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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 326 by tim, Sun Feb 13 20:05:42 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1528 by gezelter, Fri Dec 17 20:11:05 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/DarkSide/fSwitchingFunctionType.h"
59		#include "UseTheForce/doForces_interface.h"
60	<	#include "UseTheForce/notifyCutoffs_interface.h"
60	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
61	>	#include "UseTheForce/DarkSide/switcheroo_interface.h"
62		#include "utils/MemoryUtils.hpp"
63		#include "utils/simError.h"
64		#include "selection/SelectionManager.hpp"
65	+	#include "io/ForceFieldOptions.hpp"
66	+	#include "UseTheForce/ForceField.hpp"
67	+	#include "nonbonded/InteractionManager.hpp"
68
69	+
70		#ifdef IS_MPI
71		#include "UseTheForce/mpiComponentPlan.h"
72		#include "UseTheForce/DarkSide/simParallel_interface.h"
73		#endif
74
75	<	namespace oopse {
76	<
77	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
78	<	ForceField* ff, Globals* simParams) :
79	<	forceField_(ff), simParams_(simParams),
80	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
81	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
82	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
83	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
84	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
85	<	sman_(NULL), fortranInitialized_(false), selectMan_(NULL) {
86	<
87	<
79	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
75	>	using namespace std;
76	>	namespace OpenMD {
77	>
78	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
79	>	forceField_(ff), simParams_(simParams),
80	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
81	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
82	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
83	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
84	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
85	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
86	>	calcBoxDipole_(false), useAtomicVirial_(true) {
87	>
88		MoleculeStamp* molStamp;
89		int nMolWithSameStamp;
90		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
91	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
91	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
92		CutoffGroupStamp* cgStamp;
93		RigidBodyStamp* rbStamp;
94		int nRigidAtoms = 0;
95
96	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
97	<	molStamp = i->first;
98	<	nMolWithSameStamp = i->second;
99	<
100	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
101	<
102	<	//calculate atoms in molecules
103	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
104	<
105	<
106	<	//calculate atoms in cutoff groups
107	<	int nAtomsInGroups = 0;
108	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
109	<
110	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
111	<	cgStamp = molStamp->getCutoffGroup(j);
112	<	nAtomsInGroups += cgStamp->getNMembers();
113	<	}
114	<
115	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
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->getRigidBody(j);
124	<	nAtomsInRigidBodies += rbStamp->getNMembers();
125	<	}
126	<
127	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
128	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
129	<
96	>	vector<Component*> components = simParams->getComponents();
97	>
98	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
99	>	molStamp = (*i)->getMoleculeStamp();
100	>	nMolWithSameStamp = (*i)->getNMol();
101	>
102	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
103	>
104	>	//calculate atoms in molecules
105	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
106	>
107	>	//calculate atoms in cutoff groups
108	>	int nAtomsInGroups = 0;
109	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
110	>
111	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
112	>	cgStamp = molStamp->getCutoffGroupStamp(j);
113	>	nAtomsInGroups += cgStamp->getNMembers();
114	>	}
115	>
116	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
117	>
118	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
119	>
120	>	//calculate atoms in rigid bodies
121	>	int nAtomsInRigidBodies = 0;
122	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
123	>
124	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
125	>	rbStamp = molStamp->getRigidBodyStamp(j);
126	>	nAtomsInRigidBodies += rbStamp->getNMembers();
127	>	}
128	>
129	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
130	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
131	>
132		}
133	<
134	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
135	<	//therefore the total number of cutoff groups in the system is equal to
136	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
137	<	//file plus the number of cutoff groups defined in meta-data file
133	>
134	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
135	>	//group therefore the total number of cutoff groups in the system is
136	>	//equal to the total number of atoms minus number of atoms belong to
137	>	//cutoff group defined in meta-data file plus the number of cutoff
138	>	//groups defined in meta-data file
139		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
140	<
141	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
142	<	//therefore the total number of  integrable objects in the system is equal to
143	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
144	<	//file plus the number of  rigid bodies defined in meta-data file
145	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
146	<
140	>
141	>	//every free atom (atom does not belong to rigid bodies) is an
142	>	//integrable object therefore the total number of integrable objects
143	>	//in the system is equal to the total number of atoms minus number of
144	>	//atoms belong to rigid body defined in meta-data file plus the number
145	>	//of rigid bodies defined in meta-data file
146	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
147	>	+ nGlobalRigidBodies_;
148	>
149		nGlobalMols_ = molStampIds_.size();
137	–
138	–	#ifdef IS_MPI
150		molToProcMap_.resize(nGlobalMols_);
151	<	#endif
152	<
153	<	selectMan_ = new SelectionManager(this);
154	<	selectMan_->selectAll();
155	<	}
156	<
157	<	SimInfo::~SimInfo() {
158	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
159	<
149	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
150	<
151	>	}
152	>
153	>	SimInfo::~SimInfo() {
154	>	map<int, Molecule*>::iterator i;
155	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
156	>	delete i->second;
157	>	}
158	>	molecules_.clear();
159	>
160		delete sman_;
161		delete simParams_;
162		delete forceField_;
163	<	delete selectMan_;
155	<	}
163	>	}
164
157	–	int SimInfo::getNGlobalConstraints() {
158	–	int nGlobalConstraints;
159	–	#ifdef IS_MPI
160	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
161	–	MPI_COMM_WORLD);
162	–	#else
163	–	nGlobalConstraints =  nConstraints_;
164	–	#endif
165	–	return nGlobalConstraints;
166	–	}
165
166	<	bool SimInfo::addMolecule(Molecule* mol) {
166	>	bool SimInfo::addMolecule(Molecule* mol) {
167		MoleculeIterator i;
168	<
168	>
169		i = molecules_.find(mol->getGlobalIndex());
170		if (i == molecules_.end() ) {
171	<
172	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
173	<
174	<	nAtoms_ += mol->getNAtoms();
175	<	nBonds_ += mol->getNBonds();
176	<	nBends_ += mol->getNBends();
177	<	nTorsions_ += mol->getNTorsions();
178	<	nRigidBodies_ += mol->getNRigidBodies();
179	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
180	<	nCutoffGroups_ += mol->getNCutoffGroups();
181	<	nConstraints_ += mol->getNConstraintPairs();
182	<
183	<	addExcludePairs(mol);
184	<
185	<	return true;
186	<	} else {
187	<	return false;
171	>
172	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
173	>
174	>	nAtoms_ += mol->getNAtoms();
175	>	nBonds_ += mol->getNBonds();
176	>	nBends_ += mol->getNBends();
177	>	nTorsions_ += mol->getNTorsions();
178	>	nInversions_ += mol->getNInversions();
179	>	nRigidBodies_ += mol->getNRigidBodies();
180	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
181	>	nCutoffGroups_ += mol->getNCutoffGroups();
182	>	nConstraints_ += mol->getNConstraintPairs();
183	>
184	>	addInteractionPairs(mol);
185	>
186	>	return true;
187	>	} else {
188	>	return false;
189		}
190	<	}
191	<
192	<	bool SimInfo::removeMolecule(Molecule* mol) {
190	>	}
191	>
192	>	bool SimInfo::removeMolecule(Molecule* mol) {
193		MoleculeIterator i;
194		i = molecules_.find(mol->getGlobalIndex());
195
196		if (i != molecules_.end() ) {
197
198	<	assert(mol == i->second);
198	>	assert(mol == i->second);
199
200	<	nAtoms_ -= mol->getNAtoms();
201	<	nBonds_ -= mol->getNBonds();
202	<	nBends_ -= mol->getNBends();
203	<	nTorsions_ -= mol->getNTorsions();
204	<	nRigidBodies_ -= mol->getNRigidBodies();
205	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
206	<	nCutoffGroups_ -= mol->getNCutoffGroups();
207	<	nConstraints_ -= mol->getNConstraintPairs();
200	>	nAtoms_ -= mol->getNAtoms();
201	>	nBonds_ -= mol->getNBonds();
202	>	nBends_ -= mol->getNBends();
203	>	nTorsions_ -= mol->getNTorsions();
204	>	nInversions_ -= mol->getNInversions();
205	>	nRigidBodies_ -= mol->getNRigidBodies();
206	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
207	>	nCutoffGroups_ -= mol->getNCutoffGroups();
208	>	nConstraints_ -= mol->getNConstraintPairs();
209
210	<	removeExcludePairs(mol);
211	<	molecules_.erase(mol->getGlobalIndex());
210	>	removeInteractionPairs(mol);
211	>	molecules_.erase(mol->getGlobalIndex());
212
213	<	delete mol;
213	>	delete mol;
214
215	<	return true;
215	>	return true;
216		} else {
217	<	return false;
217	>	return false;
218		}
219	+	}
220
220	–
221	–	}
222	–
221
222	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
222	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
223		i = molecules_.begin();
224		return i == molecules_.end() ? NULL : i->second;
225	<	}
225	>	}
226
227	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
227	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
228		++i;
229		return i == molecules_.end() ? NULL : i->second;
230	<	}
230	>	}
231
232
233	<	void SimInfo::calcNdf() {
233	>	void SimInfo::calcNdf() {
234		int ndf_local;
235		MoleculeIterator i;
236	<	std::vector<StuntDouble*>::iterator j;
236	>	vector<StuntDouble*>::iterator j;
237		Molecule* mol;
238		StuntDouble* integrableObject;
239
240		ndf_local = 0;
241
242		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
243	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
244	<	integrableObject = mol->nextIntegrableObject(j)) {
243	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
244	>	integrableObject = mol->nextIntegrableObject(j)) {
245
246	<	ndf_local += 3;
246	>	ndf_local += 3;
247
248	<	if (integrableObject->isDirectional()) {
249	<	if (integrableObject->isLinear()) {
250	<	ndf_local += 2;
251	<	} else {
252	<	ndf_local += 3;
253	<	}
254	<	}
248	>	if (integrableObject->isDirectional()) {
249	>	if (integrableObject->isLinear()) {
250	>	ndf_local += 2;
251	>	} else {
252	>	ndf_local += 3;
253	>	}
254	>	}
255
256	<	}//end for (integrableObject)
257	<	}// end for (mol)
256	>	}
257	>	}
258
259		// n_constraints is local, so subtract them on each processor
260		ndf_local -= nConstraints_;
#	Line 271 | Line 269 | void SimInfo::calcNdf() {
269		// entire system:
270		ndf_ = ndf_ - 3 - nZconstraint_;
271
272	<	}
272	>	}
273
274	<	void SimInfo::calcNdfRaw() {
274	>	int SimInfo::getFdf() {
275	>	#ifdef IS_MPI
276	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
277	>	#else
278	>	fdf_ = fdf_local;
279	>	#endif
280	>	return fdf_;
281	>	}
282	>
283	>	void SimInfo::calcNdfRaw() {
284		int ndfRaw_local;
285
286		MoleculeIterator i;
287	<	std::vector<StuntDouble*>::iterator j;
287	>	vector<StuntDouble*>::iterator j;
288		Molecule* mol;
289		StuntDouble* integrableObject;
290
#	Line 285 | Line 292 | void SimInfo::calcNdfRaw() {
292		ndfRaw_local = 0;
293
294		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
295	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
296	<	integrableObject = mol->nextIntegrableObject(j)) {
295	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
296	>	integrableObject = mol->nextIntegrableObject(j)) {
297
298	<	ndfRaw_local += 3;
298	>	ndfRaw_local += 3;
299
300	<	if (integrableObject->isDirectional()) {
301	<	if (integrableObject->isLinear()) {
302	<	ndfRaw_local += 2;
303	<	} else {
304	<	ndfRaw_local += 3;
305	<	}
306	<	}
300	>	if (integrableObject->isDirectional()) {
301	>	if (integrableObject->isLinear()) {
302	>	ndfRaw_local += 2;
303	>	} else {
304	>	ndfRaw_local += 3;
305	>	}
306	>	}
307
308	<	}
308	>	}
309		}
310
311		#ifdef IS_MPI
#	Line 306 | Line 313 | void SimInfo::calcNdfRaw() {
313		#else
314		ndfRaw_ = ndfRaw_local;
315		#endif
316	<	}
316	>	}
317
318	<	void SimInfo::calcNdfTrans() {
318	>	void SimInfo::calcNdfTrans() {
319		int ndfTrans_local;
320
321		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 322 | Line 329 | void SimInfo::calcNdfTrans() {
329
330		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
331
332	<	}
332	>	}
333
334	<	void SimInfo::addExcludePairs(Molecule* mol) {
335	<	std::vector<Bond*>::iterator bondIter;
336	<	std::vector<Bend*>::iterator bendIter;
337	<	std::vector<Torsion*>::iterator torsionIter;
334	>	void SimInfo::addInteractionPairs(Molecule* mol) {
335	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
336	>	vector<Bond*>::iterator bondIter;
337	>	vector<Bend*>::iterator bendIter;
338	>	vector<Torsion*>::iterator torsionIter;
339	>	vector<Inversion*>::iterator inversionIter;
340		Bond* bond;
341		Bend* bend;
342		Torsion* torsion;
343	+	Inversion* inversion;
344		int a;
345		int b;
346		int c;
347		int d;
338	–
339	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
340	–	a = bond->getAtomA()->getGlobalIndex();
341	–	b = bond->getAtomB()->getGlobalIndex();
342	–	exclude_.addPair(a, b);
343	–	}
348
349	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
350	<	a = bend->getAtomA()->getGlobalIndex();
351	<	b = bend->getAtomB()->getGlobalIndex();
352	<	c = bend->getAtomC()->getGlobalIndex();
349	>	// atomGroups can be used to add special interaction maps between
350	>	// groups of atoms that are in two separate rigid bodies.
351	>	// However, most site-site interactions between two rigid bodies
352	>	// are probably not special, just the ones between the physically
353	>	// bonded atoms.  Interactions *within* a single rigid body should
354	>	// always be excluded.  These are done at the bottom of this
355	>	// function.
356
357	<	exclude_.addPair(a, b);
358	<	exclude_.addPair(a, c);
359	<	exclude_.addPair(b, c);
360	<	}
361	<
362	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
363	<	a = torsion->getAtomA()->getGlobalIndex();
364	<	b = torsion->getAtomB()->getGlobalIndex();
365	<	c = torsion->getAtomC()->getGlobalIndex();
366	<	d = torsion->getAtomD()->getGlobalIndex();
357	>	map<int, set<int> > atomGroups;
358	>	Molecule::RigidBodyIterator rbIter;
359	>	RigidBody* rb;
360	>	Molecule::IntegrableObjectIterator ii;
361	>	StuntDouble* integrableObject;
362	>
363	>	for (integrableObject = mol->beginIntegrableObject(ii);
364	>	integrableObject != NULL;
365	>	integrableObject = mol->nextIntegrableObject(ii)) {
366	>
367	>	if (integrableObject->isRigidBody()) {
368	>	rb = static_cast<RigidBody*>(integrableObject);
369	>	vector<Atom*> atoms = rb->getAtoms();
370	>	set<int> rigidAtoms;
371	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
372	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
373	>	}
374	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
375	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
376	>	}
377	>	} else {
378	>	set<int> oneAtomSet;
379	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
380	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
381	>	}
382	>	}
383	>
384	>	for (bond= mol->beginBond(bondIter); bond != NULL;
385	>	bond = mol->nextBond(bondIter)) {
386
387	<	exclude_.addPair(a, b);
388	<	exclude_.addPair(a, c);
389	<	exclude_.addPair(a, d);
390	<	exclude_.addPair(b, c);
391	<	exclude_.addPair(b, d);
392	<	exclude_.addPair(c, d);
387	>	a = bond->getAtomA()->getGlobalIndex();
388	>	b = bond->getAtomB()->getGlobalIndex();
389	>
390	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
391	>	oneTwoInteractions_.addPair(a, b);
392	>	} else {
393	>	excludedInteractions_.addPair(a, b);
394	>	}
395		}
396
397	<
398	<	}
397	>	for (bend= mol->beginBend(bendIter); bend != NULL;
398	>	bend = mol->nextBend(bendIter)) {
399
400	<	void SimInfo::removeExcludePairs(Molecule* mol) {
401	<	std::vector<Bond*>::iterator bondIter;
402	<	std::vector<Bend*>::iterator bendIter;
403	<	std::vector<Torsion*>::iterator torsionIter;
400	>	a = bend->getAtomA()->getGlobalIndex();
401	>	b = bend->getAtomB()->getGlobalIndex();
402	>	c = bend->getAtomC()->getGlobalIndex();
403	>
404	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
405	>	oneTwoInteractions_.addPair(a, b);
406	>	oneTwoInteractions_.addPair(b, c);
407	>	} else {
408	>	excludedInteractions_.addPair(a, b);
409	>	excludedInteractions_.addPair(b, c);
410	>	}
411	>
412	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
413	>	oneThreeInteractions_.addPair(a, c);
414	>	} else {
415	>	excludedInteractions_.addPair(a, c);
416	>	}
417	>	}
418	>
419	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
420	>	torsion = mol->nextTorsion(torsionIter)) {
421	>
422	>	a = torsion->getAtomA()->getGlobalIndex();
423	>	b = torsion->getAtomB()->getGlobalIndex();
424	>	c = torsion->getAtomC()->getGlobalIndex();
425	>	d = torsion->getAtomD()->getGlobalIndex();
426	>
427	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
428	>	oneTwoInteractions_.addPair(a, b);
429	>	oneTwoInteractions_.addPair(b, c);
430	>	oneTwoInteractions_.addPair(c, d);
431	>	} else {
432	>	excludedInteractions_.addPair(a, b);
433	>	excludedInteractions_.addPair(b, c);
434	>	excludedInteractions_.addPair(c, d);
435	>	}
436	>
437	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
438	>	oneThreeInteractions_.addPair(a, c);
439	>	oneThreeInteractions_.addPair(b, d);
440	>	} else {
441	>	excludedInteractions_.addPair(a, c);
442	>	excludedInteractions_.addPair(b, d);
443	>	}
444	>
445	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
446	>	oneFourInteractions_.addPair(a, d);
447	>	} else {
448	>	excludedInteractions_.addPair(a, d);
449	>	}
450	>	}
451	>
452	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
453	>	inversion = mol->nextInversion(inversionIter)) {
454	>
455	>	a = inversion->getAtomA()->getGlobalIndex();
456	>	b = inversion->getAtomB()->getGlobalIndex();
457	>	c = inversion->getAtomC()->getGlobalIndex();
458	>	d = inversion->getAtomD()->getGlobalIndex();
459	>
460	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
461	>	oneTwoInteractions_.addPair(a, b);
462	>	oneTwoInteractions_.addPair(a, c);
463	>	oneTwoInteractions_.addPair(a, d);
464	>	} else {
465	>	excludedInteractions_.addPair(a, b);
466	>	excludedInteractions_.addPair(a, c);
467	>	excludedInteractions_.addPair(a, d);
468	>	}
469	>
470	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
471	>	oneThreeInteractions_.addPair(b, c);
472	>	oneThreeInteractions_.addPair(b, d);
473	>	oneThreeInteractions_.addPair(c, d);
474	>	} else {
475	>	excludedInteractions_.addPair(b, c);
476	>	excludedInteractions_.addPair(b, d);
477	>	excludedInteractions_.addPair(c, d);
478	>	}
479	>	}
480	>
481	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
482	>	rb = mol->nextRigidBody(rbIter)) {
483	>	vector<Atom*> atoms = rb->getAtoms();
484	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
485	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
486	>	a = atoms[i]->getGlobalIndex();
487	>	b = atoms[j]->getGlobalIndex();
488	>	excludedInteractions_.addPair(a, b);
489	>	}
490	>	}
491	>	}
492	>
493	>	}
494	>
495	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
496	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
497	>	vector<Bond*>::iterator bondIter;
498	>	vector<Bend*>::iterator bendIter;
499	>	vector<Torsion*>::iterator torsionIter;
500	>	vector<Inversion*>::iterator inversionIter;
501		Bond* bond;
502		Bend* bend;
503		Torsion* torsion;
504	+	Inversion* inversion;
505		int a;
506		int b;
507		int c;
508		int d;
509	+
510	+	map<int, set<int> > atomGroups;
511	+	Molecule::RigidBodyIterator rbIter;
512	+	RigidBody* rb;
513	+	Molecule::IntegrableObjectIterator ii;
514	+	StuntDouble* integrableObject;
515
516	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
517	<	a = bond->getAtomA()->getGlobalIndex();
518	<	b = bond->getAtomB()->getGlobalIndex();
519	<	exclude_.removePair(a, b);
516	>	for (integrableObject = mol->beginIntegrableObject(ii);
517	>	integrableObject != NULL;
518	>	integrableObject = mol->nextIntegrableObject(ii)) {
519	>
520	>	if (integrableObject->isRigidBody()) {
521	>	rb = static_cast<RigidBody*>(integrableObject);
522	>	vector<Atom*> atoms = rb->getAtoms();
523	>	set<int> rigidAtoms;
524	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
525	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
526	>	}
527	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
528	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
529	>	}
530	>	} else {
531	>	set<int> oneAtomSet;
532	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
533	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
534	>	}
535	>	}
536	>
537	>	for (bond= mol->beginBond(bondIter); bond != NULL;
538	>	bond = mol->nextBond(bondIter)) {
539	>
540	>	a = bond->getAtomA()->getGlobalIndex();
541	>	b = bond->getAtomB()->getGlobalIndex();
542	>
543	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
544	>	oneTwoInteractions_.removePair(a, b);
545	>	} else {
546	>	excludedInteractions_.removePair(a, b);
547	>	}
548		}
549
550	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
551	<	a = bend->getAtomA()->getGlobalIndex();
392	<	b = bend->getAtomB()->getGlobalIndex();
393	<	c = bend->getAtomC()->getGlobalIndex();
550	>	for (bend= mol->beginBend(bendIter); bend != NULL;
551	>	bend = mol->nextBend(bendIter)) {
552
553	<	exclude_.removePair(a, b);
554	<	exclude_.removePair(a, c);
555	<	exclude_.removePair(b, c);
553	>	a = bend->getAtomA()->getGlobalIndex();
554	>	b = bend->getAtomB()->getGlobalIndex();
555	>	c = bend->getAtomC()->getGlobalIndex();
556	>
557	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
558	>	oneTwoInteractions_.removePair(a, b);
559	>	oneTwoInteractions_.removePair(b, c);
560	>	} else {
561	>	excludedInteractions_.removePair(a, b);
562	>	excludedInteractions_.removePair(b, c);
563	>	}
564	>
565	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
566	>	oneThreeInteractions_.removePair(a, c);
567	>	} else {
568	>	excludedInteractions_.removePair(a, c);
569	>	}
570		}
571
572	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
573	<	a = torsion->getAtomA()->getGlobalIndex();
402	<	b = torsion->getAtomB()->getGlobalIndex();
403	<	c = torsion->getAtomC()->getGlobalIndex();
404	<	d = torsion->getAtomD()->getGlobalIndex();
572	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
573	>	torsion = mol->nextTorsion(torsionIter)) {
574
575	<	exclude_.removePair(a, b);
576	<	exclude_.removePair(a, c);
577	<	exclude_.removePair(a, d);
578	<	exclude_.removePair(b, c);
579	<	exclude_.removePair(b, d);
580	<	exclude_.removePair(c, d);
575	>	a = torsion->getAtomA()->getGlobalIndex();
576	>	b = torsion->getAtomB()->getGlobalIndex();
577	>	c = torsion->getAtomC()->getGlobalIndex();
578	>	d = torsion->getAtomD()->getGlobalIndex();
579	>
580	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
581	>	oneTwoInteractions_.removePair(a, b);
582	>	oneTwoInteractions_.removePair(b, c);
583	>	oneTwoInteractions_.removePair(c, d);
584	>	} else {
585	>	excludedInteractions_.removePair(a, b);
586	>	excludedInteractions_.removePair(b, c);
587	>	excludedInteractions_.removePair(c, d);
588	>	}
589	>
590	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
591	>	oneThreeInteractions_.removePair(a, c);
592	>	oneThreeInteractions_.removePair(b, d);
593	>	} else {
594	>	excludedInteractions_.removePair(a, c);
595	>	excludedInteractions_.removePair(b, d);
596	>	}
597	>
598	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
599	>	oneFourInteractions_.removePair(a, d);
600	>	} else {
601	>	excludedInteractions_.removePair(a, d);
602	>	}
603		}
604
605	<	}
605	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
606	>	inversion = mol->nextInversion(inversionIter)) {
607
608	+	a = inversion->getAtomA()->getGlobalIndex();
609	+	b = inversion->getAtomB()->getGlobalIndex();
610	+	c = inversion->getAtomC()->getGlobalIndex();
611	+	d = inversion->getAtomD()->getGlobalIndex();
612
613	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
614	<	int curStampId;
613	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
614	>	oneTwoInteractions_.removePair(a, b);
615	>	oneTwoInteractions_.removePair(a, c);
616	>	oneTwoInteractions_.removePair(a, d);
617	>	} else {
618	>	excludedInteractions_.removePair(a, b);
619	>	excludedInteractions_.removePair(a, c);
620	>	excludedInteractions_.removePair(a, d);
621	>	}
622
623	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
624	+	oneThreeInteractions_.removePair(b, c);
625	+	oneThreeInteractions_.removePair(b, d);
626	+	oneThreeInteractions_.removePair(c, d);
627	+	} else {
628	+	excludedInteractions_.removePair(b, c);
629	+	excludedInteractions_.removePair(b, d);
630	+	excludedInteractions_.removePair(c, d);
631	+	}
632	+	}
633	+
634	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
635	+	rb = mol->nextRigidBody(rbIter)) {
636	+	vector<Atom*> atoms = rb->getAtoms();
637	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
638	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
639	+	a = atoms[i]->getGlobalIndex();
640	+	b = atoms[j]->getGlobalIndex();
641	+	excludedInteractions_.removePair(a, b);
642	+	}
643	+	}
644	+	}
645	+
646	+	}
647	+
648	+
649	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
650	+	int curStampId;
651	+
652		//index from 0
653		curStampId = moleculeStamps_.size();
654
655		moleculeStamps_.push_back(molStamp);
656		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
657	<	}
657	>	}
658
659	<	void SimInfo::update() {
659	>	void SimInfo::update() {
660
661		setupSimType();
662	+	setupCutoffRadius();
663	+	setupSwitchingRadius();
664	+	setupCutoffMethod();
665	+	setupSkinThickness();
666	+	setupSwitchingFunction();
667	+	setupAccumulateBoxDipole();
668
669		#ifdef IS_MPI
670		setupFortranParallel();
671		#endif
434	–
672		setupFortranSim();
673	+	fortranInitialized_ = true;
674
437	–	//setup fortran force field
438	–	/** @deprecate */
439	–	int isError = 0;
440	–	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
441	–	if(isError){
442	–	sprintf( painCave.errMsg,
443	–	"ForceField error: There was an error initializing the forceField in fortran.\n" );
444	–	painCave.isFatal = 1;
445	–	simError();
446	–	}
447	–
448	–
449	–	setupCutoff();
450	–
675		calcNdf();
676		calcNdfRaw();
677		calcNdfTrans();
678	<
679	<	fortranInitialized_ = true;
680	<	}
457	<
458	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
678	>	}
679	>
680	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
681		SimInfo::MoleculeIterator mi;
682		Molecule* mol;
683		Molecule::AtomIterator ai;
684		Atom* atom;
685	<	std::set<AtomType*> atomTypes;
686	<
685	>	set<AtomType*> atomTypes;
686	>
687		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
688	<
689	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
690	<	atomTypes.insert(atom->getAtomType());
691	<	}
692	<
688	>
689	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
690	>	atomTypes.insert(atom->getAtomType());
691	>	}
692	>
693		}
694	<
694	>
695		return atomTypes;
696	<	}
696	>	}
697
698	<	void SimInfo::setupSimType() {
699	<	std::set<AtomType*>::iterator i;
700	<	std::set<AtomType*> atomTypes;
701	<	atomTypes = getUniqueAtomTypes();
698	>	/**
699	>	* setupCutoffRadius
700	>	*
701	>	*  If the cutoffRadius was explicitly set, use that value.
702	>	*  If the cutoffRadius was not explicitly set:
703	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
704	>	*      No electrostatic atoms?  Poll the atom types present in the
705	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
706	>	*      Use the maximum suggested value that was found.
707	>	*/
708	>	void SimInfo::setupCutoffRadius() {
709
710	<	int useLennardJones = 0;
711	<	int useElectrostatic = 0;
712	<	int useEAM = 0;
713	<	int useCharge = 0;
714	<	int useDirectional = 0;
715	<	int useDipole = 0;
716	<	int useGayBerne = 0;
717	<	int useSticky = 0;
718	<	int useShape = 0;
719	<	int useFLARB = 0; //it is not in AtomType yet
720	<	int useDirectionalAtom = 0;
721	<	int useElectrostatics = 0;
722	<	//usePBC and useRF are from simParams
723	<	int usePBC = simParams_->getPBC();
724	<	int useRF = simParams_->getUseRF();
725	<
726	<	//loop over all of the atom types
727	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
728	<	useLennardJones |= (*i)->isLennardJones();
729	<	useElectrostatic |= (*i)->isElectrostatic();
730	<	useEAM |= (*i)->isEAM();
731	<	useCharge |= (*i)->isCharge();
732	<	useDirectional |= (*i)->isDirectional();
733	<	useDipole |= (*i)->isDipole();
734	<	useGayBerne |= (*i)->isGayBerne();
735	<	useSticky |= (*i)->isSticky();
736	<	useShape |= (*i)->isShape();
710	>	if (simParams_->haveCutoffRadius()) {
711	>	cutoffRadius_ = simParams_->getCutoffRadius();
712	>	} else {
713	>	if (usesElectrostaticAtoms_) {
714	>	sprintf(painCave.errMsg,
715	>	"SimInfo Warning: No value was set for the cutoffRadius.\n"
716	>	"\tOpenMD will use a default value of 12.0 angstroms"
717	>	"\tfor the cutoffRadius.\n");
718	>	painCave.isFatal = 0;
719	>	simError();
720	>	cutoffRadius_ = 12.0;
721	>	} else {
722	>	RealType thisCut;
723	>	set<AtomType*>::iterator i;
724	>	set<AtomType*> atomTypes;
725	>	atomTypes = getSimulatedAtomTypes();
726	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
727	>	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
728	>	cutoffRadius_ = max(thisCut, cutoffRadius_);
729	>	}
730	>	sprintf(painCave.errMsg,
731	>	"SimInfo Warning: No value was set for the cutoffRadius.\n"
732	>	"\tOpenMD will use %lf angstroms.\n",
733	>	cutoffRadius_);
734	>	painCave.isFatal = 0;
735	>	simError();
736	>	}
737		}
738
739	<	if (useSticky || useDipole || useGayBerne || useShape) {
740	<	useDirectionalAtom = 1;
741	<	}
739	>	InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
740	>	}
741	>
742	>	/**
743	>	* setupSwitchingRadius
744	>	*
745	>	*  If the switchingRadius was explicitly set, use that value (but check it)
746	>	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
747	>	*/
748	>	void SimInfo::setupSwitchingRadius() {
749	>
750	>	if (simParams_->haveSwitchingRadius()) {
751	>	switchingRadius_ = simParams_->getSwitchingRadius();
752	>	if (switchingRadius_ > cutoffRadius_) {
753	>	sprintf(painCave.errMsg,
754	>	"SimInfo Error: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
755	>	switchingRadius_, cutoffRadius_);
756	>	painCave.isFatal = 1;
757	>	simError();
758
759	<	if (useCharge || useDipole) {
760	<	useElectrostatics = 1;
761	<	}
759	>	}
760	>	} else {
761	>	switchingRadius_ = 0.85 * cutoffRadius_;
762	>	sprintf(painCave.errMsg,
763	>	"SimInfo Warning: No value was set for the switchingRadius.\n"
764	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
765	>	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
766	>	painCave.isFatal = 0;
767	>	simError();
768	>	}
769	>	InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
770	>	}
771
772	<	#ifdef IS_MPI
773	<	int temp;
772	>	/**
773	>	* setupSkinThickness
774	>	*
775	>	*  If the skinThickness was explicitly set, use that value (but check it)
776	>	*  If the skinThickness was not explicitly set: use 1.0 angstroms
777	>	*/
778	>	void SimInfo::setupSkinThickness() {
779	>	if (simParams_->haveSkinThickness()) {
780	>	skinThickness_ = simParams_->getSkinThickness();
781	>	} else {
782	>	skinThickness_ = 1.0;
783	>	sprintf(painCave.errMsg,
784	>	"SimInfo Warning: No value was set for the skinThickness.\n"
785	>	"\tOpenMD will use a default value of %f Angstroms\n"
786	>	"\tfor this simulation\n", skinThickness_);
787	>	painCave.isFatal = 0;
788	>	simError();
789	>	}
790	>	}
791
792	<	temp = usePBC;
793	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
792	>	void SimInfo::setupSimType() {
793	>	set<AtomType*>::iterator i;
794	>	set<AtomType*> atomTypes;
795	>	atomTypes = getSimulatedAtomTypes();
796
797	<	temp = useDirectionalAtom;
525	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
797	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
798
799	<	temp = useLennardJones;
800	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
799	>	int usesElectrostatic = 0;
800	>	int usesMetallic = 0;
801	>	int usesDirectional = 0;
802	>	//loop over all of the atom types
803	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
804	>	usesElectrostatic |= (*i)->isElectrostatic();
805	>	usesMetallic |= (*i)->isMetal();
806	>	usesDirectional |= (*i)->isDirectional();
807	>	}
808
809	<	temp = useElectrostatics;
810	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
809	>	#ifdef IS_MPI
810	>	int temp;
811	>	temp = usesDirectional;
812	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813
814	<	temp = useCharge;
815	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814	>	temp = usesMetallic;
815	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816
817	<	temp = useDipole;
818	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
538	<
539	<	temp = useSticky;
540	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
541	<
542	<	temp = useGayBerne;
543	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
544	<
545	<	temp = useEAM;
546	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
547	<
548	<	temp = useShape;
549	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
550	<
551	<	temp = useFLARB;
552	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
553	<
554	<	temp = useRF;
555	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
556	<
817	>	temp = usesElectrostatic;
818	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819		#endif
820	+	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
821	+	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
822	+	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
823	+	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
824	+	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
825	+	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
826	+	}
827
828	<	fInfo_.SIM_uses_PBC = usePBC;
560	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
561	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
562	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
563	<	fInfo_.SIM_uses_Charges = useCharge;
564	<	fInfo_.SIM_uses_Dipoles = useDipole;
565	<	fInfo_.SIM_uses_Sticky = useSticky;
566	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
567	<	fInfo_.SIM_uses_EAM = useEAM;
568	<	fInfo_.SIM_uses_Shapes = useShape;
569	<	fInfo_.SIM_uses_FLARB = useFLARB;
570	<	fInfo_.SIM_uses_RF = useRF;
571	<
572	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
573	<
574	<	if (simParams_->haveDielectric()) {
575	<	fInfo_.dielect = simParams_->getDielectric();
576	<	} else {
577	<	sprintf(painCave.errMsg,
578	<	"SimSetup Error: No Dielectric constant was set.\n"
579	<	"\tYou are trying to use Reaction Field without"
580	<	"\tsetting a dielectric constant!\n");
581	<	painCave.isFatal = 1;
582	<	simError();
583	<	}
584	<
585	<	} else {
586	<	fInfo_.dielect = 0.0;
587	<	}
588	<
589	<	}
590	<
591	<	void SimInfo::setupFortranSim() {
828	>	void SimInfo::setupFortranSim() {
829		int isError;
830	<	int nExclude;
831	<	std::vector<int> fortranGlobalGroupMembership;
830	>	int nExclude, nOneTwo, nOneThree, nOneFour;
831	>	vector<int> fortranGlobalGroupMembership;
832
833	<	nExclude = exclude_.getSize();
833	>	notifyFortranSkinThickness(&skinThickness_);
834	>
835	>	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
836	>	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
837	>	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
838	>
839		isError = 0;
840
841		//globalGroupMembership_ is filled by SimCreator
842		for (int i = 0; i < nGlobalAtoms_; i++) {
843	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
843	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
844		}
845
846		//calculate mass ratio of cutoff group
847	<	std::vector<double> mfact;
847	>	vector<RealType> mfact;
848		SimInfo::MoleculeIterator mi;
849		Molecule* mol;
850		Molecule::CutoffGroupIterator ci;
851		CutoffGroup* cg;
852		Molecule::AtomIterator ai;
853		Atom* atom;
854	<	double totalMass;
854	>	RealType totalMass;
855
856		//to avoid memory reallocation, reserve enough space for mfact
857		mfact.reserve(getNCutoffGroups());
858
859		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
860	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
860	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
861
862	<	totalMass = cg->getMass();
863	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
864	<	mfact.push_back(atom->getMass()/totalMass);
865	<	}
866	<
867	<	}
862	>	totalMass = cg->getMass();
863	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
864	>	// Check for massless groups - set mfact to 1 if true
865	>	if (totalMass != 0)
866	>	mfact.push_back(atom->getMass()/totalMass);
867	>	else
868	>	mfact.push_back( 1.0 );
869	>	}
870	>	}
871		}
872
873		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
874	<	std::vector<int> identArray;
874	>	vector<int> identArray;
875
876		//to avoid memory reallocation, reserve enough space identArray
877		identArray.reserve(getNAtoms());
878
879		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
880	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
881	<	identArray.push_back(atom->getIdent());
882	<	}
880	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
881	>	identArray.push_back(atom->getIdent());
882	>	}
883		}
884
885		//fill molMembershipArray
886		//molMembershipArray is filled by SimCreator
887	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
887	>	vector<int> molMembershipArray(nGlobalAtoms_);
888		for (int i = 0; i < nGlobalAtoms_; i++) {
889	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
889	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
890		}
891
892		//setup fortran simulation
648	–	//gloalExcludes and molMembershipArray should go away (They are never used)
649	–	//why the hell fortran need to know molecule?
650	–	//OOPSE = Object-Obfuscated Parallel Simulation Engine
651	–	int nGlobalExcludes = 0;
652	–	int* globalExcludes = NULL;
653	–	int* excludeList = exclude_.getExcludeList();
654	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
655	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
656	–	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
893
894	<	if( isError ){
894	>	nExclude = excludedInteractions_.getSize();
895	>	nOneTwo = oneTwoInteractions_.getSize();
896	>	nOneThree = oneThreeInteractions_.getSize();
897	>	nOneFour = oneFourInteractions_.getSize();
898
899	<	sprintf( painCave.errMsg,
900	<	"There was an error setting the simulation information in fortran.\n" );
901	<	painCave.isFatal = 1;
902	<	painCave.severity = OOPSE_ERROR;
664	<	simError();
665	<	}
899	>	int* excludeList = excludedInteractions_.getPairList();
900	>	int* oneTwoList = oneTwoInteractions_.getPairList();
901	>	int* oneThreeList = oneThreeInteractions_.getPairList();
902	>	int* oneFourList = oneFourInteractions_.getPairList();
903
904	<	#ifdef IS_MPI
904	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
905	>	&nExclude, excludeList,
906	>	&nOneTwo, oneTwoList,
907	>	&nOneThree, oneThreeList,
908	>	&nOneFour, oneFourList,
909	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
910	>	&fortranGlobalGroupMembership[0], &isError);
911	>
912	>	if( isError ){
913	>
914	>	sprintf( painCave.errMsg,
915	>	"There was an error setting the simulation information in fortran.\n" );
916	>	painCave.isFatal = 1;
917	>	painCave.severity = OPENMD_ERROR;
918	>	simError();
919	>	}
920	>
921	>
922		sprintf( checkPointMsg,
923	<	"succesfully sent the simulation information to fortran.\n");
924	<	MPIcheckPoint();
925	<	#endif // is_mpi
926	<	}
923	>	"succesfully sent the simulation information to fortran.\n");
924	>
925	>	errorCheckPoint();
926	>
927	>	// Setup number of neighbors in neighbor list if present
928	>	if (simParams_->haveNeighborListNeighbors()) {
929	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
930	>	setNeighbors(&nlistNeighbors);
931	>	}
932	>
933
934	+	}
935
936	<	#ifdef IS_MPI
937	<	void SimInfo::setupFortranParallel() {
938	<
936	>
937	>	void SimInfo::setupFortranParallel() {
938	>	#ifdef IS_MPI
939		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
940	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
941	<	std::vector<int> localToGlobalCutoffGroupIndex;
940	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
941	>	vector<int> localToGlobalCutoffGroupIndex;
942		SimInfo::MoleculeIterator mi;
943		Molecule::AtomIterator ai;
944		Molecule::CutoffGroupIterator ci;
#	Line 689 | Line 950 | void SimInfo::setupFortranParallel() {
950
951		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
952
953	<	//local index(index in DataStorge) of atom is important
954	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
955	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
956	<	}
953	>	//local index(index in DataStorge) of atom is important
954	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
955	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
956	>	}
957
958	<	//local index of cutoff group is trivial, it only depends on the order of travesing
959	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
960	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
961	<	}
958	>	//local index of cutoff group is trivial, it only depends on the order of travesing
959	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
960	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
961	>	}
962
963		}
964
#	Line 717 | Line 978 | void SimInfo::setupFortranParallel() {
978		&localToGlobalCutoffGroupIndex[0], &isError);
979
980		if (isError) {
981	<	sprintf(painCave.errMsg,
982	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
983	<	painCave.isFatal = 1;
984	<	simError();
981	>	sprintf(painCave.errMsg,
982	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
983	>	painCave.isFatal = 1;
984	>	simError();
985		}
986
987		sprintf(checkPointMsg, " mpiRefresh successful.\n");
988	<	MPIcheckPoint();
988	>	errorCheckPoint();
989
729	–
730	–	}
731	–
990		#endif
991	+	}
992
734	–	double SimInfo::calcMaxCutoffRadius() {
993
994	+	void SimInfo::setupSwitchingFunction() {
995	+	int ft = CUBIC;
996	+
997	+	if (simParams_->haveSwitchingFunctionType()) {
998	+	string funcType = simParams_->getSwitchingFunctionType();
999	+	toUpper(funcType);
1000	+	if (funcType == "CUBIC") {
1001	+	ft = CUBIC;
1002	+	} else {
1003	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1004	+	ft = FIFTH_ORDER_POLY;
1005	+	} else {
1006	+	// throw error
1007	+	sprintf( painCave.errMsg,
1008	+	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1009	+	painCave.isFatal = 1;
1010	+	simError();
1011	+	}
1012	+	}
1013	+	}
1014
1015	<	std::set<AtomType*> atomTypes;
1016	<	std::set<AtomType*>::iterator i;
739	<	std::vector<double> cutoffRadius;
1015	>	// send switching function notification to switcheroo
1016	>	setFunctionType(&ft);
1017
1018	<	//get the unique atom types
742	<	atomTypes = getUniqueAtomTypes();
1018	>	}
1019
1020	<	//query the max cutoff radius among these atom types
745	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
746	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
747	<	}
1020	>	void SimInfo::setupAccumulateBoxDipole() {
1021
1022	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
1023	<	#ifdef IS_MPI
1024	<	//pick the max cutoff radius among the processors
1025	<	#endif
1022	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1023	>	if ( simParams_->haveAccumulateBoxDipole() )
1024	>	if ( simParams_->getAccumulateBoxDipole() ) {
1025	>	calcBoxDipole_ = true;
1026	>	}
1027
1028	<	return maxCutoffRadius;
755	<	}
1028	>	}
1029
1030	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
758	<
759	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
760	<
761	<	if (!simParams_->haveRcut()){
762	<	sprintf(painCave.errMsg,
763	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
764	<	"\tOOPSE will use a default value of 15.0 angstroms"
765	<	"\tfor the cutoffRadius.\n");
766	<	painCave.isFatal = 0;
767	<	simError();
768	<	rcut_ = 15.0;
769	<	} else{
770	<	rcut_ = simParams_->getRcut();
771	<	}
772	<
773	<	if (!simParams_->haveRsw()){
774	<	sprintf(painCave.errMsg,
775	<	"SimCreator Warning: No value was set for switchingRadius.\n"
776	<	"\tOOPSE will use a default value of\n"
777	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
778	<	painCave.isFatal = 0;
779	<	simError();
780	<	rsw_ = 0.95 * rcut_;
781	<	} else{
782	<	rsw_ = simParams_->getRsw();
783	<	}
784	<
785	<	} else {
786	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
787	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
788	<
789	<	if (simParams_->haveRcut()) {
790	<	rcut_ = simParams_->getRcut();
791	<	} else {
792	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
793	<	rcut_ = calcMaxCutoffRadius();
794	<	}
795	<
796	<	if (simParams_->haveRsw()) {
797	<	rsw_  = simParams_->getRsw();
798	<	} else {
799	<	rsw_ = rcut_;
800	<	}
801	<
802	<	}
803	<	}
804	<
805	<	void SimInfo::setupCutoff() {
806	<	getCutoff(rcut_, rsw_);
807	<	double rnblist = rcut_ + 1; // skin of neighbor list
808	<
809	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
810	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
811	<	}
812	<
813	<	void SimInfo::addProperty(GenericData* genData) {
1030	>	void SimInfo::addProperty(GenericData* genData) {
1031		properties_.addProperty(genData);
1032	<	}
1032	>	}
1033
1034	<	void SimInfo::removeProperty(const std::string& propName) {
1034	>	void SimInfo::removeProperty(const string& propName) {
1035		properties_.removeProperty(propName);
1036	<	}
1036	>	}
1037
1038	<	void SimInfo::clearProperties() {
1038	>	void SimInfo::clearProperties() {
1039		properties_.clearProperties();
1040	<	}
1040	>	}
1041
1042	<	std::vector<std::string> SimInfo::getPropertyNames() {
1042	>	vector<string> SimInfo::getPropertyNames() {
1043		return properties_.getPropertyNames();
1044	<	}
1044	>	}
1045
1046	<	std::vector<GenericData*> SimInfo::getProperties() {
1046	>	vector<GenericData*> SimInfo::getProperties() {
1047		return properties_.getProperties();
1048	<	}
1048	>	}
1049
1050	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1050	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1051		return properties_.getPropertyByName(propName);
1052	<	}
1052	>	}
1053
1054	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1054	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1055	>	if (sman_ == sman) {
1056	>	return;
1057	>	}
1058	>	delete sman_;
1059		sman_ = sman;
1060
1061		Molecule* mol;
#	Line 846 | Line 1067 | void SimInfo::setSnapshotManager(SnapshotManager* sman
1067
1068		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1069
1070	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1071	<	atom->setSnapshotManager(sman_);
1072	<	}
1070	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1071	>	atom->setSnapshotManager(sman_);
1072	>	}
1073
1074	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1075	<	rb->setSnapshotManager(sman_);
1076	<	}
1074	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1075	>	rb->setSnapshotManager(sman_);
1076	>	}
1077		}
1078
1079	<	}
1079	>	}
1080
1081	<	Vector3d SimInfo::getComVel(){
1081	>	Vector3d SimInfo::getComVel(){
1082		SimInfo::MoleculeIterator i;
1083		Molecule* mol;
1084
1085		Vector3d comVel(0.0);
1086	<	double totalMass = 0.0;
1086	>	RealType totalMass = 0.0;
1087
1088
1089		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1090	<	double mass = mol->getMass();
1091	<	totalMass += mass;
1092	<	comVel += mass * mol->getComVel();
1090	>	RealType mass = mol->getMass();
1091	>	totalMass += mass;
1092	>	comVel += mass * mol->getComVel();
1093		}
1094
1095		#ifdef IS_MPI
1096	<	double tmpMass = totalMass;
1096	>	RealType tmpMass = totalMass;
1097		Vector3d tmpComVel(comVel);
1098	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1099	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1098	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1099	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1100		#endif
1101
1102		comVel /= totalMass;
1103
1104		return comVel;
1105	<	}
1105	>	}
1106
1107	<	Vector3d SimInfo::getCom(){
1107	>	Vector3d SimInfo::getCom(){
1108		SimInfo::MoleculeIterator i;
1109		Molecule* mol;
1110
1111		Vector3d com(0.0);
1112	<	double totalMass = 0.0;
1112	>	RealType totalMass = 0.0;
1113
1114		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1115	<	double mass = mol->getMass();
1116	<	totalMass += mass;
1117	<	com += mass * mol->getCom();
1115	>	RealType mass = mol->getMass();
1116	>	totalMass += mass;
1117	>	com += mass * mol->getCom();
1118		}
1119
1120		#ifdef IS_MPI
1121	<	double tmpMass = totalMass;
1121	>	RealType tmpMass = totalMass;
1122		Vector3d tmpCom(com);
1123	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1124	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1123	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1124	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1125		#endif
1126
1127		com /= totalMass;
1128
1129		return com;
1130
1131	<	}
1131	>	}
1132
1133	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1133	>	ostream& operator <<(ostream& o, SimInfo& info) {
1134
1135		return o;
1136	<	}
1136	>	}
1137	>
1138	>
1139	>	/*
1140	>	Returns center of mass and center of mass velocity in one function call.
1141	>	*/
1142	>
1143	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1144	>	SimInfo::MoleculeIterator i;
1145	>	Molecule* mol;
1146	>
1147	>
1148	>	RealType totalMass = 0.0;
1149	>
1150
1151	<	}//end namespace oopse
1151	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1152	>	RealType mass = mol->getMass();
1153	>	totalMass += mass;
1154	>	com += mass * mol->getCom();
1155	>	comVel += mass * mol->getComVel();
1156	>	}
1157	>
1158	>	#ifdef IS_MPI
1159	>	RealType tmpMass = totalMass;
1160	>	Vector3d tmpCom(com);
1161	>	Vector3d tmpComVel(comVel);
1162	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1163	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1164	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1165	>	#endif
1166	>
1167	>	com /= totalMass;
1168	>	comVel /= totalMass;
1169	>	}
1170	>
1171	>	/*
1172	>	Return intertia tensor for entire system and angular momentum Vector.
1173
1174	+
1175	+	[  Ixx -Ixy  -Ixz ]
1176	+	J =| -Iyx  Iyy  -Iyz |
1177	+	[ -Izx -Iyz   Izz ]
1178	+	*/
1179	+
1180	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1181	+
1182	+
1183	+	RealType xx = 0.0;
1184	+	RealType yy = 0.0;
1185	+	RealType zz = 0.0;
1186	+	RealType xy = 0.0;
1187	+	RealType xz = 0.0;
1188	+	RealType yz = 0.0;
1189	+	Vector3d com(0.0);
1190	+	Vector3d comVel(0.0);
1191	+
1192	+	getComAll(com, comVel);
1193	+
1194	+	SimInfo::MoleculeIterator i;
1195	+	Molecule* mol;
1196	+
1197	+	Vector3d thisq(0.0);
1198	+	Vector3d thisv(0.0);
1199	+
1200	+	RealType thisMass = 0.0;
1201	+
1202	+
1203	+
1204	+
1205	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1206	+
1207	+	thisq = mol->getCom()-com;
1208	+	thisv = mol->getComVel()-comVel;
1209	+	thisMass = mol->getMass();
1210	+	// Compute moment of intertia coefficients.
1211	+	xx += thisq[0]*thisq[0]*thisMass;
1212	+	yy += thisq[1]*thisq[1]*thisMass;
1213	+	zz += thisq[2]*thisq[2]*thisMass;
1214	+
1215	+	// compute products of intertia
1216	+	xy += thisq[0]*thisq[1]*thisMass;
1217	+	xz += thisq[0]*thisq[2]*thisMass;
1218	+	yz += thisq[1]*thisq[2]*thisMass;
1219	+
1220	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1221	+
1222	+	}
1223	+
1224	+
1225	+	inertiaTensor(0,0) = yy + zz;
1226	+	inertiaTensor(0,1) = -xy;
1227	+	inertiaTensor(0,2) = -xz;
1228	+	inertiaTensor(1,0) = -xy;
1229	+	inertiaTensor(1,1) = xx + zz;
1230	+	inertiaTensor(1,2) = -yz;
1231	+	inertiaTensor(2,0) = -xz;
1232	+	inertiaTensor(2,1) = -yz;
1233	+	inertiaTensor(2,2) = xx + yy;
1234	+
1235	+	#ifdef IS_MPI
1236	+	Mat3x3d tmpI(inertiaTensor);
1237	+	Vector3d tmpAngMom;
1238	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1239	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1240	+	#endif
1241	+
1242	+	return;
1243	+	}
1244	+
1245	+	//Returns the angular momentum of the system
1246	+	Vector3d SimInfo::getAngularMomentum(){
1247	+
1248	+	Vector3d com(0.0);
1249	+	Vector3d comVel(0.0);
1250	+	Vector3d angularMomentum(0.0);
1251	+
1252	+	getComAll(com,comVel);
1253	+
1254	+	SimInfo::MoleculeIterator i;
1255	+	Molecule* mol;
1256	+
1257	+	Vector3d thisr(0.0);
1258	+	Vector3d thisp(0.0);
1259	+
1260	+	RealType thisMass;
1261	+
1262	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1263	+	thisMass = mol->getMass();
1264	+	thisr = mol->getCom()-com;
1265	+	thisp = (mol->getComVel()-comVel)*thisMass;
1266	+
1267	+	angularMomentum += cross( thisr, thisp );
1268	+
1269	+	}
1270	+
1271	+	#ifdef IS_MPI
1272	+	Vector3d tmpAngMom;
1273	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1274	+	#endif
1275	+
1276	+	return angularMomentum;
1277	+	}
1278	+
1279	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1280	+	return IOIndexToIntegrableObject.at(index);
1281	+	}
1282	+
1283	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1284	+	IOIndexToIntegrableObject= v;
1285	+	}
1286	+
1287	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1288	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1289	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1290	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1291	+	*/
1292	+	void SimInfo::getGyrationalVolume(RealType &volume){
1293	+	Mat3x3d intTensor;
1294	+	RealType det;
1295	+	Vector3d dummyAngMom;
1296	+	RealType sysconstants;
1297	+	RealType geomCnst;
1298	+
1299	+	geomCnst = 3.0/2.0;
1300	+	/* Get the inertial tensor and angular momentum for free*/
1301	+	getInertiaTensor(intTensor,dummyAngMom);
1302	+
1303	+	det = intTensor.determinant();
1304	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1305	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1306	+	return;
1307	+	}
1308	+
1309	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1310	+	Mat3x3d intTensor;
1311	+	Vector3d dummyAngMom;
1312	+	RealType sysconstants;
1313	+	RealType geomCnst;
1314	+
1315	+	geomCnst = 3.0/2.0;
1316	+	/* Get the inertial tensor and angular momentum for free*/
1317	+	getInertiaTensor(intTensor,dummyAngMom);
1318	+
1319	+	detI = intTensor.determinant();
1320	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1321	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1322	+	return;
1323	+	}
1324	+	/*
1325	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1326	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1327	+	sdByGlobalIndex_ = v;
1328	+	}
1329	+
1330	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1331	+	//assert(index < nAtoms_ + nRigidBodies_);
1332	+	return sdByGlobalIndex_.at(index);
1333	+	}
1334	+	*/
1335	+	int SimInfo::getNGlobalConstraints() {
1336	+	int nGlobalConstraints;
1337	+	#ifdef IS_MPI
1338	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1339	+	MPI_COMM_WORLD);
1340	+	#else
1341	+	nGlobalConstraints =  nConstraints_;
1342	+	#endif
1343	+	return nGlobalConstraints;
1344	+	}
1345	+
1346	+	}//end namespace OpenMD
1347	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 326 by tim, Sun Feb 13 20:05:42 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1528 by gezelter, Fri Dec 17 20:11:05 2010 UTC

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