	exclude_.removePair(b, c);
580	>	a = bend->getAtomA()->getGlobalIndex();
581	>	b = bend->getAtomB()->getGlobalIndex();
582	>	c = bend->getAtomC()->getGlobalIndex();
583	>
584	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
585	>	oneTwoInteractions_.removePair(a, b);
586	>	oneTwoInteractions_.removePair(b, c);
587	>	} else {
588	>	excludedInteractions_.removePair(a, b);
589	>	excludedInteractions_.removePair(b, c);
590	>	}
591	>
592	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
593	>	oneThreeInteractions_.removePair(a, c);
594	>	} else {
595	>	excludedInteractions_.removePair(a, c);
596	>	}
597		}
598
599	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
600	<	a = torsion->getAtomA()->getGlobalIndex();
399	<	b = torsion->getAtomB()->getGlobalIndex();
400	<	c = torsion->getAtomC()->getGlobalIndex();
401	<	d = torsion->getAtomD()->getGlobalIndex();
599	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
600	>	torsion = mol->nextTorsion(torsionIter)) {
601
602	<	exclude_.removePair(a, b);
603	<	exclude_.removePair(a, c);
604	<	exclude_.removePair(a, d);
605	<	exclude_.removePair(b, c);
606	<	exclude_.removePair(b, d);
607	<	exclude_.removePair(c, d);
602	>	a = torsion->getAtomA()->getGlobalIndex();
603	>	b = torsion->getAtomB()->getGlobalIndex();
604	>	c = torsion->getAtomC()->getGlobalIndex();
605	>	d = torsion->getAtomD()->getGlobalIndex();
606	>
607	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
608	>	oneTwoInteractions_.removePair(a, b);
609	>	oneTwoInteractions_.removePair(b, c);
610	>	oneTwoInteractions_.removePair(c, d);
611	>	} else {
612	>	excludedInteractions_.removePair(a, b);
613	>	excludedInteractions_.removePair(b, c);
614	>	excludedInteractions_.removePair(c, d);
615	>	}
616	>
617	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
618	>	oneThreeInteractions_.removePair(a, c);
619	>	oneThreeInteractions_.removePair(b, d);
620	>	} else {
621	>	excludedInteractions_.removePair(a, c);
622	>	excludedInteractions_.removePair(b, d);
623	>	}
624	>
625	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
626	>	oneFourInteractions_.removePair(a, d);
627	>	} else {
628	>	excludedInteractions_.removePair(a, d);
629	>	}
630		}
631
632	<	}
632	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
633	>	inversion = mol->nextInversion(inversionIter)) {
634
635	+	a = inversion->getAtomA()->getGlobalIndex();
636	+	b = inversion->getAtomB()->getGlobalIndex();
637	+	c = inversion->getAtomC()->getGlobalIndex();
638	+	d = inversion->getAtomD()->getGlobalIndex();
639
640	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
641	<	int curStampId;
640	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
641	>	oneTwoInteractions_.removePair(a, b);
642	>	oneTwoInteractions_.removePair(a, c);
643	>	oneTwoInteractions_.removePair(a, d);
644	>	} else {
645	>	excludedInteractions_.removePair(a, b);
646	>	excludedInteractions_.removePair(a, c);
647	>	excludedInteractions_.removePair(a, d);
648	>	}
649
650	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
651	+	oneThreeInteractions_.removePair(b, c);
652	+	oneThreeInteractions_.removePair(b, d);
653	+	oneThreeInteractions_.removePair(c, d);
654	+	} else {
655	+	excludedInteractions_.removePair(b, c);
656	+	excludedInteractions_.removePair(b, d);
657	+	excludedInteractions_.removePair(c, d);
658	+	}
659	+	}
660	+
661	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
662	+	rb = mol->nextRigidBody(rbIter)) {
663	+	vector<Atom*> atoms = rb->getAtoms();
664	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
665	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
666	+	a = atoms[i]->getGlobalIndex();
667	+	b = atoms[j]->getGlobalIndex();
668	+	excludedInteractions_.removePair(a, b);
669	+	}
670	+	}
671	+	}
672	+
673	+	}
674	+
675	+
676	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
677	+	int curStampId;
678	+
679		//index from 0
680		curStampId = moleculeStamps_.size();
681
682		moleculeStamps_.push_back(molStamp);
683		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
684	<	}
684	>	}
685
424	–	void SimInfo::update() {
686
687	<	setupSimType();
688	<
689	<	#ifdef IS_MPI
690	<	setupFortranParallel();
691	<	#endif
692	<
693	<	setupFortranSim();
694	<
695	<	//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	<
687	>	/**
688	>	* update
689	>	*
690	>	*  Performs the global checks and variable settings after the
691	>	*  objects have been created.
692	>	*
693	>	*/
694	>	void SimInfo::update() {
695	>	setupSimVariables();
696		calcNdf();
697		calcNdfRaw();
698		calcNdfTrans();
699	<
700	<	fortranInitialized_ = true;
701	<	}
702	<
703	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
699	>	}
700	>
701	>	/**
702	>	* getSimulatedAtomTypes
703	>	*
704	>	* Returns an STL set of AtomType* that are actually present in this
705	>	* simulation.  Must query all processors to assemble this information.
706	>	*
707	>	*/
708	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
709		SimInfo::MoleculeIterator mi;
710		Molecule* mol;
711		Molecule::AtomIterator ai;
712		Atom* atom;
713	<	std::set<AtomType*> atomTypes;
714	<
713	>	set<AtomType*> atomTypes;
714	>
715		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
716	+	for(atom = mol->beginAtom(ai); atom != NULL;
717	+	atom = mol->nextAtom(ai)) {
718	+	atomTypes.insert(atom->getAtomType());
719	+	}
720	+	}
721	+
722	+	#ifdef IS_MPI
723
724	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
725	<	atomTypes.insert(atom->getAtomType());
726	<	}
727	<
728	<	}
724	>	// loop over the found atom types on this processor, and add their
725	>	// numerical idents to a vector:
726	>
727	>	vector<int> foundTypes;
728	>	set<AtomType*>::iterator i;
729	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
730	>	foundTypes.push_back( (*i)->getIdent() );
731
732	<	return atomTypes;
733	<	}
732	>	// count_local holds the number of found types on this processor
733	>	int count_local = foundTypes.size();
734
735	<	void SimInfo::setupSimType() {
474	<	std::set<AtomType*>::iterator i;
475	<	std::set<AtomType*> atomTypes;
476	<	atomTypes = getUniqueAtomTypes();
477	<
478	<	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();
735	>	int nproc = MPI::COMM_WORLD.Get_size();
736
737	<	//loop over all of the atom types
738	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
739	<	useLennardJones |= (*i)->isLennardJones();
740	<	useElectrostatic |= (*i)->isElectrostatic();
498	<	useEAM |= (*i)->isEAM();
499	<	useCharge |= (*i)->isCharge();
500	<	useDirectional |= (*i)->isDirectional();
501	<	useDipole |= (*i)->isDipole();
502	<	useGayBerne |= (*i)->isGayBerne();
503	<	useSticky |= (*i)->isSticky();
504	<	useShape |= (*i)->isShape();
505	<	}
737	>	// we need arrays to hold the counts and displacement vectors for
738	>	// all processors
739	>	vector<int> counts(nproc, 0);
740	>	vector<int> disps(nproc, 0);
741
742	<	if (useSticky || useDipole || useGayBerne || useShape) {
743	<	useDirectionalAtom = 1;
742	>	// fill the counts array
743	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
744	>	1, MPI::INT);
745	>
746	>	// use the processor counts to compute the displacement array
747	>	disps[0] = 0;
748	>	int totalCount = counts[0];
749	>	for (int iproc = 1; iproc < nproc; iproc++) {
750	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
751	>	totalCount += counts[iproc];
752		}
753
754	<	if (useCharge || useDipole) {
755	<	useElectrostatics = 1;
756	<	}
754	>	// we need a (possibly redundant) set of all found types:
755	>	vector<int> ftGlobal(totalCount);
756	>
757	>	// now spray out the foundTypes to all the other processors:
758	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
759	>	&ftGlobal[0], &counts[0], &disps[0],
760	>	MPI::INT);
761
762	<	#ifdef IS_MPI
516	<	int temp;
762	>	vector<int>::iterator j;
763
764	<	temp = usePBC;
765	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
764	>	// foundIdents is a stl set, so inserting an already found ident
765	>	// will have no effect.
766	>	set<int> foundIdents;
767
768	<	temp = useDirectionalAtom;
769	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
768	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
769	>	foundIdents.insert((*j));
770	>
771	>	// now iterate over the foundIdents and get the actual atom types
772	>	// that correspond to these:
773	>	set<int>::iterator it;
774	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
775	>	atomTypes.insert( forceField_->getAtomType((*it)) );
776	>
777	>	#endif
778
779	<	temp = useLennardJones;
780	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
779	>	return atomTypes;
780	>	}
781
782	<	temp = useElectrostatics;
783	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
782	>	void SimInfo::setupSimVariables() {
783	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
784	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
785	>	calcBoxDipole_ = false;
786	>	if ( simParams_->haveAccumulateBoxDipole() )
787	>	if ( simParams_->getAccumulateBoxDipole() ) {
788	>	calcBoxDipole_ = true;
789	>	}
790	>
791	>	set<AtomType*>::iterator i;
792	>	set<AtomType*> atomTypes;
793	>	atomTypes = getSimulatedAtomTypes();
794	>	int usesElectrostatic = 0;
795	>	int usesMetallic = 0;
796	>	int usesDirectional = 0;
797	>	int usesFluctuatingCharges =  0;
798	>	//loop over all of the atom types
799	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
800	>	usesElectrostatic |= (*i)->isElectrostatic();
801	>	usesMetallic |= (*i)->isMetal();
802	>	usesDirectional |= (*i)->isDirectional();
803	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
804	>	}
805	>
806	>	#ifdef IS_MPI
807	>	int temp;
808	>	temp = usesDirectional;
809	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810	>
811	>	temp = usesMetallic;
812	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813	>
814	>	temp = usesElectrostatic;
815	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816
817	<	temp = useCharge;
818	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
817	>	temp = usesFluctuatingCharges;
818	>	MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819	>	#else
820
821	<	temp = useDipole;
822	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
821	>	usesDirectionalAtoms_ = usesDirectional;
822	>	usesMetallicAtoms_ = usesMetallic;
823	>	usesElectrostaticAtoms_ = usesElectrostatic;
824	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
825
826	<	temp = useSticky;
827	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
826	>	#endif
827	>
828	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
829	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
830	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
831	>	}
832
539	–	temp = useGayBerne;
540	–	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
833
834	<	temp = useEAM;
835	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
834	>	vector<int> SimInfo::getGlobalAtomIndices() {
835	>	SimInfo::MoleculeIterator mi;
836	>	Molecule* mol;
837	>	Molecule::AtomIterator ai;
838	>	Atom* atom;
839
840	<	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);
840	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
841
842	<	#endif
842	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
843	>
844	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
845	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
846	>	}
847	>	}
848	>	return GlobalAtomIndices;
849	>	}
850
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;
851
852	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
852	>	vector<int> SimInfo::getGlobalGroupIndices() {
853	>	SimInfo::MoleculeIterator mi;
854	>	Molecule* mol;
855	>	Molecule::CutoffGroupIterator ci;
856	>	CutoffGroup* cg;
857
858	<	if (simParams_->haveDielectric()) {
859	<	fInfo_.dielect = simParams_->getDielectric();
860	<	} else {
861	<	sprintf(painCave.errMsg,
862	<	"SimSetup Error: No Dielectric constant was set.\n"
863	<	"\tYou are trying to use Reaction Field without"
864	<	"\tsetting a dielectric constant!\n");
865	<	painCave.isFatal = 1;
866	<	simError();
867	<	}
581	<
582	<	} else {
583	<	fInfo_.dielect = 0.0;
858	>	vector<int> GlobalGroupIndices;
859	>
860	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
861	>
862	>	//local index of cutoff group is trivial, it only depends on the
863	>	//order of travesing
864	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
865	>	cg = mol->nextCutoffGroup(ci)) {
866	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
867	>	}
868		}
869	+	return GlobalGroupIndices;
870	+	}
871
586	–	}
872
873	<	void SimInfo::setupFortranSim() {
874	<	int isError;
590	<	int nExclude;
591	<	std::vector<int> fortranGlobalGroupMembership;
592	<
593	<	nExclude = exclude_.getSize();
594	<	isError = 0;
873	>	void SimInfo::prepareTopology() {
874	>	int nExclude, nOneTwo, nOneThree, nOneFour;
875
596	–	//globalGroupMembership_ is filled by SimCreator
597	–	for (int i = 0; i < nGlobalAtoms_; i++) {
598	–	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
599	–	}
600	–
876		//calculate mass ratio of cutoff group
602	–	std::vector<double> mfact;
877		SimInfo::MoleculeIterator mi;
878		Molecule* mol;
879		Molecule::CutoffGroupIterator ci;
880		CutoffGroup* cg;
881		Molecule::AtomIterator ai;
882		Atom* atom;
883	<	double totalMass;
883	>	RealType totalMass;
884
885	<	//to avoid memory reallocation, reserve enough space for mfact
886	<	mfact.reserve(getNCutoffGroups());
885	>	/**
886	>	* The mass factor is the relative mass of an atom to the total
887	>	* mass of the cutoff group it belongs to.  By default, all atoms
888	>	* are their own cutoff groups, and therefore have mass factors of
889	>	* 1.  We need some special handling for massless atoms, which
890	>	* will be treated as carrying the entire mass of the cutoff
891	>	* group.
892	>	*/
893	>	massFactors_.clear();
894	>	massFactors_.resize(getNAtoms(), 1.0);
895
896		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
897	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
897	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
898	>	cg = mol->nextCutoffGroup(ci)) {
899
900	<	totalMass = cg->getMass();
901	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
902	<	mfact.push_back(atom->getMass()/totalMass);
903	<	}
904	<
905	<	}
900	>	totalMass = cg->getMass();
901	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
902	>	// Check for massless groups - set mfact to 1 if true
903	>	if (totalMass != 0)
904	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
905	>	else
906	>	massFactors_[atom->getLocalIndex()] = 1.0;
907	>	}
908	>	}
909		}
910
911	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
626	<	std::vector<int> identArray;
911	>	// Build the identArray_
912
913	<	//to avoid memory reallocation, reserve enough space identArray
914	<	identArray.reserve(getNAtoms());
630	<
913	>	identArray_.clear();
914	>	identArray_.reserve(getNAtoms());
915		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
916	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
917	<	identArray.push_back(atom->getIdent());
918	<	}
916	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
917	>	identArray_.push_back(atom->getIdent());
918	>	}
919		}
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	–	}
920
921	<	//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);
921	>	//scan topology
922
923	<	if( isError ){
923	>	nExclude = excludedInteractions_.getSize();
924	>	nOneTwo = oneTwoInteractions_.getSize();
925	>	nOneThree = oneThreeInteractions_.getSize();
926	>	nOneFour = oneFourInteractions_.getSize();
927
928	<	sprintf( painCave.errMsg,
929	<	"There was an error setting the simulation information in fortran.\n" );
930	<	painCave.isFatal = 1;
931	<	painCave.severity = OOPSE_ERROR;
661	<	simError();
662	<	}
928	>	int* excludeList = excludedInteractions_.getPairList();
929	>	int* oneTwoList = oneTwoInteractions_.getPairList();
930	>	int* oneThreeList = oneThreeInteractions_.getPairList();
931	>	int* oneFourList = oneFourInteractions_.getPairList();
932
933	<	#ifdef IS_MPI
934	<	sprintf( checkPointMsg,
666	<	"succesfully sent the simulation information to fortran.\n");
667	<	MPIcheckPoint();
668	<	#endif // is_mpi
669	<	}
933	>	topologyDone_ = true;
934	>	}
935
936	+	void SimInfo::addProperty(GenericData* genData) {
937	+	properties_.addProperty(genData);
938	+	}
939
940	<	#ifdef IS_MPI
941	<	void SimInfo::setupFortranParallel() {
942	<
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;
940	>	void SimInfo::removeProperty(const string& propName) {
941	>	properties_.removeProperty(propName);
942	>	}
943
944	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
944	>	void SimInfo::clearProperties() {
945	>	properties_.clearProperties();
946	>	}
947
948	<	//local index(index in DataStorge) of atom is important
949	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
950	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
951	<	}
948	>	vector<string> SimInfo::getPropertyNames() {
949	>	return properties_.getPropertyNames();
950	>	}
951	>
952	>	vector<GenericData*> SimInfo::getProperties() {
953	>	return properties_.getProperties();
954	>	}
955
956	<	//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) {
956	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
957		return properties_.getPropertyByName(propName);
958	<	}
958	>	}
959
960	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
960	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
961	>	if (sman_ == sman) {
962	>	return;
963	>	}
964	>	delete sman_;
965		sman_ = sman;
966
967		Molecule* mol;
968		RigidBody* rb;
969		Atom* atom;
970	+	CutoffGroup* cg;
971		SimInfo::MoleculeIterator mi;
972		Molecule::RigidBodyIterator rbIter;
973	<	Molecule::AtomIterator atomIter;;
973	>	Molecule::AtomIterator atomIter;
974	>	Molecule::CutoffGroupIterator cgIter;
975
976		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
977
978	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
979	<	atom->setSnapshotManager(sman_);
980	<	}
978	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
979	>	atom->setSnapshotManager(sman_);
980	>	}
981
982	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
983	<	rb->setSnapshotManager(sman_);
984	<	}
982	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
983	>	rb->setSnapshotManager(sman_);
984	>	}
985	>
986	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
987	>	cg->setSnapshotManager(sman_);
988	>	}
989		}
990
991	<	}
991	>	}
992
993	<	Vector3d SimInfo::getComVel(){
993	>	Vector3d SimInfo::getComVel(){
994		SimInfo::MoleculeIterator i;
995		Molecule* mol;
996
997		Vector3d comVel(0.0);
998	<	double totalMass = 0.0;
998	>	RealType totalMass = 0.0;
999
1000
1001		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1002	<	double mass = mol->getMass();
1003	<	totalMass += mass;
1004	<	comVel += mass * mol->getComVel();
1002	>	RealType mass = mol->getMass();
1003	>	totalMass += mass;
1004	>	comVel += mass * mol->getComVel();
1005		}
1006
1007		#ifdef IS_MPI
1008	<	double tmpMass = totalMass;
1008	>	RealType tmpMass = totalMass;
1009		Vector3d tmpComVel(comVel);
1010	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1011	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1010	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1011	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1012		#endif
1013
1014		comVel /= totalMass;
1015
1016		return comVel;
1017	<	}
1017	>	}
1018
1019	<	Vector3d SimInfo::getCom(){
1019	>	Vector3d SimInfo::getCom(){
1020		SimInfo::MoleculeIterator i;
1021		Molecule* mol;
1022
1023		Vector3d com(0.0);
1024	<	double totalMass = 0.0;
1024	>	RealType totalMass = 0.0;
1025
1026		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1027	<	double mass = mol->getMass();
1028	<	totalMass += mass;
1029	<	com += mass * mol->getCom();
1027	>	RealType mass = mol->getMass();
1028	>	totalMass += mass;
1029	>	com += mass * mol->getCom();
1030		}
1031
1032		#ifdef IS_MPI
1033	<	double tmpMass = totalMass;
1033	>	RealType tmpMass = totalMass;
1034		Vector3d tmpCom(com);
1035	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1036	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1035	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1036	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1037		#endif
1038
1039		com /= totalMass;
1040
1041		return com;
1042
1043	<	}
1043	>	}
1044
1045	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1045	>	ostream& operator <<(ostream& o, SimInfo& info) {
1046
1047		return o;
1048	<	}
1048	>	}
1049	>
1050	>
1051	>	/*
1052	>	Returns center of mass and center of mass velocity in one function call.
1053	>	*/
1054	>
1055	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1056	>	SimInfo::MoleculeIterator i;
1057	>	Molecule* mol;
1058	>
1059	>
1060	>	RealType totalMass = 0.0;
1061	>
1062
1063	<	}//end namespace oopse
1063	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1064	>	RealType mass = mol->getMass();
1065	>	totalMass += mass;
1066	>	com += mass * mol->getCom();
1067	>	comVel += mass * mol->getComVel();
1068	>	}
1069	>
1070	>	#ifdef IS_MPI
1071	>	RealType tmpMass = totalMass;
1072	>	Vector3d tmpCom(com);
1073	>	Vector3d tmpComVel(comVel);
1074	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1075	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1076	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1077	>	#endif
1078	>
1079	>	com /= totalMass;
1080	>	comVel /= totalMass;
1081	>	}
1082	>
1083	>	/*
1084	>	Return intertia tensor for entire system and angular momentum Vector.
1085
1086	+
1087	+	[  Ixx -Ixy  -Ixz ]
1088	+	J =| -Iyx  Iyy  -Iyz |
1089	+	[ -Izx -Iyz   Izz ]
1090	+	*/
1091	+
1092	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1093	+
1094	+
1095	+	RealType xx = 0.0;
1096	+	RealType yy = 0.0;
1097	+	RealType zz = 0.0;
1098	+	RealType xy = 0.0;
1099	+	RealType xz = 0.0;
1100	+	RealType yz = 0.0;
1101	+	Vector3d com(0.0);
1102	+	Vector3d comVel(0.0);
1103	+
1104	+	getComAll(com, comVel);
1105	+
1106	+	SimInfo::MoleculeIterator i;
1107	+	Molecule* mol;
1108	+
1109	+	Vector3d thisq(0.0);
1110	+	Vector3d thisv(0.0);
1111	+
1112	+	RealType thisMass = 0.0;
1113	+
1114	+
1115	+
1116	+
1117	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1118	+
1119	+	thisq = mol->getCom()-com;
1120	+	thisv = mol->getComVel()-comVel;
1121	+	thisMass = mol->getMass();
1122	+	// Compute moment of intertia coefficients.
1123	+	xx += thisq[0]*thisq[0]*thisMass;
1124	+	yy += thisq[1]*thisq[1]*thisMass;
1125	+	zz += thisq[2]*thisq[2]*thisMass;
1126	+
1127	+	// compute products of intertia
1128	+	xy += thisq[0]*thisq[1]*thisMass;
1129	+	xz += thisq[0]*thisq[2]*thisMass;
1130	+	yz += thisq[1]*thisq[2]*thisMass;
1131	+
1132	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1133	+
1134	+	}
1135	+
1136	+
1137	+	inertiaTensor(0,0) = yy + zz;
1138	+	inertiaTensor(0,1) = -xy;
1139	+	inertiaTensor(0,2) = -xz;
1140	+	inertiaTensor(1,0) = -xy;
1141	+	inertiaTensor(1,1) = xx + zz;
1142	+	inertiaTensor(1,2) = -yz;
1143	+	inertiaTensor(2,0) = -xz;
1144	+	inertiaTensor(2,1) = -yz;
1145	+	inertiaTensor(2,2) = xx + yy;
1146	+
1147	+	#ifdef IS_MPI
1148	+	Mat3x3d tmpI(inertiaTensor);
1149	+	Vector3d tmpAngMom;
1150	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1151	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1152	+	#endif
1153	+
1154	+	return;
1155	+	}
1156	+
1157	+	//Returns the angular momentum of the system
1158	+	Vector3d SimInfo::getAngularMomentum(){
1159	+
1160	+	Vector3d com(0.0);
1161	+	Vector3d comVel(0.0);
1162	+	Vector3d angularMomentum(0.0);
1163	+
1164	+	getComAll(com,comVel);
1165	+
1166	+	SimInfo::MoleculeIterator i;
1167	+	Molecule* mol;
1168	+
1169	+	Vector3d thisr(0.0);
1170	+	Vector3d thisp(0.0);
1171	+
1172	+	RealType thisMass;
1173	+
1174	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1175	+	thisMass = mol->getMass();
1176	+	thisr = mol->getCom()-com;
1177	+	thisp = (mol->getComVel()-comVel)*thisMass;
1178	+
1179	+	angularMomentum += cross( thisr, thisp );
1180	+
1181	+	}
1182	+
1183	+	#ifdef IS_MPI
1184	+	Vector3d tmpAngMom;
1185	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1186	+	#endif
1187	+
1188	+	return angularMomentum;
1189	+	}
1190	+
1191	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1192	+	return IOIndexToIntegrableObject.at(index);
1193	+	}
1194	+
1195	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1196	+	IOIndexToIntegrableObject= v;
1197	+	}
1198	+
1199	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1200	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1201	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1202	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1203	+	*/
1204	+	void SimInfo::getGyrationalVolume(RealType &volume){
1205	+	Mat3x3d intTensor;
1206	+	RealType det;
1207	+	Vector3d dummyAngMom;
1208	+	RealType sysconstants;
1209	+	RealType geomCnst;
1210	+
1211	+	geomCnst = 3.0/2.0;
1212	+	/* Get the inertial tensor and angular momentum for free*/
1213	+	getInertiaTensor(intTensor,dummyAngMom);
1214	+
1215	+	det = intTensor.determinant();
1216	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1217	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1218	+	return;
1219	+	}
1220	+
1221	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1222	+	Mat3x3d intTensor;
1223	+	Vector3d dummyAngMom;
1224	+	RealType sysconstants;
1225	+	RealType geomCnst;
1226	+
1227	+	geomCnst = 3.0/2.0;
1228	+	/* Get the inertial tensor and angular momentum for free*/
1229	+	getInertiaTensor(intTensor,dummyAngMom);
1230	+
1231	+	detI = intTensor.determinant();
1232	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1233	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1234	+	return;
1235	+	}
1236	+	/*
1237	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1238	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1239	+	sdByGlobalIndex_ = v;
1240	+	}
1241	+
1242	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1243	+	//assert(index < nAtoms_ + nRigidBodies_);
1244	+	return sdByGlobalIndex_.at(index);
1245	+	}
1246	+	*/
1247	+	int SimInfo::getNGlobalConstraints() {
1248	+	int nGlobalConstraints;
1249	+	#ifdef IS_MPI
1250	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1251	+	MPI_COMM_WORLD);
1252	+	#else
1253	+	nGlobalConstraints =  nConstraints_;
1254	+	#endif
1255	+	return nGlobalConstraints;
1256	+	}
1257	+
1258	+	}//end namespace OpenMD
1259	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1744 by gezelter, Tue Jun 5 18:07:08 2012 UTC

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