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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 604 by chrisfen, Fri Sep 16 19:00:12 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1597 by gezelter, Tue Jul 26 15:49:24 2011 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, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 48 | Line 48
48
49		#include <algorithm>
50		#include <set>
51	+	#include <map>
52
53		#include "brains/SimInfo.hpp"
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56	<	#include "UseTheForce/fCutoffPolicy.h"
56	<	#include "UseTheForce/Darkside/fElectrostaticSummationMethod.h"
57	<	#include "UseTheForce/doForces_interface.h"
58	<	#include "UseTheForce/notifyCutoffs_interface.h"
56	>	#include "primitives/StuntDouble.hpp"
57		#include "utils/MemoryUtils.hpp"
58		#include "utils/simError.h"
59		#include "selection/SelectionManager.hpp"
60	+	#include "io/ForceFieldOptions.hpp"
61	+	#include "UseTheForce/ForceField.hpp"
62	+	#include "nonbonded/SwitchingFunction.hpp"
63
64	<	#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
67	<	#endif
68	<
69	<	namespace oopse {
69	<
70	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
71	<	ForceField* ff, Globals* simParams) :
72	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
73	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
64	>	using namespace std;
65	>	namespace OpenMD {
66	>
67	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
68	>	forceField_(ff), simParams_(simParams),
69	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
70		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
71		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
72	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
73	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
74	<	sman_(NULL), fortranInitialized_(false) {
75	<
80	<
81	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
82	<	MoleculeStamp* molStamp;
83	<	int nMolWithSameStamp;
84	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
85	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
86	<	CutoffGroupStamp* cgStamp;
87	<	RigidBodyStamp* rbStamp;
88	<	int nRigidAtoms = 0;
72	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
73	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
74	>	nConstraints_(0), sman_(NULL), topologyDone_(false),
75	>	calcBoxDipole_(false), useAtomicVirial_(true) {
76
77	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
78	<	molStamp = i->first;
79	<	nMolWithSameStamp = i->second;
80	<
81	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
82	<
83	<	//calculate atoms in molecules
84	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
85	<
86	<
87	<	//calculate atoms in cutoff groups
88	<	int nAtomsInGroups = 0;
89	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
90	<
91	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
92	<	cgStamp = molStamp->getCutoffGroup(j);
93	<	nAtomsInGroups += cgStamp->getNMembers();
94	<	}
95	<
96	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
97	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
98	<
99	<	//calculate atoms in rigid bodies
100	<	int nAtomsInRigidBodies = 0;
101	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
102	<
116	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
117	<	rbStamp = molStamp->getRigidBody(j);
118	<	nAtomsInRigidBodies += rbStamp->getNMembers();
119	<	}
120	<
121	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
122	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
123	<
77	>	MoleculeStamp* molStamp;
78	>	int nMolWithSameStamp;
79	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
80	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
81	>	CutoffGroupStamp* cgStamp;
82	>	RigidBodyStamp* rbStamp;
83	>	int nRigidAtoms = 0;
84	>
85	>	vector<Component*> components = simParams->getComponents();
86	>
87	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
88	>	molStamp = (*i)->getMoleculeStamp();
89	>	nMolWithSameStamp = (*i)->getNMol();
90	>
91	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
92	>
93	>	//calculate atoms in molecules
94	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
95	>
96	>	//calculate atoms in cutoff groups
97	>	int nAtomsInGroups = 0;
98	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
99	>
100	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
101	>	cgStamp = molStamp->getCutoffGroupStamp(j);
102	>	nAtomsInGroups += cgStamp->getNMembers();
103		}
104	<
105	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
106	<	//therefore the total number of cutoff groups in the system is equal to
107	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
108	<	//file plus the number of cutoff groups defined in meta-data file
109	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
110	<
111	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
112	<	//therefore the total number of  integrable objects in the system is equal to
113	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
114	<	//file plus the number of  rigid bodies defined in meta-data file
115	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
116	<
117	<	nGlobalMols_ = molStampIds_.size();
118	<
119	<	#ifdef IS_MPI
120	<	molToProcMap_.resize(nGlobalMols_);
142	<	#endif
143	<
104	>
105	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
106	>
107	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
108	>
109	>	//calculate atoms in rigid bodies
110	>	int nAtomsInRigidBodies = 0;
111	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
112	>
113	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
114	>	rbStamp = molStamp->getRigidBodyStamp(j);
115	>	nAtomsInRigidBodies += rbStamp->getNMembers();
116	>	}
117	>
118	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
119	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
120	>
121		}
122	+
123	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
124	+	//group therefore the total number of cutoff groups in the system is
125	+	//equal to the total number of atoms minus number of atoms belong to
126	+	//cutoff group defined in meta-data file plus the number of cutoff
127	+	//groups defined in meta-data file
128
129	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
130	+
131	+	//every free atom (atom does not belong to rigid bodies) is an
132	+	//integrable object therefore the total number of integrable objects
133	+	//in the system is equal to the total number of atoms minus number of
134	+	//atoms belong to rigid body defined in meta-data file plus the number
135	+	//of rigid bodies defined in meta-data file
136	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
137	+	+ nGlobalRigidBodies_;
138	+
139	+	nGlobalMols_ = molStampIds_.size();
140	+	molToProcMap_.resize(nGlobalMols_);
141	+	}
142	+
143		SimInfo::~SimInfo() {
144	<	std::map<int, Molecule*>::iterator i;
144	>	map<int, Molecule*>::iterator i;
145		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
146		delete i->second;
147		}
148		molecules_.clear();
149
153	–	delete stamps_;
150		delete sman_;
151		delete simParams_;
152		delete forceField_;
153		}
154
159	–	int SimInfo::getNGlobalConstraints() {
160	–	int nGlobalConstraints;
161	–	#ifdef IS_MPI
162	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
163	–	MPI_COMM_WORLD);
164	–	#else
165	–	nGlobalConstraints =  nConstraints_;
166	–	#endif
167	–	return nGlobalConstraints;
168	–	}
155
156		bool SimInfo::addMolecule(Molecule* mol) {
157		MoleculeIterator i;
158	<
158	>
159		i = molecules_.find(mol->getGlobalIndex());
160		if (i == molecules_.end() ) {
161	<
162	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
163	<
161	>
162	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
163	>
164		nAtoms_ += mol->getNAtoms();
165		nBonds_ += mol->getNBonds();
166		nBends_ += mol->getNBends();
167		nTorsions_ += mol->getNTorsions();
168	+	nInversions_ += mol->getNInversions();
169		nRigidBodies_ += mol->getNRigidBodies();
170		nIntegrableObjects_ += mol->getNIntegrableObjects();
171		nCutoffGroups_ += mol->getNCutoffGroups();
172		nConstraints_ += mol->getNConstraintPairs();
173	<
174	<	addExcludePairs(mol);
175	<
173	>
174	>	addInteractionPairs(mol);
175	>
176		return true;
177		} else {
178		return false;
179		}
180		}
181	<
181	>
182		bool SimInfo::removeMolecule(Molecule* mol) {
183		MoleculeIterator i;
184		i = molecules_.find(mol->getGlobalIndex());
#	Line 204 | Line 191 | namespace oopse {
191		nBonds_ -= mol->getNBonds();
192		nBends_ -= mol->getNBends();
193		nTorsions_ -= mol->getNTorsions();
194	+	nInversions_ -= mol->getNInversions();
195		nRigidBodies_ -= mol->getNRigidBodies();
196		nIntegrableObjects_ -= mol->getNIntegrableObjects();
197		nCutoffGroups_ -= mol->getNCutoffGroups();
198		nConstraints_ -= mol->getNConstraintPairs();
199
200	<	removeExcludePairs(mol);
200	>	removeInteractionPairs(mol);
201		molecules_.erase(mol->getGlobalIndex());
202
203		delete mol;
#	Line 218 | Line 206 | namespace oopse {
206		} else {
207		return false;
208		}
221	–
222	–
209		}
210
211
#	Line 237 | Line 223 | namespace oopse {
223		void SimInfo::calcNdf() {
224		int ndf_local;
225		MoleculeIterator i;
226	<	std::vector<StuntDouble*>::iterator j;
226	>	vector<StuntDouble*>::iterator j;
227		Molecule* mol;
228		StuntDouble* integrableObject;
229
#	Line 257 | Line 243 | namespace oopse {
243		}
244		}
245
246	<	}//end for (integrableObject)
247	<	}// end for (mol)
246	>	}
247	>	}
248
249		// n_constraints is local, so subtract them on each processor
250		ndf_local -= nConstraints_;
#	Line 275 | Line 261 | namespace oopse {
261
262		}
263
264	+	int SimInfo::getFdf() {
265	+	#ifdef IS_MPI
266	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
267	+	#else
268	+	fdf_ = fdf_local;
269	+	#endif
270	+	return fdf_;
271	+	}
272	+
273	+	unsigned int SimInfo::getNLocalCutoffGroups(){
274	+	int nLocalCutoffAtoms = 0;
275	+	Molecule* mol;
276	+	MoleculeIterator mi;
277	+	CutoffGroup* cg;
278	+	Molecule::CutoffGroupIterator ci;
279	+
280	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
281	+
282	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
283	+	cg = mol->nextCutoffGroup(ci)) {
284	+	nLocalCutoffAtoms += cg->getNumAtom();
285	+
286	+	}
287	+	}
288	+
289	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
290	+	}
291	+
292		void SimInfo::calcNdfRaw() {
293		int ndfRaw_local;
294
295		MoleculeIterator i;
296	<	std::vector<StuntDouble*>::iterator j;
296	>	vector<StuntDouble*>::iterator j;
297		Molecule* mol;
298		StuntDouble* integrableObject;
299
#	Line 326 | Line 340 | namespace oopse {
340
341		}
342
343	<	void SimInfo::addExcludePairs(Molecule* mol) {
344	<	std::vector<Bond*>::iterator bondIter;
345	<	std::vector<Bend*>::iterator bendIter;
346	<	std::vector<Torsion*>::iterator torsionIter;
343	>	void SimInfo::addInteractionPairs(Molecule* mol) {
344	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
345	>	vector<Bond*>::iterator bondIter;
346	>	vector<Bend*>::iterator bendIter;
347	>	vector<Torsion*>::iterator torsionIter;
348	>	vector<Inversion*>::iterator inversionIter;
349		Bond* bond;
350		Bend* bend;
351		Torsion* torsion;
352	+	Inversion* inversion;
353		int a;
354		int b;
355		int c;
356		int d;
357	+
358	+	// atomGroups can be used to add special interaction maps between
359	+	// groups of atoms that are in two separate rigid bodies.
360	+	// However, most site-site interactions between two rigid bodies
361	+	// are probably not special, just the ones between the physically
362	+	// bonded atoms.  Interactions *within* a single rigid body should
363	+	// always be excluded.  These are done at the bottom of this
364	+	// function.
365	+
366	+	map<int, set<int> > atomGroups;
367	+	Molecule::RigidBodyIterator rbIter;
368	+	RigidBody* rb;
369	+	Molecule::IntegrableObjectIterator ii;
370	+	StuntDouble* integrableObject;
371
372	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
372	>	for (integrableObject = mol->beginIntegrableObject(ii);
373	>	integrableObject != NULL;
374	>	integrableObject = mol->nextIntegrableObject(ii)) {
375	>
376	>	if (integrableObject->isRigidBody()) {
377	>	rb = static_cast<RigidBody*>(integrableObject);
378	>	vector<Atom*> atoms = rb->getAtoms();
379	>	set<int> rigidAtoms;
380	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
381	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
382	>	}
383	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
384	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
385	>	}
386	>	} else {
387	>	set<int> oneAtomSet;
388	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
389	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
390	>	}
391	>	}
392	>
393	>	for (bond= mol->beginBond(bondIter); bond != NULL;
394	>	bond = mol->nextBond(bondIter)) {
395	>
396		a = bond->getAtomA()->getGlobalIndex();
397	<	b = bond->getAtomB()->getGlobalIndex();
398	<	exclude_.addPair(a, b);
397	>	b = bond->getAtomB()->getGlobalIndex();
398	>
399	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
400	>	oneTwoInteractions_.addPair(a, b);
401	>	} else {
402	>	excludedInteractions_.addPair(a, b);
403	>	}
404		}
405
406	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
406	>	for (bend= mol->beginBend(bendIter); bend != NULL;
407	>	bend = mol->nextBend(bendIter)) {
408	>
409		a = bend->getAtomA()->getGlobalIndex();
410		b = bend->getAtomB()->getGlobalIndex();
411		c = bend->getAtomC()->getGlobalIndex();
412	+
413	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
414	+	oneTwoInteractions_.addPair(a, b);
415	+	oneTwoInteractions_.addPair(b, c);
416	+	} else {
417	+	excludedInteractions_.addPair(a, b);
418	+	excludedInteractions_.addPair(b, c);
419	+	}
420
421	<	exclude_.addPair(a, b);
422	<	exclude_.addPair(a, c);
423	<	exclude_.addPair(b, c);
421	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
422	>	oneThreeInteractions_.addPair(a, c);
423	>	} else {
424	>	excludedInteractions_.addPair(a, c);
425	>	}
426		}
427
428	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
428	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
429	>	torsion = mol->nextTorsion(torsionIter)) {
430	>
431		a = torsion->getAtomA()->getGlobalIndex();
432		b = torsion->getAtomB()->getGlobalIndex();
433		c = torsion->getAtomC()->getGlobalIndex();
434	<	d = torsion->getAtomD()->getGlobalIndex();
434	>	d = torsion->getAtomD()->getGlobalIndex();
435
436	<	exclude_.addPair(a, b);
437	<	exclude_.addPair(a, c);
438	<	exclude_.addPair(a, d);
439	<	exclude_.addPair(b, c);
440	<	exclude_.addPair(b, d);
441	<	exclude_.addPair(c, d);
436	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
437	>	oneTwoInteractions_.addPair(a, b);
438	>	oneTwoInteractions_.addPair(b, c);
439	>	oneTwoInteractions_.addPair(c, d);
440	>	} else {
441	>	excludedInteractions_.addPair(a, b);
442	>	excludedInteractions_.addPair(b, c);
443	>	excludedInteractions_.addPair(c, d);
444	>	}
445	>
446	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
447	>	oneThreeInteractions_.addPair(a, c);
448	>	oneThreeInteractions_.addPair(b, d);
449	>	} else {
450	>	excludedInteractions_.addPair(a, c);
451	>	excludedInteractions_.addPair(b, d);
452	>	}
453	>
454	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
455	>	oneFourInteractions_.addPair(a, d);
456	>	} else {
457	>	excludedInteractions_.addPair(a, d);
458	>	}
459		}
460
461	<	Molecule::RigidBodyIterator rbIter;
462	<	RigidBody* rb;
463	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
464	<	std::vector<Atom*> atoms = rb->getAtoms();
465	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
466	<	for (int j = i + 1; j < atoms.size(); ++j) {
461	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
462	>	inversion = mol->nextInversion(inversionIter)) {
463	>
464	>	a = inversion->getAtomA()->getGlobalIndex();
465	>	b = inversion->getAtomB()->getGlobalIndex();
466	>	c = inversion->getAtomC()->getGlobalIndex();
467	>	d = inversion->getAtomD()->getGlobalIndex();
468	>
469	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
470	>	oneTwoInteractions_.addPair(a, b);
471	>	oneTwoInteractions_.addPair(a, c);
472	>	oneTwoInteractions_.addPair(a, d);
473	>	} else {
474	>	excludedInteractions_.addPair(a, b);
475	>	excludedInteractions_.addPair(a, c);
476	>	excludedInteractions_.addPair(a, d);
477	>	}
478	>
479	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
480	>	oneThreeInteractions_.addPair(b, c);
481	>	oneThreeInteractions_.addPair(b, d);
482	>	oneThreeInteractions_.addPair(c, d);
483	>	} else {
484	>	excludedInteractions_.addPair(b, c);
485	>	excludedInteractions_.addPair(b, d);
486	>	excludedInteractions_.addPair(c, d);
487	>	}
488	>	}
489	>
490	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
491	>	rb = mol->nextRigidBody(rbIter)) {
492	>	vector<Atom*> atoms = rb->getAtoms();
493	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
494	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
495		a = atoms[i]->getGlobalIndex();
496		b = atoms[j]->getGlobalIndex();
497	<	exclude_.addPair(a, b);
497	>	excludedInteractions_.addPair(a, b);
498		}
499		}
500		}
501
502		}
503
504	<	void SimInfo::removeExcludePairs(Molecule* mol) {
505	<	std::vector<Bond*>::iterator bondIter;
506	<	std::vector<Bend*>::iterator bendIter;
507	<	std::vector<Torsion*>::iterator torsionIter;
504	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
505	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
506	>	vector<Bond*>::iterator bondIter;
507	>	vector<Bend*>::iterator bendIter;
508	>	vector<Torsion*>::iterator torsionIter;
509	>	vector<Inversion*>::iterator inversionIter;
510		Bond* bond;
511		Bend* bend;
512		Torsion* torsion;
513	+	Inversion* inversion;
514		int a;
515		int b;
516		int c;
517		int d;
518	+
519	+	map<int, set<int> > atomGroups;
520	+	Molecule::RigidBodyIterator rbIter;
521	+	RigidBody* rb;
522	+	Molecule::IntegrableObjectIterator ii;
523	+	StuntDouble* integrableObject;
524
525	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
525	>	for (integrableObject = mol->beginIntegrableObject(ii);
526	>	integrableObject != NULL;
527	>	integrableObject = mol->nextIntegrableObject(ii)) {
528	>
529	>	if (integrableObject->isRigidBody()) {
530	>	rb = static_cast<RigidBody*>(integrableObject);
531	>	vector<Atom*> atoms = rb->getAtoms();
532	>	set<int> rigidAtoms;
533	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
534	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
535	>	}
536	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
537	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
538	>	}
539	>	} else {
540	>	set<int> oneAtomSet;
541	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
542	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
543	>	}
544	>	}
545	>
546	>	for (bond= mol->beginBond(bondIter); bond != NULL;
547	>	bond = mol->nextBond(bondIter)) {
548	>
549		a = bond->getAtomA()->getGlobalIndex();
550	<	b = bond->getAtomB()->getGlobalIndex();
551	<	exclude_.removePair(a, b);
550	>	b = bond->getAtomB()->getGlobalIndex();
551	>
552	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
553	>	oneTwoInteractions_.removePair(a, b);
554	>	} else {
555	>	excludedInteractions_.removePair(a, b);
556	>	}
557		}
558
559	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
559	>	for (bend= mol->beginBend(bendIter); bend != NULL;
560	>	bend = mol->nextBend(bendIter)) {
561	>
562		a = bend->getAtomA()->getGlobalIndex();
563		b = bend->getAtomB()->getGlobalIndex();
564		c = bend->getAtomC()->getGlobalIndex();
565	+
566	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
567	+	oneTwoInteractions_.removePair(a, b);
568	+	oneTwoInteractions_.removePair(b, c);
569	+	} else {
570	+	excludedInteractions_.removePair(a, b);
571	+	excludedInteractions_.removePair(b, c);
572	+	}
573
574	<	exclude_.removePair(a, b);
575	<	exclude_.removePair(a, c);
576	<	exclude_.removePair(b, c);
574	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
575	>	oneThreeInteractions_.removePair(a, c);
576	>	} else {
577	>	excludedInteractions_.removePair(a, c);
578	>	}
579		}
580
581	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
581	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
582	>	torsion = mol->nextTorsion(torsionIter)) {
583	>
584		a = torsion->getAtomA()->getGlobalIndex();
585		b = torsion->getAtomB()->getGlobalIndex();
586		c = torsion->getAtomC()->getGlobalIndex();
587	<	d = torsion->getAtomD()->getGlobalIndex();
587	>	d = torsion->getAtomD()->getGlobalIndex();
588	>
589	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
590	>	oneTwoInteractions_.removePair(a, b);
591	>	oneTwoInteractions_.removePair(b, c);
592	>	oneTwoInteractions_.removePair(c, d);
593	>	} else {
594	>	excludedInteractions_.removePair(a, b);
595	>	excludedInteractions_.removePair(b, c);
596	>	excludedInteractions_.removePair(c, d);
597	>	}
598
599	<	exclude_.removePair(a, b);
600	<	exclude_.removePair(a, c);
601	<	exclude_.removePair(a, d);
602	<	exclude_.removePair(b, c);
603	<	exclude_.removePair(b, d);
604	<	exclude_.removePair(c, d);
599	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
600	>	oneThreeInteractions_.removePair(a, c);
601	>	oneThreeInteractions_.removePair(b, d);
602	>	} else {
603	>	excludedInteractions_.removePair(a, c);
604	>	excludedInteractions_.removePair(b, d);
605	>	}
606	>
607	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
608	>	oneFourInteractions_.removePair(a, d);
609	>	} else {
610	>	excludedInteractions_.removePair(a, d);
611	>	}
612		}
613
614	<	Molecule::RigidBodyIterator rbIter;
615	<	RigidBody* rb;
616	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
617	<	std::vector<Atom*> atoms = rb->getAtoms();
618	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
619	<	for (int j = i + 1; j < atoms.size(); ++j) {
614	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
615	>	inversion = mol->nextInversion(inversionIter)) {
616	>
617	>	a = inversion->getAtomA()->getGlobalIndex();
618	>	b = inversion->getAtomB()->getGlobalIndex();
619	>	c = inversion->getAtomC()->getGlobalIndex();
620	>	d = inversion->getAtomD()->getGlobalIndex();
621	>
622	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
623	>	oneTwoInteractions_.removePair(a, b);
624	>	oneTwoInteractions_.removePair(a, c);
625	>	oneTwoInteractions_.removePair(a, d);
626	>	} else {
627	>	excludedInteractions_.removePair(a, b);
628	>	excludedInteractions_.removePair(a, c);
629	>	excludedInteractions_.removePair(a, d);
630	>	}
631	>
632	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
633	>	oneThreeInteractions_.removePair(b, c);
634	>	oneThreeInteractions_.removePair(b, d);
635	>	oneThreeInteractions_.removePair(c, d);
636	>	} else {
637	>	excludedInteractions_.removePair(b, c);
638	>	excludedInteractions_.removePair(b, d);
639	>	excludedInteractions_.removePair(c, d);
640	>	}
641	>	}
642	>
643	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
644	>	rb = mol->nextRigidBody(rbIter)) {
645	>	vector<Atom*> atoms = rb->getAtoms();
646	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
647	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
648		a = atoms[i]->getGlobalIndex();
649		b = atoms[j]->getGlobalIndex();
650	<	exclude_.removePair(a, b);
650	>	excludedInteractions_.removePair(a, b);
651		}
652		}
653		}
654	<
654	>
655		}
656	<
657	<
656	>
657	>
658		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
659		int curStampId;
660	<
660	>
661		//index from 0
662		curStampId = moleculeStamps_.size();
663
#	Line 451 | Line 665 | namespace oopse {
665		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
666		}
667
454	–	void SimInfo::update() {
668
669	<	setupSimType();
670	<
671	<	#ifdef IS_MPI
672	<	setupFortranParallel();
673	<	#endif
674	<
675	<	setupFortranSim();
676	<
677	<	//setup fortran force field
465	<	/** @deprecate */
466	<	int isError = 0;
467	<
468	<	setupElectrostaticSummationMethod( isError );
469	<
470	<	if(isError){
471	<	sprintf( painCave.errMsg,
472	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
473	<	painCave.isFatal = 1;
474	<	simError();
475	<	}
476	<
477	<
478	<	setupCutoff();
479	<
669	>	/**
670	>	* update
671	>	*
672	>	*  Performs the global checks and variable settings after the
673	>	*  objects have been created.
674	>	*
675	>	*/
676	>	void SimInfo::update() {
677	>	setupSimVariables();
678		calcNdf();
679		calcNdfRaw();
680		calcNdfTrans();
483	–
484	–	fortranInitialized_ = true;
681		}
682	<
683	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
682	>
683	>	/**
684	>	* getSimulatedAtomTypes
685	>	*
686	>	* Returns an STL set of AtomType* that are actually present in this
687	>	* simulation.  Must query all processors to assemble this information.
688	>	*
689	>	*/
690	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
691		SimInfo::MoleculeIterator mi;
692		Molecule* mol;
693		Molecule::AtomIterator ai;
694		Atom* atom;
695	<	std::set<AtomType*> atomTypes;
696	<
695	>	set<AtomType*> atomTypes;
696	>
697		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
698	<
699	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
698	>	for(atom = mol->beginAtom(ai); atom != NULL;
699	>	atom = mol->nextAtom(ai)) {
700		atomTypes.insert(atom->getAtomType());
701	<	}
702	<
701	>	}
702	>	}
703	>
704	>	#ifdef IS_MPI
705	>
706	>	// loop over the found atom types on this processor, and add their
707	>	// numerical idents to a vector:
708	>
709	>	vector<int> foundTypes;
710	>	set<AtomType*>::iterator i;
711	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
712	>	foundTypes.push_back( (*i)->getIdent() );
713	>
714	>	// count_local holds the number of found types on this processor
715	>	int count_local = foundTypes.size();
716	>
717	>	int nproc = MPI::COMM_WORLD.Get_size();
718	>
719	>	// we need arrays to hold the counts and displacement vectors for
720	>	// all processors
721	>	vector<int> counts(nproc, 0);
722	>	vector<int> disps(nproc, 0);
723	>
724	>	// fill the counts array
725	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
726	>	1, MPI::INT);
727	>
728	>	// use the processor counts to compute the displacement array
729	>	disps[0] = 0;
730	>	int totalCount = counts[0];
731	>	for (int iproc = 1; iproc < nproc; iproc++) {
732	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
733	>	totalCount += counts[iproc];
734		}
735
736	+	// we need a (possibly redundant) set of all found types:
737	+	vector<int> ftGlobal(totalCount);
738	+
739	+	// now spray out the foundTypes to all the other processors:
740	+	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
741	+	&ftGlobal[0], &counts[0], &disps[0],
742	+	MPI::INT);
743	+
744	+	vector<int>::iterator j;
745	+
746	+	// foundIdents is a stl set, so inserting an already found ident
747	+	// will have no effect.
748	+	set<int> foundIdents;
749	+
750	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
751	+	foundIdents.insert((*j));
752	+
753	+	// now iterate over the foundIdents and get the actual atom types
754	+	// that correspond to these:
755	+	set<int>::iterator it;
756	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
757	+	atomTypes.insert( forceField_->getAtomType((*it)) );
758	+
759	+	#endif
760	+
761		return atomTypes;
762		}
763
764	<	void SimInfo::setupSimType() {
765	<	std::set<AtomType*>::iterator i;
766	<	std::set<AtomType*> atomTypes;
767	<	atomTypes = getUniqueAtomTypes();
764	>	void SimInfo::setupSimVariables() {
765	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
766	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
767	>	calcBoxDipole_ = false;
768	>	if ( simParams_->haveAccumulateBoxDipole() )
769	>	if ( simParams_->getAccumulateBoxDipole() ) {
770	>	calcBoxDipole_ = true;
771	>	}
772
773	<	int useLennardJones = 0;
774	<	int useElectrostatic = 0;
775	<	int useEAM = 0;
776	<	int useCharge = 0;
777	<	int useDirectional = 0;
778	<	int useDipole = 0;
516	<	int useGayBerne = 0;
517	<	int useSticky = 0;
518	<	int useStickyPower = 0;
519	<	int useShape = 0;
520	<	int useFLARB = 0; //it is not in AtomType yet
521	<	int useDirectionalAtom = 0;
522	<	int useElectrostatics = 0;
523	<	//usePBC and useRF are from simParams
524	<	int usePBC = simParams_->getPBC();
525	<
773	>	set<AtomType*>::iterator i;
774	>	set<AtomType*> atomTypes;
775	>	atomTypes = getSimulatedAtomTypes();
776	>	int usesElectrostatic = 0;
777	>	int usesMetallic = 0;
778	>	int usesDirectional = 0;
779		//loop over all of the atom types
780		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
781	<	useLennardJones |= (*i)->isLennardJones();
782	<	useElectrostatic |= (*i)->isElectrostatic();
783	<	useEAM |= (*i)->isEAM();
531	<	useCharge |= (*i)->isCharge();
532	<	useDirectional |= (*i)->isDirectional();
533	<	useDipole |= (*i)->isDipole();
534	<	useGayBerne |= (*i)->isGayBerne();
535	<	useSticky |= (*i)->isSticky();
536	<	useStickyPower |= (*i)->isStickyPower();
537	<	useShape |= (*i)->isShape();
781	>	usesElectrostatic |= (*i)->isElectrostatic();
782	>	usesMetallic |= (*i)->isMetal();
783	>	usesDirectional |= (*i)->isDirectional();
784		}
785	<
540	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
541	<	useDirectionalAtom = 1;
542	<	}
543	<
544	<	if (useCharge || useDipole) {
545	<	useElectrostatics = 1;
546	<	}
547	<
785	>
786		#ifdef IS_MPI
787		int temp;
788	<
789	<	temp = usePBC;
552	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
553	<
554	<	temp = useDirectionalAtom;
555	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
556	<
557	<	temp = useLennardJones;
558	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
559	<
560	<	temp = useElectrostatics;
561	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
562	<
563	<	temp = useCharge;
564	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
565	<
566	<	temp = useDipole;
567	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
568	<
569	<	temp = useSticky;
570	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
571	<
572	<	temp = useStickyPower;
573	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
788	>	temp = usesDirectional;
789	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
790
791	<	temp = useGayBerne;
792	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
791	>	temp = usesMetallic;
792	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
793	>
794	>	temp = usesElectrostatic;
795	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
796	>	#else
797
798	<	temp = useEAM;
799	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
798	>	usesDirectionalAtoms_ = usesDirectional;
799	>	usesMetallicAtoms_ = usesMetallic;
800	>	usesElectrostaticAtoms_ = usesElectrostatic;
801
581	–	temp = useShape;
582	–	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
583	–
584	–	temp = useFLARB;
585	–	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
586	–
802		#endif
803	+
804	+	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
805	+	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
806	+	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
807	+	}
808
589	–	fInfo_.SIM_uses_PBC = usePBC;
590	–	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
591	–	fInfo_.SIM_uses_LennardJones = useLennardJones;
592	–	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
593	–	fInfo_.SIM_uses_Charges = useCharge;
594	–	fInfo_.SIM_uses_Dipoles = useDipole;
595	–	fInfo_.SIM_uses_Sticky = useSticky;
596	–	fInfo_.SIM_uses_StickyPower = useStickyPower;
597	–	fInfo_.SIM_uses_GayBerne = useGayBerne;
598	–	fInfo_.SIM_uses_EAM = useEAM;
599	–	fInfo_.SIM_uses_Shapes = useShape;
600	–	fInfo_.SIM_uses_FLARB = useFLARB;
809
810	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
810	>	vector<int> SimInfo::getGlobalAtomIndices() {
811	>	SimInfo::MoleculeIterator mi;
812	>	Molecule* mol;
813	>	Molecule::AtomIterator ai;
814	>	Atom* atom;
815
816	<	if (simParams_->haveDielectric()) {
817	<	fInfo_.dielect = simParams_->getDielectric();
818	<	} else {
819	<	sprintf(painCave.errMsg,
820	<	"SimSetup Error: No Dielectric constant was set.\n"
821	<	"\tYou are trying to use Reaction Field without"
822	<	"\tsetting a dielectric constant!\n");
611	<	painCave.isFatal = 1;
612	<	simError();
816	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
817	>
818	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
819	>
820	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
821	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
822	>	cerr << "LI = " << atom->getLocalIndex() << "GAI = " << GlobalAtomIndices[atom->getLocalIndex()] << "\n";
823		}
614	–
615	–	} else {
616	–	fInfo_.dielect = 0.0;
824		}
825	<
825	>	return GlobalAtomIndices;
826		}
827
621	–	void SimInfo::setupFortranSim() {
622	–	int isError;
623	–	int nExclude;
624	–	std::vector<int> fortranGlobalGroupMembership;
625	–
626	–	nExclude = exclude_.getSize();
627	–	isError = 0;
828
829	<	//globalGroupMembership_ is filled by SimCreator
830	<	for (int i = 0; i < nGlobalAtoms_; i++) {
831	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
829	>	vector<int> SimInfo::getGlobalGroupIndices() {
830	>	SimInfo::MoleculeIterator mi;
831	>	Molecule* mol;
832	>	Molecule::CutoffGroupIterator ci;
833	>	CutoffGroup* cg;
834	>
835	>	vector<int> GlobalGroupIndices;
836	>
837	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
838	>
839	>	//local index of cutoff group is trivial, it only depends on the
840	>	//order of travesing
841	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
842	>	cg = mol->nextCutoffGroup(ci)) {
843	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
844	>	cerr << "LI, GGI = " << GlobalGroupIndices.size() << " " << cg->getGlobalIndex() << "\n";
845	>	}
846		}
847	+	return GlobalGroupIndices;
848	+	}
849
850	+
851	+	void SimInfo::prepareTopology() {
852	+	int nExclude, nOneTwo, nOneThree, nOneFour;
853	+
854		//calculate mass ratio of cutoff group
635	–	std::vector<double> mfact;
855		SimInfo::MoleculeIterator mi;
856		Molecule* mol;
857		Molecule::CutoffGroupIterator ci;
858		CutoffGroup* cg;
859		Molecule::AtomIterator ai;
860		Atom* atom;
861	<	double totalMass;
861	>	RealType totalMass;
862
863	<	//to avoid memory reallocation, reserve enough space for mfact
864	<	mfact.reserve(getNCutoffGroups());
863	>	/**
864	>	* The mass factor is the relative mass of an atom to the total
865	>	* mass of the cutoff group it belongs to.  By default, all atoms
866	>	* are their own cutoff groups, and therefore have mass factors of
867	>	* 1.  We need some special handling for massless atoms, which
868	>	* will be treated as carrying the entire mass of the cutoff
869	>	* group.
870	>	*/
871	>	massFactors_.clear();
872	>	massFactors_.resize(getNAtoms(), 1.0);
873
874		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
875	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
875	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
876	>	cg = mol->nextCutoffGroup(ci)) {
877
878		totalMass = cg->getMass();
879		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
880	<	mfact.push_back(atom->getMass()/totalMass);
880	>	// Check for massless groups - set mfact to 1 if true
881	>	if (totalMass != 0)
882	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
883	>	else
884	>	massFactors_[atom->getLocalIndex()] = 1.0;
885		}
654	–
886		}
887		}
888
889	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
659	<	std::vector<int> identArray;
889	>	// Build the identArray_
890
891	<	//to avoid memory reallocation, reserve enough space identArray
892	<	identArray.reserve(getNAtoms());
663	<
891	>	identArray_.clear();
892	>	identArray_.reserve(getNAtoms());
893		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
894		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
895	<	identArray.push_back(atom->getIdent());
895	>	identArray_.push_back(atom->getIdent());
896		}
897		}
669	–
670	–	//fill molMembershipArray
671	–	//molMembershipArray is filled by SimCreator
672	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
673	–	for (int i = 0; i < nGlobalAtoms_; i++) {
674	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
675	–	}
898
899	<	//setup fortran simulation
678	<	int nGlobalExcludes = 0;
679	<	int* globalExcludes = NULL;
680	<	int* excludeList = exclude_.getExcludeList();
681	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
682	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
683	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
899	>	//scan topology
900
901	<	if( isError ){
901	>	nExclude = excludedInteractions_.getSize();
902	>	nOneTwo = oneTwoInteractions_.getSize();
903	>	nOneThree = oneThreeInteractions_.getSize();
904	>	nOneFour = oneFourInteractions_.getSize();
905
906	<	sprintf( painCave.errMsg,
907	<	"There was an error setting the simulation information in fortran.\n" );
908	<	painCave.isFatal = 1;
909	<	painCave.severity = OOPSE_ERROR;
691	<	simError();
692	<	}
693	<
694	<	#ifdef IS_MPI
695	<	sprintf( checkPointMsg,
696	<	"succesfully sent the simulation information to fortran.\n");
697	<	MPIcheckPoint();
698	<	#endif // is_mpi
699	<	}
700	<
701	<
702	<	#ifdef IS_MPI
703	<	void SimInfo::setupFortranParallel() {
704	<
705	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
706	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
707	<	std::vector<int> localToGlobalCutoffGroupIndex;
708	<	SimInfo::MoleculeIterator mi;
709	<	Molecule::AtomIterator ai;
710	<	Molecule::CutoffGroupIterator ci;
711	<	Molecule* mol;
712	<	Atom* atom;
713	<	CutoffGroup* cg;
714	<	mpiSimData parallelData;
715	<	int isError;
716	<
717	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
718	<
719	<	//local index(index in DataStorge) of atom is important
720	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
721	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
722	<	}
723	<
724	<	//local index of cutoff group is trivial, it only depends on the order of travesing
725	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
726	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
727	<	}
728	<
729	<	}
730	<
731	<	//fill up mpiSimData struct
732	<	parallelData.nMolGlobal = getNGlobalMolecules();
733	<	parallelData.nMolLocal = getNMolecules();
734	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
735	<	parallelData.nAtomsLocal = getNAtoms();
736	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
737	<	parallelData.nGroupsLocal = getNCutoffGroups();
738	<	parallelData.myNode = worldRank;
739	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
906	>	int* excludeList = excludedInteractions_.getPairList();
907	>	int* oneTwoList = oneTwoInteractions_.getPairList();
908	>	int* oneThreeList = oneThreeInteractions_.getPairList();
909	>	int* oneFourList = oneFourInteractions_.getPairList();
910
911	<	//pass mpiSimData struct and index arrays to fortran
742	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
743	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
744	<	&localToGlobalCutoffGroupIndex[0], &isError);
745	<
746	<	if (isError) {
747	<	sprintf(painCave.errMsg,
748	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
749	<	painCave.isFatal = 1;
750	<	simError();
751	<	}
752	<
753	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
754	<	MPIcheckPoint();
755	<
756	<
757	<	}
758	<
759	<	#endif
760	<
761	<	double SimInfo::calcMaxCutoffRadius() {
762	<
763	<
764	<	std::set<AtomType*> atomTypes;
765	<	std::set<AtomType*>::iterator i;
766	<	std::vector<double> cutoffRadius;
767	<
768	<	//get the unique atom types
769	<	atomTypes = getUniqueAtomTypes();
770	<
771	<	//query the max cutoff radius among these atom types
772	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
773	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
774	<	}
775	<
776	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
777	<	#ifdef IS_MPI
778	<	//pick the max cutoff radius among the processors
779	<	#endif
780	<
781	<	return maxCutoffRadius;
782	<	}
783	<
784	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
785	<
786	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
787	<
788	<	if (!simParams_->haveRcut()){
789	<	sprintf(painCave.errMsg,
790	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
791	<	"\tOOPSE will use a default value of 15.0 angstroms"
792	<	"\tfor the cutoffRadius.\n");
793	<	painCave.isFatal = 0;
794	<	simError();
795	<	rcut = 15.0;
796	<	} else{
797	<	rcut = simParams_->getRcut();
798	<	}
799	<
800	<	if (!simParams_->haveRsw()){
801	<	sprintf(painCave.errMsg,
802	<	"SimCreator Warning: No value was set for switchingRadius.\n"
803	<	"\tOOPSE will use a default value of\n"
804	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
805	<	painCave.isFatal = 0;
806	<	simError();
807	<	rsw = 0.95 * rcut;
808	<	} else{
809	<	rsw = simParams_->getRsw();
810	<	}
811	<
812	<	} else {
813	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
814	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
815	<
816	<	if (simParams_->haveRcut()) {
817	<	rcut = simParams_->getRcut();
818	<	} else {
819	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
820	<	rcut = calcMaxCutoffRadius();
821	<	}
822	<
823	<	if (simParams_->haveRsw()) {
824	<	rsw  = simParams_->getRsw();
825	<	} else {
826	<	rsw = rcut;
827	<	}
828	<
829	<	}
830	<	}
831	<
832	<	void SimInfo::setupCutoff() {
833	<	getCutoff(rcut_, rsw_);
834	<	double rnblist = rcut_ + 1; // skin of neighbor list
835	<
836	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
837	<
838	<	int cp =  TRADITIONAL_CUTOFF_POLICY;
839	<	if (simParams_->haveCutoffPolicy()) {
840	<	std::string myPolicy = simParams_->getCutoffPolicy();
841	<	if (myPolicy == "MIX") {
842	<	cp = MIX_CUTOFF_POLICY;
843	<	} else {
844	<	if (myPolicy == "MAX") {
845	<	cp = MAX_CUTOFF_POLICY;
846	<	} else {
847	<	if (myPolicy == "TRADITIONAL") {
848	<	cp = TRADITIONAL_CUTOFF_POLICY;
849	<	} else {
850	<	// throw error
851	<	sprintf( painCave.errMsg,
852	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
853	<	painCave.isFatal = 1;
854	<	simError();
855	<	}
856	<	}
857	<	}
858	<	}
859	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
860	<	}
861	<
862	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
863	<
864	<	int errorOut;
865	<	int esm =  NONE;
866	<	double alphaVal;
867	<
868	<	errorOut = isError;
869	<
870	<	if (simParams_->haveElectrostaticSummationMethod()) {
871	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
872	<	if (myMethod == "NONE") {
873	<	esm = NONE;
874	<	} else {
875	<	if (myMethod == "UNDAMPED_WOLF") {
876	<	esm = UNDAMPED_WOLF;
877	<	} else {
878	<	if (myMethod == "DAMPED_WOLF") {
879	<	esm = DAMPED_WOLF;
880	<	if (!simParams_->haveDampingAlpha()) {
881	<	//throw error
882	<	sprintf( painCave.errMsg,
883	<	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", simParams_->getDampingAlpha());
884	<	painCave.isFatal = 0;
885	<	simError();
886	<	}
887	<	alphaVal = simParams_->getDampingAlpha();
888	<	} else {
889	<	if (myMethod == "REACTION_FIELD") {
890	<	esm = REACTION_FIELD;
891	<	} else {
892	<	// throw error
893	<	sprintf( painCave.errMsg,
894	<	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"undamped_wolf\", \"damped_wolf\", or \"reaction_field\".", myMethod.c_str() );
895	<	painCave.isFatal = 1;
896	<	simError();
897	<	}
898	<	}
899	<	}
900	<	}
901	<	}
902	<	initFortranFF( &fInfo_.SIM_uses_RF, &esm, &alphaVal, &errorOut );
911	>	topologyDone_ = true;
912		}
913
914		void SimInfo::addProperty(GenericData* genData) {
915		properties_.addProperty(genData);
916		}
917
918	<	void SimInfo::removeProperty(const std::string& propName) {
918	>	void SimInfo::removeProperty(const string& propName) {
919		properties_.removeProperty(propName);
920		}
921
#	Line 914 | Line 923 | namespace oopse {
923		properties_.clearProperties();
924		}
925
926	<	std::vector<std::string> SimInfo::getPropertyNames() {
926	>	vector<string> SimInfo::getPropertyNames() {
927		return properties_.getPropertyNames();
928		}
929
930	<	std::vector<GenericData*> SimInfo::getProperties() {
930	>	vector<GenericData*> SimInfo::getProperties() {
931		return properties_.getProperties();
932		}
933
934	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
934	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
935		return properties_.getPropertyByName(propName);
936		}
937
#	Line 936 | Line 945 | namespace oopse {
945		Molecule* mol;
946		RigidBody* rb;
947		Atom* atom;
948	+	CutoffGroup* cg;
949		SimInfo::MoleculeIterator mi;
950		Molecule::RigidBodyIterator rbIter;
951	<	Molecule::AtomIterator atomIter;;
951	>	Molecule::AtomIterator atomIter;
952	>	Molecule::CutoffGroupIterator cgIter;
953
954		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
955
#	Line 949 | Line 960 | namespace oopse {
960		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
961		rb->setSnapshotManager(sman_);
962		}
963	+
964	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
965	+	cg->setSnapshotManager(sman_);
966	+	}
967		}
968
969		}
#	Line 958 | Line 973 | namespace oopse {
973		Molecule* mol;
974
975		Vector3d comVel(0.0);
976	<	double totalMass = 0.0;
976	>	RealType totalMass = 0.0;
977
978
979		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
980	<	double mass = mol->getMass();
980	>	RealType mass = mol->getMass();
981		totalMass += mass;
982		comVel += mass * mol->getComVel();
983		}
984
985		#ifdef IS_MPI
986	<	double tmpMass = totalMass;
986	>	RealType tmpMass = totalMass;
987		Vector3d tmpComVel(comVel);
988	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
989	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
988	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
989	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
990		#endif
991
992		comVel /= totalMass;
#	Line 984 | Line 999 | namespace oopse {
999		Molecule* mol;
1000
1001		Vector3d com(0.0);
1002	<	double totalMass = 0.0;
1002	>	RealType totalMass = 0.0;
1003
1004		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1005	<	double mass = mol->getMass();
1005	>	RealType mass = mol->getMass();
1006		totalMass += mass;
1007		com += mass * mol->getCom();
1008		}
1009
1010		#ifdef IS_MPI
1011	<	double tmpMass = totalMass;
1011	>	RealType tmpMass = totalMass;
1012		Vector3d tmpCom(com);
1013	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1014	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1013	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1014	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1015		#endif
1016
1017		com /= totalMass;
#	Line 1005 | Line 1020 | namespace oopse {
1020
1021		}
1022
1023	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1023	>	ostream& operator <<(ostream& o, SimInfo& info) {
1024
1025		return o;
1026		}
#	Line 1020 | Line 1035 | namespace oopse {
1035		Molecule* mol;
1036
1037
1038	<	double totalMass = 0.0;
1038	>	RealType totalMass = 0.0;
1039
1040
1041		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1042	<	double mass = mol->getMass();
1042	>	RealType mass = mol->getMass();
1043		totalMass += mass;
1044		com += mass * mol->getCom();
1045		comVel += mass * mol->getComVel();
1046		}
1047
1048		#ifdef IS_MPI
1049	<	double tmpMass = totalMass;
1049	>	RealType tmpMass = totalMass;
1050		Vector3d tmpCom(com);
1051		Vector3d tmpComVel(comVel);
1052	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1053	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1054	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1052	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1053	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1054	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1055		#endif
1056
1057		com /= totalMass;
#	Line 1048 | Line 1063 | namespace oopse {
1063
1064
1065		[  Ixx -Ixy  -Ixz ]
1066	<	J =| -Iyx  Iyy  -Iyz |
1066	>	J =| -Iyx  Iyy  -Iyz |
1067		[ -Izx -Iyz   Izz ]
1068		*/
1069
1070		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1071
1072
1073	<	double xx = 0.0;
1074	<	double yy = 0.0;
1075	<	double zz = 0.0;
1076	<	double xy = 0.0;
1077	<	double xz = 0.0;
1078	<	double yz = 0.0;
1073	>	RealType xx = 0.0;
1074	>	RealType yy = 0.0;
1075	>	RealType zz = 0.0;
1076	>	RealType xy = 0.0;
1077	>	RealType xz = 0.0;
1078	>	RealType yz = 0.0;
1079		Vector3d com(0.0);
1080		Vector3d comVel(0.0);
1081
#	Line 1072 | Line 1087 | namespace oopse {
1087		Vector3d thisq(0.0);
1088		Vector3d thisv(0.0);
1089
1090	<	double thisMass = 0.0;
1090	>	RealType thisMass = 0.0;
1091
1092
1093
#	Line 1110 | Line 1125 | namespace oopse {
1125		#ifdef IS_MPI
1126		Mat3x3d tmpI(inertiaTensor);
1127		Vector3d tmpAngMom;
1128	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1129	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1128	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1129	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1130		#endif
1131
1132		return;
#	Line 1132 | Line 1147 | namespace oopse {
1147		Vector3d thisr(0.0);
1148		Vector3d thisp(0.0);
1149
1150	<	double thisMass;
1150	>	RealType thisMass;
1151
1152		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1153		thisMass = mol->getMass();
#	Line 1145 | Line 1160 | namespace oopse {
1160
1161		#ifdef IS_MPI
1162		Vector3d tmpAngMom;
1163	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1163	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1164		#endif
1165
1166		return angularMomentum;
1167		}
1168
1169	<
1170	<	}//end namespace oopse
1169	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1170	>	return IOIndexToIntegrableObject.at(index);
1171	>	}
1172	>
1173	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1174	>	IOIndexToIntegrableObject= v;
1175	>	}
1176
1177	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1178	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1179	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1180	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1181	+	*/
1182	+	void SimInfo::getGyrationalVolume(RealType &volume){
1183	+	Mat3x3d intTensor;
1184	+	RealType det;
1185	+	Vector3d dummyAngMom;
1186	+	RealType sysconstants;
1187	+	RealType geomCnst;
1188	+
1189	+	geomCnst = 3.0/2.0;
1190	+	/* Get the inertial tensor and angular momentum for free*/
1191	+	getInertiaTensor(intTensor,dummyAngMom);
1192	+
1193	+	det = intTensor.determinant();
1194	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1195	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1196	+	return;
1197	+	}
1198	+
1199	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1200	+	Mat3x3d intTensor;
1201	+	Vector3d dummyAngMom;
1202	+	RealType sysconstants;
1203	+	RealType geomCnst;
1204	+
1205	+	geomCnst = 3.0/2.0;
1206	+	/* Get the inertial tensor and angular momentum for free*/
1207	+	getInertiaTensor(intTensor,dummyAngMom);
1208	+
1209	+	detI = intTensor.determinant();
1210	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1211	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1212	+	return;
1213	+	}
1214	+	/*
1215	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1216	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1217	+	sdByGlobalIndex_ = v;
1218	+	}
1219	+
1220	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1221	+	//assert(index < nAtoms_ + nRigidBodies_);
1222	+	return sdByGlobalIndex_.at(index);
1223	+	}
1224	+	*/
1225	+	int SimInfo::getNGlobalConstraints() {
1226	+	int nGlobalConstraints;
1227	+	#ifdef IS_MPI
1228	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1229	+	MPI_COMM_WORLD);
1230	+	#else
1231	+	nGlobalConstraints =  nConstraints_;
1232	+	#endif
1233	+	return nGlobalConstraints;
1234	+	}
1235	+
1236	+	}//end namespace OpenMD
1237	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 604 by chrisfen, Fri Sep 16 19:00:12 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1597 by gezelter, Tue Jul 26 15:49:24 2011 UTC

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