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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 1536 by gezelter, Wed Jan 5 14:49:05 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 "primitives/StuntDouble.hpp"
57	+	#include "UseTheForce/DarkSide/neighborLists_interface.h"
58		#include "UseTheForce/doForces_interface.h"
56	–	#include "UseTheForce/notifyCutoffs_interface.h"
59		#include "utils/MemoryUtils.hpp"
60		#include "utils/simError.h"
61		#include "selection/SelectionManager.hpp"
62	+	#include "io/ForceFieldOptions.hpp"
63	+	#include "UseTheForce/ForceField.hpp"
64	+	#include "nonbonded/SwitchingFunction.hpp"
65
66		#ifdef IS_MPI
67		#include "UseTheForce/mpiComponentPlan.h"
68		#include "UseTheForce/DarkSide/simParallel_interface.h"
69		#endif
70
71	<	namespace oopse {
72	<
73	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
74	<	ForceField* ff, Globals* simParams) :
75	<	forceField_(ff), simParams_(simParams),
76	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
77	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
78	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
79	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
80	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
81	<	sman_(NULL), fortranInitialized_(false), selectMan_(NULL) {
82	<
83	<
79	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
71	>	using namespace std;
72	>	namespace OpenMD {
73	>
74	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
75	>	forceField_(ff), simParams_(simParams),
76	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
77	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
78	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
79	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
80	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
81	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
82	>	calcBoxDipole_(false), useAtomicVirial_(true) {
83	>
84		MoleculeStamp* molStamp;
85		int nMolWithSameStamp;
86		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
87	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
88		CutoffGroupStamp* cgStamp;
89		RigidBodyStamp* rbStamp;
90		int nRigidAtoms = 0;
91
92	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
93	<	molStamp = i->first;
94	<	nMolWithSameStamp = i->second;
95	<
96	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
97	<
98	<	//calculate atoms in molecules
99	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
100	<
101	<
102	<	//calculate atoms in cutoff groups
103	<	int nAtomsInGroups = 0;
104	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
105	<
106	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
107	<	cgStamp = molStamp->getCutoffGroup(j);
108	<	nAtomsInGroups += cgStamp->getNMembers();
109	<	}
110	<
111	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
112	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
113	<
114	<	//calculate atoms in rigid bodies
115	<	int nAtomsInRigidBodies = 0;
116	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
117	<
118	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
119	<	rbStamp = molStamp->getRigidBody(j);
120	<	nAtomsInRigidBodies += rbStamp->getNMembers();
121	<	}
122	<
123	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
124	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
125	<
92	>	vector<Component*> components = simParams->getComponents();
93	>
94	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
95	>	molStamp = (*i)->getMoleculeStamp();
96	>	nMolWithSameStamp = (*i)->getNMol();
97	>
98	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
99	>
100	>	//calculate atoms in molecules
101	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
102	>
103	>	//calculate atoms in cutoff groups
104	>	int nAtomsInGroups = 0;
105	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
106	>
107	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
108	>	cgStamp = molStamp->getCutoffGroupStamp(j);
109	>	nAtomsInGroups += cgStamp->getNMembers();
110	>	}
111	>
112	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
113	>
114	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
115	>
116	>	//calculate atoms in rigid bodies
117	>	int nAtomsInRigidBodies = 0;
118	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
119	>
120	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
121	>	rbStamp = molStamp->getRigidBodyStamp(j);
122	>	nAtomsInRigidBodies += rbStamp->getNMembers();
123	>	}
124	>
125	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
126	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
127	>
128		}
129	<
130	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
131	<	//therefore the total number of cutoff groups in the system is equal to
132	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
133	<	//file plus the number of cutoff groups defined in meta-data file
129	>
130	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
131	>	//group therefore the total number of cutoff groups in the system is
132	>	//equal to the total number of atoms minus number of atoms belong to
133	>	//cutoff group defined in meta-data file plus the number of cutoff
134	>	//groups defined in meta-data file
135		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
136	<
137	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
138	<	//therefore the total number of  integrable objects in the system is equal to
139	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
140	<	//file plus the number of  rigid bodies defined in meta-data file
141	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
142	<
136	>
137	>	//every free atom (atom does not belong to rigid bodies) is an
138	>	//integrable object therefore the total number of integrable objects
139	>	//in the system is equal to the total number of atoms minus number of
140	>	//atoms belong to rigid body defined in meta-data file plus the number
141	>	//of rigid bodies defined in meta-data file
142	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
143	>	+ nGlobalRigidBodies_;
144	>
145		nGlobalMols_ = molStampIds_.size();
137	–
138	–	#ifdef IS_MPI
146		molToProcMap_.resize(nGlobalMols_);
147	<	#endif
148	<
149	<	selectMan_ = new SelectionManager(this);
150	<	selectMan_->selectAll();
151	<	}
152	<
153	<	SimInfo::~SimInfo() {
154	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
155	<
149	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
150	<
147	>	}
148	>
149	>	SimInfo::~SimInfo() {
150	>	map<int, Molecule*>::iterator i;
151	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
152	>	delete i->second;
153	>	}
154	>	molecules_.clear();
155	>
156		delete sman_;
157		delete simParams_;
158		delete forceField_;
159	<	delete selectMan_;
155	<	}
159	>	}
160
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	–	}
161
162	<	bool SimInfo::addMolecule(Molecule* mol) {
162	>	bool SimInfo::addMolecule(Molecule* mol) {
163		MoleculeIterator i;
164	<
164	>
165		i = molecules_.find(mol->getGlobalIndex());
166		if (i == molecules_.end() ) {
167	<
168	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
169	<
170	<	nAtoms_ += mol->getNAtoms();
171	<	nBonds_ += mol->getNBonds();
172	<	nBends_ += mol->getNBends();
173	<	nTorsions_ += mol->getNTorsions();
174	<	nRigidBodies_ += mol->getNRigidBodies();
175	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
176	<	nCutoffGroups_ += mol->getNCutoffGroups();
177	<	nConstraints_ += mol->getNConstraintPairs();
178	<
179	<	addExcludePairs(mol);
180	<
181	<	return true;
182	<	} else {
183	<	return false;
167	>
168	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
169	>
170	>	nAtoms_ += mol->getNAtoms();
171	>	nBonds_ += mol->getNBonds();
172	>	nBends_ += mol->getNBends();
173	>	nTorsions_ += mol->getNTorsions();
174	>	nInversions_ += mol->getNInversions();
175	>	nRigidBodies_ += mol->getNRigidBodies();
176	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
177	>	nCutoffGroups_ += mol->getNCutoffGroups();
178	>	nConstraints_ += mol->getNConstraintPairs();
179	>
180	>	addInteractionPairs(mol);
181	>
182	>	return true;
183	>	} else {
184	>	return false;
185		}
186	<	}
187	<
188	<	bool SimInfo::removeMolecule(Molecule* mol) {
186	>	}
187	>
188	>	bool SimInfo::removeMolecule(Molecule* mol) {
189		MoleculeIterator i;
190		i = molecules_.find(mol->getGlobalIndex());
191
192		if (i != molecules_.end() ) {
193
194	<	assert(mol == i->second);
194	>	assert(mol == i->second);
195
196	<	nAtoms_ -= mol->getNAtoms();
197	<	nBonds_ -= mol->getNBonds();
198	<	nBends_ -= mol->getNBends();
199	<	nTorsions_ -= mol->getNTorsions();
200	<	nRigidBodies_ -= mol->getNRigidBodies();
201	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
202	<	nCutoffGroups_ -= mol->getNCutoffGroups();
203	<	nConstraints_ -= mol->getNConstraintPairs();
196	>	nAtoms_ -= mol->getNAtoms();
197	>	nBonds_ -= mol->getNBonds();
198	>	nBends_ -= mol->getNBends();
199	>	nTorsions_ -= mol->getNTorsions();
200	>	nInversions_ -= mol->getNInversions();
201	>	nRigidBodies_ -= mol->getNRigidBodies();
202	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
203	>	nCutoffGroups_ -= mol->getNCutoffGroups();
204	>	nConstraints_ -= mol->getNConstraintPairs();
205
206	<	removeExcludePairs(mol);
207	<	molecules_.erase(mol->getGlobalIndex());
206	>	removeInteractionPairs(mol);
207	>	molecules_.erase(mol->getGlobalIndex());
208
209	<	delete mol;
209	>	delete mol;
210
211	<	return true;
211	>	return true;
212		} else {
213	<	return false;
213	>	return false;
214		}
215	+	}
216
220	–
221	–	}
222	–
217
218	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
218	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
219		i = molecules_.begin();
220		return i == molecules_.end() ? NULL : i->second;
221	<	}
221	>	}
222
223	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
223	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
224		++i;
225		return i == molecules_.end() ? NULL : i->second;
226	<	}
226	>	}
227
228
229	<	void SimInfo::calcNdf() {
229	>	void SimInfo::calcNdf() {
230		int ndf_local;
231		MoleculeIterator i;
232	<	std::vector<StuntDouble*>::iterator j;
232	>	vector<StuntDouble*>::iterator j;
233		Molecule* mol;
234		StuntDouble* integrableObject;
235
236		ndf_local = 0;
237
238		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
239	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
240	<	integrableObject = mol->nextIntegrableObject(j)) {
239	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
240	>	integrableObject = mol->nextIntegrableObject(j)) {
241
242	<	ndf_local += 3;
242	>	ndf_local += 3;
243
244	<	if (integrableObject->isDirectional()) {
245	<	if (integrableObject->isLinear()) {
246	<	ndf_local += 2;
247	<	} else {
248	<	ndf_local += 3;
249	<	}
250	<	}
244	>	if (integrableObject->isDirectional()) {
245	>	if (integrableObject->isLinear()) {
246	>	ndf_local += 2;
247	>	} else {
248	>	ndf_local += 3;
249	>	}
250	>	}
251
252	<	}//end for (integrableObject)
253	<	}// end for (mol)
252	>	}
253	>	}
254
255		// n_constraints is local, so subtract them on each processor
256		ndf_local -= nConstraints_;
#	Line 271 | Line 265 | void SimInfo::calcNdf() {
265		// entire system:
266		ndf_ = ndf_ - 3 - nZconstraint_;
267
268	<	}
268	>	}
269
270	<	void SimInfo::calcNdfRaw() {
270	>	int SimInfo::getFdf() {
271	>	#ifdef IS_MPI
272	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
273	>	#else
274	>	fdf_ = fdf_local;
275	>	#endif
276	>	return fdf_;
277	>	}
278	>
279	>	void SimInfo::calcNdfRaw() {
280		int ndfRaw_local;
281
282		MoleculeIterator i;
283	<	std::vector<StuntDouble*>::iterator j;
283	>	vector<StuntDouble*>::iterator j;
284		Molecule* mol;
285		StuntDouble* integrableObject;
286
#	Line 285 | Line 288 | void SimInfo::calcNdfRaw() {
288		ndfRaw_local = 0;
289
290		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
291	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
292	<	integrableObject = mol->nextIntegrableObject(j)) {
291	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
292	>	integrableObject = mol->nextIntegrableObject(j)) {
293
294	<	ndfRaw_local += 3;
294	>	ndfRaw_local += 3;
295
296	<	if (integrableObject->isDirectional()) {
297	<	if (integrableObject->isLinear()) {
298	<	ndfRaw_local += 2;
299	<	} else {
300	<	ndfRaw_local += 3;
301	<	}
302	<	}
296	>	if (integrableObject->isDirectional()) {
297	>	if (integrableObject->isLinear()) {
298	>	ndfRaw_local += 2;
299	>	} else {
300	>	ndfRaw_local += 3;
301	>	}
302	>	}
303
304	<	}
304	>	}
305		}
306
307		#ifdef IS_MPI
#	Line 306 | Line 309 | void SimInfo::calcNdfRaw() {
309		#else
310		ndfRaw_ = ndfRaw_local;
311		#endif
312	<	}
312	>	}
313
314	<	void SimInfo::calcNdfTrans() {
314	>	void SimInfo::calcNdfTrans() {
315		int ndfTrans_local;
316
317		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 322 | Line 325 | void SimInfo::calcNdfTrans() {
325
326		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
327
328	<	}
328	>	}
329
330	<	void SimInfo::addExcludePairs(Molecule* mol) {
331	<	std::vector<Bond*>::iterator bondIter;
332	<	std::vector<Bend*>::iterator bendIter;
333	<	std::vector<Torsion*>::iterator torsionIter;
330	>	void SimInfo::addInteractionPairs(Molecule* mol) {
331	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
332	>	vector<Bond*>::iterator bondIter;
333	>	vector<Bend*>::iterator bendIter;
334	>	vector<Torsion*>::iterator torsionIter;
335	>	vector<Inversion*>::iterator inversionIter;
336		Bond* bond;
337		Bend* bend;
338		Torsion* torsion;
339	+	Inversion* inversion;
340		int a;
341		int b;
342		int c;
343		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	–	}
344
345	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
346	<	a = bend->getAtomA()->getGlobalIndex();
347	<	b = bend->getAtomB()->getGlobalIndex();
348	<	c = bend->getAtomC()->getGlobalIndex();
345	>	// atomGroups can be used to add special interaction maps between
346	>	// groups of atoms that are in two separate rigid bodies.
347	>	// However, most site-site interactions between two rigid bodies
348	>	// are probably not special, just the ones between the physically
349	>	// bonded atoms.  Interactions *within* a single rigid body should
350	>	// always be excluded.  These are done at the bottom of this
351	>	// function.
352
353	<	exclude_.addPair(a, b);
354	<	exclude_.addPair(a, c);
355	<	exclude_.addPair(b, c);
356	<	}
357	<
358	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
359	<	a = torsion->getAtomA()->getGlobalIndex();
360	<	b = torsion->getAtomB()->getGlobalIndex();
361	<	c = torsion->getAtomC()->getGlobalIndex();
362	<	d = torsion->getAtomD()->getGlobalIndex();
353	>	map<int, set<int> > atomGroups;
354	>	Molecule::RigidBodyIterator rbIter;
355	>	RigidBody* rb;
356	>	Molecule::IntegrableObjectIterator ii;
357	>	StuntDouble* integrableObject;
358	>
359	>	for (integrableObject = mol->beginIntegrableObject(ii);
360	>	integrableObject != NULL;
361	>	integrableObject = mol->nextIntegrableObject(ii)) {
362	>
363	>	if (integrableObject->isRigidBody()) {
364	>	rb = static_cast<RigidBody*>(integrableObject);
365	>	vector<Atom*> atoms = rb->getAtoms();
366	>	set<int> rigidAtoms;
367	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
368	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
369	>	}
370	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
371	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
372	>	}
373	>	} else {
374	>	set<int> oneAtomSet;
375	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
376	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
377	>	}
378	>	}
379	>
380	>	for (bond= mol->beginBond(bondIter); bond != NULL;
381	>	bond = mol->nextBond(bondIter)) {
382
383	<	exclude_.addPair(a, b);
384	<	exclude_.addPair(a, c);
385	<	exclude_.addPair(a, d);
386	<	exclude_.addPair(b, c);
387	<	exclude_.addPair(b, d);
388	<	exclude_.addPair(c, d);
383	>	a = bond->getAtomA()->getGlobalIndex();
384	>	b = bond->getAtomB()->getGlobalIndex();
385	>
386	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
387	>	oneTwoInteractions_.addPair(a, b);
388	>	} else {
389	>	excludedInteractions_.addPair(a, b);
390	>	}
391		}
392
393	<
394	<	}
393	>	for (bend= mol->beginBend(bendIter); bend != NULL;
394	>	bend = mol->nextBend(bendIter)) {
395
396	<	void SimInfo::removeExcludePairs(Molecule* mol) {
397	<	std::vector<Bond*>::iterator bondIter;
398	<	std::vector<Bend*>::iterator bendIter;
399	<	std::vector<Torsion*>::iterator torsionIter;
396	>	a = bend->getAtomA()->getGlobalIndex();
397	>	b = bend->getAtomB()->getGlobalIndex();
398	>	c = bend->getAtomC()->getGlobalIndex();
399	>
400	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
401	>	oneTwoInteractions_.addPair(a, b);
402	>	oneTwoInteractions_.addPair(b, c);
403	>	} else {
404	>	excludedInteractions_.addPair(a, b);
405	>	excludedInteractions_.addPair(b, c);
406	>	}
407	>
408	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
409	>	oneThreeInteractions_.addPair(a, c);
410	>	} else {
411	>	excludedInteractions_.addPair(a, c);
412	>	}
413	>	}
414	>
415	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
416	>	torsion = mol->nextTorsion(torsionIter)) {
417	>
418	>	a = torsion->getAtomA()->getGlobalIndex();
419	>	b = torsion->getAtomB()->getGlobalIndex();
420	>	c = torsion->getAtomC()->getGlobalIndex();
421	>	d = torsion->getAtomD()->getGlobalIndex();
422	>
423	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
424	>	oneTwoInteractions_.addPair(a, b);
425	>	oneTwoInteractions_.addPair(b, c);
426	>	oneTwoInteractions_.addPair(c, d);
427	>	} else {
428	>	excludedInteractions_.addPair(a, b);
429	>	excludedInteractions_.addPair(b, c);
430	>	excludedInteractions_.addPair(c, d);
431	>	}
432	>
433	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
434	>	oneThreeInteractions_.addPair(a, c);
435	>	oneThreeInteractions_.addPair(b, d);
436	>	} else {
437	>	excludedInteractions_.addPair(a, c);
438	>	excludedInteractions_.addPair(b, d);
439	>	}
440	>
441	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
442	>	oneFourInteractions_.addPair(a, d);
443	>	} else {
444	>	excludedInteractions_.addPair(a, d);
445	>	}
446	>	}
447	>
448	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
449	>	inversion = mol->nextInversion(inversionIter)) {
450	>
451	>	a = inversion->getAtomA()->getGlobalIndex();
452	>	b = inversion->getAtomB()->getGlobalIndex();
453	>	c = inversion->getAtomC()->getGlobalIndex();
454	>	d = inversion->getAtomD()->getGlobalIndex();
455	>
456	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
457	>	oneTwoInteractions_.addPair(a, b);
458	>	oneTwoInteractions_.addPair(a, c);
459	>	oneTwoInteractions_.addPair(a, d);
460	>	} else {
461	>	excludedInteractions_.addPair(a, b);
462	>	excludedInteractions_.addPair(a, c);
463	>	excludedInteractions_.addPair(a, d);
464	>	}
465	>
466	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
467	>	oneThreeInteractions_.addPair(b, c);
468	>	oneThreeInteractions_.addPair(b, d);
469	>	oneThreeInteractions_.addPair(c, d);
470	>	} else {
471	>	excludedInteractions_.addPair(b, c);
472	>	excludedInteractions_.addPair(b, d);
473	>	excludedInteractions_.addPair(c, d);
474	>	}
475	>	}
476	>
477	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
478	>	rb = mol->nextRigidBody(rbIter)) {
479	>	vector<Atom*> atoms = rb->getAtoms();
480	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
481	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
482	>	a = atoms[i]->getGlobalIndex();
483	>	b = atoms[j]->getGlobalIndex();
484	>	excludedInteractions_.addPair(a, b);
485	>	}
486	>	}
487	>	}
488	>
489	>	}
490	>
491	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
492	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
493	>	vector<Bond*>::iterator bondIter;
494	>	vector<Bend*>::iterator bendIter;
495	>	vector<Torsion*>::iterator torsionIter;
496	>	vector<Inversion*>::iterator inversionIter;
497		Bond* bond;
498		Bend* bend;
499		Torsion* torsion;
500	+	Inversion* inversion;
501		int a;
502		int b;
503		int c;
504		int d;
505	+
506	+	map<int, set<int> > atomGroups;
507	+	Molecule::RigidBodyIterator rbIter;
508	+	RigidBody* rb;
509	+	Molecule::IntegrableObjectIterator ii;
510	+	StuntDouble* integrableObject;
511
512	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
513	<	a = bond->getAtomA()->getGlobalIndex();
514	<	b = bond->getAtomB()->getGlobalIndex();
515	<	exclude_.removePair(a, b);
512	>	for (integrableObject = mol->beginIntegrableObject(ii);
513	>	integrableObject != NULL;
514	>	integrableObject = mol->nextIntegrableObject(ii)) {
515	>
516	>	if (integrableObject->isRigidBody()) {
517	>	rb = static_cast<RigidBody*>(integrableObject);
518	>	vector<Atom*> atoms = rb->getAtoms();
519	>	set<int> rigidAtoms;
520	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
521	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
522	>	}
523	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
524	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
525	>	}
526	>	} else {
527	>	set<int> oneAtomSet;
528	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
529	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
530	>	}
531	>	}
532	>
533	>	for (bond= mol->beginBond(bondIter); bond != NULL;
534	>	bond = mol->nextBond(bondIter)) {
535	>
536	>	a = bond->getAtomA()->getGlobalIndex();
537	>	b = bond->getAtomB()->getGlobalIndex();
538	>
539	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
540	>	oneTwoInteractions_.removePair(a, b);
541	>	} else {
542	>	excludedInteractions_.removePair(a, b);
543	>	}
544		}
545
546	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
547	<	a = bend->getAtomA()->getGlobalIndex();
392	<	b = bend->getAtomB()->getGlobalIndex();
393	<	c = bend->getAtomC()->getGlobalIndex();
546	>	for (bend= mol->beginBend(bendIter); bend != NULL;
547	>	bend = mol->nextBend(bendIter)) {
548
549	<	exclude_.removePair(a, b);
550	<	exclude_.removePair(a, c);
551	<	exclude_.removePair(b, c);
549	>	a = bend->getAtomA()->getGlobalIndex();
550	>	b = bend->getAtomB()->getGlobalIndex();
551	>	c = bend->getAtomC()->getGlobalIndex();
552	>
553	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
554	>	oneTwoInteractions_.removePair(a, b);
555	>	oneTwoInteractions_.removePair(b, c);
556	>	} else {
557	>	excludedInteractions_.removePair(a, b);
558	>	excludedInteractions_.removePair(b, c);
559	>	}
560	>
561	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
562	>	oneThreeInteractions_.removePair(a, c);
563	>	} else {
564	>	excludedInteractions_.removePair(a, c);
565	>	}
566		}
567
568	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
569	<	a = torsion->getAtomA()->getGlobalIndex();
402	<	b = torsion->getAtomB()->getGlobalIndex();
403	<	c = torsion->getAtomC()->getGlobalIndex();
404	<	d = torsion->getAtomD()->getGlobalIndex();
568	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
569	>	torsion = mol->nextTorsion(torsionIter)) {
570
571	<	exclude_.removePair(a, b);
572	<	exclude_.removePair(a, c);
573	<	exclude_.removePair(a, d);
574	<	exclude_.removePair(b, c);
575	<	exclude_.removePair(b, d);
576	<	exclude_.removePair(c, d);
571	>	a = torsion->getAtomA()->getGlobalIndex();
572	>	b = torsion->getAtomB()->getGlobalIndex();
573	>	c = torsion->getAtomC()->getGlobalIndex();
574	>	d = torsion->getAtomD()->getGlobalIndex();
575	>
576	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
577	>	oneTwoInteractions_.removePair(a, b);
578	>	oneTwoInteractions_.removePair(b, c);
579	>	oneTwoInteractions_.removePair(c, d);
580	>	} else {
581	>	excludedInteractions_.removePair(a, b);
582	>	excludedInteractions_.removePair(b, c);
583	>	excludedInteractions_.removePair(c, d);
584	>	}
585	>
586	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
587	>	oneThreeInteractions_.removePair(a, c);
588	>	oneThreeInteractions_.removePair(b, d);
589	>	} else {
590	>	excludedInteractions_.removePair(a, c);
591	>	excludedInteractions_.removePair(b, d);
592	>	}
593	>
594	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
595	>	oneFourInteractions_.removePair(a, d);
596	>	} else {
597	>	excludedInteractions_.removePair(a, d);
598	>	}
599		}
600
601	<	}
601	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
602	>	inversion = mol->nextInversion(inversionIter)) {
603
604	+	a = inversion->getAtomA()->getGlobalIndex();
605	+	b = inversion->getAtomB()->getGlobalIndex();
606	+	c = inversion->getAtomC()->getGlobalIndex();
607	+	d = inversion->getAtomD()->getGlobalIndex();
608
609	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
610	<	int curStampId;
609	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
610	>	oneTwoInteractions_.removePair(a, b);
611	>	oneTwoInteractions_.removePair(a, c);
612	>	oneTwoInteractions_.removePair(a, d);
613	>	} else {
614	>	excludedInteractions_.removePair(a, b);
615	>	excludedInteractions_.removePair(a, c);
616	>	excludedInteractions_.removePair(a, d);
617	>	}
618
619	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
620	+	oneThreeInteractions_.removePair(b, c);
621	+	oneThreeInteractions_.removePair(b, d);
622	+	oneThreeInteractions_.removePair(c, d);
623	+	} else {
624	+	excludedInteractions_.removePair(b, c);
625	+	excludedInteractions_.removePair(b, d);
626	+	excludedInteractions_.removePair(c, d);
627	+	}
628	+	}
629	+
630	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
631	+	rb = mol->nextRigidBody(rbIter)) {
632	+	vector<Atom*> atoms = rb->getAtoms();
633	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
634	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
635	+	a = atoms[i]->getGlobalIndex();
636	+	b = atoms[j]->getGlobalIndex();
637	+	excludedInteractions_.removePair(a, b);
638	+	}
639	+	}
640	+	}
641	+
642	+	}
643	+
644	+
645	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
646	+	int curStampId;
647	+
648		//index from 0
649		curStampId = moleculeStamps_.size();
650
651		moleculeStamps_.push_back(molStamp);
652		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
653	<	}
653	>	}
654
427	–	void SimInfo::update() {
655
656	<	setupSimType();
657	<
658	<	#ifdef IS_MPI
659	<	setupFortranParallel();
660	<	#endif
661	<
662	<	setupFortranSim();
663	<
664	<	//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	<
656	>	/**
657	>	* update
658	>	*
659	>	*  Performs the global checks and variable settings after the
660	>	*  objects have been created.
661	>	*
662	>	*/
663	>	void SimInfo::update() {
664	>	setupSimVariables();
665		calcNdf();
666		calcNdfRaw();
667		calcNdfTrans();
668	<
669	<	fortranInitialized_ = true;
670	<	}
671	<
672	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
668	>	}
669	>
670	>	/**
671	>	* getSimulatedAtomTypes
672	>	*
673	>	* Returns an STL set of AtomType* that are actually present in this
674	>	* simulation.  Must query all processors to assemble this information.
675	>	*
676	>	*/
677	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
678		SimInfo::MoleculeIterator mi;
679		Molecule* mol;
680		Molecule::AtomIterator ai;
681		Atom* atom;
682	<	std::set<AtomType*> atomTypes;
682	>	set<AtomType*> atomTypes;
683	>
684	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
685	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
686	>	atomTypes.insert(atom->getAtomType());
687	>	}
688	>	}
689
690	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
690	>	#ifdef IS_MPI
691
692	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
693	<	atomTypes.insert(atom->getAtomType());
469	<	}
470	<
471	<	}
692	>	// loop over the found atom types on this processor, and add their
693	>	// numerical idents to a vector:
694
695	<	return atomTypes;
696	<	}
695	>	vector<int> foundTypes;
696	>	set<AtomType*>::iterator i;
697	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
698	>	foundTypes.push_back( (*i)->getIdent() );
699
700	<	void SimInfo::setupSimType() {
701	<	std::set<AtomType*>::iterator i;
702	<	std::set<AtomType*> atomTypes;
703	<	atomTypes = getUniqueAtomTypes();
700	>	// count_local holds the number of found types on this processor
701	>	int count_local = foundTypes.size();
702	>
703	>	// count holds the total number of found types on all processors
704	>	// (some will be redundant with the ones found locally):
705	>	int count;
706	>	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
707	>
708	>	// create a vector to hold the globally found types, and resize it:
709	>	vector<int> ftGlobal;
710	>	ftGlobal.resize(count);
711	>	vector<int> counts;
712	>
713	>	int nproc = MPI::COMM_WORLD.Get_size();
714	>	counts.resize(nproc);
715	>	vector<int> disps;
716	>	disps.resize(nproc);
717	>
718	>	// now spray out the foundTypes to all the other processors:
719
720	<	int useLennardJones = 0;
721	<	int useElectrostatic = 0;
483	<	int useEAM = 0;
484	<	int useCharge = 0;
485	<	int useDirectional = 0;
486	<	int useDipole = 0;
487	<	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();
720	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
721	>	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
722
723	+	// foundIdents is a stl set, so inserting an already found ident
724	+	// will have no effect.
725	+	set<int> foundIdents;
726	+	vector<int>::iterator j;
727	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
728	+	foundIdents.insert((*j));
729	+
730	+	// now iterate over the foundIdents and get the actual atom types
731	+	// that correspond to these:
732	+	set<int>::iterator it;
733	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
734	+	atomTypes.insert( forceField_->getAtomType((*it)) );
735	+
736	+	#endif
737	+
738	+	return atomTypes;
739	+	}
740	+
741	+	void SimInfo::setupSimVariables() {
742	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
743	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
744	+	calcBoxDipole_ = false;
745	+	if ( simParams_->haveAccumulateBoxDipole() )
746	+	if ( simParams_->getAccumulateBoxDipole() ) {
747	+	calcBoxDipole_ = true;
748	+	}
749	+
750	+	set<AtomType*>::iterator i;
751	+	set<AtomType*> atomTypes;
752	+	atomTypes = getSimulatedAtomTypes();
753	+	int usesElectrostatic = 0;
754	+	int usesMetallic = 0;
755	+	int usesDirectional = 0;
756		//loop over all of the atom types
757		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
758	<	useLennardJones |= (*i)->isLennardJones();
759	<	useElectrostatic |= (*i)->isElectrostatic();
760	<	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();
758	>	usesElectrostatic |= (*i)->isElectrostatic();
759	>	usesMetallic |= (*i)->isMetal();
760	>	usesDirectional |= (*i)->isDirectional();
761		}
762
510	–	if (useSticky || useDipole || useGayBerne || useShape) {
511	–	useDirectionalAtom = 1;
512	–	}
513	–
514	–	if (useCharge || useDipole) {
515	–	useElectrostatics = 1;
516	–	}
517	–
763		#ifdef IS_MPI
764		int temp;
765	+	temp = usesDirectional;
766	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767
768	<	temp = usePBC;
769	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
768	>	temp = usesMetallic;
769	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770
771	<	temp = useDirectionalAtom;
772	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
526	<
527	<	temp = useLennardJones;
528	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
529	<
530	<	temp = useElectrostatics;
531	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
532	<
533	<	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);
556	<
771	>	temp = usesElectrostatic;
772	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
773		#endif
774	+	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
775	+	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
776	+	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
777	+	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
778	+	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
779	+	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
780	+	}
781
782	<	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;
571	<
572	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
573	<
574	<	if (simParams_->haveDielectric()) {
575	<	fInfo_.dielect = simParams_->getDielectric();
576	<	} else {
577	<	sprintf(painCave.errMsg,
578	<	"SimSetup Error: No Dielectric constant was set.\n"
579	<	"\tYou are trying to use Reaction Field without"
580	<	"\tsetting a dielectric constant!\n");
581	<	painCave.isFatal = 1;
582	<	simError();
583	<	}
584	<
585	<	} else {
586	<	fInfo_.dielect = 0.0;
587	<	}
588	<
589	<	}
590	<
591	<	void SimInfo::setupFortranSim() {
782	>	void SimInfo::setupFortran() {
783		int isError;
784	<	int nExclude;
785	<	std::vector<int> fortranGlobalGroupMembership;
784	>	int nExclude, nOneTwo, nOneThree, nOneFour;
785	>	vector<int> fortranGlobalGroupMembership;
786
596	–	nExclude = exclude_.getSize();
787		isError = 0;
788
789		//globalGroupMembership_ is filled by SimCreator
790		for (int i = 0; i < nGlobalAtoms_; i++) {
791	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
791	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
792		}
793
794		//calculate mass ratio of cutoff group
795	<	std::vector<double> mfact;
795	>	vector<RealType> mfact;
796		SimInfo::MoleculeIterator mi;
797		Molecule* mol;
798		Molecule::CutoffGroupIterator ci;
799		CutoffGroup* cg;
800		Molecule::AtomIterator ai;
801		Atom* atom;
802	<	double totalMass;
802	>	RealType totalMass;
803
804		//to avoid memory reallocation, reserve enough space for mfact
805		mfact.reserve(getNCutoffGroups());
806
807		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
808	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
808	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
809
810	<	totalMass = cg->getMass();
811	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
812	<	mfact.push_back(atom->getMass()/totalMass);
813	<	}
814	<
815	<	}
810	>	totalMass = cg->getMass();
811	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
812	>	// Check for massless groups - set mfact to 1 if true
813	>	if (totalMass != 0)
814	>	mfact.push_back(atom->getMass()/totalMass);
815	>	else
816	>	mfact.push_back( 1.0 );
817	>	}
818	>	}
819		}
820
821	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
822	<	std::vector<int> identArray;
821	>	//fill ident array of local atoms (it is actually ident of
822	>	//AtomType, it is so confusing !!!)
823	>	vector<int> identArray;
824
825		//to avoid memory reallocation, reserve enough space identArray
826		identArray.reserve(getNAtoms());
827
828		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
829	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
830	<	identArray.push_back(atom->getIdent());
831	<	}
829	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
830	>	identArray.push_back(atom->getIdent());
831	>	}
832		}
833
834		//fill molMembershipArray
835		//molMembershipArray is filled by SimCreator
836	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
836	>	vector<int> molMembershipArray(nGlobalAtoms_);
837		for (int i = 0; i < nGlobalAtoms_; i++) {
838	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
838	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
839		}
840
841		//setup fortran simulation
648	–	//gloalExcludes and molMembershipArray should go away (They are never used)
649	–	//why the hell fortran need to know molecule?
650	–	//OOPSE = Object-Obfuscated Parallel Simulation Engine
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);
842
843	<	if( isError ){
843	>	nExclude = excludedInteractions_.getSize();
844	>	nOneTwo = oneTwoInteractions_.getSize();
845	>	nOneThree = oneThreeInteractions_.getSize();
846	>	nOneFour = oneFourInteractions_.getSize();
847
848	<	sprintf( painCave.errMsg,
849	<	"There was an error setting the simulation information in fortran.\n" );
850	<	painCave.isFatal = 1;
851	<	painCave.severity = OOPSE_ERROR;
664	<	simError();
665	<	}
848	>	int* excludeList = excludedInteractions_.getPairList();
849	>	int* oneTwoList = oneTwoInteractions_.getPairList();
850	>	int* oneThreeList = oneThreeInteractions_.getPairList();
851	>	int* oneFourList = oneFourInteractions_.getPairList();
852
853	<	#ifdef IS_MPI
853	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
854	>	&nExclude, excludeList,
855	>	&nOneTwo, oneTwoList,
856	>	&nOneThree, oneThreeList,
857	>	&nOneFour, oneFourList,
858	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
859	>	&fortranGlobalGroupMembership[0], &isError);
860	>
861	>	if( isError ){
862	>
863	>	sprintf( painCave.errMsg,
864	>	"There was an error setting the simulation information in fortran.\n" );
865	>	painCave.isFatal = 1;
866	>	painCave.severity = OPENMD_ERROR;
867	>	simError();
868	>	}
869	>
870	>
871		sprintf( checkPointMsg,
872	<	"succesfully sent the simulation information to fortran.\n");
670	<	MPIcheckPoint();
671	<	#endif // is_mpi
672	<	}
673	<
674	<
675	<	#ifdef IS_MPI
676	<	void SimInfo::setupFortranParallel() {
872	>	"succesfully sent the simulation information to fortran.\n");
873
874	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
875	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
876	<	std::vector<int> localToGlobalCutoffGroupIndex;
877	<	SimInfo::MoleculeIterator mi;
878	<	Molecule::AtomIterator ai;
879	<	Molecule::CutoffGroupIterator ci;
880	<	Molecule* mol;
881	<	Atom* atom;
882	<	CutoffGroup* cg;
874	>	errorCheckPoint();
875	>
876	>	// Setup number of neighbors in neighbor list if present
877	>	if (simParams_->haveNeighborListNeighbors()) {
878	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
879	>	setNeighbors(&nlistNeighbors);
880	>	}
881	>
882	>	#ifdef IS_MPI
883	>	//SimInfo is responsible for creating localToGlobalAtomIndex and
884	>	//localToGlobalGroupIndex
885	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
886	>	vector<int> localToGlobalCutoffGroupIndex;
887		mpiSimData parallelData;
688	–	int isError;
888
889		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
890
891	<	//local index(index in DataStorge) of atom is important
892	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
893	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
894	<	}
891	>	//local index(index in DataStorge) of atom is important
892	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
893	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
894	>	}
895
896	<	//local index of cutoff group is trivial, it only depends on the order of travesing
897	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
898	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
899	<	}
896	>	//local index of cutoff group is trivial, it only depends on the order of travesing
897	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
898	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
899	>	}
900
901		}
902
#	Line 717 | Line 916 | void SimInfo::setupFortranParallel() {
916		&localToGlobalCutoffGroupIndex[0], &isError);
917
918		if (isError) {
919	<	sprintf(painCave.errMsg,
920	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
921	<	painCave.isFatal = 1;
922	<	simError();
919	>	sprintf(painCave.errMsg,
920	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
921	>	painCave.isFatal = 1;
922	>	simError();
923		}
924
925		sprintf(checkPointMsg, " mpiRefresh successful.\n");
926	<	MPIcheckPoint();
728	<
729	<
730	<	}
731	<
926	>	errorCheckPoint();
927		#endif
928
929	<	double SimInfo::calcMaxCutoffRadius() {
929	>	initFortranFF(&isError);
930	>	if (isError) {
931	>	sprintf(painCave.errMsg,
932	>	"initFortranFF errror: fortran didn't like something we gave it.\n");
933	>	painCave.isFatal = 1;
934	>	simError();
935	>	}
936	>	fortranInitialized_ = true;
937	>	}
938
939	+	void SimInfo::addProperty(GenericData* genData) {
940	+	properties_.addProperty(genData);
941	+	}
942
943	<	std::set<AtomType*> atomTypes;
944	<	std::set<AtomType*>::iterator i;
945	<	std::vector<double> cutoffRadius;
943	>	void SimInfo::removeProperty(const string& propName) {
944	>	properties_.removeProperty(propName);
945	>	}
946
947	<	//get the unique atom types
948	<	atomTypes = getUniqueAtomTypes();
947	>	void SimInfo::clearProperties() {
948	>	properties_.clearProperties();
949	>	}
950
951	<	//query the max cutoff radius among these atom types
952	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
953	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
954	<	}
951	>	vector<string> SimInfo::getPropertyNames() {
952	>	return properties_.getPropertyNames();
953	>	}
954	>
955	>	vector<GenericData*> SimInfo::getProperties() {
956	>	return properties_.getProperties();
957	>	}
958
959	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
960	<	#ifdef IS_MPI
961	<	//pick the max cutoff radius among the processors
752	<	#endif
959	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
960	>	return properties_.getPropertyByName(propName);
961	>	}
962
963	<	return maxCutoffRadius;
964	<	}
965	<
966	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
967	<
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_;
963	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
964	>	if (sman_ == sman) {
965	>	return;
966	>	}
967	>	delete sman_;
968		sman_ = sman;
969
970		Molecule* mol;
#	Line 851 | Line 976 | void SimInfo::setSnapshotManager(SnapshotManager* sman
976
977		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
978
979	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
980	<	atom->setSnapshotManager(sman_);
981	<	}
979	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
980	>	atom->setSnapshotManager(sman_);
981	>	}
982
983	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
984	<	rb->setSnapshotManager(sman_);
985	<	}
983	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
984	>	rb->setSnapshotManager(sman_);
985	>	}
986		}
987
988	<	}
988	>	}
989
990	<	Vector3d SimInfo::getComVel(){
990	>	Vector3d SimInfo::getComVel(){
991		SimInfo::MoleculeIterator i;
992		Molecule* mol;
993
994		Vector3d comVel(0.0);
995	<	double totalMass = 0.0;
995	>	RealType totalMass = 0.0;
996
997
998		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
999	<	double mass = mol->getMass();
1000	<	totalMass += mass;
1001	<	comVel += mass * mol->getComVel();
999	>	RealType mass = mol->getMass();
1000	>	totalMass += mass;
1001	>	comVel += mass * mol->getComVel();
1002		}
1003
1004		#ifdef IS_MPI
1005	<	double tmpMass = totalMass;
1005	>	RealType tmpMass = totalMass;
1006		Vector3d tmpComVel(comVel);
1007	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1008	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1007	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1008	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1009		#endif
1010
1011		comVel /= totalMass;
1012
1013		return comVel;
1014	<	}
1014	>	}
1015
1016	<	Vector3d SimInfo::getCom(){
1016	>	Vector3d SimInfo::getCom(){
1017		SimInfo::MoleculeIterator i;
1018		Molecule* mol;
1019
1020		Vector3d com(0.0);
1021	<	double totalMass = 0.0;
1021	>	RealType totalMass = 0.0;
1022
1023		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1024	<	double mass = mol->getMass();
1025	<	totalMass += mass;
1026	<	com += mass * mol->getCom();
1024	>	RealType mass = mol->getMass();
1025	>	totalMass += mass;
1026	>	com += mass * mol->getCom();
1027		}
1028
1029		#ifdef IS_MPI
1030	<	double tmpMass = totalMass;
1030	>	RealType tmpMass = totalMass;
1031		Vector3d tmpCom(com);
1032	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1033	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1032	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1033	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1034		#endif
1035
1036		com /= totalMass;
1037
1038		return com;
1039
1040	<	}
1040	>	}
1041
1042	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1042	>	ostream& operator <<(ostream& o, SimInfo& info) {
1043
1044		return o;
1045	<	}
1045	>	}
1046	>
1047	>
1048	>	/*
1049	>	Returns center of mass and center of mass velocity in one function call.
1050	>	*/
1051	>
1052	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1053	>	SimInfo::MoleculeIterator i;
1054	>	Molecule* mol;
1055	>
1056	>
1057	>	RealType totalMass = 0.0;
1058	>
1059
1060	<	}//end namespace oopse
1060	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1061	>	RealType mass = mol->getMass();
1062	>	totalMass += mass;
1063	>	com += mass * mol->getCom();
1064	>	comVel += mass * mol->getComVel();
1065	>	}
1066	>
1067	>	#ifdef IS_MPI
1068	>	RealType tmpMass = totalMass;
1069	>	Vector3d tmpCom(com);
1070	>	Vector3d tmpComVel(comVel);
1071	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1072	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1073	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1074	>	#endif
1075	>
1076	>	com /= totalMass;
1077	>	comVel /= totalMass;
1078	>	}
1079	>
1080	>	/*
1081	>	Return intertia tensor for entire system and angular momentum Vector.
1082
1083	+
1084	+	[  Ixx -Ixy  -Ixz ]
1085	+	J =| -Iyx  Iyy  -Iyz |
1086	+	[ -Izx -Iyz   Izz ]
1087	+	*/
1088	+
1089	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1090	+
1091	+
1092	+	RealType xx = 0.0;
1093	+	RealType yy = 0.0;
1094	+	RealType zz = 0.0;
1095	+	RealType xy = 0.0;
1096	+	RealType xz = 0.0;
1097	+	RealType yz = 0.0;
1098	+	Vector3d com(0.0);
1099	+	Vector3d comVel(0.0);
1100	+
1101	+	getComAll(com, comVel);
1102	+
1103	+	SimInfo::MoleculeIterator i;
1104	+	Molecule* mol;
1105	+
1106	+	Vector3d thisq(0.0);
1107	+	Vector3d thisv(0.0);
1108	+
1109	+	RealType thisMass = 0.0;
1110	+
1111	+
1112	+
1113	+
1114	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1115	+
1116	+	thisq = mol->getCom()-com;
1117	+	thisv = mol->getComVel()-comVel;
1118	+	thisMass = mol->getMass();
1119	+	// Compute moment of intertia coefficients.
1120	+	xx += thisq[0]*thisq[0]*thisMass;
1121	+	yy += thisq[1]*thisq[1]*thisMass;
1122	+	zz += thisq[2]*thisq[2]*thisMass;
1123	+
1124	+	// compute products of intertia
1125	+	xy += thisq[0]*thisq[1]*thisMass;
1126	+	xz += thisq[0]*thisq[2]*thisMass;
1127	+	yz += thisq[1]*thisq[2]*thisMass;
1128	+
1129	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1130	+
1131	+	}
1132	+
1133	+
1134	+	inertiaTensor(0,0) = yy + zz;
1135	+	inertiaTensor(0,1) = -xy;
1136	+	inertiaTensor(0,2) = -xz;
1137	+	inertiaTensor(1,0) = -xy;
1138	+	inertiaTensor(1,1) = xx + zz;
1139	+	inertiaTensor(1,2) = -yz;
1140	+	inertiaTensor(2,0) = -xz;
1141	+	inertiaTensor(2,1) = -yz;
1142	+	inertiaTensor(2,2) = xx + yy;
1143	+
1144	+	#ifdef IS_MPI
1145	+	Mat3x3d tmpI(inertiaTensor);
1146	+	Vector3d tmpAngMom;
1147	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1148	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1149	+	#endif
1150	+
1151	+	return;
1152	+	}
1153	+
1154	+	//Returns the angular momentum of the system
1155	+	Vector3d SimInfo::getAngularMomentum(){
1156	+
1157	+	Vector3d com(0.0);
1158	+	Vector3d comVel(0.0);
1159	+	Vector3d angularMomentum(0.0);
1160	+
1161	+	getComAll(com,comVel);
1162	+
1163	+	SimInfo::MoleculeIterator i;
1164	+	Molecule* mol;
1165	+
1166	+	Vector3d thisr(0.0);
1167	+	Vector3d thisp(0.0);
1168	+
1169	+	RealType thisMass;
1170	+
1171	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1172	+	thisMass = mol->getMass();
1173	+	thisr = mol->getCom()-com;
1174	+	thisp = (mol->getComVel()-comVel)*thisMass;
1175	+
1176	+	angularMomentum += cross( thisr, thisp );
1177	+
1178	+	}
1179	+
1180	+	#ifdef IS_MPI
1181	+	Vector3d tmpAngMom;
1182	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1183	+	#endif
1184	+
1185	+	return angularMomentum;
1186	+	}
1187	+
1188	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1189	+	return IOIndexToIntegrableObject.at(index);
1190	+	}
1191	+
1192	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1193	+	IOIndexToIntegrableObject= v;
1194	+	}
1195	+
1196	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1197	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1198	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1199	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1200	+	*/
1201	+	void SimInfo::getGyrationalVolume(RealType &volume){
1202	+	Mat3x3d intTensor;
1203	+	RealType det;
1204	+	Vector3d dummyAngMom;
1205	+	RealType sysconstants;
1206	+	RealType geomCnst;
1207	+
1208	+	geomCnst = 3.0/2.0;
1209	+	/* Get the inertial tensor and angular momentum for free*/
1210	+	getInertiaTensor(intTensor,dummyAngMom);
1211	+
1212	+	det = intTensor.determinant();
1213	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1214	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1215	+	return;
1216	+	}
1217	+
1218	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1219	+	Mat3x3d intTensor;
1220	+	Vector3d dummyAngMom;
1221	+	RealType sysconstants;
1222	+	RealType geomCnst;
1223	+
1224	+	geomCnst = 3.0/2.0;
1225	+	/* Get the inertial tensor and angular momentum for free*/
1226	+	getInertiaTensor(intTensor,dummyAngMom);
1227	+
1228	+	detI = intTensor.determinant();
1229	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1230	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1231	+	return;
1232	+	}
1233	+	/*
1234	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1235	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1236	+	sdByGlobalIndex_ = v;
1237	+	}
1238	+
1239	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1240	+	//assert(index < nAtoms_ + nRigidBodies_);
1241	+	return sdByGlobalIndex_.at(index);
1242	+	}
1243	+	*/
1244	+	int SimInfo::getNGlobalConstraints() {
1245	+	int nGlobalConstraints;
1246	+	#ifdef IS_MPI
1247	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1248	+	MPI_COMM_WORLD);
1249	+	#else
1250	+	nGlobalConstraints =  nConstraints_;
1251	+	#endif
1252	+	return nGlobalConstraints;
1253	+	}
1254	+
1255	+	}//end namespace OpenMD
1256	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 334 by tim, Mon Feb 14 17:57:01 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1536 by gezelter, Wed Jan 5 14:49:05 2011 UTC

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