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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 1126 by gezelter, Fri Apr 6 21:53:43 2007 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

#	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 46 | Line 47
47		* @version 1.0
48		*/
49
50	+	#ifdef IS_MPI
51	+	#include <mpi.h>
52	+	#endif
53		#include <algorithm>
54		#include <set>
55		#include <map>
#	Line 54 | Line 58
58		#include "math/Vector3.hpp"
59		#include "primitives/Molecule.hpp"
60		#include "primitives/StuntDouble.hpp"
57	–	#include "UseTheForce/fCutoffPolicy.h"
58	–	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	–	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60	–	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61	–	#include "UseTheForce/doForces_interface.h"
62	–	#include "UseTheForce/DarkSide/neighborLists_interface.h"
63	–	#include "UseTheForce/DarkSide/electrostatic_interface.h"
64	–	#include "UseTheForce/DarkSide/switcheroo_interface.h"
61		#include "utils/MemoryUtils.hpp"
62		#include "utils/simError.h"
63		#include "selection/SelectionManager.hpp"
64		#include "io/ForceFieldOptions.hpp"
65	<	#include "UseTheForce/ForceField.hpp"
65	>	#include "brains/ForceField.hpp"
66	>	#include "nonbonded/SwitchingFunction.hpp"
67
68	<
69	<	#ifdef IS_MPI
73	<	#include "UseTheForce/mpiComponentPlan.h"
74	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
75	<	#endif
76	<
77	<	namespace oopse {
78	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79	<	std::map<int, std::set<int> >::iterator i = container.find(index);
80	<	std::set<int> result;
81	<	if (i != container.end()) {
82	<	result = i->second;
83	<	}
84	<
85	<	return result;
86	<	}
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),
73	>	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0),
74	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
75	>	nConstraints_(0), nFluctuatingCharges_(0),
76		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
77	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
78	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
79	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
80	<	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false),
81	<	useAtomicVirial_(true) {
82	<
83	<	MoleculeStamp* molStamp;
84	<	int nMolWithSameStamp;
85	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
86	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
87	<	CutoffGroupStamp* cgStamp;
88	<	RigidBodyStamp* rbStamp;
89	<	int nRigidAtoms = 0;
90	<	std::vector<Component*> components = simParams->getComponents();
91	<
92	<	for (std::vector<Component*>::iterator i = components.begin(); 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;
118	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
119	<
120	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
121	<	cgStamp = molStamp->getCutoffGroupStamp(j);
122	<	nAtomsInGroups += cgStamp->getNMembers();
123	<	}
124	<
125	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
126	<
127	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
128	<
129	<	//calculate atoms in rigid bodies
130	<	int nAtomsInRigidBodies = 0;
131	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
132	<
133	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
134	<	rbStamp = molStamp->getRigidBodyStamp(j);
135	<	nAtomsInRigidBodies += rbStamp->getNMembers();
136	<	}
137	<
138	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
139	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
140	<
77	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
78	>	nGlobalFluctuatingCharges_(0), nGlobalBonds_(0), nGlobalBends_(0),
79	>	nGlobalTorsions_(0), nGlobalInversions_(0), nGlobalConstraints_(0),
80	>	hasNGlobalConstraints_(false),
81	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
82	>	sman_(NULL), topologyDone_(false), calcBoxDipole_(false),
83	>	calcBoxQuadrupole_(false), useAtomicVirial_(true) {
84	>
85	>	MoleculeStamp* molStamp;
86	>	int nMolWithSameStamp;
87	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
88	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
89	>	CutoffGroupStamp* cgStamp;
90	>	RigidBodyStamp* rbStamp;
91	>	int nRigidAtoms = 0;
92	>
93	>	vector<Component*> components = simParams->getComponents();
94	>
95	>	for (vector<Component*>::iterator i = components.begin();
96	>	i !=components.end(); ++i) {
97	>	molStamp = (*i)->getMoleculeStamp();
98	>	if ( (*i)->haveRegion() ) {
99	>	molStamp->setRegion( (*i)->getRegion() );
100	>	} else {
101	>	// set the region to a disallowed value:
102	>	molStamp->setRegion( -1 );
103		}
104
105	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
106	<	//group therefore the total number of cutoff groups in the system is
107	<	//equal to the total number of atoms minus number of atoms belong to
108	<	//cutoff group defined in meta-data file plus the number of cutoff
109	<	//groups defined in meta-data file
110	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
111	<
112	<	//every free atom (atom does not belong to rigid bodies) is an
113	<	//integrable object therefore the total number of integrable objects
114	<	//in the system is equal to the total number of atoms minus number of
115	<	//atoms belong to rigid body defined in meta-data file plus the number
116	<	//of rigid bodies defined in meta-data file
117	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
118	<	+ nGlobalRigidBodies_;
119	<
120	<	nGlobalMols_ = molStampIds_.size();
121	<
122	<	#ifdef IS_MPI
123	<	molToProcMap_.resize(nGlobalMols_);
124	<	#endif
125	<
105	>	nMolWithSameStamp = (*i)->getNMol();
106	>
107	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
108	>
109	>	//calculate atoms in molecules
110	>	nGlobalAtoms_ += molStamp->getNAtoms() * nMolWithSameStamp;
111	>	nGlobalBonds_ += molStamp->getNBonds() * nMolWithSameStamp;
112	>	nGlobalBends_ += molStamp->getNBends() * nMolWithSameStamp;
113	>	nGlobalTorsions_ += molStamp->getNTorsions() * nMolWithSameStamp;
114	>	nGlobalInversions_ += molStamp->getNInversions() * nMolWithSameStamp;
115	>
116	>	//calculate atoms in cutoff groups
117	>	int nAtomsInGroups = 0;
118	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
119	>
120	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
121	>	cgStamp = molStamp->getCutoffGroupStamp(j);
122	>	nAtomsInGroups += cgStamp->getNMembers();
123	>	}
124	>
125	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
126	>
127	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
128	>
129	>	//calculate atoms in rigid bodies
130	>	int nAtomsInRigidBodies = 0;
131	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
132	>
133	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
134	>	rbStamp = molStamp->getRigidBodyStamp(j);
135	>	nAtomsInRigidBodies += rbStamp->getNMembers();
136	>	}
137	>
138	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
139	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
140	>
141		}
142	+
143	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
144	+	//group therefore the total number of cutoff groups in the system is
145	+	//equal to the total number of atoms minus number of atoms belong to
146	+	//cutoff group defined in meta-data file plus the number of cutoff
147	+	//groups defined in meta-data file
148
149	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
150	+
151	+	//every free atom (atom does not belong to rigid bodies) is an
152	+	//integrable object therefore the total number of integrable objects
153	+	//in the system is equal to the total number of atoms minus number of
154	+	//atoms belong to rigid body defined in meta-data file plus the number
155	+	//of rigid bodies defined in meta-data file
156	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
157	+	+ nGlobalRigidBodies_;
158	+
159	+	nGlobalMols_ = molStampIds_.size();
160	+	molToProcMap_.resize(nGlobalMols_);
161	+	}
162	+
163		SimInfo::~SimInfo() {
164	<	std::map<int, Molecule*>::iterator i;
164	>	map<int, Molecule*>::iterator i;
165		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
166		delete i->second;
167		}
#	Line 175 | Line 172 | namespace oopse {
172		delete forceField_;
173		}
174
178	–	int SimInfo::getNGlobalConstraints() {
179	–	int nGlobalConstraints;
180	–	#ifdef IS_MPI
181	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
182	–	MPI_COMM_WORLD);
183	–	#else
184	–	nGlobalConstraints =  nConstraints_;
185	–	#endif
186	–	return nGlobalConstraints;
187	–	}
175
176		bool SimInfo::addMolecule(Molecule* mol) {
177		MoleculeIterator i;
178	<
178	>
179		i = molecules_.find(mol->getGlobalIndex());
180		if (i == molecules_.end() ) {
181	<
182	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
183	<
181	>
182	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
183	>
184		nAtoms_ += mol->getNAtoms();
185		nBonds_ += mol->getNBonds();
186		nBends_ += mol->getNBends();
187		nTorsions_ += mol->getNTorsions();
188	+	nInversions_ += mol->getNInversions();
189		nRigidBodies_ += mol->getNRigidBodies();
190		nIntegrableObjects_ += mol->getNIntegrableObjects();
191		nCutoffGroups_ += mol->getNCutoffGroups();
192		nConstraints_ += mol->getNConstraintPairs();
193	<
194	<	addExcludePairs(mol);
195	<
193	>
194	>	addInteractionPairs(mol);
195	>
196		return true;
197		} else {
198		return false;
199		}
200		}
201	<
201	>
202		bool SimInfo::removeMolecule(Molecule* mol) {
203		MoleculeIterator i;
204		i = molecules_.find(mol->getGlobalIndex());
#	Line 223 | Line 211 | namespace oopse {
211		nBonds_ -= mol->getNBonds();
212		nBends_ -= mol->getNBends();
213		nTorsions_ -= mol->getNTorsions();
214	+	nInversions_ -= mol->getNInversions();
215		nRigidBodies_ -= mol->getNRigidBodies();
216		nIntegrableObjects_ -= mol->getNIntegrableObjects();
217		nCutoffGroups_ -= mol->getNCutoffGroups();
218		nConstraints_ -= mol->getNConstraintPairs();
219
220	<	removeExcludePairs(mol);
220	>	removeInteractionPairs(mol);
221		molecules_.erase(mol->getGlobalIndex());
222
223		delete mol;
#	Line 237 | Line 226 | namespace oopse {
226		} else {
227		return false;
228		}
240	–
241	–
229		}
230
231
#	Line 254 | Line 241 | namespace oopse {
241
242
243		void SimInfo::calcNdf() {
244	<	int ndf_local;
244	>	int ndf_local, nfq_local;
245		MoleculeIterator i;
246	<	std::vector<StuntDouble*>::iterator j;
246	>	vector<StuntDouble*>::iterator j;
247	>	vector<Atom*>::iterator k;
248	>
249		Molecule* mol;
250	<	StuntDouble* integrableObject;
250	>	StuntDouble* sd;
251	>	Atom* atom;
252
253		ndf_local = 0;
254	+	nfq_local = 0;
255
256		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
257	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
258	<	integrableObject = mol->nextIntegrableObject(j)) {
257	>
258	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
259	>	sd = mol->nextIntegrableObject(j)) {
260
261		ndf_local += 3;
262
263	<	if (integrableObject->isDirectional()) {
264	<	if (integrableObject->isLinear()) {
263	>	if (sd->isDirectional()) {
264	>	if (sd->isLinear()) {
265		ndf_local += 2;
266		} else {
267		ndf_local += 3;
268		}
269		}
278	–
270		}
271	+
272	+	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
273	+	atom = mol->nextFluctuatingCharge(k)) {
274	+	if (atom->isFluctuatingCharge()) {
275	+	nfq_local++;
276	+	}
277	+	}
278		}
279
280	+	ndfLocal_ = ndf_local;
281	+
282		// n_constraints is local, so subtract them on each processor
283		ndf_local -= nConstraints_;
284
285		#ifdef IS_MPI
286	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
286	>	MPI_Allreduce(&ndf_local, &ndf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
287	>	MPI_Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
288	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
289		#else
290		ndf_ = ndf_local;
291	+	nGlobalFluctuatingCharges_ = nfq_local;
292		#endif
293
294		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 296 | Line 299 | namespace oopse {
299
300		int SimInfo::getFdf() {
301		#ifdef IS_MPI
302	<	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
302	>	MPI_Allreduce(&fdf_local, &fdf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
303		#else
304		fdf_ = fdf_local;
305		#endif
306		return fdf_;
307		}
308	+
309	+	unsigned int SimInfo::getNLocalCutoffGroups(){
310	+	int nLocalCutoffAtoms = 0;
311	+	Molecule* mol;
312	+	MoleculeIterator mi;
313	+	CutoffGroup* cg;
314	+	Molecule::CutoffGroupIterator ci;
315
316	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
317	+
318	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
319	+	cg = mol->nextCutoffGroup(ci)) {
320	+	nLocalCutoffAtoms += cg->getNumAtom();
321	+
322	+	}
323	+	}
324	+
325	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
326	+	}
327	+
328		void SimInfo::calcNdfRaw() {
329		int ndfRaw_local;
330
331		MoleculeIterator i;
332	<	std::vector<StuntDouble*>::iterator j;
332	>	vector<StuntDouble*>::iterator j;
333		Molecule* mol;
334	<	StuntDouble* integrableObject;
334	>	StuntDouble* sd;
335
336		// Raw degrees of freedom that we have to set
337		ndfRaw_local = 0;
338
339		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
318	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
319	–	integrableObject = mol->nextIntegrableObject(j)) {
340
341	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
342	+	sd = mol->nextIntegrableObject(j)) {
343	+
344		ndfRaw_local += 3;
345
346	<	if (integrableObject->isDirectional()) {
347	<	if (integrableObject->isLinear()) {
346	>	if (sd->isDirectional()) {
347	>	if (sd->isLinear()) {
348		ndfRaw_local += 2;
349		} else {
350		ndfRaw_local += 3;
#	Line 332 | Line 355 | namespace oopse {
355		}
356
357		#ifdef IS_MPI
358	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
358	>	MPI_Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
359		#else
360		ndfRaw_ = ndfRaw_local;
361		#endif
#	Line 343 | Line 366 | namespace oopse {
366
367		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
368
346	–
369		#ifdef IS_MPI
370	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
370	>	MPI_Allreduce(&ndfTrans_local, &ndfTrans_, 1, MPI_INT, MPI_SUM,
371	>	MPI_COMM_WORLD);
372		#else
373		ndfTrans_ = ndfTrans_local;
374		#endif
375
376		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
354	–
377		}
378
379	<	void SimInfo::addExcludePairs(Molecule* mol) {
380	<	std::vector<Bond*>::iterator bondIter;
381	<	std::vector<Bend*>::iterator bendIter;
382	<	std::vector<Torsion*>::iterator torsionIter;
379	>	void SimInfo::addInteractionPairs(Molecule* mol) {
380	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
381	>	vector<Bond*>::iterator bondIter;
382	>	vector<Bend*>::iterator bendIter;
383	>	vector<Torsion*>::iterator torsionIter;
384	>	vector<Inversion*>::iterator inversionIter;
385		Bond* bond;
386		Bend* bend;
387		Torsion* torsion;
388	+	Inversion* inversion;
389		int a;
390		int b;
391		int c;
392		int d;
393
394	<	std::map<int, std::set<int> > atomGroups;
394	>	// atomGroups can be used to add special interaction maps between
395	>	// groups of atoms that are in two separate rigid bodies.
396	>	// However, most site-site interactions between two rigid bodies
397	>	// are probably not special, just the ones between the physically
398	>	// bonded atoms.  Interactions *within* a single rigid body should
399	>	// always be excluded.  These are done at the bottom of this
400	>	// function.
401
402	+	map<int, set<int> > atomGroups;
403		Molecule::RigidBodyIterator rbIter;
404		RigidBody* rb;
405		Molecule::IntegrableObjectIterator ii;
406	<	StuntDouble* integrableObject;
406	>	StuntDouble* sd;
407
408	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
409	<	integrableObject = mol->nextIntegrableObject(ii)) {
410	<
411	<	if (integrableObject->isRigidBody()) {
412	<	rb = static_cast<RigidBody*>(integrableObject);
413	<	std::vector<Atom*> atoms = rb->getAtoms();
414	<	std::set<int> rigidAtoms;
415	<	for (int i = 0; i < atoms.size(); ++i) {
416	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
417	<	}
418	<	for (int i = 0; i < atoms.size(); ++i) {
419	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
420	<	}
408	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
409	>	sd = mol->nextIntegrableObject(ii)) {
410	>
411	>	if (sd->isRigidBody()) {
412	>	rb = static_cast<RigidBody*>(sd);
413	>	vector<Atom*> atoms = rb->getAtoms();
414	>	set<int> rigidAtoms;
415	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
416	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
417	>	}
418	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
419	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
420	>	}
421		} else {
422	<	std::set<int> oneAtomSet;
423	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
424	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
422	>	set<int> oneAtomSet;
423	>	oneAtomSet.insert(sd->getGlobalIndex());
424	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
425		}
426		}
427
428	<
429	<
430	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
428	>
429	>	for (bond= mol->beginBond(bondIter); bond != NULL;
430	>	bond = mol->nextBond(bondIter)) {
431	>
432		a = bond->getAtomA()->getGlobalIndex();
433	<	b = bond->getAtomB()->getGlobalIndex();
434	<	exclude_.addPair(a, b);
433	>	b = bond->getAtomB()->getGlobalIndex();
434	>
435	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
436	>	oneTwoInteractions_.addPair(a, b);
437	>	} else {
438	>	excludedInteractions_.addPair(a, b);
439	>	}
440		}
441
442	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
442	>	for (bend= mol->beginBend(bendIter); bend != NULL;
443	>	bend = mol->nextBend(bendIter)) {
444	>
445		a = bend->getAtomA()->getGlobalIndex();
446		b = bend->getAtomB()->getGlobalIndex();
447		c = bend->getAtomC()->getGlobalIndex();
408	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
409	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
410	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
411	–
412	–	exclude_.addPairs(rigidSetA, rigidSetB);
413	–	exclude_.addPairs(rigidSetA, rigidSetC);
414	–	exclude_.addPairs(rigidSetB, rigidSetC);
448
449	<	//exclude_.addPair(a, b);
450	<	//exclude_.addPair(a, c);
451	<	//exclude_.addPair(b, c);
449	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
450	>	oneTwoInteractions_.addPair(a, b);
451	>	oneTwoInteractions_.addPair(b, c);
452	>	} else {
453	>	excludedInteractions_.addPair(a, b);
454	>	excludedInteractions_.addPair(b, c);
455	>	}
456	>
457	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
458	>	oneThreeInteractions_.addPair(a, c);
459	>	} else {
460	>	excludedInteractions_.addPair(a, c);
461	>	}
462		}
463
464	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
464	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
465	>	torsion = mol->nextTorsion(torsionIter)) {
466	>
467		a = torsion->getAtomA()->getGlobalIndex();
468		b = torsion->getAtomB()->getGlobalIndex();
469		c = torsion->getAtomC()->getGlobalIndex();
470	<	d = torsion->getAtomD()->getGlobalIndex();
426	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
427	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
428	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
429	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
470	>	d = torsion->getAtomD()->getGlobalIndex();
471
472	<	exclude_.addPairs(rigidSetA, rigidSetB);
473	<	exclude_.addPairs(rigidSetA, rigidSetC);
474	<	exclude_.addPairs(rigidSetA, rigidSetD);
475	<	exclude_.addPairs(rigidSetB, rigidSetC);
476	<	exclude_.addPairs(rigidSetB, rigidSetD);
477	<	exclude_.addPairs(rigidSetC, rigidSetD);
472	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
473	>	oneTwoInteractions_.addPair(a, b);
474	>	oneTwoInteractions_.addPair(b, c);
475	>	oneTwoInteractions_.addPair(c, d);
476	>	} else {
477	>	excludedInteractions_.addPair(a, b);
478	>	excludedInteractions_.addPair(b, c);
479	>	excludedInteractions_.addPair(c, d);
480	>	}
481
482	<	/*
483	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
484	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
485	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
486	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
487	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
488	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
489	<
490	<
491	<	exclude_.addPair(a, b);
492	<	exclude_.addPair(a, c);
493	<	exclude_.addPair(a, d);
494	<	exclude_.addPair(b, c);
451	<	exclude_.addPair(b, d);
452	<	exclude_.addPair(c, d);
453	<	*/
482	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
483	>	oneThreeInteractions_.addPair(a, c);
484	>	oneThreeInteractions_.addPair(b, d);
485	>	} else {
486	>	excludedInteractions_.addPair(a, c);
487	>	excludedInteractions_.addPair(b, d);
488	>	}
489	>
490	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
491	>	oneFourInteractions_.addPair(a, d);
492	>	} else {
493	>	excludedInteractions_.addPair(a, d);
494	>	}
495		}
496
497	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
498	<	std::vector<Atom*> atoms = rb->getAtoms();
499	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
500	<	for (int j = i + 1; j < atoms.size(); ++j) {
497	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
498	>	inversion = mol->nextInversion(inversionIter)) {
499	>
500	>	a = inversion->getAtomA()->getGlobalIndex();
501	>	b = inversion->getAtomB()->getGlobalIndex();
502	>	c = inversion->getAtomC()->getGlobalIndex();
503	>	d = inversion->getAtomD()->getGlobalIndex();
504	>
505	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
506	>	oneTwoInteractions_.addPair(a, b);
507	>	oneTwoInteractions_.addPair(a, c);
508	>	oneTwoInteractions_.addPair(a, d);
509	>	} else {
510	>	excludedInteractions_.addPair(a, b);
511	>	excludedInteractions_.addPair(a, c);
512	>	excludedInteractions_.addPair(a, d);
513	>	}
514	>
515	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
516	>	oneThreeInteractions_.addPair(b, c);
517	>	oneThreeInteractions_.addPair(b, d);
518	>	oneThreeInteractions_.addPair(c, d);
519	>	} else {
520	>	excludedInteractions_.addPair(b, c);
521	>	excludedInteractions_.addPair(b, d);
522	>	excludedInteractions_.addPair(c, d);
523	>	}
524	>	}
525	>
526	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
527	>	rb = mol->nextRigidBody(rbIter)) {
528	>	vector<Atom*> atoms = rb->getAtoms();
529	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
530	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
531		a = atoms[i]->getGlobalIndex();
532		b = atoms[j]->getGlobalIndex();
533	<	exclude_.addPair(a, b);
533	>	excludedInteractions_.addPair(a, b);
534		}
535		}
536		}
537
538		}
539
540	<	void SimInfo::removeExcludePairs(Molecule* mol) {
541	<	std::vector<Bond*>::iterator bondIter;
542	<	std::vector<Bend*>::iterator bendIter;
543	<	std::vector<Torsion*>::iterator torsionIter;
540	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
541	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
542	>	vector<Bond*>::iterator bondIter;
543	>	vector<Bend*>::iterator bendIter;
544	>	vector<Torsion*>::iterator torsionIter;
545	>	vector<Inversion*>::iterator inversionIter;
546		Bond* bond;
547		Bend* bend;
548		Torsion* torsion;
549	+	Inversion* inversion;
550		int a;
551		int b;
552		int c;
553		int d;
554
555	<	std::map<int, std::set<int> > atomGroups;
482	<
555	>	map<int, set<int> > atomGroups;
556		Molecule::RigidBodyIterator rbIter;
557		RigidBody* rb;
558		Molecule::IntegrableObjectIterator ii;
559	<	StuntDouble* integrableObject;
559	>	StuntDouble* sd;
560
561	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
562	<	integrableObject = mol->nextIntegrableObject(ii)) {
563	<
564	<	if (integrableObject->isRigidBody()) {
565	<	rb = static_cast<RigidBody*>(integrableObject);
566	<	std::vector<Atom*> atoms = rb->getAtoms();
567	<	std::set<int> rigidAtoms;
568	<	for (int i = 0; i < atoms.size(); ++i) {
569	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
570	<	}
571	<	for (int i = 0; i < atoms.size(); ++i) {
572	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
573	<	}
561	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
562	>	sd = mol->nextIntegrableObject(ii)) {
563	>
564	>	if (sd->isRigidBody()) {
565	>	rb = static_cast<RigidBody*>(sd);
566	>	vector<Atom*> atoms = rb->getAtoms();
567	>	set<int> rigidAtoms;
568	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
569	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
570	>	}
571	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
572	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
573	>	}
574		} else {
575	<	std::set<int> oneAtomSet;
576	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
577	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
575	>	set<int> oneAtomSet;
576	>	oneAtomSet.insert(sd->getGlobalIndex());
577	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
578		}
579		}
580
581	<
582	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
581	>	for (bond= mol->beginBond(bondIter); bond != NULL;
582	>	bond = mol->nextBond(bondIter)) {
583	>
584		a = bond->getAtomA()->getGlobalIndex();
585	<	b = bond->getAtomB()->getGlobalIndex();
586	<	exclude_.removePair(a, b);
585	>	b = bond->getAtomB()->getGlobalIndex();
586	>
587	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
588	>	oneTwoInteractions_.removePair(a, b);
589	>	} else {
590	>	excludedInteractions_.removePair(a, b);
591	>	}
592		}
593
594	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
594	>	for (bend= mol->beginBend(bendIter); bend != NULL;
595	>	bend = mol->nextBend(bendIter)) {
596	>
597		a = bend->getAtomA()->getGlobalIndex();
598		b = bend->getAtomB()->getGlobalIndex();
599		c = bend->getAtomC()->getGlobalIndex();
519	–
520	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
521	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
522	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
523	–
524	–	exclude_.removePairs(rigidSetA, rigidSetB);
525	–	exclude_.removePairs(rigidSetA, rigidSetC);
526	–	exclude_.removePairs(rigidSetB, rigidSetC);
600
601	<	//exclude_.removePair(a, b);
602	<	//exclude_.removePair(a, c);
603	<	//exclude_.removePair(b, c);
601	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
602	>	oneTwoInteractions_.removePair(a, b);
603	>	oneTwoInteractions_.removePair(b, c);
604	>	} else {
605	>	excludedInteractions_.removePair(a, b);
606	>	excludedInteractions_.removePair(b, c);
607	>	}
608	>
609	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
610	>	oneThreeInteractions_.removePair(a, c);
611	>	} else {
612	>	excludedInteractions_.removePair(a, c);
613	>	}
614		}
615
616	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
616	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
617	>	torsion = mol->nextTorsion(torsionIter)) {
618	>
619		a = torsion->getAtomA()->getGlobalIndex();
620		b = torsion->getAtomB()->getGlobalIndex();
621		c = torsion->getAtomC()->getGlobalIndex();
622	<	d = torsion->getAtomD()->getGlobalIndex();
622	>	d = torsion->getAtomD()->getGlobalIndex();
623	>
624	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
625	>	oneTwoInteractions_.removePair(a, b);
626	>	oneTwoInteractions_.removePair(b, c);
627	>	oneTwoInteractions_.removePair(c, d);
628	>	} else {
629	>	excludedInteractions_.removePair(a, b);
630	>	excludedInteractions_.removePair(b, c);
631	>	excludedInteractions_.removePair(c, d);
632	>	}
633
634	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
635	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
636	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
637	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
634	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
635	>	oneThreeInteractions_.removePair(a, c);
636	>	oneThreeInteractions_.removePair(b, d);
637	>	} else {
638	>	excludedInteractions_.removePair(a, c);
639	>	excludedInteractions_.removePair(b, d);
640	>	}
641
642	<	exclude_.removePairs(rigidSetA, rigidSetB);
643	<	exclude_.removePairs(rigidSetA, rigidSetC);
644	<	exclude_.removePairs(rigidSetA, rigidSetD);
645	<	exclude_.removePairs(rigidSetB, rigidSetC);
646	<	exclude_.removePairs(rigidSetB, rigidSetD);
647	<	exclude_.removePairs(rigidSetC, rigidSetD);
642	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
643	>	oneFourInteractions_.removePair(a, d);
644	>	} else {
645	>	excludedInteractions_.removePair(a, d);
646	>	}
647	>	}
648
649	<	/*
650	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
553	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
554	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
555	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
556	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
557	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
649	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
650	>	inversion = mol->nextInversion(inversionIter)) {
651
652	<
653	<	exclude_.removePair(a, b);
654	<	exclude_.removePair(a, c);
655	<	exclude_.removePair(a, d);
656	<	exclude_.removePair(b, c);
657	<	exclude_.removePair(b, d);
658	<	exclude_.removePair(c, d);
659	<	*/
652	>	a = inversion->getAtomA()->getGlobalIndex();
653	>	b = inversion->getAtomB()->getGlobalIndex();
654	>	c = inversion->getAtomC()->getGlobalIndex();
655	>	d = inversion->getAtomD()->getGlobalIndex();
656	>
657	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
658	>	oneTwoInteractions_.removePair(a, b);
659	>	oneTwoInteractions_.removePair(a, c);
660	>	oneTwoInteractions_.removePair(a, d);
661	>	} else {
662	>	excludedInteractions_.removePair(a, b);
663	>	excludedInteractions_.removePair(a, c);
664	>	excludedInteractions_.removePair(a, d);
665	>	}
666	>
667	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
668	>	oneThreeInteractions_.removePair(b, c);
669	>	oneThreeInteractions_.removePair(b, d);
670	>	oneThreeInteractions_.removePair(c, d);
671	>	} else {
672	>	excludedInteractions_.removePair(b, c);
673	>	excludedInteractions_.removePair(b, d);
674	>	excludedInteractions_.removePair(c, d);
675	>	}
676		}
677
678	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
679	<	std::vector<Atom*> atoms = rb->getAtoms();
680	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
681	<	for (int j = i + 1; j < atoms.size(); ++j) {
678	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
679	>	rb = mol->nextRigidBody(rbIter)) {
680	>	vector<Atom*> atoms = rb->getAtoms();
681	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
682	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
683		a = atoms[i]->getGlobalIndex();
684		b = atoms[j]->getGlobalIndex();
685	<	exclude_.removePair(a, b);
685	>	excludedInteractions_.removePair(a, b);
686		}
687		}
688		}
689	<
689	>
690		}
691	<
692	<
691	>
692	>
693		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
694		int curStampId;
695	<
695	>
696		//index from 0
697		curStampId = moleculeStamps_.size();
698
#	Line 590 | Line 700 | namespace oopse {
700		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
701		}
702
593	–	void SimInfo::update() {
703
704	<	setupSimType();
705	<
706	<	#ifdef IS_MPI
707	<	setupFortranParallel();
708	<	#endif
709	<
710	<	setupFortranSim();
711	<
712	<	//setup fortran force field
713	<	/** @deprecate */
605	<	int isError = 0;
606	<
607	<	setupCutoff();
608	<
609	<	setupElectrostaticSummationMethod( isError );
610	<	setupSwitchingFunction();
611	<	setupAccumulateBoxDipole();
612	<
613	<	if(isError){
614	<	sprintf( painCave.errMsg,
615	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
616	<	painCave.isFatal = 1;
617	<	simError();
618	<	}
619	<
704	>	/**
705	>	* update
706	>	*
707	>	*  Performs the global checks and variable settings after the
708	>	*  objects have been created.
709	>	*
710	>	*/
711	>	void SimInfo::update() {
712	>	setupSimVariables();
713	>	calcNConstraints();
714		calcNdf();
715		calcNdfRaw();
716		calcNdfTrans();
623	–
624	–	fortranInitialized_ = true;
717		}
718	<
719	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
718	>
719	>	/**
720	>	* getSimulatedAtomTypes
721	>	*
722	>	* Returns an STL set of AtomType* that are actually present in this
723	>	* simulation.  Must query all processors to assemble this information.
724	>	*
725	>	*/
726	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
727		SimInfo::MoleculeIterator mi;
728		Molecule* mol;
729		Molecule::AtomIterator ai;
730		Atom* atom;
731	<	std::set<AtomType*> atomTypes;
732	<
731	>	set<AtomType*> atomTypes;
732	>
733		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
734	<
735	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
734	>	for(atom = mol->beginAtom(ai); atom != NULL;
735	>	atom = mol->nextAtom(ai)) {
736		atomTypes.insert(atom->getAtomType());
737	<	}
738	<
640	<	}
641	<
642	<	return atomTypes;
643	<	}
644	<
645	<	void SimInfo::setupSimType() {
646	<	std::set<AtomType*>::iterator i;
647	<	std::set<AtomType*> atomTypes;
648	<	atomTypes = getUniqueAtomTypes();
737	>	}
738	>	}
739
740	<	int useLennardJones = 0;
651	<	int useElectrostatic = 0;
652	<	int useEAM = 0;
653	<	int useSC = 0;
654	<	int useCharge = 0;
655	<	int useDirectional = 0;
656	<	int useDipole = 0;
657	<	int useGayBerne = 0;
658	<	int useSticky = 0;
659	<	int useStickyPower = 0;
660	<	int useShape = 0;
661	<	int useFLARB = 0; //it is not in AtomType yet
662	<	int useDirectionalAtom = 0;
663	<	int useElectrostatics = 0;
664	<	//usePBC and useRF are from simParams
665	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
666	<	int useRF;
667	<	int useSF;
668	<	int useSP;
669	<	int useBoxDipole;
740	>	#ifdef IS_MPI
741
742	<	std::string myMethod;
743	<
673	<	// set the useRF logical
674	<	useRF = 0;
675	<	useSF = 0;
676	<	useSP = 0;
677	<
678	<
679	<	if (simParams_->haveElectrostaticSummationMethod()) {
680	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
681	<	toUpper(myMethod);
682	<	if (myMethod == "REACTION_FIELD"){
683	<	useRF = 1;
684	<	} else if (myMethod == "SHIFTED_FORCE"){
685	<	useSF = 1;
686	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
687	<	useSP = 1;
688	<	}
689	<	}
742	>	// loop over the found atom types on this processor, and add their
743	>	// numerical idents to a vector:
744
745	<	if (simParams_->haveAccumulateBoxDipole())
746	<	if (simParams_->getAccumulateBoxDipole())
747	<	useBoxDipole = 1;
745	>	vector<int> foundTypes;
746	>	set<AtomType*>::iterator i;
747	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
748	>	foundTypes.push_back( (*i)->getIdent() );
749
750	<	useAtomicVirial_ = simParams_->getUseAtomicVirial();
750	>	// count_local holds the number of found types on this processor
751	>	int count_local = foundTypes.size();
752
753	<	//loop over all of the atom types
754	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
699	<	useLennardJones |= (*i)->isLennardJones();
700	<	useElectrostatic |= (*i)->isElectrostatic();
701	<	useEAM |= (*i)->isEAM();
702	<	useSC |= (*i)->isSC();
703	<	useCharge |= (*i)->isCharge();
704	<	useDirectional |= (*i)->isDirectional();
705	<	useDipole |= (*i)->isDipole();
706	<	useGayBerne |= (*i)->isGayBerne();
707	<	useSticky |= (*i)->isSticky();
708	<	useStickyPower |= (*i)->isStickyPower();
709	<	useShape |= (*i)->isShape();
710	<	}
753	>	int nproc;
754	>	MPI_Comm_size( MPI_COMM_WORLD, &nproc);
755
756	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
757	<	useDirectionalAtom = 1;
758	<	}
756	>	// we need arrays to hold the counts and displacement vectors for
757	>	// all processors
758	>	vector<int> counts(nproc, 0);
759	>	vector<int> disps(nproc, 0);
760
761	<	if (useCharge || useDipole) {
762	<	useElectrostatics = 1;
761	>	// fill the counts array
762	>	MPI_Allgather(&count_local, 1, MPI_INT, &counts[0],
763	>	1, MPI_INT, MPI_COMM_WORLD);
764	>
765	>	// use the processor counts to compute the displacement array
766	>	disps[0] = 0;
767	>	int totalCount = counts[0];
768	>	for (int iproc = 1; iproc < nproc; iproc++) {
769	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
770	>	totalCount += counts[iproc];
771		}
772
773	<	#ifdef IS_MPI
774	<	int temp;
773	>	// we need a (possibly redundant) set of all found types:
774	>	vector<int> ftGlobal(totalCount);
775	>
776	>	// now spray out the foundTypes to all the other processors:
777	>	MPI_Allgatherv(&foundTypes[0], count_local, MPI_INT,
778	>	&ftGlobal[0], &counts[0], &disps[0],
779	>	MPI_INT, MPI_COMM_WORLD);
780
781	<	temp = usePBC;
724	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
781	>	vector<int>::iterator j;
782
783	<	temp = useDirectionalAtom;
784	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
783	>	// foundIdents is a stl set, so inserting an already found ident
784	>	// will have no effect.
785	>	set<int> foundIdents;
786
787	<	temp = useLennardJones;
788	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
787	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
788	>	foundIdents.insert((*j));
789	>
790	>	// now iterate over the foundIdents and get the actual atom types
791	>	// that correspond to these:
792	>	set<int>::iterator it;
793	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
794	>	atomTypes.insert( forceField_->getAtomType((*it)) );
795	>
796	>	#endif
797
798	<	temp = useElectrostatics;
799	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
798	>	return atomTypes;
799	>	}
800
735	–	temp = useCharge;
736	–	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
801
802	<	temp = useDipole;
803	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
802	>	int getGlobalCountOfType(AtomType* atype) {
803	>	/*
804	>	set<AtomType*> atypes = getSimulatedAtomTypes();
805	>	map<AtomType*, int> counts_;
806
807	<	temp = useSticky;
808	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
807	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
808	>	for(atom = mol->beginAtom(ai); atom != NULL;
809	>	atom = mol->nextAtom(ai)) {
810	>	atom->getAtomType();
811	>	}
812	>	}
813	>	*/
814	>	return 0;
815	>	}
816
817	<	temp = useStickyPower;
818	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
817	>	void SimInfo::setupSimVariables() {
818	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
819	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
820	>	// parameter is true
821	>	calcBoxDipole_ = false;
822	>	if ( simParams_->haveAccumulateBoxDipole() )
823	>	if ( simParams_->getAccumulateBoxDipole() ) {
824	>	calcBoxDipole_ = true;
825	>	}
826	>	// we only call setAccumulateBoxQuadrupole if the accumulateBoxQuadrupole
827	>	// parameter is true
828	>	calcBoxQuadrupole_ = false;
829	>	if ( simParams_->haveAccumulateBoxQuadrupole() )
830	>	if ( simParams_->getAccumulateBoxQuadrupole() ) {
831	>	calcBoxQuadrupole_ = true;
832	>	}
833
834	<	temp = useGayBerne;
835	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
834	>	set<AtomType*>::iterator i;
835	>	set<AtomType*> atomTypes;
836	>	atomTypes = getSimulatedAtomTypes();
837	>	bool usesElectrostatic = false;
838	>	bool usesMetallic = false;
839	>	bool usesDirectional = false;
840	>	bool usesFluctuatingCharges =  false;
841	>	//loop over all of the atom types
842	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
843	>	usesElectrostatic |= (*i)->isElectrostatic();
844	>	usesMetallic |= (*i)->isMetal();
845	>	usesDirectional |= (*i)->isDirectional();
846	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
847	>	}
848
849	<	temp = useEAM;
850	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
849	>	#ifdef IS_MPI
850	>	int temp;
851
852	<	temp = useSC;
853	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
852	>	temp = usesDirectional;
853	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
854	>	usesDirectionalAtoms_ = (temp == 0) ? false : true;
855
856	<	temp = useShape;
857	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
856	>	temp = usesMetallic;
857	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
858	>	usesMetallicAtoms_ = (temp == 0) ? false : true;
859
860	<	temp = useFLARB;
861	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860	>	temp = usesElectrostatic;
861	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
862	>	usesElectrostaticAtoms_ = (temp == 0) ? false : true;
863
864	<	temp = useRF;
865	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
864	>	temp = usesFluctuatingCharges;
865	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
866	>	usesFluctuatingCharges_ = (temp == 0) ? false : true;
867	>	#else
868
869	<	temp = useSF;
870	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
869	>	usesDirectionalAtoms_ = usesDirectional;
870	>	usesMetallicAtoms_ = usesMetallic;
871	>	usesElectrostaticAtoms_ = usesElectrostatic;
872	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
873
874	<	temp = useSP;
875	<	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
874	>	#endif
875	>
876	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
877	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
878	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
879	>	}
880
771	–	temp = useBoxDipole;
772	–	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
881
882	<	temp = useAtomicVirial_;
883	<	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
882	>	vector<int> SimInfo::getGlobalAtomIndices() {
883	>	SimInfo::MoleculeIterator mi;
884	>	Molecule* mol;
885	>	Molecule::AtomIterator ai;
886	>	Atom* atom;
887
888	<	#endif
889	<
890	<	fInfo_.SIM_uses_PBC = usePBC;
891	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
892	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
893	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
894	<	fInfo_.SIM_uses_Charges = useCharge;
895	<	fInfo_.SIM_uses_Dipoles = useDipole;
896	<	fInfo_.SIM_uses_Sticky = useSticky;
786	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
787	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
788	<	fInfo_.SIM_uses_EAM = useEAM;
789	<	fInfo_.SIM_uses_SC = useSC;
790	<	fInfo_.SIM_uses_Shapes = useShape;
791	<	fInfo_.SIM_uses_FLARB = useFLARB;
792	<	fInfo_.SIM_uses_RF = useRF;
793	<	fInfo_.SIM_uses_SF = useSF;
794	<	fInfo_.SIM_uses_SP = useSP;
795	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
796	<	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
888	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
889	>
890	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
891	>
892	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
893	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
894	>	}
895	>	}
896	>	return GlobalAtomIndices;
897		}
898
799	–	void SimInfo::setupFortranSim() {
800	–	int isError;
801	–	int nExclude;
802	–	std::vector<int> fortranGlobalGroupMembership;
803	–
804	–	nExclude = exclude_.getSize();
805	–	isError = 0;
899
900	<	//globalGroupMembership_ is filled by SimCreator
901	<	for (int i = 0; i < nGlobalAtoms_; i++) {
902	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
900	>	vector<int> SimInfo::getGlobalGroupIndices() {
901	>	SimInfo::MoleculeIterator mi;
902	>	Molecule* mol;
903	>	Molecule::CutoffGroupIterator ci;
904	>	CutoffGroup* cg;
905	>
906	>	vector<int> GlobalGroupIndices;
907	>
908	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
909	>
910	>	//local index of cutoff group is trivial, it only depends on the
911	>	//order of travesing
912	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
913	>	cg = mol->nextCutoffGroup(ci)) {
914	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
915	>	}
916		}
917	+	return GlobalGroupIndices;
918	+	}
919
920	+
921	+	void SimInfo::prepareTopology() {
922	+
923		//calculate mass ratio of cutoff group
813	–	std::vector<RealType> mfact;
924		SimInfo::MoleculeIterator mi;
925		Molecule* mol;
926		Molecule::CutoffGroupIterator ci;
#	Line 819 | Line 929 | namespace oopse {
929		Atom* atom;
930		RealType totalMass;
931
932	<	//to avoid memory reallocation, reserve enough space for mfact
933	<	mfact.reserve(getNCutoffGroups());
932	>	/**
933	>	* The mass factor is the relative mass of an atom to the total
934	>	* mass of the cutoff group it belongs to.  By default, all atoms
935	>	* are their own cutoff groups, and therefore have mass factors of
936	>	* 1.  We need some special handling for massless atoms, which
937	>	* will be treated as carrying the entire mass of the cutoff
938	>	* group.
939	>	*/
940	>	massFactors_.clear();
941	>	massFactors_.resize(getNAtoms(), 1.0);
942
943		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
944	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
944	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
945	>	cg = mol->nextCutoffGroup(ci)) {
946
947		totalMass = cg->getMass();
948		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
949		// Check for massless groups - set mfact to 1 if true
950	<	if (totalMass != 0)
951	<	mfact.push_back(atom->getMass()/totalMass);
950	>	if (totalMass != 0)
951	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
952		else
953	<	mfact.push_back( 1.0 );
953	>	massFactors_[atom->getLocalIndex()] = 1.0;
954		}
836	–
955		}
838	–	}
839	–
840	–	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
841	–	std::vector<int> identArray;
842	–
843	–	//to avoid memory reallocation, reserve enough space identArray
844	–	identArray.reserve(getNAtoms());
845	–
846	–	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
847	–	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
848	–	identArray.push_back(atom->getIdent());
849	–	}
850	–	}
851	–
852	–	//fill molMembershipArray
853	–	//molMembershipArray is filled by SimCreator
854	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
855	–	for (int i = 0; i < nGlobalAtoms_; i++) {
856	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
857	–	}
858	–
859	–	//setup fortran simulation
860	–	int nGlobalExcludes = 0;
861	–	int* globalExcludes = NULL;
862	–	int* excludeList = exclude_.getExcludeList();
863	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
864	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
865	–	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
866	–
867	–	if( isError ){
868	–
869	–	sprintf( painCave.errMsg,
870	–	"There was an error setting the simulation information in fortran.\n" );
871	–	painCave.isFatal = 1;
872	–	painCave.severity = OOPSE_ERROR;
873	–	simError();
874	–	}
875	–
876	–	#ifdef IS_MPI
877	–	sprintf( checkPointMsg,
878	–	"succesfully sent the simulation information to fortran.\n");
879	–	MPIcheckPoint();
880	–	#endif // is_mpi
881	–
882	–	// Setup number of neighbors in neighbor list if present
883	–	if (simParams_->haveNeighborListNeighbors()) {
884	–	int nlistNeighbors = simParams_->getNeighborListNeighbors();
885	–	setNeighbors(&nlistNeighbors);
886	–	}
887	–
888	–
889	–	}
890	–
891	–
892	–	#ifdef IS_MPI
893	–	void SimInfo::setupFortranParallel() {
894	–
895	–	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
896	–	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
897	–	std::vector<int> localToGlobalCutoffGroupIndex;
898	–	SimInfo::MoleculeIterator mi;
899	–	Molecule::AtomIterator ai;
900	–	Molecule::CutoffGroupIterator ci;
901	–	Molecule* mol;
902	–	Atom* atom;
903	–	CutoffGroup* cg;
904	–	mpiSimData parallelData;
905	–	int isError;
906	–
907	–	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
908	–
909	–	//local index(index in DataStorge) of atom is important
910	–	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
911	–	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
912	–	}
913	–
914	–	//local index of cutoff group is trivial, it only depends on the order of travesing
915	–	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
916	–	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
917	–	}
918	–
956		}
957
958	<	//fill up mpiSimData struct
922	<	parallelData.nMolGlobal = getNGlobalMolecules();
923	<	parallelData.nMolLocal = getNMolecules();
924	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
925	<	parallelData.nAtomsLocal = getNAtoms();
926	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
927	<	parallelData.nGroupsLocal = getNCutoffGroups();
928	<	parallelData.myNode = worldRank;
929	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
958	>	// Build the identArray_ and regions_
959
960	<	//pass mpiSimData struct and index arrays to fortran
961	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
962	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
963	<	&localToGlobalCutoffGroupIndex[0], &isError);
964	<
965	<	if (isError) {
966	<	sprintf(painCave.errMsg,
967	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
968	<	painCave.isFatal = 1;
969	<	simError();
941	<	}
942	<
943	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
944	<	MPIcheckPoint();
945	<
946	<
947	<	}
948	<
949	<	#endif
950	<
951	<	void SimInfo::setupCutoff() {
952	<
953	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
954	<
955	<	// Check the cutoff policy
956	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
957	<
958	<	std::string myPolicy;
959	<	if (forceFieldOptions_.haveCutoffPolicy()){
960	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
961	<	}else if (simParams_->haveCutoffPolicy()) {
962	<	myPolicy = simParams_->getCutoffPolicy();
963	<	}
964	<
965	<	if (!myPolicy.empty()){
966	<	toUpper(myPolicy);
967	<	if (myPolicy == "MIX") {
968	<	cp = MIX_CUTOFF_POLICY;
969	<	} else {
970	<	if (myPolicy == "MAX") {
971	<	cp = MAX_CUTOFF_POLICY;
972	<	} else {
973	<	if (myPolicy == "TRADITIONAL") {
974	<	cp = TRADITIONAL_CUTOFF_POLICY;
975	<	} else {
976	<	// throw error
977	<	sprintf( painCave.errMsg,
978	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
979	<	painCave.isFatal = 1;
980	<	simError();
981	<	}
982	<	}
983	<	}
984	<	}
985	<	notifyFortranCutoffPolicy(&cp);
986	<
987	<	// Check the Skin Thickness for neighborlists
988	<	RealType skin;
989	<	if (simParams_->haveSkinThickness()) {
990	<	skin = simParams_->getSkinThickness();
991	<	notifyFortranSkinThickness(&skin);
992	<	}
993	<
994	<	// Check if the cutoff was set explicitly:
995	<	if (simParams_->haveCutoffRadius()) {
996	<	rcut_ = simParams_->getCutoffRadius();
997	<	if (simParams_->haveSwitchingRadius()) {
998	<	rsw_  = simParams_->getSwitchingRadius();
999	<	} else {
1000	<	if (fInfo_.SIM_uses_Charges |
1001	<	fInfo_.SIM_uses_Dipoles |
1002	<	fInfo_.SIM_uses_RF) {
1003	<
1004	<	rsw_ = 0.85 * rcut_;
1005	<	sprintf(painCave.errMsg,
1006	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1007	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1008	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1009	<	painCave.isFatal = 0;
1010	<	simError();
1011	<	} else {
1012	<	rsw_ = rcut_;
1013	<	sprintf(painCave.errMsg,
1014	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1015	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
1016	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1017	<	painCave.isFatal = 0;
1018	<	simError();
1019	<	}
1020	<	}
1021	<
1022	<	notifyFortranCutoffs(&rcut_, &rsw_);
1023	<
1024	<	} else {
1025	<
1026	<	// For electrostatic atoms, we'll assume a large safe value:
1027	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1028	<	sprintf(painCave.errMsg,
1029	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1030	<	"\tOOPSE will use a default value of 15.0 angstroms"
1031	<	"\tfor the cutoffRadius.\n");
1032	<	painCave.isFatal = 0;
1033	<	simError();
1034	<	rcut_ = 15.0;
1035	<
1036	<	if (simParams_->haveElectrostaticSummationMethod()) {
1037	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1038	<	toUpper(myMethod);
1039	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1040	<	if (simParams_->haveSwitchingRadius()){
1041	<	sprintf(painCave.errMsg,
1042	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1043	<	"\teven though the electrostaticSummationMethod was\n"
1044	<	"\tset to %s\n", myMethod.c_str());
1045	<	painCave.isFatal = 1;
1046	<	simError();
1047	<	}
1048	<	}
1049	<	}
1050	<
1051	<	if (simParams_->haveSwitchingRadius()){
1052	<	rsw_ = simParams_->getSwitchingRadius();
1053	<	} else {
1054	<	sprintf(painCave.errMsg,
1055	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1056	<	"\tOOPSE will use a default value of\n"
1057	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1058	<	painCave.isFatal = 0;
1059	<	simError();
1060	<	rsw_ = 0.85 * rcut_;
1061	<	}
1062	<	notifyFortranCutoffs(&rcut_, &rsw_);
1063	<	} else {
1064	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1065	<	// We'll punt and let fortran figure out the cutoffs later.
1066	<
1067	<	notifyFortranYouAreOnYourOwn();
1068	<
1069	<	}
1070	<	}
1071	<	}
1072	<
1073	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1074	<
1075	<	int errorOut;
1076	<	int esm =  NONE;
1077	<	int sm = UNDAMPED;
1078	<	RealType alphaVal;
1079	<	RealType dielectric;
1080	<
1081	<	errorOut = isError;
1082	<
1083	<	if (simParams_->haveElectrostaticSummationMethod()) {
1084	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1085	<	toUpper(myMethod);
1086	<	if (myMethod == "NONE") {
1087	<	esm = NONE;
1088	<	} else {
1089	<	if (myMethod == "SWITCHING_FUNCTION") {
1090	<	esm = SWITCHING_FUNCTION;
1091	<	} else {
1092	<	if (myMethod == "SHIFTED_POTENTIAL") {
1093	<	esm = SHIFTED_POTENTIAL;
1094	<	} else {
1095	<	if (myMethod == "SHIFTED_FORCE") {
1096	<	esm = SHIFTED_FORCE;
1097	<	} else {
1098	<	if (myMethod == "REACTION_FIELD") {
1099	<	esm = REACTION_FIELD;
1100	<	dielectric = simParams_->getDielectric();
1101	<	if (!simParams_->haveDielectric()) {
1102	<	// throw warning
1103	<	sprintf( painCave.errMsg,
1104	<	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1105	<	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1106	<	painCave.isFatal = 0;
1107	<	simError();
1108	<	}
1109	<	} else {
1110	<	// throw error
1111	<	sprintf( painCave.errMsg,
1112	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1113	<	"\t(Input file specified %s .)\n"
1114	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1115	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1116	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1117	<	painCave.isFatal = 1;
1118	<	simError();
1119	<	}
1120	<	}
1121	<	}
1122	<	}
960	>	identArray_.clear();
961	>	identArray_.reserve(getNAtoms());
962	>	regions_.clear();
963	>	regions_.reserve(getNAtoms());
964	>
965	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
966	>	int reg = mol->getRegion();
967	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
968	>	identArray_.push_back(atom->getIdent());
969	>	regions_.push_back(reg);
970		}
971	<	}
972	<
973	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1127	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1128	<	toUpper(myScreen);
1129	<	if (myScreen == "UNDAMPED") {
1130	<	sm = UNDAMPED;
1131	<	} else {
1132	<	if (myScreen == "DAMPED") {
1133	<	sm = DAMPED;
1134	<	if (!simParams_->haveDampingAlpha()) {
1135	<	// first set a cutoff dependent alpha value
1136	<	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1137	<	alphaVal = 0.5125 - rcut_* 0.025;
1138	<	// for values rcut > 20.5, alpha is zero
1139	<	if (alphaVal < 0) alphaVal = 0;
1140	<
1141	<	// throw warning
1142	<	sprintf( painCave.errMsg,
1143	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1144	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1145	<	painCave.isFatal = 0;
1146	<	simError();
1147	<	} else {
1148	<	alphaVal = simParams_->getDampingAlpha();
1149	<	}
1150	<
1151	<	} else {
1152	<	// throw error
1153	<	sprintf( painCave.errMsg,
1154	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1155	<	"\t(Input file specified %s .)\n"
1156	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1157	<	"or \"damped\".\n", myScreen.c_str() );
1158	<	painCave.isFatal = 1;
1159	<	simError();
1160	<	}
1161	<	}
1162	<	}
1163	<
1164	<	// let's pass some summation method variables to fortran
1165	<	setElectrostaticSummationMethod( &esm );
1166	<	setFortranElectrostaticMethod( &esm );
1167	<	setScreeningMethod( &sm );
1168	<	setDampingAlpha( &alphaVal );
1169	<	setReactionFieldDielectric( &dielectric );
1170	<	initFortranFF( &errorOut );
971	>	}
972	>
973	>	topologyDone_ = true;
974		}
975
1173	–	void SimInfo::setupSwitchingFunction() {
1174	–	int ft = CUBIC;
1175	–
1176	–	if (simParams_->haveSwitchingFunctionType()) {
1177	–	std::string funcType = simParams_->getSwitchingFunctionType();
1178	–	toUpper(funcType);
1179	–	if (funcType == "CUBIC") {
1180	–	ft = CUBIC;
1181	–	} else {
1182	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1183	–	ft = FIFTH_ORDER_POLY;
1184	–	} else {
1185	–	// throw error
1186	–	sprintf( painCave.errMsg,
1187	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1188	–	painCave.isFatal = 1;
1189	–	simError();
1190	–	}
1191	–	}
1192	–	}
1193	–
1194	–	// send switching function notification to switcheroo
1195	–	setFunctionType(&ft);
1196	–
1197	–	}
1198	–
1199	–	void SimInfo::setupAccumulateBoxDipole() {
1200	–
1201	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1202	–	if ( simParams_->haveAccumulateBoxDipole() )
1203	–	if ( simParams_->getAccumulateBoxDipole() ) {
1204	–	setAccumulateBoxDipole();
1205	–	calcBoxDipole_ = true;
1206	–	}
1207	–
1208	–	}
1209	–
976		void SimInfo::addProperty(GenericData* genData) {
977		properties_.addProperty(genData);
978		}
979
980	<	void SimInfo::removeProperty(const std::string& propName) {
980	>	void SimInfo::removeProperty(const string& propName) {
981		properties_.removeProperty(propName);
982		}
983
#	Line 1219 | Line 985 | namespace oopse {
985		properties_.clearProperties();
986		}
987
988	<	std::vector<std::string> SimInfo::getPropertyNames() {
988	>	vector<string> SimInfo::getPropertyNames() {
989		return properties_.getPropertyNames();
990		}
991
992	<	std::vector<GenericData*> SimInfo::getProperties() {
992	>	vector<GenericData*> SimInfo::getProperties() {
993		return properties_.getProperties();
994		}
995
996	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
996	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
997		return properties_.getPropertyByName(propName);
998		}
999
#	Line 1238 | Line 1004 | namespace oopse {
1004		delete sman_;
1005		sman_ = sman;
1006
1241	–	Molecule* mol;
1242	–	RigidBody* rb;
1243	–	Atom* atom;
1007		SimInfo::MoleculeIterator mi;
1008	+	Molecule::AtomIterator ai;
1009		Molecule::RigidBodyIterator rbIter;
1010	<	Molecule::AtomIterator atomIter;;
1010	>	Molecule::CutoffGroupIterator cgIter;
1011	>	Molecule::BondIterator bondIter;
1012	>	Molecule::BendIterator bendIter;
1013	>	Molecule::TorsionIterator torsionIter;
1014	>	Molecule::InversionIterator inversionIter;
1015
1016	+	Molecule* mol;
1017	+	Atom* atom;
1018	+	RigidBody* rb;
1019	+	CutoffGroup* cg;
1020	+	Bond* bond;
1021	+	Bend* bend;
1022	+	Torsion* torsion;
1023	+	Inversion* inversion;
1024	+
1025		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1026
1027	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1027	>	for (atom = mol->beginAtom(ai); atom != NULL;
1028	>	atom = mol->nextAtom(ai)) {
1029		atom->setSnapshotManager(sman_);
1030	<	}
1031	<
1032	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1030	>	}
1031	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1032	>	rb = mol->nextRigidBody(rbIter)) {
1033		rb->setSnapshotManager(sman_);
1034		}
1035	<	}
1036	<
1035	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1036	>	cg = mol->nextCutoffGroup(cgIter)) {
1037	>	cg->setSnapshotManager(sman_);
1038	>	}
1039	>	for (bond = mol->beginBond(bondIter); bond != NULL;
1040	>	bond = mol->nextBond(bondIter)) {
1041	>	bond->setSnapshotManager(sman_);
1042	>	}
1043	>	for (bend = mol->beginBend(bendIter); bend != NULL;
1044	>	bend = mol->nextBend(bendIter)) {
1045	>	bend->setSnapshotManager(sman_);
1046	>	}
1047	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
1048	>	torsion = mol->nextTorsion(torsionIter)) {
1049	>	torsion->setSnapshotManager(sman_);
1050	>	}
1051	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
1052	>	inversion = mol->nextInversion(inversionIter)) {
1053	>	inversion->setSnapshotManager(sman_);
1054	>	}
1055	>	}
1056		}
1057
1261	–	Vector3d SimInfo::getComVel(){
1262	–	SimInfo::MoleculeIterator i;
1263	–	Molecule* mol;
1058
1059	<	Vector3d comVel(0.0);
1266	<	RealType totalMass = 0.0;
1267	<
1268	<
1269	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1270	<	RealType mass = mol->getMass();
1271	<	totalMass += mass;
1272	<	comVel += mass * mol->getComVel();
1273	<	}
1274	<
1275	<	#ifdef IS_MPI
1276	<	RealType tmpMass = totalMass;
1277	<	Vector3d tmpComVel(comVel);
1278	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1279	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1280	<	#endif
1281	<
1282	<	comVel /= totalMass;
1283	<
1284	<	return comVel;
1285	<	}
1286	<
1287	<	Vector3d SimInfo::getCom(){
1288	<	SimInfo::MoleculeIterator i;
1289	<	Molecule* mol;
1290	<
1291	<	Vector3d com(0.0);
1292	<	RealType totalMass = 0.0;
1293	<
1294	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1295	<	RealType mass = mol->getMass();
1296	<	totalMass += mass;
1297	<	com += mass * mol->getCom();
1298	<	}
1299	<
1300	<	#ifdef IS_MPI
1301	<	RealType tmpMass = totalMass;
1302	<	Vector3d tmpCom(com);
1303	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1304	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1305	<	#endif
1306	<
1307	<	com /= totalMass;
1308	<
1309	<	return com;
1059	>	ostream& operator <<(ostream& o, SimInfo& info) {
1060
1311	–	}
1312	–
1313	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1314	–
1061		return o;
1062		}
1063
1064	<
1319	<	/*
1320	<	Returns center of mass and center of mass velocity in one function call.
1321	<	*/
1322	<
1323	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1324	<	SimInfo::MoleculeIterator i;
1325	<	Molecule* mol;
1326	<
1327	<
1328	<	RealType totalMass = 0.0;
1329	<
1330	<
1331	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1332	<	RealType mass = mol->getMass();
1333	<	totalMass += mass;
1334	<	com += mass * mol->getCom();
1335	<	comVel += mass * mol->getComVel();
1336	<	}
1337	<
1338	<	#ifdef IS_MPI
1339	<	RealType tmpMass = totalMass;
1340	<	Vector3d tmpCom(com);
1341	<	Vector3d tmpComVel(comVel);
1342	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1343	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1344	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1345	<	#endif
1346	<
1347	<	com /= totalMass;
1348	<	comVel /= totalMass;
1349	<	}
1350	<
1351	<	/*
1352	<	Return intertia tensor for entire system and angular momentum Vector.
1353	<
1354	<
1355	<	[  Ixx -Ixy  -Ixz ]
1356	<	J =| -Iyx  Iyy  -Iyz |
1357	<	[ -Izx -Iyz   Izz ]
1358	<	*/
1359	<
1360	<	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1361	<
1362	<
1363	<	RealType xx = 0.0;
1364	<	RealType yy = 0.0;
1365	<	RealType zz = 0.0;
1366	<	RealType xy = 0.0;
1367	<	RealType xz = 0.0;
1368	<	RealType yz = 0.0;
1369	<	Vector3d com(0.0);
1370	<	Vector3d comVel(0.0);
1371	<
1372	<	getComAll(com, comVel);
1373	<
1374	<	SimInfo::MoleculeIterator i;
1375	<	Molecule* mol;
1376	<
1377	<	Vector3d thisq(0.0);
1378	<	Vector3d thisv(0.0);
1379	<
1380	<	RealType thisMass = 0.0;
1381	<
1382	<
1383	<
1384	<
1385	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1386	<
1387	<	thisq = mol->getCom()-com;
1388	<	thisv = mol->getComVel()-comVel;
1389	<	thisMass = mol->getMass();
1390	<	// Compute moment of intertia coefficients.
1391	<	xx += thisq[0]*thisq[0]*thisMass;
1392	<	yy += thisq[1]*thisq[1]*thisMass;
1393	<	zz += thisq[2]*thisq[2]*thisMass;
1394	<
1395	<	// compute products of intertia
1396	<	xy += thisq[0]*thisq[1]*thisMass;
1397	<	xz += thisq[0]*thisq[2]*thisMass;
1398	<	yz += thisq[1]*thisq[2]*thisMass;
1399	<
1400	<	angularMomentum += cross( thisq, thisv ) * thisMass;
1401	<
1402	<	}
1403	<
1404	<
1405	<	inertiaTensor(0,0) = yy + zz;
1406	<	inertiaTensor(0,1) = -xy;
1407	<	inertiaTensor(0,2) = -xz;
1408	<	inertiaTensor(1,0) = -xy;
1409	<	inertiaTensor(1,1) = xx + zz;
1410	<	inertiaTensor(1,2) = -yz;
1411	<	inertiaTensor(2,0) = -xz;
1412	<	inertiaTensor(2,1) = -yz;
1413	<	inertiaTensor(2,2) = xx + yy;
1414	<
1415	<	#ifdef IS_MPI
1416	<	Mat3x3d tmpI(inertiaTensor);
1417	<	Vector3d tmpAngMom;
1418	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1419	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1420	<	#endif
1421	<
1422	<	return;
1423	<	}
1424	<
1425	<	//Returns the angular momentum of the system
1426	<	Vector3d SimInfo::getAngularMomentum(){
1427	<
1428	<	Vector3d com(0.0);
1429	<	Vector3d comVel(0.0);
1430	<	Vector3d angularMomentum(0.0);
1431	<
1432	<	getComAll(com,comVel);
1433	<
1434	<	SimInfo::MoleculeIterator i;
1435	<	Molecule* mol;
1436	<
1437	<	Vector3d thisr(0.0);
1438	<	Vector3d thisp(0.0);
1439	<
1440	<	RealType thisMass;
1441	<
1442	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1443	<	thisMass = mol->getMass();
1444	<	thisr = mol->getCom()-com;
1445	<	thisp = (mol->getComVel()-comVel)*thisMass;
1446	<
1447	<	angularMomentum += cross( thisr, thisp );
1448	<
1449	<	}
1450	<
1451	<	#ifdef IS_MPI
1452	<	Vector3d tmpAngMom;
1453	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1454	<	#endif
1455	<
1456	<	return angularMomentum;
1457	<	}
1458	<
1064	>
1065		StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1066	<	return IOIndexToIntegrableObject.at(index);
1066	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1067	>	sprintf(painCave.errMsg,
1068	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1069	>	"\tindex exceeds number of known objects!\n");
1070	>	painCave.isFatal = 1;
1071	>	simError();
1072	>	return NULL;
1073	>	} else
1074	>	return IOIndexToIntegrableObject.at(index);
1075		}
1076
1077	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1077	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1078		IOIndexToIntegrableObject= v;
1079		}
1080
1081	<	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1082	<	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1083	<	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1084	<	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1085	<	*/
1086	<	void SimInfo::getGyrationalVolume(RealType &volume){
1087	<	Mat3x3d intTensor;
1474	<	RealType det;
1475	<	Vector3d dummyAngMom;
1476	<	RealType sysconstants;
1477	<	RealType geomCnst;
1478	<
1479	<	geomCnst = 3.0/2.0;
1480	<	/* Get the inertial tensor and angular momentum for free*/
1481	<	getInertiaTensor(intTensor,dummyAngMom);
1482	<
1483	<	det = intTensor.determinant();
1484	<	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1485	<	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1486	<	return;
1081	>	void SimInfo::calcNConstraints() {
1082	>	#ifdef IS_MPI
1083	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints_, 1,
1084	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1085	>	#else
1086	>	nGlobalConstraints_ =  nConstraints_;
1087	>	#endif
1088		}
1089
1090	<	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1490	<	Mat3x3d intTensor;
1491	<	Vector3d dummyAngMom;
1492	<	RealType sysconstants;
1493	<	RealType geomCnst;
1090	>	}//end namespace OpenMD
1091
1495	–	geomCnst = 3.0/2.0;
1496	–	/* Get the inertial tensor and angular momentum for free*/
1497	–	getInertiaTensor(intTensor,dummyAngMom);
1498	–
1499	–	detI = intTensor.determinant();
1500	–	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1501	–	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1502	–	return;
1503	–	}
1504	–	/*
1505	–	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1506	–	assert( v.size() == nAtoms_ + nRigidBodies_);
1507	–	sdByGlobalIndex_ = v;
1508	–	}
1509	–
1510	–	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1511	–	//assert(index < nAtoms_ + nRigidBodies_);
1512	–	return sdByGlobalIndex_.at(index);
1513	–	}
1514	–	*/
1515	–	}//end namespace oopse
1516	–

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 1126 by gezelter, Fri Apr 6 21:53:43 2007 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

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