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root/OpenMD/trunk/src/brains/SimInfo.cpp

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 555 by chuckv, Mon May 30 14:01:52 2005 UTC vs.
Revision 1929 by gezelter, Mon Aug 19 13:12:00 2013 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 48 | Line 49
49
50		#include <algorithm>
51		#include <set>
52	+	#include <map>
53
54		#include "brains/SimInfo.hpp"
55		#include "math/Vector3.hpp"
56		#include "primitives/Molecule.hpp"
57	<	#include "UseTheForce/doForces_interface.h"
56	<	#include "UseTheForce/notifyCutoffs_interface.h"
57	>	#include "primitives/StuntDouble.hpp"
58		#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60		#include "selection/SelectionManager.hpp"
61	<
61	>	#include "io/ForceFieldOptions.hpp"
62	>	#include "brains/ForceField.hpp"
63	>	#include "nonbonded/SwitchingFunction.hpp"
64		#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
64	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68	<	namespace oopse {
69	<
70	<	SimInfo::SimInfo(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	<
78	<
79	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
80	<	MoleculeStamp* molStamp;
81	<	int nMolWithSameStamp;
82	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
83	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
84	<	CutoffGroupStamp* cgStamp;
85	<	RigidBodyStamp* rbStamp;
86	<	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	<	}
106	<
107	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
108	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
109	<
110	<	//calculate atoms in rigid bodies
111	<	int nAtomsInRigidBodies = 0;
112	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
113	<
114	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
115	<	rbStamp = molStamp->getRigidBody(j);
116	<	nAtomsInRigidBodies += rbStamp->getNMembers();
117	<	}
118	<
119	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
120	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
121	<
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();
92	>	i !=components.end(); ++i) {
93	>	molStamp = (*i)->getMoleculeStamp();
94	>	if ( (*i)->haveRegion() ) {
95	>	molStamp->setRegion( (*i)->getRegion() );
96	>	} else {
97	>	// set the region to a disallowed value:
98	>	molStamp->setRegion( -1 );
99		}
100
101	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
102	<	//therefore the total number of cutoff groups in the system is equal to
103	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
104	<	//file plus the number of cutoff groups defined in meta-data file
105	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
106	<
107	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
108	<	//therefore the total number of  integrable objects in the system is equal to
109	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
110	<	//file plus the number of  rigid bodies defined in meta-data file
111	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
112	<
113	<	nGlobalMols_ = molStampIds_.size();
114	<
115	<	#ifdef IS_MPI
116	<	molToProcMap_.resize(nGlobalMols_);
117	<	#endif
118	<
101	>	nMolWithSameStamp = (*i)->getNMol();
102	>
103	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
104	>
105	>	//calculate atoms in molecules
106	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
107	>
108	>	//calculate atoms in cutoff groups
109	>	int nAtomsInGroups = 0;
110	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
111	>
112	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
113	>	cgStamp = molStamp->getCutoffGroupStamp(j);
114	>	nAtomsInGroups += cgStamp->getNMembers();
115	>	}
116	>
117	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
118	>
119	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
120	>
121	>	//calculate atoms in rigid bodies
122	>	int nAtomsInRigidBodies = 0;
123	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
124	>
125	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
126	>	rbStamp = molStamp->getRigidBodyStamp(j);
127	>	nAtomsInRigidBodies += rbStamp->getNMembers();
128	>	}
129	>
130	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
131	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
132	>
133		}
134	+
135	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
136	+	//group therefore the total number of cutoff groups in the system is
137	+	//equal to the total number of atoms minus number of atoms belong to
138	+	//cutoff group defined in meta-data file plus the number of cutoff
139	+	//groups defined in meta-data file
140
141	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
142	+
143	+	//every free atom (atom does not belong to rigid bodies) is an
144	+	//integrable object therefore the total number of integrable objects
145	+	//in the system is equal to the total number of atoms minus number of
146	+	//atoms belong to rigid body defined in meta-data file plus the number
147	+	//of rigid bodies defined in meta-data file
148	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
149	+	+ nGlobalRigidBodies_;
150	+
151	+	nGlobalMols_ = molStampIds_.size();
152	+	molToProcMap_.resize(nGlobalMols_);
153	+	}
154	+
155		SimInfo::~SimInfo() {
156	<	std::map<int, Molecule*>::iterator i;
156	>	map<int, Molecule*>::iterator i;
157		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
158		delete i->second;
159		}
160		molecules_.clear();
161
151	–	delete stamps_;
162		delete sman_;
163		delete simParams_;
164		delete forceField_;
165		}
166
157	–	int SimInfo::getNGlobalConstraints() {
158	–	int nGlobalConstraints;
159	–	#ifdef IS_MPI
160	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
161	–	MPI_COMM_WORLD);
162	–	#else
163	–	nGlobalConstraints =  nConstraints_;
164	–	#endif
165	–	return nGlobalConstraints;
166	–	}
167
168		bool SimInfo::addMolecule(Molecule* mol) {
169		MoleculeIterator i;
170	<
170	>
171		i = molecules_.find(mol->getGlobalIndex());
172		if (i == molecules_.end() ) {
173	<
174	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
175	<
173	>
174	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
175	>
176		nAtoms_ += mol->getNAtoms();
177		nBonds_ += mol->getNBonds();
178		nBends_ += mol->getNBends();
179		nTorsions_ += mol->getNTorsions();
180	+	nInversions_ += mol->getNInversions();
181		nRigidBodies_ += mol->getNRigidBodies();
182		nIntegrableObjects_ += mol->getNIntegrableObjects();
183		nCutoffGroups_ += mol->getNCutoffGroups();
184		nConstraints_ += mol->getNConstraintPairs();
185	<
186	<	addExcludePairs(mol);
187	<
185	>
186	>	addInteractionPairs(mol);
187	>
188		return true;
189		} else {
190		return false;
191		}
192		}
193	<
193	>
194		bool SimInfo::removeMolecule(Molecule* mol) {
195		MoleculeIterator i;
196		i = molecules_.find(mol->getGlobalIndex());
#	Line 202 | Line 203 | namespace oopse {
203		nBonds_ -= mol->getNBonds();
204		nBends_ -= mol->getNBends();
205		nTorsions_ -= mol->getNTorsions();
206	+	nInversions_ -= mol->getNInversions();
207		nRigidBodies_ -= mol->getNRigidBodies();
208		nIntegrableObjects_ -= mol->getNIntegrableObjects();
209		nCutoffGroups_ -= mol->getNCutoffGroups();
210		nConstraints_ -= mol->getNConstraintPairs();
211
212	<	removeExcludePairs(mol);
212	>	removeInteractionPairs(mol);
213		molecules_.erase(mol->getGlobalIndex());
214
215		delete mol;
#	Line 216 | Line 218 | namespace oopse {
218		} else {
219		return false;
220		}
219	–
220	–
221		}
222
223
#	Line 233 | Line 233 | namespace oopse {
233
234
235		void SimInfo::calcNdf() {
236	<	int ndf_local;
236	>	int ndf_local, nfq_local;
237		MoleculeIterator i;
238	<	std::vector<StuntDouble*>::iterator j;
238	>	vector<StuntDouble*>::iterator j;
239	>	vector<Atom*>::iterator k;
240	>
241		Molecule* mol;
242	<	StuntDouble* integrableObject;
242	>	StuntDouble* sd;
243	>	Atom* atom;
244
245		ndf_local = 0;
246	+	nfq_local = 0;
247
248		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
245	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
246	–	integrableObject = mol->nextIntegrableObject(j)) {
249
250	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
251	+	sd = mol->nextIntegrableObject(j)) {
252	+
253		ndf_local += 3;
254
255	<	if (integrableObject->isDirectional()) {
256	<	if (integrableObject->isLinear()) {
255	>	if (sd->isDirectional()) {
256	>	if (sd->isLinear()) {
257		ndf_local += 2;
258		} else {
259		ndf_local += 3;
260		}
261		}
262	<
263	<	}//end for (integrableObject)
264	<	}// end for (mol)
262	>	}
263	>
264	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
265	>	atom = mol->nextFluctuatingCharge(k)) {
266	>	if (atom->isFluctuatingCharge()) {
267	>	nfq_local++;
268	>	}
269	>	}
270	>	}
271
272	+	ndfLocal_ = ndf_local;
273	+
274		// n_constraints is local, so subtract them on each processor
275		ndf_local -= nConstraints_;
276
277		#ifdef IS_MPI
278	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
278	>	MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
279	>	MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
280	>	MPI::INT, MPI::SUM);
281		#else
282		ndf_ = ndf_local;
283	+	nGlobalFluctuatingCharges_ = nfq_local;
284		#endif
285
286		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 273 | Line 289 | namespace oopse {
289
290		}
291
292	+	int SimInfo::getFdf() {
293	+	#ifdef IS_MPI
294	+	MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
295	+	#else
296	+	fdf_ = fdf_local;
297	+	#endif
298	+	return fdf_;
299	+	}
300	+
301	+	unsigned int SimInfo::getNLocalCutoffGroups(){
302	+	int nLocalCutoffAtoms = 0;
303	+	Molecule* mol;
304	+	MoleculeIterator mi;
305	+	CutoffGroup* cg;
306	+	Molecule::CutoffGroupIterator ci;
307	+
308	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
309	+
310	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
311	+	cg = mol->nextCutoffGroup(ci)) {
312	+	nLocalCutoffAtoms += cg->getNumAtom();
313	+
314	+	}
315	+	}
316	+
317	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
318	+	}
319	+
320		void SimInfo::calcNdfRaw() {
321		int ndfRaw_local;
322
323		MoleculeIterator i;
324	<	std::vector<StuntDouble*>::iterator j;
324	>	vector<StuntDouble*>::iterator j;
325		Molecule* mol;
326	<	StuntDouble* integrableObject;
326	>	StuntDouble* sd;
327
328		// Raw degrees of freedom that we have to set
329		ndfRaw_local = 0;
330
331		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
288	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
289	–	integrableObject = mol->nextIntegrableObject(j)) {
332
333	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
334	+	sd = mol->nextIntegrableObject(j)) {
335	+
336		ndfRaw_local += 3;
337
338	<	if (integrableObject->isDirectional()) {
339	<	if (integrableObject->isLinear()) {
338	>	if (sd->isDirectional()) {
339	>	if (sd->isLinear()) {
340		ndfRaw_local += 2;
341		} else {
342		ndfRaw_local += 3;
#	Line 302 | Line 347 | namespace oopse {
347		}
348
349		#ifdef IS_MPI
350	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
350	>	MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
351		#else
352		ndfRaw_ = ndfRaw_local;
353		#endif
#	Line 315 | Line 360 | namespace oopse {
360
361
362		#ifdef IS_MPI
363	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
363	>	MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
364	>	MPI::INT, MPI::SUM);
365		#else
366		ndfTrans_ = ndfTrans_local;
367		#endif
#	Line 324 | Line 370 | namespace oopse {
370
371		}
372
373	<	void SimInfo::addExcludePairs(Molecule* mol) {
374	<	std::vector<Bond*>::iterator bondIter;
375	<	std::vector<Bend*>::iterator bendIter;
376	<	std::vector<Torsion*>::iterator torsionIter;
373	>	void SimInfo::addInteractionPairs(Molecule* mol) {
374	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
375	>	vector<Bond*>::iterator bondIter;
376	>	vector<Bend*>::iterator bendIter;
377	>	vector<Torsion*>::iterator torsionIter;
378	>	vector<Inversion*>::iterator inversionIter;
379		Bond* bond;
380		Bend* bend;
381		Torsion* torsion;
382	+	Inversion* inversion;
383		int a;
384		int b;
385		int c;
386		int d;
387	+
388	+	// atomGroups can be used to add special interaction maps between
389	+	// groups of atoms that are in two separate rigid bodies.
390	+	// However, most site-site interactions between two rigid bodies
391	+	// are probably not special, just the ones between the physically
392	+	// bonded atoms.  Interactions *within* a single rigid body should
393	+	// always be excluded.  These are done at the bottom of this
394	+	// function.
395	+
396	+	map<int, set<int> > atomGroups;
397	+	Molecule::RigidBodyIterator rbIter;
398	+	RigidBody* rb;
399	+	Molecule::IntegrableObjectIterator ii;
400	+	StuntDouble* sd;
401
402	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
402	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
403	>	sd = mol->nextIntegrableObject(ii)) {
404	>
405	>	if (sd->isRigidBody()) {
406	>	rb = static_cast<RigidBody*>(sd);
407	>	vector<Atom*> atoms = rb->getAtoms();
408	>	set<int> rigidAtoms;
409	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
410	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
411	>	}
412	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
413	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
414	>	}
415	>	} else {
416	>	set<int> oneAtomSet;
417	>	oneAtomSet.insert(sd->getGlobalIndex());
418	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
419	>	}
420	>	}
421	>
422	>	for (bond= mol->beginBond(bondIter); bond != NULL;
423	>	bond = mol->nextBond(bondIter)) {
424	>
425		a = bond->getAtomA()->getGlobalIndex();
426	<	b = bond->getAtomB()->getGlobalIndex();
427	<	exclude_.addPair(a, b);
426	>	b = bond->getAtomB()->getGlobalIndex();
427	>
428	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
429	>	oneTwoInteractions_.addPair(a, b);
430	>	} else {
431	>	excludedInteractions_.addPair(a, b);
432	>	}
433		}
434
435	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
435	>	for (bend= mol->beginBend(bendIter); bend != NULL;
436	>	bend = mol->nextBend(bendIter)) {
437	>
438		a = bend->getAtomA()->getGlobalIndex();
439		b = bend->getAtomB()->getGlobalIndex();
440		c = bend->getAtomC()->getGlobalIndex();
441	+
442	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
443	+	oneTwoInteractions_.addPair(a, b);
444	+	oneTwoInteractions_.addPair(b, c);
445	+	} else {
446	+	excludedInteractions_.addPair(a, b);
447	+	excludedInteractions_.addPair(b, c);
448	+	}
449
450	<	exclude_.addPair(a, b);
451	<	exclude_.addPair(a, c);
452	<	exclude_.addPair(b, c);
450	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
451	>	oneThreeInteractions_.addPair(a, c);
452	>	} else {
453	>	excludedInteractions_.addPair(a, c);
454	>	}
455		}
456
457	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
457	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
458	>	torsion = mol->nextTorsion(torsionIter)) {
459	>
460		a = torsion->getAtomA()->getGlobalIndex();
461		b = torsion->getAtomB()->getGlobalIndex();
462		c = torsion->getAtomC()->getGlobalIndex();
463	<	d = torsion->getAtomD()->getGlobalIndex();
463	>	d = torsion->getAtomD()->getGlobalIndex();
464
465	<	exclude_.addPair(a, b);
466	<	exclude_.addPair(a, c);
467	<	exclude_.addPair(a, d);
468	<	exclude_.addPair(b, c);
469	<	exclude_.addPair(b, d);
470	<	exclude_.addPair(c, d);
465	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
466	>	oneTwoInteractions_.addPair(a, b);
467	>	oneTwoInteractions_.addPair(b, c);
468	>	oneTwoInteractions_.addPair(c, d);
469	>	} else {
470	>	excludedInteractions_.addPair(a, b);
471	>	excludedInteractions_.addPair(b, c);
472	>	excludedInteractions_.addPair(c, d);
473	>	}
474	>
475	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
476	>	oneThreeInteractions_.addPair(a, c);
477	>	oneThreeInteractions_.addPair(b, d);
478	>	} else {
479	>	excludedInteractions_.addPair(a, c);
480	>	excludedInteractions_.addPair(b, d);
481	>	}
482	>
483	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
484	>	oneFourInteractions_.addPair(a, d);
485	>	} else {
486	>	excludedInteractions_.addPair(a, d);
487	>	}
488		}
489
490	<	Molecule::RigidBodyIterator rbIter;
491	<	RigidBody* rb;
492	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
493	<	std::vector<Atom*> atoms = rb->getAtoms();
494	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
495	<	for (int j = i + 1; j < atoms.size(); ++j) {
490	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
491	>	inversion = mol->nextInversion(inversionIter)) {
492	>
493	>	a = inversion->getAtomA()->getGlobalIndex();
494	>	b = inversion->getAtomB()->getGlobalIndex();
495	>	c = inversion->getAtomC()->getGlobalIndex();
496	>	d = inversion->getAtomD()->getGlobalIndex();
497	>
498	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
499	>	oneTwoInteractions_.addPair(a, b);
500	>	oneTwoInteractions_.addPair(a, c);
501	>	oneTwoInteractions_.addPair(a, d);
502	>	} else {
503	>	excludedInteractions_.addPair(a, b);
504	>	excludedInteractions_.addPair(a, c);
505	>	excludedInteractions_.addPair(a, d);
506	>	}
507	>
508	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
509	>	oneThreeInteractions_.addPair(b, c);
510	>	oneThreeInteractions_.addPair(b, d);
511	>	oneThreeInteractions_.addPair(c, d);
512	>	} else {
513	>	excludedInteractions_.addPair(b, c);
514	>	excludedInteractions_.addPair(b, d);
515	>	excludedInteractions_.addPair(c, d);
516	>	}
517	>	}
518	>
519	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
520	>	rb = mol->nextRigidBody(rbIter)) {
521	>	vector<Atom*> atoms = rb->getAtoms();
522	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
523	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
524		a = atoms[i]->getGlobalIndex();
525		b = atoms[j]->getGlobalIndex();
526	<	exclude_.addPair(a, b);
526	>	excludedInteractions_.addPair(a, b);
527		}
528		}
529		}
530
531		}
532
533	<	void SimInfo::removeExcludePairs(Molecule* mol) {
534	<	std::vector<Bond*>::iterator bondIter;
535	<	std::vector<Bend*>::iterator bendIter;
536	<	std::vector<Torsion*>::iterator torsionIter;
533	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
534	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
535	>	vector<Bond*>::iterator bondIter;
536	>	vector<Bend*>::iterator bendIter;
537	>	vector<Torsion*>::iterator torsionIter;
538	>	vector<Inversion*>::iterator inversionIter;
539		Bond* bond;
540		Bend* bend;
541		Torsion* torsion;
542	+	Inversion* inversion;
543		int a;
544		int b;
545		int c;
546		int d;
547	+
548	+	map<int, set<int> > atomGroups;
549	+	Molecule::RigidBodyIterator rbIter;
550	+	RigidBody* rb;
551	+	Molecule::IntegrableObjectIterator ii;
552	+	StuntDouble* sd;
553
554	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
554	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
555	>	sd = mol->nextIntegrableObject(ii)) {
556	>
557	>	if (sd->isRigidBody()) {
558	>	rb = static_cast<RigidBody*>(sd);
559	>	vector<Atom*> atoms = rb->getAtoms();
560	>	set<int> rigidAtoms;
561	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
562	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
563	>	}
564	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
565	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
566	>	}
567	>	} else {
568	>	set<int> oneAtomSet;
569	>	oneAtomSet.insert(sd->getGlobalIndex());
570	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
571	>	}
572	>	}
573	>
574	>	for (bond= mol->beginBond(bondIter); bond != NULL;
575	>	bond = mol->nextBond(bondIter)) {
576	>
577		a = bond->getAtomA()->getGlobalIndex();
578	<	b = bond->getAtomB()->getGlobalIndex();
579	<	exclude_.removePair(a, b);
578	>	b = bond->getAtomB()->getGlobalIndex();
579	>
580	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
581	>	oneTwoInteractions_.removePair(a, b);
582	>	} else {
583	>	excludedInteractions_.removePair(a, b);
584	>	}
585		}
586
587	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
587	>	for (bend= mol->beginBend(bendIter); bend != NULL;
588	>	bend = mol->nextBend(bendIter)) {
589	>
590		a = bend->getAtomA()->getGlobalIndex();
591		b = bend->getAtomB()->getGlobalIndex();
592		c = bend->getAtomC()->getGlobalIndex();
593	+
594	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
595	+	oneTwoInteractions_.removePair(a, b);
596	+	oneTwoInteractions_.removePair(b, c);
597	+	} else {
598	+	excludedInteractions_.removePair(a, b);
599	+	excludedInteractions_.removePair(b, c);
600	+	}
601
602	<	exclude_.removePair(a, b);
603	<	exclude_.removePair(a, c);
604	<	exclude_.removePair(b, c);
602	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
603	>	oneThreeInteractions_.removePair(a, c);
604	>	} else {
605	>	excludedInteractions_.removePair(a, c);
606	>	}
607		}
608
609	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
609	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
610	>	torsion = mol->nextTorsion(torsionIter)) {
611	>
612		a = torsion->getAtomA()->getGlobalIndex();
613		b = torsion->getAtomB()->getGlobalIndex();
614		c = torsion->getAtomC()->getGlobalIndex();
615	<	d = torsion->getAtomD()->getGlobalIndex();
615	>	d = torsion->getAtomD()->getGlobalIndex();
616	>
617	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
618	>	oneTwoInteractions_.removePair(a, b);
619	>	oneTwoInteractions_.removePair(b, c);
620	>	oneTwoInteractions_.removePair(c, d);
621	>	} else {
622	>	excludedInteractions_.removePair(a, b);
623	>	excludedInteractions_.removePair(b, c);
624	>	excludedInteractions_.removePair(c, d);
625	>	}
626
627	<	exclude_.removePair(a, b);
628	<	exclude_.removePair(a, c);
629	<	exclude_.removePair(a, d);
630	<	exclude_.removePair(b, c);
631	<	exclude_.removePair(b, d);
632	<	exclude_.removePair(c, d);
627	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
628	>	oneThreeInteractions_.removePair(a, c);
629	>	oneThreeInteractions_.removePair(b, d);
630	>	} else {
631	>	excludedInteractions_.removePair(a, c);
632	>	excludedInteractions_.removePair(b, d);
633	>	}
634	>
635	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
636	>	oneFourInteractions_.removePair(a, d);
637	>	} else {
638	>	excludedInteractions_.removePair(a, d);
639	>	}
640		}
641
642	<	Molecule::RigidBodyIterator rbIter;
643	<	RigidBody* rb;
644	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
645	<	std::vector<Atom*> atoms = rb->getAtoms();
646	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
647	<	for (int j = i + 1; j < atoms.size(); ++j) {
642	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
643	>	inversion = mol->nextInversion(inversionIter)) {
644	>
645	>	a = inversion->getAtomA()->getGlobalIndex();
646	>	b = inversion->getAtomB()->getGlobalIndex();
647	>	c = inversion->getAtomC()->getGlobalIndex();
648	>	d = inversion->getAtomD()->getGlobalIndex();
649	>
650	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
651	>	oneTwoInteractions_.removePair(a, b);
652	>	oneTwoInteractions_.removePair(a, c);
653	>	oneTwoInteractions_.removePair(a, d);
654	>	} else {
655	>	excludedInteractions_.removePair(a, b);
656	>	excludedInteractions_.removePair(a, c);
657	>	excludedInteractions_.removePair(a, d);
658	>	}
659	>
660	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
661	>	oneThreeInteractions_.removePair(b, c);
662	>	oneThreeInteractions_.removePair(b, d);
663	>	oneThreeInteractions_.removePair(c, d);
664	>	} else {
665	>	excludedInteractions_.removePair(b, c);
666	>	excludedInteractions_.removePair(b, d);
667	>	excludedInteractions_.removePair(c, d);
668	>	}
669	>	}
670	>
671	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
672	>	rb = mol->nextRigidBody(rbIter)) {
673	>	vector<Atom*> atoms = rb->getAtoms();
674	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
675	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
676		a = atoms[i]->getGlobalIndex();
677		b = atoms[j]->getGlobalIndex();
678	<	exclude_.removePair(a, b);
678	>	excludedInteractions_.removePair(a, b);
679		}
680		}
681		}
682	<
682	>
683		}
684	<
685	<
684	>
685	>
686		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
687		int curStampId;
688	<
688	>
689		//index from 0
690		curStampId = moleculeStamps_.size();
691
#	Line 449 | Line 693 | namespace oopse {
693		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
694		}
695
452	–	void SimInfo::update() {
696
697	<	setupSimType();
698	<
699	<	#ifdef IS_MPI
700	<	setupFortranParallel();
701	<	#endif
702	<
703	<	setupFortranSim();
704	<
705	<	//setup fortran force field
463	<	/** @deprecate */
464	<	int isError = 0;
465	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
466	<	if(isError){
467	<	sprintf( painCave.errMsg,
468	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
469	<	painCave.isFatal = 1;
470	<	simError();
471	<	}
472	<
473	<
474	<	setupCutoff();
475	<
697	>	/**
698	>	* update
699	>	*
700	>	*  Performs the global checks and variable settings after the
701	>	*  objects have been created.
702	>	*
703	>	*/
704	>	void SimInfo::update() {
705	>	setupSimVariables();
706		calcNdf();
707		calcNdfRaw();
708		calcNdfTrans();
479	–
480	–	fortranInitialized_ = true;
709		}
710	<
711	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
710	>
711	>	/**
712	>	* getSimulatedAtomTypes
713	>	*
714	>	* Returns an STL set of AtomType* that are actually present in this
715	>	* simulation.  Must query all processors to assemble this information.
716	>	*
717	>	*/
718	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
719		SimInfo::MoleculeIterator mi;
720		Molecule* mol;
721		Molecule::AtomIterator ai;
722		Atom* atom;
723	<	std::set<AtomType*> atomTypes;
724	<
723	>	set<AtomType*> atomTypes;
724	>
725		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
726	<
727	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
726	>	for(atom = mol->beginAtom(ai); atom != NULL;
727	>	atom = mol->nextAtom(ai)) {
728		atomTypes.insert(atom->getAtomType());
729	<	}
730	<
729	>	}
730	>	}
731	>
732	>	#ifdef IS_MPI
733	>
734	>	// loop over the found atom types on this processor, and add their
735	>	// numerical idents to a vector:
736	>
737	>	vector<int> foundTypes;
738	>	set<AtomType*>::iterator i;
739	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
740	>	foundTypes.push_back( (*i)->getIdent() );
741	>
742	>	// count_local holds the number of found types on this processor
743	>	int count_local = foundTypes.size();
744	>
745	>	int nproc = MPI::COMM_WORLD.Get_size();
746	>
747	>	// we need arrays to hold the counts and displacement vectors for
748	>	// all processors
749	>	vector<int> counts(nproc, 0);
750	>	vector<int> disps(nproc, 0);
751	>
752	>	// fill the counts array
753	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
754	>	1, MPI::INT);
755	>
756	>	// use the processor counts to compute the displacement array
757	>	disps[0] = 0;
758	>	int totalCount = counts[0];
759	>	for (int iproc = 1; iproc < nproc; iproc++) {
760	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
761	>	totalCount += counts[iproc];
762		}
763	+
764	+	// we need a (possibly redundant) set of all found types:
765	+	vector<int> ftGlobal(totalCount);
766	+
767	+	// now spray out the foundTypes to all the other processors:
768	+	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
769	+	&ftGlobal[0], &counts[0], &disps[0],
770	+	MPI::INT);
771
772	+	vector<int>::iterator j;
773	+
774	+	// foundIdents is a stl set, so inserting an already found ident
775	+	// will have no effect.
776	+	set<int> foundIdents;
777	+
778	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
779	+	foundIdents.insert((*j));
780	+
781	+	// now iterate over the foundIdents and get the actual atom types
782	+	// that correspond to these:
783	+	set<int>::iterator it;
784	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
785	+	atomTypes.insert( forceField_->getAtomType((*it)) );
786	+
787	+	#endif
788	+
789		return atomTypes;
790		}
791
501	–	void SimInfo::setupSimType() {
502	–	std::set<AtomType*>::iterator i;
503	–	std::set<AtomType*> atomTypes;
504	–	atomTypes = getUniqueAtomTypes();
505	–
506	–	int useLennardJones = 0;
507	–	int useElectrostatic = 0;
508	–	int useEAM = 0;
509	–	int useCharge = 0;
510	–	int useDirectional = 0;
511	–	int useDipole = 0;
512	–	int useGayBerne = 0;
513	–	int useSticky = 0;
514	–	int useStickyPower = 0;
515	–	int useShape = 0;
516	–	int useFLARB = 0; //it is not in AtomType yet
517	–	int useDirectionalAtom = 0;
518	–	int useElectrostatics = 0;
519	–	//usePBC and useRF are from simParams
520	–	int usePBC = simParams_->getPBC();
521	–	int useRF = simParams_->getUseRF();
792
793	+	int getGlobalCountOfType(AtomType* atype) {
794	+	/*
795	+	set<AtomType*> atypes = getSimulatedAtomTypes();
796	+	map<AtomType*, int> counts_;
797	+
798	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
799	+	for(atom = mol->beginAtom(ai); atom != NULL;
800	+	atom = mol->nextAtom(ai)) {
801	+	atom->getAtomType();
802	+	}
803	+	}
804	+	*/
805	+	return 0;
806	+	}
807	+
808	+	void SimInfo::setupSimVariables() {
809	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
810	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
811	+	// parameter is true
812	+	calcBoxDipole_ = false;
813	+	if ( simParams_->haveAccumulateBoxDipole() )
814	+	if ( simParams_->getAccumulateBoxDipole() ) {
815	+	calcBoxDipole_ = true;
816	+	}
817	+
818	+	set<AtomType*>::iterator i;
819	+	set<AtomType*> atomTypes;
820	+	atomTypes = getSimulatedAtomTypes();
821	+	bool usesElectrostatic = false;
822	+	bool usesMetallic = false;
823	+	bool usesDirectional = false;
824	+	bool usesFluctuatingCharges =  false;
825		//loop over all of the atom types
826		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
827	<	useLennardJones |= (*i)->isLennardJones();
828	<	useElectrostatic |= (*i)->isElectrostatic();
829	<	useEAM |= (*i)->isEAM();
830	<	useCharge |= (*i)->isCharge();
529	<	useDirectional |= (*i)->isDirectional();
530	<	useDipole |= (*i)->isDipole();
531	<	useGayBerne |= (*i)->isGayBerne();
532	<	useSticky |= (*i)->isSticky();
533	<	useStickyPower |= (*i)->isStickyPower();
534	<	useShape |= (*i)->isShape();
827	>	usesElectrostatic |= (*i)->isElectrostatic();
828	>	usesMetallic |= (*i)->isMetal();
829	>	usesDirectional |= (*i)->isDirectional();
830	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
831		}
832
833	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
834	<	useDirectionalAtom = 1;
835	<	}
833	>	#ifdef IS_MPI
834	>	bool temp;
835	>	temp = usesDirectional;
836	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
837	>	MPI::LOR);
838	>
839	>	temp = usesMetallic;
840	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
841	>	MPI::LOR);
842	>
843	>	temp = usesElectrostatic;
844	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
845	>	MPI::LOR);
846
847	<	if (useCharge || useDipole) {
848	<	useElectrostatics = 1;
849	<	}
847	>	temp = usesFluctuatingCharges;
848	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
849	>	MPI::LOR);
850	>	#else
851
852	<	#ifdef IS_MPI
853	<	int temp;
852	>	usesDirectionalAtoms_ = usesDirectional;
853	>	usesMetallicAtoms_ = usesMetallic;
854	>	usesElectrostaticAtoms_ = usesElectrostatic;
855	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
856
857	<	temp = usePBC;
549	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
550	<
551	<	temp = useDirectionalAtom;
552	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
553	<
554	<	temp = useLennardJones;
555	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
556	<
557	<	temp = useElectrostatics;
558	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
559	<
560	<	temp = useCharge;
561	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
562	<
563	<	temp = useDipole;
564	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
565	<
566	<	temp = useSticky;
567	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
568	<
569	<	temp = useStickyPower;
570	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
857	>	#endif
858
859	<	temp = useGayBerne;
860	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
859	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
860	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
861	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
862	>	}
863
575	–	temp = useEAM;
576	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
864
865	<	temp = useShape;
866	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
865	>	vector<int> SimInfo::getGlobalAtomIndices() {
866	>	SimInfo::MoleculeIterator mi;
867	>	Molecule* mol;
868	>	Molecule::AtomIterator ai;
869	>	Atom* atom;
870
871	<	temp = useFLARB;
582	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
583	<
584	<	temp = useRF;
585	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
871	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
872
873	<	#endif
873	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
874	>
875	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
876	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
877	>	}
878	>	}
879	>	return GlobalAtomIndices;
880	>	}
881
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;
601	–	fInfo_.SIM_uses_RF = useRF;
882
883	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
883	>	vector<int> SimInfo::getGlobalGroupIndices() {
884	>	SimInfo::MoleculeIterator mi;
885	>	Molecule* mol;
886	>	Molecule::CutoffGroupIterator ci;
887	>	CutoffGroup* cg;
888
889	<	if (simParams_->haveDielectric()) {
890	<	fInfo_.dielect = simParams_->getDielectric();
891	<	} else {
892	<	sprintf(painCave.errMsg,
893	<	"SimSetup Error: No Dielectric constant was set.\n"
894	<	"\tYou are trying to use Reaction Field without"
895	<	"\tsetting a dielectric constant!\n");
896	<	painCave.isFatal = 1;
897	<	simError();
898	<	}
615	<
616	<	} else {
617	<	fInfo_.dielect = 0.0;
889	>	vector<int> GlobalGroupIndices;
890	>
891	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
892	>
893	>	//local index of cutoff group is trivial, it only depends on the
894	>	//order of travesing
895	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
896	>	cg = mol->nextCutoffGroup(ci)) {
897	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
898	>	}
899		}
900	<
900	>	return GlobalGroupIndices;
901		}
902
622	–	void SimInfo::setupFortranSim() {
623	–	int isError;
624	–	int nExclude;
625	–	std::vector<int> fortranGlobalGroupMembership;
626	–
627	–	nExclude = exclude_.getSize();
628	–	isError = 0;
903
904	<	//globalGroupMembership_ is filled by SimCreator
631	<	for (int i = 0; i < nGlobalAtoms_; i++) {
632	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
633	<	}
904	>	void SimInfo::prepareTopology() {
905
906		//calculate mass ratio of cutoff group
636	–	std::vector<double> mfact;
907		SimInfo::MoleculeIterator mi;
908		Molecule* mol;
909		Molecule::CutoffGroupIterator ci;
910		CutoffGroup* cg;
911		Molecule::AtomIterator ai;
912		Atom* atom;
913	<	double totalMass;
913	>	RealType totalMass;
914
915	<	//to avoid memory reallocation, reserve enough space for mfact
916	<	mfact.reserve(getNCutoffGroups());
915	>	/**
916	>	* The mass factor is the relative mass of an atom to the total
917	>	* mass of the cutoff group it belongs to.  By default, all atoms
918	>	* are their own cutoff groups, and therefore have mass factors of
919	>	* 1.  We need some special handling for massless atoms, which
920	>	* will be treated as carrying the entire mass of the cutoff
921	>	* group.
922	>	*/
923	>	massFactors_.clear();
924	>	massFactors_.resize(getNAtoms(), 1.0);
925
926		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
927	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
927	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
928	>	cg = mol->nextCutoffGroup(ci)) {
929
930		totalMass = cg->getMass();
931		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
932	<	mfact.push_back(atom->getMass()/totalMass);
932	>	// Check for massless groups - set mfact to 1 if true
933	>	if (totalMass != 0)
934	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
935	>	else
936	>	massFactors_[atom->getLocalIndex()] = 1.0;
937		}
655	–
938		}
939		}
940
941	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
660	<	std::vector<int> identArray;
941	>	// Build the identArray_ and regions_
942
943	<	//to avoid memory reallocation, reserve enough space identArray
944	<	identArray.reserve(getNAtoms());
945	<
946	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
943	>	identArray_.clear();
944	>	identArray_.reserve(getNAtoms());
945	>	regions_.clear();
946	>	regions_.reserve(getNAtoms());
947	>
948	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
949	>	int reg = mol->getRegion();
950		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
951	<	identArray.push_back(atom->getIdent());
951	>	identArray_.push_back(atom->getIdent());
952	>	regions_.push_back(reg);
953		}
954		}
955	<
956	<	//fill molMembershipArray
672	<	//molMembershipArray is filled by SimCreator
673	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
674	<	for (int i = 0; i < nGlobalAtoms_; i++) {
675	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
676	<	}
677	<
678	<	//setup fortran simulation
679	<	int nGlobalExcludes = 0;
680	<	int* globalExcludes = NULL;
681	<	int* excludeList = exclude_.getExcludeList();
682	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
683	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
684	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
685	<
686	<	if( isError ){
687	<
688	<	sprintf( painCave.errMsg,
689	<	"There was an error setting the simulation information in fortran.\n" );
690	<	painCave.isFatal = 1;
691	<	painCave.severity = OOPSE_ERROR;
692	<	simError();
693	<	}
694	<
695	<	#ifdef IS_MPI
696	<	sprintf( checkPointMsg,
697	<	"succesfully sent the simulation information to fortran.\n");
698	<	MPIcheckPoint();
699	<	#endif // is_mpi
700	<	}
701	<
702	<
703	<	#ifdef IS_MPI
704	<	void SimInfo::setupFortranParallel() {
705	<
706	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
707	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
708	<	std::vector<int> localToGlobalCutoffGroupIndex;
709	<	SimInfo::MoleculeIterator mi;
710	<	Molecule::AtomIterator ai;
711	<	Molecule::CutoffGroupIterator ci;
712	<	Molecule* mol;
713	<	Atom* atom;
714	<	CutoffGroup* cg;
715	<	mpiSimData parallelData;
716	<	int isError;
717	<
718	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
719	<
720	<	//local index(index in DataStorge) of atom is important
721	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
722	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
723	<	}
724	<
725	<	//local index of cutoff group is trivial, it only depends on the order of travesing
726	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
727	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
728	<	}
729	<
730	<	}
731	<
732	<	//fill up mpiSimData struct
733	<	parallelData.nMolGlobal = getNGlobalMolecules();
734	<	parallelData.nMolLocal = getNMolecules();
735	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
736	<	parallelData.nAtomsLocal = getNAtoms();
737	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
738	<	parallelData.nGroupsLocal = getNCutoffGroups();
739	<	parallelData.myNode = worldRank;
740	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
741	<
742	<	//pass mpiSimData struct and index arrays to fortran
743	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
744	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
745	<	&localToGlobalCutoffGroupIndex[0], &isError);
746	<
747	<	if (isError) {
748	<	sprintf(painCave.errMsg,
749	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
750	<	painCave.isFatal = 1;
751	<	simError();
752	<	}
753	<
754	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
755	<	MPIcheckPoint();
756	<
757	<
955	>
956	>	topologyDone_ = true;
957		}
958
760	–	#endif
761	–
762	–	double SimInfo::calcMaxCutoffRadius() {
763	–
764	–
765	–	std::set<AtomType*> atomTypes;
766	–	std::set<AtomType*>::iterator i;
767	–	std::vector<double> cutoffRadius;
768	–
769	–	//get the unique atom types
770	–	atomTypes = getUniqueAtomTypes();
771	–
772	–	//query the max cutoff radius among these atom types
773	–	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
774	–	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
775	–	}
776	–
777	–	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
778	–	#ifdef IS_MPI
779	–	//pick the max cutoff radius among the processors
780	–	#endif
781	–
782	–	return maxCutoffRadius;
783	–	}
784	–
785	–	void SimInfo::getCutoff(double& rcut, double& rsw) {
786	–
787	–	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
788	–
789	–	if (!simParams_->haveRcut()){
790	–	sprintf(painCave.errMsg,
791	–	"SimCreator Warning: No value was set for the cutoffRadius.\n"
792	–	"\tOOPSE will use a default value of 15.0 angstroms"
793	–	"\tfor the cutoffRadius.\n");
794	–	painCave.isFatal = 0;
795	–	simError();
796	–	rcut = 15.0;
797	–	} else{
798	–	rcut = simParams_->getRcut();
799	–	}
800	–
801	–	if (!simParams_->haveRsw()){
802	–	sprintf(painCave.errMsg,
803	–	"SimCreator Warning: No value was set for switchingRadius.\n"
804	–	"\tOOPSE will use a default value of\n"
805	–	"\t0.95 * cutoffRadius for the switchingRadius\n");
806	–	painCave.isFatal = 0;
807	–	simError();
808	–	rsw = 0.95 * rcut;
809	–	} else{
810	–	rsw = simParams_->getRsw();
811	–	}
812	–
813	–	} else {
814	–	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
815	–	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
816	–
817	–	if (simParams_->haveRcut()) {
818	–	rcut = simParams_->getRcut();
819	–	} else {
820	–	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
821	–	rcut = calcMaxCutoffRadius();
822	–	}
823	–
824	–	if (simParams_->haveRsw()) {
825	–	rsw  = simParams_->getRsw();
826	–	} else {
827	–	rsw = rcut;
828	–	}
829	–
830	–	}
831	–	}
832	–
833	–	void SimInfo::setupCutoff() {
834	–	getCutoff(rcut_, rsw_);
835	–	double rnblist = rcut_ + 1; // skin of neighbor list
836	–
837	–	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
838	–	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
839	–	}
840	–
959		void SimInfo::addProperty(GenericData* genData) {
960		properties_.addProperty(genData);
961		}
962
963	<	void SimInfo::removeProperty(const std::string& propName) {
963	>	void SimInfo::removeProperty(const string& propName) {
964		properties_.removeProperty(propName);
965		}
966
#	Line 850 | Line 968 | namespace oopse {
968		properties_.clearProperties();
969		}
970
971	<	std::vector<std::string> SimInfo::getPropertyNames() {
971	>	vector<string> SimInfo::getPropertyNames() {
972		return properties_.getPropertyNames();
973		}
974
975	<	std::vector<GenericData*> SimInfo::getProperties() {
975	>	vector<GenericData*> SimInfo::getProperties() {
976		return properties_.getProperties();
977		}
978
979	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
979	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
980		return properties_.getPropertyByName(propName);
981		}
982
#	Line 872 | Line 990 | namespace oopse {
990		Molecule* mol;
991		RigidBody* rb;
992		Atom* atom;
993	+	CutoffGroup* cg;
994		SimInfo::MoleculeIterator mi;
995		Molecule::RigidBodyIterator rbIter;
996	<	Molecule::AtomIterator atomIter;;
996	>	Molecule::AtomIterator atomIter;
997	>	Molecule::CutoffGroupIterator cgIter;
998
999		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1000
1001	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1001	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
1002	>	atom = mol->nextAtom(atomIter)) {
1003		atom->setSnapshotManager(sman_);
1004		}
1005
1006	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1006	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1007	>	rb = mol->nextRigidBody(rbIter)) {
1008		rb->setSnapshotManager(sman_);
1009		}
1010	+
1011	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1012	+	cg = mol->nextCutoffGroup(cgIter)) {
1013	+	cg->setSnapshotManager(sman_);
1014	+	}
1015		}
1016
1017		}
1018
892	–	Vector3d SimInfo::getComVel(){
893	–	SimInfo::MoleculeIterator i;
894	–	Molecule* mol;
1019
1020	<	Vector3d comVel(0.0);
897	<	double totalMass = 0.0;
898	<
899	<
900	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
901	<	double mass = mol->getMass();
902	<	totalMass += mass;
903	<	comVel += mass * mol->getComVel();
904	<	}
1020	>	ostream& operator <<(ostream& o, SimInfo& info) {
1021
906	–	#ifdef IS_MPI
907	–	double tmpMass = totalMass;
908	–	Vector3d tmpComVel(comVel);
909	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
910	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
911	–	#endif
912	–
913	–	comVel /= totalMass;
914	–
915	–	return comVel;
916	–	}
917	–
918	–	Vector3d SimInfo::getCom(){
919	–	SimInfo::MoleculeIterator i;
920	–	Molecule* mol;
921	–
922	–	Vector3d com(0.0);
923	–	double totalMass = 0.0;
924	–
925	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
926	–	double mass = mol->getMass();
927	–	totalMass += mass;
928	–	com += mass * mol->getCom();
929	–	}
930	–
931	–	#ifdef IS_MPI
932	–	double tmpMass = totalMass;
933	–	Vector3d tmpCom(com);
934	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
935	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
936	–	#endif
937	–
938	–	com /= totalMass;
939	–
940	–	return com;
941	–
942	–	}
943	–
944	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
945	–
1022		return o;
1023		}
1024
1025	<
1026	<	/*
1027	<	Returns center of mass and center of mass velocity in one function call.
1028	<	*/
1029	<
1030	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1031	<	SimInfo::MoleculeIterator i;
1032	<	Molecule* mol;
1033	<
1034	<
1035	<	double totalMass = 0.0;
1036	<
1025	>
1026	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1027	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1028	>	sprintf(painCave.errMsg,
1029	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1030	>	"\tindex exceeds number of known objects!\n");
1031	>	painCave.isFatal = 1;
1032	>	simError();
1033	>	return NULL;
1034	>	} else
1035	>	return IOIndexToIntegrableObject.at(index);
1036	>	}
1037	>
1038	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1039	>	IOIndexToIntegrableObject= v;
1040	>	}
1041
1042	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1043	<	double mass = mol->getMass();
964	<	totalMass += mass;
965	<	com += mass * mol->getCom();
966	<	comVel += mass * mol->getComVel();
967	<	}
968	<
1042	>	int SimInfo::getNGlobalConstraints() {
1043	>	int nGlobalConstraints;
1044		#ifdef IS_MPI
1045	<	double tmpMass = totalMass;
1046	<	Vector3d tmpCom(com);
1047	<	Vector3d tmpComVel(comVel);
1048	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
974	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
975	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1045	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1046	>	MPI::INT, MPI::SUM);
1047	>	#else
1048	>	nGlobalConstraints =  nConstraints_;
1049		#endif
1050	<
1051	<	com /= totalMass;
979	<	comVel /= totalMass;
980	<	}
981	<
982	<	/*
983	<	Return intertia tensor for entire system and angular momentum Vector.
984	<	*/
1050	>	return nGlobalConstraints;
1051	>	}
1052
1053	<	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
987	<
988	<
989	<	double xx = 0.0;
990	<	double yy = 0.0;
991	<	double zz = 0.0;
992	<	double xy = 0.0;
993	<	double xz = 0.0;
994	<	double yz = 0.0;
995	<	Vector3d com(0.0);
996	<	Vector3d comVel(0.0);
997	<
998	<	getComAll(com, comVel);
999	<
1000	<	SimInfo::MoleculeIterator i;
1001	<	Molecule* mol;
1002	<
1003	<	Vector3d thisq(0.0);
1004	<	Vector3d thisv(0.0);
1053	>	}//end namespace OpenMD
1054
1006	–	double thisMass = 0.0;
1007	–
1008	–
1009	–
1010	–
1011	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1012	–
1013	–	thisq = mol->getCom()-com;
1014	–	thisv = mol->getComVel()-comVel;
1015	–	thisMass = mol->getMass();
1016	–	// Compute moment of intertia coefficients.
1017	–	xx += thisq[0]*thisq[0]*thisMass;
1018	–	yy += thisq[1]*thisq[1]*thisMass;
1019	–	zz += thisq[2]*thisq[2]*thisMass;
1020	–
1021	–	// compute products of intertia
1022	–	xy += thisq[0]*thisq[1]*thisMass;
1023	–	xz += thisq[0]*thisq[2]*thisMass;
1024	–	yz += thisq[1]*thisq[2]*thisMass;
1025	–
1026	–	angularMomentum += cross( thisq, thisv ) * thisMass;
1027	–
1028	–	}
1029	–
1030	–
1031	–	inertiaTensor(0,0) = yy + zz;
1032	–	inertiaTensor(0,1) = -xy;
1033	–	inertiaTensor(0,2) = -xz;
1034	–	inertiaTensor(1,0) = -xy;
1035	–	inertiaTensor(2,0) = xx + zz;
1036	–	inertiaTensor(1,2) = -yz;
1037	–	inertiaTensor(2,0) = -xz;
1038	–	inertiaTensor(2,1) = -yz;
1039	–	inertiaTensor(2,2) = xx + yy;
1040	–
1041	–	#ifdef IS_MPI
1042	–	Mat3x3d tmpI(inertiaTensor);
1043	–	Vector3d tmpAngMom;
1044	–	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1045	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1046	–	#endif
1047	–
1048	–	return;
1049	–	}
1050	–
1051	–	//Returns the angular momentum of the system
1052	–	Vector3d SimInfo::getAngularMomentum(){
1053	–
1054	–	Vector3d com(0.0);
1055	–	Vector3d comVel(0.0);
1056	–	Vector3d angularMomentum(0.0);
1057	–
1058	–	getComAll(com,comVel);
1059	–
1060	–	SimInfo::MoleculeIterator i;
1061	–	Molecule* mol;
1062	–
1063	–	Vector3d thisq(0.0);
1064	–	Vector3d thisv(0.0);
1065	–
1066	–	double thisMass = 0.0;
1067	–
1068	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1069	–	thisq = mol->getCom()-com;
1070	–	thisv = mol->getComVel()-comVel;
1071	–	thisMass = mol->getMass();
1072	–	angularMomentum += cross( thisq, thisv ) * thisMass;
1073	–
1074	–	}
1075	–
1076	–	#ifdef IS_MPI
1077	–	Vector3d tmpAngMom;
1078	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1079	–	#endif
1080	–
1081	–	return angularMomentum;
1082	–	}
1083	–
1084	–
1085	–	}//end namespace oopse
1086	–

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 555 by chuckv, Mon May 30 14:01:52 2005 UTC vs.
Revision 1929 by gezelter, Mon Aug 19 13:12:00 2013 UTC

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