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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1779 by gezelter, Mon Aug 20 17:51:39 2012 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 48 | Line 49
49
50		#include <algorithm>
51		#include <set>
52	+	#include <map>
53
54		#include "brains/SimInfo.hpp"
55		#include "math/Vector3.hpp"
56		#include "primitives/Molecule.hpp"
57	<	#include "UseTheForce/doForces_interface.h"
56	<	#include "UseTheForce/notifyCutoffs_interface.h"
57	>	#include "primitives/StuntDouble.hpp"
58		#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60		#include "selection/SelectionManager.hpp"
61	<
61	>	#include "io/ForceFieldOptions.hpp"
62	>	#include "brains/ForceField.hpp"
63	>	#include "nonbonded/SwitchingFunction.hpp"
64		#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
64	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68	<	namespace oopse {
69	<
70	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
71	<	ForceField* ff, Globals* simParams) :
72	<	forceField_(ff), simParams_(simParams),
73	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
77	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
78	<	sman_(NULL), fortranInitialized_(false) {
79	<
80	<
79	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
68	>	using namespace std;
69	>	namespace OpenMD {
70	>
71	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72	>	forceField_(ff), simParams_(simParams),
73	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0),
76	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79	>	calcBoxDipole_(false), useAtomicVirial_(true) {
80	>
81		MoleculeStamp* molStamp;
82		int nMolWithSameStamp;
83		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
84	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
85		CutoffGroupStamp* cgStamp;
86		RigidBodyStamp* rbStamp;
87		int nRigidAtoms = 0;
88
89	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
90	<	molStamp = i->first;
91	<	nMolWithSameStamp = i->second;
92	<
93	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
94	<
95	<	//calculate atoms in molecules
96	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
97	<
98	<
99	<	//calculate atoms in cutoff groups
100	<	int nAtomsInGroups = 0;
101	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
102	<
103	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
104	<	cgStamp = molStamp->getCutoffGroup(j);
105	<	nAtomsInGroups += cgStamp->getNMembers();
106	<	}
107	<
108	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
109	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
110	<
111	<	//calculate atoms in rigid bodies
112	<	int nAtomsInRigidBodies = 0;
113	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
114	<
115	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
116	<	rbStamp = molStamp->getRigidBody(j);
117	<	nAtomsInRigidBodies += rbStamp->getNMembers();
118	<	}
119	<
120	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
121	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
122	<
89	>	vector<Component*> components = simParams->getComponents();
90	>
91	>	for (vector<Component*>::iterator i = components.begin();
92	>	i !=components.end(); ++i) {
93	>	molStamp = (*i)->getMoleculeStamp();
94	>	nMolWithSameStamp = (*i)->getNMol();
95	>
96	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
97	>
98	>	//calculate atoms in molecules
99	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
100	>
101	>	//calculate atoms in cutoff groups
102	>	int nAtomsInGroups = 0;
103	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
104	>
105	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
106	>	cgStamp = molStamp->getCutoffGroupStamp(j);
107	>	nAtomsInGroups += cgStamp->getNMembers();
108	>	}
109	>
110	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
111	>
112	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
113	>
114	>	//calculate atoms in rigid bodies
115	>	int nAtomsInRigidBodies = 0;
116	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
117	>
118	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
119	>	rbStamp = molStamp->getRigidBodyStamp(j);
120	>	nAtomsInRigidBodies += rbStamp->getNMembers();
121	>	}
122	>
123	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
124	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
125	>
126		}
127	+
128	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
129	+	//group therefore the total number of cutoff groups in the system is
130	+	//equal to the total number of atoms minus number of atoms belong to
131	+	//cutoff group defined in meta-data file plus the number of cutoff
132	+	//groups defined in meta-data file
133
124	–	//every free atom (atom does not belong to cutoff groups) is a cutoff group
125	–	//therefore the total number of cutoff groups in the system is equal to
126	–	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
127	–	//file plus the number of cutoff groups defined in meta-data file
134		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
135	<
136	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
137	<	//therefore the total number of  integrable objects in the system is equal to
138	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
139	<	//file plus the number of  rigid bodies defined in meta-data file
140	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
141	<
135	>
136	>	//every free atom (atom does not belong to rigid bodies) is an
137	>	//integrable object therefore the total number of integrable objects
138	>	//in the system is equal to the total number of atoms minus number of
139	>	//atoms belong to rigid body defined in meta-data file plus the number
140	>	//of rigid bodies defined in meta-data file
141	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
142	>	+ nGlobalRigidBodies_;
143	>
144		nGlobalMols_ = molStampIds_.size();
137	–
138	–	#ifdef IS_MPI
145		molToProcMap_.resize(nGlobalMols_);
146	<	#endif
147	<
148	<	}
149	<
144	<	SimInfo::~SimInfo() {
145	<	std::map<int, Molecule*>::iterator i;
146	>	}
147	>
148	>	SimInfo::~SimInfo() {
149	>	map<int, Molecule*>::iterator i;
150		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
151	<	delete i->second;
151	>	delete i->second;
152		}
153		molecules_.clear();
154	<
151	<	MemoryUtils::deletePointers(moleculeStamps_);
152	<
154	>
155		delete sman_;
156		delete simParams_;
157		delete forceField_;
158	<	}
158	>	}
159
158	–	int SimInfo::getNGlobalConstraints() {
159	–	int nGlobalConstraints;
160	–	#ifdef IS_MPI
161	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
162	–	MPI_COMM_WORLD);
163	–	#else
164	–	nGlobalConstraints =  nConstraints_;
165	–	#endif
166	–	return nGlobalConstraints;
167	–	}
160
161	<	bool SimInfo::addMolecule(Molecule* mol) {
161	>	bool SimInfo::addMolecule(Molecule* mol) {
162		MoleculeIterator i;
163	<
163	>
164		i = molecules_.find(mol->getGlobalIndex());
165		if (i == molecules_.end() ) {
166	<
167	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
168	<
169	<	nAtoms_ += mol->getNAtoms();
170	<	nBonds_ += mol->getNBonds();
171	<	nBends_ += mol->getNBends();
172	<	nTorsions_ += mol->getNTorsions();
173	<	nRigidBodies_ += mol->getNRigidBodies();
174	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
175	<	nCutoffGroups_ += mol->getNCutoffGroups();
176	<	nConstraints_ += mol->getNConstraintPairs();
177	<
178	<	addExcludePairs(mol);
179	<
180	<	return true;
181	<	} else {
182	<	return false;
166	>
167	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
168	>
169	>	nAtoms_ += mol->getNAtoms();
170	>	nBonds_ += mol->getNBonds();
171	>	nBends_ += mol->getNBends();
172	>	nTorsions_ += mol->getNTorsions();
173	>	nInversions_ += mol->getNInversions();
174	>	nRigidBodies_ += mol->getNRigidBodies();
175	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
176	>	nCutoffGroups_ += mol->getNCutoffGroups();
177	>	nConstraints_ += mol->getNConstraintPairs();
178	>
179	>	addInteractionPairs(mol);
180	>
181	>	return true;
182	>	} else {
183	>	return false;
184		}
185	<	}
186	<
187	<	bool SimInfo::removeMolecule(Molecule* mol) {
185	>	}
186	>
187	>	bool SimInfo::removeMolecule(Molecule* mol) {
188		MoleculeIterator i;
189		i = molecules_.find(mol->getGlobalIndex());
190
191		if (i != molecules_.end() ) {
192
193	<	assert(mol == i->second);
193	>	assert(mol == i->second);
194
195	<	nAtoms_ -= mol->getNAtoms();
196	<	nBonds_ -= mol->getNBonds();
197	<	nBends_ -= mol->getNBends();
198	<	nTorsions_ -= mol->getNTorsions();
199	<	nRigidBodies_ -= mol->getNRigidBodies();
200	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
201	<	nCutoffGroups_ -= mol->getNCutoffGroups();
202	<	nConstraints_ -= mol->getNConstraintPairs();
195	>	nAtoms_ -= mol->getNAtoms();
196	>	nBonds_ -= mol->getNBonds();
197	>	nBends_ -= mol->getNBends();
198	>	nTorsions_ -= mol->getNTorsions();
199	>	nInversions_ -= mol->getNInversions();
200	>	nRigidBodies_ -= mol->getNRigidBodies();
201	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
202	>	nCutoffGroups_ -= mol->getNCutoffGroups();
203	>	nConstraints_ -= mol->getNConstraintPairs();
204
205	<	removeExcludePairs(mol);
206	<	molecules_.erase(mol->getGlobalIndex());
205	>	removeInteractionPairs(mol);
206	>	molecules_.erase(mol->getGlobalIndex());
207
208	<	delete mol;
208	>	delete mol;
209
210	<	return true;
210	>	return true;
211		} else {
212	<	return false;
212	>	return false;
213		}
214	+	}
215
221	–
222	–	}
223	–
216
217	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
217	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
218		i = molecules_.begin();
219		return i == molecules_.end() ? NULL : i->second;
220	<	}
220	>	}
221
222	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
222	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
223		++i;
224		return i == molecules_.end() ? NULL : i->second;
225	<	}
225	>	}
226
227
228	<	void SimInfo::calcNdf() {
229	<	int ndf_local;
228	>	void SimInfo::calcNdf() {
229	>	int ndf_local, nfq_local;
230		MoleculeIterator i;
231	<	std::vector<StuntDouble*>::iterator j;
231	>	vector<StuntDouble*>::iterator j;
232	>	vector<Atom*>::iterator k;
233	>
234		Molecule* mol;
235	<	StuntDouble* integrableObject;
235	>	StuntDouble* sd;
236	>	Atom* atom;
237
238		ndf_local = 0;
239	+	nfq_local = 0;
240
241		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
246	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
247	–	integrableObject = mol->nextIntegrableObject(j)) {
242
243	<	ndf_local += 3;
243	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
244	>	sd = mol->nextIntegrableObject(j)) {
245
246	<	if (integrableObject->isDirectional()) {
247	<	if (integrableObject->isLinear()) {
248	<	ndf_local += 2;
249	<	} else {
250	<	ndf_local += 3;
251	<	}
252	<	}
253	<
254	<	}//end for (integrableObject)
255	<	}// end for (mol)
246	>	ndf_local += 3;
247	>
248	>	if (sd->isDirectional()) {
249	>	if (sd->isLinear()) {
250	>	ndf_local += 2;
251	>	} else {
252	>	ndf_local += 3;
253	>	}
254	>	}
255	>	}
256	>
257	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
258	>	atom = mol->nextFluctuatingCharge(k)) {
259	>	if (atom->isFluctuatingCharge()) {
260	>	nfq_local++;
261	>	}
262	>	}
263	>	}
264
265	+	ndfLocal_ = ndf_local;
266	+
267		// n_constraints is local, so subtract them on each processor
268		ndf_local -= nConstraints_;
269
270		#ifdef IS_MPI
271		MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
272	+	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
273		#else
274		ndf_ = ndf_local;
275	+	nGlobalFluctuatingCharges_ = nfq_local;
276		#endif
277
278		// nZconstraints_ is global, as are the 3 COM translations for the
279		// entire system:
280		ndf_ = ndf_ - 3 - nZconstraint_;
281
282	<	}
282	>	}
283
284	<	void SimInfo::calcNdfRaw() {
284	>	int SimInfo::getFdf() {
285	>	#ifdef IS_MPI
286	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
287	>	#else
288	>	fdf_ = fdf_local;
289	>	#endif
290	>	return fdf_;
291	>	}
292	>
293	>	unsigned int SimInfo::getNLocalCutoffGroups(){
294	>	int nLocalCutoffAtoms = 0;
295	>	Molecule* mol;
296	>	MoleculeIterator mi;
297	>	CutoffGroup* cg;
298	>	Molecule::CutoffGroupIterator ci;
299	>
300	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
301	>
302	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
303	>	cg = mol->nextCutoffGroup(ci)) {
304	>	nLocalCutoffAtoms += cg->getNumAtom();
305	>
306	>	}
307	>	}
308	>
309	>	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
310	>	}
311	>
312	>	void SimInfo::calcNdfRaw() {
313		int ndfRaw_local;
314
315		MoleculeIterator i;
316	<	std::vector<StuntDouble*>::iterator j;
316	>	vector<StuntDouble*>::iterator j;
317		Molecule* mol;
318	<	StuntDouble* integrableObject;
318	>	StuntDouble* sd;
319
320		// Raw degrees of freedom that we have to set
321		ndfRaw_local = 0;
322
323		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
289	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
290	–	integrableObject = mol->nextIntegrableObject(j)) {
324
325	<	ndfRaw_local += 3;
325	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
326	>	sd = mol->nextIntegrableObject(j)) {
327
328	<	if (integrableObject->isDirectional()) {
329	<	if (integrableObject->isLinear()) {
330	<	ndfRaw_local += 2;
331	<	} else {
332	<	ndfRaw_local += 3;
333	<	}
334	<	}
328	>	ndfRaw_local += 3;
329	>
330	>	if (sd->isDirectional()) {
331	>	if (sd->isLinear()) {
332	>	ndfRaw_local += 2;
333	>	} else {
334	>	ndfRaw_local += 3;
335	>	}
336	>	}
337
338	<	}
338	>	}
339		}
340
341		#ifdef IS_MPI
#	Line 307 | Line 343 | void SimInfo::calcNdfRaw() {
343		#else
344		ndfRaw_ = ndfRaw_local;
345		#endif
346	<	}
346	>	}
347
348	<	void SimInfo::calcNdfTrans() {
348	>	void SimInfo::calcNdfTrans() {
349		int ndfTrans_local;
350
351		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 323 | Line 359 | void SimInfo::calcNdfTrans() {
359
360		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
361
362	<	}
362	>	}
363
364	<	void SimInfo::addExcludePairs(Molecule* mol) {
365	<	std::vector<Bond*>::iterator bondIter;
366	<	std::vector<Bend*>::iterator bendIter;
367	<	std::vector<Torsion*>::iterator torsionIter;
364	>	void SimInfo::addInteractionPairs(Molecule* mol) {
365	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
366	>	vector<Bond*>::iterator bondIter;
367	>	vector<Bend*>::iterator bendIter;
368	>	vector<Torsion*>::iterator torsionIter;
369	>	vector<Inversion*>::iterator inversionIter;
370		Bond* bond;
371		Bend* bend;
372		Torsion* torsion;
373	+	Inversion* inversion;
374		int a;
375		int b;
376		int c;
377		int d;
378	+
379	+	// atomGroups can be used to add special interaction maps between
380	+	// groups of atoms that are in two separate rigid bodies.
381	+	// However, most site-site interactions between two rigid bodies
382	+	// are probably not special, just the ones between the physically
383	+	// bonded atoms.  Interactions *within* a single rigid body should
384	+	// always be excluded.  These are done at the bottom of this
385	+	// function.
386	+
387	+	map<int, set<int> > atomGroups;
388	+	Molecule::RigidBodyIterator rbIter;
389	+	RigidBody* rb;
390	+	Molecule::IntegrableObjectIterator ii;
391	+	StuntDouble* sd;
392
393	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
394	<	a = bond->getAtomA()->getGlobalIndex();
395	<	b = bond->getAtomB()->getGlobalIndex();
396	<	exclude_.addPair(a, b);
393	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
394	>	sd = mol->nextIntegrableObject(ii)) {
395	>
396	>	if (sd->isRigidBody()) {
397	>	rb = static_cast<RigidBody*>(sd);
398	>	vector<Atom*> atoms = rb->getAtoms();
399	>	set<int> rigidAtoms;
400	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
401	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
402	>	}
403	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
404	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
405	>	}
406	>	} else {
407	>	set<int> oneAtomSet;
408	>	oneAtomSet.insert(sd->getGlobalIndex());
409	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
410	>	}
411	>	}
412	>
413	>	for (bond= mol->beginBond(bondIter); bond != NULL;
414	>	bond = mol->nextBond(bondIter)) {
415	>
416	>	a = bond->getAtomA()->getGlobalIndex();
417	>	b = bond->getAtomB()->getGlobalIndex();
418	>
419	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
420	>	oneTwoInteractions_.addPair(a, b);
421	>	} else {
422	>	excludedInteractions_.addPair(a, b);
423	>	}
424		}
425
426	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
427	<	a = bend->getAtomA()->getGlobalIndex();
348	<	b = bend->getAtomB()->getGlobalIndex();
349	<	c = bend->getAtomC()->getGlobalIndex();
426	>	for (bend= mol->beginBend(bendIter); bend != NULL;
427	>	bend = mol->nextBend(bendIter)) {
428
429	<	exclude_.addPair(a, b);
430	<	exclude_.addPair(a, c);
431	<	exclude_.addPair(b, c);
429	>	a = bend->getAtomA()->getGlobalIndex();
430	>	b = bend->getAtomB()->getGlobalIndex();
431	>	c = bend->getAtomC()->getGlobalIndex();
432	>
433	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
434	>	oneTwoInteractions_.addPair(a, b);
435	>	oneTwoInteractions_.addPair(b, c);
436	>	} else {
437	>	excludedInteractions_.addPair(a, b);
438	>	excludedInteractions_.addPair(b, c);
439	>	}
440	>
441	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
442	>	oneThreeInteractions_.addPair(a, c);
443	>	} else {
444	>	excludedInteractions_.addPair(a, c);
445	>	}
446		}
447
448	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
449	<	a = torsion->getAtomA()->getGlobalIndex();
358	<	b = torsion->getAtomB()->getGlobalIndex();
359	<	c = torsion->getAtomC()->getGlobalIndex();
360	<	d = torsion->getAtomD()->getGlobalIndex();
448	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
449	>	torsion = mol->nextTorsion(torsionIter)) {
450
451	<	exclude_.addPair(a, b);
452	<	exclude_.addPair(a, c);
453	<	exclude_.addPair(a, d);
454	<	exclude_.addPair(b, c);
455	<	exclude_.addPair(b, d);
456	<	exclude_.addPair(c, d);
451	>	a = torsion->getAtomA()->getGlobalIndex();
452	>	b = torsion->getAtomB()->getGlobalIndex();
453	>	c = torsion->getAtomC()->getGlobalIndex();
454	>	d = torsion->getAtomD()->getGlobalIndex();
455	>
456	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
457	>	oneTwoInteractions_.addPair(a, b);
458	>	oneTwoInteractions_.addPair(b, c);
459	>	oneTwoInteractions_.addPair(c, d);
460	>	} else {
461	>	excludedInteractions_.addPair(a, b);
462	>	excludedInteractions_.addPair(b, c);
463	>	excludedInteractions_.addPair(c, d);
464	>	}
465	>
466	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
467	>	oneThreeInteractions_.addPair(a, c);
468	>	oneThreeInteractions_.addPair(b, d);
469	>	} else {
470	>	excludedInteractions_.addPair(a, c);
471	>	excludedInteractions_.addPair(b, d);
472	>	}
473	>
474	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
475	>	oneFourInteractions_.addPair(a, d);
476	>	} else {
477	>	excludedInteractions_.addPair(a, d);
478	>	}
479		}
480
481	<
482	<	}
481	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
482	>	inversion = mol->nextInversion(inversionIter)) {
483
484	<	void SimInfo::removeExcludePairs(Molecule* mol) {
485	<	std::vector<Bond*>::iterator bondIter;
486	<	std::vector<Bend*>::iterator bendIter;
487	<	std::vector<Torsion*>::iterator torsionIter;
484	>	a = inversion->getAtomA()->getGlobalIndex();
485	>	b = inversion->getAtomB()->getGlobalIndex();
486	>	c = inversion->getAtomC()->getGlobalIndex();
487	>	d = inversion->getAtomD()->getGlobalIndex();
488	>
489	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
490	>	oneTwoInteractions_.addPair(a, b);
491	>	oneTwoInteractions_.addPair(a, c);
492	>	oneTwoInteractions_.addPair(a, d);
493	>	} else {
494	>	excludedInteractions_.addPair(a, b);
495	>	excludedInteractions_.addPair(a, c);
496	>	excludedInteractions_.addPair(a, d);
497	>	}
498	>
499	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
500	>	oneThreeInteractions_.addPair(b, c);
501	>	oneThreeInteractions_.addPair(b, d);
502	>	oneThreeInteractions_.addPair(c, d);
503	>	} else {
504	>	excludedInteractions_.addPair(b, c);
505	>	excludedInteractions_.addPair(b, d);
506	>	excludedInteractions_.addPair(c, d);
507	>	}
508	>	}
509	>
510	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
511	>	rb = mol->nextRigidBody(rbIter)) {
512	>	vector<Atom*> atoms = rb->getAtoms();
513	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
514	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
515	>	a = atoms[i]->getGlobalIndex();
516	>	b = atoms[j]->getGlobalIndex();
517	>	excludedInteractions_.addPair(a, b);
518	>	}
519	>	}
520	>	}
521	>
522	>	}
523	>
524	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
525	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
526	>	vector<Bond*>::iterator bondIter;
527	>	vector<Bend*>::iterator bendIter;
528	>	vector<Torsion*>::iterator torsionIter;
529	>	vector<Inversion*>::iterator inversionIter;
530		Bond* bond;
531		Bend* bend;
532		Torsion* torsion;
533	+	Inversion* inversion;
534		int a;
535		int b;
536		int c;
537		int d;
538	+
539	+	map<int, set<int> > atomGroups;
540	+	Molecule::RigidBodyIterator rbIter;
541	+	RigidBody* rb;
542	+	Molecule::IntegrableObjectIterator ii;
543	+	StuntDouble* sd;
544
545	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
546	<	a = bond->getAtomA()->getGlobalIndex();
547	<	b = bond->getAtomB()->getGlobalIndex();
548	<	exclude_.removePair(a, b);
545	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
546	>	sd = mol->nextIntegrableObject(ii)) {
547	>
548	>	if (sd->isRigidBody()) {
549	>	rb = static_cast<RigidBody*>(sd);
550	>	vector<Atom*> atoms = rb->getAtoms();
551	>	set<int> rigidAtoms;
552	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
553	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
554	>	}
555	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
556	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
557	>	}
558	>	} else {
559	>	set<int> oneAtomSet;
560	>	oneAtomSet.insert(sd->getGlobalIndex());
561	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
562	>	}
563	>	}
564	>
565	>	for (bond= mol->beginBond(bondIter); bond != NULL;
566	>	bond = mol->nextBond(bondIter)) {
567	>
568	>	a = bond->getAtomA()->getGlobalIndex();
569	>	b = bond->getAtomB()->getGlobalIndex();
570	>
571	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
572	>	oneTwoInteractions_.removePair(a, b);
573	>	} else {
574	>	excludedInteractions_.removePair(a, b);
575	>	}
576		}
577
578	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
579	<	a = bend->getAtomA()->getGlobalIndex();
393	<	b = bend->getAtomB()->getGlobalIndex();
394	<	c = bend->getAtomC()->getGlobalIndex();
578	>	for (bend= mol->beginBend(bendIter); bend != NULL;
579	>	bend = mol->nextBend(bendIter)) {
580
581	<	exclude_.removePair(a, b);
582	<	exclude_.removePair(a, c);
583	<	exclude_.removePair(b, c);
581	>	a = bend->getAtomA()->getGlobalIndex();
582	>	b = bend->getAtomB()->getGlobalIndex();
583	>	c = bend->getAtomC()->getGlobalIndex();
584	>
585	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
586	>	oneTwoInteractions_.removePair(a, b);
587	>	oneTwoInteractions_.removePair(b, c);
588	>	} else {
589	>	excludedInteractions_.removePair(a, b);
590	>	excludedInteractions_.removePair(b, c);
591	>	}
592	>
593	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
594	>	oneThreeInteractions_.removePair(a, c);
595	>	} else {
596	>	excludedInteractions_.removePair(a, c);
597	>	}
598		}
599
600	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
601	<	a = torsion->getAtomA()->getGlobalIndex();
403	<	b = torsion->getAtomB()->getGlobalIndex();
404	<	c = torsion->getAtomC()->getGlobalIndex();
405	<	d = torsion->getAtomD()->getGlobalIndex();
600	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
601	>	torsion = mol->nextTorsion(torsionIter)) {
602
603	<	exclude_.removePair(a, b);
604	<	exclude_.removePair(a, c);
605	<	exclude_.removePair(a, d);
606	<	exclude_.removePair(b, c);
607	<	exclude_.removePair(b, d);
608	<	exclude_.removePair(c, d);
603	>	a = torsion->getAtomA()->getGlobalIndex();
604	>	b = torsion->getAtomB()->getGlobalIndex();
605	>	c = torsion->getAtomC()->getGlobalIndex();
606	>	d = torsion->getAtomD()->getGlobalIndex();
607	>
608	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
609	>	oneTwoInteractions_.removePair(a, b);
610	>	oneTwoInteractions_.removePair(b, c);
611	>	oneTwoInteractions_.removePair(c, d);
612	>	} else {
613	>	excludedInteractions_.removePair(a, b);
614	>	excludedInteractions_.removePair(b, c);
615	>	excludedInteractions_.removePair(c, d);
616	>	}
617	>
618	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
619	>	oneThreeInteractions_.removePair(a, c);
620	>	oneThreeInteractions_.removePair(b, d);
621	>	} else {
622	>	excludedInteractions_.removePair(a, c);
623	>	excludedInteractions_.removePair(b, d);
624	>	}
625	>
626	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
627	>	oneFourInteractions_.removePair(a, d);
628	>	} else {
629	>	excludedInteractions_.removePair(a, d);
630	>	}
631		}
632
633	<	}
633	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
634	>	inversion = mol->nextInversion(inversionIter)) {
635
636	+	a = inversion->getAtomA()->getGlobalIndex();
637	+	b = inversion->getAtomB()->getGlobalIndex();
638	+	c = inversion->getAtomC()->getGlobalIndex();
639	+	d = inversion->getAtomD()->getGlobalIndex();
640
641	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
642	<	int curStampId;
641	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
642	>	oneTwoInteractions_.removePair(a, b);
643	>	oneTwoInteractions_.removePair(a, c);
644	>	oneTwoInteractions_.removePair(a, d);
645	>	} else {
646	>	excludedInteractions_.removePair(a, b);
647	>	excludedInteractions_.removePair(a, c);
648	>	excludedInteractions_.removePair(a, d);
649	>	}
650
651	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
652	+	oneThreeInteractions_.removePair(b, c);
653	+	oneThreeInteractions_.removePair(b, d);
654	+	oneThreeInteractions_.removePair(c, d);
655	+	} else {
656	+	excludedInteractions_.removePair(b, c);
657	+	excludedInteractions_.removePair(b, d);
658	+	excludedInteractions_.removePair(c, d);
659	+	}
660	+	}
661	+
662	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
663	+	rb = mol->nextRigidBody(rbIter)) {
664	+	vector<Atom*> atoms = rb->getAtoms();
665	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
666	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
667	+	a = atoms[i]->getGlobalIndex();
668	+	b = atoms[j]->getGlobalIndex();
669	+	excludedInteractions_.removePair(a, b);
670	+	}
671	+	}
672	+	}
673	+
674	+	}
675	+
676	+
677	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
678	+	int curStampId;
679	+
680		//index from 0
681		curStampId = moleculeStamps_.size();
682
683		moleculeStamps_.push_back(molStamp);
684		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
685	<	}
685	>	}
686
428	–	void SimInfo::update() {
687
688	<	setupSimType();
689	<
690	<	#ifdef IS_MPI
691	<	setupFortranParallel();
692	<	#endif
693	<
694	<	setupFortranSim();
695	<
696	<	//setup fortran force field
439	<	/** @deprecate */
440	<	int isError = 0;
441	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
442	<	if(isError){
443	<	sprintf( painCave.errMsg,
444	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
445	<	painCave.isFatal = 1;
446	<	simError();
447	<	}
448	<
449	<
450	<	setupCutoff();
451	<
688	>	/**
689	>	* update
690	>	*
691	>	*  Performs the global checks and variable settings after the
692	>	*  objects have been created.
693	>	*
694	>	*/
695	>	void SimInfo::update() {
696	>	setupSimVariables();
697		calcNdf();
698		calcNdfRaw();
699		calcNdfTrans();
700	<
701	<	fortranInitialized_ = true;
702	<	}
703	<
704	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
700	>	}
701	>
702	>	/**
703	>	* getSimulatedAtomTypes
704	>	*
705	>	* Returns an STL set of AtomType* that are actually present in this
706	>	* simulation.  Must query all processors to assemble this information.
707	>	*
708	>	*/
709	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
710		SimInfo::MoleculeIterator mi;
711		Molecule* mol;
712		Molecule::AtomIterator ai;
713		Atom* atom;
714	<	std::set<AtomType*> atomTypes;
715	<
714	>	set<AtomType*> atomTypes;
715	>
716		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
717	+	for(atom = mol->beginAtom(ai); atom != NULL;
718	+	atom = mol->nextAtom(ai)) {
719	+	atomTypes.insert(atom->getAtomType());
720	+	}
721	+	}
722	+
723	+	#ifdef IS_MPI
724
725	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
726	<	atomTypes.insert(atom->getAtomType());
727	<	}
728	<
729	<	}
725	>	// loop over the found atom types on this processor, and add their
726	>	// numerical idents to a vector:
727	>
728	>	vector<int> foundTypes;
729	>	set<AtomType*>::iterator i;
730	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
731	>	foundTypes.push_back( (*i)->getIdent() );
732
733	<	return atomTypes;
734	<	}
733	>	// count_local holds the number of found types on this processor
734	>	int count_local = foundTypes.size();
735
736	<	void SimInfo::setupSimType() {
478	<	std::set<AtomType*>::iterator i;
479	<	std::set<AtomType*> atomTypes;
480	<	atomTypes = getUniqueAtomTypes();
481	<
482	<	int useLennardJones = 0;
483	<	int useElectrostatic = 0;
484	<	int useEAM = 0;
485	<	int useCharge = 0;
486	<	int useDirectional = 0;
487	<	int useDipole = 0;
488	<	int useGayBerne = 0;
489	<	int useSticky = 0;
490	<	int useShape = 0;
491	<	int useFLARB = 0; //it is not in AtomType yet
492	<	int useDirectionalAtom = 0;
493	<	int useElectrostatics = 0;
494	<	//usePBC and useRF are from simParams
495	<	int usePBC = simParams_->getPBC();
496	<	int useRF = simParams_->getUseRF();
736	>	int nproc = MPI::COMM_WORLD.Get_size();
737
738	<	//loop over all of the atom types
739	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
740	<	useLennardJones |= (*i)->isLennardJones();
741	<	useElectrostatic |= (*i)->isElectrostatic();
502	<	useEAM |= (*i)->isEAM();
503	<	useCharge |= (*i)->isCharge();
504	<	useDirectional |= (*i)->isDirectional();
505	<	useDipole |= (*i)->isDipole();
506	<	useGayBerne |= (*i)->isGayBerne();
507	<	useSticky |= (*i)->isSticky();
508	<	useShape |= (*i)->isShape();
509	<	}
738	>	// we need arrays to hold the counts and displacement vectors for
739	>	// all processors
740	>	vector<int> counts(nproc, 0);
741	>	vector<int> disps(nproc, 0);
742
743	<	if (useSticky || useDipole || useGayBerne || useShape) {
744	<	useDirectionalAtom = 1;
743	>	// fill the counts array
744	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
745	>	1, MPI::INT);
746	>
747	>	// use the processor counts to compute the displacement array
748	>	disps[0] = 0;
749	>	int totalCount = counts[0];
750	>	for (int iproc = 1; iproc < nproc; iproc++) {
751	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
752	>	totalCount += counts[iproc];
753		}
754
755	<	if (useCharge || useDipole) {
756	<	useElectrostatics = 1;
757	<	}
755	>	// we need a (possibly redundant) set of all found types:
756	>	vector<int> ftGlobal(totalCount);
757	>
758	>	// now spray out the foundTypes to all the other processors:
759	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
760	>	&ftGlobal[0], &counts[0], &disps[0],
761	>	MPI::INT);
762
763	<	#ifdef IS_MPI
520	<	int temp;
763	>	vector<int>::iterator j;
764
765	<	temp = usePBC;
766	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
765	>	// foundIdents is a stl set, so inserting an already found ident
766	>	// will have no effect.
767	>	set<int> foundIdents;
768
769	<	temp = useDirectionalAtom;
770	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
770	>	foundIdents.insert((*j));
771	>
772	>	// now iterate over the foundIdents and get the actual atom types
773	>	// that correspond to these:
774	>	set<int>::iterator it;
775	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
776	>	atomTypes.insert( forceField_->getAtomType((*it)) );
777	>
778	>	#endif
779
780	<	temp = useLennardJones;
781	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
780	>	return atomTypes;
781	>	}
782
783	<	temp = useElectrostatics;
784	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
783	>	void SimInfo::setupSimVariables() {
784	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
785	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
786	>	// parameter is true
787	>	calcBoxDipole_ = false;
788	>	if ( simParams_->haveAccumulateBoxDipole() )
789	>	if ( simParams_->getAccumulateBoxDipole() ) {
790	>	calcBoxDipole_ = true;
791	>	}
792	>
793	>	set<AtomType*>::iterator i;
794	>	set<AtomType*> atomTypes;
795	>	atomTypes = getSimulatedAtomTypes();
796	>	bool usesElectrostatic = false;
797	>	bool usesMetallic = false;
798	>	bool usesDirectional = false;
799	>	bool usesFluctuatingCharges =  false;
800	>	//loop over all of the atom types
801	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
802	>	usesElectrostatic |= (*i)->isElectrostatic();
803	>	usesMetallic |= (*i)->isMetal();
804	>	usesDirectional |= (*i)->isDirectional();
805	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
806	>	}
807
808	<	temp = useCharge;
809	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
808	>	#ifdef IS_MPI
809	>	bool temp;
810	>	temp = usesDirectional;
811	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
812	>	MPI::LOR);
813	>
814	>	temp = usesMetallic;
815	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
816	>	MPI::LOR);
817	>
818	>	temp = usesElectrostatic;
819	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
820	>	MPI::LOR);
821
822	<	temp = useDipole;
823	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
822	>	temp = usesFluctuatingCharges;
823	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
824	>	MPI::LOR);
825	>	#else
826
827	<	temp = useSticky;
828	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
827	>	usesDirectionalAtoms_ = usesDirectional;
828	>	usesMetallicAtoms_ = usesMetallic;
829	>	usesElectrostaticAtoms_ = usesElectrostatic;
830	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
831
832	<	temp = useGayBerne;
833	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
832	>	#endif
833	>
834	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
835	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
836	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
837	>	}
838
546	–	temp = useEAM;
547	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
839
840	<	temp = useShape;
841	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
840	>	vector<int> SimInfo::getGlobalAtomIndices() {
841	>	SimInfo::MoleculeIterator mi;
842	>	Molecule* mol;
843	>	Molecule::AtomIterator ai;
844	>	Atom* atom;
845
846	<	temp = useFLARB;
553	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
554	<
555	<	temp = useRF;
556	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
846	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
847
848	<	#endif
848	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
849	>
850	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
851	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
852	>	}
853	>	}
854	>	return GlobalAtomIndices;
855	>	}
856
560	–	fInfo_.SIM_uses_PBC = usePBC;
561	–	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
562	–	fInfo_.SIM_uses_LennardJones = useLennardJones;
563	–	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
564	–	fInfo_.SIM_uses_Charges = useCharge;
565	–	fInfo_.SIM_uses_Dipoles = useDipole;
566	–	fInfo_.SIM_uses_Sticky = useSticky;
567	–	fInfo_.SIM_uses_GayBerne = useGayBerne;
568	–	fInfo_.SIM_uses_EAM = useEAM;
569	–	fInfo_.SIM_uses_Shapes = useShape;
570	–	fInfo_.SIM_uses_FLARB = useFLARB;
571	–	fInfo_.SIM_uses_RF = useRF;
857
858	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
858	>	vector<int> SimInfo::getGlobalGroupIndices() {
859	>	SimInfo::MoleculeIterator mi;
860	>	Molecule* mol;
861	>	Molecule::CutoffGroupIterator ci;
862	>	CutoffGroup* cg;
863
864	<	if (simParams_->haveDielectric()) {
865	<	fInfo_.dielect = simParams_->getDielectric();
866	<	} else {
867	<	sprintf(painCave.errMsg,
868	<	"SimSetup Error: No Dielectric constant was set.\n"
869	<	"\tYou are trying to use Reaction Field without"
870	<	"\tsetting a dielectric constant!\n");
871	<	painCave.isFatal = 1;
872	<	simError();
873	<	}
585	<
586	<	} else {
587	<	fInfo_.dielect = 0.0;
864	>	vector<int> GlobalGroupIndices;
865	>
866	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
867	>
868	>	//local index of cutoff group is trivial, it only depends on the
869	>	//order of travesing
870	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
871	>	cg = mol->nextCutoffGroup(ci)) {
872	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
873	>	}
874		}
875	+	return GlobalGroupIndices;
876	+	}
877
590	–	}
878
879	<	void SimInfo::setupFortranSim() {
880	<	int isError;
594	<	int nExclude;
595	<	std::vector<int> fortranGlobalGroupMembership;
596	<
597	<	nExclude = exclude_.getSize();
598	<	isError = 0;
879	>	void SimInfo::prepareTopology() {
880	>	int nExclude, nOneTwo, nOneThree, nOneFour;
881
600	–	//globalGroupMembership_ is filled by SimCreator
601	–	for (int i = 0; i < nGlobalAtoms_; i++) {
602	–	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
603	–	}
604	–
882		//calculate mass ratio of cutoff group
606	–	std::vector<double> mfact;
883		SimInfo::MoleculeIterator mi;
884		Molecule* mol;
885		Molecule::CutoffGroupIterator ci;
886		CutoffGroup* cg;
887		Molecule::AtomIterator ai;
888		Atom* atom;
889	<	double totalMass;
889	>	RealType totalMass;
890
891	<	//to avoid memory reallocation, reserve enough space for mfact
892	<	mfact.reserve(getNCutoffGroups());
891	>	/**
892	>	* The mass factor is the relative mass of an atom to the total
893	>	* mass of the cutoff group it belongs to.  By default, all atoms
894	>	* are their own cutoff groups, and therefore have mass factors of
895	>	* 1.  We need some special handling for massless atoms, which
896	>	* will be treated as carrying the entire mass of the cutoff
897	>	* group.
898	>	*/
899	>	massFactors_.clear();
900	>	massFactors_.resize(getNAtoms(), 1.0);
901
902		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
903	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
903	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
904	>	cg = mol->nextCutoffGroup(ci)) {
905
906	<	totalMass = cg->getMass();
907	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
908	<	mfact.push_back(atom->getMass()/totalMass);
909	<	}
910	<
911	<	}
906	>	totalMass = cg->getMass();
907	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
908	>	// Check for massless groups - set mfact to 1 if true
909	>	if (totalMass != 0)
910	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
911	>	else
912	>	massFactors_[atom->getLocalIndex()] = 1.0;
913	>	}
914	>	}
915		}
916
917	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
630	<	std::vector<int> identArray;
917	>	// Build the identArray_
918
919	<	//to avoid memory reallocation, reserve enough space identArray
920	<	identArray.reserve(getNAtoms());
634	<
919	>	identArray_.clear();
920	>	identArray_.reserve(getNAtoms());
921		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
922	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
923	<	identArray.push_back(atom->getIdent());
924	<	}
922	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
923	>	identArray_.push_back(atom->getIdent());
924	>	}
925		}
640	–
641	–	//fill molMembershipArray
642	–	//molMembershipArray is filled by SimCreator
643	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
644	–	for (int i = 0; i < nGlobalAtoms_; i++) {
645	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
646	–	}
926
927	<	//setup fortran simulation
649	<	//gloalExcludes and molMembershipArray should go away (They are never used)
650	<	//why the hell fortran need to know molecule?
651	<	//OOPSE = Object-Obfuscated Parallel Simulation Engine
652	<	int nGlobalExcludes = 0;
653	<	int* globalExcludes = NULL;
654	<	int* excludeList = exclude_.getExcludeList();
655	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
656	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
657	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
927	>	//scan topology
928
929	<	if( isError ){
929	>	nExclude = excludedInteractions_.getSize();
930	>	nOneTwo = oneTwoInteractions_.getSize();
931	>	nOneThree = oneThreeInteractions_.getSize();
932	>	nOneFour = oneFourInteractions_.getSize();
933
934	<	sprintf( painCave.errMsg,
935	<	"There was an error setting the simulation information in fortran.\n" );
936	<	painCave.isFatal = 1;
937	<	painCave.severity = OOPSE_ERROR;
665	<	simError();
666	<	}
934	>	int* excludeList = excludedInteractions_.getPairList();
935	>	int* oneTwoList = oneTwoInteractions_.getPairList();
936	>	int* oneThreeList = oneThreeInteractions_.getPairList();
937	>	int* oneFourList = oneFourInteractions_.getPairList();
938
939	<	#ifdef IS_MPI
940	<	sprintf( checkPointMsg,
670	<	"succesfully sent the simulation information to fortran.\n");
671	<	MPIcheckPoint();
672	<	#endif // is_mpi
673	<	}
939	>	topologyDone_ = true;
940	>	}
941
942	<
676	<	#ifdef IS_MPI
677	<	void SimInfo::setupFortranParallel() {
678	<
679	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
680	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
681	<	std::vector<int> localToGlobalCutoffGroupIndex;
682	<	SimInfo::MoleculeIterator mi;
683	<	Molecule::AtomIterator ai;
684	<	Molecule::CutoffGroupIterator ci;
685	<	Molecule* mol;
686	<	Atom* atom;
687	<	CutoffGroup* cg;
688	<	mpiSimData parallelData;
689	<	int isError;
690	<
691	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
692	<
693	<	//local index(index in DataStorge) of atom is important
694	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
695	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
696	<	}
697	<
698	<	//local index of cutoff group is trivial, it only depends on the order of travesing
699	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
700	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
701	<	}
702	<
703	<	}
704	<
705	<	//fill up mpiSimData struct
706	<	parallelData.nMolGlobal = getNGlobalMolecules();
707	<	parallelData.nMolLocal = getNMolecules();
708	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
709	<	parallelData.nAtomsLocal = getNAtoms();
710	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
711	<	parallelData.nGroupsLocal = getNCutoffGroups();
712	<	parallelData.myNode = worldRank;
713	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
714	<
715	<	//pass mpiSimData struct and index arrays to fortran
716	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
717	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
718	<	&localToGlobalCutoffGroupIndex[0], &isError);
719	<
720	<	if (isError) {
721	<	sprintf(painCave.errMsg,
722	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
723	<	painCave.isFatal = 1;
724	<	simError();
725	<	}
726	<
727	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
728	<	MPIcheckPoint();
729	<
730	<
731	<	}
732	<
733	<	#endif
734	<
735	<	double SimInfo::calcMaxCutoffRadius() {
736	<
737	<
738	<	std::set<AtomType*> atomTypes;
739	<	std::set<AtomType*>::iterator i;
740	<	std::vector<double> cutoffRadius;
741	<
742	<	//get the unique atom types
743	<	atomTypes = getUniqueAtomTypes();
744	<
745	<	//query the max cutoff radius among these atom types
746	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
747	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
748	<	}
749	<
750	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
751	<	#ifdef IS_MPI
752	<	//pick the max cutoff radius among the processors
753	<	#endif
754	<
755	<	return maxCutoffRadius;
756	<	}
757	<
758	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
759	<
760	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
761	<
762	<	if (!simParams_->haveRcut()){
763	<	sprintf(painCave.errMsg,
764	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
765	<	"\tOOPSE will use a default value of 15.0 angstroms"
766	<	"\tfor the cutoffRadius.\n");
767	<	painCave.isFatal = 0;
768	<	simError();
769	<	rcut = 15.0;
770	<	} else{
771	<	rcut = simParams_->getRcut();
772	<	}
773	<
774	<	if (!simParams_->haveRsw()){
775	<	sprintf(painCave.errMsg,
776	<	"SimCreator Warning: No value was set for switchingRadius.\n"
777	<	"\tOOPSE will use a default value of\n"
778	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
779	<	painCave.isFatal = 0;
780	<	simError();
781	<	rsw = 0.95 * rcut;
782	<	} else{
783	<	rsw = simParams_->getRsw();
784	<	}
785	<
786	<	} else {
787	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
788	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
789	<
790	<	if (simParams_->haveRcut()) {
791	<	rcut = simParams_->getRcut();
792	<	} else {
793	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
794	<	rcut = calcMaxCutoffRadius();
795	<	}
796	<
797	<	if (simParams_->haveRsw()) {
798	<	rsw  = simParams_->getRsw();
799	<	} else {
800	<	rsw = rcut;
801	<	}
802	<
803	<	}
804	<	}
805	<
806	<	void SimInfo::setupCutoff() {
807	<	getCutoff(rcut_, rsw_);
808	<	double rnblist = rcut_ + 1; // skin of neighbor list
809	<
810	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
811	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
812	<	}
813	<
814	<	void SimInfo::addProperty(GenericData* genData) {
942	>	void SimInfo::addProperty(GenericData* genData) {
943		properties_.addProperty(genData);
944	<	}
944	>	}
945
946	<	void SimInfo::removeProperty(const std::string& propName) {
946	>	void SimInfo::removeProperty(const string& propName) {
947		properties_.removeProperty(propName);
948	<	}
948	>	}
949
950	<	void SimInfo::clearProperties() {
950	>	void SimInfo::clearProperties() {
951		properties_.clearProperties();
952	<	}
952	>	}
953
954	<	std::vector<std::string> SimInfo::getPropertyNames() {
954	>	vector<string> SimInfo::getPropertyNames() {
955		return properties_.getPropertyNames();
956	<	}
956	>	}
957
958	<	std::vector<GenericData*> SimInfo::getProperties() {
958	>	vector<GenericData*> SimInfo::getProperties() {
959		return properties_.getProperties();
960	<	}
960	>	}
961
962	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
962	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
963		return properties_.getPropertyByName(propName);
964	<	}
964	>	}
965
966	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
967	<	//if (sman_ == sman_) {
968	<	//    return;
969	<	//}
970	<
843	<	//delete sman_;
966	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
967	>	if (sman_ == sman) {
968	>	return;
969	>	}
970	>	delete sman_;
971		sman_ = sman;
972
973		Molecule* mol;
974		RigidBody* rb;
975		Atom* atom;
976	+	CutoffGroup* cg;
977		SimInfo::MoleculeIterator mi;
978		Molecule::RigidBodyIterator rbIter;
979	<	Molecule::AtomIterator atomIter;;
979	>	Molecule::AtomIterator atomIter;
980	>	Molecule::CutoffGroupIterator cgIter;
981
982		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
983
984	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
985	<	atom->setSnapshotManager(sman_);
986	<	}
984	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
985	>	atom = mol->nextAtom(atomIter)) {
986	>	atom->setSnapshotManager(sman_);
987	>	}
988
989	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
990	<	rb->setSnapshotManager(sman_);
991	<	}
989	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
990	>	rb = mol->nextRigidBody(rbIter)) {
991	>	rb->setSnapshotManager(sman_);
992	>	}
993	>
994	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
995	>	cg = mol->nextCutoffGroup(cgIter)) {
996	>	cg->setSnapshotManager(sman_);
997	>	}
998		}
999
1000	<	}
1000	>	}
1001
866	–	Vector3d SimInfo::getComVel(){
867	–	SimInfo::MoleculeIterator i;
868	–	Molecule* mol;
1002
1003	<	Vector3d comVel(0.0);
871	<	double totalMass = 0.0;
872	<
873	<
874	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
875	<	double mass = mol->getMass();
876	<	totalMass += mass;
877	<	comVel += mass * mol->getComVel();
878	<	}
1003	>	ostream& operator <<(ostream& o, SimInfo& info) {
1004
1005	<	#ifdef IS_MPI
1006	<	double tmpMass = totalMass;
1007	<	Vector3d tmpComVel(comVel);
1008	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1009	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1010	<	#endif
1005	>	return o;
1006	>	}
1007	>
1008	>
1009	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1010	>	if (index >= IOIndexToIntegrableObject.size()) {
1011	>	sprintf(painCave.errMsg,
1012	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1013	>	"\tindex exceeds number of known objects!\n");
1014	>	painCave.isFatal = 1;
1015	>	simError();
1016	>	return NULL;
1017	>	} else
1018	>	return IOIndexToIntegrableObject.at(index);
1019	>	}
1020	>
1021	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1022	>	IOIndexToIntegrableObject= v;
1023	>	}
1024
1025	<	comVel /= totalMass;
1026	<
889	<	return comVel;
890	<	}
891	<
892	<	Vector3d SimInfo::getCom(){
893	<	SimInfo::MoleculeIterator i;
894	<	Molecule* mol;
895	<
896	<	Vector3d com(0.0);
897	<	double totalMass = 0.0;
898	<
899	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
900	<	double mass = mol->getMass();
901	<	totalMass += mass;
902	<	com += mass * mol->getCom();
903	<	}
904	<
1025	>	int SimInfo::getNGlobalConstraints() {
1026	>	int nGlobalConstraints;
1027		#ifdef IS_MPI
1028	<	double tmpMass = totalMass;
1029	<	Vector3d tmpCom(com);
1030	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1031	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1028	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1029	>	MPI_COMM_WORLD);
1030	>	#else
1031	>	nGlobalConstraints =  nConstraints_;
1032		#endif
1033	+	return nGlobalConstraints;
1034	+	}
1035
1036	<	com /= totalMass;
1036	>	}//end namespace OpenMD
1037
914	–	return com;
915	–
916	–	}
917	–
918	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
919	–
920	–	return o;
921	–	}
922	–
923	–	}//end namespace oopse
924	–

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1779 by gezelter, Mon Aug 20 17:51:39 2012 UTC

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