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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 334 by tim, Mon Feb 14 17:57:01 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1874 by gezelter, Wed May 15 15:09:35 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), selectMan_(NULL) {
79	<
80	<
79	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
68	>	using namespace std;
69	>	namespace OpenMD {
70	>
71	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72	>	forceField_(ff), simParams_(simParams),
73	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0),
76	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79	>	calcBoxDipole_(false), useAtomicVirial_(true) {
80	>
81		MoleculeStamp* molStamp;
82		int nMolWithSameStamp;
83		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
84	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
85		CutoffGroupStamp* cgStamp;
86		RigidBodyStamp* rbStamp;
87		int nRigidAtoms = 0;
88
89	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
90	<	molStamp = i->first;
91	<	nMolWithSameStamp = i->second;
92	<
93	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
94	<
95	<	//calculate atoms in molecules
96	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
97	<
98	<
99	<	//calculate atoms in cutoff groups
100	<	int nAtomsInGroups = 0;
101	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
102	<
103	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
104	<	cgStamp = molStamp->getCutoffGroup(j);
105	<	nAtomsInGroups += cgStamp->getNMembers();
106	<	}
107	<
108	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
109	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
110	<
111	<	//calculate atoms in rigid bodies
112	<	int nAtomsInRigidBodies = 0;
113	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
114	<
115	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
116	<	rbStamp = molStamp->getRigidBody(j);
117	<	nAtomsInRigidBodies += rbStamp->getNMembers();
118	<	}
119	<
120	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
121	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
122	<
89	>	vector<Component*> components = simParams->getComponents();
90	>
91	>	for (vector<Component*>::iterator i = components.begin();
92	>	i !=components.end(); ++i) {
93	>	molStamp = (*i)->getMoleculeStamp();
94	>	nMolWithSameStamp = (*i)->getNMol();
95	>
96	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
97	>
98	>	//calculate atoms in molecules
99	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
100	>
101	>	//calculate atoms in cutoff groups
102	>	int nAtomsInGroups = 0;
103	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
104	>
105	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
106	>	cgStamp = molStamp->getCutoffGroupStamp(j);
107	>	nAtomsInGroups += cgStamp->getNMembers();
108	>	}
109	>
110	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
111	>
112	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
113	>
114	>	//calculate atoms in rigid bodies
115	>	int nAtomsInRigidBodies = 0;
116	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
117	>
118	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
119	>	rbStamp = molStamp->getRigidBodyStamp(j);
120	>	nAtomsInRigidBodies += rbStamp->getNMembers();
121	>	}
122	>
123	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
124	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
125	>
126		}
127	+
128	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
129	+	//group therefore the total number of cutoff groups in the system is
130	+	//equal to the total number of atoms minus number of atoms belong to
131	+	//cutoff group defined in meta-data file plus the number of cutoff
132	+	//groups defined in meta-data file
133
124	–	//every free atom (atom does not belong to cutoff groups) is a cutoff group
125	–	//therefore the total number of cutoff groups in the system is equal to
126	–	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
127	–	//file plus the number of cutoff groups defined in meta-data file
134		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
135	<
136	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
137	<	//therefore the total number of  integrable objects in the system is equal to
138	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
139	<	//file plus the number of  rigid bodies defined in meta-data file
140	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
141	<
135	>
136	>	//every free atom (atom does not belong to rigid bodies) is an
137	>	//integrable object therefore the total number of integrable objects
138	>	//in the system is equal to the total number of atoms minus number of
139	>	//atoms belong to rigid body defined in meta-data file plus the number
140	>	//of rigid bodies defined in meta-data file
141	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
142	>	+ nGlobalRigidBodies_;
143	>
144		nGlobalMols_ = molStampIds_.size();
137	–
138	–	#ifdef IS_MPI
145		molToProcMap_.resize(nGlobalMols_);
146	<	#endif
147	<
148	<	selectMan_ = new SelectionManager(this);
149	<	selectMan_->selectAll();
150	<	}
151	<
152	<	SimInfo::~SimInfo() {
153	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
154	<
149	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
150	<
146	>	}
147	>
148	>	SimInfo::~SimInfo() {
149	>	map<int, Molecule*>::iterator i;
150	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
151	>	delete i->second;
152	>	}
153	>	molecules_.clear();
154	>
155		delete sman_;
156		delete simParams_;
157		delete forceField_;
158	<	delete selectMan_;
155	<	}
158	>	}
159
157	–	int SimInfo::getNGlobalConstraints() {
158	–	int nGlobalConstraints;
159	–	#ifdef IS_MPI
160	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
161	–	MPI_COMM_WORLD);
162	–	#else
163	–	nGlobalConstraints =  nConstraints_;
164	–	#endif
165	–	return nGlobalConstraints;
166	–	}
160
161	<	bool SimInfo::addMolecule(Molecule* mol) {
161	>	bool SimInfo::addMolecule(Molecule* mol) {
162		MoleculeIterator i;
163	<
163	>
164		i = molecules_.find(mol->getGlobalIndex());
165		if (i == molecules_.end() ) {
166	<
167	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
168	<
169	<	nAtoms_ += mol->getNAtoms();
170	<	nBonds_ += mol->getNBonds();
171	<	nBends_ += mol->getNBends();
172	<	nTorsions_ += mol->getNTorsions();
173	<	nRigidBodies_ += mol->getNRigidBodies();
174	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
175	<	nCutoffGroups_ += mol->getNCutoffGroups();
176	<	nConstraints_ += mol->getNConstraintPairs();
177	<
178	<	addExcludePairs(mol);
179	<
180	<	return true;
166	>
167	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
168	>
169	>	nAtoms_ += mol->getNAtoms();
170	>	nBonds_ += mol->getNBonds();
171	>	nBends_ += mol->getNBends();
172	>	nTorsions_ += mol->getNTorsions();
173	>	nInversions_ += mol->getNInversions();
174	>	nRigidBodies_ += mol->getNRigidBodies();
175	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
176	>	nCutoffGroups_ += mol->getNCutoffGroups();
177	>	nConstraints_ += mol->getNConstraintPairs();
178	>
179	>	addInteractionPairs(mol);
180	>
181	>	return true;
182		} else {
183	<	return false;
183	>	return false;
184		}
185	<	}
186	<
187	<	bool SimInfo::removeMolecule(Molecule* mol) {
185	>	}
186	>
187	>	bool SimInfo::removeMolecule(Molecule* mol) {
188		MoleculeIterator i;
189		i = molecules_.find(mol->getGlobalIndex());
190
191		if (i != molecules_.end() ) {
192
193	<	assert(mol == i->second);
193	>	assert(mol == i->second);
194
195	<	nAtoms_ -= mol->getNAtoms();
196	<	nBonds_ -= mol->getNBonds();
197	<	nBends_ -= mol->getNBends();
198	<	nTorsions_ -= mol->getNTorsions();
199	<	nRigidBodies_ -= mol->getNRigidBodies();
200	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
201	<	nCutoffGroups_ -= mol->getNCutoffGroups();
202	<	nConstraints_ -= mol->getNConstraintPairs();
195	>	nAtoms_ -= mol->getNAtoms();
196	>	nBonds_ -= mol->getNBonds();
197	>	nBends_ -= mol->getNBends();
198	>	nTorsions_ -= mol->getNTorsions();
199	>	nInversions_ -= mol->getNInversions();
200	>	nRigidBodies_ -= mol->getNRigidBodies();
201	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
202	>	nCutoffGroups_ -= mol->getNCutoffGroups();
203	>	nConstraints_ -= mol->getNConstraintPairs();
204
205	<	removeExcludePairs(mol);
206	<	molecules_.erase(mol->getGlobalIndex());
205	>	removeInteractionPairs(mol);
206	>	molecules_.erase(mol->getGlobalIndex());
207
208	<	delete mol;
208	>	delete mol;
209
210	<	return true;
210	>	return true;
211		} else {
212	<	return false;
212	>	return false;
213		}
214	+	}
215
220	–
221	–	}
222	–
216
217	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
217	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
218		i = molecules_.begin();
219		return i == molecules_.end() ? NULL : i->second;
220	<	}
220	>	}
221
222	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
222	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
223		++i;
224		return i == molecules_.end() ? NULL : i->second;
225	<	}
225	>	}
226
227
228	<	void SimInfo::calcNdf() {
229	<	int ndf_local;
228	>	void SimInfo::calcNdf() {
229	>	int ndf_local, nfq_local;
230		MoleculeIterator i;
231	<	std::vector<StuntDouble*>::iterator j;
231	>	vector<StuntDouble*>::iterator j;
232	>	vector<Atom*>::iterator k;
233	>
234		Molecule* mol;
235	<	StuntDouble* integrableObject;
235	>	StuntDouble* sd;
236	>	Atom* atom;
237
238		ndf_local = 0;
239	+	nfq_local = 0;
240
241		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
245	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
246	–	integrableObject = mol->nextIntegrableObject(j)) {
242
243	<	ndf_local += 3;
243	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
244	>	sd = mol->nextIntegrableObject(j)) {
245
246	<	if (integrableObject->isDirectional()) {
247	<	if (integrableObject->isLinear()) {
248	<	ndf_local += 2;
249	<	} else {
250	<	ndf_local += 3;
251	<	}
252	<	}
253	<
254	<	}//end for (integrableObject)
255	<	}// end for (mol)
246	>	ndf_local += 3;
247	>
248	>	if (sd->isDirectional()) {
249	>	if (sd->isLinear()) {
250	>	ndf_local += 2;
251	>	} else {
252	>	ndf_local += 3;
253	>	}
254	>	}
255	>	}
256	>
257	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
258	>	atom = mol->nextFluctuatingCharge(k)) {
259	>	if (atom->isFluctuatingCharge()) {
260	>	nfq_local++;
261	>	}
262	>	}
263	>	}
264
265	+	ndfLocal_ = ndf_local;
266	+
267		// n_constraints is local, so subtract them on each processor
268		ndf_local -= nConstraints_;
269
270		#ifdef IS_MPI
271	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
271	>	MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
272	>	MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
273	>	MPI::INT, MPI::SUM);
274		#else
275		ndf_ = ndf_local;
276	+	nGlobalFluctuatingCharges_ = nfq_local;
277		#endif
278
279		// nZconstraints_ is global, as are the 3 COM translations for the
280		// entire system:
281		ndf_ = ndf_ - 3 - nZconstraint_;
282
283	<	}
283	>	}
284
285	<	void SimInfo::calcNdfRaw() {
285	>	int SimInfo::getFdf() {
286	>	#ifdef IS_MPI
287	>	MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
288	>	#else
289	>	fdf_ = fdf_local;
290	>	#endif
291	>	return fdf_;
292	>	}
293	>
294	>	unsigned int SimInfo::getNLocalCutoffGroups(){
295	>	int nLocalCutoffAtoms = 0;
296	>	Molecule* mol;
297	>	MoleculeIterator mi;
298	>	CutoffGroup* cg;
299	>	Molecule::CutoffGroupIterator ci;
300	>
301	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
302	>
303	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
304	>	cg = mol->nextCutoffGroup(ci)) {
305	>	nLocalCutoffAtoms += cg->getNumAtom();
306	>
307	>	}
308	>	}
309	>
310	>	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
311	>	}
312	>
313	>	void SimInfo::calcNdfRaw() {
314		int ndfRaw_local;
315
316		MoleculeIterator i;
317	<	std::vector<StuntDouble*>::iterator j;
317	>	vector<StuntDouble*>::iterator j;
318		Molecule* mol;
319	<	StuntDouble* integrableObject;
319	>	StuntDouble* sd;
320
321		// Raw degrees of freedom that we have to set
322		ndfRaw_local = 0;
323
324		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
288	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
289	–	integrableObject = mol->nextIntegrableObject(j)) {
325
326	<	ndfRaw_local += 3;
326	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
327	>	sd = mol->nextIntegrableObject(j)) {
328
329	<	if (integrableObject->isDirectional()) {
330	<	if (integrableObject->isLinear()) {
331	<	ndfRaw_local += 2;
332	<	} else {
333	<	ndfRaw_local += 3;
334	<	}
335	<	}
329	>	ndfRaw_local += 3;
330	>
331	>	if (sd->isDirectional()) {
332	>	if (sd->isLinear()) {
333	>	ndfRaw_local += 2;
334	>	} else {
335	>	ndfRaw_local += 3;
336	>	}
337	>	}
338
339	<	}
339	>	}
340		}
341
342		#ifdef IS_MPI
343	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
343	>	MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
344		#else
345		ndfRaw_ = ndfRaw_local;
346		#endif
347	<	}
347	>	}
348
349	<	void SimInfo::calcNdfTrans() {
349	>	void SimInfo::calcNdfTrans() {
350		int ndfTrans_local;
351
352		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
353
354
355		#ifdef IS_MPI
356	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
356	>	MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
357	>	MPI::INT, MPI::SUM);
358		#else
359		ndfTrans_ = ndfTrans_local;
360		#endif
361
362		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
363
364	<	}
364	>	}
365
366	<	void SimInfo::addExcludePairs(Molecule* mol) {
367	<	std::vector<Bond*>::iterator bondIter;
368	<	std::vector<Bend*>::iterator bendIter;
369	<	std::vector<Torsion*>::iterator torsionIter;
366	>	void SimInfo::addInteractionPairs(Molecule* mol) {
367	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
368	>	vector<Bond*>::iterator bondIter;
369	>	vector<Bend*>::iterator bendIter;
370	>	vector<Torsion*>::iterator torsionIter;
371	>	vector<Inversion*>::iterator inversionIter;
372		Bond* bond;
373		Bend* bend;
374		Torsion* torsion;
375	+	Inversion* inversion;
376		int a;
377		int b;
378		int c;
379		int d;
380	+
381	+	// atomGroups can be used to add special interaction maps between
382	+	// groups of atoms that are in two separate rigid bodies.
383	+	// However, most site-site interactions between two rigid bodies
384	+	// are probably not special, just the ones between the physically
385	+	// bonded atoms.  Interactions *within* a single rigid body should
386	+	// always be excluded.  These are done at the bottom of this
387	+	// function.
388	+
389	+	map<int, set<int> > atomGroups;
390	+	Molecule::RigidBodyIterator rbIter;
391	+	RigidBody* rb;
392	+	Molecule::IntegrableObjectIterator ii;
393	+	StuntDouble* sd;
394
395	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
396	<	a = bond->getAtomA()->getGlobalIndex();
397	<	b = bond->getAtomB()->getGlobalIndex();
398	<	exclude_.addPair(a, b);
395	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
396	>	sd = mol->nextIntegrableObject(ii)) {
397	>
398	>	if (sd->isRigidBody()) {
399	>	rb = static_cast<RigidBody*>(sd);
400	>	vector<Atom*> atoms = rb->getAtoms();
401	>	set<int> rigidAtoms;
402	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
403	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
404	>	}
405	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
406	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
407	>	}
408	>	} else {
409	>	set<int> oneAtomSet;
410	>	oneAtomSet.insert(sd->getGlobalIndex());
411	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
412	>	}
413	>	}
414	>
415	>	for (bond= mol->beginBond(bondIter); bond != NULL;
416	>	bond = mol->nextBond(bondIter)) {
417	>
418	>	a = bond->getAtomA()->getGlobalIndex();
419	>	b = bond->getAtomB()->getGlobalIndex();
420	>
421	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
422	>	oneTwoInteractions_.addPair(a, b);
423	>	} else {
424	>	excludedInteractions_.addPair(a, b);
425	>	}
426		}
427
428	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
429	<	a = bend->getAtomA()->getGlobalIndex();
347	<	b = bend->getAtomB()->getGlobalIndex();
348	<	c = bend->getAtomC()->getGlobalIndex();
428	>	for (bend= mol->beginBend(bendIter); bend != NULL;
429	>	bend = mol->nextBend(bendIter)) {
430
431	<	exclude_.addPair(a, b);
432	<	exclude_.addPair(a, c);
433	<	exclude_.addPair(b, c);
431	>	a = bend->getAtomA()->getGlobalIndex();
432	>	b = bend->getAtomB()->getGlobalIndex();
433	>	c = bend->getAtomC()->getGlobalIndex();
434	>
435	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
436	>	oneTwoInteractions_.addPair(a, b);
437	>	oneTwoInteractions_.addPair(b, c);
438	>	} else {
439	>	excludedInteractions_.addPair(a, b);
440	>	excludedInteractions_.addPair(b, c);
441	>	}
442	>
443	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
444	>	oneThreeInteractions_.addPair(a, c);
445	>	} else {
446	>	excludedInteractions_.addPair(a, c);
447	>	}
448		}
449
450	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
451	<	a = torsion->getAtomA()->getGlobalIndex();
357	<	b = torsion->getAtomB()->getGlobalIndex();
358	<	c = torsion->getAtomC()->getGlobalIndex();
359	<	d = torsion->getAtomD()->getGlobalIndex();
450	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
451	>	torsion = mol->nextTorsion(torsionIter)) {
452
453	<	exclude_.addPair(a, b);
454	<	exclude_.addPair(a, c);
455	<	exclude_.addPair(a, d);
456	<	exclude_.addPair(b, c);
457	<	exclude_.addPair(b, d);
458	<	exclude_.addPair(c, d);
453	>	a = torsion->getAtomA()->getGlobalIndex();
454	>	b = torsion->getAtomB()->getGlobalIndex();
455	>	c = torsion->getAtomC()->getGlobalIndex();
456	>	d = torsion->getAtomD()->getGlobalIndex();
457	>
458	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
459	>	oneTwoInteractions_.addPair(a, b);
460	>	oneTwoInteractions_.addPair(b, c);
461	>	oneTwoInteractions_.addPair(c, d);
462	>	} else {
463	>	excludedInteractions_.addPair(a, b);
464	>	excludedInteractions_.addPair(b, c);
465	>	excludedInteractions_.addPair(c, d);
466	>	}
467	>
468	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
469	>	oneThreeInteractions_.addPair(a, c);
470	>	oneThreeInteractions_.addPair(b, d);
471	>	} else {
472	>	excludedInteractions_.addPair(a, c);
473	>	excludedInteractions_.addPair(b, d);
474	>	}
475	>
476	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
477	>	oneFourInteractions_.addPair(a, d);
478	>	} else {
479	>	excludedInteractions_.addPair(a, d);
480	>	}
481		}
482
483	<
484	<	}
483	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
484	>	inversion = mol->nextInversion(inversionIter)) {
485
486	<	void SimInfo::removeExcludePairs(Molecule* mol) {
487	<	std::vector<Bond*>::iterator bondIter;
488	<	std::vector<Bend*>::iterator bendIter;
489	<	std::vector<Torsion*>::iterator torsionIter;
486	>	a = inversion->getAtomA()->getGlobalIndex();
487	>	b = inversion->getAtomB()->getGlobalIndex();
488	>	c = inversion->getAtomC()->getGlobalIndex();
489	>	d = inversion->getAtomD()->getGlobalIndex();
490	>
491	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
492	>	oneTwoInteractions_.addPair(a, b);
493	>	oneTwoInteractions_.addPair(a, c);
494	>	oneTwoInteractions_.addPair(a, d);
495	>	} else {
496	>	excludedInteractions_.addPair(a, b);
497	>	excludedInteractions_.addPair(a, c);
498	>	excludedInteractions_.addPair(a, d);
499	>	}
500	>
501	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
502	>	oneThreeInteractions_.addPair(b, c);
503	>	oneThreeInteractions_.addPair(b, d);
504	>	oneThreeInteractions_.addPair(c, d);
505	>	} else {
506	>	excludedInteractions_.addPair(b, c);
507	>	excludedInteractions_.addPair(b, d);
508	>	excludedInteractions_.addPair(c, d);
509	>	}
510	>	}
511	>
512	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
513	>	rb = mol->nextRigidBody(rbIter)) {
514	>	vector<Atom*> atoms = rb->getAtoms();
515	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
516	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
517	>	a = atoms[i]->getGlobalIndex();
518	>	b = atoms[j]->getGlobalIndex();
519	>	excludedInteractions_.addPair(a, b);
520	>	}
521	>	}
522	>	}
523	>
524	>	}
525	>
526	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
527	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
528	>	vector<Bond*>::iterator bondIter;
529	>	vector<Bend*>::iterator bendIter;
530	>	vector<Torsion*>::iterator torsionIter;
531	>	vector<Inversion*>::iterator inversionIter;
532		Bond* bond;
533		Bend* bend;
534		Torsion* torsion;
535	+	Inversion* inversion;
536		int a;
537		int b;
538		int c;
539		int d;
540	+
541	+	map<int, set<int> > atomGroups;
542	+	Molecule::RigidBodyIterator rbIter;
543	+	RigidBody* rb;
544	+	Molecule::IntegrableObjectIterator ii;
545	+	StuntDouble* sd;
546
547	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
548	<	a = bond->getAtomA()->getGlobalIndex();
549	<	b = bond->getAtomB()->getGlobalIndex();
550	<	exclude_.removePair(a, b);
547	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
548	>	sd = mol->nextIntegrableObject(ii)) {
549	>
550	>	if (sd->isRigidBody()) {
551	>	rb = static_cast<RigidBody*>(sd);
552	>	vector<Atom*> atoms = rb->getAtoms();
553	>	set<int> rigidAtoms;
554	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
555	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
556	>	}
557	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
558	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
559	>	}
560	>	} else {
561	>	set<int> oneAtomSet;
562	>	oneAtomSet.insert(sd->getGlobalIndex());
563	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
564	>	}
565	>	}
566	>
567	>	for (bond= mol->beginBond(bondIter); bond != NULL;
568	>	bond = mol->nextBond(bondIter)) {
569	>
570	>	a = bond->getAtomA()->getGlobalIndex();
571	>	b = bond->getAtomB()->getGlobalIndex();
572	>
573	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
574	>	oneTwoInteractions_.removePair(a, b);
575	>	} else {
576	>	excludedInteractions_.removePair(a, b);
577	>	}
578		}
579
580	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
581	<	a = bend->getAtomA()->getGlobalIndex();
392	<	b = bend->getAtomB()->getGlobalIndex();
393	<	c = bend->getAtomC()->getGlobalIndex();
580	>	for (bend= mol->beginBend(bendIter); bend != NULL;
581	>	bend = mol->nextBend(bendIter)) {
582
583	<	exclude_.removePair(a, b);
584	<	exclude_.removePair(a, c);
585	<	exclude_.removePair(b, c);
583	>	a = bend->getAtomA()->getGlobalIndex();
584	>	b = bend->getAtomB()->getGlobalIndex();
585	>	c = bend->getAtomC()->getGlobalIndex();
586	>
587	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
588	>	oneTwoInteractions_.removePair(a, b);
589	>	oneTwoInteractions_.removePair(b, c);
590	>	} else {
591	>	excludedInteractions_.removePair(a, b);
592	>	excludedInteractions_.removePair(b, c);
593	>	}
594	>
595	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
596	>	oneThreeInteractions_.removePair(a, c);
597	>	} else {
598	>	excludedInteractions_.removePair(a, c);
599	>	}
600		}
601
602	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
603	<	a = torsion->getAtomA()->getGlobalIndex();
402	<	b = torsion->getAtomB()->getGlobalIndex();
403	<	c = torsion->getAtomC()->getGlobalIndex();
404	<	d = torsion->getAtomD()->getGlobalIndex();
602	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
603	>	torsion = mol->nextTorsion(torsionIter)) {
604
605	<	exclude_.removePair(a, b);
606	<	exclude_.removePair(a, c);
607	<	exclude_.removePair(a, d);
608	<	exclude_.removePair(b, c);
609	<	exclude_.removePair(b, d);
610	<	exclude_.removePair(c, d);
605	>	a = torsion->getAtomA()->getGlobalIndex();
606	>	b = torsion->getAtomB()->getGlobalIndex();
607	>	c = torsion->getAtomC()->getGlobalIndex();
608	>	d = torsion->getAtomD()->getGlobalIndex();
609	>
610	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
611	>	oneTwoInteractions_.removePair(a, b);
612	>	oneTwoInteractions_.removePair(b, c);
613	>	oneTwoInteractions_.removePair(c, d);
614	>	} else {
615	>	excludedInteractions_.removePair(a, b);
616	>	excludedInteractions_.removePair(b, c);
617	>	excludedInteractions_.removePair(c, d);
618	>	}
619	>
620	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
621	>	oneThreeInteractions_.removePair(a, c);
622	>	oneThreeInteractions_.removePair(b, d);
623	>	} else {
624	>	excludedInteractions_.removePair(a, c);
625	>	excludedInteractions_.removePair(b, d);
626	>	}
627	>
628	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
629	>	oneFourInteractions_.removePair(a, d);
630	>	} else {
631	>	excludedInteractions_.removePair(a, d);
632	>	}
633		}
634
635	<	}
635	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
636	>	inversion = mol->nextInversion(inversionIter)) {
637
638	+	a = inversion->getAtomA()->getGlobalIndex();
639	+	b = inversion->getAtomB()->getGlobalIndex();
640	+	c = inversion->getAtomC()->getGlobalIndex();
641	+	d = inversion->getAtomD()->getGlobalIndex();
642
643	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
644	<	int curStampId;
643	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
644	>	oneTwoInteractions_.removePair(a, b);
645	>	oneTwoInteractions_.removePair(a, c);
646	>	oneTwoInteractions_.removePair(a, d);
647	>	} else {
648	>	excludedInteractions_.removePair(a, b);
649	>	excludedInteractions_.removePair(a, c);
650	>	excludedInteractions_.removePair(a, d);
651	>	}
652
653	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
654	+	oneThreeInteractions_.removePair(b, c);
655	+	oneThreeInteractions_.removePair(b, d);
656	+	oneThreeInteractions_.removePair(c, d);
657	+	} else {
658	+	excludedInteractions_.removePair(b, c);
659	+	excludedInteractions_.removePair(b, d);
660	+	excludedInteractions_.removePair(c, d);
661	+	}
662	+	}
663	+
664	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
665	+	rb = mol->nextRigidBody(rbIter)) {
666	+	vector<Atom*> atoms = rb->getAtoms();
667	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
668	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
669	+	a = atoms[i]->getGlobalIndex();
670	+	b = atoms[j]->getGlobalIndex();
671	+	excludedInteractions_.removePair(a, b);
672	+	}
673	+	}
674	+	}
675	+
676	+	}
677	+
678	+
679	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
680	+	int curStampId;
681	+
682		//index from 0
683		curStampId = moleculeStamps_.size();
684
685		moleculeStamps_.push_back(molStamp);
686		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
687	<	}
687	>	}
688
427	–	void SimInfo::update() {
689
690	<	setupSimType();
691	<
692	<	#ifdef IS_MPI
693	<	setupFortranParallel();
694	<	#endif
695	<
696	<	setupFortranSim();
697	<
698	<	//setup fortran force field
438	<	/** @deprecate */
439	<	int isError = 0;
440	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
441	<	if(isError){
442	<	sprintf( painCave.errMsg,
443	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
444	<	painCave.isFatal = 1;
445	<	simError();
446	<	}
447	<
448	<
449	<	setupCutoff();
450	<
690	>	/**
691	>	* update
692	>	*
693	>	*  Performs the global checks and variable settings after the
694	>	*  objects have been created.
695	>	*
696	>	*/
697	>	void SimInfo::update() {
698	>	setupSimVariables();
699		calcNdf();
700		calcNdfRaw();
701		calcNdfTrans();
702	<
703	<	fortranInitialized_ = true;
704	<	}
705	<
706	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
702	>	}
703	>
704	>	/**
705	>	* getSimulatedAtomTypes
706	>	*
707	>	* Returns an STL set of AtomType* that are actually present in this
708	>	* simulation.  Must query all processors to assemble this information.
709	>	*
710	>	*/
711	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
712		SimInfo::MoleculeIterator mi;
713		Molecule* mol;
714		Molecule::AtomIterator ai;
715		Atom* atom;
716	<	std::set<AtomType*> atomTypes;
717	<
716	>	set<AtomType*> atomTypes;
717	>
718		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
719	+	for(atom = mol->beginAtom(ai); atom != NULL;
720	+	atom = mol->nextAtom(ai)) {
721	+	atomTypes.insert(atom->getAtomType());
722	+	}
723	+	}
724	+
725	+	#ifdef IS_MPI
726
727	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
728	<	atomTypes.insert(atom->getAtomType());
729	<	}
730	<
731	<	}
727	>	// loop over the found atom types on this processor, and add their
728	>	// numerical idents to a vector:
729	>
730	>	vector<int> foundTypes;
731	>	set<AtomType*>::iterator i;
732	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
733	>	foundTypes.push_back( (*i)->getIdent() );
734
735	<	return atomTypes;
736	<	}
735	>	// count_local holds the number of found types on this processor
736	>	int count_local = foundTypes.size();
737
738	<	void SimInfo::setupSimType() {
477	<	std::set<AtomType*>::iterator i;
478	<	std::set<AtomType*> atomTypes;
479	<	atomTypes = getUniqueAtomTypes();
480	<
481	<	int useLennardJones = 0;
482	<	int useElectrostatic = 0;
483	<	int useEAM = 0;
484	<	int useCharge = 0;
485	<	int useDirectional = 0;
486	<	int useDipole = 0;
487	<	int useGayBerne = 0;
488	<	int useSticky = 0;
489	<	int useShape = 0;
490	<	int useFLARB = 0; //it is not in AtomType yet
491	<	int useDirectionalAtom = 0;
492	<	int useElectrostatics = 0;
493	<	//usePBC and useRF are from simParams
494	<	int usePBC = simParams_->getPBC();
495	<	int useRF = simParams_->getUseRF();
738	>	int nproc = MPI::COMM_WORLD.Get_size();
739
740	<	//loop over all of the atom types
741	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
742	<	useLennardJones |= (*i)->isLennardJones();
743	<	useElectrostatic |= (*i)->isElectrostatic();
501	<	useEAM |= (*i)->isEAM();
502	<	useCharge |= (*i)->isCharge();
503	<	useDirectional |= (*i)->isDirectional();
504	<	useDipole |= (*i)->isDipole();
505	<	useGayBerne |= (*i)->isGayBerne();
506	<	useSticky |= (*i)->isSticky();
507	<	useShape |= (*i)->isShape();
508	<	}
740	>	// we need arrays to hold the counts and displacement vectors for
741	>	// all processors
742	>	vector<int> counts(nproc, 0);
743	>	vector<int> disps(nproc, 0);
744
745	<	if (useSticky || useDipole || useGayBerne || useShape) {
746	<	useDirectionalAtom = 1;
745	>	// fill the counts array
746	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
747	>	1, MPI::INT);
748	>
749	>	// use the processor counts to compute the displacement array
750	>	disps[0] = 0;
751	>	int totalCount = counts[0];
752	>	for (int iproc = 1; iproc < nproc; iproc++) {
753	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
754	>	totalCount += counts[iproc];
755		}
756
757	<	if (useCharge || useDipole) {
758	<	useElectrostatics = 1;
759	<	}
757	>	// we need a (possibly redundant) set of all found types:
758	>	vector<int> ftGlobal(totalCount);
759	>
760	>	// now spray out the foundTypes to all the other processors:
761	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
762	>	&ftGlobal[0], &counts[0], &disps[0],
763	>	MPI::INT);
764
765	<	#ifdef IS_MPI
519	<	int temp;
765	>	vector<int>::iterator j;
766
767	<	temp = usePBC;
768	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767	>	// foundIdents is a stl set, so inserting an already found ident
768	>	// will have no effect.
769	>	set<int> foundIdents;
770
771	<	temp = useDirectionalAtom;
772	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
771	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
772	>	foundIdents.insert((*j));
773	>
774	>	// now iterate over the foundIdents and get the actual atom types
775	>	// that correspond to these:
776	>	set<int>::iterator it;
777	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
778	>	atomTypes.insert( forceField_->getAtomType((*it)) );
779	>
780	>	#endif
781
782	<	temp = useLennardJones;
783	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
782	>	return atomTypes;
783	>	}
784
530	–	temp = useElectrostatics;
531	–	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
785
786	<	temp = useCharge;
787	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
786	>	int getGlobalCountOfType(AtomType* atype) {
787	>	/*
788	>	set<AtomType*> atypes = getSimulatedAtomTypes();
789	>	map<AtomType*, int> counts_;
790
791	<	temp = useDipole;
792	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
791	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
792	>	for(atom = mol->beginAtom(ai); atom != NULL;
793	>	atom = mol->nextAtom(ai)) {
794	>	atom->getAtomType();
795	>	}
796	>	}
797	>	*/
798	>	return 0;
799	>	}
800
801	<	temp = useSticky;
802	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
801	>	void SimInfo::setupSimVariables() {
802	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
803	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
804	>	// parameter is true
805	>	calcBoxDipole_ = false;
806	>	if ( simParams_->haveAccumulateBoxDipole() )
807	>	if ( simParams_->getAccumulateBoxDipole() ) {
808	>	calcBoxDipole_ = true;
809	>	}
810	>
811	>	set<AtomType*>::iterator i;
812	>	set<AtomType*> atomTypes;
813	>	atomTypes = getSimulatedAtomTypes();
814	>	bool usesElectrostatic = false;
815	>	bool usesMetallic = false;
816	>	bool usesDirectional = false;
817	>	bool usesFluctuatingCharges =  false;
818	>	//loop over all of the atom types
819	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
820	>	usesElectrostatic |= (*i)->isElectrostatic();
821	>	usesMetallic |= (*i)->isMetal();
822	>	usesDirectional |= (*i)->isDirectional();
823	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
824	>	}
825
826	<	temp = useGayBerne;
827	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
826	>	#ifdef IS_MPI
827	>	bool temp;
828	>	temp = usesDirectional;
829	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
830	>	MPI::LOR);
831	>
832	>	temp = usesMetallic;
833	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
834	>	MPI::LOR);
835	>
836	>	temp = usesElectrostatic;
837	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
838	>	MPI::LOR);
839
840	<	temp = useEAM;
841	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
840	>	temp = usesFluctuatingCharges;
841	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
842	>	MPI::LOR);
843	>	#else
844
845	<	temp = useShape;
846	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
845	>	usesDirectionalAtoms_ = usesDirectional;
846	>	usesMetallicAtoms_ = usesMetallic;
847	>	usesElectrostaticAtoms_ = usesElectrostatic;
848	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
849
551	–	temp = useFLARB;
552	–	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
553	–
554	–	temp = useRF;
555	–	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
556	–
850		#endif
851	+
852	+	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
853	+	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
854	+	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
855	+	}
856
559	–	fInfo_.SIM_uses_PBC = usePBC;
560	–	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
561	–	fInfo_.SIM_uses_LennardJones = useLennardJones;
562	–	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
563	–	fInfo_.SIM_uses_Charges = useCharge;
564	–	fInfo_.SIM_uses_Dipoles = useDipole;
565	–	fInfo_.SIM_uses_Sticky = useSticky;
566	–	fInfo_.SIM_uses_GayBerne = useGayBerne;
567	–	fInfo_.SIM_uses_EAM = useEAM;
568	–	fInfo_.SIM_uses_Shapes = useShape;
569	–	fInfo_.SIM_uses_FLARB = useFLARB;
570	–	fInfo_.SIM_uses_RF = useRF;
857
858	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
858	>	vector<int> SimInfo::getGlobalAtomIndices() {
859	>	SimInfo::MoleculeIterator mi;
860	>	Molecule* mol;
861	>	Molecule::AtomIterator ai;
862	>	Atom* atom;
863
864	<	if (simParams_->haveDielectric()) {
865	<	fInfo_.dielect = simParams_->getDielectric();
866	<	} else {
867	<	sprintf(painCave.errMsg,
868	<	"SimSetup Error: No Dielectric constant was set.\n"
869	<	"\tYou are trying to use Reaction Field without"
870	<	"\tsetting a dielectric constant!\n");
581	<	painCave.isFatal = 1;
582	<	simError();
583	<	}
584	<
585	<	} else {
586	<	fInfo_.dielect = 0.0;
864	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
865	>
866	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
867	>
868	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
869	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
870	>	}
871		}
872	+	return GlobalAtomIndices;
873	+	}
874
589	–	}
875
876	<	void SimInfo::setupFortranSim() {
877	<	int isError;
878	<	int nExclude;
879	<	std::vector<int> fortranGlobalGroupMembership;
880	<
596	<	nExclude = exclude_.getSize();
597	<	isError = 0;
876	>	vector<int> SimInfo::getGlobalGroupIndices() {
877	>	SimInfo::MoleculeIterator mi;
878	>	Molecule* mol;
879	>	Molecule::CutoffGroupIterator ci;
880	>	CutoffGroup* cg;
881
882	<	//globalGroupMembership_ is filled by SimCreator
883	<	for (int i = 0; i < nGlobalAtoms_; i++) {
884	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
882	>	vector<int> GlobalGroupIndices;
883	>
884	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
885	>
886	>	//local index of cutoff group is trivial, it only depends on the
887	>	//order of travesing
888	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
889	>	cg = mol->nextCutoffGroup(ci)) {
890	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
891	>	}
892		}
893	+	return GlobalGroupIndices;
894	+	}
895
896	+
897	+	void SimInfo::prepareTopology() {
898	+
899		//calculate mass ratio of cutoff group
605	–	std::vector<double> mfact;
900		SimInfo::MoleculeIterator mi;
901		Molecule* mol;
902		Molecule::CutoffGroupIterator ci;
903		CutoffGroup* cg;
904		Molecule::AtomIterator ai;
905		Atom* atom;
906	<	double totalMass;
906	>	RealType totalMass;
907
908	<	//to avoid memory reallocation, reserve enough space for mfact
909	<	mfact.reserve(getNCutoffGroups());
908	>	/**
909	>	* The mass factor is the relative mass of an atom to the total
910	>	* mass of the cutoff group it belongs to.  By default, all atoms
911	>	* are their own cutoff groups, and therefore have mass factors of
912	>	* 1.  We need some special handling for massless atoms, which
913	>	* will be treated as carrying the entire mass of the cutoff
914	>	* group.
915	>	*/
916	>	massFactors_.clear();
917	>	massFactors_.resize(getNAtoms(), 1.0);
918
919		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
920	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
920	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
921	>	cg = mol->nextCutoffGroup(ci)) {
922
923	<	totalMass = cg->getMass();
924	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
925	<	mfact.push_back(atom->getMass()/totalMass);
926	<	}
927	<
928	<	}
923	>	totalMass = cg->getMass();
924	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
925	>	// Check for massless groups - set mfact to 1 if true
926	>	if (totalMass != 0)
927	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
928	>	else
929	>	massFactors_[atom->getLocalIndex()] = 1.0;
930	>	}
931	>	}
932		}
933
934	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
629	<	std::vector<int> identArray;
934	>	// Build the identArray_
935
936	<	//to avoid memory reallocation, reserve enough space identArray
937	<	identArray.reserve(getNAtoms());
633	<
936	>	identArray_.clear();
937	>	identArray_.reserve(getNAtoms());
938		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
939	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
940	<	identArray.push_back(atom->getIdent());
941	<	}
939	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
940	>	identArray_.push_back(atom->getIdent());
941	>	}
942		}
943	+
944	+	topologyDone_ = true;
945	+	}
946
947	<	//fill molMembershipArray
641	<	//molMembershipArray is filled by SimCreator
642	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
643	<	for (int i = 0; i < nGlobalAtoms_; i++) {
644	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
645	<	}
646	<
647	<	//setup fortran simulation
648	<	//gloalExcludes and molMembershipArray should go away (They are never used)
649	<	//why the hell fortran need to know molecule?
650	<	//OOPSE = Object-Obfuscated Parallel Simulation Engine
651	<	int nGlobalExcludes = 0;
652	<	int* globalExcludes = NULL;
653	<	int* excludeList = exclude_.getExcludeList();
654	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
655	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
656	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
657	<
658	<	if( isError ){
659	<
660	<	sprintf( painCave.errMsg,
661	<	"There was an error setting the simulation information in fortran.\n" );
662	<	painCave.isFatal = 1;
663	<	painCave.severity = OOPSE_ERROR;
664	<	simError();
665	<	}
666	<
667	<	#ifdef IS_MPI
668	<	sprintf( checkPointMsg,
669	<	"succesfully sent the simulation information to fortran.\n");
670	<	MPIcheckPoint();
671	<	#endif // is_mpi
672	<	}
673	<
674	<
675	<	#ifdef IS_MPI
676	<	void SimInfo::setupFortranParallel() {
677	<
678	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
679	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
680	<	std::vector<int> localToGlobalCutoffGroupIndex;
681	<	SimInfo::MoleculeIterator mi;
682	<	Molecule::AtomIterator ai;
683	<	Molecule::CutoffGroupIterator ci;
684	<	Molecule* mol;
685	<	Atom* atom;
686	<	CutoffGroup* cg;
687	<	mpiSimData parallelData;
688	<	int isError;
689	<
690	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
691	<
692	<	//local index(index in DataStorge) of atom is important
693	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
694	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
695	<	}
696	<
697	<	//local index of cutoff group is trivial, it only depends on the order of travesing
698	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
699	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
700	<	}
701	<
702	<	}
703	<
704	<	//fill up mpiSimData struct
705	<	parallelData.nMolGlobal = getNGlobalMolecules();
706	<	parallelData.nMolLocal = getNMolecules();
707	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
708	<	parallelData.nAtomsLocal = getNAtoms();
709	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
710	<	parallelData.nGroupsLocal = getNCutoffGroups();
711	<	parallelData.myNode = worldRank;
712	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
713	<
714	<	//pass mpiSimData struct and index arrays to fortran
715	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
716	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
717	<	&localToGlobalCutoffGroupIndex[0], &isError);
718	<
719	<	if (isError) {
720	<	sprintf(painCave.errMsg,
721	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
722	<	painCave.isFatal = 1;
723	<	simError();
724	<	}
725	<
726	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
727	<	MPIcheckPoint();
728	<
729	<
730	<	}
731	<
732	<	#endif
733	<
734	<	double SimInfo::calcMaxCutoffRadius() {
735	<
736	<
737	<	std::set<AtomType*> atomTypes;
738	<	std::set<AtomType*>::iterator i;
739	<	std::vector<double> cutoffRadius;
740	<
741	<	//get the unique atom types
742	<	atomTypes = getUniqueAtomTypes();
743	<
744	<	//query the max cutoff radius among these atom types
745	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
746	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
747	<	}
748	<
749	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
750	<	#ifdef IS_MPI
751	<	//pick the max cutoff radius among the processors
752	<	#endif
753	<
754	<	return maxCutoffRadius;
755	<	}
756	<
757	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
758	<
759	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
760	<
761	<	if (!simParams_->haveRcut()){
762	<	sprintf(painCave.errMsg,
763	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
764	<	"\tOOPSE will use a default value of 15.0 angstroms"
765	<	"\tfor the cutoffRadius.\n");
766	<	painCave.isFatal = 0;
767	<	simError();
768	<	rcut = 15.0;
769	<	} else{
770	<	rcut = simParams_->getRcut();
771	<	}
772	<
773	<	if (!simParams_->haveRsw()){
774	<	sprintf(painCave.errMsg,
775	<	"SimCreator Warning: No value was set for switchingRadius.\n"
776	<	"\tOOPSE will use a default value of\n"
777	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
778	<	painCave.isFatal = 0;
779	<	simError();
780	<	rsw = 0.95 * rcut;
781	<	} else{
782	<	rsw = simParams_->getRsw();
783	<	}
784	<
785	<	} else {
786	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
787	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
788	<
789	<	if (simParams_->haveRcut()) {
790	<	rcut = simParams_->getRcut();
791	<	} else {
792	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
793	<	rcut = calcMaxCutoffRadius();
794	<	}
795	<
796	<	if (simParams_->haveRsw()) {
797	<	rsw  = simParams_->getRsw();
798	<	} else {
799	<	rsw = rcut;
800	<	}
801	<
802	<	}
803	<	}
804	<
805	<	void SimInfo::setupCutoff() {
806	<	getCutoff(rcut_, rsw_);
807	<	double rnblist = rcut_ + 1; // skin of neighbor list
808	<
809	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
810	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
811	<	}
812	<
813	<	void SimInfo::addProperty(GenericData* genData) {
947	>	void SimInfo::addProperty(GenericData* genData) {
948		properties_.addProperty(genData);
949	<	}
949	>	}
950
951	<	void SimInfo::removeProperty(const std::string& propName) {
951	>	void SimInfo::removeProperty(const string& propName) {
952		properties_.removeProperty(propName);
953	<	}
953	>	}
954
955	<	void SimInfo::clearProperties() {
955	>	void SimInfo::clearProperties() {
956		properties_.clearProperties();
957	<	}
957	>	}
958
959	<	std::vector<std::string> SimInfo::getPropertyNames() {
959	>	vector<string> SimInfo::getPropertyNames() {
960		return properties_.getPropertyNames();
961	<	}
961	>	}
962
963	<	std::vector<GenericData*> SimInfo::getProperties() {
963	>	vector<GenericData*> SimInfo::getProperties() {
964		return properties_.getProperties();
965	<	}
965	>	}
966
967	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
967	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
968		return properties_.getPropertyByName(propName);
969	<	}
969	>	}
970
971	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
972	<	//if (sman_ == sman_) {
973	<	//    return;
974	<	//}
975	<
842	<	//delete sman_;
971	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
972	>	if (sman_ == sman) {
973	>	return;
974	>	}
975	>	delete sman_;
976		sman_ = sman;
977
978		Molecule* mol;
979		RigidBody* rb;
980		Atom* atom;
981	+	CutoffGroup* cg;
982		SimInfo::MoleculeIterator mi;
983		Molecule::RigidBodyIterator rbIter;
984	<	Molecule::AtomIterator atomIter;;
984	>	Molecule::AtomIterator atomIter;
985	>	Molecule::CutoffGroupIterator cgIter;
986
987		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
988
989	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
990	<	atom->setSnapshotManager(sman_);
991	<	}
989	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
990	>	atom = mol->nextAtom(atomIter)) {
991	>	atom->setSnapshotManager(sman_);
992	>	}
993
994	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
995	<	rb->setSnapshotManager(sman_);
996	<	}
994	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
995	>	rb = mol->nextRigidBody(rbIter)) {
996	>	rb->setSnapshotManager(sman_);
997	>	}
998	>
999	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1000	>	cg = mol->nextCutoffGroup(cgIter)) {
1001	>	cg->setSnapshotManager(sman_);
1002	>	}
1003		}
1004
1005	<	}
1005	>	}
1006
865	–	Vector3d SimInfo::getComVel(){
866	–	SimInfo::MoleculeIterator i;
867	–	Molecule* mol;
1007
1008	<	Vector3d comVel(0.0);
870	<	double totalMass = 0.0;
871	<
872	<
873	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
874	<	double mass = mol->getMass();
875	<	totalMass += mass;
876	<	comVel += mass * mol->getComVel();
877	<	}
1008	>	ostream& operator <<(ostream& o, SimInfo& info) {
1009
1010	<	#ifdef IS_MPI
1011	<	double tmpMass = totalMass;
1012	<	Vector3d tmpComVel(comVel);
1013	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1014	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1015	<	#endif
1010	>	return o;
1011	>	}
1012	>
1013	>
1014	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1015	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1016	>	sprintf(painCave.errMsg,
1017	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1018	>	"\tindex exceeds number of known objects!\n");
1019	>	painCave.isFatal = 1;
1020	>	simError();
1021	>	return NULL;
1022	>	} else
1023	>	return IOIndexToIntegrableObject.at(index);
1024	>	}
1025	>
1026	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1027	>	IOIndexToIntegrableObject= v;
1028	>	}
1029
1030	<	comVel /= totalMass;
1031	<
888	<	return comVel;
889	<	}
890	<
891	<	Vector3d SimInfo::getCom(){
892	<	SimInfo::MoleculeIterator i;
893	<	Molecule* mol;
894	<
895	<	Vector3d com(0.0);
896	<	double totalMass = 0.0;
897	<
898	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
899	<	double mass = mol->getMass();
900	<	totalMass += mass;
901	<	com += mass * mol->getCom();
902	<	}
903	<
1030	>	int SimInfo::getNGlobalConstraints() {
1031	>	int nGlobalConstraints;
1032		#ifdef IS_MPI
1033	<	double tmpMass = totalMass;
1034	<	Vector3d tmpCom(com);
1035	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1036	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1033	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1034	>	MPI::INT, MPI::SUM);
1035	>	#else
1036	>	nGlobalConstraints =  nConstraints_;
1037		#endif
1038	+	return nGlobalConstraints;
1039	+	}
1040
1041	<	com /= totalMass;
1041	>	}//end namespace OpenMD
1042
913	–	return com;
914	–
915	–	}
916	–
917	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
918	–
919	–	return o;
920	–	}
921	–
922	–	}//end namespace oopse
923	–

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 334 by tim, Mon Feb 14 17:57:01 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

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