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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1530 by gezelter, Tue Dec 28 21:47:55 2010 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/fCutoffPolicy.h"
58		#include "UseTheForce/doForces_interface.h"
59	<	#include "UseTheForce/notifyCutoffs_interface.h"
59	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
60		#include "utils/MemoryUtils.hpp"
61		#include "utils/simError.h"
62		#include "selection/SelectionManager.hpp"
63	+	#include "io/ForceFieldOptions.hpp"
64	+	#include "UseTheForce/ForceField.hpp"
65	+	#include "nonbonded/SwitchingFunction.hpp"
66
67	+
68		#ifdef IS_MPI
69		#include "UseTheForce/mpiComponentPlan.h"
70		#include "UseTheForce/DarkSide/simParallel_interface.h"
71		#endif
72
73	<	namespace oopse {
74	<
75	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
76	<	ForceField* ff, Globals* simParams) :
77	<	forceField_(ff), simParams_(simParams),
78	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
79	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
80	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
81	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
82	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
83	<	sman_(NULL), fortranInitialized_(false) {
84	<
85	<
79	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
73	>	using namespace std;
74	>	namespace OpenMD {
75	>
76	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
77	>	forceField_(ff), simParams_(simParams),
78	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
79	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
80	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
81	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
82	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
83	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
84	>	calcBoxDipole_(false), useAtomicVirial_(true) {
85	>
86		MoleculeStamp* molStamp;
87		int nMolWithSameStamp;
88		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
89	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
89	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
90		CutoffGroupStamp* cgStamp;
91		RigidBodyStamp* rbStamp;
92		int nRigidAtoms = 0;
93
94	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
95	<	molStamp = i->first;
96	<	nMolWithSameStamp = i->second;
97	<
98	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
99	<
100	<	//calculate atoms in molecules
101	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
102	<
103	<
104	<	//calculate atoms in cutoff groups
105	<	int nAtomsInGroups = 0;
106	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
107	<
108	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
109	<	cgStamp = molStamp->getCutoffGroup(j);
110	<	nAtomsInGroups += cgStamp->getNMembers();
111	<	}
112	<
113	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
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->getRigidBody(j);
122	<	nAtomsInRigidBodies += rbStamp->getNMembers();
123	<	}
124	<
125	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
126	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
127	<
94	>	vector<Component*> components = simParams->getComponents();
95	>
96	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
97	>	molStamp = (*i)->getMoleculeStamp();
98	>	nMolWithSameStamp = (*i)->getNMol();
99	>
100	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
101	>
102	>	//calculate atoms in molecules
103	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
104	>
105	>	//calculate atoms in cutoff groups
106	>	int nAtomsInGroups = 0;
107	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
108	>
109	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
110	>	cgStamp = molStamp->getCutoffGroupStamp(j);
111	>	nAtomsInGroups += cgStamp->getNMembers();
112	>	}
113	>
114	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
115	>
116	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
117	>
118	>	//calculate atoms in rigid bodies
119	>	int nAtomsInRigidBodies = 0;
120	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
121	>
122	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
123	>	rbStamp = molStamp->getRigidBodyStamp(j);
124	>	nAtomsInRigidBodies += rbStamp->getNMembers();
125	>	}
126	>
127	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
128	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
129	>
130		}
131	<
132	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
133	<	//therefore the total number of cutoff groups in the system is equal to
134	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
135	<	//file plus the number of cutoff groups defined in meta-data file
131	>
132	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
133	>	//group therefore the total number of cutoff groups in the system is
134	>	//equal to the total number of atoms minus number of atoms belong to
135	>	//cutoff group defined in meta-data file plus the number of cutoff
136	>	//groups defined in meta-data file
137		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
138	<
139	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
140	<	//therefore the total number of  integrable objects in the system is equal to
141	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
142	<	//file plus the number of  rigid bodies defined in meta-data file
143	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
144	<
138	>
139	>	//every free atom (atom does not belong to rigid bodies) is an
140	>	//integrable object therefore the total number of integrable objects
141	>	//in the system is equal to the total number of atoms minus number of
142	>	//atoms belong to rigid body defined in meta-data file plus the number
143	>	//of rigid bodies defined in meta-data file
144	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
145	>	+ nGlobalRigidBodies_;
146	>
147		nGlobalMols_ = molStampIds_.size();
137	–
138	–	#ifdef IS_MPI
148		molToProcMap_.resize(nGlobalMols_);
149	<	#endif
150	<
151	<	}
152	<
144	<	SimInfo::~SimInfo() {
145	<	std::map<int, Molecule*>::iterator i;
149	>	}
150	>
151	>	SimInfo::~SimInfo() {
152	>	map<int, Molecule*>::iterator i;
153		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
154	<	delete i->second;
154	>	delete i->second;
155		}
156		molecules_.clear();
157	<
151	<	MemoryUtils::deletePointers(moleculeStamps_);
152	<
157	>
158		delete sman_;
159		delete simParams_;
160		delete forceField_;
161	<	}
161	>	}
162
158	–	int SimInfo::getNGlobalConstraints() {
159	–	int nGlobalConstraints;
160	–	#ifdef IS_MPI
161	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
162	–	MPI_COMM_WORLD);
163	–	#else
164	–	nGlobalConstraints =  nConstraints_;
165	–	#endif
166	–	return nGlobalConstraints;
167	–	}
163
164	<	bool SimInfo::addMolecule(Molecule* mol) {
164	>	bool SimInfo::addMolecule(Molecule* mol) {
165		MoleculeIterator i;
166	<
166	>
167		i = molecules_.find(mol->getGlobalIndex());
168		if (i == molecules_.end() ) {
169	<
170	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
171	<
172	<	nAtoms_ += mol->getNAtoms();
173	<	nBonds_ += mol->getNBonds();
174	<	nBends_ += mol->getNBends();
175	<	nTorsions_ += mol->getNTorsions();
176	<	nRigidBodies_ += mol->getNRigidBodies();
177	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
178	<	nCutoffGroups_ += mol->getNCutoffGroups();
179	<	nConstraints_ += mol->getNConstraintPairs();
180	<
181	<	addExcludePairs(mol);
182	<
183	<	return true;
169	>
170	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
171	>
172	>	nAtoms_ += mol->getNAtoms();
173	>	nBonds_ += mol->getNBonds();
174	>	nBends_ += mol->getNBends();
175	>	nTorsions_ += mol->getNTorsions();
176	>	nInversions_ += mol->getNInversions();
177	>	nRigidBodies_ += mol->getNRigidBodies();
178	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
179	>	nCutoffGroups_ += mol->getNCutoffGroups();
180	>	nConstraints_ += mol->getNConstraintPairs();
181	>
182	>	addInteractionPairs(mol);
183	>
184	>	return true;
185		} else {
186	<	return false;
186	>	return false;
187		}
188	<	}
189	<
190	<	bool SimInfo::removeMolecule(Molecule* mol) {
188	>	}
189	>
190	>	bool SimInfo::removeMolecule(Molecule* mol) {
191		MoleculeIterator i;
192		i = molecules_.find(mol->getGlobalIndex());
193
194		if (i != molecules_.end() ) {
195
196	<	assert(mol == i->second);
196	>	assert(mol == i->second);
197
198	<	nAtoms_ -= mol->getNAtoms();
199	<	nBonds_ -= mol->getNBonds();
200	<	nBends_ -= mol->getNBends();
201	<	nTorsions_ -= mol->getNTorsions();
202	<	nRigidBodies_ -= mol->getNRigidBodies();
203	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
204	<	nCutoffGroups_ -= mol->getNCutoffGroups();
205	<	nConstraints_ -= mol->getNConstraintPairs();
198	>	nAtoms_ -= mol->getNAtoms();
199	>	nBonds_ -= mol->getNBonds();
200	>	nBends_ -= mol->getNBends();
201	>	nTorsions_ -= mol->getNTorsions();
202	>	nInversions_ -= mol->getNInversions();
203	>	nRigidBodies_ -= mol->getNRigidBodies();
204	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
205	>	nCutoffGroups_ -= mol->getNCutoffGroups();
206	>	nConstraints_ -= mol->getNConstraintPairs();
207
208	<	removeExcludePairs(mol);
209	<	molecules_.erase(mol->getGlobalIndex());
208	>	removeInteractionPairs(mol);
209	>	molecules_.erase(mol->getGlobalIndex());
210
211	<	delete mol;
211	>	delete mol;
212
213	<	return true;
213	>	return true;
214		} else {
215	<	return false;
215	>	return false;
216		}
217	+	}
218
221	–
222	–	}
223	–
219
220	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
220	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
221		i = molecules_.begin();
222		return i == molecules_.end() ? NULL : i->second;
223	<	}
223	>	}
224
225	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
225	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
226		++i;
227		return i == molecules_.end() ? NULL : i->second;
228	<	}
228	>	}
229
230
231	<	void SimInfo::calcNdf() {
231	>	void SimInfo::calcNdf() {
232		int ndf_local;
233		MoleculeIterator i;
234	<	std::vector<StuntDouble*>::iterator j;
234	>	vector<StuntDouble*>::iterator j;
235		Molecule* mol;
236		StuntDouble* integrableObject;
237
238		ndf_local = 0;
239
240		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
241	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
242	<	integrableObject = mol->nextIntegrableObject(j)) {
241	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
242	>	integrableObject = mol->nextIntegrableObject(j)) {
243
244	<	ndf_local += 3;
244	>	ndf_local += 3;
245
246	<	if (integrableObject->isDirectional()) {
247	<	if (integrableObject->isLinear()) {
248	<	ndf_local += 2;
249	<	} else {
250	<	ndf_local += 3;
251	<	}
252	<	}
246	>	if (integrableObject->isDirectional()) {
247	>	if (integrableObject->isLinear()) {
248	>	ndf_local += 2;
249	>	} else {
250	>	ndf_local += 3;
251	>	}
252	>	}
253
254	<	}//end for (integrableObject)
255	<	}// end for (mol)
254	>	}
255	>	}
256
257		// n_constraints is local, so subtract them on each processor
258		ndf_local -= nConstraints_;
#	Line 272 | Line 267 | void SimInfo::calcNdf() {
267		// entire system:
268		ndf_ = ndf_ - 3 - nZconstraint_;
269
270	<	}
270	>	}
271
272	<	void SimInfo::calcNdfRaw() {
272	>	int SimInfo::getFdf() {
273	>	#ifdef IS_MPI
274	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
275	>	#else
276	>	fdf_ = fdf_local;
277	>	#endif
278	>	return fdf_;
279	>	}
280	>
281	>	void SimInfo::calcNdfRaw() {
282		int ndfRaw_local;
283
284		MoleculeIterator i;
285	<	std::vector<StuntDouble*>::iterator j;
285	>	vector<StuntDouble*>::iterator j;
286		Molecule* mol;
287		StuntDouble* integrableObject;
288
#	Line 286 | Line 290 | void SimInfo::calcNdfRaw() {
290		ndfRaw_local = 0;
291
292		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
293	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
294	<	integrableObject = mol->nextIntegrableObject(j)) {
293	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
294	>	integrableObject = mol->nextIntegrableObject(j)) {
295
296	<	ndfRaw_local += 3;
296	>	ndfRaw_local += 3;
297
298	<	if (integrableObject->isDirectional()) {
299	<	if (integrableObject->isLinear()) {
300	<	ndfRaw_local += 2;
301	<	} else {
302	<	ndfRaw_local += 3;
303	<	}
304	<	}
298	>	if (integrableObject->isDirectional()) {
299	>	if (integrableObject->isLinear()) {
300	>	ndfRaw_local += 2;
301	>	} else {
302	>	ndfRaw_local += 3;
303	>	}
304	>	}
305
306	<	}
306	>	}
307		}
308
309		#ifdef IS_MPI
#	Line 307 | Line 311 | void SimInfo::calcNdfRaw() {
311		#else
312		ndfRaw_ = ndfRaw_local;
313		#endif
314	<	}
314	>	}
315
316	<	void SimInfo::calcNdfTrans() {
316	>	void SimInfo::calcNdfTrans() {
317		int ndfTrans_local;
318
319		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 323 | Line 327 | void SimInfo::calcNdfTrans() {
327
328		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
329
330	<	}
330	>	}
331
332	<	void SimInfo::addExcludePairs(Molecule* mol) {
333	<	std::vector<Bond*>::iterator bondIter;
334	<	std::vector<Bend*>::iterator bendIter;
335	<	std::vector<Torsion*>::iterator torsionIter;
332	>	void SimInfo::addInteractionPairs(Molecule* mol) {
333	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
334	>	vector<Bond*>::iterator bondIter;
335	>	vector<Bend*>::iterator bendIter;
336	>	vector<Torsion*>::iterator torsionIter;
337	>	vector<Inversion*>::iterator inversionIter;
338		Bond* bond;
339		Bend* bend;
340		Torsion* torsion;
341	+	Inversion* inversion;
342		int a;
343		int b;
344		int c;
345		int d;
339	–
340	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
341	–	a = bond->getAtomA()->getGlobalIndex();
342	–	b = bond->getAtomB()->getGlobalIndex();
343	–	exclude_.addPair(a, b);
344	–	}
346
347	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
348	<	a = bend->getAtomA()->getGlobalIndex();
349	<	b = bend->getAtomB()->getGlobalIndex();
350	<	c = bend->getAtomC()->getGlobalIndex();
347	>	// atomGroups can be used to add special interaction maps between
348	>	// groups of atoms that are in two separate rigid bodies.
349	>	// However, most site-site interactions between two rigid bodies
350	>	// are probably not special, just the ones between the physically
351	>	// bonded atoms.  Interactions *within* a single rigid body should
352	>	// always be excluded.  These are done at the bottom of this
353	>	// function.
354
355	<	exclude_.addPair(a, b);
356	<	exclude_.addPair(a, c);
357	<	exclude_.addPair(b, c);
355	>	map<int, set<int> > atomGroups;
356	>	Molecule::RigidBodyIterator rbIter;
357	>	RigidBody* rb;
358	>	Molecule::IntegrableObjectIterator ii;
359	>	StuntDouble* integrableObject;
360	>
361	>	for (integrableObject = mol->beginIntegrableObject(ii);
362	>	integrableObject != NULL;
363	>	integrableObject = mol->nextIntegrableObject(ii)) {
364	>
365	>	if (integrableObject->isRigidBody()) {
366	>	rb = static_cast<RigidBody*>(integrableObject);
367	>	vector<Atom*> atoms = rb->getAtoms();
368	>	set<int> rigidAtoms;
369	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
370	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
371	>	}
372	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
373	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
374	>	}
375	>	} else {
376	>	set<int> oneAtomSet;
377	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
378	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
379	>	}
380	>	}
381	>
382	>	for (bond= mol->beginBond(bondIter); bond != NULL;
383	>	bond = mol->nextBond(bondIter)) {
384	>
385	>	a = bond->getAtomA()->getGlobalIndex();
386	>	b = bond->getAtomB()->getGlobalIndex();
387	>
388	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
389	>	oneTwoInteractions_.addPair(a, b);
390	>	} else {
391	>	excludedInteractions_.addPair(a, b);
392	>	}
393		}
394
395	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
396	<	a = torsion->getAtomA()->getGlobalIndex();
358	<	b = torsion->getAtomB()->getGlobalIndex();
359	<	c = torsion->getAtomC()->getGlobalIndex();
360	<	d = torsion->getAtomD()->getGlobalIndex();
395	>	for (bend= mol->beginBend(bendIter); bend != NULL;
396	>	bend = mol->nextBend(bendIter)) {
397
398	<	exclude_.addPair(a, b);
399	<	exclude_.addPair(a, c);
400	<	exclude_.addPair(a, d);
401	<	exclude_.addPair(b, c);
402	<	exclude_.addPair(b, d);
403	<	exclude_.addPair(c, d);
398	>	a = bend->getAtomA()->getGlobalIndex();
399	>	b = bend->getAtomB()->getGlobalIndex();
400	>	c = bend->getAtomC()->getGlobalIndex();
401	>
402	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
403	>	oneTwoInteractions_.addPair(a, b);
404	>	oneTwoInteractions_.addPair(b, c);
405	>	} else {
406	>	excludedInteractions_.addPair(a, b);
407	>	excludedInteractions_.addPair(b, c);
408	>	}
409	>
410	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
411	>	oneThreeInteractions_.addPair(a, c);
412	>	} else {
413	>	excludedInteractions_.addPair(a, c);
414	>	}
415		}
416
417	<
418	<	}
417	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
418	>	torsion = mol->nextTorsion(torsionIter)) {
419
420	<	void SimInfo::removeExcludePairs(Molecule* mol) {
421	<	std::vector<Bond*>::iterator bondIter;
422	<	std::vector<Bend*>::iterator bendIter;
423	<	std::vector<Torsion*>::iterator torsionIter;
420	>	a = torsion->getAtomA()->getGlobalIndex();
421	>	b = torsion->getAtomB()->getGlobalIndex();
422	>	c = torsion->getAtomC()->getGlobalIndex();
423	>	d = torsion->getAtomD()->getGlobalIndex();
424	>
425	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
426	>	oneTwoInteractions_.addPair(a, b);
427	>	oneTwoInteractions_.addPair(b, c);
428	>	oneTwoInteractions_.addPair(c, d);
429	>	} else {
430	>	excludedInteractions_.addPair(a, b);
431	>	excludedInteractions_.addPair(b, c);
432	>	excludedInteractions_.addPair(c, d);
433	>	}
434	>
435	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
436	>	oneThreeInteractions_.addPair(a, c);
437	>	oneThreeInteractions_.addPair(b, d);
438	>	} else {
439	>	excludedInteractions_.addPair(a, c);
440	>	excludedInteractions_.addPair(b, d);
441	>	}
442	>
443	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
444	>	oneFourInteractions_.addPair(a, d);
445	>	} else {
446	>	excludedInteractions_.addPair(a, d);
447	>	}
448	>	}
449	>
450	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
451	>	inversion = mol->nextInversion(inversionIter)) {
452	>
453	>	a = inversion->getAtomA()->getGlobalIndex();
454	>	b = inversion->getAtomB()->getGlobalIndex();
455	>	c = inversion->getAtomC()->getGlobalIndex();
456	>	d = inversion->getAtomD()->getGlobalIndex();
457	>
458	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
459	>	oneTwoInteractions_.addPair(a, b);
460	>	oneTwoInteractions_.addPair(a, c);
461	>	oneTwoInteractions_.addPair(a, d);
462	>	} else {
463	>	excludedInteractions_.addPair(a, b);
464	>	excludedInteractions_.addPair(a, c);
465	>	excludedInteractions_.addPair(a, d);
466	>	}
467	>
468	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
469	>	oneThreeInteractions_.addPair(b, c);
470	>	oneThreeInteractions_.addPair(b, d);
471	>	oneThreeInteractions_.addPair(c, d);
472	>	} else {
473	>	excludedInteractions_.addPair(b, c);
474	>	excludedInteractions_.addPair(b, d);
475	>	excludedInteractions_.addPair(c, d);
476	>	}
477	>	}
478	>
479	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
480	>	rb = mol->nextRigidBody(rbIter)) {
481	>	vector<Atom*> atoms = rb->getAtoms();
482	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
483	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
484	>	a = atoms[i]->getGlobalIndex();
485	>	b = atoms[j]->getGlobalIndex();
486	>	excludedInteractions_.addPair(a, b);
487	>	}
488	>	}
489	>	}
490	>
491	>	}
492	>
493	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
494	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
495	>	vector<Bond*>::iterator bondIter;
496	>	vector<Bend*>::iterator bendIter;
497	>	vector<Torsion*>::iterator torsionIter;
498	>	vector<Inversion*>::iterator inversionIter;
499		Bond* bond;
500		Bend* bend;
501		Torsion* torsion;
502	+	Inversion* inversion;
503		int a;
504		int b;
505		int c;
506		int d;
507	+
508	+	map<int, set<int> > atomGroups;
509	+	Molecule::RigidBodyIterator rbIter;
510	+	RigidBody* rb;
511	+	Molecule::IntegrableObjectIterator ii;
512	+	StuntDouble* integrableObject;
513
514	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
515	<	a = bond->getAtomA()->getGlobalIndex();
516	<	b = bond->getAtomB()->getGlobalIndex();
517	<	exclude_.removePair(a, b);
514	>	for (integrableObject = mol->beginIntegrableObject(ii);
515	>	integrableObject != NULL;
516	>	integrableObject = mol->nextIntegrableObject(ii)) {
517	>
518	>	if (integrableObject->isRigidBody()) {
519	>	rb = static_cast<RigidBody*>(integrableObject);
520	>	vector<Atom*> atoms = rb->getAtoms();
521	>	set<int> rigidAtoms;
522	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
523	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
524	>	}
525	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
526	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
527	>	}
528	>	} else {
529	>	set<int> oneAtomSet;
530	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
531	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
532	>	}
533	>	}
534	>
535	>	for (bond= mol->beginBond(bondIter); bond != NULL;
536	>	bond = mol->nextBond(bondIter)) {
537	>
538	>	a = bond->getAtomA()->getGlobalIndex();
539	>	b = bond->getAtomB()->getGlobalIndex();
540	>
541	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
542	>	oneTwoInteractions_.removePair(a, b);
543	>	} else {
544	>	excludedInteractions_.removePair(a, b);
545	>	}
546		}
547
548	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
549	<	a = bend->getAtomA()->getGlobalIndex();
393	<	b = bend->getAtomB()->getGlobalIndex();
394	<	c = bend->getAtomC()->getGlobalIndex();
548	>	for (bend= mol->beginBend(bendIter); bend != NULL;
549	>	bend = mol->nextBend(bendIter)) {
550
551	<	exclude_.removePair(a, b);
552	<	exclude_.removePair(a, c);
553	<	exclude_.removePair(b, c);
551	>	a = bend->getAtomA()->getGlobalIndex();
552	>	b = bend->getAtomB()->getGlobalIndex();
553	>	c = bend->getAtomC()->getGlobalIndex();
554	>
555	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
556	>	oneTwoInteractions_.removePair(a, b);
557	>	oneTwoInteractions_.removePair(b, c);
558	>	} else {
559	>	excludedInteractions_.removePair(a, b);
560	>	excludedInteractions_.removePair(b, c);
561	>	}
562	>
563	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
564	>	oneThreeInteractions_.removePair(a, c);
565	>	} else {
566	>	excludedInteractions_.removePair(a, c);
567	>	}
568		}
569
570	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
571	<	a = torsion->getAtomA()->getGlobalIndex();
403	<	b = torsion->getAtomB()->getGlobalIndex();
404	<	c = torsion->getAtomC()->getGlobalIndex();
405	<	d = torsion->getAtomD()->getGlobalIndex();
570	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
571	>	torsion = mol->nextTorsion(torsionIter)) {
572
573	<	exclude_.removePair(a, b);
574	<	exclude_.removePair(a, c);
575	<	exclude_.removePair(a, d);
576	<	exclude_.removePair(b, c);
577	<	exclude_.removePair(b, d);
578	<	exclude_.removePair(c, d);
573	>	a = torsion->getAtomA()->getGlobalIndex();
574	>	b = torsion->getAtomB()->getGlobalIndex();
575	>	c = torsion->getAtomC()->getGlobalIndex();
576	>	d = torsion->getAtomD()->getGlobalIndex();
577	>
578	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
579	>	oneTwoInteractions_.removePair(a, b);
580	>	oneTwoInteractions_.removePair(b, c);
581	>	oneTwoInteractions_.removePair(c, d);
582	>	} else {
583	>	excludedInteractions_.removePair(a, b);
584	>	excludedInteractions_.removePair(b, c);
585	>	excludedInteractions_.removePair(c, d);
586	>	}
587	>
588	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
589	>	oneThreeInteractions_.removePair(a, c);
590	>	oneThreeInteractions_.removePair(b, d);
591	>	} else {
592	>	excludedInteractions_.removePair(a, c);
593	>	excludedInteractions_.removePair(b, d);
594	>	}
595	>
596	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
597	>	oneFourInteractions_.removePair(a, d);
598	>	} else {
599	>	excludedInteractions_.removePair(a, d);
600	>	}
601		}
602
603	<	}
603	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
604	>	inversion = mol->nextInversion(inversionIter)) {
605
606	+	a = inversion->getAtomA()->getGlobalIndex();
607	+	b = inversion->getAtomB()->getGlobalIndex();
608	+	c = inversion->getAtomC()->getGlobalIndex();
609	+	d = inversion->getAtomD()->getGlobalIndex();
610
611	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
612	<	int curStampId;
611	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
612	>	oneTwoInteractions_.removePair(a, b);
613	>	oneTwoInteractions_.removePair(a, c);
614	>	oneTwoInteractions_.removePair(a, d);
615	>	} else {
616	>	excludedInteractions_.removePair(a, b);
617	>	excludedInteractions_.removePair(a, c);
618	>	excludedInteractions_.removePair(a, d);
619	>	}
620
621	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
622	+	oneThreeInteractions_.removePair(b, c);
623	+	oneThreeInteractions_.removePair(b, d);
624	+	oneThreeInteractions_.removePair(c, d);
625	+	} else {
626	+	excludedInteractions_.removePair(b, c);
627	+	excludedInteractions_.removePair(b, d);
628	+	excludedInteractions_.removePair(c, d);
629	+	}
630	+	}
631	+
632	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
633	+	rb = mol->nextRigidBody(rbIter)) {
634	+	vector<Atom*> atoms = rb->getAtoms();
635	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
636	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
637	+	a = atoms[i]->getGlobalIndex();
638	+	b = atoms[j]->getGlobalIndex();
639	+	excludedInteractions_.removePair(a, b);
640	+	}
641	+	}
642	+	}
643	+
644	+	}
645	+
646	+
647	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
648	+	int curStampId;
649	+
650		//index from 0
651		curStampId = moleculeStamps_.size();
652
653		moleculeStamps_.push_back(molStamp);
654		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
655	<	}
655	>	}
656
428	–	void SimInfo::update() {
657
658	<	setupSimType();
658	>	/**
659	>	* update
660	>	*
661	>	*  Performs the global checks and variable settings after the objects have been
662	>	*  created.
663	>	*
664	>	*/
665	>	void SimInfo::update() {
666	>
667	>	setupSimVariables();
668	>	setupCutoffs();
669	>	setupSwitching();
670	>	setupElectrostatics();
671	>	setupNeighborlists();
672
673		#ifdef IS_MPI
674		setupFortranParallel();
675		#endif
435	–
676		setupFortranSim();
677	+	fortranInitialized_ = true;
678
438	–	//setup fortran force field
439	–	/** @deprecate */
440	–	int isError = 0;
441	–	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
442	–	if(isError){
443	–	sprintf( painCave.errMsg,
444	–	"ForceField error: There was an error initializing the forceField in fortran.\n" );
445	–	painCave.isFatal = 1;
446	–	simError();
447	–	}
448	–
449	–
450	–	setupCutoff();
451	–
679		calcNdf();
680		calcNdfRaw();
681		calcNdfTrans();
682	<
683	<	fortranInitialized_ = true;
684	<	}
458	<
459	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
682	>	}
683	>
684	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
685		SimInfo::MoleculeIterator mi;
686		Molecule* mol;
687		Molecule::AtomIterator ai;
688		Atom* atom;
689	<	std::set<AtomType*> atomTypes;
689	>	set<AtomType*> atomTypes;
690	>
691	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
692	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
693	>	atomTypes.insert(atom->getAtomType());
694	>	}
695	>	}
696	>	return atomTypes;
697	>	}
698
699	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
700	<
701	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
702	<	atomTypes.insert(atom->getAtomType());
699	>	/**
700	>	* setupCutoffs
701	>	*
702	>	* Sets the values of cutoffRadius and cutoffMethod
703	>	*
704	>	* cutoffRadius : realType
705	>	*  If the cutoffRadius was explicitly set, use that value.
706	>	*  If the cutoffRadius was not explicitly set:
707	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
708	>	*      No electrostatic atoms?  Poll the atom types present in the
709	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
710	>	*      Use the maximum suggested value that was found.
711	>	*
712	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
713	>	*      If cutoffMethod was explicitly set, use that choice.
714	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
715	>	*/
716	>	void SimInfo::setupCutoffs() {
717	>
718	>	if (simParams_->haveCutoffRadius()) {
719	>	cutoffRadius_ = simParams_->getCutoffRadius();
720	>	} else {
721	>	if (usesElectrostaticAtoms_) {
722	>	sprintf(painCave.errMsg,
723	>	"SimInfo: No value was set for the cutoffRadius.\n"
724	>	"\tOpenMD will use a default value of 12.0 angstroms"
725	>	"\tfor the cutoffRadius.\n");
726	>	painCave.isFatal = 0;
727	>	painCave.severity = OPENMD_INFO;
728	>	simError();
729	>	cutoffRadius_ = 12.0;
730	>	} else {
731	>	RealType thisCut;
732	>	set<AtomType*>::iterator i;
733	>	set<AtomType*> atomTypes;
734	>	atomTypes = getSimulatedAtomTypes();
735	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
736	>	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
737	>	cutoffRadius_ = max(thisCut, cutoffRadius_);
738		}
739	<
739	>	sprintf(painCave.errMsg,
740	>	"SimInfo: No value was set for the cutoffRadius.\n"
741	>	"\tOpenMD will use %lf angstroms.\n",
742	>	cutoffRadius_);
743	>	painCave.isFatal = 0;
744	>	painCave.severity = OPENMD_INFO;
745	>	simError();
746	>	}
747		}
748
749	<	return atomTypes;
475	<	}
749	>	InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
750
751	<	void SimInfo::setupSimType() {
752	<	std::set<AtomType*>::iterator i;
753	<	std::set<AtomType*> atomTypes;
754	<	atomTypes = getUniqueAtomTypes();
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;
763	<	int useSticky = 0;
764	<	int useShape = 0;
765	<	int useFLARB = 0; //it is not in AtomType yet
766	<	int useDirectionalAtom = 0;
767	<	int useElectrostatics = 0;
768	<	//usePBC and useRF are from simParams
769	<	int usePBC = simParams_->getPBC();
770	<	int useRF = simParams_->getUseRF();
771	<
772	<	//loop over all of the atom types
773	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
774	<	useLennardJones |= (*i)->isLennardJones();
775	<	useElectrostatic |= (*i)->isElectrostatic();
776	<	useEAM |= (*i)->isEAM();
777	<	useCharge |= (*i)->isCharge();
778	<	useDirectional |= (*i)->isDirectional();
779	<	useDipole |= (*i)->isDipole();
780	<	useGayBerne |= (*i)->isGayBerne();
507	<	useSticky |= (*i)->isSticky();
508	<	useShape |= (*i)->isShape();
751	>	map<string, CutoffMethod> stringToCutoffMethod;
752	>	stringToCutoffMethod["HARD"] = HARD;
753	>	stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
754	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
755	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
756	>
757	>	if (simParams_->haveCutoffMethod()) {
758	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
759	>	map<string, CutoffMethod>::iterator i;
760	>	i = stringToCutoffMethod.find(cutMeth);
761	>	if (i == stringToCutoffMethod.end()) {
762	>	sprintf(painCave.errMsg,
763	>	"SimInfo: Could not find chosen cutoffMethod %s\n"
764	>	"\tShould be one of: "
765	>	"HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
766	>	cutMeth.c_str());
767	>	painCave.isFatal = 1;
768	>	painCave.severity = OPENMD_ERROR;
769	>	simError();
770	>	} else {
771	>	cutoffMethod_ = i->second;
772	>	}
773	>	} else {
774	>	sprintf(painCave.errMsg,
775	>	"SimInfo: No value was set for the cutoffMethod.\n"
776	>	"\tOpenMD will use SHIFTED_FORCE.\n");
777	>	painCave.isFatal = 0;
778	>	painCave.severity = OPENMD_INFO;
779	>	simError();
780	>	cutoffMethod_ = SHIFTED_FORCE;
781		}
782
783	<	if (useSticky || useDipole || useGayBerne || useShape) {
784	<	useDirectionalAtom = 1;
785	<	}
783	>	InteractionManager::Instance()->setCutoffMethod(cutoffMethod_);
784	>	}
785	>
786	>	/**
787	>	* setupSwitching
788	>	*
789	>	* Sets the values of switchingRadius and
790	>	*  If the switchingRadius was explicitly set, use that value (but check it)
791	>	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
792	>	*/
793	>	void SimInfo::setupSwitching() {
794	>
795	>	if (simParams_->haveSwitchingRadius()) {
796	>	switchingRadius_ = simParams_->getSwitchingRadius();
797	>	if (switchingRadius_ > cutoffRadius_) {
798	>	sprintf(painCave.errMsg,
799	>	"SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
800	>	switchingRadius_, cutoffRadius_);
801	>	painCave.isFatal = 1;
802	>	painCave.severity = OPENMD_ERROR;
803	>	simError();
804	>	}
805	>	} else {
806	>	switchingRadius_ = 0.85 * cutoffRadius_;
807	>	sprintf(painCave.errMsg,
808	>	"SimInfo: No value was set for the switchingRadius.\n"
809	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
810	>	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
811	>	painCave.isFatal = 0;
812	>	painCave.severity = OPENMD_WARNING;
813	>	simError();
814	>	}
815	>
816	>	InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
817
818	<	if (useCharge || useDipole) {
819	<	useElectrostatics = 1;
818	>	SwitchingFunctionType ft;
819	>
820	>	if (simParams_->haveSwitchingFunctionType()) {
821	>	string funcType = simParams_->getSwitchingFunctionType();
822	>	toUpper(funcType);
823	>	if (funcType == "CUBIC") {
824	>	ft = cubic;
825	>	} else {
826	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
827	>	ft = fifth_order_poly;
828	>	} else {
829	>	// throw error
830	>	sprintf( painCave.errMsg,
831	>	"SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
832	>	"\tswitchingFunctionType must be one of: "
833	>	"\"cubic\" or \"fifth_order_polynomial\".",
834	>	funcType.c_str() );
835	>	painCave.isFatal = 1;
836	>	painCave.severity = OPENMD_ERROR;
837	>	simError();
838	>	}
839	>	}
840		}
841
842	<	#ifdef IS_MPI
843	<	int temp;
842	>	InteractionManager::Instance()->setSwitchingFunctionType(ft);
843	>	}
844
845	<	temp = usePBC;
846	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
845	>	/**
846	>	* setupSkinThickness
847	>	*
848	>	*  If the skinThickness was explicitly set, use that value (but check it)
849	>	*  If the skinThickness was not explicitly set: use 1.0 angstroms
850	>	*/
851	>	void SimInfo::setupSkinThickness() {
852	>	if (simParams_->haveSkinThickness()) {
853	>	skinThickness_ = simParams_->getSkinThickness();
854	>	} else {
855	>	skinThickness_ = 1.0;
856	>	sprintf(painCave.errMsg,
857	>	"SimInfo Warning: No value was set for the skinThickness.\n"
858	>	"\tOpenMD will use a default value of %f Angstroms\n"
859	>	"\tfor this simulation\n", skinThickness_);
860	>	painCave.isFatal = 0;
861	>	simError();
862	>	}
863	>	}
864
865	<	temp = useDirectionalAtom;
866	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
865	>	void SimInfo::setupSimType() {
866	>	set<AtomType*>::iterator i;
867	>	set<AtomType*> atomTypes;
868	>	atomTypes = getSimulatedAtomTypes();
869
870	<	temp = useLennardJones;
529	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
870	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
871
872	<	temp = useElectrostatics;
873	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
872	>	int usesElectrostatic = 0;
873	>	int usesMetallic = 0;
874	>	int usesDirectional = 0;
875	>	//loop over all of the atom types
876	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
877	>	usesElectrostatic |= (*i)->isElectrostatic();
878	>	usesMetallic |= (*i)->isMetal();
879	>	usesDirectional |= (*i)->isDirectional();
880	>	}
881
882	<	temp = useCharge;
883	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
882	>	#ifdef IS_MPI
883	>	int temp;
884	>	temp = usesDirectional;
885	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
886
887	<	temp = useDipole;
888	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
887	>	temp = usesMetallic;
888	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
889
890	<	temp = useSticky;
891	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
542	<
543	<	temp = useGayBerne;
544	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
545	<
546	<	temp = useEAM;
547	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
548	<
549	<	temp = useShape;
550	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
551	<
552	<	temp = useFLARB;
553	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
554	<
555	<	temp = useRF;
556	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
557	<
890	>	temp = usesElectrostatic;
891	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
892		#endif
893	+	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
894	+	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
895	+	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
896	+	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
897	+	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
898	+	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
899	+	}
900
901	<	fInfo_.SIM_uses_PBC = usePBC;
902	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
903	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
904	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
905	<	fInfo_.SIM_uses_Charges = useCharge;
906	<	fInfo_.SIM_uses_Dipoles = useDipole;
566	<	fInfo_.SIM_uses_Sticky = useSticky;
567	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
568	<	fInfo_.SIM_uses_EAM = useEAM;
569	<	fInfo_.SIM_uses_Shapes = useShape;
570	<	fInfo_.SIM_uses_FLARB = useFLARB;
571	<	fInfo_.SIM_uses_RF = useRF;
572	<
573	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
574	<
575	<	if (simParams_->haveDielectric()) {
576	<	fInfo_.dielect = simParams_->getDielectric();
577	<	} else {
578	<	sprintf(painCave.errMsg,
579	<	"SimSetup Error: No Dielectric constant was set.\n"
580	<	"\tYou are trying to use Reaction Field without"
581	<	"\tsetting a dielectric constant!\n");
582	<	painCave.isFatal = 1;
583	<	simError();
584	<	}
585	<
586	<	} else {
587	<	fInfo_.dielect = 0.0;
588	<	}
901	>	void SimInfo::setupFortranSim() {
902	>	int isError;
903	>	int nExclude, nOneTwo, nOneThree, nOneFour;
904	>	vector<int> fortranGlobalGroupMembership;
905	>
906	>	notifyFortranSkinThickness(&skinThickness_);
907
908	<	}
908	>	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
909	>	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
910	>	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
911
592	–	void SimInfo::setupFortranSim() {
593	–	int isError;
594	–	int nExclude;
595	–	std::vector<int> fortranGlobalGroupMembership;
596	–
597	–	nExclude = exclude_.getSize();
912		isError = 0;
913
914		//globalGroupMembership_ is filled by SimCreator
915		for (int i = 0; i < nGlobalAtoms_; i++) {
916	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
916	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
917		}
918
919		//calculate mass ratio of cutoff group
920	<	std::vector<double> mfact;
920	>	vector<RealType> mfact;
921		SimInfo::MoleculeIterator mi;
922		Molecule* mol;
923		Molecule::CutoffGroupIterator ci;
924		CutoffGroup* cg;
925		Molecule::AtomIterator ai;
926		Atom* atom;
927	<	double totalMass;
927	>	RealType totalMass;
928
929		//to avoid memory reallocation, reserve enough space for mfact
930		mfact.reserve(getNCutoffGroups());
931
932		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
933	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
933	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
934
935	<	totalMass = cg->getMass();
936	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
937	<	mfact.push_back(atom->getMass()/totalMass);
938	<	}
939	<
940	<	}
935	>	totalMass = cg->getMass();
936	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
937	>	// Check for massless groups - set mfact to 1 if true
938	>	if (totalMass != 0)
939	>	mfact.push_back(atom->getMass()/totalMass);
940	>	else
941	>	mfact.push_back( 1.0 );
942	>	}
943	>	}
944		}
945
946		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
947	<	std::vector<int> identArray;
947	>	vector<int> identArray;
948
949		//to avoid memory reallocation, reserve enough space identArray
950		identArray.reserve(getNAtoms());
951
952		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
953	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
954	<	identArray.push_back(atom->getIdent());
955	<	}
953	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
954	>	identArray.push_back(atom->getIdent());
955	>	}
956		}
957
958		//fill molMembershipArray
959		//molMembershipArray is filled by SimCreator
960	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
960	>	vector<int> molMembershipArray(nGlobalAtoms_);
961		for (int i = 0; i < nGlobalAtoms_; i++) {
962	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
962	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
963		}
964
965		//setup fortran simulation
649	–	//gloalExcludes and molMembershipArray should go away (They are never used)
650	–	//why the hell fortran need to know molecule?
651	–	//OOPSE = Object-Obfuscated Parallel Simulation Engine
652	–	int nGlobalExcludes = 0;
653	–	int* globalExcludes = NULL;
654	–	int* excludeList = exclude_.getExcludeList();
655	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
656	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
657	–	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
966
967	<	if( isError ){
967	>	nExclude = excludedInteractions_.getSize();
968	>	nOneTwo = oneTwoInteractions_.getSize();
969	>	nOneThree = oneThreeInteractions_.getSize();
970	>	nOneFour = oneFourInteractions_.getSize();
971
972	<	sprintf( painCave.errMsg,
973	<	"There was an error setting the simulation information in fortran.\n" );
974	<	painCave.isFatal = 1;
975	<	painCave.severity = OOPSE_ERROR;
665	<	simError();
666	<	}
972	>	int* excludeList = excludedInteractions_.getPairList();
973	>	int* oneTwoList = oneTwoInteractions_.getPairList();
974	>	int* oneThreeList = oneThreeInteractions_.getPairList();
975	>	int* oneFourList = oneFourInteractions_.getPairList();
976
977	<	#ifdef IS_MPI
977	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
978	>	&nExclude, excludeList,
979	>	&nOneTwo, oneTwoList,
980	>	&nOneThree, oneThreeList,
981	>	&nOneFour, oneFourList,
982	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
983	>	&fortranGlobalGroupMembership[0], &isError);
984	>
985	>	if( isError ){
986	>
987	>	sprintf( painCave.errMsg,
988	>	"There was an error setting the simulation information in fortran.\n" );
989	>	painCave.isFatal = 1;
990	>	painCave.severity = OPENMD_ERROR;
991	>	simError();
992	>	}
993	>
994	>
995		sprintf( checkPointMsg,
996	<	"succesfully sent the simulation information to fortran.\n");
997	<	MPIcheckPoint();
998	<	#endif // is_mpi
999	<	}
996	>	"succesfully sent the simulation information to fortran.\n");
997	>
998	>	errorCheckPoint();
999	>
1000	>	// Setup number of neighbors in neighbor list if present
1001	>	if (simParams_->haveNeighborListNeighbors()) {
1002	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
1003	>	setNeighbors(&nlistNeighbors);
1004	>	}
1005	>
1006
1007	+	}
1008
1009	<	#ifdef IS_MPI
1010	<	void SimInfo::setupFortranParallel() {
1011	<
1009	>
1010	>	void SimInfo::setupFortranParallel() {
1011	>	#ifdef IS_MPI
1012		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1013	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1014	<	std::vector<int> localToGlobalCutoffGroupIndex;
1013	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1014	>	vector<int> localToGlobalCutoffGroupIndex;
1015		SimInfo::MoleculeIterator mi;
1016		Molecule::AtomIterator ai;
1017		Molecule::CutoffGroupIterator ci;
#	Line 690 | Line 1023 | void SimInfo::setupFortranParallel() {
1023
1024		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1025
1026	<	//local index(index in DataStorge) of atom is important
1027	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1028	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1029	<	}
1026	>	//local index(index in DataStorge) of atom is important
1027	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1028	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1029	>	}
1030
1031	<	//local index of cutoff group is trivial, it only depends on the order of travesing
1032	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1033	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1034	<	}
1031	>	//local index of cutoff group is trivial, it only depends on the order of travesing
1032	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1033	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1034	>	}
1035
1036		}
1037
#	Line 718 | Line 1051 | void SimInfo::setupFortranParallel() {
1051		&localToGlobalCutoffGroupIndex[0], &isError);
1052
1053		if (isError) {
1054	<	sprintf(painCave.errMsg,
1055	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1056	<	painCave.isFatal = 1;
1057	<	simError();
1054	>	sprintf(painCave.errMsg,
1055	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1056	>	painCave.isFatal = 1;
1057	>	simError();
1058		}
1059
1060		sprintf(checkPointMsg, " mpiRefresh successful.\n");
1061	<	MPIcheckPoint();
1061	>	errorCheckPoint();
1062
1063	+	#endif
1064	+	}
1065
731	–	}
1066
1067	<	#endif
1067	>	void SimInfo::setupSwitchingFunction() {
1068
1069	<	double SimInfo::calcMaxCutoffRadius() {
1069	>	}
1070
1071	+	void SimInfo::setupAccumulateBoxDipole() {
1072
1073	<	std::set<AtomType*> atomTypes;
1074	<	std::set<AtomType*>::iterator i;
1075	<	std::vector<double> cutoffRadius;
1073	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1074	>	if ( simParams_->haveAccumulateBoxDipole() )
1075	>	if ( simParams_->getAccumulateBoxDipole() ) {
1076	>	calcBoxDipole_ = true;
1077	>	}
1078
1079	<	//get the unique atom types
743	<	atomTypes = getUniqueAtomTypes();
1079	>	}
1080
1081	<	//query the max cutoff radius among these atom types
1082	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
1083	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
748	<	}
1081	>	void SimInfo::addProperty(GenericData* genData) {
1082	>	properties_.addProperty(genData);
1083	>	}
1084
1085	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
1086	<	#ifdef IS_MPI
1087	<	//pick the max cutoff radius among the processors
753	<	#endif
1085	>	void SimInfo::removeProperty(const string& propName) {
1086	>	properties_.removeProperty(propName);
1087	>	}
1088
1089	<	return maxCutoffRadius;
1090	<	}
1089	>	void SimInfo::clearProperties() {
1090	>	properties_.clearProperties();
1091	>	}
1092
1093	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
759	<
760	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
761	<
762	<	if (!simParams_->haveRcut()){
763	<	sprintf(painCave.errMsg,
764	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
765	<	"\tOOPSE will use a default value of 15.0 angstroms"
766	<	"\tfor the cutoffRadius.\n");
767	<	painCave.isFatal = 0;
768	<	simError();
769	<	rcut = 15.0;
770	<	} else{
771	<	rcut = simParams_->getRcut();
772	<	}
773	<
774	<	if (!simParams_->haveRsw()){
775	<	sprintf(painCave.errMsg,
776	<	"SimCreator Warning: No value was set for switchingRadius.\n"
777	<	"\tOOPSE will use a default value of\n"
778	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
779	<	painCave.isFatal = 0;
780	<	simError();
781	<	rsw = 0.95 * rcut;
782	<	} else{
783	<	rsw = simParams_->getRsw();
784	<	}
785	<
786	<	} else {
787	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
788	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
789	<
790	<	if (simParams_->haveRcut()) {
791	<	rcut = simParams_->getRcut();
792	<	} else {
793	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
794	<	rcut = calcMaxCutoffRadius();
795	<	}
796	<
797	<	if (simParams_->haveRsw()) {
798	<	rsw  = simParams_->getRsw();
799	<	} else {
800	<	rsw = rcut;
801	<	}
802	<
803	<	}
804	<	}
805	<
806	<	void SimInfo::setupCutoff() {
807	<	getCutoff(rcut_, rsw_);
808	<	double rnblist = rcut_ + 1; // skin of neighbor list
809	<
810	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
811	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
812	<	}
813	<
814	<	void SimInfo::addProperty(GenericData* genData) {
815	<	properties_.addProperty(genData);
816	<	}
817	<
818	<	void SimInfo::removeProperty(const std::string& propName) {
819	<	properties_.removeProperty(propName);
820	<	}
821	<
822	<	void SimInfo::clearProperties() {
823	<	properties_.clearProperties();
824	<	}
825	<
826	<	std::vector<std::string> SimInfo::getPropertyNames() {
1093	>	vector<string> SimInfo::getPropertyNames() {
1094		return properties_.getPropertyNames();
1095	<	}
1095	>	}
1096
1097	<	std::vector<GenericData*> SimInfo::getProperties() {
1097	>	vector<GenericData*> SimInfo::getProperties() {
1098		return properties_.getProperties();
1099	<	}
1099	>	}
1100
1101	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1101	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1102		return properties_.getPropertyByName(propName);
1103	<	}
1103	>	}
1104
1105	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1106	<	//if (sman_ == sman_) {
1107	<	//    return;
1108	<	//}
1109	<
843	<	//delete sman_;
1105	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1106	>	if (sman_ == sman) {
1107	>	return;
1108	>	}
1109	>	delete sman_;
1110		sman_ = sman;
1111
1112		Molecule* mol;
#	Line 852 | Line 1118 | void SimInfo::setSnapshotManager(SnapshotManager* sman
1118
1119		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1120
1121	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1122	<	atom->setSnapshotManager(sman_);
1123	<	}
1121	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1122	>	atom->setSnapshotManager(sman_);
1123	>	}
1124
1125	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1126	<	rb->setSnapshotManager(sman_);
1127	<	}
1125	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1126	>	rb->setSnapshotManager(sman_);
1127	>	}
1128		}
1129
1130	<	}
1130	>	}
1131
1132	<	Vector3d SimInfo::getComVel(){
1132	>	Vector3d SimInfo::getComVel(){
1133		SimInfo::MoleculeIterator i;
1134		Molecule* mol;
1135
1136		Vector3d comVel(0.0);
1137	<	double totalMass = 0.0;
1137	>	RealType totalMass = 0.0;
1138
1139
1140		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1141	<	double mass = mol->getMass();
1142	<	totalMass += mass;
1143	<	comVel += mass * mol->getComVel();
1141	>	RealType mass = mol->getMass();
1142	>	totalMass += mass;
1143	>	comVel += mass * mol->getComVel();
1144		}
1145
1146		#ifdef IS_MPI
1147	<	double tmpMass = totalMass;
1147	>	RealType tmpMass = totalMass;
1148		Vector3d tmpComVel(comVel);
1149	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1150	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1149	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1150	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1151		#endif
1152
1153		comVel /= totalMass;
1154
1155		return comVel;
1156	<	}
1156	>	}
1157
1158	<	Vector3d SimInfo::getCom(){
1158	>	Vector3d SimInfo::getCom(){
1159		SimInfo::MoleculeIterator i;
1160		Molecule* mol;
1161
1162		Vector3d com(0.0);
1163	<	double totalMass = 0.0;
1163	>	RealType totalMass = 0.0;
1164
1165		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1166	<	double mass = mol->getMass();
1167	<	totalMass += mass;
1168	<	com += mass * mol->getCom();
1166	>	RealType mass = mol->getMass();
1167	>	totalMass += mass;
1168	>	com += mass * mol->getCom();
1169		}
1170
1171		#ifdef IS_MPI
1172	<	double tmpMass = totalMass;
1172	>	RealType tmpMass = totalMass;
1173		Vector3d tmpCom(com);
1174	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1175	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1174	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1175	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1176		#endif
1177
1178		com /= totalMass;
1179
1180		return com;
1181
1182	<	}
1182	>	}
1183
1184	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1184	>	ostream& operator <<(ostream& o, SimInfo& info) {
1185
1186		return o;
1187	<	}
1187	>	}
1188	>
1189	>
1190	>	/*
1191	>	Returns center of mass and center of mass velocity in one function call.
1192	>	*/
1193	>
1194	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1195	>	SimInfo::MoleculeIterator i;
1196	>	Molecule* mol;
1197	>
1198	>
1199	>	RealType totalMass = 0.0;
1200	>
1201
1202	<	}//end namespace oopse
1202	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1203	>	RealType mass = mol->getMass();
1204	>	totalMass += mass;
1205	>	com += mass * mol->getCom();
1206	>	comVel += mass * mol->getComVel();
1207	>	}
1208	>
1209	>	#ifdef IS_MPI
1210	>	RealType tmpMass = totalMass;
1211	>	Vector3d tmpCom(com);
1212	>	Vector3d tmpComVel(comVel);
1213	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1214	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1215	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1216	>	#endif
1217	>
1218	>	com /= totalMass;
1219	>	comVel /= totalMass;
1220	>	}
1221	>
1222	>	/*
1223	>	Return intertia tensor for entire system and angular momentum Vector.
1224
1225	+
1226	+	[  Ixx -Ixy  -Ixz ]
1227	+	J =| -Iyx  Iyy  -Iyz |
1228	+	[ -Izx -Iyz   Izz ]
1229	+	*/
1230	+
1231	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1232	+
1233	+
1234	+	RealType xx = 0.0;
1235	+	RealType yy = 0.0;
1236	+	RealType zz = 0.0;
1237	+	RealType xy = 0.0;
1238	+	RealType xz = 0.0;
1239	+	RealType yz = 0.0;
1240	+	Vector3d com(0.0);
1241	+	Vector3d comVel(0.0);
1242	+
1243	+	getComAll(com, comVel);
1244	+
1245	+	SimInfo::MoleculeIterator i;
1246	+	Molecule* mol;
1247	+
1248	+	Vector3d thisq(0.0);
1249	+	Vector3d thisv(0.0);
1250	+
1251	+	RealType thisMass = 0.0;
1252	+
1253	+
1254	+
1255	+
1256	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1257	+
1258	+	thisq = mol->getCom()-com;
1259	+	thisv = mol->getComVel()-comVel;
1260	+	thisMass = mol->getMass();
1261	+	// Compute moment of intertia coefficients.
1262	+	xx += thisq[0]*thisq[0]*thisMass;
1263	+	yy += thisq[1]*thisq[1]*thisMass;
1264	+	zz += thisq[2]*thisq[2]*thisMass;
1265	+
1266	+	// compute products of intertia
1267	+	xy += thisq[0]*thisq[1]*thisMass;
1268	+	xz += thisq[0]*thisq[2]*thisMass;
1269	+	yz += thisq[1]*thisq[2]*thisMass;
1270	+
1271	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1272	+
1273	+	}
1274	+
1275	+
1276	+	inertiaTensor(0,0) = yy + zz;
1277	+	inertiaTensor(0,1) = -xy;
1278	+	inertiaTensor(0,2) = -xz;
1279	+	inertiaTensor(1,0) = -xy;
1280	+	inertiaTensor(1,1) = xx + zz;
1281	+	inertiaTensor(1,2) = -yz;
1282	+	inertiaTensor(2,0) = -xz;
1283	+	inertiaTensor(2,1) = -yz;
1284	+	inertiaTensor(2,2) = xx + yy;
1285	+
1286	+	#ifdef IS_MPI
1287	+	Mat3x3d tmpI(inertiaTensor);
1288	+	Vector3d tmpAngMom;
1289	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1290	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1291	+	#endif
1292	+
1293	+	return;
1294	+	}
1295	+
1296	+	//Returns the angular momentum of the system
1297	+	Vector3d SimInfo::getAngularMomentum(){
1298	+
1299	+	Vector3d com(0.0);
1300	+	Vector3d comVel(0.0);
1301	+	Vector3d angularMomentum(0.0);
1302	+
1303	+	getComAll(com,comVel);
1304	+
1305	+	SimInfo::MoleculeIterator i;
1306	+	Molecule* mol;
1307	+
1308	+	Vector3d thisr(0.0);
1309	+	Vector3d thisp(0.0);
1310	+
1311	+	RealType thisMass;
1312	+
1313	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1314	+	thisMass = mol->getMass();
1315	+	thisr = mol->getCom()-com;
1316	+	thisp = (mol->getComVel()-comVel)*thisMass;
1317	+
1318	+	angularMomentum += cross( thisr, thisp );
1319	+
1320	+	}
1321	+
1322	+	#ifdef IS_MPI
1323	+	Vector3d tmpAngMom;
1324	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1325	+	#endif
1326	+
1327	+	return angularMomentum;
1328	+	}
1329	+
1330	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1331	+	return IOIndexToIntegrableObject.at(index);
1332	+	}
1333	+
1334	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1335	+	IOIndexToIntegrableObject= v;
1336	+	}
1337	+
1338	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1339	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1340	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1341	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1342	+	*/
1343	+	void SimInfo::getGyrationalVolume(RealType &volume){
1344	+	Mat3x3d intTensor;
1345	+	RealType det;
1346	+	Vector3d dummyAngMom;
1347	+	RealType sysconstants;
1348	+	RealType geomCnst;
1349	+
1350	+	geomCnst = 3.0/2.0;
1351	+	/* Get the inertial tensor and angular momentum for free*/
1352	+	getInertiaTensor(intTensor,dummyAngMom);
1353	+
1354	+	det = intTensor.determinant();
1355	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1356	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1357	+	return;
1358	+	}
1359	+
1360	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1361	+	Mat3x3d intTensor;
1362	+	Vector3d dummyAngMom;
1363	+	RealType sysconstants;
1364	+	RealType geomCnst;
1365	+
1366	+	geomCnst = 3.0/2.0;
1367	+	/* Get the inertial tensor and angular momentum for free*/
1368	+	getInertiaTensor(intTensor,dummyAngMom);
1369	+
1370	+	detI = intTensor.determinant();
1371	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1372	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1373	+	return;
1374	+	}
1375	+	/*
1376	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1377	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1378	+	sdByGlobalIndex_ = v;
1379	+	}
1380	+
1381	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1382	+	//assert(index < nAtoms_ + nRigidBodies_);
1383	+	return sdByGlobalIndex_.at(index);
1384	+	}
1385	+	*/
1386	+	int SimInfo::getNGlobalConstraints() {
1387	+	int nGlobalConstraints;
1388	+	#ifdef IS_MPI
1389	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1390	+	MPI_COMM_WORLD);
1391	+	#else
1392	+	nGlobalConstraints =  nConstraints_;
1393	+	#endif
1394	+	return nGlobalConstraints;
1395	+	}
1396	+
1397	+	}//end namespace OpenMD
1398	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1530 by gezelter, Tue Dec 28 21:47:55 2010 UTC

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