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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 334 by tim, Mon Feb 14 17:57:01 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 48 | Line 48
48
49		#include <algorithm>
50		#include <set>
51	+	#include <map>
52
53		#include "brains/SimInfo.hpp"
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56	<	#include "UseTheForce/doForces_interface.h"
56	<	#include "UseTheForce/notifyCutoffs_interface.h"
56	>	#include "primitives/StuntDouble.hpp"
57		#include "utils/MemoryUtils.hpp"
58		#include "utils/simError.h"
59		#include "selection/SelectionManager.hpp"
60	<
60	>	#include "io/ForceFieldOptions.hpp"
61	>	#include "UseTheForce/ForceField.hpp"
62	>	#include "nonbonded/SwitchingFunction.hpp"
63		#ifdef IS_MPI
64	<	#include "UseTheForce/mpiComponentPlan.h"
65	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
64	<	#endif
64	>	#include <mpi.h>
65	>	#endif
66
67	<	namespace oopse {
68	<
69	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
70	<	ForceField* ff, Globals* simParams) :
71	<	forceField_(ff), simParams_(simParams),
72	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
73	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
74	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
75	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
76	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
77	<	sman_(NULL), fortranInitialized_(false), selectMan_(NULL) {
78	<
79	<
79	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
67	>	using namespace std;
68	>	namespace OpenMD {
69	>
70	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
71	>	forceField_(ff), simParams_(simParams),
72	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
73	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
74	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
75	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
76	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
77	>	nConstraints_(0), sman_(NULL), topologyDone_(false),
78	>	calcBoxDipole_(false), useAtomicVirial_(true) {
79	>
80		MoleculeStamp* molStamp;
81		int nMolWithSameStamp;
82		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
83	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
83	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
84		CutoffGroupStamp* cgStamp;
85		RigidBodyStamp* rbStamp;
86		int nRigidAtoms = 0;
87
88	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
89	<	molStamp = i->first;
90	<	nMolWithSameStamp = i->second;
91	<
92	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
93	<
94	<	//calculate atoms in molecules
95	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
96	<
97	<
98	<	//calculate atoms in cutoff groups
99	<	int nAtomsInGroups = 0;
100	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
101	<
102	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
103	<	cgStamp = molStamp->getCutoffGroup(j);
104	<	nAtomsInGroups += cgStamp->getNMembers();
105	<	}
106	<
107	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
108	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
109	<
110	<	//calculate atoms in rigid bodies
111	<	int nAtomsInRigidBodies = 0;
112	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
113	<
114	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
115	<	rbStamp = molStamp->getRigidBody(j);
116	<	nAtomsInRigidBodies += rbStamp->getNMembers();
117	<	}
118	<
119	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
120	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
121	<
88	>	vector<Component*> components = simParams->getComponents();
89	>
90	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
91	>	molStamp = (*i)->getMoleculeStamp();
92	>	nMolWithSameStamp = (*i)->getNMol();
93	>
94	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
95	>
96	>	//calculate atoms in molecules
97	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
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->getCutoffGroupStamp(j);
105	>	nAtomsInGroups += cgStamp->getNMembers();
106	>	}
107	>
108	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
109	>
110	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
111	>
112	>	//calculate atoms in rigid bodies
113	>	int nAtomsInRigidBodies = 0;
114	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
115	>
116	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
117	>	rbStamp = molStamp->getRigidBodyStamp(j);
118	>	nAtomsInRigidBodies += rbStamp->getNMembers();
119	>	}
120	>
121	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
122	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
123	>
124		}
125	+
126	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
127	+	//group therefore the total number of cutoff groups in the system is
128	+	//equal to the total number of atoms minus number of atoms belong to
129	+	//cutoff group defined in meta-data file plus the number of cutoff
130	+	//groups defined in meta-data file
131
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
132		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
133	<
134	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
135	<	//therefore the total number of  integrable objects in the system is equal to
136	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
137	<	//file plus the number of  rigid bodies defined in meta-data file
138	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
139	<
133	>
134	>	//every free atom (atom does not belong to rigid bodies) is an
135	>	//integrable object therefore the total number of integrable objects
136	>	//in the system is equal to the total number of atoms minus number of
137	>	//atoms belong to rigid body defined in meta-data file plus the number
138	>	//of rigid bodies defined in meta-data file
139	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
140	>	+ nGlobalRigidBodies_;
141	>
142		nGlobalMols_ = molStampIds_.size();
137	–
138	–	#ifdef IS_MPI
143		molToProcMap_.resize(nGlobalMols_);
144	<	#endif
145	<
146	<	selectMan_ = new SelectionManager(this);
147	<	selectMan_->selectAll();
148	<	}
149	<
150	<	SimInfo::~SimInfo() {
151	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
152	<
149	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
150	<
144	>	}
145	>
146	>	SimInfo::~SimInfo() {
147	>	map<int, Molecule*>::iterator i;
148	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
149	>	delete i->second;
150	>	}
151	>	molecules_.clear();
152	>
153		delete sman_;
154		delete simParams_;
155		delete forceField_;
156	<	delete selectMan_;
155	<	}
156	>	}
157
157	–	int SimInfo::getNGlobalConstraints() {
158	–	int nGlobalConstraints;
159	–	#ifdef IS_MPI
160	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
161	–	MPI_COMM_WORLD);
162	–	#else
163	–	nGlobalConstraints =  nConstraints_;
164	–	#endif
165	–	return nGlobalConstraints;
166	–	}
158
159	<	bool SimInfo::addMolecule(Molecule* mol) {
159	>	bool SimInfo::addMolecule(Molecule* mol) {
160		MoleculeIterator i;
161	<
161	>
162		i = molecules_.find(mol->getGlobalIndex());
163		if (i == molecules_.end() ) {
164	<
165	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
166	<
167	<	nAtoms_ += mol->getNAtoms();
168	<	nBonds_ += mol->getNBonds();
169	<	nBends_ += mol->getNBends();
170	<	nTorsions_ += mol->getNTorsions();
171	<	nRigidBodies_ += mol->getNRigidBodies();
172	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
173	<	nCutoffGroups_ += mol->getNCutoffGroups();
174	<	nConstraints_ += mol->getNConstraintPairs();
175	<
176	<	addExcludePairs(mol);
177	<
178	<	return true;
179	<	} else {
180	<	return false;
164	>
165	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
166	>
167	>	nAtoms_ += mol->getNAtoms();
168	>	nBonds_ += mol->getNBonds();
169	>	nBends_ += mol->getNBends();
170	>	nTorsions_ += mol->getNTorsions();
171	>	nInversions_ += mol->getNInversions();
172	>	nRigidBodies_ += mol->getNRigidBodies();
173	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
174	>	nCutoffGroups_ += mol->getNCutoffGroups();
175	>	nConstraints_ += mol->getNConstraintPairs();
176	>
177	>	addInteractionPairs(mol);
178	>
179	>	return true;
180	>	} else {
181	>	return false;
182		}
183	<	}
184	<
185	<	bool SimInfo::removeMolecule(Molecule* mol) {
183	>	}
184	>
185	>	bool SimInfo::removeMolecule(Molecule* mol) {
186		MoleculeIterator i;
187		i = molecules_.find(mol->getGlobalIndex());
188
189		if (i != molecules_.end() ) {
190
191	<	assert(mol == i->second);
191	>	assert(mol == i->second);
192
193	<	nAtoms_ -= mol->getNAtoms();
194	<	nBonds_ -= mol->getNBonds();
195	<	nBends_ -= mol->getNBends();
196	<	nTorsions_ -= mol->getNTorsions();
197	<	nRigidBodies_ -= mol->getNRigidBodies();
198	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
199	<	nCutoffGroups_ -= mol->getNCutoffGroups();
200	<	nConstraints_ -= mol->getNConstraintPairs();
193	>	nAtoms_ -= mol->getNAtoms();
194	>	nBonds_ -= mol->getNBonds();
195	>	nBends_ -= mol->getNBends();
196	>	nTorsions_ -= mol->getNTorsions();
197	>	nInversions_ -= mol->getNInversions();
198	>	nRigidBodies_ -= mol->getNRigidBodies();
199	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
200	>	nCutoffGroups_ -= mol->getNCutoffGroups();
201	>	nConstraints_ -= mol->getNConstraintPairs();
202
203	<	removeExcludePairs(mol);
204	<	molecules_.erase(mol->getGlobalIndex());
203	>	removeInteractionPairs(mol);
204	>	molecules_.erase(mol->getGlobalIndex());
205
206	<	delete mol;
206	>	delete mol;
207
208	<	return true;
208	>	return true;
209		} else {
210	<	return false;
210	>	return false;
211		}
212	+	}
213
220	–
221	–	}
222	–
214
215	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
215	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
216		i = molecules_.begin();
217		return i == molecules_.end() ? NULL : i->second;
218	<	}
218	>	}
219
220	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
220	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
221		++i;
222		return i == molecules_.end() ? NULL : i->second;
223	<	}
223	>	}
224
225
226	<	void SimInfo::calcNdf() {
226	>	void SimInfo::calcNdf() {
227		int ndf_local;
228		MoleculeIterator i;
229	<	std::vector<StuntDouble*>::iterator j;
229	>	vector<StuntDouble*>::iterator j;
230		Molecule* mol;
231		StuntDouble* integrableObject;
232
233		ndf_local = 0;
234
235		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
236	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
237	<	integrableObject = mol->nextIntegrableObject(j)) {
236	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
237	>	integrableObject = mol->nextIntegrableObject(j)) {
238
239	<	ndf_local += 3;
239	>	ndf_local += 3;
240
241	<	if (integrableObject->isDirectional()) {
242	<	if (integrableObject->isLinear()) {
243	<	ndf_local += 2;
244	<	} else {
245	<	ndf_local += 3;
246	<	}
247	<	}
241	>	if (integrableObject->isDirectional()) {
242	>	if (integrableObject->isLinear()) {
243	>	ndf_local += 2;
244	>	} else {
245	>	ndf_local += 3;
246	>	}
247	>	}
248
249	<	}//end for (integrableObject)
250	<	}// end for (mol)
249	>	}
250	>	}
251
252		// n_constraints is local, so subtract them on each processor
253		ndf_local -= nConstraints_;
#	Line 271 | Line 262 | void SimInfo::calcNdf() {
262		// entire system:
263		ndf_ = ndf_ - 3 - nZconstraint_;
264
265	<	}
265	>	}
266
267	<	void SimInfo::calcNdfRaw() {
267	>	int SimInfo::getFdf() {
268	>	#ifdef IS_MPI
269	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
270	>	#else
271	>	fdf_ = fdf_local;
272	>	#endif
273	>	return fdf_;
274	>	}
275	>
276	>	unsigned int SimInfo::getNLocalCutoffGroups(){
277	>	int nLocalCutoffAtoms = 0;
278	>	Molecule* mol;
279	>	MoleculeIterator mi;
280	>	CutoffGroup* cg;
281	>	Molecule::CutoffGroupIterator ci;
282	>
283	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
284	>
285	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
286	>	cg = mol->nextCutoffGroup(ci)) {
287	>	nLocalCutoffAtoms += cg->getNumAtom();
288	>
289	>	}
290	>	}
291	>
292	>	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
293	>	}
294	>
295	>	void SimInfo::calcNdfRaw() {
296		int ndfRaw_local;
297
298		MoleculeIterator i;
299	<	std::vector<StuntDouble*>::iterator j;
299	>	vector<StuntDouble*>::iterator j;
300		Molecule* mol;
301		StuntDouble* integrableObject;
302
#	Line 285 | Line 304 | void SimInfo::calcNdfRaw() {
304		ndfRaw_local = 0;
305
306		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
307	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
308	<	integrableObject = mol->nextIntegrableObject(j)) {
307	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
308	>	integrableObject = mol->nextIntegrableObject(j)) {
309
310	<	ndfRaw_local += 3;
310	>	ndfRaw_local += 3;
311
312	<	if (integrableObject->isDirectional()) {
313	<	if (integrableObject->isLinear()) {
314	<	ndfRaw_local += 2;
315	<	} else {
316	<	ndfRaw_local += 3;
317	<	}
318	<	}
312	>	if (integrableObject->isDirectional()) {
313	>	if (integrableObject->isLinear()) {
314	>	ndfRaw_local += 2;
315	>	} else {
316	>	ndfRaw_local += 3;
317	>	}
318	>	}
319
320	<	}
320	>	}
321		}
322
323		#ifdef IS_MPI
#	Line 306 | Line 325 | void SimInfo::calcNdfRaw() {
325		#else
326		ndfRaw_ = ndfRaw_local;
327		#endif
328	<	}
328	>	}
329
330	<	void SimInfo::calcNdfTrans() {
330	>	void SimInfo::calcNdfTrans() {
331		int ndfTrans_local;
332
333		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 322 | Line 341 | void SimInfo::calcNdfTrans() {
341
342		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
343
344	<	}
344	>	}
345
346	<	void SimInfo::addExcludePairs(Molecule* mol) {
347	<	std::vector<Bond*>::iterator bondIter;
348	<	std::vector<Bend*>::iterator bendIter;
349	<	std::vector<Torsion*>::iterator torsionIter;
346	>	void SimInfo::addInteractionPairs(Molecule* mol) {
347	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
348	>	vector<Bond*>::iterator bondIter;
349	>	vector<Bend*>::iterator bendIter;
350	>	vector<Torsion*>::iterator torsionIter;
351	>	vector<Inversion*>::iterator inversionIter;
352		Bond* bond;
353		Bend* bend;
354		Torsion* torsion;
355	+	Inversion* inversion;
356		int a;
357		int b;
358		int c;
359		int d;
338	–
339	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
340	–	a = bond->getAtomA()->getGlobalIndex();
341	–	b = bond->getAtomB()->getGlobalIndex();
342	–	exclude_.addPair(a, b);
343	–	}
360
361	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
362	<	a = bend->getAtomA()->getGlobalIndex();
363	<	b = bend->getAtomB()->getGlobalIndex();
364	<	c = bend->getAtomC()->getGlobalIndex();
361	>	// atomGroups can be used to add special interaction maps between
362	>	// groups of atoms that are in two separate rigid bodies.
363	>	// However, most site-site interactions between two rigid bodies
364	>	// are probably not special, just the ones between the physically
365	>	// bonded atoms.  Interactions *within* a single rigid body should
366	>	// always be excluded.  These are done at the bottom of this
367	>	// function.
368
369	<	exclude_.addPair(a, b);
370	<	exclude_.addPair(a, c);
371	<	exclude_.addPair(b, c);
372	<	}
373	<
374	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
375	<	a = torsion->getAtomA()->getGlobalIndex();
376	<	b = torsion->getAtomB()->getGlobalIndex();
377	<	c = torsion->getAtomC()->getGlobalIndex();
378	<	d = torsion->getAtomD()->getGlobalIndex();
369	>	map<int, set<int> > atomGroups;
370	>	Molecule::RigidBodyIterator rbIter;
371	>	RigidBody* rb;
372	>	Molecule::IntegrableObjectIterator ii;
373	>	StuntDouble* integrableObject;
374	>
375	>	for (integrableObject = mol->beginIntegrableObject(ii);
376	>	integrableObject != NULL;
377	>	integrableObject = mol->nextIntegrableObject(ii)) {
378	>
379	>	if (integrableObject->isRigidBody()) {
380	>	rb = static_cast<RigidBody*>(integrableObject);
381	>	vector<Atom*> atoms = rb->getAtoms();
382	>	set<int> rigidAtoms;
383	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
384	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
385	>	}
386	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
387	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
388	>	}
389	>	} else {
390	>	set<int> oneAtomSet;
391	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
392	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
393	>	}
394	>	}
395	>
396	>	for (bond= mol->beginBond(bondIter); bond != NULL;
397	>	bond = mol->nextBond(bondIter)) {
398
399	<	exclude_.addPair(a, b);
400	<	exclude_.addPair(a, c);
401	<	exclude_.addPair(a, d);
402	<	exclude_.addPair(b, c);
403	<	exclude_.addPair(b, d);
404	<	exclude_.addPair(c, d);
399	>	a = bond->getAtomA()->getGlobalIndex();
400	>	b = bond->getAtomB()->getGlobalIndex();
401	>
402	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
403	>	oneTwoInteractions_.addPair(a, b);
404	>	} else {
405	>	excludedInteractions_.addPair(a, b);
406	>	}
407		}
408
409	<
410	<	}
409	>	for (bend= mol->beginBend(bendIter); bend != NULL;
410	>	bend = mol->nextBend(bendIter)) {
411
412	<	void SimInfo::removeExcludePairs(Molecule* mol) {
413	<	std::vector<Bond*>::iterator bondIter;
414	<	std::vector<Bend*>::iterator bendIter;
415	<	std::vector<Torsion*>::iterator torsionIter;
412	>	a = bend->getAtomA()->getGlobalIndex();
413	>	b = bend->getAtomB()->getGlobalIndex();
414	>	c = bend->getAtomC()->getGlobalIndex();
415	>
416	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
417	>	oneTwoInteractions_.addPair(a, b);
418	>	oneTwoInteractions_.addPair(b, c);
419	>	} else {
420	>	excludedInteractions_.addPair(a, b);
421	>	excludedInteractions_.addPair(b, c);
422	>	}
423	>
424	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
425	>	oneThreeInteractions_.addPair(a, c);
426	>	} else {
427	>	excludedInteractions_.addPair(a, c);
428	>	}
429	>	}
430	>
431	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
432	>	torsion = mol->nextTorsion(torsionIter)) {
433	>
434	>	a = torsion->getAtomA()->getGlobalIndex();
435	>	b = torsion->getAtomB()->getGlobalIndex();
436	>	c = torsion->getAtomC()->getGlobalIndex();
437	>	d = torsion->getAtomD()->getGlobalIndex();
438	>
439	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
440	>	oneTwoInteractions_.addPair(a, b);
441	>	oneTwoInteractions_.addPair(b, c);
442	>	oneTwoInteractions_.addPair(c, d);
443	>	} else {
444	>	excludedInteractions_.addPair(a, b);
445	>	excludedInteractions_.addPair(b, c);
446	>	excludedInteractions_.addPair(c, d);
447	>	}
448	>
449	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
450	>	oneThreeInteractions_.addPair(a, c);
451	>	oneThreeInteractions_.addPair(b, d);
452	>	} else {
453	>	excludedInteractions_.addPair(a, c);
454	>	excludedInteractions_.addPair(b, d);
455	>	}
456	>
457	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
458	>	oneFourInteractions_.addPair(a, d);
459	>	} else {
460	>	excludedInteractions_.addPair(a, d);
461	>	}
462	>	}
463	>
464	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
465	>	inversion = mol->nextInversion(inversionIter)) {
466	>
467	>	a = inversion->getAtomA()->getGlobalIndex();
468	>	b = inversion->getAtomB()->getGlobalIndex();
469	>	c = inversion->getAtomC()->getGlobalIndex();
470	>	d = inversion->getAtomD()->getGlobalIndex();
471	>
472	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
473	>	oneTwoInteractions_.addPair(a, b);
474	>	oneTwoInteractions_.addPair(a, c);
475	>	oneTwoInteractions_.addPair(a, d);
476	>	} else {
477	>	excludedInteractions_.addPair(a, b);
478	>	excludedInteractions_.addPair(a, c);
479	>	excludedInteractions_.addPair(a, d);
480	>	}
481	>
482	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
483	>	oneThreeInteractions_.addPair(b, c);
484	>	oneThreeInteractions_.addPair(b, d);
485	>	oneThreeInteractions_.addPair(c, d);
486	>	} else {
487	>	excludedInteractions_.addPair(b, c);
488	>	excludedInteractions_.addPair(b, d);
489	>	excludedInteractions_.addPair(c, d);
490	>	}
491	>	}
492	>
493	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
494	>	rb = mol->nextRigidBody(rbIter)) {
495	>	vector<Atom*> atoms = rb->getAtoms();
496	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
497	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
498	>	a = atoms[i]->getGlobalIndex();
499	>	b = atoms[j]->getGlobalIndex();
500	>	excludedInteractions_.addPair(a, b);
501	>	}
502	>	}
503	>	}
504	>
505	>	}
506	>
507	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
508	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
509	>	vector<Bond*>::iterator bondIter;
510	>	vector<Bend*>::iterator bendIter;
511	>	vector<Torsion*>::iterator torsionIter;
512	>	vector<Inversion*>::iterator inversionIter;
513		Bond* bond;
514		Bend* bend;
515		Torsion* torsion;
516	+	Inversion* inversion;
517		int a;
518		int b;
519		int c;
520		int d;
521	+
522	+	map<int, set<int> > atomGroups;
523	+	Molecule::RigidBodyIterator rbIter;
524	+	RigidBody* rb;
525	+	Molecule::IntegrableObjectIterator ii;
526	+	StuntDouble* integrableObject;
527
528	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
529	<	a = bond->getAtomA()->getGlobalIndex();
530	<	b = bond->getAtomB()->getGlobalIndex();
531	<	exclude_.removePair(a, b);
528	>	for (integrableObject = mol->beginIntegrableObject(ii);
529	>	integrableObject != NULL;
530	>	integrableObject = mol->nextIntegrableObject(ii)) {
531	>
532	>	if (integrableObject->isRigidBody()) {
533	>	rb = static_cast<RigidBody*>(integrableObject);
534	>	vector<Atom*> atoms = rb->getAtoms();
535	>	set<int> rigidAtoms;
536	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
537	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
538	>	}
539	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
540	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
541	>	}
542	>	} else {
543	>	set<int> oneAtomSet;
544	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
545	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
546	>	}
547	>	}
548	>
549	>	for (bond= mol->beginBond(bondIter); bond != NULL;
550	>	bond = mol->nextBond(bondIter)) {
551	>
552	>	a = bond->getAtomA()->getGlobalIndex();
553	>	b = bond->getAtomB()->getGlobalIndex();
554	>
555	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
556	>	oneTwoInteractions_.removePair(a, b);
557	>	} else {
558	>	excludedInteractions_.removePair(a, b);
559	>	}
560		}
561
562	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
563	<	a = bend->getAtomA()->getGlobalIndex();
392	<	b = bend->getAtomB()->getGlobalIndex();
393	<	c = bend->getAtomC()->getGlobalIndex();
562	>	for (bend= mol->beginBend(bendIter); bend != NULL;
563	>	bend = mol->nextBend(bendIter)) {
564
565	<	exclude_.removePair(a, b);
566	<	exclude_.removePair(a, c);
567	<	exclude_.removePair(b, c);
565	>	a = bend->getAtomA()->getGlobalIndex();
566	>	b = bend->getAtomB()->getGlobalIndex();
567	>	c = bend->getAtomC()->getGlobalIndex();
568	>
569	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
570	>	oneTwoInteractions_.removePair(a, b);
571	>	oneTwoInteractions_.removePair(b, c);
572	>	} else {
573	>	excludedInteractions_.removePair(a, b);
574	>	excludedInteractions_.removePair(b, c);
575	>	}
576	>
577	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
578	>	oneThreeInteractions_.removePair(a, c);
579	>	} else {
580	>	excludedInteractions_.removePair(a, c);
581	>	}
582		}
583
584	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
585	<	a = torsion->getAtomA()->getGlobalIndex();
402	<	b = torsion->getAtomB()->getGlobalIndex();
403	<	c = torsion->getAtomC()->getGlobalIndex();
404	<	d = torsion->getAtomD()->getGlobalIndex();
584	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
585	>	torsion = mol->nextTorsion(torsionIter)) {
586
587	<	exclude_.removePair(a, b);
588	<	exclude_.removePair(a, c);
589	<	exclude_.removePair(a, d);
590	<	exclude_.removePair(b, c);
591	<	exclude_.removePair(b, d);
592	<	exclude_.removePair(c, d);
587	>	a = torsion->getAtomA()->getGlobalIndex();
588	>	b = torsion->getAtomB()->getGlobalIndex();
589	>	c = torsion->getAtomC()->getGlobalIndex();
590	>	d = torsion->getAtomD()->getGlobalIndex();
591	>
592	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
593	>	oneTwoInteractions_.removePair(a, b);
594	>	oneTwoInteractions_.removePair(b, c);
595	>	oneTwoInteractions_.removePair(c, d);
596	>	} else {
597	>	excludedInteractions_.removePair(a, b);
598	>	excludedInteractions_.removePair(b, c);
599	>	excludedInteractions_.removePair(c, d);
600	>	}
601	>
602	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
603	>	oneThreeInteractions_.removePair(a, c);
604	>	oneThreeInteractions_.removePair(b, d);
605	>	} else {
606	>	excludedInteractions_.removePair(a, c);
607	>	excludedInteractions_.removePair(b, d);
608	>	}
609	>
610	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
611	>	oneFourInteractions_.removePair(a, d);
612	>	} else {
613	>	excludedInteractions_.removePair(a, d);
614	>	}
615		}
616
617	<	}
617	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
618	>	inversion = mol->nextInversion(inversionIter)) {
619
620	+	a = inversion->getAtomA()->getGlobalIndex();
621	+	b = inversion->getAtomB()->getGlobalIndex();
622	+	c = inversion->getAtomC()->getGlobalIndex();
623	+	d = inversion->getAtomD()->getGlobalIndex();
624
625	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
626	<	int curStampId;
625	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
626	>	oneTwoInteractions_.removePair(a, b);
627	>	oneTwoInteractions_.removePair(a, c);
628	>	oneTwoInteractions_.removePair(a, d);
629	>	} else {
630	>	excludedInteractions_.removePair(a, b);
631	>	excludedInteractions_.removePair(a, c);
632	>	excludedInteractions_.removePair(a, d);
633	>	}
634
635	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
636	+	oneThreeInteractions_.removePair(b, c);
637	+	oneThreeInteractions_.removePair(b, d);
638	+	oneThreeInteractions_.removePair(c, d);
639	+	} else {
640	+	excludedInteractions_.removePair(b, c);
641	+	excludedInteractions_.removePair(b, d);
642	+	excludedInteractions_.removePair(c, d);
643	+	}
644	+	}
645	+
646	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
647	+	rb = mol->nextRigidBody(rbIter)) {
648	+	vector<Atom*> atoms = rb->getAtoms();
649	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
650	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
651	+	a = atoms[i]->getGlobalIndex();
652	+	b = atoms[j]->getGlobalIndex();
653	+	excludedInteractions_.removePair(a, b);
654	+	}
655	+	}
656	+	}
657	+
658	+	}
659	+
660	+
661	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
662	+	int curStampId;
663	+
664		//index from 0
665		curStampId = moleculeStamps_.size();
666
667		moleculeStamps_.push_back(molStamp);
668		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
669	<	}
669	>	}
670
427	–	void SimInfo::update() {
671
672	<	setupSimType();
673	<
674	<	#ifdef IS_MPI
675	<	setupFortranParallel();
676	<	#endif
677	<
678	<	setupFortranSim();
679	<
680	<	//setup fortran force field
438	<	/** @deprecate */
439	<	int isError = 0;
440	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
441	<	if(isError){
442	<	sprintf( painCave.errMsg,
443	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
444	<	painCave.isFatal = 1;
445	<	simError();
446	<	}
447	<
448	<
449	<	setupCutoff();
450	<
672	>	/**
673	>	* update
674	>	*
675	>	*  Performs the global checks and variable settings after the
676	>	*  objects have been created.
677	>	*
678	>	*/
679	>	void SimInfo::update() {
680	>	setupSimVariables();
681		calcNdf();
682		calcNdfRaw();
683		calcNdfTrans();
684	<
685	<	fortranInitialized_ = true;
686	<	}
687	<
688	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
684	>	}
685	>
686	>	/**
687	>	* getSimulatedAtomTypes
688	>	*
689	>	* Returns an STL set of AtomType* that are actually present in this
690	>	* simulation.  Must query all processors to assemble this information.
691	>	*
692	>	*/
693	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
694		SimInfo::MoleculeIterator mi;
695		Molecule* mol;
696		Molecule::AtomIterator ai;
697		Atom* atom;
698	<	std::set<AtomType*> atomTypes;
699	<
698	>	set<AtomType*> atomTypes;
699	>
700		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
701	+	for(atom = mol->beginAtom(ai); atom != NULL;
702	+	atom = mol->nextAtom(ai)) {
703	+	atomTypes.insert(atom->getAtomType());
704	+	}
705	+	}
706	+
707	+	#ifdef IS_MPI
708
709	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
710	<	atomTypes.insert(atom->getAtomType());
711	<	}
712	<
709	>	// loop over the found atom types on this processor, and add their
710	>	// numerical idents to a vector:
711	>
712	>	vector<int> foundTypes;
713	>	set<AtomType*>::iterator i;
714	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
715	>	foundTypes.push_back( (*i)->getIdent() );
716	>
717	>	// count_local holds the number of found types on this processor
718	>	int count_local = foundTypes.size();
719	>
720	>	int nproc = MPI::COMM_WORLD.Get_size();
721	>
722	>	// we need arrays to hold the counts and displacement vectors for
723	>	// all processors
724	>	vector<int> counts(nproc, 0);
725	>	vector<int> disps(nproc, 0);
726	>
727	>	// fill the counts array
728	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
729	>	1, MPI::INT);
730	>
731	>	// use the processor counts to compute the displacement array
732	>	disps[0] = 0;
733	>	int totalCount = counts[0];
734	>	for (int iproc = 1; iproc < nproc; iproc++) {
735	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
736	>	totalCount += counts[iproc];
737		}
738
739	<	return atomTypes;
740	<	}
739	>	// we need a (possibly redundant) set of all found types:
740	>	vector<int> ftGlobal(totalCount);
741	>
742	>	// now spray out the foundTypes to all the other processors:
743	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
744	>	&ftGlobal[0], &counts[0], &disps[0],
745	>	MPI::INT);
746
747	<	void SimInfo::setupSimType() {
748	<	std::set<AtomType*>::iterator i;
749	<	std::set<AtomType*> atomTypes;
750	<	atomTypes = getUniqueAtomTypes();
747	>	vector<int>::iterator j;
748	>
749	>	// foundIdents is a stl set, so inserting an already found ident
750	>	// will have no effect.
751	>	set<int> foundIdents;
752	>
753	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
754	>	foundIdents.insert((*j));
755
756	<	int useLennardJones = 0;
757	<	int useElectrostatic = 0;
758	<	int useEAM = 0;
759	<	int useCharge = 0;
760	<	int useDirectional = 0;
761	<	int useDipole = 0;
762	<	int useGayBerne = 0;
488	<	int useSticky = 0;
489	<	int useShape = 0;
490	<	int useFLARB = 0; //it is not in AtomType yet
491	<	int useDirectionalAtom = 0;
492	<	int useElectrostatics = 0;
493	<	//usePBC and useRF are from simParams
494	<	int usePBC = simParams_->getPBC();
495	<	int useRF = simParams_->getUseRF();
756	>	// now iterate over the foundIdents and get the actual atom types
757	>	// that correspond to these:
758	>	set<int>::iterator it;
759	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
760	>	atomTypes.insert( forceField_->getAtomType((*it)) );
761	>
762	>	#endif
763
764	+	return atomTypes;
765	+	}
766	+
767	+	void SimInfo::setupSimVariables() {
768	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
769	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
770	+	calcBoxDipole_ = false;
771	+	if ( simParams_->haveAccumulateBoxDipole() )
772	+	if ( simParams_->getAccumulateBoxDipole() ) {
773	+	calcBoxDipole_ = true;
774	+	}
775	+
776	+	set<AtomType*>::iterator i;
777	+	set<AtomType*> atomTypes;
778	+	atomTypes = getSimulatedAtomTypes();
779	+	int usesElectrostatic = 0;
780	+	int usesMetallic = 0;
781	+	int usesDirectional = 0;
782		//loop over all of the atom types
783		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
784	<	useLennardJones |= (*i)->isLennardJones();
785	<	useElectrostatic |= (*i)->isElectrostatic();
786	<	useEAM |= (*i)->isEAM();
502	<	useCharge |= (*i)->isCharge();
503	<	useDirectional |= (*i)->isDirectional();
504	<	useDipole |= (*i)->isDipole();
505	<	useGayBerne |= (*i)->isGayBerne();
506	<	useSticky |= (*i)->isSticky();
507	<	useShape |= (*i)->isShape();
784	>	usesElectrostatic |= (*i)->isElectrostatic();
785	>	usesMetallic |= (*i)->isMetal();
786	>	usesDirectional |= (*i)->isDirectional();
787		}
788	<
510	<	if (useSticky || useDipole || useGayBerne || useShape) {
511	<	useDirectionalAtom = 1;
512	<	}
513	<
514	<	if (useCharge || useDipole) {
515	<	useElectrostatics = 1;
516	<	}
517	<
788	>
789		#ifdef IS_MPI
790		int temp;
791	+	temp = usesDirectional;
792	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
793	+
794	+	temp = usesMetallic;
795	+	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
796	+
797	+	temp = usesElectrostatic;
798	+	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
799	+	#else
800
801	<	temp = usePBC;
802	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
801	>	usesDirectionalAtoms_ = usesDirectional;
802	>	usesMetallicAtoms_ = usesMetallic;
803	>	usesElectrostaticAtoms_ = usesElectrostatic;
804
805	<	temp = useDirectionalAtom;
806	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
805	>	#endif
806	>
807	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
808	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
809	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
810	>	}
811
527	–	temp = useLennardJones;
528	–	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
812
813	<	temp = useElectrostatics;
814	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813	>	vector<int> SimInfo::getGlobalAtomIndices() {
814	>	SimInfo::MoleculeIterator mi;
815	>	Molecule* mol;
816	>	Molecule::AtomIterator ai;
817	>	Atom* atom;
818
819	<	temp = useCharge;
534	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
535	<
536	<	temp = useDipole;
537	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
538	<
539	<	temp = useSticky;
540	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
541	<
542	<	temp = useGayBerne;
543	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
544	<
545	<	temp = useEAM;
546	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
547	<
548	<	temp = useShape;
549	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
550	<
551	<	temp = useFLARB;
552	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
553	<
554	<	temp = useRF;
555	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
820
821	<	#endif
821	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
822	>
823	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
824	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
825	>	}
826	>	}
827	>	return GlobalAtomIndices;
828	>	}
829
559	–	fInfo_.SIM_uses_PBC = usePBC;
560	–	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
561	–	fInfo_.SIM_uses_LennardJones = useLennardJones;
562	–	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
563	–	fInfo_.SIM_uses_Charges = useCharge;
564	–	fInfo_.SIM_uses_Dipoles = useDipole;
565	–	fInfo_.SIM_uses_Sticky = useSticky;
566	–	fInfo_.SIM_uses_GayBerne = useGayBerne;
567	–	fInfo_.SIM_uses_EAM = useEAM;
568	–	fInfo_.SIM_uses_Shapes = useShape;
569	–	fInfo_.SIM_uses_FLARB = useFLARB;
570	–	fInfo_.SIM_uses_RF = useRF;
830
831	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
831	>	vector<int> SimInfo::getGlobalGroupIndices() {
832	>	SimInfo::MoleculeIterator mi;
833	>	Molecule* mol;
834	>	Molecule::CutoffGroupIterator ci;
835	>	CutoffGroup* cg;
836
837	<	if (simParams_->haveDielectric()) {
838	<	fInfo_.dielect = simParams_->getDielectric();
839	<	} else {
840	<	sprintf(painCave.errMsg,
841	<	"SimSetup Error: No Dielectric constant was set.\n"
842	<	"\tYou are trying to use Reaction Field without"
843	<	"\tsetting a dielectric constant!\n");
844	<	painCave.isFatal = 1;
845	<	simError();
846	<	}
584	<
585	<	} else {
586	<	fInfo_.dielect = 0.0;
837	>	vector<int> GlobalGroupIndices;
838	>
839	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
840	>
841	>	//local index of cutoff group is trivial, it only depends on the
842	>	//order of travesing
843	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
844	>	cg = mol->nextCutoffGroup(ci)) {
845	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
846	>	}
847		}
848	+	return GlobalGroupIndices;
849	+	}
850
589	–	}
851
852	<	void SimInfo::setupFortranSim() {
853	<	int isError;
593	<	int nExclude;
594	<	std::vector<int> fortranGlobalGroupMembership;
595	<
596	<	nExclude = exclude_.getSize();
597	<	isError = 0;
852	>	void SimInfo::prepareTopology() {
853	>	int nExclude, nOneTwo, nOneThree, nOneFour;
854
599	–	//globalGroupMembership_ is filled by SimCreator
600	–	for (int i = 0; i < nGlobalAtoms_; i++) {
601	–	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
602	–	}
603	–
855		//calculate mass ratio of cutoff group
605	–	std::vector<double> mfact;
856		SimInfo::MoleculeIterator mi;
857		Molecule* mol;
858		Molecule::CutoffGroupIterator ci;
859		CutoffGroup* cg;
860		Molecule::AtomIterator ai;
861		Atom* atom;
862	<	double totalMass;
862	>	RealType totalMass;
863
864	<	//to avoid memory reallocation, reserve enough space for mfact
865	<	mfact.reserve(getNCutoffGroups());
864	>	/**
865	>	* The mass factor is the relative mass of an atom to the total
866	>	* mass of the cutoff group it belongs to.  By default, all atoms
867	>	* are their own cutoff groups, and therefore have mass factors of
868	>	* 1.  We need some special handling for massless atoms, which
869	>	* will be treated as carrying the entire mass of the cutoff
870	>	* group.
871	>	*/
872	>	massFactors_.clear();
873	>	massFactors_.resize(getNAtoms(), 1.0);
874
875		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
876	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
876	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
877	>	cg = mol->nextCutoffGroup(ci)) {
878
879	<	totalMass = cg->getMass();
880	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
881	<	mfact.push_back(atom->getMass()/totalMass);
882	<	}
883	<
884	<	}
879	>	totalMass = cg->getMass();
880	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
881	>	// Check for massless groups - set mfact to 1 if true
882	>	if (totalMass != 0)
883	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
884	>	else
885	>	massFactors_[atom->getLocalIndex()] = 1.0;
886	>	}
887	>	}
888		}
889
890	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
629	<	std::vector<int> identArray;
890	>	// Build the identArray_
891
892	<	//to avoid memory reallocation, reserve enough space identArray
893	<	identArray.reserve(getNAtoms());
633	<
892	>	identArray_.clear();
893	>	identArray_.reserve(getNAtoms());
894		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
895	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
896	<	identArray.push_back(atom->getIdent());
897	<	}
895	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
896	>	identArray_.push_back(atom->getIdent());
897	>	}
898		}
639	–
640	–	//fill molMembershipArray
641	–	//molMembershipArray is filled by SimCreator
642	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
643	–	for (int i = 0; i < nGlobalAtoms_; i++) {
644	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
645	–	}
899
900	<	//setup fortran simulation
648	<	//gloalExcludes and molMembershipArray should go away (They are never used)
649	<	//why the hell fortran need to know molecule?
650	<	//OOPSE = Object-Obfuscated Parallel Simulation Engine
651	<	int nGlobalExcludes = 0;
652	<	int* globalExcludes = NULL;
653	<	int* excludeList = exclude_.getExcludeList();
654	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
655	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
656	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
900	>	//scan topology
901
902	<	if( isError ){
902	>	nExclude = excludedInteractions_.getSize();
903	>	nOneTwo = oneTwoInteractions_.getSize();
904	>	nOneThree = oneThreeInteractions_.getSize();
905	>	nOneFour = oneFourInteractions_.getSize();
906
907	<	sprintf( painCave.errMsg,
908	<	"There was an error setting the simulation information in fortran.\n" );
909	<	painCave.isFatal = 1;
910	<	painCave.severity = OOPSE_ERROR;
664	<	simError();
665	<	}
907	>	int* excludeList = excludedInteractions_.getPairList();
908	>	int* oneTwoList = oneTwoInteractions_.getPairList();
909	>	int* oneThreeList = oneThreeInteractions_.getPairList();
910	>	int* oneFourList = oneFourInteractions_.getPairList();
911
912	<	#ifdef IS_MPI
913	<	sprintf( checkPointMsg,
669	<	"succesfully sent the simulation information to fortran.\n");
670	<	MPIcheckPoint();
671	<	#endif // is_mpi
672	<	}
912	>	topologyDone_ = true;
913	>	}
914
915	+	void SimInfo::addProperty(GenericData* genData) {
916	+	properties_.addProperty(genData);
917	+	}
918
919	<	#ifdef IS_MPI
920	<	void SimInfo::setupFortranParallel() {
921	<
678	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
679	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
680	<	std::vector<int> localToGlobalCutoffGroupIndex;
681	<	SimInfo::MoleculeIterator mi;
682	<	Molecule::AtomIterator ai;
683	<	Molecule::CutoffGroupIterator ci;
684	<	Molecule* mol;
685	<	Atom* atom;
686	<	CutoffGroup* cg;
687	<	mpiSimData parallelData;
688	<	int isError;
919	>	void SimInfo::removeProperty(const string& propName) {
920	>	properties_.removeProperty(propName);
921	>	}
922
923	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
923	>	void SimInfo::clearProperties() {
924	>	properties_.clearProperties();
925	>	}
926
927	<	//local index(index in DataStorge) of atom is important
928	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
929	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
930	<	}
927	>	vector<string> SimInfo::getPropertyNames() {
928	>	return properties_.getPropertyNames();
929	>	}
930	>
931	>	vector<GenericData*> SimInfo::getProperties() {
932	>	return properties_.getProperties();
933	>	}
934
935	<	//local index of cutoff group is trivial, it only depends on the order of travesing
936	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
937	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
700	<	}
701	<
702	<	}
935	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
936	>	return properties_.getPropertyByName(propName);
937	>	}
938
939	<	//fill up mpiSimData struct
940	<	parallelData.nMolGlobal = getNGlobalMolecules();
941	<	parallelData.nMolLocal = getNMolecules();
942	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
943	<	parallelData.nAtomsLocal = getNAtoms();
709	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
710	<	parallelData.nGroupsLocal = getNCutoffGroups();
711	<	parallelData.myNode = worldRank;
712	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
713	<
714	<	//pass mpiSimData struct and index arrays to fortran
715	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
716	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
717	<	&localToGlobalCutoffGroupIndex[0], &isError);
718	<
719	<	if (isError) {
720	<	sprintf(painCave.errMsg,
721	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
722	<	painCave.isFatal = 1;
723	<	simError();
724	<	}
725	<
726	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
727	<	MPIcheckPoint();
728	<
729	<
730	<	}
731	<
732	<	#endif
733	<
734	<	double SimInfo::calcMaxCutoffRadius() {
735	<
736	<
737	<	std::set<AtomType*> atomTypes;
738	<	std::set<AtomType*>::iterator i;
739	<	std::vector<double> cutoffRadius;
740	<
741	<	//get the unique atom types
742	<	atomTypes = getUniqueAtomTypes();
743	<
744	<	//query the max cutoff radius among these atom types
745	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
746	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
747	<	}
748	<
749	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
750	<	#ifdef IS_MPI
751	<	//pick the max cutoff radius among the processors
752	<	#endif
753	<
754	<	return maxCutoffRadius;
755	<	}
756	<
757	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
758	<
759	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
760	<
761	<	if (!simParams_->haveRcut()){
762	<	sprintf(painCave.errMsg,
763	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
764	<	"\tOOPSE will use a default value of 15.0 angstroms"
765	<	"\tfor the cutoffRadius.\n");
766	<	painCave.isFatal = 0;
767	<	simError();
768	<	rcut = 15.0;
769	<	} else{
770	<	rcut = simParams_->getRcut();
771	<	}
772	<
773	<	if (!simParams_->haveRsw()){
774	<	sprintf(painCave.errMsg,
775	<	"SimCreator Warning: No value was set for switchingRadius.\n"
776	<	"\tOOPSE will use a default value of\n"
777	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
778	<	painCave.isFatal = 0;
779	<	simError();
780	<	rsw = 0.95 * rcut;
781	<	} else{
782	<	rsw = simParams_->getRsw();
783	<	}
784	<
785	<	} else {
786	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
787	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
788	<
789	<	if (simParams_->haveRcut()) {
790	<	rcut = simParams_->getRcut();
791	<	} else {
792	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
793	<	rcut = calcMaxCutoffRadius();
794	<	}
795	<
796	<	if (simParams_->haveRsw()) {
797	<	rsw  = simParams_->getRsw();
798	<	} else {
799	<	rsw = rcut;
800	<	}
801	<
802	<	}
803	<	}
804	<
805	<	void SimInfo::setupCutoff() {
806	<	getCutoff(rcut_, rsw_);
807	<	double rnblist = rcut_ + 1; // skin of neighbor list
808	<
809	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
810	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
811	<	}
812	<
813	<	void SimInfo::addProperty(GenericData* genData) {
814	<	properties_.addProperty(genData);
815	<	}
816	<
817	<	void SimInfo::removeProperty(const std::string& propName) {
818	<	properties_.removeProperty(propName);
819	<	}
820	<
821	<	void SimInfo::clearProperties() {
822	<	properties_.clearProperties();
823	<	}
824	<
825	<	std::vector<std::string> SimInfo::getPropertyNames() {
826	<	return properties_.getPropertyNames();
827	<	}
828	<
829	<	std::vector<GenericData*> SimInfo::getProperties() {
830	<	return properties_.getProperties();
831	<	}
832	<
833	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
834	<	return properties_.getPropertyByName(propName);
835	<	}
836	<
837	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
838	<	//if (sman_ == sman_) {
839	<	//    return;
840	<	//}
841	<
842	<	//delete sman_;
939	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
940	>	if (sman_ == sman) {
941	>	return;
942	>	}
943	>	delete sman_;
944		sman_ = sman;
945
946		Molecule* mol;
947		RigidBody* rb;
948		Atom* atom;
949	+	CutoffGroup* cg;
950		SimInfo::MoleculeIterator mi;
951		Molecule::RigidBodyIterator rbIter;
952	<	Molecule::AtomIterator atomIter;;
952	>	Molecule::AtomIterator atomIter;
953	>	Molecule::CutoffGroupIterator cgIter;
954
955		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
956
957	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
958	<	atom->setSnapshotManager(sman_);
959	<	}
957	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
958	>	atom->setSnapshotManager(sman_);
959	>	}
960
961	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
962	<	rb->setSnapshotManager(sman_);
963	<	}
961	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
962	>	rb->setSnapshotManager(sman_);
963	>	}
964	>
965	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
966	>	cg->setSnapshotManager(sman_);
967	>	}
968		}
969
970	<	}
970	>	}
971
972	<	Vector3d SimInfo::getComVel(){
972	>	Vector3d SimInfo::getComVel(){
973		SimInfo::MoleculeIterator i;
974		Molecule* mol;
975
976		Vector3d comVel(0.0);
977	<	double totalMass = 0.0;
977	>	RealType totalMass = 0.0;
978
979
980		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
981	<	double mass = mol->getMass();
982	<	totalMass += mass;
983	<	comVel += mass * mol->getComVel();
981	>	RealType mass = mol->getMass();
982	>	totalMass += mass;
983	>	comVel += mass * mol->getComVel();
984		}
985
986		#ifdef IS_MPI
987	<	double tmpMass = totalMass;
987	>	RealType tmpMass = totalMass;
988		Vector3d tmpComVel(comVel);
989	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
990	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
989	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
990	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
991		#endif
992
993		comVel /= totalMass;
994
995		return comVel;
996	<	}
996	>	}
997
998	<	Vector3d SimInfo::getCom(){
998	>	Vector3d SimInfo::getCom(){
999		SimInfo::MoleculeIterator i;
1000		Molecule* mol;
1001
1002		Vector3d com(0.0);
1003	<	double totalMass = 0.0;
1003	>	RealType totalMass = 0.0;
1004
1005		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1006	<	double mass = mol->getMass();
1007	<	totalMass += mass;
1008	<	com += mass * mol->getCom();
1006	>	RealType mass = mol->getMass();
1007	>	totalMass += mass;
1008	>	com += mass * mol->getCom();
1009		}
1010
1011		#ifdef IS_MPI
1012	<	double tmpMass = totalMass;
1012	>	RealType tmpMass = totalMass;
1013		Vector3d tmpCom(com);
1014	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1015	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1014	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1015	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1016		#endif
1017
1018		com /= totalMass;
1019
1020		return com;
1021
1022	<	}
1022	>	}
1023
1024	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1024	>	ostream& operator <<(ostream& o, SimInfo& info) {
1025
1026		return o;
1027	<	}
1027	>	}
1028	>
1029	>
1030	>	/*
1031	>	Returns center of mass and center of mass velocity in one function call.
1032	>	*/
1033	>
1034	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1035	>	SimInfo::MoleculeIterator i;
1036	>	Molecule* mol;
1037	>
1038	>
1039	>	RealType totalMass = 0.0;
1040	>
1041
1042	<	}//end namespace oopse
1042	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1043	>	RealType mass = mol->getMass();
1044	>	totalMass += mass;
1045	>	com += mass * mol->getCom();
1046	>	comVel += mass * mol->getComVel();
1047	>	}
1048	>
1049	>	#ifdef IS_MPI
1050	>	RealType tmpMass = totalMass;
1051	>	Vector3d tmpCom(com);
1052	>	Vector3d tmpComVel(comVel);
1053	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1054	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1055	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1056	>	#endif
1057	>
1058	>	com /= totalMass;
1059	>	comVel /= totalMass;
1060	>	}
1061	>
1062	>	/*
1063	>	Return intertia tensor for entire system and angular momentum Vector.
1064
1065	+
1066	+	[  Ixx -Ixy  -Ixz ]
1067	+	J =| -Iyx  Iyy  -Iyz |
1068	+	[ -Izx -Iyz   Izz ]
1069	+	*/
1070	+
1071	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1072	+
1073	+
1074	+	RealType xx = 0.0;
1075	+	RealType yy = 0.0;
1076	+	RealType zz = 0.0;
1077	+	RealType xy = 0.0;
1078	+	RealType xz = 0.0;
1079	+	RealType yz = 0.0;
1080	+	Vector3d com(0.0);
1081	+	Vector3d comVel(0.0);
1082	+
1083	+	getComAll(com, comVel);
1084	+
1085	+	SimInfo::MoleculeIterator i;
1086	+	Molecule* mol;
1087	+
1088	+	Vector3d thisq(0.0);
1089	+	Vector3d thisv(0.0);
1090	+
1091	+	RealType thisMass = 0.0;
1092	+
1093	+
1094	+
1095	+
1096	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1097	+
1098	+	thisq = mol->getCom()-com;
1099	+	thisv = mol->getComVel()-comVel;
1100	+	thisMass = mol->getMass();
1101	+	// Compute moment of intertia coefficients.
1102	+	xx += thisq[0]*thisq[0]*thisMass;
1103	+	yy += thisq[1]*thisq[1]*thisMass;
1104	+	zz += thisq[2]*thisq[2]*thisMass;
1105	+
1106	+	// compute products of intertia
1107	+	xy += thisq[0]*thisq[1]*thisMass;
1108	+	xz += thisq[0]*thisq[2]*thisMass;
1109	+	yz += thisq[1]*thisq[2]*thisMass;
1110	+
1111	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1112	+
1113	+	}
1114	+
1115	+
1116	+	inertiaTensor(0,0) = yy + zz;
1117	+	inertiaTensor(0,1) = -xy;
1118	+	inertiaTensor(0,2) = -xz;
1119	+	inertiaTensor(1,0) = -xy;
1120	+	inertiaTensor(1,1) = xx + zz;
1121	+	inertiaTensor(1,2) = -yz;
1122	+	inertiaTensor(2,0) = -xz;
1123	+	inertiaTensor(2,1) = -yz;
1124	+	inertiaTensor(2,2) = xx + yy;
1125	+
1126	+	#ifdef IS_MPI
1127	+	Mat3x3d tmpI(inertiaTensor);
1128	+	Vector3d tmpAngMom;
1129	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1130	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1131	+	#endif
1132	+
1133	+	return;
1134	+	}
1135	+
1136	+	//Returns the angular momentum of the system
1137	+	Vector3d SimInfo::getAngularMomentum(){
1138	+
1139	+	Vector3d com(0.0);
1140	+	Vector3d comVel(0.0);
1141	+	Vector3d angularMomentum(0.0);
1142	+
1143	+	getComAll(com,comVel);
1144	+
1145	+	SimInfo::MoleculeIterator i;
1146	+	Molecule* mol;
1147	+
1148	+	Vector3d thisr(0.0);
1149	+	Vector3d thisp(0.0);
1150	+
1151	+	RealType thisMass;
1152	+
1153	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1154	+	thisMass = mol->getMass();
1155	+	thisr = mol->getCom()-com;
1156	+	thisp = (mol->getComVel()-comVel)*thisMass;
1157	+
1158	+	angularMomentum += cross( thisr, thisp );
1159	+
1160	+	}
1161	+
1162	+	#ifdef IS_MPI
1163	+	Vector3d tmpAngMom;
1164	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1165	+	#endif
1166	+
1167	+	return angularMomentum;
1168	+	}
1169	+
1170	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1171	+	return IOIndexToIntegrableObject.at(index);
1172	+	}
1173	+
1174	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1175	+	IOIndexToIntegrableObject= v;
1176	+	}
1177	+
1178	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1179	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1180	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1181	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1182	+	*/
1183	+	void SimInfo::getGyrationalVolume(RealType &volume){
1184	+	Mat3x3d intTensor;
1185	+	RealType det;
1186	+	Vector3d dummyAngMom;
1187	+	RealType sysconstants;
1188	+	RealType geomCnst;
1189	+
1190	+	geomCnst = 3.0/2.0;
1191	+	/* Get the inertial tensor and angular momentum for free*/
1192	+	getInertiaTensor(intTensor,dummyAngMom);
1193	+
1194	+	det = intTensor.determinant();
1195	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1196	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1197	+	return;
1198	+	}
1199	+
1200	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1201	+	Mat3x3d intTensor;
1202	+	Vector3d dummyAngMom;
1203	+	RealType sysconstants;
1204	+	RealType geomCnst;
1205	+
1206	+	geomCnst = 3.0/2.0;
1207	+	/* Get the inertial tensor and angular momentum for free*/
1208	+	getInertiaTensor(intTensor,dummyAngMom);
1209	+
1210	+	detI = intTensor.determinant();
1211	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1212	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1213	+	return;
1214	+	}
1215	+	/*
1216	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1217	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1218	+	sdByGlobalIndex_ = v;
1219	+	}
1220	+
1221	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1222	+	//assert(index < nAtoms_ + nRigidBodies_);
1223	+	return sdByGlobalIndex_.at(index);
1224	+	}
1225	+	*/
1226	+	int SimInfo::getNGlobalConstraints() {
1227	+	int nGlobalConstraints;
1228	+	#ifdef IS_MPI
1229	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1230	+	MPI_COMM_WORLD);
1231	+	#else
1232	+	nGlobalConstraints =  nConstraints_;
1233	+	#endif
1234	+	return nGlobalConstraints;
1235	+	}
1236	+
1237	+	}//end namespace OpenMD
1238	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 334 by tim, Mon Feb 14 17:57:01 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC

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