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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 316 by tim, Fri Feb 11 22:41:02 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1532 by gezelter, Wed Dec 29 19:59:21 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	+
67		#ifdef IS_MPI
68		#include "UseTheForce/mpiComponentPlan.h"
69		#include "UseTheForce/DarkSide/simParallel_interface.h"
70		#endif
71
72	<	namespace oopse {
73	<
74	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
75	<	ForceField* ff, Globals* simParams) :
76	<	forceField_(ff), simParams_(simParams),
77	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
78	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
79	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
80	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
81	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
82	<	sman_(NULL), fortranInitialized_(false), selectMan_(NULL) {
83	<
84	<
79	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
72	>	using namespace std;
73	>	namespace OpenMD {
74	>
75	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
76	>	forceField_(ff), simParams_(simParams),
77	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
78	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
79	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
80	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
81	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
82	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
83	>	calcBoxDipole_(false), useAtomicVirial_(true) {
84	>
85		MoleculeStamp* molStamp;
86		int nMolWithSameStamp;
87		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
88	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
88	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
89		CutoffGroupStamp* cgStamp;
90		RigidBodyStamp* rbStamp;
91		int nRigidAtoms = 0;
92
93	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
94	<	molStamp = i->first;
95	<	nMolWithSameStamp = i->second;
96	<
97	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
98	<
99	<	//calculate atoms in molecules
100	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
101	<
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->getCutoffGroup(j);
109	<	nAtomsInGroups += cgStamp->getNMembers();
110	<	}
111	<
112	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
113	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
114	<
115	<	//calculate atoms in rigid bodies
116	<	int nAtomsInRigidBodies = 0;
117	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
118	<
119	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
120	<	rbStamp = molStamp->getRigidBody(j);
121	<	nAtomsInRigidBodies += rbStamp->getNMembers();
122	<	}
123	<
124	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
125	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
126	<
93	>	vector<Component*> components = simParams->getComponents();
94	>
95	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
96	>	molStamp = (*i)->getMoleculeStamp();
97	>	nMolWithSameStamp = (*i)->getNMol();
98	>
99	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
100	>
101	>	//calculate atoms in molecules
102	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
103	>
104	>	//calculate atoms in cutoff groups
105	>	int nAtomsInGroups = 0;
106	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
107	>
108	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
109	>	cgStamp = molStamp->getCutoffGroupStamp(j);
110	>	nAtomsInGroups += cgStamp->getNMembers();
111	>	}
112	>
113	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
114	>
115	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
116	>
117	>	//calculate atoms in rigid bodies
118	>	int nAtomsInRigidBodies = 0;
119	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
120	>
121	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
122	>	rbStamp = molStamp->getRigidBodyStamp(j);
123	>	nAtomsInRigidBodies += rbStamp->getNMembers();
124	>	}
125	>
126	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
127	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
128	>
129		}
130	<
131	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
132	<	//therefore the total number of cutoff groups in the system is equal to
133	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
134	<	//file plus the number of cutoff groups defined in meta-data file
130	>
131	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
132	>	//group therefore the total number of cutoff groups in the system is
133	>	//equal to the total number of atoms minus number of atoms belong to
134	>	//cutoff group defined in meta-data file plus the number of cutoff
135	>	//groups defined in meta-data file
136		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
137	<
138	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
139	<	//therefore the total number of  integrable objects in the system is equal to
140	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
141	<	//file plus the number of  rigid bodies defined in meta-data file
142	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
143	<
137	>
138	>	//every free atom (atom does not belong to rigid bodies) is an
139	>	//integrable object therefore the total number of integrable objects
140	>	//in the system is equal to the total number of atoms minus number of
141	>	//atoms belong to rigid body defined in meta-data file plus the number
142	>	//of rigid bodies defined in meta-data file
143	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
144	>	+ nGlobalRigidBodies_;
145	>
146		nGlobalMols_ = molStampIds_.size();
137	–
138	–	#ifdef IS_MPI
147		molToProcMap_.resize(nGlobalMols_);
148	<	#endif
149	<
150	<	selectMan_ = new SelectionManager(this);
151	<	selectMan_->selectAll();
152	<	}
153	<
154	<	SimInfo::~SimInfo() {
155	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
156	<
149	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
150	<
148	>	}
149	>
150	>	SimInfo::~SimInfo() {
151	>	map<int, Molecule*>::iterator i;
152	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
153	>	delete i->second;
154	>	}
155	>	molecules_.clear();
156	>
157		delete sman_;
158		delete simParams_;
159		delete forceField_;
160	<	delete selectMan_;
155	<	}
160	>	}
161
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	–	}
162
163	<	bool SimInfo::addMolecule(Molecule* mol) {
163	>	bool SimInfo::addMolecule(Molecule* mol) {
164		MoleculeIterator i;
165	<
165	>
166		i = molecules_.find(mol->getGlobalIndex());
167		if (i == molecules_.end() ) {
168	<
169	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
170	<
171	<	nAtoms_ += mol->getNAtoms();
172	<	nBonds_ += mol->getNBonds();
173	<	nBends_ += mol->getNBends();
174	<	nTorsions_ += mol->getNTorsions();
175	<	nRigidBodies_ += mol->getNRigidBodies();
176	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
177	<	nCutoffGroups_ += mol->getNCutoffGroups();
178	<	nConstraints_ += mol->getNConstraintPairs();
179	<
180	<	addExcludePairs(mol);
181	<
182	<	return true;
168	>
169	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
170	>
171	>	nAtoms_ += mol->getNAtoms();
172	>	nBonds_ += mol->getNBonds();
173	>	nBends_ += mol->getNBends();
174	>	nTorsions_ += mol->getNTorsions();
175	>	nInversions_ += mol->getNInversions();
176	>	nRigidBodies_ += mol->getNRigidBodies();
177	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
178	>	nCutoffGroups_ += mol->getNCutoffGroups();
179	>	nConstraints_ += mol->getNConstraintPairs();
180	>
181	>	addInteractionPairs(mol);
182	>
183	>	return true;
184		} else {
185	<	return false;
185	>	return false;
186		}
187	<	}
188	<
189	<	bool SimInfo::removeMolecule(Molecule* mol) {
187	>	}
188	>
189	>	bool SimInfo::removeMolecule(Molecule* mol) {
190		MoleculeIterator i;
191		i = molecules_.find(mol->getGlobalIndex());
192
193		if (i != molecules_.end() ) {
194
195	<	assert(mol == i->second);
195	>	assert(mol == i->second);
196
197	<	nAtoms_ -= mol->getNAtoms();
198	<	nBonds_ -= mol->getNBonds();
199	<	nBends_ -= mol->getNBends();
200	<	nTorsions_ -= mol->getNTorsions();
201	<	nRigidBodies_ -= mol->getNRigidBodies();
202	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
203	<	nCutoffGroups_ -= mol->getNCutoffGroups();
204	<	nConstraints_ -= mol->getNConstraintPairs();
197	>	nAtoms_ -= mol->getNAtoms();
198	>	nBonds_ -= mol->getNBonds();
199	>	nBends_ -= mol->getNBends();
200	>	nTorsions_ -= mol->getNTorsions();
201	>	nInversions_ -= mol->getNInversions();
202	>	nRigidBodies_ -= mol->getNRigidBodies();
203	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
204	>	nCutoffGroups_ -= mol->getNCutoffGroups();
205	>	nConstraints_ -= mol->getNConstraintPairs();
206
207	<	removeExcludePairs(mol);
208	<	molecules_.erase(mol->getGlobalIndex());
207	>	removeInteractionPairs(mol);
208	>	molecules_.erase(mol->getGlobalIndex());
209
210	<	delete mol;
210	>	delete mol;
211
212	<	return true;
212	>	return true;
213		} else {
214	<	return false;
214	>	return false;
215		}
216	+	}
217
220	–
221	–	}
222	–
218
219	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
219	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
220		i = molecules_.begin();
221		return i == molecules_.end() ? NULL : i->second;
222	<	}
222	>	}
223
224	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
224	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
225		++i;
226		return i == molecules_.end() ? NULL : i->second;
227	<	}
227	>	}
228
229
230	<	void SimInfo::calcNdf() {
230	>	void SimInfo::calcNdf() {
231		int ndf_local;
232		MoleculeIterator i;
233	<	std::vector<StuntDouble*>::iterator j;
233	>	vector<StuntDouble*>::iterator j;
234		Molecule* mol;
235		StuntDouble* integrableObject;
236
237		ndf_local = 0;
238
239		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
240	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
241	<	integrableObject = mol->nextIntegrableObject(j)) {
240	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
241	>	integrableObject = mol->nextIntegrableObject(j)) {
242
243	<	ndf_local += 3;
243	>	ndf_local += 3;
244
245	<	if (integrableObject->isDirectional()) {
246	<	if (integrableObject->isLinear()) {
247	<	ndf_local += 2;
248	<	} else {
249	<	ndf_local += 3;
250	<	}
251	<	}
245	>	if (integrableObject->isDirectional()) {
246	>	if (integrableObject->isLinear()) {
247	>	ndf_local += 2;
248	>	} else {
249	>	ndf_local += 3;
250	>	}
251	>	}
252
253	<	}//end for (integrableObject)
254	<	}// end for (mol)
253	>	}
254	>	}
255
256		// n_constraints is local, so subtract them on each processor
257		ndf_local -= nConstraints_;
#	Line 271 | Line 266 | void SimInfo::calcNdf() {
266		// entire system:
267		ndf_ = ndf_ - 3 - nZconstraint_;
268
269	<	}
269	>	}
270
271	<	void SimInfo::calcNdfRaw() {
271	>	int SimInfo::getFdf() {
272	>	#ifdef IS_MPI
273	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
274	>	#else
275	>	fdf_ = fdf_local;
276	>	#endif
277	>	return fdf_;
278	>	}
279	>
280	>	void SimInfo::calcNdfRaw() {
281		int ndfRaw_local;
282
283		MoleculeIterator i;
284	<	std::vector<StuntDouble*>::iterator j;
284	>	vector<StuntDouble*>::iterator j;
285		Molecule* mol;
286		StuntDouble* integrableObject;
287
#	Line 285 | Line 289 | void SimInfo::calcNdfRaw() {
289		ndfRaw_local = 0;
290
291		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
292	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
293	<	integrableObject = mol->nextIntegrableObject(j)) {
292	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
293	>	integrableObject = mol->nextIntegrableObject(j)) {
294
295	<	ndfRaw_local += 3;
295	>	ndfRaw_local += 3;
296
297	<	if (integrableObject->isDirectional()) {
298	<	if (integrableObject->isLinear()) {
299	<	ndfRaw_local += 2;
300	<	} else {
301	<	ndfRaw_local += 3;
302	<	}
303	<	}
297	>	if (integrableObject->isDirectional()) {
298	>	if (integrableObject->isLinear()) {
299	>	ndfRaw_local += 2;
300	>	} else {
301	>	ndfRaw_local += 3;
302	>	}
303	>	}
304
305	<	}
305	>	}
306		}
307
308		#ifdef IS_MPI
#	Line 306 | Line 310 | void SimInfo::calcNdfRaw() {
310		#else
311		ndfRaw_ = ndfRaw_local;
312		#endif
313	<	}
313	>	}
314
315	<	void SimInfo::calcNdfTrans() {
315	>	void SimInfo::calcNdfTrans() {
316		int ndfTrans_local;
317
318		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 322 | Line 326 | void SimInfo::calcNdfTrans() {
326
327		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
328
329	<	}
329	>	}
330
331	<	void SimInfo::addExcludePairs(Molecule* mol) {
332	<	std::vector<Bond*>::iterator bondIter;
333	<	std::vector<Bend*>::iterator bendIter;
334	<	std::vector<Torsion*>::iterator torsionIter;
331	>	void SimInfo::addInteractionPairs(Molecule* mol) {
332	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
333	>	vector<Bond*>::iterator bondIter;
334	>	vector<Bend*>::iterator bendIter;
335	>	vector<Torsion*>::iterator torsionIter;
336	>	vector<Inversion*>::iterator inversionIter;
337		Bond* bond;
338		Bend* bend;
339		Torsion* torsion;
340	+	Inversion* inversion;
341		int a;
342		int b;
343		int c;
344		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	–	}
345
346	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
347	<	a = bend->getAtomA()->getGlobalIndex();
348	<	b = bend->getAtomB()->getGlobalIndex();
349	<	c = bend->getAtomC()->getGlobalIndex();
346	>	// atomGroups can be used to add special interaction maps between
347	>	// groups of atoms that are in two separate rigid bodies.
348	>	// However, most site-site interactions between two rigid bodies
349	>	// are probably not special, just the ones between the physically
350	>	// bonded atoms.  Interactions *within* a single rigid body should
351	>	// always be excluded.  These are done at the bottom of this
352	>	// function.
353
354	<	exclude_.addPair(a, b);
355	<	exclude_.addPair(a, c);
356	<	exclude_.addPair(b, c);
354	>	map<int, set<int> > atomGroups;
355	>	Molecule::RigidBodyIterator rbIter;
356	>	RigidBody* rb;
357	>	Molecule::IntegrableObjectIterator ii;
358	>	StuntDouble* integrableObject;
359	>
360	>	for (integrableObject = mol->beginIntegrableObject(ii);
361	>	integrableObject != NULL;
362	>	integrableObject = mol->nextIntegrableObject(ii)) {
363	>
364	>	if (integrableObject->isRigidBody()) {
365	>	rb = static_cast<RigidBody*>(integrableObject);
366	>	vector<Atom*> atoms = rb->getAtoms();
367	>	set<int> rigidAtoms;
368	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
369	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
370	>	}
371	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
372	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
373	>	}
374	>	} else {
375	>	set<int> oneAtomSet;
376	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
377	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
378	>	}
379	>	}
380	>
381	>	for (bond= mol->beginBond(bondIter); bond != NULL;
382	>	bond = mol->nextBond(bondIter)) {
383	>
384	>	a = bond->getAtomA()->getGlobalIndex();
385	>	b = bond->getAtomB()->getGlobalIndex();
386	>
387	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
388	>	oneTwoInteractions_.addPair(a, b);
389	>	} else {
390	>	excludedInteractions_.addPair(a, b);
391	>	}
392		}
393
394	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
395	<	a = torsion->getAtomA()->getGlobalIndex();
357	<	b = torsion->getAtomB()->getGlobalIndex();
358	<	c = torsion->getAtomC()->getGlobalIndex();
359	<	d = torsion->getAtomD()->getGlobalIndex();
394	>	for (bend= mol->beginBend(bendIter); bend != NULL;
395	>	bend = mol->nextBend(bendIter)) {
396
397	<	exclude_.addPair(a, b);
398	<	exclude_.addPair(a, c);
399	<	exclude_.addPair(a, d);
400	<	exclude_.addPair(b, c);
401	<	exclude_.addPair(b, d);
402	<	exclude_.addPair(c, d);
397	>	a = bend->getAtomA()->getGlobalIndex();
398	>	b = bend->getAtomB()->getGlobalIndex();
399	>	c = bend->getAtomC()->getGlobalIndex();
400	>
401	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
402	>	oneTwoInteractions_.addPair(a, b);
403	>	oneTwoInteractions_.addPair(b, c);
404	>	} else {
405	>	excludedInteractions_.addPair(a, b);
406	>	excludedInteractions_.addPair(b, c);
407	>	}
408	>
409	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
410	>	oneThreeInteractions_.addPair(a, c);
411	>	} else {
412	>	excludedInteractions_.addPair(a, c);
413	>	}
414		}
415
416	<
417	<	}
416	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
417	>	torsion = mol->nextTorsion(torsionIter)) {
418
419	<	void SimInfo::removeExcludePairs(Molecule* mol) {
420	<	std::vector<Bond*>::iterator bondIter;
421	<	std::vector<Bend*>::iterator bendIter;
422	<	std::vector<Torsion*>::iterator torsionIter;
419	>	a = torsion->getAtomA()->getGlobalIndex();
420	>	b = torsion->getAtomB()->getGlobalIndex();
421	>	c = torsion->getAtomC()->getGlobalIndex();
422	>	d = torsion->getAtomD()->getGlobalIndex();
423	>
424	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
425	>	oneTwoInteractions_.addPair(a, b);
426	>	oneTwoInteractions_.addPair(b, c);
427	>	oneTwoInteractions_.addPair(c, d);
428	>	} else {
429	>	excludedInteractions_.addPair(a, b);
430	>	excludedInteractions_.addPair(b, c);
431	>	excludedInteractions_.addPair(c, d);
432	>	}
433	>
434	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
435	>	oneThreeInteractions_.addPair(a, c);
436	>	oneThreeInteractions_.addPair(b, d);
437	>	} else {
438	>	excludedInteractions_.addPair(a, c);
439	>	excludedInteractions_.addPair(b, d);
440	>	}
441	>
442	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
443	>	oneFourInteractions_.addPair(a, d);
444	>	} else {
445	>	excludedInteractions_.addPair(a, d);
446	>	}
447	>	}
448	>
449	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
450	>	inversion = mol->nextInversion(inversionIter)) {
451	>
452	>	a = inversion->getAtomA()->getGlobalIndex();
453	>	b = inversion->getAtomB()->getGlobalIndex();
454	>	c = inversion->getAtomC()->getGlobalIndex();
455	>	d = inversion->getAtomD()->getGlobalIndex();
456	>
457	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
458	>	oneTwoInteractions_.addPair(a, b);
459	>	oneTwoInteractions_.addPair(a, c);
460	>	oneTwoInteractions_.addPair(a, d);
461	>	} else {
462	>	excludedInteractions_.addPair(a, b);
463	>	excludedInteractions_.addPair(a, c);
464	>	excludedInteractions_.addPair(a, d);
465	>	}
466	>
467	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
468	>	oneThreeInteractions_.addPair(b, c);
469	>	oneThreeInteractions_.addPair(b, d);
470	>	oneThreeInteractions_.addPair(c, d);
471	>	} else {
472	>	excludedInteractions_.addPair(b, c);
473	>	excludedInteractions_.addPair(b, d);
474	>	excludedInteractions_.addPair(c, d);
475	>	}
476	>	}
477	>
478	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
479	>	rb = mol->nextRigidBody(rbIter)) {
480	>	vector<Atom*> atoms = rb->getAtoms();
481	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
482	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
483	>	a = atoms[i]->getGlobalIndex();
484	>	b = atoms[j]->getGlobalIndex();
485	>	excludedInteractions_.addPair(a, b);
486	>	}
487	>	}
488	>	}
489	>
490	>	}
491	>
492	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
493	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
494	>	vector<Bond*>::iterator bondIter;
495	>	vector<Bend*>::iterator bendIter;
496	>	vector<Torsion*>::iterator torsionIter;
497	>	vector<Inversion*>::iterator inversionIter;
498		Bond* bond;
499		Bend* bend;
500		Torsion* torsion;
501	+	Inversion* inversion;
502		int a;
503		int b;
504		int c;
505		int d;
506	+
507	+	map<int, set<int> > atomGroups;
508	+	Molecule::RigidBodyIterator rbIter;
509	+	RigidBody* rb;
510	+	Molecule::IntegrableObjectIterator ii;
511	+	StuntDouble* integrableObject;
512
513	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
514	<	a = bond->getAtomA()->getGlobalIndex();
515	<	b = bond->getAtomB()->getGlobalIndex();
516	<	exclude_.removePair(a, b);
513	>	for (integrableObject = mol->beginIntegrableObject(ii);
514	>	integrableObject != NULL;
515	>	integrableObject = mol->nextIntegrableObject(ii)) {
516	>
517	>	if (integrableObject->isRigidBody()) {
518	>	rb = static_cast<RigidBody*>(integrableObject);
519	>	vector<Atom*> atoms = rb->getAtoms();
520	>	set<int> rigidAtoms;
521	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
522	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
523	>	}
524	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
525	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
526	>	}
527	>	} else {
528	>	set<int> oneAtomSet;
529	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
530	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
531	>	}
532	>	}
533	>
534	>	for (bond= mol->beginBond(bondIter); bond != NULL;
535	>	bond = mol->nextBond(bondIter)) {
536	>
537	>	a = bond->getAtomA()->getGlobalIndex();
538	>	b = bond->getAtomB()->getGlobalIndex();
539	>
540	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
541	>	oneTwoInteractions_.removePair(a, b);
542	>	} else {
543	>	excludedInteractions_.removePair(a, b);
544	>	}
545		}
546
547	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
548	<	a = bend->getAtomA()->getGlobalIndex();
392	<	b = bend->getAtomB()->getGlobalIndex();
393	<	c = bend->getAtomC()->getGlobalIndex();
547	>	for (bend= mol->beginBend(bendIter); bend != NULL;
548	>	bend = mol->nextBend(bendIter)) {
549
550	<	exclude_.removePair(a, b);
551	<	exclude_.removePair(a, c);
552	<	exclude_.removePair(b, c);
550	>	a = bend->getAtomA()->getGlobalIndex();
551	>	b = bend->getAtomB()->getGlobalIndex();
552	>	c = bend->getAtomC()->getGlobalIndex();
553	>
554	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
555	>	oneTwoInteractions_.removePair(a, b);
556	>	oneTwoInteractions_.removePair(b, c);
557	>	} else {
558	>	excludedInteractions_.removePair(a, b);
559	>	excludedInteractions_.removePair(b, c);
560	>	}
561	>
562	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
563	>	oneThreeInteractions_.removePair(a, c);
564	>	} else {
565	>	excludedInteractions_.removePair(a, c);
566	>	}
567		}
568
569	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
570	<	a = torsion->getAtomA()->getGlobalIndex();
402	<	b = torsion->getAtomB()->getGlobalIndex();
403	<	c = torsion->getAtomC()->getGlobalIndex();
404	<	d = torsion->getAtomD()->getGlobalIndex();
569	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
570	>	torsion = mol->nextTorsion(torsionIter)) {
571
572	<	exclude_.removePair(a, b);
573	<	exclude_.removePair(a, c);
574	<	exclude_.removePair(a, d);
575	<	exclude_.removePair(b, c);
576	<	exclude_.removePair(b, d);
577	<	exclude_.removePair(c, d);
572	>	a = torsion->getAtomA()->getGlobalIndex();
573	>	b = torsion->getAtomB()->getGlobalIndex();
574	>	c = torsion->getAtomC()->getGlobalIndex();
575	>	d = torsion->getAtomD()->getGlobalIndex();
576	>
577	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
578	>	oneTwoInteractions_.removePair(a, b);
579	>	oneTwoInteractions_.removePair(b, c);
580	>	oneTwoInteractions_.removePair(c, d);
581	>	} else {
582	>	excludedInteractions_.removePair(a, b);
583	>	excludedInteractions_.removePair(b, c);
584	>	excludedInteractions_.removePair(c, d);
585	>	}
586	>
587	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
588	>	oneThreeInteractions_.removePair(a, c);
589	>	oneThreeInteractions_.removePair(b, d);
590	>	} else {
591	>	excludedInteractions_.removePair(a, c);
592	>	excludedInteractions_.removePair(b, d);
593	>	}
594	>
595	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
596	>	oneFourInteractions_.removePair(a, d);
597	>	} else {
598	>	excludedInteractions_.removePair(a, d);
599	>	}
600		}
601
602	<	}
602	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
603	>	inversion = mol->nextInversion(inversionIter)) {
604
605	+	a = inversion->getAtomA()->getGlobalIndex();
606	+	b = inversion->getAtomB()->getGlobalIndex();
607	+	c = inversion->getAtomC()->getGlobalIndex();
608	+	d = inversion->getAtomD()->getGlobalIndex();
609
610	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
611	<	int curStampId;
610	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
611	>	oneTwoInteractions_.removePair(a, b);
612	>	oneTwoInteractions_.removePair(a, c);
613	>	oneTwoInteractions_.removePair(a, d);
614	>	} else {
615	>	excludedInteractions_.removePair(a, b);
616	>	excludedInteractions_.removePair(a, c);
617	>	excludedInteractions_.removePair(a, d);
618	>	}
619
620	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
621	+	oneThreeInteractions_.removePair(b, c);
622	+	oneThreeInteractions_.removePair(b, d);
623	+	oneThreeInteractions_.removePair(c, d);
624	+	} else {
625	+	excludedInteractions_.removePair(b, c);
626	+	excludedInteractions_.removePair(b, d);
627	+	excludedInteractions_.removePair(c, d);
628	+	}
629	+	}
630	+
631	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
632	+	rb = mol->nextRigidBody(rbIter)) {
633	+	vector<Atom*> atoms = rb->getAtoms();
634	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
635	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
636	+	a = atoms[i]->getGlobalIndex();
637	+	b = atoms[j]->getGlobalIndex();
638	+	excludedInteractions_.removePair(a, b);
639	+	}
640	+	}
641	+	}
642	+
643	+	}
644	+
645	+
646	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
647	+	int curStampId;
648	+
649		//index from 0
650		curStampId = moleculeStamps_.size();
651
652		moleculeStamps_.push_back(molStamp);
653		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
654	<	}
654	>	}
655
427	–	void SimInfo::update() {
656
657	<	setupSimType();
657	>	/**
658	>	* update
659	>	*
660	>	*  Performs the global checks and variable settings after the objects have been
661	>	*  created.
662	>	*
663	>	*/
664	>	void SimInfo::update() {
665	>
666	>	setupSimVariables();
667	>	setupCutoffs();
668	>	setupSwitching();
669	>	setupElectrostatics();
670	>	setupNeighborlists();
671
672		#ifdef IS_MPI
673		setupFortranParallel();
674		#endif
434	–
675		setupFortranSim();
676	+	fortranInitialized_ = true;
677
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	–
678		calcNdf();
679		calcNdfRaw();
680		calcNdfTrans();
681	<
682	<	fortranInitialized_ = true;
683	<	}
457	<
458	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
681	>	}
682	>
683	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
684		SimInfo::MoleculeIterator mi;
685		Molecule* mol;
686		Molecule::AtomIterator ai;
687		Atom* atom;
688	<	std::set<AtomType*> atomTypes;
688	>	set<AtomType*> atomTypes;
689	>
690	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
691	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
692	>	atomTypes.insert(atom->getAtomType());
693	>	}
694	>	}
695	>	return atomTypes;
696	>	}
697
698	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
699	<
700	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
701	<	atomTypes.insert(atom->getAtomType());
698	>	/**
699	>	* setupCutoffs
700	>	*
701	>	* Sets the values of cutoffRadius and cutoffMethod
702	>	*
703	>	* cutoffRadius : realType
704	>	*  If the cutoffRadius was explicitly set, use that value.
705	>	*  If the cutoffRadius was not explicitly set:
706	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
707	>	*      No electrostatic atoms?  Poll the atom types present in the
708	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
709	>	*      Use the maximum suggested value that was found.
710	>	*
711	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
712	>	*      If cutoffMethod was explicitly set, use that choice.
713	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
714	>	*/
715	>	void SimInfo::setupCutoffs() {
716	>
717	>	if (simParams_->haveCutoffRadius()) {
718	>	cutoffRadius_ = simParams_->getCutoffRadius();
719	>	} else {
720	>	if (usesElectrostaticAtoms_) {
721	>	sprintf(painCave.errMsg,
722	>	"SimInfo: No value was set for the cutoffRadius.\n"
723	>	"\tOpenMD will use a default value of 12.0 angstroms"
724	>	"\tfor the cutoffRadius.\n");
725	>	painCave.isFatal = 0;
726	>	painCave.severity = OPENMD_INFO;
727	>	simError();
728	>	cutoffRadius_ = 12.0;
729	>	} else {
730	>	RealType thisCut;
731	>	set<AtomType*>::iterator i;
732	>	set<AtomType*> atomTypes;
733	>	atomTypes = getSimulatedAtomTypes();
734	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
735	>	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
736	>	cutoffRadius_ = max(thisCut, cutoffRadius_);
737		}
738	<
738	>	sprintf(painCave.errMsg,
739	>	"SimInfo: No value was set for the cutoffRadius.\n"
740	>	"\tOpenMD will use %lf angstroms.\n",
741	>	cutoffRadius_);
742	>	painCave.isFatal = 0;
743	>	painCave.severity = OPENMD_INFO;
744	>	simError();
745	>	}
746		}
747
748	<	return atomTypes;
474	<	}
748	>	InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
749
750	<	void SimInfo::setupSimType() {
751	<	std::set<AtomType*>::iterator i;
752	<	std::set<AtomType*> atomTypes;
753	<	atomTypes = getUniqueAtomTypes();
754	<
755	<	int useLennardJones = 0;
756	<	int useElectrostatic = 0;
757	<	int useEAM = 0;
758	<	int useCharge = 0;
759	<	int useDirectional = 0;
760	<	int useDipole = 0;
761	<	int useGayBerne = 0;
762	<	int useSticky = 0;
763	<	int useShape = 0;
764	<	int useFLARB = 0; //it is not in AtomType yet
765	<	int useDirectionalAtom = 0;
766	<	int useElectrostatics = 0;
767	<	//usePBC and useRF are from simParams
768	<	int usePBC = simParams_->getPBC();
769	<	int useRF = simParams_->getUseRF();
770	<
771	<	//loop over all of the atom types
772	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
773	<	useLennardJones |= (*i)->isLennardJones();
774	<	useElectrostatic |= (*i)->isElectrostatic();
775	<	useEAM |= (*i)->isEAM();
776	<	useCharge |= (*i)->isCharge();
777	<	useDirectional |= (*i)->isDirectional();
778	<	useDipole |= (*i)->isDipole();
779	<	useGayBerne |= (*i)->isGayBerne();
506	<	useSticky |= (*i)->isSticky();
507	<	useShape |= (*i)->isShape();
750	>	map<string, CutoffMethod> stringToCutoffMethod;
751	>	stringToCutoffMethod["HARD"] = HARD;
752	>	stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
753	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
754	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
755	>
756	>	if (simParams_->haveCutoffMethod()) {
757	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
758	>	map<string, CutoffMethod>::iterator i;
759	>	i = stringToCutoffMethod.find(cutMeth);
760	>	if (i == stringToCutoffMethod.end()) {
761	>	sprintf(painCave.errMsg,
762	>	"SimInfo: Could not find chosen cutoffMethod %s\n"
763	>	"\tShould be one of: "
764	>	"HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
765	>	cutMeth.c_str());
766	>	painCave.isFatal = 1;
767	>	painCave.severity = OPENMD_ERROR;
768	>	simError();
769	>	} else {
770	>	cutoffMethod_ = i->second;
771	>	}
772	>	} else {
773	>	sprintf(painCave.errMsg,
774	>	"SimInfo: No value was set for the cutoffMethod.\n"
775	>	"\tOpenMD will use SHIFTED_FORCE.\n");
776	>	painCave.isFatal = 0;
777	>	painCave.severity = OPENMD_INFO;
778	>	simError();
779	>	cutoffMethod_ = SHIFTED_FORCE;
780		}
781
782	<	if (useSticky || useDipole || useGayBerne || useShape) {
783	<	useDirectionalAtom = 1;
784	<	}
782	>	InteractionManager::Instance()->setCutoffMethod(cutoffMethod_);
783	>	}
784	>
785	>	/**
786	>	* setupSwitching
787	>	*
788	>	* Sets the values of switchingRadius and
789	>	*  If the switchingRadius was explicitly set, use that value (but check it)
790	>	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
791	>	*/
792	>	void SimInfo::setupSwitching() {
793	>
794	>	if (simParams_->haveSwitchingRadius()) {
795	>	switchingRadius_ = simParams_->getSwitchingRadius();
796	>	if (switchingRadius_ > cutoffRadius_) {
797	>	sprintf(painCave.errMsg,
798	>	"SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
799	>	switchingRadius_, cutoffRadius_);
800	>	painCave.isFatal = 1;
801	>	painCave.severity = OPENMD_ERROR;
802	>	simError();
803	>	}
804	>	} else {
805	>	switchingRadius_ = 0.85 * cutoffRadius_;
806	>	sprintf(painCave.errMsg,
807	>	"SimInfo: No value was set for the switchingRadius.\n"
808	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
809	>	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
810	>	painCave.isFatal = 0;
811	>	painCave.severity = OPENMD_WARNING;
812	>	simError();
813	>	}
814	>
815	>	InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
816
817	<	if (useCharge || useDipole) {
818	<	useElectrostatics = 1;
817	>	SwitchingFunctionType ft;
818	>
819	>	if (simParams_->haveSwitchingFunctionType()) {
820	>	string funcType = simParams_->getSwitchingFunctionType();
821	>	toUpper(funcType);
822	>	if (funcType == "CUBIC") {
823	>	ft = cubic;
824	>	} else {
825	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
826	>	ft = fifth_order_poly;
827	>	} else {
828	>	// throw error
829	>	sprintf( painCave.errMsg,
830	>	"SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
831	>	"\tswitchingFunctionType must be one of: "
832	>	"\"cubic\" or \"fifth_order_polynomial\".",
833	>	funcType.c_str() );
834	>	painCave.isFatal = 1;
835	>	painCave.severity = OPENMD_ERROR;
836	>	simError();
837	>	}
838	>	}
839		}
840
841	<	#ifdef IS_MPI
842	<	int temp;
841	>	InteractionManager::Instance()->setSwitchingFunctionType(ft);
842	>	}
843
844	<	temp = usePBC;
845	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
844	>	/**
845	>	* setupSkinThickness
846	>	*
847	>	*  If the skinThickness was explicitly set, use that value (but check it)
848	>	*  If the skinThickness was not explicitly set: use 1.0 angstroms
849	>	*/
850	>	void SimInfo::setupSkinThickness() {
851	>	if (simParams_->haveSkinThickness()) {
852	>	skinThickness_ = simParams_->getSkinThickness();
853	>	} else {
854	>	skinThickness_ = 1.0;
855	>	sprintf(painCave.errMsg,
856	>	"SimInfo Warning: No value was set for the skinThickness.\n"
857	>	"\tOpenMD will use a default value of %f Angstroms\n"
858	>	"\tfor this simulation\n", skinThickness_);
859	>	painCave.isFatal = 0;
860	>	simError();
861	>	}
862	>	}
863
864	<	temp = useDirectionalAtom;
865	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
864	>	void SimInfo::setupSimType() {
865	>	set<AtomType*>::iterator i;
866	>	set<AtomType*> atomTypes;
867	>	atomTypes = getSimulatedAtomTypes();
868
869	<	temp = useLennardJones;
528	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
869	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
870
871	<	temp = useElectrostatics;
872	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
871	>	int usesElectrostatic = 0;
872	>	int usesMetallic = 0;
873	>	int usesDirectional = 0;
874	>	//loop over all of the atom types
875	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
876	>	usesElectrostatic |= (*i)->isElectrostatic();
877	>	usesMetallic |= (*i)->isMetal();
878	>	usesDirectional |= (*i)->isDirectional();
879	>	}
880
881	<	temp = useCharge;
882	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
881	>	#ifdef IS_MPI
882	>	int temp;
883	>	temp = usesDirectional;
884	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
885
886	<	temp = useDipole;
887	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
886	>	temp = usesMetallic;
887	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
888
889	<	temp = useSticky;
890	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
889	>	temp = usesElectrostatic;
890	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
891	>	#endif
892	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
893	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
894	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
895	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
896	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
897	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
898	>	}
899
900	<	temp = useGayBerne;
901	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
902	<
903	<	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);
900	>	void SimInfo::setupFortranSim() {
901	>	int isError;
902	>	int nExclude, nOneTwo, nOneThree, nOneFour;
903	>	vector<int> fortranGlobalGroupMembership;
904
905	<	#endif
905	>	notifyFortranSkinThickness(&skinThickness_);
906
907	<	fInfo_.SIM_uses_PBC = usePBC;
908	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
909	<	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	<	}
907	>	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
908	>	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
909	>	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
910
589	–	}
590	–
591	–	void SimInfo::setupFortranSim() {
592	–	int isError;
593	–	int nExclude;
594	–	std::vector<int> fortranGlobalGroupMembership;
595	–
596	–	nExclude = exclude_.getSize();
911		isError = 0;
912
913		//globalGroupMembership_ is filled by SimCreator
914		for (int i = 0; i < nGlobalAtoms_; i++) {
915	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
915	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
916		}
917
918		//calculate mass ratio of cutoff group
919	<	std::vector<double> mfact;
919	>	vector<RealType> mfact;
920		SimInfo::MoleculeIterator mi;
921		Molecule* mol;
922		Molecule::CutoffGroupIterator ci;
923		CutoffGroup* cg;
924		Molecule::AtomIterator ai;
925		Atom* atom;
926	<	double totalMass;
926	>	RealType totalMass;
927
928		//to avoid memory reallocation, reserve enough space for mfact
929		mfact.reserve(getNCutoffGroups());
930
931		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
932	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
932	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
933
934	<	totalMass = cg->getMass();
935	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
936	<	mfact.push_back(atom->getMass()/totalMass);
937	<	}
938	<
939	<	}
934	>	totalMass = cg->getMass();
935	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
936	>	// Check for massless groups - set mfact to 1 if true
937	>	if (totalMass != 0)
938	>	mfact.push_back(atom->getMass()/totalMass);
939	>	else
940	>	mfact.push_back( 1.0 );
941	>	}
942	>	}
943		}
944
945		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
946	<	std::vector<int> identArray;
946	>	vector<int> identArray;
947
948		//to avoid memory reallocation, reserve enough space identArray
949		identArray.reserve(getNAtoms());
950
951		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
952	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
953	<	identArray.push_back(atom->getIdent());
954	<	}
952	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
953	>	identArray.push_back(atom->getIdent());
954	>	}
955		}
956
957		//fill molMembershipArray
958		//molMembershipArray is filled by SimCreator
959	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
959	>	vector<int> molMembershipArray(nGlobalAtoms_);
960		for (int i = 0; i < nGlobalAtoms_; i++) {
961	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
961	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
962		}
963
964		//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);
965
966	<	if( isError ){
966	>	nExclude = excludedInteractions_.getSize();
967	>	nOneTwo = oneTwoInteractions_.getSize();
968	>	nOneThree = oneThreeInteractions_.getSize();
969	>	nOneFour = oneFourInteractions_.getSize();
970
971	<	sprintf( painCave.errMsg,
972	<	"There was an error setting the simulation information in fortran.\n" );
973	<	painCave.isFatal = 1;
974	<	painCave.severity = OOPSE_ERROR;
664	<	simError();
665	<	}
971	>	int* excludeList = excludedInteractions_.getPairList();
972	>	int* oneTwoList = oneTwoInteractions_.getPairList();
973	>	int* oneThreeList = oneThreeInteractions_.getPairList();
974	>	int* oneFourList = oneFourInteractions_.getPairList();
975
976	<	#ifdef IS_MPI
976	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
977	>	&nExclude, excludeList,
978	>	&nOneTwo, oneTwoList,
979	>	&nOneThree, oneThreeList,
980	>	&nOneFour, oneFourList,
981	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
982	>	&fortranGlobalGroupMembership[0], &isError);
983	>
984	>	if( isError ){
985	>
986	>	sprintf( painCave.errMsg,
987	>	"There was an error setting the simulation information in fortran.\n" );
988	>	painCave.isFatal = 1;
989	>	painCave.severity = OPENMD_ERROR;
990	>	simError();
991	>	}
992	>
993	>
994		sprintf( checkPointMsg,
995	<	"succesfully sent the simulation information to fortran.\n");
996	<	MPIcheckPoint();
997	<	#endif // is_mpi
998	<	}
995	>	"succesfully sent the simulation information to fortran.\n");
996	>
997	>	errorCheckPoint();
998	>
999	>	// Setup number of neighbors in neighbor list if present
1000	>	if (simParams_->haveNeighborListNeighbors()) {
1001	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
1002	>	setNeighbors(&nlistNeighbors);
1003	>	}
1004	>
1005
1006	+	}
1007
1008	<	#ifdef IS_MPI
1009	<	void SimInfo::setupFortranParallel() {
1010	<
1008	>
1009	>	void SimInfo::setupFortranParallel() {
1010	>	#ifdef IS_MPI
1011		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1012	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1013	<	std::vector<int> localToGlobalCutoffGroupIndex;
1012	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1013	>	vector<int> localToGlobalCutoffGroupIndex;
1014		SimInfo::MoleculeIterator mi;
1015		Molecule::AtomIterator ai;
1016		Molecule::CutoffGroupIterator ci;
#	Line 689 | Line 1022 | void SimInfo::setupFortranParallel() {
1022
1023		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1024
1025	<	//local index(index in DataStorge) of atom is important
1026	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1027	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1028	<	}
1025	>	//local index(index in DataStorge) of atom is important
1026	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1027	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1028	>	}
1029
1030	<	//local index of cutoff group is trivial, it only depends on the order of travesing
1031	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1032	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1033	<	}
1030	>	//local index of cutoff group is trivial, it only depends on the order of travesing
1031	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1032	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1033	>	}
1034
1035		}
1036
#	Line 717 | Line 1050 | void SimInfo::setupFortranParallel() {
1050		&localToGlobalCutoffGroupIndex[0], &isError);
1051
1052		if (isError) {
1053	<	sprintf(painCave.errMsg,
1054	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1055	<	painCave.isFatal = 1;
1056	<	simError();
1053	>	sprintf(painCave.errMsg,
1054	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1055	>	painCave.isFatal = 1;
1056	>	simError();
1057		}
1058
1059		sprintf(checkPointMsg, " mpiRefresh successful.\n");
1060	<	MPIcheckPoint();
1060	>	errorCheckPoint();
1061
729	–
730	–	}
731	–
1062		#endif
1063	+	}
1064
734	–	double SimInfo::calcMaxCutoffRadius() {
1065
1066	+	void SimInfo::setupSwitchingFunction() {
1067
1068	<	std::set<AtomType*> atomTypes;
738	<	std::set<AtomType*>::iterator i;
739	<	std::vector<double> cutoffRadius;
1068	>	}
1069
1070	<	//get the unique atom types
742	<	atomTypes = getUniqueAtomTypes();
1070	>	void SimInfo::setupAccumulateBoxDipole() {
1071
1072	<	//query the max cutoff radius among these atom types
1073	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
1074	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
1075	<	}
1072	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1073	>	if ( simParams_->haveAccumulateBoxDipole() )
1074	>	if ( simParams_->getAccumulateBoxDipole() ) {
1075	>	calcBoxDipole_ = true;
1076	>	}
1077
1078	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
750	<	#ifdef IS_MPI
751	<	//pick the max cutoff radius among the processors
752	<	#endif
1078	>	}
1079
1080	<	return maxCutoffRadius;
1081	<	}
1082	<
1083	<	void SimInfo::setupCutoff() {
1084	<	double rcut_;  //cutoff radius
759	<	double rsw_; //switching radius
760	<
761	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
762	<
763	<	if (!simParams_->haveRcut()){
764	<	sprintf(painCave.errMsg,
765	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
766	<	"\tOOPSE will use a default value of 15.0 angstroms"
767	<	"\tfor the cutoffRadius.\n");
768	<	painCave.isFatal = 0;
769	<	simError();
770	<	rcut_ = 15.0;
771	<	} else{
772	<	rcut_ = simParams_->getRcut();
773	<	}
774	<
775	<	if (!simParams_->haveRsw()){
776	<	sprintf(painCave.errMsg,
777	<	"SimCreator Warning: No value was set for switchingRadius.\n"
778	<	"\tOOPSE will use a default value of\n"
779	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
780	<	painCave.isFatal = 0;
781	<	simError();
782	<	rsw_ = 0.95 * rcut_;
783	<	} else{
784	<	rsw_ = simParams_->getRsw();
785	<	}
786	<
787	<	} else {
788	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
789	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
790	<
791	<	if (simParams_->haveRcut()) {
792	<	rcut_ = simParams_->getRcut();
793	<	} else {
794	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
795	<	rcut_ = calcMaxCutoffRadius();
796	<	}
797	<
798	<	if (simParams_->haveRsw()) {
799	<	rsw_  = simParams_->getRsw();
800	<	} else {
801	<	rsw_ = rcut_;
802	<	}
803	<
804	<	}
805	<
806	<	double rnblist = rcut_ + 1; // skin of neighbor list
807	<
808	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
809	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
810	<	}
811	<
812	<	void SimInfo::addProperty(GenericData* genData) {
813	<	properties_.addProperty(genData);
814	<	}
815	<
816	<	void SimInfo::removeProperty(const std::string& propName) {
1080	>	void SimInfo::addProperty(GenericData* genData) {
1081	>	properties_.addProperty(genData);
1082	>	}
1083	>
1084	>	void SimInfo::removeProperty(const string& propName) {
1085		properties_.removeProperty(propName);
1086	<	}
1086	>	}
1087
1088	<	void SimInfo::clearProperties() {
1088	>	void SimInfo::clearProperties() {
1089		properties_.clearProperties();
1090	<	}
1090	>	}
1091
1092	<	std::vector<std::string> SimInfo::getPropertyNames() {
1092	>	vector<string> SimInfo::getPropertyNames() {
1093		return properties_.getPropertyNames();
1094	<	}
1094	>	}
1095
1096	<	std::vector<GenericData*> SimInfo::getProperties() {
1096	>	vector<GenericData*> SimInfo::getProperties() {
1097		return properties_.getProperties();
1098	<	}
1098	>	}
1099
1100	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1100	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1101		return properties_.getPropertyByName(propName);
1102	<	}
1102	>	}
1103
1104	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1104	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1105	>	if (sman_ == sman) {
1106	>	return;
1107	>	}
1108	>	delete sman_;
1109		sman_ = sman;
1110
1111		Molecule* mol;
#	Line 845 | Line 1117 | void SimInfo::setSnapshotManager(SnapshotManager* sman
1117
1118		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1119
1120	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1121	<	atom->setSnapshotManager(sman_);
1122	<	}
1120	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1121	>	atom->setSnapshotManager(sman_);
1122	>	}
1123
1124	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1125	<	rb->setSnapshotManager(sman_);
1126	<	}
1124	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1125	>	rb->setSnapshotManager(sman_);
1126	>	}
1127		}
1128
1129	<	}
1129	>	}
1130
1131	<	Vector3d SimInfo::getComVel(){
1131	>	Vector3d SimInfo::getComVel(){
1132		SimInfo::MoleculeIterator i;
1133		Molecule* mol;
1134
1135		Vector3d comVel(0.0);
1136	<	double totalMass = 0.0;
1136	>	RealType totalMass = 0.0;
1137
1138
1139		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1140	<	double mass = mol->getMass();
1141	<	totalMass += mass;
1142	<	comVel += mass * mol->getComVel();
1140	>	RealType mass = mol->getMass();
1141	>	totalMass += mass;
1142	>	comVel += mass * mol->getComVel();
1143		}
1144
1145		#ifdef IS_MPI
1146	<	double tmpMass = totalMass;
1146	>	RealType tmpMass = totalMass;
1147		Vector3d tmpComVel(comVel);
1148	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1149	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1148	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1149	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1150		#endif
1151
1152		comVel /= totalMass;
1153
1154		return comVel;
1155	<	}
1155	>	}
1156
1157	<	Vector3d SimInfo::getCom(){
1157	>	Vector3d SimInfo::getCom(){
1158		SimInfo::MoleculeIterator i;
1159		Molecule* mol;
1160
1161		Vector3d com(0.0);
1162	<	double totalMass = 0.0;
1162	>	RealType totalMass = 0.0;
1163
1164		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1165	<	double mass = mol->getMass();
1166	<	totalMass += mass;
1167	<	com += mass * mol->getCom();
1165	>	RealType mass = mol->getMass();
1166	>	totalMass += mass;
1167	>	com += mass * mol->getCom();
1168		}
1169
1170		#ifdef IS_MPI
1171	<	double tmpMass = totalMass;
1171	>	RealType tmpMass = totalMass;
1172		Vector3d tmpCom(com);
1173	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1174	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1173	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1174	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1175		#endif
1176
1177		com /= totalMass;
1178
1179		return com;
1180
1181	<	}
1181	>	}
1182
1183	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1183	>	ostream& operator <<(ostream& o, SimInfo& info) {
1184
1185		return o;
1186	<	}
1186	>	}
1187	>
1188	>
1189	>	/*
1190	>	Returns center of mass and center of mass velocity in one function call.
1191	>	*/
1192	>
1193	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1194	>	SimInfo::MoleculeIterator i;
1195	>	Molecule* mol;
1196	>
1197	>
1198	>	RealType totalMass = 0.0;
1199	>
1200
1201	<	}//end namespace oopse
1201	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1202	>	RealType mass = mol->getMass();
1203	>	totalMass += mass;
1204	>	com += mass * mol->getCom();
1205	>	comVel += mass * mol->getComVel();
1206	>	}
1207	>
1208	>	#ifdef IS_MPI
1209	>	RealType tmpMass = totalMass;
1210	>	Vector3d tmpCom(com);
1211	>	Vector3d tmpComVel(comVel);
1212	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1213	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1214	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1215	>	#endif
1216	>
1217	>	com /= totalMass;
1218	>	comVel /= totalMass;
1219	>	}
1220	>
1221	>	/*
1222	>	Return intertia tensor for entire system and angular momentum Vector.
1223
1224	+
1225	+	[  Ixx -Ixy  -Ixz ]
1226	+	J =| -Iyx  Iyy  -Iyz |
1227	+	[ -Izx -Iyz   Izz ]
1228	+	*/
1229	+
1230	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1231	+
1232	+
1233	+	RealType xx = 0.0;
1234	+	RealType yy = 0.0;
1235	+	RealType zz = 0.0;
1236	+	RealType xy = 0.0;
1237	+	RealType xz = 0.0;
1238	+	RealType yz = 0.0;
1239	+	Vector3d com(0.0);
1240	+	Vector3d comVel(0.0);
1241	+
1242	+	getComAll(com, comVel);
1243	+
1244	+	SimInfo::MoleculeIterator i;
1245	+	Molecule* mol;
1246	+
1247	+	Vector3d thisq(0.0);
1248	+	Vector3d thisv(0.0);
1249	+
1250	+	RealType thisMass = 0.0;
1251	+
1252	+
1253	+
1254	+
1255	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1256	+
1257	+	thisq = mol->getCom()-com;
1258	+	thisv = mol->getComVel()-comVel;
1259	+	thisMass = mol->getMass();
1260	+	// Compute moment of intertia coefficients.
1261	+	xx += thisq[0]*thisq[0]*thisMass;
1262	+	yy += thisq[1]*thisq[1]*thisMass;
1263	+	zz += thisq[2]*thisq[2]*thisMass;
1264	+
1265	+	// compute products of intertia
1266	+	xy += thisq[0]*thisq[1]*thisMass;
1267	+	xz += thisq[0]*thisq[2]*thisMass;
1268	+	yz += thisq[1]*thisq[2]*thisMass;
1269	+
1270	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1271	+
1272	+	}
1273	+
1274	+
1275	+	inertiaTensor(0,0) = yy + zz;
1276	+	inertiaTensor(0,1) = -xy;
1277	+	inertiaTensor(0,2) = -xz;
1278	+	inertiaTensor(1,0) = -xy;
1279	+	inertiaTensor(1,1) = xx + zz;
1280	+	inertiaTensor(1,2) = -yz;
1281	+	inertiaTensor(2,0) = -xz;
1282	+	inertiaTensor(2,1) = -yz;
1283	+	inertiaTensor(2,2) = xx + yy;
1284	+
1285	+	#ifdef IS_MPI
1286	+	Mat3x3d tmpI(inertiaTensor);
1287	+	Vector3d tmpAngMom;
1288	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1289	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1290	+	#endif
1291	+
1292	+	return;
1293	+	}
1294	+
1295	+	//Returns the angular momentum of the system
1296	+	Vector3d SimInfo::getAngularMomentum(){
1297	+
1298	+	Vector3d com(0.0);
1299	+	Vector3d comVel(0.0);
1300	+	Vector3d angularMomentum(0.0);
1301	+
1302	+	getComAll(com,comVel);
1303	+
1304	+	SimInfo::MoleculeIterator i;
1305	+	Molecule* mol;
1306	+
1307	+	Vector3d thisr(0.0);
1308	+	Vector3d thisp(0.0);
1309	+
1310	+	RealType thisMass;
1311	+
1312	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1313	+	thisMass = mol->getMass();
1314	+	thisr = mol->getCom()-com;
1315	+	thisp = (mol->getComVel()-comVel)*thisMass;
1316	+
1317	+	angularMomentum += cross( thisr, thisp );
1318	+
1319	+	}
1320	+
1321	+	#ifdef IS_MPI
1322	+	Vector3d tmpAngMom;
1323	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1324	+	#endif
1325	+
1326	+	return angularMomentum;
1327	+	}
1328	+
1329	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1330	+	return IOIndexToIntegrableObject.at(index);
1331	+	}
1332	+
1333	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1334	+	IOIndexToIntegrableObject= v;
1335	+	}
1336	+
1337	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1338	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1339	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1340	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1341	+	*/
1342	+	void SimInfo::getGyrationalVolume(RealType &volume){
1343	+	Mat3x3d intTensor;
1344	+	RealType det;
1345	+	Vector3d dummyAngMom;
1346	+	RealType sysconstants;
1347	+	RealType geomCnst;
1348	+
1349	+	geomCnst = 3.0/2.0;
1350	+	/* Get the inertial tensor and angular momentum for free*/
1351	+	getInertiaTensor(intTensor,dummyAngMom);
1352	+
1353	+	det = intTensor.determinant();
1354	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1355	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1356	+	return;
1357	+	}
1358	+
1359	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1360	+	Mat3x3d intTensor;
1361	+	Vector3d dummyAngMom;
1362	+	RealType sysconstants;
1363	+	RealType geomCnst;
1364	+
1365	+	geomCnst = 3.0/2.0;
1366	+	/* Get the inertial tensor and angular momentum for free*/
1367	+	getInertiaTensor(intTensor,dummyAngMom);
1368	+
1369	+	detI = intTensor.determinant();
1370	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1371	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1372	+	return;
1373	+	}
1374	+	/*
1375	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1376	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1377	+	sdByGlobalIndex_ = v;
1378	+	}
1379	+
1380	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1381	+	//assert(index < nAtoms_ + nRigidBodies_);
1382	+	return sdByGlobalIndex_.at(index);
1383	+	}
1384	+	*/
1385	+	int SimInfo::getNGlobalConstraints() {
1386	+	int nGlobalConstraints;
1387	+	#ifdef IS_MPI
1388	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1389	+	MPI_COMM_WORLD);
1390	+	#else
1391	+	nGlobalConstraints =  nConstraints_;
1392	+	#endif
1393	+	return nGlobalConstraints;
1394	+	}
1395	+
1396	+	}//end namespace OpenMD
1397	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 316 by tim, Fri Feb 11 22:41:02 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC

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