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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
Revision 1908 by gezelter, Fri Jul 19 21:25:45 2013 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, 234107 (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);
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	>	if ( (*i)->haveRegion() ) {
95	>	molStamp->setRegion( (*i)->getRegion() );
96	>	} else {
97	>	// set the region to a disallowed value:
98	>	molStamp->setRegion( -1 );
99	>	}
100
101	<	//calculate atoms in molecules
102	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
103	<
104	<
105	<	//calculate atoms in cutoff groups
106	<	int nAtomsInGroups = 0;
107	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
108	<
109	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
110	<	cgStamp = molStamp->getCutoffGroup(j);
111	<	nAtomsInGroups += cgStamp->getNMembers();
112	<	}
113	<
114	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
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->getRigidBody(j);
123	<	nAtomsInRigidBodies += rbStamp->getNMembers();
124	<	}
125	<
126	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
127	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
128	<
101	>	nMolWithSameStamp = (*i)->getNMol();
102	>
103	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
104	>
105	>	//calculate atoms in molecules
106	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
107	>
108	>	//calculate atoms in cutoff groups
109	>	int nAtomsInGroups = 0;
110	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
111	>
112	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
113	>	cgStamp = molStamp->getCutoffGroupStamp(j);
114	>	nAtomsInGroups += cgStamp->getNMembers();
115	>	}
116	>
117	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
118	>
119	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
120	>
121	>	//calculate atoms in rigid bodies
122	>	int nAtomsInRigidBodies = 0;
123	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
124	>
125	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
126	>	rbStamp = molStamp->getRigidBodyStamp(j);
127	>	nAtomsInRigidBodies += rbStamp->getNMembers();
128	>	}
129	>
130	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
131	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
132	>
133		}
134	+
135	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
136	+	//group therefore the total number of cutoff groups in the system is
137	+	//equal to the total number of atoms minus number of atoms belong to
138	+	//cutoff group defined in meta-data file plus the number of cutoff
139	+	//groups defined in meta-data file
140
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
141		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
142	<
143	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
144	<	//therefore the total number of  integrable objects in the system is equal to
145	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
146	<	//file plus the number of  rigid bodies defined in meta-data file
147	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
148	<
142	>
143	>	//every free atom (atom does not belong to rigid bodies) is an
144	>	//integrable object therefore the total number of integrable objects
145	>	//in the system is equal to the total number of atoms minus number of
146	>	//atoms belong to rigid body defined in meta-data file plus the number
147	>	//of rigid bodies defined in meta-data file
148	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
149	>	+ nGlobalRigidBodies_;
150	>
151		nGlobalMols_ = molStampIds_.size();
137	–
138	–	#ifdef IS_MPI
152		molToProcMap_.resize(nGlobalMols_);
153	<	#endif
154	<
155	<	}
156	<
144	<	SimInfo::~SimInfo() {
145	<	std::map<int, Molecule*>::iterator i;
153	>	}
154	>
155	>	SimInfo::~SimInfo() {
156	>	map<int, Molecule*>::iterator i;
157		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
158	<	delete i->second;
158	>	delete i->second;
159		}
160		molecules_.clear();
161	<
151	<	MemoryUtils::deletePointers(moleculeStamps_);
152	<
161	>
162		delete sman_;
163		delete simParams_;
164		delete forceField_;
165	<	}
165	>	}
166
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	–	}
167
168	<	bool SimInfo::addMolecule(Molecule* mol) {
168	>	bool SimInfo::addMolecule(Molecule* mol) {
169		MoleculeIterator i;
170	<
170	>
171		i = molecules_.find(mol->getGlobalIndex());
172		if (i == molecules_.end() ) {
173	<
174	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
175	<
176	<	nAtoms_ += mol->getNAtoms();
177	<	nBonds_ += mol->getNBonds();
178	<	nBends_ += mol->getNBends();
179	<	nTorsions_ += mol->getNTorsions();
180	<	nRigidBodies_ += mol->getNRigidBodies();
181	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
182	<	nCutoffGroups_ += mol->getNCutoffGroups();
183	<	nConstraints_ += mol->getNConstraintPairs();
184	<
185	<	addExcludePairs(mol);
186	<
187	<	return true;
173	>
174	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
175	>
176	>	nAtoms_ += mol->getNAtoms();
177	>	nBonds_ += mol->getNBonds();
178	>	nBends_ += mol->getNBends();
179	>	nTorsions_ += mol->getNTorsions();
180	>	nInversions_ += mol->getNInversions();
181	>	nRigidBodies_ += mol->getNRigidBodies();
182	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
183	>	nCutoffGroups_ += mol->getNCutoffGroups();
184	>	nConstraints_ += mol->getNConstraintPairs();
185	>
186	>	addInteractionPairs(mol);
187	>
188	>	return true;
189		} else {
190	<	return false;
190	>	return false;
191		}
192	<	}
193	<
194	<	bool SimInfo::removeMolecule(Molecule* mol) {
192	>	}
193	>
194	>	bool SimInfo::removeMolecule(Molecule* mol) {
195		MoleculeIterator i;
196		i = molecules_.find(mol->getGlobalIndex());
197
198		if (i != molecules_.end() ) {
199
200	<	assert(mol == i->second);
200	>	assert(mol == i->second);
201
202	<	nAtoms_ -= mol->getNAtoms();
203	<	nBonds_ -= mol->getNBonds();
204	<	nBends_ -= mol->getNBends();
205	<	nTorsions_ -= mol->getNTorsions();
206	<	nRigidBodies_ -= mol->getNRigidBodies();
207	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
208	<	nCutoffGroups_ -= mol->getNCutoffGroups();
209	<	nConstraints_ -= mol->getNConstraintPairs();
202	>	nAtoms_ -= mol->getNAtoms();
203	>	nBonds_ -= mol->getNBonds();
204	>	nBends_ -= mol->getNBends();
205	>	nTorsions_ -= mol->getNTorsions();
206	>	nInversions_ -= mol->getNInversions();
207	>	nRigidBodies_ -= mol->getNRigidBodies();
208	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
209	>	nCutoffGroups_ -= mol->getNCutoffGroups();
210	>	nConstraints_ -= mol->getNConstraintPairs();
211
212	<	removeExcludePairs(mol);
213	<	molecules_.erase(mol->getGlobalIndex());
212	>	removeInteractionPairs(mol);
213	>	molecules_.erase(mol->getGlobalIndex());
214
215	<	delete mol;
215	>	delete mol;
216
217	<	return true;
217	>	return true;
218		} else {
219	<	return false;
219	>	return false;
220		}
221	+	}
222
221	–
222	–	}
223	–
223
224	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
224	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
225		i = molecules_.begin();
226		return i == molecules_.end() ? NULL : i->second;
227	<	}
227	>	}
228
229	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
229	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
230		++i;
231		return i == molecules_.end() ? NULL : i->second;
232	<	}
232	>	}
233
234
235	<	void SimInfo::calcNdf() {
236	<	int ndf_local;
235	>	void SimInfo::calcNdf() {
236	>	int ndf_local, nfq_local;
237		MoleculeIterator i;
238	<	std::vector<StuntDouble*>::iterator j;
238	>	vector<StuntDouble*>::iterator j;
239	>	vector<Atom*>::iterator k;
240	>
241		Molecule* mol;
242	<	StuntDouble* integrableObject;
242	>	StuntDouble* sd;
243	>	Atom* atom;
244
245		ndf_local = 0;
246	+	nfq_local = 0;
247
248		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
246	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
247	–	integrableObject = mol->nextIntegrableObject(j)) {
249
250	<	ndf_local += 3;
250	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
251	>	sd = mol->nextIntegrableObject(j)) {
252
253	<	if (integrableObject->isDirectional()) {
254	<	if (integrableObject->isLinear()) {
255	<	ndf_local += 2;
256	<	} else {
257	<	ndf_local += 3;
258	<	}
259	<	}
260	<
261	<	}//end for (integrableObject)
262	<	}// end for (mol)
253	>	ndf_local += 3;
254	>
255	>	if (sd->isDirectional()) {
256	>	if (sd->isLinear()) {
257	>	ndf_local += 2;
258	>	} else {
259	>	ndf_local += 3;
260	>	}
261	>	}
262	>	}
263	>
264	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
265	>	atom = mol->nextFluctuatingCharge(k)) {
266	>	if (atom->isFluctuatingCharge()) {
267	>	nfq_local++;
268	>	}
269	>	}
270	>	}
271
272	+	ndfLocal_ = ndf_local;
273	+
274		// n_constraints is local, so subtract them on each processor
275		ndf_local -= nConstraints_;
276
277		#ifdef IS_MPI
278	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
278	>	MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
279	>	MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
280	>	MPI::INT, MPI::SUM);
281		#else
282		ndf_ = ndf_local;
283	+	nGlobalFluctuatingCharges_ = nfq_local;
284		#endif
285
286		// nZconstraints_ is global, as are the 3 COM translations for the
287		// entire system:
288		ndf_ = ndf_ - 3 - nZconstraint_;
289
290	<	}
290	>	}
291
292	<	void SimInfo::calcNdfRaw() {
292	>	int SimInfo::getFdf() {
293	>	#ifdef IS_MPI
294	>	MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
295	>	#else
296	>	fdf_ = fdf_local;
297	>	#endif
298	>	return fdf_;
299	>	}
300	>
301	>	unsigned int SimInfo::getNLocalCutoffGroups(){
302	>	int nLocalCutoffAtoms = 0;
303	>	Molecule* mol;
304	>	MoleculeIterator mi;
305	>	CutoffGroup* cg;
306	>	Molecule::CutoffGroupIterator ci;
307	>
308	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
309	>
310	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
311	>	cg = mol->nextCutoffGroup(ci)) {
312	>	nLocalCutoffAtoms += cg->getNumAtom();
313	>
314	>	}
315	>	}
316	>
317	>	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
318	>	}
319	>
320	>	void SimInfo::calcNdfRaw() {
321		int ndfRaw_local;
322
323		MoleculeIterator i;
324	<	std::vector<StuntDouble*>::iterator j;
324	>	vector<StuntDouble*>::iterator j;
325		Molecule* mol;
326	<	StuntDouble* integrableObject;
326	>	StuntDouble* sd;
327
328		// Raw degrees of freedom that we have to set
329		ndfRaw_local = 0;
330
331		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
289	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
290	–	integrableObject = mol->nextIntegrableObject(j)) {
332
333	<	ndfRaw_local += 3;
333	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
334	>	sd = mol->nextIntegrableObject(j)) {
335
336	<	if (integrableObject->isDirectional()) {
337	<	if (integrableObject->isLinear()) {
338	<	ndfRaw_local += 2;
339	<	} else {
340	<	ndfRaw_local += 3;
341	<	}
342	<	}
336	>	ndfRaw_local += 3;
337	>
338	>	if (sd->isDirectional()) {
339	>	if (sd->isLinear()) {
340	>	ndfRaw_local += 2;
341	>	} else {
342	>	ndfRaw_local += 3;
343	>	}
344	>	}
345
346	<	}
346	>	}
347		}
348
349		#ifdef IS_MPI
350	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
350	>	MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
351		#else
352		ndfRaw_ = ndfRaw_local;
353		#endif
354	<	}
354	>	}
355
356	<	void SimInfo::calcNdfTrans() {
356	>	void SimInfo::calcNdfTrans() {
357		int ndfTrans_local;
358
359		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
360
361
362		#ifdef IS_MPI
363	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
363	>	MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
364	>	MPI::INT, MPI::SUM);
365		#else
366		ndfTrans_ = ndfTrans_local;
367		#endif
368
369		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
370
371	<	}
371	>	}
372
373	<	void SimInfo::addExcludePairs(Molecule* mol) {
374	<	std::vector<Bond*>::iterator bondIter;
375	<	std::vector<Bend*>::iterator bendIter;
376	<	std::vector<Torsion*>::iterator torsionIter;
373	>	void SimInfo::addInteractionPairs(Molecule* mol) {
374	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
375	>	vector<Bond*>::iterator bondIter;
376	>	vector<Bend*>::iterator bendIter;
377	>	vector<Torsion*>::iterator torsionIter;
378	>	vector<Inversion*>::iterator inversionIter;
379		Bond* bond;
380		Bend* bend;
381		Torsion* torsion;
382	+	Inversion* inversion;
383		int a;
384		int b;
385		int c;
386		int d;
387	+
388	+	// atomGroups can be used to add special interaction maps between
389	+	// groups of atoms that are in two separate rigid bodies.
390	+	// However, most site-site interactions between two rigid bodies
391	+	// are probably not special, just the ones between the physically
392	+	// bonded atoms.  Interactions *within* a single rigid body should
393	+	// always be excluded.  These are done at the bottom of this
394	+	// function.
395	+
396	+	map<int, set<int> > atomGroups;
397	+	Molecule::RigidBodyIterator rbIter;
398	+	RigidBody* rb;
399	+	Molecule::IntegrableObjectIterator ii;
400	+	StuntDouble* sd;
401
402	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
403	<	a = bond->getAtomA()->getGlobalIndex();
404	<	b = bond->getAtomB()->getGlobalIndex();
405	<	exclude_.addPair(a, b);
402	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
403	>	sd = mol->nextIntegrableObject(ii)) {
404	>
405	>	if (sd->isRigidBody()) {
406	>	rb = static_cast<RigidBody*>(sd);
407	>	vector<Atom*> atoms = rb->getAtoms();
408	>	set<int> rigidAtoms;
409	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
410	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
411	>	}
412	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
413	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
414	>	}
415	>	} else {
416	>	set<int> oneAtomSet;
417	>	oneAtomSet.insert(sd->getGlobalIndex());
418	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
419	>	}
420	>	}
421	>
422	>	for (bond= mol->beginBond(bondIter); bond != NULL;
423	>	bond = mol->nextBond(bondIter)) {
424	>
425	>	a = bond->getAtomA()->getGlobalIndex();
426	>	b = bond->getAtomB()->getGlobalIndex();
427	>
428	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
429	>	oneTwoInteractions_.addPair(a, b);
430	>	} else {
431	>	excludedInteractions_.addPair(a, b);
432	>	}
433		}
434
435	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
436	<	a = bend->getAtomA()->getGlobalIndex();
348	<	b = bend->getAtomB()->getGlobalIndex();
349	<	c = bend->getAtomC()->getGlobalIndex();
435	>	for (bend= mol->beginBend(bendIter); bend != NULL;
436	>	bend = mol->nextBend(bendIter)) {
437
438	<	exclude_.addPair(a, b);
439	<	exclude_.addPair(a, c);
440	<	exclude_.addPair(b, c);
438	>	a = bend->getAtomA()->getGlobalIndex();
439	>	b = bend->getAtomB()->getGlobalIndex();
440	>	c = bend->getAtomC()->getGlobalIndex();
441	>
442	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
443	>	oneTwoInteractions_.addPair(a, b);
444	>	oneTwoInteractions_.addPair(b, c);
445	>	} else {
446	>	excludedInteractions_.addPair(a, b);
447	>	excludedInteractions_.addPair(b, c);
448	>	}
449	>
450	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
451	>	oneThreeInteractions_.addPair(a, c);
452	>	} else {
453	>	excludedInteractions_.addPair(a, c);
454	>	}
455		}
456
457	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
458	<	a = torsion->getAtomA()->getGlobalIndex();
358	<	b = torsion->getAtomB()->getGlobalIndex();
359	<	c = torsion->getAtomC()->getGlobalIndex();
360	<	d = torsion->getAtomD()->getGlobalIndex();
457	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
458	>	torsion = mol->nextTorsion(torsionIter)) {
459
460	<	exclude_.addPair(a, b);
461	<	exclude_.addPair(a, c);
462	<	exclude_.addPair(a, d);
463	<	exclude_.addPair(b, c);
464	<	exclude_.addPair(b, d);
465	<	exclude_.addPair(c, d);
460	>	a = torsion->getAtomA()->getGlobalIndex();
461	>	b = torsion->getAtomB()->getGlobalIndex();
462	>	c = torsion->getAtomC()->getGlobalIndex();
463	>	d = torsion->getAtomD()->getGlobalIndex();
464	>
465	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
466	>	oneTwoInteractions_.addPair(a, b);
467	>	oneTwoInteractions_.addPair(b, c);
468	>	oneTwoInteractions_.addPair(c, d);
469	>	} else {
470	>	excludedInteractions_.addPair(a, b);
471	>	excludedInteractions_.addPair(b, c);
472	>	excludedInteractions_.addPair(c, d);
473	>	}
474	>
475	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
476	>	oneThreeInteractions_.addPair(a, c);
477	>	oneThreeInteractions_.addPair(b, d);
478	>	} else {
479	>	excludedInteractions_.addPair(a, c);
480	>	excludedInteractions_.addPair(b, d);
481	>	}
482	>
483	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
484	>	oneFourInteractions_.addPair(a, d);
485	>	} else {
486	>	excludedInteractions_.addPair(a, d);
487	>	}
488		}
489
490	<
491	<	}
490	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
491	>	inversion = mol->nextInversion(inversionIter)) {
492
493	<	void SimInfo::removeExcludePairs(Molecule* mol) {
494	<	std::vector<Bond*>::iterator bondIter;
495	<	std::vector<Bend*>::iterator bendIter;
496	<	std::vector<Torsion*>::iterator torsionIter;
493	>	a = inversion->getAtomA()->getGlobalIndex();
494	>	b = inversion->getAtomB()->getGlobalIndex();
495	>	c = inversion->getAtomC()->getGlobalIndex();
496	>	d = inversion->getAtomD()->getGlobalIndex();
497	>
498	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
499	>	oneTwoInteractions_.addPair(a, b);
500	>	oneTwoInteractions_.addPair(a, c);
501	>	oneTwoInteractions_.addPair(a, d);
502	>	} else {
503	>	excludedInteractions_.addPair(a, b);
504	>	excludedInteractions_.addPair(a, c);
505	>	excludedInteractions_.addPair(a, d);
506	>	}
507	>
508	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
509	>	oneThreeInteractions_.addPair(b, c);
510	>	oneThreeInteractions_.addPair(b, d);
511	>	oneThreeInteractions_.addPair(c, d);
512	>	} else {
513	>	excludedInteractions_.addPair(b, c);
514	>	excludedInteractions_.addPair(b, d);
515	>	excludedInteractions_.addPair(c, d);
516	>	}
517	>	}
518	>
519	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
520	>	rb = mol->nextRigidBody(rbIter)) {
521	>	vector<Atom*> atoms = rb->getAtoms();
522	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
523	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
524	>	a = atoms[i]->getGlobalIndex();
525	>	b = atoms[j]->getGlobalIndex();
526	>	excludedInteractions_.addPair(a, b);
527	>	}
528	>	}
529	>	}
530	>
531	>	}
532	>
533	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
534	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
535	>	vector<Bond*>::iterator bondIter;
536	>	vector<Bend*>::iterator bendIter;
537	>	vector<Torsion*>::iterator torsionIter;
538	>	vector<Inversion*>::iterator inversionIter;
539		Bond* bond;
540		Bend* bend;
541		Torsion* torsion;
542	+	Inversion* inversion;
543		int a;
544		int b;
545		int c;
546		int d;
547	+
548	+	map<int, set<int> > atomGroups;
549	+	Molecule::RigidBodyIterator rbIter;
550	+	RigidBody* rb;
551	+	Molecule::IntegrableObjectIterator ii;
552	+	StuntDouble* sd;
553
554	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
555	<	a = bond->getAtomA()->getGlobalIndex();
556	<	b = bond->getAtomB()->getGlobalIndex();
557	<	exclude_.removePair(a, b);
554	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
555	>	sd = mol->nextIntegrableObject(ii)) {
556	>
557	>	if (sd->isRigidBody()) {
558	>	rb = static_cast<RigidBody*>(sd);
559	>	vector<Atom*> atoms = rb->getAtoms();
560	>	set<int> rigidAtoms;
561	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
562	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
563	>	}
564	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
565	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
566	>	}
567	>	} else {
568	>	set<int> oneAtomSet;
569	>	oneAtomSet.insert(sd->getGlobalIndex());
570	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
571	>	}
572	>	}
573	>
574	>	for (bond= mol->beginBond(bondIter); bond != NULL;
575	>	bond = mol->nextBond(bondIter)) {
576	>
577	>	a = bond->getAtomA()->getGlobalIndex();
578	>	b = bond->getAtomB()->getGlobalIndex();
579	>
580	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
581	>	oneTwoInteractions_.removePair(a, b);
582	>	} else {
583	>	excludedInteractions_.removePair(a, b);
584	>	}
585		}
586
587	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
588	<	a = bend->getAtomA()->getGlobalIndex();
393	<	b = bend->getAtomB()->getGlobalIndex();
394	<	c = bend->getAtomC()->getGlobalIndex();
587	>	for (bend= mol->beginBend(bendIter); bend != NULL;
588	>	bend = mol->nextBend(bendIter)) {
589
590	<	exclude_.removePair(a, b);
591	<	exclude_.removePair(a, c);
592	<	exclude_.removePair(b, c);
590	>	a = bend->getAtomA()->getGlobalIndex();
591	>	b = bend->getAtomB()->getGlobalIndex();
592	>	c = bend->getAtomC()->getGlobalIndex();
593	>
594	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
595	>	oneTwoInteractions_.removePair(a, b);
596	>	oneTwoInteractions_.removePair(b, c);
597	>	} else {
598	>	excludedInteractions_.removePair(a, b);
599	>	excludedInteractions_.removePair(b, c);
600	>	}
601	>
602	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
603	>	oneThreeInteractions_.removePair(a, c);
604	>	} else {
605	>	excludedInteractions_.removePair(a, c);
606	>	}
607		}
608
609	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
610	<	a = torsion->getAtomA()->getGlobalIndex();
403	<	b = torsion->getAtomB()->getGlobalIndex();
404	<	c = torsion->getAtomC()->getGlobalIndex();
405	<	d = torsion->getAtomD()->getGlobalIndex();
609	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
610	>	torsion = mol->nextTorsion(torsionIter)) {
611
612	<	exclude_.removePair(a, b);
613	<	exclude_.removePair(a, c);
614	<	exclude_.removePair(a, d);
615	<	exclude_.removePair(b, c);
616	<	exclude_.removePair(b, d);
617	<	exclude_.removePair(c, d);
612	>	a = torsion->getAtomA()->getGlobalIndex();
613	>	b = torsion->getAtomB()->getGlobalIndex();
614	>	c = torsion->getAtomC()->getGlobalIndex();
615	>	d = torsion->getAtomD()->getGlobalIndex();
616	>
617	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
618	>	oneTwoInteractions_.removePair(a, b);
619	>	oneTwoInteractions_.removePair(b, c);
620	>	oneTwoInteractions_.removePair(c, d);
621	>	} else {
622	>	excludedInteractions_.removePair(a, b);
623	>	excludedInteractions_.removePair(b, c);
624	>	excludedInteractions_.removePair(c, d);
625	>	}
626	>
627	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
628	>	oneThreeInteractions_.removePair(a, c);
629	>	oneThreeInteractions_.removePair(b, d);
630	>	} else {
631	>	excludedInteractions_.removePair(a, c);
632	>	excludedInteractions_.removePair(b, d);
633	>	}
634	>
635	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
636	>	oneFourInteractions_.removePair(a, d);
637	>	} else {
638	>	excludedInteractions_.removePair(a, d);
639	>	}
640		}
641
642	<	}
642	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
643	>	inversion = mol->nextInversion(inversionIter)) {
644
645	+	a = inversion->getAtomA()->getGlobalIndex();
646	+	b = inversion->getAtomB()->getGlobalIndex();
647	+	c = inversion->getAtomC()->getGlobalIndex();
648	+	d = inversion->getAtomD()->getGlobalIndex();
649
650	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
651	<	int curStampId;
650	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
651	>	oneTwoInteractions_.removePair(a, b);
652	>	oneTwoInteractions_.removePair(a, c);
653	>	oneTwoInteractions_.removePair(a, d);
654	>	} else {
655	>	excludedInteractions_.removePair(a, b);
656	>	excludedInteractions_.removePair(a, c);
657	>	excludedInteractions_.removePair(a, d);
658	>	}
659
660	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
661	+	oneThreeInteractions_.removePair(b, c);
662	+	oneThreeInteractions_.removePair(b, d);
663	+	oneThreeInteractions_.removePair(c, d);
664	+	} else {
665	+	excludedInteractions_.removePair(b, c);
666	+	excludedInteractions_.removePair(b, d);
667	+	excludedInteractions_.removePair(c, d);
668	+	}
669	+	}
670	+
671	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
672	+	rb = mol->nextRigidBody(rbIter)) {
673	+	vector<Atom*> atoms = rb->getAtoms();
674	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
675	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
676	+	a = atoms[i]->getGlobalIndex();
677	+	b = atoms[j]->getGlobalIndex();
678	+	excludedInteractions_.removePair(a, b);
679	+	}
680	+	}
681	+	}
682	+
683	+	}
684	+
685	+
686	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
687	+	int curStampId;
688	+
689		//index from 0
690		curStampId = moleculeStamps_.size();
691
692		moleculeStamps_.push_back(molStamp);
693		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
694	<	}
694	>	}
695
428	–	void SimInfo::update() {
696
697	<	setupSimType();
698	<
699	<	#ifdef IS_MPI
700	<	setupFortranParallel();
701	<	#endif
702	<
703	<	setupFortranSim();
704	<
705	<	//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	<
697	>	/**
698	>	* update
699	>	*
700	>	*  Performs the global checks and variable settings after the
701	>	*  objects have been created.
702	>	*
703	>	*/
704	>	void SimInfo::update() {
705	>	setupSimVariables();
706		calcNdf();
707		calcNdfRaw();
708		calcNdfTrans();
709	<
710	<	fortranInitialized_ = true;
711	<	}
712	<
713	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
709	>	}
710	>
711	>	/**
712	>	* getSimulatedAtomTypes
713	>	*
714	>	* Returns an STL set of AtomType* that are actually present in this
715	>	* simulation.  Must query all processors to assemble this information.
716	>	*
717	>	*/
718	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
719		SimInfo::MoleculeIterator mi;
720		Molecule* mol;
721		Molecule::AtomIterator ai;
722		Atom* atom;
723	<	std::set<AtomType*> atomTypes;
724	<
723	>	set<AtomType*> atomTypes;
724	>
725		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
726	+	for(atom = mol->beginAtom(ai); atom != NULL;
727	+	atom = mol->nextAtom(ai)) {
728	+	atomTypes.insert(atom->getAtomType());
729	+	}
730	+	}
731	+
732	+	#ifdef IS_MPI
733
734	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
735	<	atomTypes.insert(atom->getAtomType());
736	<	}
737	<
738	<	}
734	>	// loop over the found atom types on this processor, and add their
735	>	// numerical idents to a vector:
736	>
737	>	vector<int> foundTypes;
738	>	set<AtomType*>::iterator i;
739	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
740	>	foundTypes.push_back( (*i)->getIdent() );
741
742	<	return atomTypes;
743	<	}
742	>	// count_local holds the number of found types on this processor
743	>	int count_local = foundTypes.size();
744
745	<	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();
745	>	int nproc = MPI::COMM_WORLD.Get_size();
746
747	<	//loop over all of the atom types
748	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
749	<	useLennardJones |= (*i)->isLennardJones();
750	<	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	<	}
747	>	// we need arrays to hold the counts and displacement vectors for
748	>	// all processors
749	>	vector<int> counts(nproc, 0);
750	>	vector<int> disps(nproc, 0);
751
752	<	if (useSticky || useDipole || useGayBerne || useShape) {
753	<	useDirectionalAtom = 1;
752	>	// fill the counts array
753	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
754	>	1, MPI::INT);
755	>
756	>	// use the processor counts to compute the displacement array
757	>	disps[0] = 0;
758	>	int totalCount = counts[0];
759	>	for (int iproc = 1; iproc < nproc; iproc++) {
760	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
761	>	totalCount += counts[iproc];
762		}
763
764	<	if (useCharge || useDipole) {
765	<	useElectrostatics = 1;
766	<	}
764	>	// we need a (possibly redundant) set of all found types:
765	>	vector<int> ftGlobal(totalCount);
766	>
767	>	// now spray out the foundTypes to all the other processors:
768	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
769	>	&ftGlobal[0], &counts[0], &disps[0],
770	>	MPI::INT);
771
772	<	#ifdef IS_MPI
520	<	int temp;
772	>	vector<int>::iterator j;
773
774	<	temp = usePBC;
775	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
774	>	// foundIdents is a stl set, so inserting an already found ident
775	>	// will have no effect.
776	>	set<int> foundIdents;
777
778	<	temp = useDirectionalAtom;
779	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
778	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
779	>	foundIdents.insert((*j));
780	>
781	>	// now iterate over the foundIdents and get the actual atom types
782	>	// that correspond to these:
783	>	set<int>::iterator it;
784	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
785	>	atomTypes.insert( forceField_->getAtomType((*it)) );
786	>
787	>	#endif
788
789	<	temp = useLennardJones;
790	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
789	>	return atomTypes;
790	>	}
791
531	–	temp = useElectrostatics;
532	–	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
792
793	<	temp = useCharge;
794	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
793	>	int getGlobalCountOfType(AtomType* atype) {
794	>	/*
795	>	set<AtomType*> atypes = getSimulatedAtomTypes();
796	>	map<AtomType*, int> counts_;
797
798	<	temp = useDipole;
799	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
798	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
799	>	for(atom = mol->beginAtom(ai); atom != NULL;
800	>	atom = mol->nextAtom(ai)) {
801	>	atom->getAtomType();
802	>	}
803	>	}
804	>	*/
805	>	return 0;
806	>	}
807
808	<	temp = useSticky;
809	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
808	>	void SimInfo::setupSimVariables() {
809	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
810	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
811	>	// parameter is true
812	>	calcBoxDipole_ = false;
813	>	if ( simParams_->haveAccumulateBoxDipole() )
814	>	if ( simParams_->getAccumulateBoxDipole() ) {
815	>	calcBoxDipole_ = true;
816	>	}
817	>
818	>	set<AtomType*>::iterator i;
819	>	set<AtomType*> atomTypes;
820	>	atomTypes = getSimulatedAtomTypes();
821	>	bool usesElectrostatic = false;
822	>	bool usesMetallic = false;
823	>	bool usesDirectional = false;
824	>	bool usesFluctuatingCharges =  false;
825	>	//loop over all of the atom types
826	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
827	>	usesElectrostatic |= (*i)->isElectrostatic();
828	>	usesMetallic |= (*i)->isMetal();
829	>	usesDirectional |= (*i)->isDirectional();
830	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
831	>	}
832
833	<	temp = useGayBerne;
834	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
833	>	#ifdef IS_MPI
834	>	bool temp;
835	>	temp = usesDirectional;
836	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
837	>	MPI::LOR);
838	>
839	>	temp = usesMetallic;
840	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
841	>	MPI::LOR);
842	>
843	>	temp = usesElectrostatic;
844	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
845	>	MPI::LOR);
846
847	<	temp = useEAM;
848	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
847	>	temp = usesFluctuatingCharges;
848	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
849	>	MPI::LOR);
850	>	#else
851
852	<	temp = useShape;
853	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
852	>	usesDirectionalAtoms_ = usesDirectional;
853	>	usesMetallicAtoms_ = usesMetallic;
854	>	usesElectrostaticAtoms_ = usesElectrostatic;
855	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
856
552	–	temp = useFLARB;
553	–	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
554	–
555	–	temp = useRF;
556	–	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
557	–
857		#endif
858	+
859	+	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
860	+	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
861	+	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
862	+	}
863
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;
864
865	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
865	>	vector<int> SimInfo::getGlobalAtomIndices() {
866	>	SimInfo::MoleculeIterator mi;
867	>	Molecule* mol;
868	>	Molecule::AtomIterator ai;
869	>	Atom* atom;
870
871	<	if (simParams_->haveDielectric()) {
872	<	fInfo_.dielect = simParams_->getDielectric();
873	<	} else {
874	<	sprintf(painCave.errMsg,
875	<	"SimSetup Error: No Dielectric constant was set.\n"
876	<	"\tYou are trying to use Reaction Field without"
877	<	"\tsetting a dielectric constant!\n");
582	<	painCave.isFatal = 1;
583	<	simError();
584	<	}
585	<
586	<	} else {
587	<	fInfo_.dielect = 0.0;
871	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
872	>
873	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
874	>
875	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
876	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
877	>	}
878		}
879	+	return GlobalAtomIndices;
880	+	}
881
590	–	}
882
883	<	void SimInfo::setupFortranSim() {
884	<	int isError;
885	<	int nExclude;
886	<	std::vector<int> fortranGlobalGroupMembership;
887	<
597	<	nExclude = exclude_.getSize();
598	<	isError = 0;
883	>	vector<int> SimInfo::getGlobalGroupIndices() {
884	>	SimInfo::MoleculeIterator mi;
885	>	Molecule* mol;
886	>	Molecule::CutoffGroupIterator ci;
887	>	CutoffGroup* cg;
888
889	<	//globalGroupMembership_ is filled by SimCreator
890	<	for (int i = 0; i < nGlobalAtoms_; i++) {
891	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
889	>	vector<int> GlobalGroupIndices;
890	>
891	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
892	>
893	>	//local index of cutoff group is trivial, it only depends on the
894	>	//order of travesing
895	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
896	>	cg = mol->nextCutoffGroup(ci)) {
897	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
898	>	}
899		}
900	+	return GlobalGroupIndices;
901	+	}
902
903	+
904	+	void SimInfo::prepareTopology() {
905	+
906		//calculate mass ratio of cutoff group
606	–	std::vector<double> mfact;
907		SimInfo::MoleculeIterator mi;
908		Molecule* mol;
909		Molecule::CutoffGroupIterator ci;
910		CutoffGroup* cg;
911		Molecule::AtomIterator ai;
912		Atom* atom;
913	<	double totalMass;
913	>	RealType totalMass;
914
915	<	//to avoid memory reallocation, reserve enough space for mfact
916	<	mfact.reserve(getNCutoffGroups());
915	>	/**
916	>	* The mass factor is the relative mass of an atom to the total
917	>	* mass of the cutoff group it belongs to.  By default, all atoms
918	>	* are their own cutoff groups, and therefore have mass factors of
919	>	* 1.  We need some special handling for massless atoms, which
920	>	* will be treated as carrying the entire mass of the cutoff
921	>	* group.
922	>	*/
923	>	massFactors_.clear();
924	>	massFactors_.resize(getNAtoms(), 1.0);
925
926		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
927	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
927	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
928	>	cg = mol->nextCutoffGroup(ci)) {
929
930	<	totalMass = cg->getMass();
931	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
932	<	mfact.push_back(atom->getMass()/totalMass);
933	<	}
934	<
935	<	}
930	>	totalMass = cg->getMass();
931	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
932	>	// Check for massless groups - set mfact to 1 if true
933	>	if (totalMass != 0)
934	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
935	>	else
936	>	massFactors_[atom->getLocalIndex()] = 1.0;
937	>	}
938	>	}
939		}
940
941	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
630	<	std::vector<int> identArray;
941	>	// Build the identArray_
942
943	<	//to avoid memory reallocation, reserve enough space identArray
944	<	identArray.reserve(getNAtoms());
634	<
943	>	identArray_.clear();
944	>	identArray_.reserve(getNAtoms());
945		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
946	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
947	<	identArray.push_back(atom->getIdent());
948	<	}
946	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
947	>	identArray_.push_back(atom->getIdent());
948	>	}
949		}
950	+
951	+	topologyDone_ = true;
952	+	}
953
954	<	//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	<	}
647	<
648	<	//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);
658	<
659	<	if( isError ){
660	<
661	<	sprintf( painCave.errMsg,
662	<	"There was an error setting the simulation information in fortran.\n" );
663	<	painCave.isFatal = 1;
664	<	painCave.severity = OOPSE_ERROR;
665	<	simError();
666	<	}
667	<
668	<	#ifdef IS_MPI
669	<	sprintf( checkPointMsg,
670	<	"succesfully sent the simulation information to fortran.\n");
671	<	MPIcheckPoint();
672	<	#endif // is_mpi
673	<	}
674	<
675	<
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) {
954	>	void SimInfo::addProperty(GenericData* genData) {
955		properties_.addProperty(genData);
956	<	}
956	>	}
957
958	<	void SimInfo::removeProperty(const std::string& propName) {
958	>	void SimInfo::removeProperty(const string& propName) {
959		properties_.removeProperty(propName);
960	<	}
960	>	}
961
962	<	void SimInfo::clearProperties() {
962	>	void SimInfo::clearProperties() {
963		properties_.clearProperties();
964	<	}
964	>	}
965
966	<	std::vector<std::string> SimInfo::getPropertyNames() {
966	>	vector<string> SimInfo::getPropertyNames() {
967		return properties_.getPropertyNames();
968	<	}
968	>	}
969
970	<	std::vector<GenericData*> SimInfo::getProperties() {
970	>	vector<GenericData*> SimInfo::getProperties() {
971		return properties_.getProperties();
972	<	}
972	>	}
973
974	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
974	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
975		return properties_.getPropertyByName(propName);
976	<	}
976	>	}
977
978	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
979	<	//if (sman_ == sman_) {
980	<	//    return;
981	<	//}
982	<
843	<	//delete sman_;
978	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
979	>	if (sman_ == sman) {
980	>	return;
981	>	}
982	>	delete sman_;
983		sman_ = sman;
984
985		Molecule* mol;
986		RigidBody* rb;
987		Atom* atom;
988	+	CutoffGroup* cg;
989		SimInfo::MoleculeIterator mi;
990		Molecule::RigidBodyIterator rbIter;
991	<	Molecule::AtomIterator atomIter;;
991	>	Molecule::AtomIterator atomIter;
992	>	Molecule::CutoffGroupIterator cgIter;
993
994		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
995
996	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
997	<	atom->setSnapshotManager(sman_);
998	<	}
996	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
997	>	atom = mol->nextAtom(atomIter)) {
998	>	atom->setSnapshotManager(sman_);
999	>	}
1000
1001	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1002	<	rb->setSnapshotManager(sman_);
1003	<	}
1001	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1002	>	rb = mol->nextRigidBody(rbIter)) {
1003	>	rb->setSnapshotManager(sman_);
1004	>	}
1005	>
1006	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1007	>	cg = mol->nextCutoffGroup(cgIter)) {
1008	>	cg->setSnapshotManager(sman_);
1009	>	}
1010		}
1011
1012	<	}
1012	>	}
1013
866	–	Vector3d SimInfo::getComVel(){
867	–	SimInfo::MoleculeIterator i;
868	–	Molecule* mol;
1014
1015	<	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	<	}
1015	>	ostream& operator <<(ostream& o, SimInfo& info) {
1016
1017	<	#ifdef IS_MPI
1018	<	double tmpMass = totalMass;
1019	<	Vector3d tmpComVel(comVel);
1020	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1021	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1022	<	#endif
1017	>	return o;
1018	>	}
1019	>
1020	>
1021	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1022	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1023	>	sprintf(painCave.errMsg,
1024	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1025	>	"\tindex exceeds number of known objects!\n");
1026	>	painCave.isFatal = 1;
1027	>	simError();
1028	>	return NULL;
1029	>	} else
1030	>	return IOIndexToIntegrableObject.at(index);
1031	>	}
1032	>
1033	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1034	>	IOIndexToIntegrableObject= v;
1035	>	}
1036
1037	<	comVel /= totalMass;
1038	<
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	<
1037	>	int SimInfo::getNGlobalConstraints() {
1038	>	int nGlobalConstraints;
1039		#ifdef IS_MPI
1040	<	double tmpMass = totalMass;
1041	<	Vector3d tmpCom(com);
1042	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1043	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1040	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1041	>	MPI::INT, MPI::SUM);
1042	>	#else
1043	>	nGlobalConstraints =  nConstraints_;
1044		#endif
1045	+	return nGlobalConstraints;
1046	+	}
1047
1048	<	com /= totalMass;
1048	>	}//end namespace OpenMD
1049
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.
Revision 1908 by gezelter, Fri Jul 19 21:25:45 2013 UTC

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