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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 598 by chrisfen, Thu Sep 15 00:14:35 2005 UTC vs.
Revision 1908 by gezelter, Fri Jul 19 21:25:45 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/fCutoffPolicy.h"
56	<	#include "UseTheForce/fCoulombicCorrection.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	<	}
108	<
109	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
110	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
111	<
112	<	//calculate atoms in rigid bodies
113	<	int nAtomsInRigidBodies = 0;
114	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
115	<
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();
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
153	–	delete stamps_;
162		delete sman_;
163		delete simParams_;
164		delete forceField_;
165		}
166
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	–	}
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 204 | 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 218 | Line 218 | namespace oopse {
218		} else {
219		return false;
220		}
221	–
222	–
221		}
222
223
#	Line 235 | 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)) {
247	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
248	–	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 275 | 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)) {
290	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291	–	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 304 | 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 317 | 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 326 | 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 451 | Line 693 | namespace oopse {
693		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
694		}
695
454	–	void SimInfo::update() {
696
697	<	setupSimType();
698	<
699	<	#ifdef IS_MPI
700	<	setupFortranParallel();
701	<	#endif
702	<
703	<	setupFortranSim();
704	<
705	<	//setup fortran force field
465	<	/** @deprecate */
466	<	int isError = 0;
467	<
468	<	setupCoulombicCorrection( 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	<
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();
483	–
484	–	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
792	<	void SimInfo::setupSimType() {
793	<	std::set<AtomType*>::iterator i;
794	<	std::set<AtomType*> atomTypes;
795	<	atomTypes = getUniqueAtomTypes();
796	<
797	<	int useLennardJones = 0;
798	<	int useElectrostatic = 0;
799	<	int useEAM = 0;
800	<	int useCharge = 0;
801	<	int useDirectional = 0;
802	<	int useDipole = 0;
803	<	int useGayBerne = 0;
804	<	int useSticky = 0;
805	<	int useStickyPower = 0;
806	<	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	<	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();
533	<	useDirectional |= (*i)->isDirectional();
534	<	useDipole |= (*i)->isDipole();
535	<	useGayBerne |= (*i)->isGayBerne();
536	<	useSticky |= (*i)->isSticky();
537	<	useStickyPower |= (*i)->isStickyPower();
538	<	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;
553	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
554	<
555	<	temp = useDirectionalAtom;
556	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
557	<
558	<	temp = useLennardJones;
559	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
560	<
561	<	temp = useElectrostatics;
562	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
563	<
564	<	temp = useCharge;
565	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
566	<
567	<	temp = useDipole;
568	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
569	<
570	<	temp = useSticky;
571	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
572	<
573	<	temp = useStickyPower;
574	<	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
579	–	temp = useEAM;
580	–	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;
586	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
587	<
588	<	temp = useRF;
589	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
590	<
591	<	temp = useUW;
592	<	MPI_Allreduce(&temp, &useUW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
593	<
594	<	temp = useDW;
595	<	MPI_Allreduce(&temp, &useDW, 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
599	–	fInfo_.SIM_uses_PBC = usePBC;
600	–	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
601	–	fInfo_.SIM_uses_LennardJones = useLennardJones;
602	–	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
603	–	fInfo_.SIM_uses_Charges = useCharge;
604	–	fInfo_.SIM_uses_Dipoles = useDipole;
605	–	fInfo_.SIM_uses_Sticky = useSticky;
606	–	fInfo_.SIM_uses_StickyPower = useStickyPower;
607	–	fInfo_.SIM_uses_GayBerne = useGayBerne;
608	–	fInfo_.SIM_uses_EAM = useEAM;
609	–	fInfo_.SIM_uses_Shapes = useShape;
610	–	fInfo_.SIM_uses_FLARB = useFLARB;
611	–	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	<	}
625	<
626	<	} else {
627	<	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
632	–	void SimInfo::setupFortranSim() {
633	–	int isError;
634	–	int nExclude;
635	–	std::vector<int> fortranGlobalGroupMembership;
636	–
637	–	nExclude = exclude_.getSize();
638	–	isError = 0;
903
904	<	//globalGroupMembership_ is filled by SimCreator
641	<	for (int i = 0; i < nGlobalAtoms_; i++) {
642	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
643	<	}
904	>	void SimInfo::prepareTopology() {
905
906		//calculate mass ratio of cutoff group
646	–	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		}
665	–
938		}
939		}
940
941	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
670	<	std::vector<int> identArray;
941	>	// Build the identArray_
942
943	<	//to avoid memory reallocation, reserve enough space identArray
944	<	identArray.reserve(getNAtoms());
674	<
943	>	identArray_.clear();
944	>	identArray_.reserve(getNAtoms());
945		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
946		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
947	<	identArray.push_back(atom->getIdent());
947	>	identArray_.push_back(atom->getIdent());
948		}
949		}
680	–
681	–	//fill molMembershipArray
682	–	//molMembershipArray is filled by SimCreator
683	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
684	–	for (int i = 0; i < nGlobalAtoms_; i++) {
685	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
686	–	}
950
951	<	//setup fortran simulation
689	<	int nGlobalExcludes = 0;
690	<	int* globalExcludes = NULL;
691	<	int* excludeList = exclude_.getExcludeList();
692	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
693	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
694	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
695	<
696	<	if( isError ){
697	<
698	<	sprintf( painCave.errMsg,
699	<	"There was an error setting the simulation information in fortran.\n" );
700	<	painCave.isFatal = 1;
701	<	painCave.severity = OOPSE_ERROR;
702	<	simError();
703	<	}
704	<
705	<	#ifdef IS_MPI
706	<	sprintf( checkPointMsg,
707	<	"succesfully sent the simulation information to fortran.\n");
708	<	MPIcheckPoint();
709	<	#endif // is_mpi
710	<	}
711	<
712	<
713	<	#ifdef IS_MPI
714	<	void SimInfo::setupFortranParallel() {
715	<
716	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
717	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
718	<	std::vector<int> localToGlobalCutoffGroupIndex;
719	<	SimInfo::MoleculeIterator mi;
720	<	Molecule::AtomIterator ai;
721	<	Molecule::CutoffGroupIterator ci;
722	<	Molecule* mol;
723	<	Atom* atom;
724	<	CutoffGroup* cg;
725	<	mpiSimData parallelData;
726	<	int isError;
727	<
728	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
729	<
730	<	//local index(index in DataStorge) of atom is important
731	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
732	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
733	<	}
734	<
735	<	//local index of cutoff group is trivial, it only depends on the order of travesing
736	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
737	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
738	<	}
739	<
740	<	}
741	<
742	<	//fill up mpiSimData struct
743	<	parallelData.nMolGlobal = getNGlobalMolecules();
744	<	parallelData.nMolLocal = getNMolecules();
745	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
746	<	parallelData.nAtomsLocal = getNAtoms();
747	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
748	<	parallelData.nGroupsLocal = getNCutoffGroups();
749	<	parallelData.myNode = worldRank;
750	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
751	<
752	<	//pass mpiSimData struct and index arrays to fortran
753	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
754	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
755	<	&localToGlobalCutoffGroupIndex[0], &isError);
756	<
757	<	if (isError) {
758	<	sprintf(painCave.errMsg,
759	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
760	<	painCave.isFatal = 1;
761	<	simError();
762	<	}
763	<
764	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
765	<	MPIcheckPoint();
766	<
767	<
768	<	}
769	<
770	<	#endif
771	<
772	<	double SimInfo::calcMaxCutoffRadius() {
773	<
774	<
775	<	std::set<AtomType*> atomTypes;
776	<	std::set<AtomType*>::iterator i;
777	<	std::vector<double> cutoffRadius;
778	<
779	<	//get the unique atom types
780	<	atomTypes = getUniqueAtomTypes();
781	<
782	<	//query the max cutoff radius among these atom types
783	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
784	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
785	<	}
786	<
787	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
788	<	#ifdef IS_MPI
789	<	//pick the max cutoff radius among the processors
790	<	#endif
791	<
792	<	return maxCutoffRadius;
793	<	}
794	<
795	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
796	<
797	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
798	<
799	<	if (!simParams_->haveRcut()){
800	<	sprintf(painCave.errMsg,
801	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
802	<	"\tOOPSE will use a default value of 15.0 angstroms"
803	<	"\tfor the cutoffRadius.\n");
804	<	painCave.isFatal = 0;
805	<	simError();
806	<	rcut = 15.0;
807	<	} else{
808	<	rcut = simParams_->getRcut();
809	<	}
810	<
811	<	if (!simParams_->haveRsw()){
812	<	sprintf(painCave.errMsg,
813	<	"SimCreator Warning: No value was set for switchingRadius.\n"
814	<	"\tOOPSE will use a default value of\n"
815	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
816	<	painCave.isFatal = 0;
817	<	simError();
818	<	rsw = 0.95 * rcut;
819	<	} else{
820	<	rsw = simParams_->getRsw();
821	<	}
822	<
823	<	} else {
824	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
825	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
826	<
827	<	if (simParams_->haveRcut()) {
828	<	rcut = simParams_->getRcut();
829	<	} else {
830	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
831	<	rcut = calcMaxCutoffRadius();
832	<	}
833	<
834	<	if (simParams_->haveRsw()) {
835	<	rsw  = simParams_->getRsw();
836	<	} else {
837	<	rsw = rcut;
838	<	}
839	<
840	<	}
951	>	topologyDone_ = true;
952		}
953
843	–	void SimInfo::setupCutoff() {
844	–	getCutoff(rcut_, rsw_);
845	–	double rnblist = rcut_ + 1; // skin of neighbor list
846	–
847	–	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
848	–
849	–	int cp =  TRADITIONAL_CUTOFF_POLICY;
850	–	if (simParams_->haveCutoffPolicy()) {
851	–	std::string myPolicy = simParams_->getCutoffPolicy();
852	–	if (myPolicy == "MIX") {
853	–	cp = MIX_CUTOFF_POLICY;
854	–	} else {
855	–	if (myPolicy == "MAX") {
856	–	cp = MAX_CUTOFF_POLICY;
857	–	} else {
858	–	if (myPolicy == "TRADITIONAL") {
859	–	cp = TRADITIONAL_CUTOFF_POLICY;
860	–	} else {
861	–	// throw error
862	–	sprintf( painCave.errMsg,
863	–	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
864	–	painCave.isFatal = 1;
865	–	simError();
866	–	}
867	–	}
868	–	}
869	–	}
870	–	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
871	–	}
872	–
873	–	void SimInfo::setupCoulombicCorrection( int isError ) {
874	–
875	–	int errorOut;
876	–	int cc =  NONE;
877	–	double alphaVal;
878	–
879	–	errorOut = isError;
880	–
881	–	if (simParams_->haveCoulombicCorrection()) {
882	–	std::string myCorrection = simParams_->getCoulombicCorrection();
883	–	if (myCorrection == "NONE") {
884	–	cc = NONE;
885	–	} else {
886	–	if (myCorrection == "UNDAMPED_WOLF") {
887	–	cc = UNDAMPED_WOLF;
888	–	} else {
889	–	if (myCorrection == "WOLF") {
890	–	cc = WOLF;
891	–	if (!simParams_->haveDampingAlpha()) {
892	–	//throw error
893	–	sprintf( painCave.errMsg,
894	–	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Wolf Coulombic Correction.", simParams_->getDampingAlpha());
895	–	painCave.isFatal = 0;
896	–	simError();
897	–	}
898	–	alphaVal = simParams_->getDampingAlpha();
899	–	} else {
900	–	if (myCorrection == "REACTION_FIELD") {
901	–	cc = REACTION_FIELD;
902	–	} else {
903	–	// throw error
904	–	sprintf( painCave.errMsg,
905	–	"SimInfo error: Unknown coulombicCorrection. (Input file specified %s .)\n\tcoulombicCorrection must be one of: \"none\", \"undamped_wolf\", \"wolf\", or \"reaction_field\".", myCorrection.c_str() );
906	–	painCave.isFatal = 1;
907	–	simError();
908	–	}
909	–	}
910	–	}
911	–	}
912	–	}
913	–	initFortranFF( &fInfo_.SIM_uses_RF, &cc, &alphaVal, &errorOut );
914	–	}
915	–
954		void SimInfo::addProperty(GenericData* genData) {
955		properties_.addProperty(genData);
956		}
957
958	<	void SimInfo::removeProperty(const std::string& propName) {
958	>	void SimInfo::removeProperty(const string& propName) {
959		properties_.removeProperty(propName);
960		}
961
#	Line 925 | Line 963 | namespace oopse {
963		properties_.clearProperties();
964		}
965
966	<	std::vector<std::string> SimInfo::getPropertyNames() {
966	>	vector<string> SimInfo::getPropertyNames() {
967		return properties_.getPropertyNames();
968		}
969
970	<	std::vector<GenericData*> SimInfo::getProperties() {
970	>	vector<GenericData*> SimInfo::getProperties() {
971		return properties_.getProperties();
972		}
973
974	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
974	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
975		return properties_.getPropertyByName(propName);
976		}
977
#	Line 947 | Line 985 | namespace oopse {
985		Molecule* mol;
986		RigidBody* rb;
987		Atom* atom;
988	+	CutoffGroup* cg;
989		SimInfo::MoleculeIterator mi;
990		Molecule::RigidBodyIterator rbIter;
991	<	Molecule::AtomIterator atomIter;;
991	>	Molecule::AtomIterator atomIter;
992	>	Molecule::CutoffGroupIterator cgIter;
993
994		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
995
996	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
996	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
997	>	atom = mol->nextAtom(atomIter)) {
998		atom->setSnapshotManager(sman_);
999		}
1000
1001	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1001	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1002	>	rb = mol->nextRigidBody(rbIter)) {
1003		rb->setSnapshotManager(sman_);
1004		}
1005	+
1006	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1007	+	cg = mol->nextCutoffGroup(cgIter)) {
1008	+	cg->setSnapshotManager(sman_);
1009	+	}
1010		}
1011
1012		}
1013
967	–	Vector3d SimInfo::getComVel(){
968	–	SimInfo::MoleculeIterator i;
969	–	Molecule* mol;
1014
1015	<	Vector3d comVel(0.0);
972	<	double totalMass = 0.0;
973	<
974	<
975	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
976	<	double mass = mol->getMass();
977	<	totalMass += mass;
978	<	comVel += mass * mol->getComVel();
979	<	}
1015	>	ostream& operator <<(ostream& o, SimInfo& info) {
1016
981	–	#ifdef IS_MPI
982	–	double tmpMass = totalMass;
983	–	Vector3d tmpComVel(comVel);
984	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
985	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
986	–	#endif
987	–
988	–	comVel /= totalMass;
989	–
990	–	return comVel;
991	–	}
992	–
993	–	Vector3d SimInfo::getCom(){
994	–	SimInfo::MoleculeIterator i;
995	–	Molecule* mol;
996	–
997	–	Vector3d com(0.0);
998	–	double totalMass = 0.0;
999	–
1000	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1001	–	double mass = mol->getMass();
1002	–	totalMass += mass;
1003	–	com += mass * mol->getCom();
1004	–	}
1005	–
1006	–	#ifdef IS_MPI
1007	–	double tmpMass = totalMass;
1008	–	Vector3d tmpCom(com);
1009	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1010	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1011	–	#endif
1012	–
1013	–	com /= totalMass;
1014	–
1015	–	return com;
1016	–
1017	–	}
1018	–
1019	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1020	–
1017		return o;
1018		}
1019
1020	<
1021	<	/*
1022	<	Returns center of mass and center of mass velocity in one function call.
1023	<	*/
1024	<
1025	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1026	<	SimInfo::MoleculeIterator i;
1027	<	Molecule* mol;
1028	<
1029	<
1030	<	double totalMass = 0.0;
1031	<
1020	>
1021	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1022	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1023	>	sprintf(painCave.errMsg,
1024	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1025	>	"\tindex exceeds number of known objects!\n");
1026	>	painCave.isFatal = 1;
1027	>	simError();
1028	>	return NULL;
1029	>	} else
1030	>	return IOIndexToIntegrableObject.at(index);
1031	>	}
1032	>
1033	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1034	>	IOIndexToIntegrableObject= v;
1035	>	}
1036
1037	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1038	<	double mass = mol->getMass();
1039	<	totalMass += mass;
1040	<	com += mass * mol->getCom();
1041	<	comVel += mass * mol->getComVel();
1042	<	}
1043	<
1037	>	int SimInfo::getNGlobalConstraints() {
1038	>	int nGlobalConstraints;
1039		#ifdef IS_MPI
1040	<	double tmpMass = totalMass;
1041	<	Vector3d tmpCom(com);
1042	<	Vector3d tmpComVel(comVel);
1043	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1049	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1050	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1040	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1041	>	MPI::INT, MPI::SUM);
1042	>	#else
1043	>	nGlobalConstraints =  nConstraints_;
1044		#endif
1045	<
1046	<	com /= totalMass;
1054	<	comVel /= totalMass;
1055	<	}
1056	<
1057	<	/*
1058	<	Return intertia tensor for entire system and angular momentum Vector.
1045	>	return nGlobalConstraints;
1046	>	}
1047
1048	+	}//end namespace OpenMD
1049
1061	–	[  Ixx -Ixy  -Ixz ]
1062	–	J =| -Iyx  Iyy  -Iyz |
1063	–	[ -Izx -Iyz   Izz ]
1064	–	*/
1065	–
1066	–	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1067	–
1068	–
1069	–	double xx = 0.0;
1070	–	double yy = 0.0;
1071	–	double zz = 0.0;
1072	–	double xy = 0.0;
1073	–	double xz = 0.0;
1074	–	double yz = 0.0;
1075	–	Vector3d com(0.0);
1076	–	Vector3d comVel(0.0);
1077	–
1078	–	getComAll(com, comVel);
1079	–
1080	–	SimInfo::MoleculeIterator i;
1081	–	Molecule* mol;
1082	–
1083	–	Vector3d thisq(0.0);
1084	–	Vector3d thisv(0.0);
1085	–
1086	–	double thisMass = 0.0;
1087	–
1088	–
1089	–
1090	–
1091	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1092	–
1093	–	thisq = mol->getCom()-com;
1094	–	thisv = mol->getComVel()-comVel;
1095	–	thisMass = mol->getMass();
1096	–	// Compute moment of intertia coefficients.
1097	–	xx += thisq[0]*thisq[0]*thisMass;
1098	–	yy += thisq[1]*thisq[1]*thisMass;
1099	–	zz += thisq[2]*thisq[2]*thisMass;
1100	–
1101	–	// compute products of intertia
1102	–	xy += thisq[0]*thisq[1]*thisMass;
1103	–	xz += thisq[0]*thisq[2]*thisMass;
1104	–	yz += thisq[1]*thisq[2]*thisMass;
1105	–
1106	–	angularMomentum += cross( thisq, thisv ) * thisMass;
1107	–
1108	–	}
1109	–
1110	–
1111	–	inertiaTensor(0,0) = yy + zz;
1112	–	inertiaTensor(0,1) = -xy;
1113	–	inertiaTensor(0,2) = -xz;
1114	–	inertiaTensor(1,0) = -xy;
1115	–	inertiaTensor(1,1) = xx + zz;
1116	–	inertiaTensor(1,2) = -yz;
1117	–	inertiaTensor(2,0) = -xz;
1118	–	inertiaTensor(2,1) = -yz;
1119	–	inertiaTensor(2,2) = xx + yy;
1120	–
1121	–	#ifdef IS_MPI
1122	–	Mat3x3d tmpI(inertiaTensor);
1123	–	Vector3d tmpAngMom;
1124	–	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1125	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1126	–	#endif
1127	–
1128	–	return;
1129	–	}
1130	–
1131	–	//Returns the angular momentum of the system
1132	–	Vector3d SimInfo::getAngularMomentum(){
1133	–
1134	–	Vector3d com(0.0);
1135	–	Vector3d comVel(0.0);
1136	–	Vector3d angularMomentum(0.0);
1137	–
1138	–	getComAll(com,comVel);
1139	–
1140	–	SimInfo::MoleculeIterator i;
1141	–	Molecule* mol;
1142	–
1143	–	Vector3d thisr(0.0);
1144	–	Vector3d thisp(0.0);
1145	–
1146	–	double thisMass;
1147	–
1148	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1149	–	thisMass = mol->getMass();
1150	–	thisr = mol->getCom()-com;
1151	–	thisp = (mol->getComVel()-comVel)*thisMass;
1152	–
1153	–	angularMomentum += cross( thisr, thisp );
1154	–
1155	–	}
1156	–
1157	–	#ifdef IS_MPI
1158	–	Vector3d tmpAngMom;
1159	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1160	–	#endif
1161	–
1162	–	return angularMomentum;
1163	–	}
1164	–
1165	–
1166	–	}//end namespace oopse
1167	–

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 598 by chrisfen, Thu Sep 15 00:14:35 2005 UTC vs.
Revision 1908 by gezelter, Fri Jul 19 21:25:45 2013 UTC

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