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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 608 by chrisfen, Fri Sep 16 21:07:45 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1744 by gezelter, Tue Jun 5 18:07:08 2012 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 48 | Line 49
49
50		#include <algorithm>
51		#include <set>
52	+	#include <map>
53
54		#include "brains/SimInfo.hpp"
55		#include "math/Vector3.hpp"
56		#include "primitives/Molecule.hpp"
57	<	#include "UseTheForce/fCutoffPolicy.h"
56	<	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
57	<	#include "UseTheForce/doForces_interface.h"
58	<	#include "UseTheForce/notifyCutoffs_interface.h"
57	>	#include "primitives/StuntDouble.hpp"
58		#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60		#include "selection/SelectionManager.hpp"
61	<
61	>	#include "io/ForceFieldOptions.hpp"
62	>	#include "brains/ForceField.hpp"
63	>	#include "nonbonded/SwitchingFunction.hpp"
64		#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
66	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68	<	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),
68	>	using namespace std;
69	>	namespace OpenMD {
70	>
71	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72	>	forceField_(ff), simParams_(simParams),
73	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
77	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
78	<	sman_(NULL), fortranInitialized_(false) {
79	<
80	<
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;
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0),
76	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79	>	calcBoxDipole_(false), useAtomicVirial_(true) {
80
81	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
82	<	molStamp = i->first;
83	<	nMolWithSameStamp = i->second;
84	<
85	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
86	<
87	<	//calculate atoms in molecules
88	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
89	<
90	<
91	<	//calculate atoms in cutoff groups
92	<	int nAtomsInGroups = 0;
93	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
94	<
95	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
96	<	cgStamp = molStamp->getCutoffGroup(j);
97	<	nAtomsInGroups += cgStamp->getNMembers();
98	<	}
99	<
100	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
101	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
102	<
103	<	//calculate atoms in rigid bodies
104	<	int nAtomsInRigidBodies = 0;
105	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
106	<
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	<
81	>	MoleculeStamp* molStamp;
82	>	int nMolWithSameStamp;
83	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
85	>	CutoffGroupStamp* cgStamp;
86	>	RigidBodyStamp* rbStamp;
87	>	int nRigidAtoms = 0;
88	>
89	>	vector<Component*> components = simParams->getComponents();
90	>
91	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
92	>	molStamp = (*i)->getMoleculeStamp();
93	>	nMolWithSameStamp = (*i)->getNMol();
94	>
95	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
96	>
97	>	//calculate atoms in molecules
98	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
99	>
100	>	//calculate atoms in cutoff groups
101	>	int nAtomsInGroups = 0;
102	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
103	>
104	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
105	>	cgStamp = molStamp->getCutoffGroupStamp(j);
106	>	nAtomsInGroups += cgStamp->getNMembers();
107		}
108	<
109	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
110	<	//therefore the total number of cutoff groups in the system is equal to
111	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
112	<	//file plus the number of cutoff groups defined in meta-data file
113	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
114	<
115	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
116	<	//therefore the total number of  integrable objects in the system is equal to
117	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
118	<	//file plus the number of  rigid bodies defined in meta-data file
119	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
120	<
121	<	nGlobalMols_ = molStampIds_.size();
122	<
123	<	#ifdef IS_MPI
124	<	molToProcMap_.resize(nGlobalMols_);
142	<	#endif
143	<
108	>
109	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
110	>
111	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
112	>
113	>	//calculate atoms in rigid bodies
114	>	int nAtomsInRigidBodies = 0;
115	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
116	>
117	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
118	>	rbStamp = molStamp->getRigidBodyStamp(j);
119	>	nAtomsInRigidBodies += rbStamp->getNMembers();
120	>	}
121	>
122	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
123	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
124	>
125		}
126	+
127	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
128	+	//group therefore the total number of cutoff groups in the system is
129	+	//equal to the total number of atoms minus number of atoms belong to
130	+	//cutoff group defined in meta-data file plus the number of cutoff
131	+	//groups defined in meta-data file
132
133	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134	+
135	+	//every free atom (atom does not belong to rigid bodies) is an
136	+	//integrable object therefore the total number of integrable objects
137	+	//in the system is equal to the total number of atoms minus number of
138	+	//atoms belong to rigid body defined in meta-data file plus the number
139	+	//of rigid bodies defined in meta-data file
140	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
141	+	+ nGlobalRigidBodies_;
142	+
143	+	nGlobalMols_ = molStampIds_.size();
144	+	molToProcMap_.resize(nGlobalMols_);
145	+	}
146	+
147		SimInfo::~SimInfo() {
148	<	std::map<int, Molecule*>::iterator i;
148	>	map<int, Molecule*>::iterator i;
149		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
150		delete i->second;
151		}
152		molecules_.clear();
153
153	–	delete stamps_;
154		delete sman_;
155		delete simParams_;
156		delete forceField_;
157		}
158
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	–	}
159
160		bool SimInfo::addMolecule(Molecule* mol) {
161		MoleculeIterator i;
162	<
162	>
163		i = molecules_.find(mol->getGlobalIndex());
164		if (i == molecules_.end() ) {
165	<
166	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
167	<
165	>
166	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
167	>
168		nAtoms_ += mol->getNAtoms();
169		nBonds_ += mol->getNBonds();
170		nBends_ += mol->getNBends();
171		nTorsions_ += mol->getNTorsions();
172	+	nInversions_ += mol->getNInversions();
173		nRigidBodies_ += mol->getNRigidBodies();
174		nIntegrableObjects_ += mol->getNIntegrableObjects();
175		nCutoffGroups_ += mol->getNCutoffGroups();
176		nConstraints_ += mol->getNConstraintPairs();
177	<
178	<	addExcludePairs(mol);
179	<
177	>
178	>	addInteractionPairs(mol);
179	>
180		return true;
181		} else {
182		return false;
183		}
184		}
185	<
185	>
186		bool SimInfo::removeMolecule(Molecule* mol) {
187		MoleculeIterator i;
188		i = molecules_.find(mol->getGlobalIndex());
#	Line 204 | Line 195 | namespace oopse {
195		nBonds_ -= mol->getNBonds();
196		nBends_ -= mol->getNBends();
197		nTorsions_ -= mol->getNTorsions();
198	+	nInversions_ -= mol->getNInversions();
199		nRigidBodies_ -= mol->getNRigidBodies();
200		nIntegrableObjects_ -= mol->getNIntegrableObjects();
201		nCutoffGroups_ -= mol->getNCutoffGroups();
202		nConstraints_ -= mol->getNConstraintPairs();
203
204	<	removeExcludePairs(mol);
204	>	removeInteractionPairs(mol);
205		molecules_.erase(mol->getGlobalIndex());
206
207		delete mol;
#	Line 218 | Line 210 | namespace oopse {
210		} else {
211		return false;
212		}
221	–
222	–
213		}
214
215
#	Line 235 | Line 225 | namespace oopse {
225
226
227		void SimInfo::calcNdf() {
228	<	int ndf_local;
228	>	int ndf_local, nfq_local;
229		MoleculeIterator i;
230	<	std::vector<StuntDouble*>::iterator j;
230	>	vector<StuntDouble*>::iterator j;
231	>	vector<Atom*>::iterator k;
232	>
233		Molecule* mol;
234		StuntDouble* integrableObject;
235	+	Atom* atom;
236
237		ndf_local = 0;
238	+	nfq_local = 0;
239
240		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
241		for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
#	Line 256 | Line 250 | namespace oopse {
250		ndf_local += 3;
251		}
252		}
253	<
254	<	}//end for (integrableObject)
255	<	}// end for (mol)
253	>	}
254	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
255	>	atom = mol->nextFluctuatingCharge(k)) {
256	>	if (atom->isFluctuatingCharge()) {
257	>	nfq_local++;
258	>	}
259	>	}
260	>	}
261
262	+	ndfLocal_ = ndf_local;
263	+	cerr << "ndfLocal_ = " << ndfLocal_ << "\n";
264	+
265		// n_constraints is local, so subtract them on each processor
266		ndf_local -= nConstraints_;
267
268		#ifdef IS_MPI
269		MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
270	+	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
271		#else
272		ndf_ = ndf_local;
273	+	nGlobalFluctuatingCharges_ = nfq_local;
274		#endif
275
276		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 275 | Line 279 | namespace oopse {
279
280		}
281
282	+	int SimInfo::getFdf() {
283	+	#ifdef IS_MPI
284	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
285	+	#else
286	+	fdf_ = fdf_local;
287	+	#endif
288	+	return fdf_;
289	+	}
290	+
291	+	unsigned int SimInfo::getNLocalCutoffGroups(){
292	+	int nLocalCutoffAtoms = 0;
293	+	Molecule* mol;
294	+	MoleculeIterator mi;
295	+	CutoffGroup* cg;
296	+	Molecule::CutoffGroupIterator ci;
297	+
298	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
299	+
300	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
301	+	cg = mol->nextCutoffGroup(ci)) {
302	+	nLocalCutoffAtoms += cg->getNumAtom();
303	+
304	+	}
305	+	}
306	+
307	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
308	+	}
309	+
310		void SimInfo::calcNdfRaw() {
311		int ndfRaw_local;
312
313		MoleculeIterator i;
314	<	std::vector<StuntDouble*>::iterator j;
314	>	vector<StuntDouble*>::iterator j;
315		Molecule* mol;
316		StuntDouble* integrableObject;
317
#	Line 326 | Line 358 | namespace oopse {
358
359		}
360
361	<	void SimInfo::addExcludePairs(Molecule* mol) {
362	<	std::vector<Bond*>::iterator bondIter;
363	<	std::vector<Bend*>::iterator bendIter;
364	<	std::vector<Torsion*>::iterator torsionIter;
361	>	void SimInfo::addInteractionPairs(Molecule* mol) {
362	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
363	>	vector<Bond*>::iterator bondIter;
364	>	vector<Bend*>::iterator bendIter;
365	>	vector<Torsion*>::iterator torsionIter;
366	>	vector<Inversion*>::iterator inversionIter;
367		Bond* bond;
368		Bend* bend;
369		Torsion* torsion;
370	+	Inversion* inversion;
371		int a;
372		int b;
373		int c;
374		int d;
375	+
376	+	// atomGroups can be used to add special interaction maps between
377	+	// groups of atoms that are in two separate rigid bodies.
378	+	// However, most site-site interactions between two rigid bodies
379	+	// are probably not special, just the ones between the physically
380	+	// bonded atoms.  Interactions *within* a single rigid body should
381	+	// always be excluded.  These are done at the bottom of this
382	+	// function.
383	+
384	+	map<int, set<int> > atomGroups;
385	+	Molecule::RigidBodyIterator rbIter;
386	+	RigidBody* rb;
387	+	Molecule::IntegrableObjectIterator ii;
388	+	StuntDouble* integrableObject;
389
390	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
390	>	for (integrableObject = mol->beginIntegrableObject(ii);
391	>	integrableObject != NULL;
392	>	integrableObject = mol->nextIntegrableObject(ii)) {
393	>
394	>	if (integrableObject->isRigidBody()) {
395	>	rb = static_cast<RigidBody*>(integrableObject);
396	>	vector<Atom*> atoms = rb->getAtoms();
397	>	set<int> rigidAtoms;
398	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
399	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
400	>	}
401	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
402	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
403	>	}
404	>	} else {
405	>	set<int> oneAtomSet;
406	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
407	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
408	>	}
409	>	}
410	>
411	>	for (bond= mol->beginBond(bondIter); bond != NULL;
412	>	bond = mol->nextBond(bondIter)) {
413	>
414		a = bond->getAtomA()->getGlobalIndex();
415	<	b = bond->getAtomB()->getGlobalIndex();
416	<	exclude_.addPair(a, b);
415	>	b = bond->getAtomB()->getGlobalIndex();
416	>
417	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
418	>	oneTwoInteractions_.addPair(a, b);
419	>	} else {
420	>	excludedInteractions_.addPair(a, b);
421	>	}
422		}
423
424	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
424	>	for (bend= mol->beginBend(bendIter); bend != NULL;
425	>	bend = mol->nextBend(bendIter)) {
426	>
427		a = bend->getAtomA()->getGlobalIndex();
428		b = bend->getAtomB()->getGlobalIndex();
429		c = bend->getAtomC()->getGlobalIndex();
430	<
431	<	exclude_.addPair(a, b);
432	<	exclude_.addPair(a, c);
433	<	exclude_.addPair(b, c);
430	>
431	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
432	>	oneTwoInteractions_.addPair(a, b);
433	>	oneTwoInteractions_.addPair(b, c);
434	>	} else {
435	>	excludedInteractions_.addPair(a, b);
436	>	excludedInteractions_.addPair(b, c);
437	>	}
438	>
439	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
440	>	oneThreeInteractions_.addPair(a, c);
441	>	} else {
442	>	excludedInteractions_.addPair(a, c);
443	>	}
444		}
445
446	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
446	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
447	>	torsion = mol->nextTorsion(torsionIter)) {
448	>
449		a = torsion->getAtomA()->getGlobalIndex();
450		b = torsion->getAtomB()->getGlobalIndex();
451		c = torsion->getAtomC()->getGlobalIndex();
452	<	d = torsion->getAtomD()->getGlobalIndex();
452	>	d = torsion->getAtomD()->getGlobalIndex();
453
454	<	exclude_.addPair(a, b);
455	<	exclude_.addPair(a, c);
456	<	exclude_.addPair(a, d);
457	<	exclude_.addPair(b, c);
458	<	exclude_.addPair(b, d);
459	<	exclude_.addPair(c, d);
454	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
455	>	oneTwoInteractions_.addPair(a, b);
456	>	oneTwoInteractions_.addPair(b, c);
457	>	oneTwoInteractions_.addPair(c, d);
458	>	} else {
459	>	excludedInteractions_.addPair(a, b);
460	>	excludedInteractions_.addPair(b, c);
461	>	excludedInteractions_.addPair(c, d);
462	>	}
463	>
464	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
465	>	oneThreeInteractions_.addPair(a, c);
466	>	oneThreeInteractions_.addPair(b, d);
467	>	} else {
468	>	excludedInteractions_.addPair(a, c);
469	>	excludedInteractions_.addPair(b, d);
470	>	}
471	>
472	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
473	>	oneFourInteractions_.addPair(a, d);
474	>	} else {
475	>	excludedInteractions_.addPair(a, d);
476	>	}
477		}
478
479	<	Molecule::RigidBodyIterator rbIter;
480	<	RigidBody* rb;
481	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
482	<	std::vector<Atom*> atoms = rb->getAtoms();
483	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
484	<	for (int j = i + 1; j < atoms.size(); ++j) {
479	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
480	>	inversion = mol->nextInversion(inversionIter)) {
481	>
482	>	a = inversion->getAtomA()->getGlobalIndex();
483	>	b = inversion->getAtomB()->getGlobalIndex();
484	>	c = inversion->getAtomC()->getGlobalIndex();
485	>	d = inversion->getAtomD()->getGlobalIndex();
486	>
487	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
488	>	oneTwoInteractions_.addPair(a, b);
489	>	oneTwoInteractions_.addPair(a, c);
490	>	oneTwoInteractions_.addPair(a, d);
491	>	} else {
492	>	excludedInteractions_.addPair(a, b);
493	>	excludedInteractions_.addPair(a, c);
494	>	excludedInteractions_.addPair(a, d);
495	>	}
496	>
497	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
498	>	oneThreeInteractions_.addPair(b, c);
499	>	oneThreeInteractions_.addPair(b, d);
500	>	oneThreeInteractions_.addPair(c, d);
501	>	} else {
502	>	excludedInteractions_.addPair(b, c);
503	>	excludedInteractions_.addPair(b, d);
504	>	excludedInteractions_.addPair(c, d);
505	>	}
506	>	}
507	>
508	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
509	>	rb = mol->nextRigidBody(rbIter)) {
510	>	vector<Atom*> atoms = rb->getAtoms();
511	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
512	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
513		a = atoms[i]->getGlobalIndex();
514		b = atoms[j]->getGlobalIndex();
515	<	exclude_.addPair(a, b);
515	>	excludedInteractions_.addPair(a, b);
516		}
517		}
518		}
519
520		}
521
522	<	void SimInfo::removeExcludePairs(Molecule* mol) {
523	<	std::vector<Bond*>::iterator bondIter;
524	<	std::vector<Bend*>::iterator bendIter;
525	<	std::vector<Torsion*>::iterator torsionIter;
522	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
523	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
524	>	vector<Bond*>::iterator bondIter;
525	>	vector<Bend*>::iterator bendIter;
526	>	vector<Torsion*>::iterator torsionIter;
527	>	vector<Inversion*>::iterator inversionIter;
528		Bond* bond;
529		Bend* bend;
530		Torsion* torsion;
531	+	Inversion* inversion;
532		int a;
533		int b;
534		int c;
535		int d;
536	+
537	+	map<int, set<int> > atomGroups;
538	+	Molecule::RigidBodyIterator rbIter;
539	+	RigidBody* rb;
540	+	Molecule::IntegrableObjectIterator ii;
541	+	StuntDouble* integrableObject;
542
543	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
543	>	for (integrableObject = mol->beginIntegrableObject(ii);
544	>	integrableObject != NULL;
545	>	integrableObject = mol->nextIntegrableObject(ii)) {
546	>
547	>	if (integrableObject->isRigidBody()) {
548	>	rb = static_cast<RigidBody*>(integrableObject);
549	>	vector<Atom*> atoms = rb->getAtoms();
550	>	set<int> rigidAtoms;
551	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
552	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
553	>	}
554	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
555	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
556	>	}
557	>	} else {
558	>	set<int> oneAtomSet;
559	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
560	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
561	>	}
562	>	}
563	>
564	>	for (bond= mol->beginBond(bondIter); bond != NULL;
565	>	bond = mol->nextBond(bondIter)) {
566	>
567		a = bond->getAtomA()->getGlobalIndex();
568	<	b = bond->getAtomB()->getGlobalIndex();
569	<	exclude_.removePair(a, b);
568	>	b = bond->getAtomB()->getGlobalIndex();
569	>
570	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
571	>	oneTwoInteractions_.removePair(a, b);
572	>	} else {
573	>	excludedInteractions_.removePair(a, b);
574	>	}
575		}
576
577	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
577	>	for (bend= mol->beginBend(bendIter); bend != NULL;
578	>	bend = mol->nextBend(bendIter)) {
579	>
580		a = bend->getAtomA()->getGlobalIndex();
581		b = bend->getAtomB()->getGlobalIndex();
582		c = bend->getAtomC()->getGlobalIndex();
583	+
584	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
585	+	oneTwoInteractions_.removePair(a, b);
586	+	oneTwoInteractions_.removePair(b, c);
587	+	} else {
588	+	excludedInteractions_.removePair(a, b);
589	+	excludedInteractions_.removePair(b, c);
590	+	}
591
592	<	exclude_.removePair(a, b);
593	<	exclude_.removePair(a, c);
594	<	exclude_.removePair(b, c);
592	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
593	>	oneThreeInteractions_.removePair(a, c);
594	>	} else {
595	>	excludedInteractions_.removePair(a, c);
596	>	}
597		}
598
599	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
599	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
600	>	torsion = mol->nextTorsion(torsionIter)) {
601	>
602		a = torsion->getAtomA()->getGlobalIndex();
603		b = torsion->getAtomB()->getGlobalIndex();
604		c = torsion->getAtomC()->getGlobalIndex();
605	<	d = torsion->getAtomD()->getGlobalIndex();
605	>	d = torsion->getAtomD()->getGlobalIndex();
606	>
607	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
608	>	oneTwoInteractions_.removePair(a, b);
609	>	oneTwoInteractions_.removePair(b, c);
610	>	oneTwoInteractions_.removePair(c, d);
611	>	} else {
612	>	excludedInteractions_.removePair(a, b);
613	>	excludedInteractions_.removePair(b, c);
614	>	excludedInteractions_.removePair(c, d);
615	>	}
616
617	<	exclude_.removePair(a, b);
618	<	exclude_.removePair(a, c);
619	<	exclude_.removePair(a, d);
620	<	exclude_.removePair(b, c);
621	<	exclude_.removePair(b, d);
622	<	exclude_.removePair(c, d);
617	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
618	>	oneThreeInteractions_.removePair(a, c);
619	>	oneThreeInteractions_.removePair(b, d);
620	>	} else {
621	>	excludedInteractions_.removePair(a, c);
622	>	excludedInteractions_.removePair(b, d);
623	>	}
624	>
625	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
626	>	oneFourInteractions_.removePair(a, d);
627	>	} else {
628	>	excludedInteractions_.removePair(a, d);
629	>	}
630		}
631
632	<	Molecule::RigidBodyIterator rbIter;
633	<	RigidBody* rb;
634	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
635	<	std::vector<Atom*> atoms = rb->getAtoms();
636	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
637	<	for (int j = i + 1; j < atoms.size(); ++j) {
632	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
633	>	inversion = mol->nextInversion(inversionIter)) {
634	>
635	>	a = inversion->getAtomA()->getGlobalIndex();
636	>	b = inversion->getAtomB()->getGlobalIndex();
637	>	c = inversion->getAtomC()->getGlobalIndex();
638	>	d = inversion->getAtomD()->getGlobalIndex();
639	>
640	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
641	>	oneTwoInteractions_.removePair(a, b);
642	>	oneTwoInteractions_.removePair(a, c);
643	>	oneTwoInteractions_.removePair(a, d);
644	>	} else {
645	>	excludedInteractions_.removePair(a, b);
646	>	excludedInteractions_.removePair(a, c);
647	>	excludedInteractions_.removePair(a, d);
648	>	}
649	>
650	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
651	>	oneThreeInteractions_.removePair(b, c);
652	>	oneThreeInteractions_.removePair(b, d);
653	>	oneThreeInteractions_.removePair(c, d);
654	>	} else {
655	>	excludedInteractions_.removePair(b, c);
656	>	excludedInteractions_.removePair(b, d);
657	>	excludedInteractions_.removePair(c, d);
658	>	}
659	>	}
660	>
661	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
662	>	rb = mol->nextRigidBody(rbIter)) {
663	>	vector<Atom*> atoms = rb->getAtoms();
664	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
665	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
666		a = atoms[i]->getGlobalIndex();
667		b = atoms[j]->getGlobalIndex();
668	<	exclude_.removePair(a, b);
668	>	excludedInteractions_.removePair(a, b);
669		}
670		}
671		}
672	<
672	>
673		}
674	<
675	<
674	>
675	>
676		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
677		int curStampId;
678	<
678	>
679		//index from 0
680		curStampId = moleculeStamps_.size();
681
#	Line 451 | Line 683 | namespace oopse {
683		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
684		}
685
454	–	void SimInfo::update() {
686
687	<	setupSimType();
688	<
689	<	#ifdef IS_MPI
690	<	setupFortranParallel();
691	<	#endif
692	<
693	<	setupFortranSim();
694	<
695	<	//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	<
687	>	/**
688	>	* update
689	>	*
690	>	*  Performs the global checks and variable settings after the
691	>	*  objects have been created.
692	>	*
693	>	*/
694	>	void SimInfo::update() {
695	>	setupSimVariables();
696		calcNdf();
697		calcNdfRaw();
698		calcNdfTrans();
483	–
484	–	fortranInitialized_ = true;
699		}
700	<
701	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
700	>
701	>	/**
702	>	* getSimulatedAtomTypes
703	>	*
704	>	* Returns an STL set of AtomType* that are actually present in this
705	>	* simulation.  Must query all processors to assemble this information.
706	>	*
707	>	*/
708	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
709		SimInfo::MoleculeIterator mi;
710		Molecule* mol;
711		Molecule::AtomIterator ai;
712		Atom* atom;
713	<	std::set<AtomType*> atomTypes;
714	<
713	>	set<AtomType*> atomTypes;
714	>
715		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
716	<
717	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
716	>	for(atom = mol->beginAtom(ai); atom != NULL;
717	>	atom = mol->nextAtom(ai)) {
718		atomTypes.insert(atom->getAtomType());
719	<	}
720	<
719	>	}
720	>	}
721	>
722	>	#ifdef IS_MPI
723	>
724	>	// loop over the found atom types on this processor, and add their
725	>	// numerical idents to a vector:
726	>
727	>	vector<int> foundTypes;
728	>	set<AtomType*>::iterator i;
729	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
730	>	foundTypes.push_back( (*i)->getIdent() );
731	>
732	>	// count_local holds the number of found types on this processor
733	>	int count_local = foundTypes.size();
734	>
735	>	int nproc = MPI::COMM_WORLD.Get_size();
736	>
737	>	// we need arrays to hold the counts and displacement vectors for
738	>	// all processors
739	>	vector<int> counts(nproc, 0);
740	>	vector<int> disps(nproc, 0);
741	>
742	>	// fill the counts array
743	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
744	>	1, MPI::INT);
745	>
746	>	// use the processor counts to compute the displacement array
747	>	disps[0] = 0;
748	>	int totalCount = counts[0];
749	>	for (int iproc = 1; iproc < nproc; iproc++) {
750	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
751	>	totalCount += counts[iproc];
752		}
753
754	+	// we need a (possibly redundant) set of all found types:
755	+	vector<int> ftGlobal(totalCount);
756	+
757	+	// now spray out the foundTypes to all the other processors:
758	+	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
759	+	&ftGlobal[0], &counts[0], &disps[0],
760	+	MPI::INT);
761	+
762	+	vector<int>::iterator j;
763	+
764	+	// foundIdents is a stl set, so inserting an already found ident
765	+	// will have no effect.
766	+	set<int> foundIdents;
767	+
768	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
769	+	foundIdents.insert((*j));
770	+
771	+	// now iterate over the foundIdents and get the actual atom types
772	+	// that correspond to these:
773	+	set<int>::iterator it;
774	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
775	+	atomTypes.insert( forceField_->getAtomType((*it)) );
776	+
777	+	#endif
778	+
779		return atomTypes;
780		}
781
782	<	void SimInfo::setupSimType() {
783	<	std::set<AtomType*>::iterator i;
784	<	std::set<AtomType*> atomTypes;
785	<	atomTypes = getUniqueAtomTypes();
782	>	void SimInfo::setupSimVariables() {
783	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
784	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
785	>	calcBoxDipole_ = false;
786	>	if ( simParams_->haveAccumulateBoxDipole() )
787	>	if ( simParams_->getAccumulateBoxDipole() ) {
788	>	calcBoxDipole_ = true;
789	>	}
790
791	<	int useLennardJones = 0;
792	<	int useElectrostatic = 0;
793	<	int useEAM = 0;
794	<	int useCharge = 0;
795	<	int useDirectional = 0;
796	<	int useDipole = 0;
797	<	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	<
791	>	set<AtomType*>::iterator i;
792	>	set<AtomType*> atomTypes;
793	>	atomTypes = getSimulatedAtomTypes();
794	>	int usesElectrostatic = 0;
795	>	int usesMetallic = 0;
796	>	int usesDirectional = 0;
797	>	int usesFluctuatingCharges =  0;
798		//loop over all of the atom types
799		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
800	<	useLennardJones |= (*i)->isLennardJones();
801	<	useElectrostatic |= (*i)->isElectrostatic();
802	<	useEAM |= (*i)->isEAM();
803	<	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();
800	>	usesElectrostatic |= (*i)->isElectrostatic();
801	>	usesMetallic |= (*i)->isMetal();
802	>	usesDirectional |= (*i)->isDirectional();
803	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
804		}
805	<
540	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
541	<	useDirectionalAtom = 1;
542	<	}
543	<
544	<	if (useCharge || useDipole) {
545	<	useElectrostatics = 1;
546	<	}
547	<
805	>
806		#ifdef IS_MPI
807		int temp;
808	<
809	<	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);
808	>	temp = usesDirectional;
809	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810
811	<	temp = useGayBerne;
812	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
811	>	temp = usesMetallic;
812	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813	>
814	>	temp = usesElectrostatic;
815	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816
817	<	temp = useEAM;
818	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
817	>	temp = usesFluctuatingCharges;
818	>	MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819	>	#else
820
821	<	temp = useShape;
822	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
821	>	usesDirectionalAtoms_ = usesDirectional;
822	>	usesMetallicAtoms_ = usesMetallic;
823	>	usesElectrostaticAtoms_ = usesElectrostatic;
824	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
825
584	–	temp = useFLARB;
585	–	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
586	–
826		#endif
827	+
828	+	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
829	+	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
830	+	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
831	+	}
832
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;
833
834	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
834	>	vector<int> SimInfo::getGlobalAtomIndices() {
835	>	SimInfo::MoleculeIterator mi;
836	>	Molecule* mol;
837	>	Molecule::AtomIterator ai;
838	>	Atom* atom;
839
840	<	if (simParams_->haveDielectric()) {
841	<	fInfo_.dielect = simParams_->getDielectric();
842	<	} else {
843	<	sprintf(painCave.errMsg,
844	<	"SimSetup Error: No Dielectric constant was set.\n"
845	<	"\tYou are trying to use Reaction Field without"
610	<	"\tsetting a dielectric constant!\n");
611	<	painCave.isFatal = 1;
612	<	simError();
840	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
841	>
842	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
843	>
844	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
845	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
846		}
614	–
615	–	} else {
616	–	fInfo_.dielect = 0.0;
847		}
848	<
848	>	return GlobalAtomIndices;
849		}
850
621	–	void SimInfo::setupFortranSim() {
622	–	int isError;
623	–	int nExclude;
624	–	std::vector<int> fortranGlobalGroupMembership;
625	–
626	–	nExclude = exclude_.getSize();
627	–	isError = 0;
851
852	<	//globalGroupMembership_ is filled by SimCreator
853	<	for (int i = 0; i < nGlobalAtoms_; i++) {
854	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
852	>	vector<int> SimInfo::getGlobalGroupIndices() {
853	>	SimInfo::MoleculeIterator mi;
854	>	Molecule* mol;
855	>	Molecule::CutoffGroupIterator ci;
856	>	CutoffGroup* cg;
857	>
858	>	vector<int> GlobalGroupIndices;
859	>
860	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
861	>
862	>	//local index of cutoff group is trivial, it only depends on the
863	>	//order of travesing
864	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
865	>	cg = mol->nextCutoffGroup(ci)) {
866	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
867	>	}
868		}
869	+	return GlobalGroupIndices;
870	+	}
871
872	+
873	+	void SimInfo::prepareTopology() {
874	+	int nExclude, nOneTwo, nOneThree, nOneFour;
875	+
876		//calculate mass ratio of cutoff group
635	–	std::vector<double> mfact;
877		SimInfo::MoleculeIterator mi;
878		Molecule* mol;
879		Molecule::CutoffGroupIterator ci;
880		CutoffGroup* cg;
881		Molecule::AtomIterator ai;
882		Atom* atom;
883	<	double totalMass;
883	>	RealType totalMass;
884
885	<	//to avoid memory reallocation, reserve enough space for mfact
886	<	mfact.reserve(getNCutoffGroups());
885	>	/**
886	>	* The mass factor is the relative mass of an atom to the total
887	>	* mass of the cutoff group it belongs to.  By default, all atoms
888	>	* are their own cutoff groups, and therefore have mass factors of
889	>	* 1.  We need some special handling for massless atoms, which
890	>	* will be treated as carrying the entire mass of the cutoff
891	>	* group.
892	>	*/
893	>	massFactors_.clear();
894	>	massFactors_.resize(getNAtoms(), 1.0);
895
896		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
897	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
897	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
898	>	cg = mol->nextCutoffGroup(ci)) {
899
900		totalMass = cg->getMass();
901		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
902	<	mfact.push_back(atom->getMass()/totalMass);
902	>	// Check for massless groups - set mfact to 1 if true
903	>	if (totalMass != 0)
904	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
905	>	else
906	>	massFactors_[atom->getLocalIndex()] = 1.0;
907		}
654	–
908		}
909		}
910
911	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
659	<	std::vector<int> identArray;
911	>	// Build the identArray_
912
913	<	//to avoid memory reallocation, reserve enough space identArray
914	<	identArray.reserve(getNAtoms());
663	<
913	>	identArray_.clear();
914	>	identArray_.reserve(getNAtoms());
915		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
916		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
917	<	identArray.push_back(atom->getIdent());
917	>	identArray_.push_back(atom->getIdent());
918		}
919		}
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	–	}
920
921	<	//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);
921	>	//scan topology
922
923	<	if( isError ){
923	>	nExclude = excludedInteractions_.getSize();
924	>	nOneTwo = oneTwoInteractions_.getSize();
925	>	nOneThree = oneThreeInteractions_.getSize();
926	>	nOneFour = oneFourInteractions_.getSize();
927
928	<	sprintf( painCave.errMsg,
929	<	"There was an error setting the simulation information in fortran.\n" );
930	<	painCave.isFatal = 1;
931	<	painCave.severity = OOPSE_ERROR;
691	<	simError();
692	<	}
928	>	int* excludeList = excludedInteractions_.getPairList();
929	>	int* oneTwoList = oneTwoInteractions_.getPairList();
930	>	int* oneThreeList = oneThreeInteractions_.getPairList();
931	>	int* oneFourList = oneFourInteractions_.getPairList();
932
933	<	#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));
740	<
741	<	//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( &esm, &alphaVal, &errorOut );
933	>	topologyDone_ = true;
934		}
935
936		void SimInfo::addProperty(GenericData* genData) {
937		properties_.addProperty(genData);
938		}
939
940	<	void SimInfo::removeProperty(const std::string& propName) {
940	>	void SimInfo::removeProperty(const string& propName) {
941		properties_.removeProperty(propName);
942		}
943
#	Line 914 | Line 945 | namespace oopse {
945		properties_.clearProperties();
946		}
947
948	<	std::vector<std::string> SimInfo::getPropertyNames() {
948	>	vector<string> SimInfo::getPropertyNames() {
949		return properties_.getPropertyNames();
950		}
951
952	<	std::vector<GenericData*> SimInfo::getProperties() {
952	>	vector<GenericData*> SimInfo::getProperties() {
953		return properties_.getProperties();
954		}
955
956	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
956	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
957		return properties_.getPropertyByName(propName);
958		}
959
#	Line 936 | Line 967 | namespace oopse {
967		Molecule* mol;
968		RigidBody* rb;
969		Atom* atom;
970	+	CutoffGroup* cg;
971		SimInfo::MoleculeIterator mi;
972		Molecule::RigidBodyIterator rbIter;
973	<	Molecule::AtomIterator atomIter;;
973	>	Molecule::AtomIterator atomIter;
974	>	Molecule::CutoffGroupIterator cgIter;
975
976		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
977
#	Line 949 | Line 982 | namespace oopse {
982		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
983		rb->setSnapshotManager(sman_);
984		}
985	+
986	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
987	+	cg->setSnapshotManager(sman_);
988	+	}
989		}
990
991		}
#	Line 958 | Line 995 | namespace oopse {
995		Molecule* mol;
996
997		Vector3d comVel(0.0);
998	<	double totalMass = 0.0;
998	>	RealType totalMass = 0.0;
999
1000
1001		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1002	<	double mass = mol->getMass();
1002	>	RealType mass = mol->getMass();
1003		totalMass += mass;
1004		comVel += mass * mol->getComVel();
1005		}
1006
1007		#ifdef IS_MPI
1008	<	double tmpMass = totalMass;
1008	>	RealType tmpMass = totalMass;
1009		Vector3d tmpComVel(comVel);
1010	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1011	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1010	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1011	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1012		#endif
1013
1014		comVel /= totalMass;
#	Line 984 | Line 1021 | namespace oopse {
1021		Molecule* mol;
1022
1023		Vector3d com(0.0);
1024	<	double totalMass = 0.0;
1024	>	RealType totalMass = 0.0;
1025
1026		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1027	<	double mass = mol->getMass();
1027	>	RealType mass = mol->getMass();
1028		totalMass += mass;
1029		com += mass * mol->getCom();
1030		}
1031
1032		#ifdef IS_MPI
1033	<	double tmpMass = totalMass;
1033	>	RealType tmpMass = totalMass;
1034		Vector3d tmpCom(com);
1035	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1036	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1035	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1036	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1037		#endif
1038
1039		com /= totalMass;
#	Line 1005 | Line 1042 | namespace oopse {
1042
1043		}
1044
1045	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1045	>	ostream& operator <<(ostream& o, SimInfo& info) {
1046
1047		return o;
1048		}
#	Line 1020 | Line 1057 | namespace oopse {
1057		Molecule* mol;
1058
1059
1060	<	double totalMass = 0.0;
1060	>	RealType totalMass = 0.0;
1061
1062
1063		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1064	<	double mass = mol->getMass();
1064	>	RealType mass = mol->getMass();
1065		totalMass += mass;
1066		com += mass * mol->getCom();
1067		comVel += mass * mol->getComVel();
1068		}
1069
1070		#ifdef IS_MPI
1071	<	double tmpMass = totalMass;
1071	>	RealType tmpMass = totalMass;
1072		Vector3d tmpCom(com);
1073		Vector3d tmpComVel(comVel);
1074	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1075	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1076	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1074	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1075	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1076	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1077		#endif
1078
1079		com /= totalMass;
#	Line 1048 | Line 1085 | namespace oopse {
1085
1086
1087		[  Ixx -Ixy  -Ixz ]
1088	<	J =| -Iyx  Iyy  -Iyz |
1088	>	J =| -Iyx  Iyy  -Iyz |
1089		[ -Izx -Iyz   Izz ]
1090		*/
1091
1092		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1093
1094
1095	<	double xx = 0.0;
1096	<	double yy = 0.0;
1097	<	double zz = 0.0;
1098	<	double xy = 0.0;
1099	<	double xz = 0.0;
1100	<	double yz = 0.0;
1095	>	RealType xx = 0.0;
1096	>	RealType yy = 0.0;
1097	>	RealType zz = 0.0;
1098	>	RealType xy = 0.0;
1099	>	RealType xz = 0.0;
1100	>	RealType yz = 0.0;
1101		Vector3d com(0.0);
1102		Vector3d comVel(0.0);
1103
#	Line 1072 | Line 1109 | namespace oopse {
1109		Vector3d thisq(0.0);
1110		Vector3d thisv(0.0);
1111
1112	<	double thisMass = 0.0;
1112	>	RealType thisMass = 0.0;
1113
1114
1115
#	Line 1110 | Line 1147 | namespace oopse {
1147		#ifdef IS_MPI
1148		Mat3x3d tmpI(inertiaTensor);
1149		Vector3d tmpAngMom;
1150	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1151	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1150	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1151	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1152		#endif
1153
1154		return;
#	Line 1132 | Line 1169 | namespace oopse {
1169		Vector3d thisr(0.0);
1170		Vector3d thisp(0.0);
1171
1172	<	double thisMass;
1172	>	RealType thisMass;
1173
1174		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1175		thisMass = mol->getMass();
#	Line 1145 | Line 1182 | namespace oopse {
1182
1183		#ifdef IS_MPI
1184		Vector3d tmpAngMom;
1185	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1185	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1186		#endif
1187
1188		return angularMomentum;
1189		}
1190
1191	<
1192	<	}//end namespace oopse
1191	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1192	>	return IOIndexToIntegrableObject.at(index);
1193	>	}
1194	>
1195	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1196	>	IOIndexToIntegrableObject= v;
1197	>	}
1198
1199	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1200	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1201	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1202	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1203	+	*/
1204	+	void SimInfo::getGyrationalVolume(RealType &volume){
1205	+	Mat3x3d intTensor;
1206	+	RealType det;
1207	+	Vector3d dummyAngMom;
1208	+	RealType sysconstants;
1209	+	RealType geomCnst;
1210	+
1211	+	geomCnst = 3.0/2.0;
1212	+	/* Get the inertial tensor and angular momentum for free*/
1213	+	getInertiaTensor(intTensor,dummyAngMom);
1214	+
1215	+	det = intTensor.determinant();
1216	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1217	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1218	+	return;
1219	+	}
1220	+
1221	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1222	+	Mat3x3d intTensor;
1223	+	Vector3d dummyAngMom;
1224	+	RealType sysconstants;
1225	+	RealType geomCnst;
1226	+
1227	+	geomCnst = 3.0/2.0;
1228	+	/* Get the inertial tensor and angular momentum for free*/
1229	+	getInertiaTensor(intTensor,dummyAngMom);
1230	+
1231	+	detI = intTensor.determinant();
1232	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1233	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1234	+	return;
1235	+	}
1236	+	/*
1237	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1238	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1239	+	sdByGlobalIndex_ = v;
1240	+	}
1241	+
1242	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1243	+	//assert(index < nAtoms_ + nRigidBodies_);
1244	+	return sdByGlobalIndex_.at(index);
1245	+	}
1246	+	*/
1247	+	int SimInfo::getNGlobalConstraints() {
1248	+	int nGlobalConstraints;
1249	+	#ifdef IS_MPI
1250	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1251	+	MPI_COMM_WORLD);
1252	+	#else
1253	+	nGlobalConstraints =  nConstraints_;
1254	+	#endif
1255	+	return nGlobalConstraints;
1256	+	}
1257	+
1258	+	}//end namespace OpenMD
1259	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 608 by chrisfen, Fri Sep 16 21:07:45 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1744 by gezelter, Tue Jun 5 18:07:08 2012 UTC

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