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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 274 by tim, Tue Jan 25 21:59:18 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1534 by gezelter, Wed Dec 29 21:53:28 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/doForces_interface.h"
58	<	#include "UseTheForce/notifyCutoffs_interface.h"
58	>	#include "UseTheForce/DarkSide/neighborLists_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) {
82	<
83	<
78	<	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;
128	–
129	–	//every free atom (atom does not belong to rigid bodies) is an integrable object
130	–	//therefore the total number of  integrable objects in the system is equal to
131	–	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
132	–	//file plus the number of  rigid bodies defined in meta-data file
133	–	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
134	–
135	–	nGlobalMols_ = molStampIds_.size();
136	–
137	–	#ifdef IS_MPI
138	–	molToProcMap_.resize(nGlobalMols_);
139	–	#endif
136
137	<	}
138	<
139	<	SimInfo::~SimInfo() {
140	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
141	<
142	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
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();
146	+	molToProcMap_.resize(nGlobalMols_);
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	+	}
160
152	–	}
161
162	<	int SimInfo::getNGlobalConstraints() {
155	<	int nGlobalConstraints;
156	<	#ifdef IS_MPI
157	<	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
158	<	MPI_COMM_WORLD);
159	<	#else
160	<	nGlobalConstraints =  nConstraints_;
161	<	#endif
162	<	return nGlobalConstraints;
163	<	}
164	<
165	<	bool SimInfo::addMolecule(Molecule* mol) {
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;
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;
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
217	–
218	–	}
219	–
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 268 | 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 282 | 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 303 | 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 319 | 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;
335	–
336	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
337	–	a = bond->getAtomA()->getGlobalIndex();
338	–	b = bond->getAtomB()->getGlobalIndex();
339	–	exclude_.addPair(a, b);
340	–	}
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);
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	>	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	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
394	<	a = torsion->getAtomA()->getGlobalIndex();
354	<	b = torsion->getAtomB()->getGlobalIndex();
355	<	c = torsion->getAtomC()->getGlobalIndex();
356	<	d = torsion->getAtomD()->getGlobalIndex();
393	>	for (bend= mol->beginBend(bendIter); bend != NULL;
394	>	bend = mol->nextBend(bendIter)) {
395
396	<	exclude_.addPair(a, b);
397	<	exclude_.addPair(a, c);
398	<	exclude_.addPair(a, d);
399	<	exclude_.addPair(b, c);
400	<	exclude_.addPair(b, d);
401	<	exclude_.addPair(c, d);
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	<
416	<	}
415	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
416	>	torsion = mol->nextTorsion(torsionIter)) {
417
418	<	void SimInfo::removeExcludePairs(Molecule* mol) {
419	<	std::vector<Bond*>::iterator bondIter;
420	<	std::vector<Bend*>::iterator bendIter;
421	<	std::vector<Torsion*>::iterator torsionIter;
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();
389	<	b = bend->getAtomB()->getGlobalIndex();
390	<	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();
399	<	b = torsion->getAtomB()->getGlobalIndex();
400	<	c = torsion->getAtomC()->getGlobalIndex();
401	<	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
424	–	void SimInfo::update() {
655
656	<	setupSimType();
656	>	/**
657	>	* update
658	>	*
659	>	*  Performs the global checks and variable settings after the objects have been
660	>	*  created.
661	>	*
662	>	*/
663	>	void SimInfo::update() {
664	>
665	>	setupSimVariables();
666	>	setupCutoffs();
667	>	setupSwitching();
668	>	setupElectrostatics();
669	>	setupNeighborlists();
670
671		#ifdef IS_MPI
672		setupFortranParallel();
673		#endif
431	–
674		setupFortranSim();
675	+	fortranInitialized_ = true;
676
434	–	//setup fortran force field
435	–	/** @deprecate */
436	–	int isError = 0;
437	–	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
438	–	if(isError){
439	–	sprintf( painCave.errMsg,
440	–	"ForceField error: There was an error initializing the forceField in fortran.\n" );
441	–	painCave.isFatal = 1;
442	–	simError();
443	–	}
444	–
445	–
446	–	setupCutoff();
447	–
677		calcNdf();
678		calcNdfRaw();
679		calcNdfTrans();
680	<
681	<	fortranInitialized_ = true;
682	<	}
454	<
455	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
680	>	}
681	>
682	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
683		SimInfo::MoleculeIterator mi;
684		Molecule* mol;
685		Molecule::AtomIterator ai;
686		Atom* atom;
687	<	std::set<AtomType*> atomTypes;
688	<
689	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
690	<
691	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
692	<	atomTypes.insert(atom->getAtomType());
693	<	}
467	<
468	<	}
469	<
687	>	set<AtomType*> atomTypes;
688	>
689	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
690	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
691	>	atomTypes.insert(atom->getAtomType());
692	>	}
693	>	}
694		return atomTypes;
695	<	}
695	>	}
696
697	<	void SimInfo::setupSimType() {
698	<	std::set<AtomType*>::iterator i;
699	<	std::set<AtomType*> atomTypes;
700	<	atomTypes = getUniqueAtomTypes();
697	>	/**
698	>	* setupCutoffs
699	>	*
700	>	* Sets the values of cutoffRadius and cutoffMethod
701	>	*
702	>	* cutoffRadius : realType
703	>	*  If the cutoffRadius was explicitly set, use that value.
704	>	*  If the cutoffRadius was not explicitly set:
705	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
706	>	*      No electrostatic atoms?  Poll the atom types present in the
707	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
708	>	*      Use the maximum suggested value that was found.
709	>	*
710	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
711	>	*      If cutoffMethod was explicitly set, use that choice.
712	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
713	>	*/
714	>	void SimInfo::setupCutoffs() {
715
716	<	int useLennardJones = 0;
717	<	int useElectrostatic = 0;
718	<	int useEAM = 0;
719	<	int useCharge = 0;
720	<	int useDirectional = 0;
721	<	int useDipole = 0;
722	<	int useGayBerne = 0;
723	<	int useSticky = 0;
724	<	int useShape = 0;
725	<	int useFLARB = 0; //it is not in AtomType yet
726	<	int useDirectionalAtom = 0;
727	<	int useElectrostatics = 0;
728	<	//usePBC and useRF are from simParams
729	<	int usePBC = simParams_->getPBC();
730	<	int useRF = simParams_->getUseRF();
731	<
732	<	//loop over all of the atom types
733	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
734	<	useLennardJones |= (*i)->isLennardJones();
735	<	useElectrostatic |= (*i)->isElectrostatic();
736	<	useEAM |= (*i)->isEAM();
737	<	useCharge |= (*i)->isCharge();
738	<	useDirectional |= (*i)->isDirectional();
739	<	useDipole |= (*i)->isDipole();
740	<	useGayBerne |= (*i)->isGayBerne();
741	<	useSticky |= (*i)->isSticky();
742	<	useShape |= (*i)->isShape();
716	>	if (simParams_->haveCutoffRadius()) {
717	>	cutoffRadius_ = simParams_->getCutoffRadius();
718	>	} else {
719	>	if (usesElectrostaticAtoms_) {
720	>	sprintf(painCave.errMsg,
721	>	"SimInfo: No value was set for the cutoffRadius.\n"
722	>	"\tOpenMD will use a default value of 12.0 angstroms"
723	>	"\tfor the cutoffRadius.\n");
724	>	painCave.isFatal = 0;
725	>	painCave.severity = OPENMD_INFO;
726	>	simError();
727	>	cutoffRadius_ = 12.0;
728	>	} else {
729	>	RealType thisCut;
730	>	set<AtomType*>::iterator i;
731	>	set<AtomType*> atomTypes;
732	>	atomTypes = getSimulatedAtomTypes();
733	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
734	>	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
735	>	cutoffRadius_ = max(thisCut, cutoffRadius_);
736	>	}
737	>	sprintf(painCave.errMsg,
738	>	"SimInfo: No value was set for the cutoffRadius.\n"
739	>	"\tOpenMD will use %lf angstroms.\n",
740	>	cutoffRadius_);
741	>	painCave.isFatal = 0;
742	>	painCave.severity = OPENMD_INFO;
743	>	simError();
744	>	}
745		}
746
747	<	if (useSticky || useDipole || useGayBerne || useShape) {
748	<	useDirectionalAtom = 1;
747	>	map<string, CutoffMethod> stringToCutoffMethod;
748	>	stringToCutoffMethod["HARD"] = HARD;
749	>	stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
750	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
751	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
752	>
753	>	if (simParams_->haveCutoffMethod()) {
754	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
755	>	map<string, CutoffMethod>::iterator i;
756	>	i = stringToCutoffMethod.find(cutMeth);
757	>	if (i == stringToCutoffMethod.end()) {
758	>	sprintf(painCave.errMsg,
759	>	"SimInfo: Could not find chosen cutoffMethod %s\n"
760	>	"\tShould be one of: "
761	>	"HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
762	>	cutMeth.c_str());
763	>	painCave.isFatal = 1;
764	>	painCave.severity = OPENMD_ERROR;
765	>	simError();
766	>	} else {
767	>	cutoffMethod_ = i->second;
768	>	}
769	>	} else {
770	>	sprintf(painCave.errMsg,
771	>	"SimInfo: No value was set for the cutoffMethod.\n"
772	>	"\tOpenMD will use SHIFTED_FORCE.\n");
773	>	painCave.isFatal = 0;
774	>	painCave.severity = OPENMD_INFO;
775	>	simError();
776	>	cutoffMethod_ = SHIFTED_FORCE;
777		}
778	+	}
779	+
780	+	/**
781	+	* setupSwitching
782	+	*
783	+	* Sets the values of switchingRadius and
784	+	*  If the switchingRadius was explicitly set, use that value (but check it)
785	+	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
786	+	*/
787	+	void SimInfo::setupSwitching() {
788	+
789	+	if (simParams_->haveSwitchingRadius()) {
790	+	switchingRadius_ = simParams_->getSwitchingRadius();
791	+	if (switchingRadius_ > cutoffRadius_) {
792	+	sprintf(painCave.errMsg,
793	+	"SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
794	+	switchingRadius_, cutoffRadius_);
795	+	painCave.isFatal = 1;
796	+	painCave.severity = OPENMD_ERROR;
797	+	simError();
798	+	}
799	+	} else {
800	+	switchingRadius_ = 0.85 * cutoffRadius_;
801	+	sprintf(painCave.errMsg,
802	+	"SimInfo: No value was set for the switchingRadius.\n"
803	+	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
804	+	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
805	+	painCave.isFatal = 0;
806	+	painCave.severity = OPENMD_WARNING;
807	+	simError();
808	+	}
809	+
810	+	if (simParams_->haveSwitchingFunctionType()) {
811	+	string funcType = simParams_->getSwitchingFunctionType();
812	+	toUpper(funcType);
813	+	if (funcType == "CUBIC") {
814	+	sft_ = cubic;
815	+	} else {
816	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
817	+	sft_ = fifth_order_poly;
818	+	} else {
819	+	// throw error
820	+	sprintf( painCave.errMsg,
821	+	"SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
822	+	"\tswitchingFunctionType must be one of: "
823	+	"\"cubic\" or \"fifth_order_polynomial\".",
824	+	funcType.c_str() );
825	+	painCave.isFatal = 1;
826	+	painCave.severity = OPENMD_ERROR;
827	+	simError();
828	+	}
829	+	}
830	+	}
831	+	}
832
833	<	if (useCharge || useDipole) {
834	<	useElectrostatics = 1;
833	>	/**
834	>	* setupNeighborlists
835	>	*
836	>	*  If the skinThickness was explicitly set, use that value (but check it)
837	>	*  If the skinThickness was not explicitly set: use 1.0 angstroms
838	>	*/
839	>	void SimInfo::setupNeighborlists() {
840	>	if (simParams_->haveSkinThickness()) {
841	>	skinThickness_ = simParams_->getSkinThickness();
842	>	} else {
843	>	skinThickness_ = 1.0;
844	>	sprintf(painCave.errMsg,
845	>	"SimInfo: No value was set for the skinThickness.\n"
846	>	"\tOpenMD will use a default value of %f Angstroms\n"
847	>	"\tfor this simulation\n", skinThickness_);
848	>	painCave.severity = OPENMD_INFO;
849	>	painCave.isFatal = 0;
850	>	simError();
851	>	}
852	>	}
853	>
854	>	void SimInfo::setupSimVariables() {
855	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
856	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
857	>	calcBoxDipole_ = false;
858	>	if ( simParams_->haveAccumulateBoxDipole() )
859	>	if ( simParams_->getAccumulateBoxDipole() ) {
860	>	calcBoxDipole_ = true;
861	>	}
862	>
863	>	set<AtomType*>::iterator i;
864	>	set<AtomType*> atomTypes;
865	>	atomTypes = getSimulatedAtomTypes();
866	>	int usesElectrostatic = 0;
867	>	int usesMetallic = 0;
868	>	int usesDirectional = 0;
869	>	//loop over all of the atom types
870	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
871	>	usesElectrostatic |= (*i)->isElectrostatic();
872	>	usesMetallic |= (*i)->isMetal();
873	>	usesDirectional |= (*i)->isDirectional();
874		}
875
876		#ifdef IS_MPI
877		int temp;
878	+	temp = usesDirectional;
879	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
880
881	<	temp = usePBC;
882	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
881	>	temp = usesMetallic;
882	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
883
884	<	temp = useDirectionalAtom;
885	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
523	<
524	<	temp = useLennardJones;
525	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
526	<
527	<	temp = useElectrostatics;
528	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
529	<
530	<	temp = useCharge;
531	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
532	<
533	<	temp = useDipole;
534	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
535	<
536	<	temp = useSticky;
537	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
538	<
539	<	temp = useGayBerne;
540	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
541	<
542	<	temp = useEAM;
543	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
544	<
545	<	temp = useShape;
546	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
547	<
548	<	temp = useFLARB;
549	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
550	<
551	<	temp = useRF;
552	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
553	<
884	>	temp = usesElectrostatic;
885	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
886		#endif
887	+	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
888	+	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
889	+	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
890	+	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
891	+	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
892	+	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
893	+	}
894
895	<	fInfo_.SIM_uses_PBC = usePBC;
896	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
897	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
898	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
899	<	fInfo_.SIM_uses_Charges = useCharge;
900	<	fInfo_.SIM_uses_Dipoles = useDipole;
562	<	fInfo_.SIM_uses_Sticky = useSticky;
563	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
564	<	fInfo_.SIM_uses_EAM = useEAM;
565	<	fInfo_.SIM_uses_Shapes = useShape;
566	<	fInfo_.SIM_uses_FLARB = useFLARB;
567	<	fInfo_.SIM_uses_RF = useRF;
568	<
569	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
895	>	void SimInfo::setupFortranSim() {
896	>	int isError;
897	>	int nExclude, nOneTwo, nOneThree, nOneFour;
898	>	vector<int> fortranGlobalGroupMembership;
899	>
900	>	notifyFortranSkinThickness(&skinThickness_);
901
902	<	if (simParams_->haveDielectric()) {
903	<	fInfo_.dielect = simParams_->getDielectric();
904	<	} else {
574	<	sprintf(painCave.errMsg,
575	<	"SimSetup Error: No Dielectric constant was set.\n"
576	<	"\tYou are trying to use Reaction Field without"
577	<	"\tsetting a dielectric constant!\n");
578	<	painCave.isFatal = 1;
579	<	simError();
580	<	}
581	<
582	<	} else {
583	<	fInfo_.dielect = 0.0;
584	<	}
902	>	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
903	>	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
904	>	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
905
586	–	}
587	–
588	–	void SimInfo::setupFortranSim() {
589	–	int isError;
590	–	int nExclude;
591	–	std::vector<int> fortranGlobalGroupMembership;
592	–
593	–	nExclude = exclude_.getSize();
906		isError = 0;
907
908		//globalGroupMembership_ is filled by SimCreator
909		for (int i = 0; i < nGlobalAtoms_; i++) {
910	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
910	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
911		}
912
913		//calculate mass ratio of cutoff group
914	<	std::vector<double> mfact;
914	>	vector<RealType> mfact;
915		SimInfo::MoleculeIterator mi;
916		Molecule* mol;
917		Molecule::CutoffGroupIterator ci;
918		CutoffGroup* cg;
919		Molecule::AtomIterator ai;
920		Atom* atom;
921	<	double totalMass;
921	>	RealType totalMass;
922
923		//to avoid memory reallocation, reserve enough space for mfact
924		mfact.reserve(getNCutoffGroups());
925
926		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
927	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
927	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
928
929	<	totalMass = cg->getMass();
930	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
931	<	mfact.push_back(atom->getMass()/totalMass);
932	<	}
933	<
934	<	}
929	>	totalMass = cg->getMass();
930	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
931	>	// Check for massless groups - set mfact to 1 if true
932	>	if (totalMass != 0)
933	>	mfact.push_back(atom->getMass()/totalMass);
934	>	else
935	>	mfact.push_back( 1.0 );
936	>	}
937	>	}
938		}
939
940		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
941	<	std::vector<int> identArray;
941	>	vector<int> identArray;
942
943		//to avoid memory reallocation, reserve enough space identArray
944		identArray.reserve(getNAtoms());
945
946		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
947	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
948	<	identArray.push_back(atom->getIdent());
949	<	}
947	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
948	>	identArray.push_back(atom->getIdent());
949	>	}
950		}
951
952		//fill molMembershipArray
953		//molMembershipArray is filled by SimCreator
954	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
954	>	vector<int> molMembershipArray(nGlobalAtoms_);
955		for (int i = 0; i < nGlobalAtoms_; i++) {
956	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
956	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
957		}
958
959		//setup fortran simulation
645	–	//gloalExcludes and molMembershipArray should go away (They are never used)
646	–	//why the hell fortran need to know molecule?
647	–	//OOPSE = Object-Obfuscated Parallel Simulation Engine
648	–	int nGlobalExcludes = 0;
649	–	int* globalExcludes = NULL;
650	–	int* excludeList = exclude_.getExcludeList();
651	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
652	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
653	–	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
960
961	<	if( isError ){
961	>	nExclude = excludedInteractions_.getSize();
962	>	nOneTwo = oneTwoInteractions_.getSize();
963	>	nOneThree = oneThreeInteractions_.getSize();
964	>	nOneFour = oneFourInteractions_.getSize();
965
966	<	sprintf( painCave.errMsg,
967	<	"There was an error setting the simulation information in fortran.\n" );
968	<	painCave.isFatal = 1;
969	<	painCave.severity = OOPSE_ERROR;
661	<	simError();
662	<	}
966	>	int* excludeList = excludedInteractions_.getPairList();
967	>	int* oneTwoList = oneTwoInteractions_.getPairList();
968	>	int* oneThreeList = oneThreeInteractions_.getPairList();
969	>	int* oneFourList = oneFourInteractions_.getPairList();
970
971	<	#ifdef IS_MPI
971	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
972	>	&nExclude, excludeList,
973	>	&nOneTwo, oneTwoList,
974	>	&nOneThree, oneThreeList,
975	>	&nOneFour, oneFourList,
976	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
977	>	&fortranGlobalGroupMembership[0], &isError);
978	>
979	>	if( isError ){
980	>
981	>	sprintf( painCave.errMsg,
982	>	"There was an error setting the simulation information in fortran.\n" );
983	>	painCave.isFatal = 1;
984	>	painCave.severity = OPENMD_ERROR;
985	>	simError();
986	>	}
987	>
988	>
989		sprintf( checkPointMsg,
990	<	"succesfully sent the simulation information to fortran.\n");
991	<	MPIcheckPoint();
992	<	#endif // is_mpi
993	<	}
990	>	"succesfully sent the simulation information to fortran.\n");
991	>
992	>	errorCheckPoint();
993	>
994	>	// Setup number of neighbors in neighbor list if present
995	>	if (simParams_->haveNeighborListNeighbors()) {
996	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
997	>	setNeighbors(&nlistNeighbors);
998	>	}
999	>
1000
1001	+	}
1002
1003	<	#ifdef IS_MPI
1004	<	void SimInfo::setupFortranParallel() {
1005	<
1003	>
1004	>	void SimInfo::setupFortranParallel() {
1005	>	#ifdef IS_MPI
1006		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1007	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1008	<	std::vector<int> localToGlobalCutoffGroupIndex;
1007	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1008	>	vector<int> localToGlobalCutoffGroupIndex;
1009		SimInfo::MoleculeIterator mi;
1010		Molecule::AtomIterator ai;
1011		Molecule::CutoffGroupIterator ci;
#	Line 686 | Line 1017 | void SimInfo::setupFortranParallel() {
1017
1018		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1019
1020	<	//local index(index in DataStorge) of atom is important
1021	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1022	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1023	<	}
1020	>	//local index(index in DataStorge) of atom is important
1021	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1022	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1023	>	}
1024
1025	<	//local index of cutoff group is trivial, it only depends on the order of travesing
1026	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1027	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1028	<	}
1025	>	//local index of cutoff group is trivial, it only depends on the order of travesing
1026	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1027	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1028	>	}
1029
1030		}
1031
#	Line 714 | Line 1045 | void SimInfo::setupFortranParallel() {
1045		&localToGlobalCutoffGroupIndex[0], &isError);
1046
1047		if (isError) {
1048	<	sprintf(painCave.errMsg,
1049	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1050	<	painCave.isFatal = 1;
1051	<	simError();
1048	>	sprintf(painCave.errMsg,
1049	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1050	>	painCave.isFatal = 1;
1051	>	simError();
1052		}
1053
1054		sprintf(checkPointMsg, " mpiRefresh successful.\n");
1055	<	MPIcheckPoint();
1055	>	errorCheckPoint();
1056
726	–
727	–	}
728	–
1057		#endif
1058	+	}
1059
731	–	double SimInfo::calcMaxCutoffRadius() {
1060
1061	+	void SimInfo::setupAccumulateBoxDipole() {
1062
734	–	std::set<AtomType*> atomTypes;
735	–	std::set<AtomType*>::iterator i;
736	–	std::vector<double> cutoffRadius;
1063
1064	<	//get the unique atom types
739	<	atomTypes = getUniqueAtomTypes();
1064	>	}
1065
1066	<	//query the max cutoff radius among these atom types
1067	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
1068	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
744	<	}
1066	>	void SimInfo::addProperty(GenericData* genData) {
1067	>	properties_.addProperty(genData);
1068	>	}
1069
1070	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
1071	<	#ifdef IS_MPI
1072	<	//pick the max cutoff radius among the processors
749	<	#endif
1070	>	void SimInfo::removeProperty(const string& propName) {
1071	>	properties_.removeProperty(propName);
1072	>	}
1073
1074	<	return maxCutoffRadius;
752	<	}
753	<
754	<	void SimInfo::setupCutoff() {
755	<	double rcut_;  //cutoff radius
756	<	double rsw_; //switching radius
757	<
758	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
759	<
760	<	if (!simParams_->haveRcut()){
761	<	sprintf(painCave.errMsg,
762	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
763	<	"\tOOPSE will use a default value of 15.0 angstroms"
764	<	"\tfor the cutoffRadius.\n");
765	<	painCave.isFatal = 0;
766	<	simError();
767	<	rcut_ = 15.0;
768	<	} else{
769	<	rcut_ = simParams_->getRcut();
770	<	}
771	<
772	<	if (!simParams_->haveRsw()){
773	<	sprintf(painCave.errMsg,
774	<	"SimCreator Warning: No value was set for switchingRadius.\n"
775	<	"\tOOPSE will use a default value of\n"
776	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
777	<	painCave.isFatal = 0;
778	<	simError();
779	<	rsw_ = 0.95 * rcut_;
780	<	} else{
781	<	rsw_ = simParams_->getRsw();
782	<	}
783	<
784	<	} else {
785	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
786	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
787	<
788	<	if (simParams_->haveRcut()) {
789	<	rcut_ = simParams_->getRcut();
790	<	} else {
791	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
792	<	rcut_ = calcMaxCutoffRadius();
793	<	}
794	<
795	<	if (simParams_->haveRsw()) {
796	<	rsw_  = simParams_->getRsw();
797	<	} else {
798	<	rsw_ = rcut_;
799	<	}
800	<
801	<	}
802	<
803	<	double rnblist = rcut_ + 1; // skin of neighbor list
804	<
805	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
806	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
807	<	}
808	<
809	<	void SimInfo::addProperty(GenericData* genData) {
810	<	properties_.addProperty(genData);
811	<	}
812	<
813	<	void SimInfo::removeProperty(const std::string& propName) {
814	<	properties_.removeProperty(propName);
815	<	}
816	<
817	<	void SimInfo::clearProperties() {
1074	>	void SimInfo::clearProperties() {
1075		properties_.clearProperties();
1076	<	}
1076	>	}
1077
1078	<	std::vector<std::string> SimInfo::getPropertyNames() {
1078	>	vector<string> SimInfo::getPropertyNames() {
1079		return properties_.getPropertyNames();
1080	<	}
1080	>	}
1081
1082	<	std::vector<GenericData*> SimInfo::getProperties() {
1082	>	vector<GenericData*> SimInfo::getProperties() {
1083		return properties_.getProperties();
1084	<	}
1084	>	}
1085
1086	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1086	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1087		return properties_.getPropertyByName(propName);
1088	<	}
1088	>	}
1089
1090	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1090	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1091	>	if (sman_ == sman) {
1092	>	return;
1093	>	}
1094	>	delete sman_;
1095		sman_ = sman;
1096
1097		Molecule* mol;
#	Line 842 | Line 1103 | void SimInfo::setSnapshotManager(SnapshotManager* sman
1103
1104		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1105
1106	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1107	<	atom->setSnapshotManager(sman_);
1108	<	}
1106	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1107	>	atom->setSnapshotManager(sman_);
1108	>	}
1109
1110	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1111	<	rb->setSnapshotManager(sman_);
1112	<	}
1110	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1111	>	rb->setSnapshotManager(sman_);
1112	>	}
1113		}
1114
1115	<	}
1115	>	}
1116
1117	<	Vector3d SimInfo::getComVel(){
1117	>	Vector3d SimInfo::getComVel(){
1118		SimInfo::MoleculeIterator i;
1119		Molecule* mol;
1120
1121		Vector3d comVel(0.0);
1122	<	double totalMass = 0.0;
1122	>	RealType totalMass = 0.0;
1123
1124
1125		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1126	<	double mass = mol->getMass();
1127	<	totalMass += mass;
1128	<	comVel += mass * mol->getComVel();
1126	>	RealType mass = mol->getMass();
1127	>	totalMass += mass;
1128	>	comVel += mass * mol->getComVel();
1129		}
1130
1131		#ifdef IS_MPI
1132	<	double tmpMass = totalMass;
1132	>	RealType tmpMass = totalMass;
1133		Vector3d tmpComVel(comVel);
1134	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1135	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1134	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1135	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1136		#endif
1137
1138		comVel /= totalMass;
1139
1140		return comVel;
1141	<	}
1141	>	}
1142
1143	<	Vector3d SimInfo::getCom(){
1143	>	Vector3d SimInfo::getCom(){
1144		SimInfo::MoleculeIterator i;
1145		Molecule* mol;
1146
1147		Vector3d com(0.0);
1148	<	double totalMass = 0.0;
1148	>	RealType totalMass = 0.0;
1149
1150		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1151	<	double mass = mol->getMass();
1152	<	totalMass += mass;
1153	<	com += mass * mol->getCom();
1151	>	RealType mass = mol->getMass();
1152	>	totalMass += mass;
1153	>	com += mass * mol->getCom();
1154		}
1155
1156		#ifdef IS_MPI
1157	<	double tmpMass = totalMass;
1157	>	RealType tmpMass = totalMass;
1158		Vector3d tmpCom(com);
1159	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1160	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1159	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1160	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1161		#endif
1162
1163		com /= totalMass;
1164
1165		return com;
1166
1167	<	}
1167	>	}
1168
1169	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1169	>	ostream& operator <<(ostream& o, SimInfo& info) {
1170
1171		return o;
1172	<	}
1172	>	}
1173	>
1174	>
1175	>	/*
1176	>	Returns center of mass and center of mass velocity in one function call.
1177	>	*/
1178	>
1179	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1180	>	SimInfo::MoleculeIterator i;
1181	>	Molecule* mol;
1182	>
1183	>
1184	>	RealType totalMass = 0.0;
1185	>
1186
1187	<	}//end namespace oopse
1187	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1188	>	RealType mass = mol->getMass();
1189	>	totalMass += mass;
1190	>	com += mass * mol->getCom();
1191	>	comVel += mass * mol->getComVel();
1192	>	}
1193	>
1194	>	#ifdef IS_MPI
1195	>	RealType tmpMass = totalMass;
1196	>	Vector3d tmpCom(com);
1197	>	Vector3d tmpComVel(comVel);
1198	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1199	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1200	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1201	>	#endif
1202	>
1203	>	com /= totalMass;
1204	>	comVel /= totalMass;
1205	>	}
1206	>
1207	>	/*
1208	>	Return intertia tensor for entire system and angular momentum Vector.
1209
1210	+
1211	+	[  Ixx -Ixy  -Ixz ]
1212	+	J =| -Iyx  Iyy  -Iyz |
1213	+	[ -Izx -Iyz   Izz ]
1214	+	*/
1215	+
1216	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1217	+
1218	+
1219	+	RealType xx = 0.0;
1220	+	RealType yy = 0.0;
1221	+	RealType zz = 0.0;
1222	+	RealType xy = 0.0;
1223	+	RealType xz = 0.0;
1224	+	RealType yz = 0.0;
1225	+	Vector3d com(0.0);
1226	+	Vector3d comVel(0.0);
1227	+
1228	+	getComAll(com, comVel);
1229	+
1230	+	SimInfo::MoleculeIterator i;
1231	+	Molecule* mol;
1232	+
1233	+	Vector3d thisq(0.0);
1234	+	Vector3d thisv(0.0);
1235	+
1236	+	RealType thisMass = 0.0;
1237	+
1238	+
1239	+
1240	+
1241	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1242	+
1243	+	thisq = mol->getCom()-com;
1244	+	thisv = mol->getComVel()-comVel;
1245	+	thisMass = mol->getMass();
1246	+	// Compute moment of intertia coefficients.
1247	+	xx += thisq[0]*thisq[0]*thisMass;
1248	+	yy += thisq[1]*thisq[1]*thisMass;
1249	+	zz += thisq[2]*thisq[2]*thisMass;
1250	+
1251	+	// compute products of intertia
1252	+	xy += thisq[0]*thisq[1]*thisMass;
1253	+	xz += thisq[0]*thisq[2]*thisMass;
1254	+	yz += thisq[1]*thisq[2]*thisMass;
1255	+
1256	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1257	+
1258	+	}
1259	+
1260	+
1261	+	inertiaTensor(0,0) = yy + zz;
1262	+	inertiaTensor(0,1) = -xy;
1263	+	inertiaTensor(0,2) = -xz;
1264	+	inertiaTensor(1,0) = -xy;
1265	+	inertiaTensor(1,1) = xx + zz;
1266	+	inertiaTensor(1,2) = -yz;
1267	+	inertiaTensor(2,0) = -xz;
1268	+	inertiaTensor(2,1) = -yz;
1269	+	inertiaTensor(2,2) = xx + yy;
1270	+
1271	+	#ifdef IS_MPI
1272	+	Mat3x3d tmpI(inertiaTensor);
1273	+	Vector3d tmpAngMom;
1274	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1275	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1276	+	#endif
1277	+
1278	+	return;
1279	+	}
1280	+
1281	+	//Returns the angular momentum of the system
1282	+	Vector3d SimInfo::getAngularMomentum(){
1283	+
1284	+	Vector3d com(0.0);
1285	+	Vector3d comVel(0.0);
1286	+	Vector3d angularMomentum(0.0);
1287	+
1288	+	getComAll(com,comVel);
1289	+
1290	+	SimInfo::MoleculeIterator i;
1291	+	Molecule* mol;
1292	+
1293	+	Vector3d thisr(0.0);
1294	+	Vector3d thisp(0.0);
1295	+
1296	+	RealType thisMass;
1297	+
1298	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1299	+	thisMass = mol->getMass();
1300	+	thisr = mol->getCom()-com;
1301	+	thisp = (mol->getComVel()-comVel)*thisMass;
1302	+
1303	+	angularMomentum += cross( thisr, thisp );
1304	+
1305	+	}
1306	+
1307	+	#ifdef IS_MPI
1308	+	Vector3d tmpAngMom;
1309	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1310	+	#endif
1311	+
1312	+	return angularMomentum;
1313	+	}
1314	+
1315	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1316	+	return IOIndexToIntegrableObject.at(index);
1317	+	}
1318	+
1319	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1320	+	IOIndexToIntegrableObject= v;
1321	+	}
1322	+
1323	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1324	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1325	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1326	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1327	+	*/
1328	+	void SimInfo::getGyrationalVolume(RealType &volume){
1329	+	Mat3x3d intTensor;
1330	+	RealType det;
1331	+	Vector3d dummyAngMom;
1332	+	RealType sysconstants;
1333	+	RealType geomCnst;
1334	+
1335	+	geomCnst = 3.0/2.0;
1336	+	/* Get the inertial tensor and angular momentum for free*/
1337	+	getInertiaTensor(intTensor,dummyAngMom);
1338	+
1339	+	det = intTensor.determinant();
1340	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1341	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1342	+	return;
1343	+	}
1344	+
1345	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1346	+	Mat3x3d intTensor;
1347	+	Vector3d dummyAngMom;
1348	+	RealType sysconstants;
1349	+	RealType geomCnst;
1350	+
1351	+	geomCnst = 3.0/2.0;
1352	+	/* Get the inertial tensor and angular momentum for free*/
1353	+	getInertiaTensor(intTensor,dummyAngMom);
1354	+
1355	+	detI = intTensor.determinant();
1356	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1357	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1358	+	return;
1359	+	}
1360	+	/*
1361	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1362	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1363	+	sdByGlobalIndex_ = v;
1364	+	}
1365	+
1366	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1367	+	//assert(index < nAtoms_ + nRigidBodies_);
1368	+	return sdByGlobalIndex_.at(index);
1369	+	}
1370	+	*/
1371	+	int SimInfo::getNGlobalConstraints() {
1372	+	int nGlobalConstraints;
1373	+	#ifdef IS_MPI
1374	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1375	+	MPI_COMM_WORLD);
1376	+	#else
1377	+	nGlobalConstraints =  nConstraints_;
1378	+	#endif
1379	+	return nGlobalConstraints;
1380	+	}
1381	+
1382	+	}//end namespace OpenMD
1383	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 274 by tim, Tue Jan 25 21:59:18 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1534 by gezelter, Wed Dec 29 21:53:28 2010 UTC

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