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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 1769 by gezelter, Mon Jul 9 14:15:52 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(); i !=components.end(); ++i) {
92	>	molStamp = (*i)->getMoleculeStamp();
93	>	nMolWithSameStamp = (*i)->getNMol();
94	>
95	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
96	>
97	>	//calculate atoms in molecules
98	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
99	>
100	>	//calculate atoms in cutoff groups
101	>	int nAtomsInGroups = 0;
102	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
103	>
104	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
105	>	cgStamp = molStamp->getCutoffGroupStamp(j);
106	>	nAtomsInGroups += cgStamp->getNMembers();
107	>	}
108	>
109	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
110	>
111	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
112	>
113	>	//calculate atoms in rigid bodies
114	>	int nAtomsInRigidBodies = 0;
115	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
116	>
117	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
118	>	rbStamp = molStamp->getRigidBodyStamp(j);
119	>	nAtomsInRigidBodies += rbStamp->getNMembers();
120	>	}
121	>
122	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
123	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
124	>
125		}
126	+
127	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
128	+	//group therefore the total number of cutoff groups in the system is
129	+	//equal to the total number of atoms minus number of atoms belong to
130	+	//cutoff group defined in meta-data file plus the number of cutoff
131	+	//groups defined in meta-data file
132
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
133		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134	<
135	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
136	<	//therefore the total number of  integrable objects in the system is equal to
137	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
138	<	//file plus the number of  rigid bodies defined in meta-data file
139	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
140	<
134	>
135	>	//every free atom (atom does not belong to rigid bodies) is an
136	>	//integrable object therefore the total number of integrable objects
137	>	//in the system is equal to the total number of atoms minus number of
138	>	//atoms belong to rigid body defined in meta-data file plus the number
139	>	//of rigid bodies defined in meta-data file
140	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
141	>	+ nGlobalRigidBodies_;
142	>
143		nGlobalMols_ = molStampIds_.size();
137	–
138	–	#ifdef IS_MPI
144		molToProcMap_.resize(nGlobalMols_);
145	<	#endif
146	<
147	<	}
148	<
144	<	SimInfo::~SimInfo() {
145	<	std::map<int, Molecule*>::iterator i;
145	>	}
146	>
147	>	SimInfo::~SimInfo() {
148	>	map<int, Molecule*>::iterator i;
149		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
150	<	delete i->second;
150	>	delete i->second;
151		}
152		molecules_.clear();
153	<
151	<	MemoryUtils::deletePointers(moleculeStamps_);
152	<
153	>
154		delete sman_;
155		delete simParams_;
156		delete forceField_;
157	<	}
157	>	}
158
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	–	}
159
160	<	bool SimInfo::addMolecule(Molecule* mol) {
160	>	bool SimInfo::addMolecule(Molecule* mol) {
161		MoleculeIterator i;
162	<
162	>
163		i = molecules_.find(mol->getGlobalIndex());
164		if (i == molecules_.end() ) {
165	<
166	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
167	<
168	<	nAtoms_ += mol->getNAtoms();
169	<	nBonds_ += mol->getNBonds();
170	<	nBends_ += mol->getNBends();
171	<	nTorsions_ += mol->getNTorsions();
172	<	nRigidBodies_ += mol->getNRigidBodies();
173	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
174	<	nCutoffGroups_ += mol->getNCutoffGroups();
175	<	nConstraints_ += mol->getNConstraintPairs();
176	<
177	<	addExcludePairs(mol);
178	<
179	<	return true;
180	<	} else {
181	<	return false;
165	>
166	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
167	>
168	>	nAtoms_ += mol->getNAtoms();
169	>	nBonds_ += mol->getNBonds();
170	>	nBends_ += mol->getNBends();
171	>	nTorsions_ += mol->getNTorsions();
172	>	nInversions_ += mol->getNInversions();
173	>	nRigidBodies_ += mol->getNRigidBodies();
174	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
175	>	nCutoffGroups_ += mol->getNCutoffGroups();
176	>	nConstraints_ += mol->getNConstraintPairs();
177	>
178	>	addInteractionPairs(mol);
179	>
180	>	return true;
181	>	} else {
182	>	return false;
183		}
184	<	}
185	<
186	<	bool SimInfo::removeMolecule(Molecule* mol) {
184	>	}
185	>
186	>	bool SimInfo::removeMolecule(Molecule* mol) {
187		MoleculeIterator i;
188		i = molecules_.find(mol->getGlobalIndex());
189
190		if (i != molecules_.end() ) {
191
192	<	assert(mol == i->second);
192	>	assert(mol == i->second);
193
194	<	nAtoms_ -= mol->getNAtoms();
195	<	nBonds_ -= mol->getNBonds();
196	<	nBends_ -= mol->getNBends();
197	<	nTorsions_ -= mol->getNTorsions();
198	<	nRigidBodies_ -= mol->getNRigidBodies();
199	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
200	<	nCutoffGroups_ -= mol->getNCutoffGroups();
201	<	nConstraints_ -= mol->getNConstraintPairs();
194	>	nAtoms_ -= mol->getNAtoms();
195	>	nBonds_ -= mol->getNBonds();
196	>	nBends_ -= mol->getNBends();
197	>	nTorsions_ -= mol->getNTorsions();
198	>	nInversions_ -= mol->getNInversions();
199	>	nRigidBodies_ -= mol->getNRigidBodies();
200	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
201	>	nCutoffGroups_ -= mol->getNCutoffGroups();
202	>	nConstraints_ -= mol->getNConstraintPairs();
203
204	<	removeExcludePairs(mol);
205	<	molecules_.erase(mol->getGlobalIndex());
204	>	removeInteractionPairs(mol);
205	>	molecules_.erase(mol->getGlobalIndex());
206
207	<	delete mol;
207	>	delete mol;
208
209	<	return true;
209	>	return true;
210		} else {
211	<	return false;
211	>	return false;
212		}
213	+	}
214
221	–
222	–	}
223	–
215
216	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
216	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
217		i = molecules_.begin();
218		return i == molecules_.end() ? NULL : i->second;
219	<	}
219	>	}
220
221	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
221	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
222		++i;
223		return i == molecules_.end() ? NULL : i->second;
224	<	}
224	>	}
225
226
227	<	void SimInfo::calcNdf() {
228	<	int ndf_local;
227	>	void SimInfo::calcNdf() {
228	>	int ndf_local, nfq_local;
229		MoleculeIterator i;
230	<	std::vector<StuntDouble*>::iterator j;
230	>	vector<StuntDouble*>::iterator j;
231	>	vector<Atom*>::iterator k;
232	>
233		Molecule* mol;
234	<	StuntDouble* integrableObject;
234	>	StuntDouble* sd;
235	>	Atom* atom;
236
237		ndf_local = 0;
238	+	nfq_local = 0;
239
240		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
246	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
247	–	integrableObject = mol->nextIntegrableObject(j)) {
241
242	<	ndf_local += 3;
242	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
243	>	sd = mol->nextIntegrableObject(j)) {
244
245	<	if (integrableObject->isDirectional()) {
246	<	if (integrableObject->isLinear()) {
247	<	ndf_local += 2;
248	<	} else {
249	<	ndf_local += 3;
250	<	}
251	<	}
252	<
253	<	}//end for (integrableObject)
254	<	}// end for (mol)
245	>	ndf_local += 3;
246	>
247	>	if (sd->isDirectional()) {
248	>	if (sd->isLinear()) {
249	>	ndf_local += 2;
250	>	} else {
251	>	ndf_local += 3;
252	>	}
253	>	}
254	>	}
255	>
256	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
257	>	atom = mol->nextFluctuatingCharge(k)) {
258	>	if (atom->isFluctuatingCharge()) {
259	>	nfq_local++;
260	>	}
261	>	}
262	>	}
263
264	+	ndfLocal_ = ndf_local;
265	+
266		// n_constraints is local, so subtract them on each processor
267		ndf_local -= nConstraints_;
268
269		#ifdef IS_MPI
270		MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
271	+	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
272		#else
273		ndf_ = ndf_local;
274	+	nGlobalFluctuatingCharges_ = nfq_local;
275		#endif
276
277		// nZconstraints_ is global, as are the 3 COM translations for the
278		// entire system:
279		ndf_ = ndf_ - 3 - nZconstraint_;
280
281	<	}
281	>	}
282
283	<	void SimInfo::calcNdfRaw() {
283	>	int SimInfo::getFdf() {
284	>	#ifdef IS_MPI
285	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
286	>	#else
287	>	fdf_ = fdf_local;
288	>	#endif
289	>	return fdf_;
290	>	}
291	>
292	>	unsigned int SimInfo::getNLocalCutoffGroups(){
293	>	int nLocalCutoffAtoms = 0;
294	>	Molecule* mol;
295	>	MoleculeIterator mi;
296	>	CutoffGroup* cg;
297	>	Molecule::CutoffGroupIterator ci;
298	>
299	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
300	>
301	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
302	>	cg = mol->nextCutoffGroup(ci)) {
303	>	nLocalCutoffAtoms += cg->getNumAtom();
304	>
305	>	}
306	>	}
307	>
308	>	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
309	>	}
310	>
311	>	void SimInfo::calcNdfRaw() {
312		int ndfRaw_local;
313
314		MoleculeIterator i;
315	<	std::vector<StuntDouble*>::iterator j;
315	>	vector<StuntDouble*>::iterator j;
316		Molecule* mol;
317	<	StuntDouble* integrableObject;
317	>	StuntDouble* sd;
318
319		// Raw degrees of freedom that we have to set
320		ndfRaw_local = 0;
321
322		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
289	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
290	–	integrableObject = mol->nextIntegrableObject(j)) {
323
324	<	ndfRaw_local += 3;
324	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
325	>	sd = mol->nextIntegrableObject(j)) {
326
327	<	if (integrableObject->isDirectional()) {
328	<	if (integrableObject->isLinear()) {
329	<	ndfRaw_local += 2;
330	<	} else {
331	<	ndfRaw_local += 3;
332	<	}
333	<	}
327	>	ndfRaw_local += 3;
328	>
329	>	if (sd->isDirectional()) {
330	>	if (sd->isLinear()) {
331	>	ndfRaw_local += 2;
332	>	} else {
333	>	ndfRaw_local += 3;
334	>	}
335	>	}
336
337	<	}
337	>	}
338		}
339
340		#ifdef IS_MPI
#	Line 307 | Line 342 | void SimInfo::calcNdfRaw() {
342		#else
343		ndfRaw_ = ndfRaw_local;
344		#endif
345	<	}
345	>	}
346
347	<	void SimInfo::calcNdfTrans() {
347	>	void SimInfo::calcNdfTrans() {
348		int ndfTrans_local;
349
350		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 323 | Line 358 | void SimInfo::calcNdfTrans() {
358
359		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
360
361	<	}
361	>	}
362
363	<	void SimInfo::addExcludePairs(Molecule* mol) {
364	<	std::vector<Bond*>::iterator bondIter;
365	<	std::vector<Bend*>::iterator bendIter;
366	<	std::vector<Torsion*>::iterator torsionIter;
363	>	void SimInfo::addInteractionPairs(Molecule* mol) {
364	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
365	>	vector<Bond*>::iterator bondIter;
366	>	vector<Bend*>::iterator bendIter;
367	>	vector<Torsion*>::iterator torsionIter;
368	>	vector<Inversion*>::iterator inversionIter;
369		Bond* bond;
370		Bend* bend;
371		Torsion* torsion;
372	+	Inversion* inversion;
373		int a;
374		int b;
375		int c;
376		int d;
377	+
378	+	// atomGroups can be used to add special interaction maps between
379	+	// groups of atoms that are in two separate rigid bodies.
380	+	// However, most site-site interactions between two rigid bodies
381	+	// are probably not special, just the ones between the physically
382	+	// bonded atoms.  Interactions *within* a single rigid body should
383	+	// always be excluded.  These are done at the bottom of this
384	+	// function.
385	+
386	+	map<int, set<int> > atomGroups;
387	+	Molecule::RigidBodyIterator rbIter;
388	+	RigidBody* rb;
389	+	Molecule::IntegrableObjectIterator ii;
390	+	StuntDouble* sd;
391
392	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
393	<	a = bond->getAtomA()->getGlobalIndex();
394	<	b = bond->getAtomB()->getGlobalIndex();
395	<	exclude_.addPair(a, b);
392	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
393	>	sd = mol->nextIntegrableObject(ii)) {
394	>
395	>	if (sd->isRigidBody()) {
396	>	rb = static_cast<RigidBody*>(sd);
397	>	vector<Atom*> atoms = rb->getAtoms();
398	>	set<int> rigidAtoms;
399	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
400	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
401	>	}
402	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
403	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
404	>	}
405	>	} else {
406	>	set<int> oneAtomSet;
407	>	oneAtomSet.insert(sd->getGlobalIndex());
408	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
409	>	}
410	>	}
411	>
412	>	for (bond= mol->beginBond(bondIter); bond != NULL;
413	>	bond = mol->nextBond(bondIter)) {
414	>
415	>	a = bond->getAtomA()->getGlobalIndex();
416	>	b = bond->getAtomB()->getGlobalIndex();
417	>
418	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
419	>	oneTwoInteractions_.addPair(a, b);
420	>	} else {
421	>	excludedInteractions_.addPair(a, b);
422	>	}
423		}
424
425	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
426	<	a = bend->getAtomA()->getGlobalIndex();
348	<	b = bend->getAtomB()->getGlobalIndex();
349	<	c = bend->getAtomC()->getGlobalIndex();
425	>	for (bend= mol->beginBend(bendIter); bend != NULL;
426	>	bend = mol->nextBend(bendIter)) {
427
428	<	exclude_.addPair(a, b);
429	<	exclude_.addPair(a, c);
430	<	exclude_.addPair(b, c);
428	>	a = bend->getAtomA()->getGlobalIndex();
429	>	b = bend->getAtomB()->getGlobalIndex();
430	>	c = bend->getAtomC()->getGlobalIndex();
431	>
432	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
433	>	oneTwoInteractions_.addPair(a, b);
434	>	oneTwoInteractions_.addPair(b, c);
435	>	} else {
436	>	excludedInteractions_.addPair(a, b);
437	>	excludedInteractions_.addPair(b, c);
438	>	}
439	>
440	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
441	>	oneThreeInteractions_.addPair(a, c);
442	>	} else {
443	>	excludedInteractions_.addPair(a, c);
444	>	}
445		}
446
447	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
448	<	a = torsion->getAtomA()->getGlobalIndex();
358	<	b = torsion->getAtomB()->getGlobalIndex();
359	<	c = torsion->getAtomC()->getGlobalIndex();
360	<	d = torsion->getAtomD()->getGlobalIndex();
447	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
448	>	torsion = mol->nextTorsion(torsionIter)) {
449
450	<	exclude_.addPair(a, b);
451	<	exclude_.addPair(a, c);
452	<	exclude_.addPair(a, d);
453	<	exclude_.addPair(b, c);
454	<	exclude_.addPair(b, d);
455	<	exclude_.addPair(c, d);
450	>	a = torsion->getAtomA()->getGlobalIndex();
451	>	b = torsion->getAtomB()->getGlobalIndex();
452	>	c = torsion->getAtomC()->getGlobalIndex();
453	>	d = torsion->getAtomD()->getGlobalIndex();
454	>
455	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
456	>	oneTwoInteractions_.addPair(a, b);
457	>	oneTwoInteractions_.addPair(b, c);
458	>	oneTwoInteractions_.addPair(c, d);
459	>	} else {
460	>	excludedInteractions_.addPair(a, b);
461	>	excludedInteractions_.addPair(b, c);
462	>	excludedInteractions_.addPair(c, d);
463	>	}
464	>
465	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
466	>	oneThreeInteractions_.addPair(a, c);
467	>	oneThreeInteractions_.addPair(b, d);
468	>	} else {
469	>	excludedInteractions_.addPair(a, c);
470	>	excludedInteractions_.addPair(b, d);
471	>	}
472	>
473	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
474	>	oneFourInteractions_.addPair(a, d);
475	>	} else {
476	>	excludedInteractions_.addPair(a, d);
477	>	}
478		}
479
480	<
481	<	}
480	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
481	>	inversion = mol->nextInversion(inversionIter)) {
482
483	<	void SimInfo::removeExcludePairs(Molecule* mol) {
484	<	std::vector<Bond*>::iterator bondIter;
485	<	std::vector<Bend*>::iterator bendIter;
486	<	std::vector<Torsion*>::iterator torsionIter;
483	>	a = inversion->getAtomA()->getGlobalIndex();
484	>	b = inversion->getAtomB()->getGlobalIndex();
485	>	c = inversion->getAtomC()->getGlobalIndex();
486	>	d = inversion->getAtomD()->getGlobalIndex();
487	>
488	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
489	>	oneTwoInteractions_.addPair(a, b);
490	>	oneTwoInteractions_.addPair(a, c);
491	>	oneTwoInteractions_.addPair(a, d);
492	>	} else {
493	>	excludedInteractions_.addPair(a, b);
494	>	excludedInteractions_.addPair(a, c);
495	>	excludedInteractions_.addPair(a, d);
496	>	}
497	>
498	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
499	>	oneThreeInteractions_.addPair(b, c);
500	>	oneThreeInteractions_.addPair(b, d);
501	>	oneThreeInteractions_.addPair(c, d);
502	>	} else {
503	>	excludedInteractions_.addPair(b, c);
504	>	excludedInteractions_.addPair(b, d);
505	>	excludedInteractions_.addPair(c, d);
506	>	}
507	>	}
508	>
509	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
510	>	rb = mol->nextRigidBody(rbIter)) {
511	>	vector<Atom*> atoms = rb->getAtoms();
512	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
513	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
514	>	a = atoms[i]->getGlobalIndex();
515	>	b = atoms[j]->getGlobalIndex();
516	>	excludedInteractions_.addPair(a, b);
517	>	}
518	>	}
519	>	}
520	>
521	>	}
522	>
523	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
524	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
525	>	vector<Bond*>::iterator bondIter;
526	>	vector<Bend*>::iterator bendIter;
527	>	vector<Torsion*>::iterator torsionIter;
528	>	vector<Inversion*>::iterator inversionIter;
529		Bond* bond;
530		Bend* bend;
531		Torsion* torsion;
532	+	Inversion* inversion;
533		int a;
534		int b;
535		int c;
536		int d;
537	+
538	+	map<int, set<int> > atomGroups;
539	+	Molecule::RigidBodyIterator rbIter;
540	+	RigidBody* rb;
541	+	Molecule::IntegrableObjectIterator ii;
542	+	StuntDouble* sd;
543
544	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
545	<	a = bond->getAtomA()->getGlobalIndex();
546	<	b = bond->getAtomB()->getGlobalIndex();
547	<	exclude_.removePair(a, b);
544	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
545	>	sd = mol->nextIntegrableObject(ii)) {
546	>
547	>	if (sd->isRigidBody()) {
548	>	rb = static_cast<RigidBody*>(sd);
549	>	vector<Atom*> atoms = rb->getAtoms();
550	>	set<int> rigidAtoms;
551	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
552	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
553	>	}
554	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
555	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
556	>	}
557	>	} else {
558	>	set<int> oneAtomSet;
559	>	oneAtomSet.insert(sd->getGlobalIndex());
560	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
561	>	}
562	>	}
563	>
564	>	for (bond= mol->beginBond(bondIter); bond != NULL;
565	>	bond = mol->nextBond(bondIter)) {
566	>
567	>	a = bond->getAtomA()->getGlobalIndex();
568	>	b = bond->getAtomB()->getGlobalIndex();
569	>
570	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
571	>	oneTwoInteractions_.removePair(a, b);
572	>	} else {
573	>	excludedInteractions_.removePair(a, b);
574	>	}
575		}
576
577	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
578	<	a = bend->getAtomA()->getGlobalIndex();
393	<	b = bend->getAtomB()->getGlobalIndex();
394	<	c = bend->getAtomC()->getGlobalIndex();
577	>	for (bend= mol->beginBend(bendIter); bend != NULL;
578	>	bend = mol->nextBend(bendIter)) {
579
580	<	exclude_.removePair(a, b);
581	<	exclude_.removePair(a, c);
582	<	exclude_.removePair(b, c);
580	>	a = bend->getAtomA()->getGlobalIndex();
581	>	b = bend->getAtomB()->getGlobalIndex();
582	>	c = bend->getAtomC()->getGlobalIndex();
583	>
584	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
585	>	oneTwoInteractions_.removePair(a, b);
586	>	oneTwoInteractions_.removePair(b, c);
587	>	} else {
588	>	excludedInteractions_.removePair(a, b);
589	>	excludedInteractions_.removePair(b, c);
590	>	}
591	>
592	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
593	>	oneThreeInteractions_.removePair(a, c);
594	>	} else {
595	>	excludedInteractions_.removePair(a, c);
596	>	}
597		}
598
599	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
600	<	a = torsion->getAtomA()->getGlobalIndex();
403	<	b = torsion->getAtomB()->getGlobalIndex();
404	<	c = torsion->getAtomC()->getGlobalIndex();
405	<	d = torsion->getAtomD()->getGlobalIndex();
599	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
600	>	torsion = mol->nextTorsion(torsionIter)) {
601
602	<	exclude_.removePair(a, b);
603	<	exclude_.removePair(a, c);
604	<	exclude_.removePair(a, d);
605	<	exclude_.removePair(b, c);
606	<	exclude_.removePair(b, d);
607	<	exclude_.removePair(c, d);
602	>	a = torsion->getAtomA()->getGlobalIndex();
603	>	b = torsion->getAtomB()->getGlobalIndex();
604	>	c = torsion->getAtomC()->getGlobalIndex();
605	>	d = torsion->getAtomD()->getGlobalIndex();
606	>
607	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
608	>	oneTwoInteractions_.removePair(a, b);
609	>	oneTwoInteractions_.removePair(b, c);
610	>	oneTwoInteractions_.removePair(c, d);
611	>	} else {
612	>	excludedInteractions_.removePair(a, b);
613	>	excludedInteractions_.removePair(b, c);
614	>	excludedInteractions_.removePair(c, d);
615	>	}
616	>
617	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
618	>	oneThreeInteractions_.removePair(a, c);
619	>	oneThreeInteractions_.removePair(b, d);
620	>	} else {
621	>	excludedInteractions_.removePair(a, c);
622	>	excludedInteractions_.removePair(b, d);
623	>	}
624	>
625	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
626	>	oneFourInteractions_.removePair(a, d);
627	>	} else {
628	>	excludedInteractions_.removePair(a, d);
629	>	}
630		}
631
632	<	}
632	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
633	>	inversion = mol->nextInversion(inversionIter)) {
634
635	+	a = inversion->getAtomA()->getGlobalIndex();
636	+	b = inversion->getAtomB()->getGlobalIndex();
637	+	c = inversion->getAtomC()->getGlobalIndex();
638	+	d = inversion->getAtomD()->getGlobalIndex();
639
640	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
641	<	int curStampId;
640	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
641	>	oneTwoInteractions_.removePair(a, b);
642	>	oneTwoInteractions_.removePair(a, c);
643	>	oneTwoInteractions_.removePair(a, d);
644	>	} else {
645	>	excludedInteractions_.removePair(a, b);
646	>	excludedInteractions_.removePair(a, c);
647	>	excludedInteractions_.removePair(a, d);
648	>	}
649
650	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
651	+	oneThreeInteractions_.removePair(b, c);
652	+	oneThreeInteractions_.removePair(b, d);
653	+	oneThreeInteractions_.removePair(c, d);
654	+	} else {
655	+	excludedInteractions_.removePair(b, c);
656	+	excludedInteractions_.removePair(b, d);
657	+	excludedInteractions_.removePair(c, d);
658	+	}
659	+	}
660	+
661	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
662	+	rb = mol->nextRigidBody(rbIter)) {
663	+	vector<Atom*> atoms = rb->getAtoms();
664	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
665	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
666	+	a = atoms[i]->getGlobalIndex();
667	+	b = atoms[j]->getGlobalIndex();
668	+	excludedInteractions_.removePair(a, b);
669	+	}
670	+	}
671	+	}
672	+
673	+	}
674	+
675	+
676	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
677	+	int curStampId;
678	+
679		//index from 0
680		curStampId = moleculeStamps_.size();
681
682		moleculeStamps_.push_back(molStamp);
683		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
684	<	}
684	>	}
685
428	–	void SimInfo::update() {
686
687	<	setupSimType();
688	<
689	<	#ifdef IS_MPI
690	<	setupFortranParallel();
691	<	#endif
692	<
693	<	setupFortranSim();
694	<
695	<	//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	<
687	>	/**
688	>	* update
689	>	*
690	>	*  Performs the global checks and variable settings after the
691	>	*  objects have been created.
692	>	*
693	>	*/
694	>	void SimInfo::update() {
695	>	setupSimVariables();
696		calcNdf();
697		calcNdfRaw();
698		calcNdfTrans();
699	<
700	<	fortranInitialized_ = true;
701	<	}
702	<
703	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
699	>	}
700	>
701	>	/**
702	>	* getSimulatedAtomTypes
703	>	*
704	>	* Returns an STL set of AtomType* that are actually present in this
705	>	* simulation.  Must query all processors to assemble this information.
706	>	*
707	>	*/
708	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
709		SimInfo::MoleculeIterator mi;
710		Molecule* mol;
711		Molecule::AtomIterator ai;
712		Atom* atom;
713	<	std::set<AtomType*> atomTypes;
714	<
713	>	set<AtomType*> atomTypes;
714	>
715		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
716	+	for(atom = mol->beginAtom(ai); atom != NULL;
717	+	atom = mol->nextAtom(ai)) {
718	+	atomTypes.insert(atom->getAtomType());
719	+	}
720	+	}
721	+
722	+	#ifdef IS_MPI
723
724	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
725	<	atomTypes.insert(atom->getAtomType());
726	<	}
727	<
728	<	}
724	>	// loop over the found atom types on this processor, and add their
725	>	// numerical idents to a vector:
726	>
727	>	vector<int> foundTypes;
728	>	set<AtomType*>::iterator i;
729	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
730	>	foundTypes.push_back( (*i)->getIdent() );
731
732	<	return atomTypes;
733	<	}
732	>	// count_local holds the number of found types on this processor
733	>	int count_local = foundTypes.size();
734
735	<	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();
735	>	int nproc = MPI::COMM_WORLD.Get_size();
736
737	<	//loop over all of the atom types
738	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
739	<	useLennardJones |= (*i)->isLennardJones();
740	<	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	<	}
737	>	// we need arrays to hold the counts and displacement vectors for
738	>	// all processors
739	>	vector<int> counts(nproc, 0);
740	>	vector<int> disps(nproc, 0);
741
742	<	if (useSticky || useDipole || useGayBerne || useShape) {
743	<	useDirectionalAtom = 1;
742	>	// fill the counts array
743	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
744	>	1, MPI::INT);
745	>
746	>	// use the processor counts to compute the displacement array
747	>	disps[0] = 0;
748	>	int totalCount = counts[0];
749	>	for (int iproc = 1; iproc < nproc; iproc++) {
750	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
751	>	totalCount += counts[iproc];
752		}
753
754	<	if (useCharge || useDipole) {
755	<	useElectrostatics = 1;
756	<	}
754	>	// we need a (possibly redundant) set of all found types:
755	>	vector<int> ftGlobal(totalCount);
756	>
757	>	// now spray out the foundTypes to all the other processors:
758	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
759	>	&ftGlobal[0], &counts[0], &disps[0],
760	>	MPI::INT);
761
762	<	#ifdef IS_MPI
520	<	int temp;
762	>	vector<int>::iterator j;
763
764	<	temp = usePBC;
765	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
764	>	// foundIdents is a stl set, so inserting an already found ident
765	>	// will have no effect.
766	>	set<int> foundIdents;
767
768	<	temp = useDirectionalAtom;
769	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
768	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
769	>	foundIdents.insert((*j));
770	>
771	>	// now iterate over the foundIdents and get the actual atom types
772	>	// that correspond to these:
773	>	set<int>::iterator it;
774	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
775	>	atomTypes.insert( forceField_->getAtomType((*it)) );
776	>
777	>	#endif
778
779	<	temp = useLennardJones;
780	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
779	>	return atomTypes;
780	>	}
781
782	<	temp = useElectrostatics;
783	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
782	>	void SimInfo::setupSimVariables() {
783	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
784	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
785	>	calcBoxDipole_ = false;
786	>	if ( simParams_->haveAccumulateBoxDipole() )
787	>	if ( simParams_->getAccumulateBoxDipole() ) {
788	>	calcBoxDipole_ = true;
789	>	}
790	>
791	>	set<AtomType*>::iterator i;
792	>	set<AtomType*> atomTypes;
793	>	atomTypes = getSimulatedAtomTypes();
794	>	bool usesElectrostatic = false;
795	>	bool usesMetallic = false;
796	>	bool usesDirectional = false;
797	>	bool usesFluctuatingCharges =  false;
798	>	//loop over all of the atom types
799	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
800	>	usesElectrostatic |= (*i)->isElectrostatic();
801	>	usesMetallic |= (*i)->isMetal();
802	>	usesDirectional |= (*i)->isDirectional();
803	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
804	>	}
805
806	<	temp = useCharge;
807	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
806	>	#ifdef IS_MPI
807	>	bool temp;
808	>	temp = usesDirectional;
809	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
810	>	MPI::LOR);
811	>
812	>	temp = usesMetallic;
813	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
814	>	MPI::LOR);
815	>
816	>	temp = usesElectrostatic;
817	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
818	>	MPI::LOR);
819
820	<	temp = useDipole;
821	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
820	>	temp = usesFluctuatingCharges;
821	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
822	>	MPI::LOR);
823	>	#else
824
825	<	temp = useSticky;
826	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
825	>	usesDirectionalAtoms_ = usesDirectional;
826	>	usesMetallicAtoms_ = usesMetallic;
827	>	usesElectrostaticAtoms_ = usesElectrostatic;
828	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
829
830	<	temp = useGayBerne;
831	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
830	>	#endif
831	>
832	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
833	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
834	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
835	>	}
836
546	–	temp = useEAM;
547	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
837
838	<	temp = useShape;
839	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
838	>	vector<int> SimInfo::getGlobalAtomIndices() {
839	>	SimInfo::MoleculeIterator mi;
840	>	Molecule* mol;
841	>	Molecule::AtomIterator ai;
842	>	Atom* atom;
843
844	<	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);
844	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
845
846	<	#endif
846	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
847	>
848	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
849	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
850	>	}
851	>	}
852	>	return GlobalAtomIndices;
853	>	}
854
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;
855
856	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
856	>	vector<int> SimInfo::getGlobalGroupIndices() {
857	>	SimInfo::MoleculeIterator mi;
858	>	Molecule* mol;
859	>	Molecule::CutoffGroupIterator ci;
860	>	CutoffGroup* cg;
861
862	<	if (simParams_->haveDielectric()) {
863	<	fInfo_.dielect = simParams_->getDielectric();
864	<	} else {
865	<	sprintf(painCave.errMsg,
866	<	"SimSetup Error: No Dielectric constant was set.\n"
867	<	"\tYou are trying to use Reaction Field without"
868	<	"\tsetting a dielectric constant!\n");
869	<	painCave.isFatal = 1;
870	<	simError();
871	<	}
585	<
586	<	} else {
587	<	fInfo_.dielect = 0.0;
862	>	vector<int> GlobalGroupIndices;
863	>
864	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
865	>
866	>	//local index of cutoff group is trivial, it only depends on the
867	>	//order of travesing
868	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
869	>	cg = mol->nextCutoffGroup(ci)) {
870	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
871	>	}
872		}
873	+	return GlobalGroupIndices;
874	+	}
875
590	–	}
876
877	<	void SimInfo::setupFortranSim() {
878	<	int isError;
594	<	int nExclude;
595	<	std::vector<int> fortranGlobalGroupMembership;
596	<
597	<	nExclude = exclude_.getSize();
598	<	isError = 0;
877	>	void SimInfo::prepareTopology() {
878	>	int nExclude, nOneTwo, nOneThree, nOneFour;
879
600	–	//globalGroupMembership_ is filled by SimCreator
601	–	for (int i = 0; i < nGlobalAtoms_; i++) {
602	–	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
603	–	}
604	–
880		//calculate mass ratio of cutoff group
606	–	std::vector<double> mfact;
881		SimInfo::MoleculeIterator mi;
882		Molecule* mol;
883		Molecule::CutoffGroupIterator ci;
884		CutoffGroup* cg;
885		Molecule::AtomIterator ai;
886		Atom* atom;
887	<	double totalMass;
887	>	RealType totalMass;
888
889	<	//to avoid memory reallocation, reserve enough space for mfact
890	<	mfact.reserve(getNCutoffGroups());
889	>	/**
890	>	* The mass factor is the relative mass of an atom to the total
891	>	* mass of the cutoff group it belongs to.  By default, all atoms
892	>	* are their own cutoff groups, and therefore have mass factors of
893	>	* 1.  We need some special handling for massless atoms, which
894	>	* will be treated as carrying the entire mass of the cutoff
895	>	* group.
896	>	*/
897	>	massFactors_.clear();
898	>	massFactors_.resize(getNAtoms(), 1.0);
899
900		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
901	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
901	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
902	>	cg = mol->nextCutoffGroup(ci)) {
903
904	<	totalMass = cg->getMass();
905	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
906	<	mfact.push_back(atom->getMass()/totalMass);
907	<	}
908	<
909	<	}
904	>	totalMass = cg->getMass();
905	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
906	>	// Check for massless groups - set mfact to 1 if true
907	>	if (totalMass != 0)
908	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
909	>	else
910	>	massFactors_[atom->getLocalIndex()] = 1.0;
911	>	}
912	>	}
913		}
914
915	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
630	<	std::vector<int> identArray;
915	>	// Build the identArray_
916
917	<	//to avoid memory reallocation, reserve enough space identArray
918	<	identArray.reserve(getNAtoms());
634	<
917	>	identArray_.clear();
918	>	identArray_.reserve(getNAtoms());
919		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
920	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
921	<	identArray.push_back(atom->getIdent());
922	<	}
920	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
921	>	identArray_.push_back(atom->getIdent());
922	>	}
923		}
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	–	}
924
925	<	//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);
925	>	//scan topology
926
927	<	if( isError ){
927	>	nExclude = excludedInteractions_.getSize();
928	>	nOneTwo = oneTwoInteractions_.getSize();
929	>	nOneThree = oneThreeInteractions_.getSize();
930	>	nOneFour = oneFourInteractions_.getSize();
931
932	<	sprintf( painCave.errMsg,
933	<	"There was an error setting the simulation information in fortran.\n" );
934	<	painCave.isFatal = 1;
935	<	painCave.severity = OOPSE_ERROR;
665	<	simError();
666	<	}
932	>	int* excludeList = excludedInteractions_.getPairList();
933	>	int* oneTwoList = oneTwoInteractions_.getPairList();
934	>	int* oneThreeList = oneThreeInteractions_.getPairList();
935	>	int* oneFourList = oneFourInteractions_.getPairList();
936
937	<	#ifdef IS_MPI
938	<	sprintf( checkPointMsg,
670	<	"succesfully sent the simulation information to fortran.\n");
671	<	MPIcheckPoint();
672	<	#endif // is_mpi
673	<	}
937	>	topologyDone_ = true;
938	>	}
939
940	<
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) {
940	>	void SimInfo::addProperty(GenericData* genData) {
941		properties_.addProperty(genData);
942	<	}
942	>	}
943
944	<	void SimInfo::removeProperty(const std::string& propName) {
944	>	void SimInfo::removeProperty(const string& propName) {
945		properties_.removeProperty(propName);
946	<	}
946	>	}
947
948	<	void SimInfo::clearProperties() {
948	>	void SimInfo::clearProperties() {
949		properties_.clearProperties();
950	<	}
950	>	}
951
952	<	std::vector<std::string> SimInfo::getPropertyNames() {
952	>	vector<string> SimInfo::getPropertyNames() {
953		return properties_.getPropertyNames();
954	<	}
954	>	}
955
956	<	std::vector<GenericData*> SimInfo::getProperties() {
956	>	vector<GenericData*> SimInfo::getProperties() {
957		return properties_.getProperties();
958	<	}
958	>	}
959
960	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
960	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
961		return properties_.getPropertyByName(propName);
962	<	}
962	>	}
963
964	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
965	<	//if (sman_ == sman_) {
966	<	//    return;
967	<	//}
968	<
843	<	//delete sman_;
964	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
965	>	if (sman_ == sman) {
966	>	return;
967	>	}
968	>	delete sman_;
969		sman_ = sman;
970
971		Molecule* mol;
972		RigidBody* rb;
973		Atom* atom;
974	+	CutoffGroup* cg;
975		SimInfo::MoleculeIterator mi;
976		Molecule::RigidBodyIterator rbIter;
977	<	Molecule::AtomIterator atomIter;;
977	>	Molecule::AtomIterator atomIter;
978	>	Molecule::CutoffGroupIterator cgIter;
979
980		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
981
982	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
983	<	atom->setSnapshotManager(sman_);
984	<	}
982	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
983	>	atom->setSnapshotManager(sman_);
984	>	}
985
986	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
987	<	rb->setSnapshotManager(sman_);
988	<	}
986	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
987	>	rb->setSnapshotManager(sman_);
988	>	}
989	>
990	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
991	>	cg->setSnapshotManager(sman_);
992	>	}
993		}
994
995	<	}
995	>	}
996
866	–	Vector3d SimInfo::getComVel(){
867	–	SimInfo::MoleculeIterator i;
868	–	Molecule* mol;
997
998	<	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	<	}
998	>	ostream& operator <<(ostream& o, SimInfo& info) {
999
1000	<	#ifdef IS_MPI
1001	<	double tmpMass = totalMass;
1002	<	Vector3d tmpComVel(comVel);
1003	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1004	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1005	<	#endif
1000	>	return o;
1001	>	}
1002	>
1003	>
1004	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1005	>	return IOIndexToIntegrableObject.at(index);
1006	>	}
1007	>
1008	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1009	>	IOIndexToIntegrableObject= v;
1010	>	}
1011	>	/*
1012	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1013	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1014	>	sdByGlobalIndex_ = v;
1015	>	}
1016
1017	<	comVel /= totalMass;
1018	<
1019	<	return comVel;
1020	<	}
1021	<
1022	<	Vector3d SimInfo::getCom(){
1023	<	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	<
1017	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1018	>	//assert(index < nAtoms_ + nRigidBodies_);
1019	>	return sdByGlobalIndex_.at(index);
1020	>	}
1021	>	*/
1022	>	int SimInfo::getNGlobalConstraints() {
1023	>	int nGlobalConstraints;
1024		#ifdef IS_MPI
1025	<	double tmpMass = totalMass;
1026	<	Vector3d tmpCom(com);
1027	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1028	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1025	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1026	>	MPI_COMM_WORLD);
1027	>	#else
1028	>	nGlobalConstraints =  nConstraints_;
1029		#endif
1030	+	return nGlobalConstraints;
1031	+	}
1032
1033	<	com /= totalMass;
1033	>	}//end namespace OpenMD
1034
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 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC

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