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

Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC

#	Line 36 | Line 36
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38		* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
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 54 | Line 55
55		#include "math/Vector3.hpp"
56		#include "primitives/Molecule.hpp"
57		#include "primitives/StuntDouble.hpp"
57	–	#include "UseTheForce/fCutoffPolicy.h"
58	–	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	–	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60	–	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61	–	#include "UseTheForce/doForces_interface.h"
62	–	#include "UseTheForce/DarkSide/neighborLists_interface.h"
63	–	#include "UseTheForce/DarkSide/electrostatic_interface.h"
64	–	#include "UseTheForce/DarkSide/switcheroo_interface.h"
58		#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60		#include "selection/SelectionManager.hpp"
61		#include "io/ForceFieldOptions.hpp"
62	<	#include "UseTheForce/ForceField.hpp"
63	<
71	<
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"
75	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68	+	using namespace std;
69		namespace OpenMD {
78	–	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79	–	std::map<int, std::set<int> >::iterator i = container.find(index);
80	–	std::set<int> result;
81	–	if (i != container.end()) {
82	–	result = i->second;
83	–	}
84	–
85	–	return result;
86	–	}
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),
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), sman_(NULL), fortranInitialized_(false),
79	<	calcBoxDipole_(false), useAtomicVirial_(true) {
80	<
81	<
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;
89	<
90	<	std::vector<Component*> components = simParams->getComponents();
78	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79	>	calcBoxDipole_(false), useAtomicVirial_(true) {
80	>
81	>	MoleculeStamp* molStamp;
82	>	int nMolWithSameStamp;
83	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
85	>	CutoffGroupStamp* cgStamp;
86	>	RigidBodyStamp* rbStamp;
87	>	int nRigidAtoms = 0;
88	>
89	>	vector<Component*> components = simParams->getComponents();
90	>
91	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
92	>	molStamp = (*i)->getMoleculeStamp();
93	>	nMolWithSameStamp = (*i)->getNMol();
94
95	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
96	<	molStamp = (*i)->getMoleculeStamp();
97	<	nMolWithSameStamp = (*i)->getNMol();
98	<
99	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
100	<
101	<	//calculate atoms in molecules
102	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
103	<
104	<	//calculate atoms in cutoff groups
105	<	int nAtomsInGroups = 0;
106	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
121	<
122	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
123	<	cgStamp = molStamp->getCutoffGroupStamp(j);
124	<	nAtomsInGroups += cgStamp->getNMembers();
125	<	}
126	<
127	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
128	<
129	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
130	<
131	<	//calculate atoms in rigid bodies
132	<	int nAtomsInRigidBodies = 0;
133	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
134	<
135	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
136	<	rbStamp = molStamp->getRigidBodyStamp(j);
137	<	nAtomsInRigidBodies += rbStamp->getNMembers();
138	<	}
139	<
140	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
141	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
142	<
95	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
96	>
97	>	//calculate atoms in molecules
98	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
99	>
100	>	//calculate atoms in cutoff groups
101	>	int nAtomsInGroups = 0;
102	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
103	>
104	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
105	>	cgStamp = molStamp->getCutoffGroupStamp(j);
106	>	nAtomsInGroups += cgStamp->getNMembers();
107		}
108	<
109	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
110	<	//group therefore the total number of cutoff groups in the system is
111	<	//equal to the total number of atoms minus number of atoms belong to
112	<	//cutoff group defined in meta-data file plus the number of cutoff
113	<	//groups defined in meta-data file
114	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
115	<
116	<	//every free atom (atom does not belong to rigid bodies) is an
117	<	//integrable object therefore the total number of integrable objects
118	<	//in the system is equal to the total number of atoms minus number of
119	<	//atoms belong to rigid body defined in meta-data file plus the number
120	<	//of rigid bodies defined in meta-data file
121	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
122	<	+ nGlobalRigidBodies_;
123	<
124	<	nGlobalMols_ = molStampIds_.size();
161	<	molToProcMap_.resize(nGlobalMols_);
108	>
109	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
110	>
111	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
112	>
113	>	//calculate atoms in rigid bodies
114	>	int nAtomsInRigidBodies = 0;
115	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
116	>
117	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
118	>	rbStamp = molStamp->getRigidBodyStamp(j);
119	>	nAtomsInRigidBodies += rbStamp->getNMembers();
120	>	}
121	>
122	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
123	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
124	>
125		}
126	+
127	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
128	+	//group therefore the total number of cutoff groups in the system is
129	+	//equal to the total number of atoms minus number of atoms belong to
130	+	//cutoff group defined in meta-data file plus the number of cutoff
131	+	//groups defined in meta-data file
132
133	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134	+
135	+	//every free atom (atom does not belong to rigid bodies) is an
136	+	//integrable object therefore the total number of integrable objects
137	+	//in the system is equal to the total number of atoms minus number of
138	+	//atoms belong to rigid body defined in meta-data file plus the number
139	+	//of rigid bodies defined in meta-data file
140	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
141	+	+ nGlobalRigidBodies_;
142	+
143	+	nGlobalMols_ = molStampIds_.size();
144	+	molToProcMap_.resize(nGlobalMols_);
145	+	}
146	+
147		SimInfo::~SimInfo() {
148	<	std::map<int, Molecule*>::iterator i;
148	>	map<int, Molecule*>::iterator i;
149		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
150		delete i->second;
151		}
#	Line 173 | Line 156 | namespace OpenMD {
156		delete forceField_;
157		}
158
176	–	int SimInfo::getNGlobalConstraints() {
177	–	int nGlobalConstraints;
178	–	#ifdef IS_MPI
179	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
180	–	MPI_COMM_WORLD);
181	–	#else
182	–	nGlobalConstraints =  nConstraints_;
183	–	#endif
184	–	return nGlobalConstraints;
185	–	}
159
160		bool SimInfo::addMolecule(Molecule* mol) {
161		MoleculeIterator i;
162	<
162	>
163		i = molecules_.find(mol->getGlobalIndex());
164		if (i == molecules_.end() ) {
165	<
166	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
167	<
165	>
166	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
167	>
168		nAtoms_ += mol->getNAtoms();
169		nBonds_ += mol->getNBonds();
170		nBends_ += mol->getNBends();
#	Line 201 | Line 174 | namespace OpenMD {
174		nIntegrableObjects_ += mol->getNIntegrableObjects();
175		nCutoffGroups_ += mol->getNCutoffGroups();
176		nConstraints_ += mol->getNConstraintPairs();
177	<
177	>
178		addInteractionPairs(mol);
179	<
179	>
180		return true;
181		} else {
182		return false;
183		}
184		}
185	<
185	>
186		bool SimInfo::removeMolecule(Molecule* mol) {
187		MoleculeIterator i;
188		i = molecules_.find(mol->getGlobalIndex());
#	Line 237 | Line 210 | namespace OpenMD {
210		} else {
211		return false;
212		}
240	–
241	–
213		}
214
215
#	Line 254 | Line 225 | namespace OpenMD {
225
226
227		void SimInfo::calcNdf() {
228	<	int ndf_local;
228	>	int ndf_local, nfq_local;
229		MoleculeIterator i;
230	<	std::vector<StuntDouble*>::iterator j;
230	>	vector<StuntDouble*>::iterator j;
231	>	vector<Atom*>::iterator k;
232	>
233		Molecule* mol;
234	<	StuntDouble* integrableObject;
234	>	StuntDouble* sd;
235	>	Atom* atom;
236
237		ndf_local = 0;
238	+	nfq_local = 0;
239
240		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
266	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
267	–	integrableObject = mol->nextIntegrableObject(j)) {
241
242	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
243	+	sd = mol->nextIntegrableObject(j)) {
244	+
245		ndf_local += 3;
246
247	<	if (integrableObject->isDirectional()) {
248	<	if (integrableObject->isLinear()) {
247	>	if (sd->isDirectional()) {
248	>	if (sd->isLinear()) {
249		ndf_local += 2;
250		} else {
251		ndf_local += 3;
252		}
253		}
278	–
254		}
255	+
256	+	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
257	+	atom = mol->nextFluctuatingCharge(k)) {
258	+	if (atom->isFluctuatingCharge()) {
259	+	nfq_local++;
260	+	}
261	+	}
262		}
263
264	+	ndfLocal_ = ndf_local;
265	+
266		// n_constraints is local, so subtract them on each processor
267		ndf_local -= nConstraints_;
268
269		#ifdef IS_MPI
270		MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
271	+	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
272		#else
273		ndf_ = ndf_local;
274	+	nGlobalFluctuatingCharges_ = nfq_local;
275		#endif
276
277		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 302 | Line 288 | namespace OpenMD {
288		#endif
289		return fdf_;
290		}
291	+
292	+	unsigned int SimInfo::getNLocalCutoffGroups(){
293	+	int nLocalCutoffAtoms = 0;
294	+	Molecule* mol;
295	+	MoleculeIterator mi;
296	+	CutoffGroup* cg;
297	+	Molecule::CutoffGroupIterator ci;
298
299	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
300	+
301	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
302	+	cg = mol->nextCutoffGroup(ci)) {
303	+	nLocalCutoffAtoms += cg->getNumAtom();
304	+
305	+	}
306	+	}
307	+
308	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
309	+	}
310	+
311		void SimInfo::calcNdfRaw() {
312		int ndfRaw_local;
313
314		MoleculeIterator i;
315	<	std::vector<StuntDouble*>::iterator j;
315	>	vector<StuntDouble*>::iterator j;
316		Molecule* mol;
317	<	StuntDouble* integrableObject;
317	>	StuntDouble* sd;
318
319		// Raw degrees of freedom that we have to set
320		ndfRaw_local = 0;
321
322		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
318	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
319	–	integrableObject = mol->nextIntegrableObject(j)) {
323
324	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
325	+	sd = mol->nextIntegrableObject(j)) {
326	+
327		ndfRaw_local += 3;
328
329	<	if (integrableObject->isDirectional()) {
330	<	if (integrableObject->isLinear()) {
329	>	if (sd->isDirectional()) {
330	>	if (sd->isLinear()) {
331		ndfRaw_local += 2;
332		} else {
333		ndfRaw_local += 3;
#	Line 356 | Line 362 | namespace OpenMD {
362
363		void SimInfo::addInteractionPairs(Molecule* mol) {
364		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
365	<	std::vector<Bond*>::iterator bondIter;
366	<	std::vector<Bend*>::iterator bendIter;
367	<	std::vector<Torsion*>::iterator torsionIter;
368	<	std::vector<Inversion*>::iterator inversionIter;
365	>	vector<Bond*>::iterator bondIter;
366	>	vector<Bend*>::iterator bendIter;
367	>	vector<Torsion*>::iterator torsionIter;
368	>	vector<Inversion*>::iterator inversionIter;
369		Bond* bond;
370		Bend* bend;
371		Torsion* torsion;
#	Line 377 | Line 383 | namespace OpenMD {
383		// always be excluded.  These are done at the bottom of this
384		// function.
385
386	<	std::map<int, std::set<int> > atomGroups;
386	>	map<int, set<int> > atomGroups;
387		Molecule::RigidBodyIterator rbIter;
388		RigidBody* rb;
389		Molecule::IntegrableObjectIterator ii;
390	<	StuntDouble* integrableObject;
390	>	StuntDouble* sd;
391
392	<	for (integrableObject = mol->beginIntegrableObject(ii);
393	<	integrableObject != NULL;
388	<	integrableObject = mol->nextIntegrableObject(ii)) {
392	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
393	>	sd = mol->nextIntegrableObject(ii)) {
394
395	<	if (integrableObject->isRigidBody()) {
396	<	rb = static_cast<RigidBody*>(integrableObject);
397	<	std::vector<Atom*> atoms = rb->getAtoms();
398	<	std::set<int> rigidAtoms;
395	>	if (sd->isRigidBody()) {
396	>	rb = static_cast<RigidBody*>(sd);
397	>	vector<Atom*> atoms = rb->getAtoms();
398	>	set<int> rigidAtoms;
399		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
400		rigidAtoms.insert(atoms[i]->getGlobalIndex());
401		}
402		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
403	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
403	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
404		}
405		} else {
406	<	std::set<int> oneAtomSet;
407	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
408	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
406	>	set<int> oneAtomSet;
407	>	oneAtomSet.insert(sd->getGlobalIndex());
408	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
409		}
410		}
411
#	Line 503 | Line 508 | namespace OpenMD {
508
509		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
510		rb = mol->nextRigidBody(rbIter)) {
511	<	std::vector<Atom*> atoms = rb->getAtoms();
511	>	vector<Atom*> atoms = rb->getAtoms();
512		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
513		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
514		a = atoms[i]->getGlobalIndex();
#	Line 517 | Line 522 | namespace OpenMD {
522
523		void SimInfo::removeInteractionPairs(Molecule* mol) {
524		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
525	<	std::vector<Bond*>::iterator bondIter;
526	<	std::vector<Bend*>::iterator bendIter;
527	<	std::vector<Torsion*>::iterator torsionIter;
528	<	std::vector<Inversion*>::iterator inversionIter;
525	>	vector<Bond*>::iterator bondIter;
526	>	vector<Bend*>::iterator bendIter;
527	>	vector<Torsion*>::iterator torsionIter;
528	>	vector<Inversion*>::iterator inversionIter;
529		Bond* bond;
530		Bend* bend;
531		Torsion* torsion;
#	Line 530 | Line 535 | namespace OpenMD {
535		int c;
536		int d;
537
538	<	std::map<int, std::set<int> > atomGroups;
538	>	map<int, set<int> > atomGroups;
539		Molecule::RigidBodyIterator rbIter;
540		RigidBody* rb;
541		Molecule::IntegrableObjectIterator ii;
542	<	StuntDouble* integrableObject;
542	>	StuntDouble* sd;
543
544	<	for (integrableObject = mol->beginIntegrableObject(ii);
545	<	integrableObject != NULL;
541	<	integrableObject = mol->nextIntegrableObject(ii)) {
544	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
545	>	sd = mol->nextIntegrableObject(ii)) {
546
547	<	if (integrableObject->isRigidBody()) {
548	<	rb = static_cast<RigidBody*>(integrableObject);
549	<	std::vector<Atom*> atoms = rb->getAtoms();
550	<	std::set<int> rigidAtoms;
547	>	if (sd->isRigidBody()) {
548	>	rb = static_cast<RigidBody*>(sd);
549	>	vector<Atom*> atoms = rb->getAtoms();
550	>	set<int> rigidAtoms;
551		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
552		rigidAtoms.insert(atoms[i]->getGlobalIndex());
553		}
554		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
555	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
555	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
556		}
557		} else {
558	<	std::set<int> oneAtomSet;
559	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
560	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
558	>	set<int> oneAtomSet;
559	>	oneAtomSet.insert(sd->getGlobalIndex());
560	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
561		}
562		}
563
#	Line 656 | Line 660 | namespace OpenMD {
660
661		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
662		rb = mol->nextRigidBody(rbIter)) {
663	<	std::vector<Atom*> atoms = rb->getAtoms();
663	>	vector<Atom*> atoms = rb->getAtoms();
664		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
665		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
666		a = atoms[i]->getGlobalIndex();
#	Line 679 | Line 683 | namespace OpenMD {
683		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
684		}
685
682	–	void SimInfo::update() {
686
687	<	setupSimType();
688	<
689	<	#ifdef IS_MPI
690	<	setupFortranParallel();
691	<	#endif
692	<
693	<	setupFortranSim();
694	<
695	<	//setup fortran force field
693	<	/** @deprecate */
694	<	int isError = 0;
695	<
696	<	setupCutoff();
697	<
698	<	setupElectrostaticSummationMethod( isError );
699	<	setupSwitchingFunction();
700	<	setupAccumulateBoxDipole();
701	<
702	<	if(isError){
703	<	sprintf( painCave.errMsg,
704	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
705	<	painCave.isFatal = 1;
706	<	simError();
707	<	}
708	<
687	>	/**
688	>	* update
689	>	*
690	>	*  Performs the global checks and variable settings after the
691	>	*  objects have been created.
692	>	*
693	>	*/
694	>	void SimInfo::update() {
695	>	setupSimVariables();
696		calcNdf();
697		calcNdfRaw();
698		calcNdfTrans();
712	–
713	–	fortranInitialized_ = true;
699		}
700	<
701	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
700	>
701	>	/**
702	>	* getSimulatedAtomTypes
703	>	*
704	>	* Returns an STL set of AtomType* that are actually present in this
705	>	* simulation.  Must query all processors to assemble this information.
706	>	*
707	>	*/
708	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
709		SimInfo::MoleculeIterator mi;
710		Molecule* mol;
711		Molecule::AtomIterator ai;
712		Atom* atom;
713	<	std::set<AtomType*> atomTypes;
714	<
713	>	set<AtomType*> atomTypes;
714	>
715		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
716	<
717	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
716	>	for(atom = mol->beginAtom(ai); atom != NULL;
717	>	atom = mol->nextAtom(ai)) {
718		atomTypes.insert(atom->getAtomType());
719	<	}
720	<
729	<	}
730	<
731	<	return atomTypes;
732	<	}
733	<
734	<	void SimInfo::setupSimType() {
735	<	std::set<AtomType*>::iterator i;
736	<	std::set<AtomType*> atomTypes;
737	<	atomTypes = getUniqueAtomTypes();
719	>	}
720	>	}
721
722	<	int useLennardJones = 0;
740	<	int useElectrostatic = 0;
741	<	int useEAM = 0;
742	<	int useSC = 0;
743	<	int useCharge = 0;
744	<	int useDirectional = 0;
745	<	int useDipole = 0;
746	<	int useGayBerne = 0;
747	<	int useSticky = 0;
748	<	int useStickyPower = 0;
749	<	int useShape = 0;
750	<	int useFLARB = 0; //it is not in AtomType yet
751	<	int useDirectionalAtom = 0;
752	<	int useElectrostatics = 0;
753	<	//usePBC and useRF are from simParams
754	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
755	<	int useRF;
756	<	int useSF;
757	<	int useSP;
758	<	int useBoxDipole;
722	>	#ifdef IS_MPI
723
724	<	std::string myMethod;
725	<
762	<	// set the useRF logical
763	<	useRF = 0;
764	<	useSF = 0;
765	<	useSP = 0;
766	<	useBoxDipole = 0;
767	<
768	<
769	<	if (simParams_->haveElectrostaticSummationMethod()) {
770	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
771	<	toUpper(myMethod);
772	<	if (myMethod == "REACTION_FIELD"){
773	<	useRF = 1;
774	<	} else if (myMethod == "SHIFTED_FORCE"){
775	<	useSF = 1;
776	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
777	<	useSP = 1;
778	<	}
779	<	}
724	>	// loop over the found atom types on this processor, and add their
725	>	// numerical idents to a vector:
726
727	<	if (simParams_->haveAccumulateBoxDipole())
728	<	if (simParams_->getAccumulateBoxDipole())
729	<	useBoxDipole = 1;
727	>	vector<int> foundTypes;
728	>	set<AtomType*>::iterator i;
729	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
730	>	foundTypes.push_back( (*i)->getIdent() );
731
732	<	useAtomicVirial_ = simParams_->getUseAtomicVirial();
732	>	// count_local holds the number of found types on this processor
733	>	int count_local = foundTypes.size();
734
735	<	//loop over all of the atom types
788	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
789	<	useLennardJones |= (*i)->isLennardJones();
790	<	useElectrostatic |= (*i)->isElectrostatic();
791	<	useEAM |= (*i)->isEAM();
792	<	useSC |= (*i)->isSC();
793	<	useCharge |= (*i)->isCharge();
794	<	useDirectional |= (*i)->isDirectional();
795	<	useDipole |= (*i)->isDipole();
796	<	useGayBerne |= (*i)->isGayBerne();
797	<	useSticky |= (*i)->isSticky();
798	<	useStickyPower |= (*i)->isStickyPower();
799	<	useShape |= (*i)->isShape();
800	<	}
735	>	int nproc = MPI::COMM_WORLD.Get_size();
736
737	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
738	<	useDirectionalAtom = 1;
739	<	}
737	>	// we need arrays to hold the counts and displacement vectors for
738	>	// all processors
739	>	vector<int> counts(nproc, 0);
740	>	vector<int> disps(nproc, 0);
741
742	<	if (useCharge || useDipole) {
743	<	useElectrostatics = 1;
742	>	// fill the counts array
743	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
744	>	1, MPI::INT);
745	>
746	>	// use the processor counts to compute the displacement array
747	>	disps[0] = 0;
748	>	int totalCount = counts[0];
749	>	for (int iproc = 1; iproc < nproc; iproc++) {
750	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
751	>	totalCount += counts[iproc];
752		}
753
754	<	#ifdef IS_MPI
755	<	int temp;
754	>	// we need a (possibly redundant) set of all found types:
755	>	vector<int> ftGlobal(totalCount);
756	>
757	>	// now spray out the foundTypes to all the other processors:
758	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
759	>	&ftGlobal[0], &counts[0], &disps[0],
760	>	MPI::INT);
761
762	<	temp = usePBC;
814	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
762	>	vector<int>::iterator j;
763
764	<	temp = useDirectionalAtom;
765	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
764	>	// foundIdents is a stl set, so inserting an already found ident
765	>	// will have no effect.
766	>	set<int> foundIdents;
767
768	<	temp = useLennardJones;
769	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
768	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
769	>	foundIdents.insert((*j));
770	>
771	>	// now iterate over the foundIdents and get the actual atom types
772	>	// that correspond to these:
773	>	set<int>::iterator it;
774	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
775	>	atomTypes.insert( forceField_->getAtomType((*it)) );
776	>
777	>	#endif
778
779	<	temp = useElectrostatics;
780	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
779	>	return atomTypes;
780	>	}
781
782	<	temp = useCharge;
783	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
784	<
785	<	temp = useDipole;
786	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
787	<
788	<	temp = useSticky;
789	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
833	<
834	<	temp = useStickyPower;
835	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
782	>	void SimInfo::setupSimVariables() {
783	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
784	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
785	>	calcBoxDipole_ = false;
786	>	if ( simParams_->haveAccumulateBoxDipole() )
787	>	if ( simParams_->getAccumulateBoxDipole() ) {
788	>	calcBoxDipole_ = true;
789	>	}
790
791	<	temp = useGayBerne;
792	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
791	>	set<AtomType*>::iterator i;
792	>	set<AtomType*> atomTypes;
793	>	atomTypes = getSimulatedAtomTypes();
794	>	bool usesElectrostatic = false;
795	>	bool usesMetallic = false;
796	>	bool usesDirectional = false;
797	>	bool usesFluctuatingCharges =  false;
798	>	//loop over all of the atom types
799	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
800	>	usesElectrostatic |= (*i)->isElectrostatic();
801	>	usesMetallic |= (*i)->isMetal();
802	>	usesDirectional |= (*i)->isDirectional();
803	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
804	>	}
805
806	<	temp = useEAM;
807	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
808	<
809	<	temp = useSC;
810	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
806	>	#ifdef IS_MPI
807	>	bool temp;
808	>	temp = usesDirectional;
809	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
810	>	MPI::LOR);
811	>
812	>	temp = usesMetallic;
813	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
814	>	MPI::LOR);
815
816	<	temp = useShape;
817	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816	>	temp = usesElectrostatic;
817	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
818	>	MPI::LOR);
819
820	<	temp = useFLARB;
821	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
820	>	temp = usesFluctuatingCharges;
821	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
822	>	MPI::LOR);
823	>	#else
824
825	<	temp = useRF;
826	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
825	>	usesDirectionalAtoms_ = usesDirectional;
826	>	usesMetallicAtoms_ = usesMetallic;
827	>	usesElectrostaticAtoms_ = usesElectrostatic;
828	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
829
830	<	temp = useSF;
831	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
830	>	#endif
831	>
832	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
833	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
834	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
835	>	}
836
858	–	temp = useSP;
859	–	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
837
838	<	temp = useBoxDipole;
839	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
838	>	vector<int> SimInfo::getGlobalAtomIndices() {
839	>	SimInfo::MoleculeIterator mi;
840	>	Molecule* mol;
841	>	Molecule::AtomIterator ai;
842	>	Atom* atom;
843
844	<	temp = useAtomicVirial_;
845	<	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
844	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
845	>
846	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
847	>
848	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
849	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
850	>	}
851	>	}
852	>	return GlobalAtomIndices;
853	>	}
854
867	–	#endif
855
856	<	fInfo_.SIM_uses_PBC = usePBC;
857	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
858	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
859	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
860	<	fInfo_.SIM_uses_Charges = useCharge;
874	<	fInfo_.SIM_uses_Dipoles = useDipole;
875	<	fInfo_.SIM_uses_Sticky = useSticky;
876	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
877	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
878	<	fInfo_.SIM_uses_EAM = useEAM;
879	<	fInfo_.SIM_uses_SC = useSC;
880	<	fInfo_.SIM_uses_Shapes = useShape;
881	<	fInfo_.SIM_uses_FLARB = useFLARB;
882	<	fInfo_.SIM_uses_RF = useRF;
883	<	fInfo_.SIM_uses_SF = useSF;
884	<	fInfo_.SIM_uses_SP = useSP;
885	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
886	<	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
887	<	}
856	>	vector<int> SimInfo::getGlobalGroupIndices() {
857	>	SimInfo::MoleculeIterator mi;
858	>	Molecule* mol;
859	>	Molecule::CutoffGroupIterator ci;
860	>	CutoffGroup* cg;
861
862	<	void SimInfo::setupFortranSim() {
890	<	int isError;
891	<	int nExclude, nOneTwo, nOneThree, nOneFour;
892	<	std::vector<int> fortranGlobalGroupMembership;
862	>	vector<int> GlobalGroupIndices;
863
864	<	isError = 0;
865	<
866	<	//globalGroupMembership_ is filled by SimCreator
867	<	for (int i = 0; i < nGlobalAtoms_; i++) {
868	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
864	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
865	>
866	>	//local index of cutoff group is trivial, it only depends on the
867	>	//order of travesing
868	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
869	>	cg = mol->nextCutoffGroup(ci)) {
870	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
871	>	}
872		}
873	+	return GlobalGroupIndices;
874	+	}
875
876	+
877	+	void SimInfo::prepareTopology() {
878	+	int nExclude, nOneTwo, nOneThree, nOneFour;
879	+
880		//calculate mass ratio of cutoff group
902	–	std::vector<RealType> mfact;
881		SimInfo::MoleculeIterator mi;
882		Molecule* mol;
883		Molecule::CutoffGroupIterator ci;
#	Line 908 | Line 886 | namespace OpenMD {
886		Atom* atom;
887		RealType totalMass;
888
889	<	//to avoid memory reallocation, reserve enough space for mfact
890	<	mfact.reserve(getNCutoffGroups());
889	>	/**
890	>	* The mass factor is the relative mass of an atom to the total
891	>	* mass of the cutoff group it belongs to.  By default, all atoms
892	>	* are their own cutoff groups, and therefore have mass factors of
893	>	* 1.  We need some special handling for massless atoms, which
894	>	* will be treated as carrying the entire mass of the cutoff
895	>	* group.
896	>	*/
897	>	massFactors_.clear();
898	>	massFactors_.resize(getNAtoms(), 1.0);
899
900		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
901	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
901	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
902	>	cg = mol->nextCutoffGroup(ci)) {
903
904		totalMass = cg->getMass();
905		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
906		// Check for massless groups - set mfact to 1 if true
907	<	if (totalMass != 0)
908	<	mfact.push_back(atom->getMass()/totalMass);
907	>	if (totalMass != 0)
908	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
909		else
910	<	mfact.push_back( 1.0 );
910	>	massFactors_[atom->getLocalIndex()] = 1.0;
911		}
912		}
913		}
914
915	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
929	<	std::vector<int> identArray;
915	>	// Build the identArray_
916
917	<	//to avoid memory reallocation, reserve enough space identArray
918	<	identArray.reserve(getNAtoms());
933	<
917	>	identArray_.clear();
918	>	identArray_.reserve(getNAtoms());
919		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
920		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
921	<	identArray.push_back(atom->getIdent());
921	>	identArray_.push_back(atom->getIdent());
922		}
923		}
939	–
940	–	//fill molMembershipArray
941	–	//molMembershipArray is filled by SimCreator
942	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
943	–	for (int i = 0; i < nGlobalAtoms_; i++) {
944	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
945	–	}
924
925	<	//setup fortran simulation
925	>	//scan topology
926
927		nExclude = excludedInteractions_.getSize();
928		nOneTwo = oneTwoInteractions_.getSize();
#	Line 956 | Line 934 | namespace OpenMD {
934		int* oneThreeList = oneThreeInteractions_.getPairList();
935		int* oneFourList = oneFourInteractions_.getPairList();
936
937	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
938	<	&nExclude, excludeList,
961	<	&nOneTwo, oneTwoList,
962	<	&nOneThree, oneThreeList,
963	<	&nOneFour, oneFourList,
964	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
965	<	&fortranGlobalGroupMembership[0], &isError);
966	<
967	<	if( isError ){
968	<
969	<	sprintf( painCave.errMsg,
970	<	"There was an error setting the simulation information in fortran.\n" );
971	<	painCave.isFatal = 1;
972	<	painCave.severity = OPENMD_ERROR;
973	<	simError();
974	<	}
975	<
976	<
977	<	sprintf( checkPointMsg,
978	<	"succesfully sent the simulation information to fortran.\n");
979	<
980	<	errorCheckPoint();
981	<
982	<	// Setup number of neighbors in neighbor list if present
983	<	if (simParams_->haveNeighborListNeighbors()) {
984	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
985	<	setNeighbors(&nlistNeighbors);
986	<	}
987	<
937	>	topologyDone_ = true;
938	>	}
939
940	+	void SimInfo::addProperty(GenericData* genData) {
941	+	properties_.addProperty(genData);
942		}
943
944	+	void SimInfo::removeProperty(const string& propName) {
945	+	properties_.removeProperty(propName);
946	+	}
947
948	<	void SimInfo::setupFortranParallel() {
949	<	#ifdef IS_MPI
994	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
995	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
996	<	std::vector<int> localToGlobalCutoffGroupIndex;
997	<	SimInfo::MoleculeIterator mi;
998	<	Molecule::AtomIterator ai;
999	<	Molecule::CutoffGroupIterator ci;
1000	<	Molecule* mol;
1001	<	Atom* atom;
1002	<	CutoffGroup* cg;
1003	<	mpiSimData parallelData;
1004	<	int isError;
1005	<
1006	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1007	<
1008	<	//local index(index in DataStorge) of atom is important
1009	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1010	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1011	<	}
1012	<
1013	<	//local index of cutoff group is trivial, it only depends on the order of travesing
1014	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1015	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1016	<	}
1017	<
1018	<	}
1019	<
1020	<	//fill up mpiSimData struct
1021	<	parallelData.nMolGlobal = getNGlobalMolecules();
1022	<	parallelData.nMolLocal = getNMolecules();
1023	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
1024	<	parallelData.nAtomsLocal = getNAtoms();
1025	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1026	<	parallelData.nGroupsLocal = getNCutoffGroups();
1027	<	parallelData.myNode = worldRank;
1028	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1029	<
1030	<	//pass mpiSimData struct and index arrays to fortran
1031	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1032	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1033	<	&localToGlobalCutoffGroupIndex[0], &isError);
1034	<
1035	<	if (isError) {
1036	<	sprintf(painCave.errMsg,
1037	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1038	<	painCave.isFatal = 1;
1039	<	simError();
1040	<	}
1041	<
1042	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
1043	<	errorCheckPoint();
1044	<
1045	<	#endif
948	>	void SimInfo::clearProperties() {
949	>	properties_.clearProperties();
950		}
951
952	<	void SimInfo::setupCutoff() {
953	<
954	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1051	<
1052	<	// Check the cutoff policy
1053	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1054	<
1055	<	// Set LJ shifting bools to false
1056	<	ljsp_ = 0;
1057	<	ljsf_ = 0;
1058	<
1059	<	std::string myPolicy;
1060	<	if (forceFieldOptions_.haveCutoffPolicy()){
1061	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
1062	<	}else if (simParams_->haveCutoffPolicy()) {
1063	<	myPolicy = simParams_->getCutoffPolicy();
1064	<	}
1065	<
1066	<	if (!myPolicy.empty()){
1067	<	toUpper(myPolicy);
1068	<	if (myPolicy == "MIX") {
1069	<	cp = MIX_CUTOFF_POLICY;
1070	<	} else {
1071	<	if (myPolicy == "MAX") {
1072	<	cp = MAX_CUTOFF_POLICY;
1073	<	} else {
1074	<	if (myPolicy == "TRADITIONAL") {
1075	<	cp = TRADITIONAL_CUTOFF_POLICY;
1076	<	} else {
1077	<	// throw error
1078	<	sprintf( painCave.errMsg,
1079	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1080	<	painCave.isFatal = 1;
1081	<	simError();
1082	<	}
1083	<	}
1084	<	}
1085	<	}
1086	<	notifyFortranCutoffPolicy(&cp);
1087	<
1088	<	// Check the Skin Thickness for neighborlists
1089	<	RealType skin;
1090	<	if (simParams_->haveSkinThickness()) {
1091	<	skin = simParams_->getSkinThickness();
1092	<	notifyFortranSkinThickness(&skin);
1093	<	}
1094	<
1095	<	// Check if the cutoff was set explicitly:
1096	<	if (simParams_->haveCutoffRadius()) {
1097	<	rcut_ = simParams_->getCutoffRadius();
1098	<	if (simParams_->haveSwitchingRadius()) {
1099	<	rsw_  = simParams_->getSwitchingRadius();
1100	<	} else {
1101	<	if (fInfo_.SIM_uses_Charges |
1102	<	fInfo_.SIM_uses_Dipoles |
1103	<	fInfo_.SIM_uses_RF) {
1104	<
1105	<	rsw_ = 0.85 * rcut_;
1106	<	sprintf(painCave.errMsg,
1107	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1108	<	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1109	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1110	<	painCave.isFatal = 0;
1111	<	simError();
1112	<	} else {
1113	<	rsw_ = rcut_;
1114	<	sprintf(painCave.errMsg,
1115	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1116	<	"\tOpenMD will use the same value as the cutoffRadius.\n"
1117	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1118	<	painCave.isFatal = 0;
1119	<	simError();
1120	<	}
1121	<	}
1122	<
1123	<	if (simParams_->haveElectrostaticSummationMethod()) {
1124	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1125	<	toUpper(myMethod);
1126	<
1127	<	if (myMethod == "SHIFTED_POTENTIAL") {
1128	<	ljsp_ = 1;
1129	<	} else if (myMethod == "SHIFTED_FORCE") {
1130	<	ljsf_ = 1;
1131	<	}
1132	<	}
1133	<
1134	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
952	>	vector<string> SimInfo::getPropertyNames() {
953	>	return properties_.getPropertyNames();
954	>	}
955
956	<	} else {
957	<
1138	<	// For electrostatic atoms, we'll assume a large safe value:
1139	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1140	<	sprintf(painCave.errMsg,
1141	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1142	<	"\tOpenMD will use a default value of 15.0 angstroms"
1143	<	"\tfor the cutoffRadius.\n");
1144	<	painCave.isFatal = 0;
1145	<	simError();
1146	<	rcut_ = 15.0;
1147	<
1148	<	if (simParams_->haveElectrostaticSummationMethod()) {
1149	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1150	<	toUpper(myMethod);
1151	<
1152	<	// For the time being, we're tethering the LJ shifted behavior to the
1153	<	// electrostaticSummationMethod keyword options
1154	<	if (myMethod == "SHIFTED_POTENTIAL") {
1155	<	ljsp_ = 1;
1156	<	} else if (myMethod == "SHIFTED_FORCE") {
1157	<	ljsf_ = 1;
1158	<	}
1159	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1160	<	if (simParams_->haveSwitchingRadius()){
1161	<	sprintf(painCave.errMsg,
1162	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1163	<	"\teven though the electrostaticSummationMethod was\n"
1164	<	"\tset to %s\n", myMethod.c_str());
1165	<	painCave.isFatal = 1;
1166	<	simError();
1167	<	}
1168	<	}
1169	<	}
1170	<
1171	<	if (simParams_->haveSwitchingRadius()){
1172	<	rsw_ = simParams_->getSwitchingRadius();
1173	<	} else {
1174	<	sprintf(painCave.errMsg,
1175	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1176	<	"\tOpenMD will use a default value of\n"
1177	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1178	<	painCave.isFatal = 0;
1179	<	simError();
1180	<	rsw_ = 0.85 * rcut_;
1181	<	}
1182	<
1183	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1184	<
1185	<	} else {
1186	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1187	<	// We'll punt and let fortran figure out the cutoffs later.
1188	<
1189	<	notifyFortranYouAreOnYourOwn();
1190	<
1191	<	}
1192	<	}
956	>	vector<GenericData*> SimInfo::getProperties() {
957	>	return properties_.getProperties();
958		}
959
960	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1196	<
1197	<	int errorOut;
1198	<	int esm =  NONE;
1199	<	int sm = UNDAMPED;
1200	<	RealType alphaVal;
1201	<	RealType dielectric;
1202	<
1203	<	errorOut = isError;
1204	<
1205	<	if (simParams_->haveElectrostaticSummationMethod()) {
1206	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1207	<	toUpper(myMethod);
1208	<	if (myMethod == "NONE") {
1209	<	esm = NONE;
1210	<	} else {
1211	<	if (myMethod == "SWITCHING_FUNCTION") {
1212	<	esm = SWITCHING_FUNCTION;
1213	<	} else {
1214	<	if (myMethod == "SHIFTED_POTENTIAL") {
1215	<	esm = SHIFTED_POTENTIAL;
1216	<	} else {
1217	<	if (myMethod == "SHIFTED_FORCE") {
1218	<	esm = SHIFTED_FORCE;
1219	<	} else {
1220	<	if (myMethod == "REACTION_FIELD") {
1221	<	esm = REACTION_FIELD;
1222	<	dielectric = simParams_->getDielectric();
1223	<	if (!simParams_->haveDielectric()) {
1224	<	// throw warning
1225	<	sprintf( painCave.errMsg,
1226	<	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1227	<	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1228	<	painCave.isFatal = 0;
1229	<	simError();
1230	<	}
1231	<	} else {
1232	<	// throw error
1233	<	sprintf( painCave.errMsg,
1234	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1235	<	"\t(Input file specified %s .)\n"
1236	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1237	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1238	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1239	<	painCave.isFatal = 1;
1240	<	simError();
1241	<	}
1242	<	}
1243	<	}
1244	<	}
1245	<	}
1246	<	}
1247	<
1248	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1249	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1250	<	toUpper(myScreen);
1251	<	if (myScreen == "UNDAMPED") {
1252	<	sm = UNDAMPED;
1253	<	} else {
1254	<	if (myScreen == "DAMPED") {
1255	<	sm = DAMPED;
1256	<	if (!simParams_->haveDampingAlpha()) {
1257	<	// first set a cutoff dependent alpha value
1258	<	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1259	<	alphaVal = 0.5125 - rcut_* 0.025;
1260	<	// for values rcut > 20.5, alpha is zero
1261	<	if (alphaVal < 0) alphaVal = 0;
1262	<
1263	<	// throw warning
1264	<	sprintf( painCave.errMsg,
1265	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1266	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1267	<	painCave.isFatal = 0;
1268	<	simError();
1269	<	} else {
1270	<	alphaVal = simParams_->getDampingAlpha();
1271	<	}
1272	<
1273	<	} else {
1274	<	// throw error
1275	<	sprintf( painCave.errMsg,
1276	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1277	<	"\t(Input file specified %s .)\n"
1278	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1279	<	"or \"damped\".\n", myScreen.c_str() );
1280	<	painCave.isFatal = 1;
1281	<	simError();
1282	<	}
1283	<	}
1284	<	}
1285	<
1286	<	// let's pass some summation method variables to fortran
1287	<	setElectrostaticSummationMethod( &esm );
1288	<	setFortranElectrostaticMethod( &esm );
1289	<	setScreeningMethod( &sm );
1290	<	setDampingAlpha( &alphaVal );
1291	<	setReactionFieldDielectric( &dielectric );
1292	<	initFortranFF( &errorOut );
1293	<	}
1294	<
1295	<	void SimInfo::setupSwitchingFunction() {
1296	<	int ft = CUBIC;
1297	<
1298	<	if (simParams_->haveSwitchingFunctionType()) {
1299	<	std::string funcType = simParams_->getSwitchingFunctionType();
1300	<	toUpper(funcType);
1301	<	if (funcType == "CUBIC") {
1302	<	ft = CUBIC;
1303	<	} else {
1304	<	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1305	<	ft = FIFTH_ORDER_POLY;
1306	<	} else {
1307	<	// throw error
1308	<	sprintf( painCave.errMsg,
1309	<	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1310	<	painCave.isFatal = 1;
1311	<	simError();
1312	<	}
1313	<	}
1314	<	}
1315	<
1316	<	// send switching function notification to switcheroo
1317	<	setFunctionType(&ft);
1318	<
1319	<	}
1320	<
1321	<	void SimInfo::setupAccumulateBoxDipole() {
1322	<
1323	<	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1324	<	if ( simParams_->haveAccumulateBoxDipole() )
1325	<	if ( simParams_->getAccumulateBoxDipole() ) {
1326	<	setAccumulateBoxDipole();
1327	<	calcBoxDipole_ = true;
1328	<	}
1329	<
1330	<	}
1331	<
1332	<	void SimInfo::addProperty(GenericData* genData) {
1333	<	properties_.addProperty(genData);
1334	<	}
1335	<
1336	<	void SimInfo::removeProperty(const std::string& propName) {
1337	<	properties_.removeProperty(propName);
1338	<	}
1339	<
1340	<	void SimInfo::clearProperties() {
1341	<	properties_.clearProperties();
1342	<	}
1343	<
1344	<	std::vector<std::string> SimInfo::getPropertyNames() {
1345	<	return properties_.getPropertyNames();
1346	<	}
1347	<
1348	<	std::vector<GenericData*> SimInfo::getProperties() {
1349	<	return properties_.getProperties();
1350	<	}
1351	<
1352	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
960	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
961		return properties_.getPropertyByName(propName);
962		}
963
#	Line 1363 | Line 971 | namespace OpenMD {
971		Molecule* mol;
972		RigidBody* rb;
973		Atom* atom;
974	+	CutoffGroup* cg;
975		SimInfo::MoleculeIterator mi;
976		Molecule::RigidBodyIterator rbIter;
977	<	Molecule::AtomIterator atomIter;;
977	>	Molecule::AtomIterator atomIter;
978	>	Molecule::CutoffGroupIterator cgIter;
979
980		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
981
#	Line 1376 | Line 986 | namespace OpenMD {
986		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
987		rb->setSnapshotManager(sman_);
988		}
989	+
990	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
991	+	cg->setSnapshotManager(sman_);
992	+	}
993		}
994
995		}
996
1383	–	Vector3d SimInfo::getComVel(){
1384	–	SimInfo::MoleculeIterator i;
1385	–	Molecule* mol;
997
998	<	Vector3d comVel(0.0);
1388	<	RealType totalMass = 0.0;
1389	<
1390	<
1391	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1392	<	RealType mass = mol->getMass();
1393	<	totalMass += mass;
1394	<	comVel += mass * mol->getComVel();
1395	<	}
998	>	ostream& operator <<(ostream& o, SimInfo& info) {
999
1397	–	#ifdef IS_MPI
1398	–	RealType tmpMass = totalMass;
1399	–	Vector3d tmpComVel(comVel);
1400	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1401	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1402	–	#endif
1403	–
1404	–	comVel /= totalMass;
1405	–
1406	–	return comVel;
1407	–	}
1408	–
1409	–	Vector3d SimInfo::getCom(){
1410	–	SimInfo::MoleculeIterator i;
1411	–	Molecule* mol;
1412	–
1413	–	Vector3d com(0.0);
1414	–	RealType totalMass = 0.0;
1415	–
1416	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1417	–	RealType mass = mol->getMass();
1418	–	totalMass += mass;
1419	–	com += mass * mol->getCom();
1420	–	}
1421	–
1422	–	#ifdef IS_MPI
1423	–	RealType tmpMass = totalMass;
1424	–	Vector3d tmpCom(com);
1425	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1426	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1427	–	#endif
1428	–
1429	–	com /= totalMass;
1430	–
1431	–	return com;
1432	–
1433	–	}
1434	–
1435	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1436	–
1000		return o;
1001		}
1002
1003	<
1441	<	/*
1442	<	Returns center of mass and center of mass velocity in one function call.
1443	<	*/
1444	<
1445	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1446	<	SimInfo::MoleculeIterator i;
1447	<	Molecule* mol;
1448	<
1449	<
1450	<	RealType totalMass = 0.0;
1451	<
1452	<
1453	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1454	<	RealType mass = mol->getMass();
1455	<	totalMass += mass;
1456	<	com += mass * mol->getCom();
1457	<	comVel += mass * mol->getComVel();
1458	<	}
1459	<
1460	<	#ifdef IS_MPI
1461	<	RealType tmpMass = totalMass;
1462	<	Vector3d tmpCom(com);
1463	<	Vector3d tmpComVel(comVel);
1464	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1465	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1466	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1467	<	#endif
1468	<
1469	<	com /= totalMass;
1470	<	comVel /= totalMass;
1471	<	}
1472	<
1473	<	/*
1474	<	Return intertia tensor for entire system and angular momentum Vector.
1475	<
1476	<
1477	<	[  Ixx -Ixy  -Ixz ]
1478	<	J =| -Iyx  Iyy  -Iyz |
1479	<	[ -Izx -Iyz   Izz ]
1480	<	*/
1481	<
1482	<	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1483	<
1484	<
1485	<	RealType xx = 0.0;
1486	<	RealType yy = 0.0;
1487	<	RealType zz = 0.0;
1488	<	RealType xy = 0.0;
1489	<	RealType xz = 0.0;
1490	<	RealType yz = 0.0;
1491	<	Vector3d com(0.0);
1492	<	Vector3d comVel(0.0);
1493	<
1494	<	getComAll(com, comVel);
1495	<
1496	<	SimInfo::MoleculeIterator i;
1497	<	Molecule* mol;
1498	<
1499	<	Vector3d thisq(0.0);
1500	<	Vector3d thisv(0.0);
1501	<
1502	<	RealType thisMass = 0.0;
1503	<
1504	<
1505	<
1506	<
1507	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1508	<
1509	<	thisq = mol->getCom()-com;
1510	<	thisv = mol->getComVel()-comVel;
1511	<	thisMass = mol->getMass();
1512	<	// Compute moment of intertia coefficients.
1513	<	xx += thisq[0]*thisq[0]*thisMass;
1514	<	yy += thisq[1]*thisq[1]*thisMass;
1515	<	zz += thisq[2]*thisq[2]*thisMass;
1516	<
1517	<	// compute products of intertia
1518	<	xy += thisq[0]*thisq[1]*thisMass;
1519	<	xz += thisq[0]*thisq[2]*thisMass;
1520	<	yz += thisq[1]*thisq[2]*thisMass;
1521	<
1522	<	angularMomentum += cross( thisq, thisv ) * thisMass;
1523	<
1524	<	}
1525	<
1526	<
1527	<	inertiaTensor(0,0) = yy + zz;
1528	<	inertiaTensor(0,1) = -xy;
1529	<	inertiaTensor(0,2) = -xz;
1530	<	inertiaTensor(1,0) = -xy;
1531	<	inertiaTensor(1,1) = xx + zz;
1532	<	inertiaTensor(1,2) = -yz;
1533	<	inertiaTensor(2,0) = -xz;
1534	<	inertiaTensor(2,1) = -yz;
1535	<	inertiaTensor(2,2) = xx + yy;
1536	<
1537	<	#ifdef IS_MPI
1538	<	Mat3x3d tmpI(inertiaTensor);
1539	<	Vector3d tmpAngMom;
1540	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1541	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1542	<	#endif
1543	<
1544	<	return;
1545	<	}
1546	<
1547	<	//Returns the angular momentum of the system
1548	<	Vector3d SimInfo::getAngularMomentum(){
1549	<
1550	<	Vector3d com(0.0);
1551	<	Vector3d comVel(0.0);
1552	<	Vector3d angularMomentum(0.0);
1553	<
1554	<	getComAll(com,comVel);
1555	<
1556	<	SimInfo::MoleculeIterator i;
1557	<	Molecule* mol;
1558	<
1559	<	Vector3d thisr(0.0);
1560	<	Vector3d thisp(0.0);
1561	<
1562	<	RealType thisMass;
1563	<
1564	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1565	<	thisMass = mol->getMass();
1566	<	thisr = mol->getCom()-com;
1567	<	thisp = (mol->getComVel()-comVel)*thisMass;
1568	<
1569	<	angularMomentum += cross( thisr, thisp );
1570	<
1571	<	}
1572	<
1573	<	#ifdef IS_MPI
1574	<	Vector3d tmpAngMom;
1575	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1576	<	#endif
1577	<
1578	<	return angularMomentum;
1579	<	}
1580	<
1003	>
1004		StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1005		return IOIndexToIntegrableObject.at(index);
1006		}
1007
1008	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1008	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1009		IOIndexToIntegrableObject= v;
1010		}
1588	–
1589	–	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1590	–	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1591	–	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1592	–	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1593	–	*/
1594	–	void SimInfo::getGyrationalVolume(RealType &volume){
1595	–	Mat3x3d intTensor;
1596	–	RealType det;
1597	–	Vector3d dummyAngMom;
1598	–	RealType sysconstants;
1599	–	RealType geomCnst;
1600	–
1601	–	geomCnst = 3.0/2.0;
1602	–	/* Get the inertial tensor and angular momentum for free*/
1603	–	getInertiaTensor(intTensor,dummyAngMom);
1604	–
1605	–	det = intTensor.determinant();
1606	–	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1607	–	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1608	–	return;
1609	–	}
1610	–
1611	–	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1612	–	Mat3x3d intTensor;
1613	–	Vector3d dummyAngMom;
1614	–	RealType sysconstants;
1615	–	RealType geomCnst;
1616	–
1617	–	geomCnst = 3.0/2.0;
1618	–	/* Get the inertial tensor and angular momentum for free*/
1619	–	getInertiaTensor(intTensor,dummyAngMom);
1620	–
1621	–	detI = intTensor.determinant();
1622	–	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1623	–	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1624	–	return;
1625	–	}
1011		/*
1012	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1012	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1013		assert( v.size() == nAtoms_ + nRigidBodies_);
1014		sdByGlobalIndex_ = v;
1015		}
#	Line 1634 | Line 1019 | namespace OpenMD {
1019		return sdByGlobalIndex_.at(index);
1020		}
1021		*/
1022	+	int SimInfo::getNGlobalConstraints() {
1023	+	int nGlobalConstraints;
1024	+	#ifdef IS_MPI
1025	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1026	+	MPI_COMM_WORLD);
1027	+	#else
1028	+	nGlobalConstraints =  nConstraints_;
1029	+	#endif
1030	+	return nGlobalConstraints;
1031	+	}
1032	+
1033		}//end namespace OpenMD
1034

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