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

Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1505 by gezelter, Sun Oct 3 22:18:59 2010 UTC vs.
Revision 1779 by gezelter, Mon Aug 20 17:51:39 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/fSwitchingFunctionType.h"
59	–	#include "UseTheForce/doForces_interface.h"
60	–	#include "UseTheForce/DarkSide/neighborLists_interface.h"
61	–	#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	<
68	<
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"
72	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68	+	using namespace std;
69		namespace OpenMD {
75	–	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
76	–	std::map<int, std::set<int> >::iterator i = container.find(index);
77	–	std::set<int> result;
78	–	if (i != container.end()) {
79	–	result = i->second;
80	–	}
81	–
82	–	return result;
83	–	}
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();
92	>	i !=components.end(); ++i) {
93	>	molStamp = (*i)->getMoleculeStamp();
94	>	nMolWithSameStamp = (*i)->getNMol();
95
96	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
97	<	molStamp = (*i)->getMoleculeStamp();
98	<	nMolWithSameStamp = (*i)->getNMol();
99	<
100	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
101	<
102	<	//calculate atoms in molecules
103	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
104	<
105	<	//calculate atoms in cutoff groups
106	<	int nAtomsInGroups = 0;
107	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
118	<
119	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
120	<	cgStamp = molStamp->getCutoffGroupStamp(j);
121	<	nAtomsInGroups += cgStamp->getNMembers();
122	<	}
123	<
124	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
125	<
126	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
127	<
128	<	//calculate atoms in rigid bodies
129	<	int nAtomsInRigidBodies = 0;
130	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
131	<
132	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
133	<	rbStamp = molStamp->getRigidBodyStamp(j);
134	<	nAtomsInRigidBodies += rbStamp->getNMembers();
135	<	}
136	<
137	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
138	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
139	<
96	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
97	>
98	>	//calculate atoms in molecules
99	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
100	>
101	>	//calculate atoms in cutoff groups
102	>	int nAtomsInGroups = 0;
103	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
104	>
105	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
106	>	cgStamp = molStamp->getCutoffGroupStamp(j);
107	>	nAtomsInGroups += cgStamp->getNMembers();
108		}
109	<
110	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
111	<	//group therefore the total number of cutoff groups in the system is
112	<	//equal to the total number of atoms minus number of atoms belong to
113	<	//cutoff group defined in meta-data file plus the number of cutoff
114	<	//groups defined in meta-data file
115	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
116	<
117	<	//every free atom (atom does not belong to rigid bodies) is an
118	<	//integrable object therefore the total number of integrable objects
119	<	//in the system is equal to the total number of atoms minus number of
120	<	//atoms belong to rigid body defined in meta-data file plus the number
121	<	//of rigid bodies defined in meta-data file
122	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
123	<	+ nGlobalRigidBodies_;
124	<
125	<	nGlobalMols_ = molStampIds_.size();
158	<	molToProcMap_.resize(nGlobalMols_);
109	>
110	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
111	>
112	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
113	>
114	>	//calculate atoms in rigid bodies
115	>	int nAtomsInRigidBodies = 0;
116	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
117	>
118	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
119	>	rbStamp = molStamp->getRigidBodyStamp(j);
120	>	nAtomsInRigidBodies += rbStamp->getNMembers();
121	>	}
122	>
123	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
124	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
125	>
126		}
127	+
128	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
129	+	//group therefore the total number of cutoff groups in the system is
130	+	//equal to the total number of atoms minus number of atoms belong to
131	+	//cutoff group defined in meta-data file plus the number of cutoff
132	+	//groups defined in meta-data file
133
134	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
135	+
136	+	//every free atom (atom does not belong to rigid bodies) is an
137	+	//integrable object therefore the total number of integrable objects
138	+	//in the system is equal to the total number of atoms minus number of
139	+	//atoms belong to rigid body defined in meta-data file plus the number
140	+	//of rigid bodies defined in meta-data file
141	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
142	+	+ nGlobalRigidBodies_;
143	+
144	+	nGlobalMols_ = molStampIds_.size();
145	+	molToProcMap_.resize(nGlobalMols_);
146	+	}
147	+
148		SimInfo::~SimInfo() {
149	<	std::map<int, Molecule*>::iterator i;
149	>	map<int, Molecule*>::iterator i;
150		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
151		delete i->second;
152		}
#	Line 170 | Line 157 | namespace OpenMD {
157		delete forceField_;
158		}
159
173	–	int SimInfo::getNGlobalConstraints() {
174	–	int nGlobalConstraints;
175	–	#ifdef IS_MPI
176	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
177	–	MPI_COMM_WORLD);
178	–	#else
179	–	nGlobalConstraints =  nConstraints_;
180	–	#endif
181	–	return nGlobalConstraints;
182	–	}
160
161		bool SimInfo::addMolecule(Molecule* mol) {
162		MoleculeIterator i;
163	<
163	>
164		i = molecules_.find(mol->getGlobalIndex());
165		if (i == molecules_.end() ) {
166	<
167	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
168	<
166	>
167	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
168	>
169		nAtoms_ += mol->getNAtoms();
170		nBonds_ += mol->getNBonds();
171		nBends_ += mol->getNBends();
#	Line 198 | Line 175 | namespace OpenMD {
175		nIntegrableObjects_ += mol->getNIntegrableObjects();
176		nCutoffGroups_ += mol->getNCutoffGroups();
177		nConstraints_ += mol->getNConstraintPairs();
178	<
178	>
179		addInteractionPairs(mol);
180	<
180	>
181		return true;
182		} else {
183		return false;
184		}
185		}
186	<
186	>
187		bool SimInfo::removeMolecule(Molecule* mol) {
188		MoleculeIterator i;
189		i = molecules_.find(mol->getGlobalIndex());
#	Line 234 | Line 211 | namespace OpenMD {
211		} else {
212		return false;
213		}
237	–
238	–
214		}
215
216
#	Line 251 | Line 226 | namespace OpenMD {
226
227
228		void SimInfo::calcNdf() {
229	<	int ndf_local;
229	>	int ndf_local, nfq_local;
230		MoleculeIterator i;
231	<	std::vector<StuntDouble*>::iterator j;
231	>	vector<StuntDouble*>::iterator j;
232	>	vector<Atom*>::iterator k;
233	>
234		Molecule* mol;
235	<	StuntDouble* integrableObject;
235	>	StuntDouble* sd;
236	>	Atom* atom;
237
238		ndf_local = 0;
239	+	nfq_local = 0;
240
241		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
263	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
264	–	integrableObject = mol->nextIntegrableObject(j)) {
242
243	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
244	+	sd = mol->nextIntegrableObject(j)) {
245	+
246		ndf_local += 3;
247
248	<	if (integrableObject->isDirectional()) {
249	<	if (integrableObject->isLinear()) {
248	>	if (sd->isDirectional()) {
249	>	if (sd->isLinear()) {
250		ndf_local += 2;
251		} else {
252		ndf_local += 3;
253		}
254		}
275	–
255		}
256	+
257	+	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
258	+	atom = mol->nextFluctuatingCharge(k)) {
259	+	if (atom->isFluctuatingCharge()) {
260	+	nfq_local++;
261	+	}
262	+	}
263		}
264
265	+	ndfLocal_ = ndf_local;
266	+
267		// n_constraints is local, so subtract them on each processor
268		ndf_local -= nConstraints_;
269
270		#ifdef IS_MPI
271		MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
272	+	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
273		#else
274		ndf_ = ndf_local;
275	+	nGlobalFluctuatingCharges_ = nfq_local;
276		#endif
277
278		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 299 | Line 289 | namespace OpenMD {
289		#endif
290		return fdf_;
291		}
292	+
293	+	unsigned int SimInfo::getNLocalCutoffGroups(){
294	+	int nLocalCutoffAtoms = 0;
295	+	Molecule* mol;
296	+	MoleculeIterator mi;
297	+	CutoffGroup* cg;
298	+	Molecule::CutoffGroupIterator ci;
299
300	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
301	+
302	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
303	+	cg = mol->nextCutoffGroup(ci)) {
304	+	nLocalCutoffAtoms += cg->getNumAtom();
305	+
306	+	}
307	+	}
308	+
309	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
310	+	}
311	+
312		void SimInfo::calcNdfRaw() {
313		int ndfRaw_local;
314
315		MoleculeIterator i;
316	<	std::vector<StuntDouble*>::iterator j;
316	>	vector<StuntDouble*>::iterator j;
317		Molecule* mol;
318	<	StuntDouble* integrableObject;
318	>	StuntDouble* sd;
319
320		// Raw degrees of freedom that we have to set
321		ndfRaw_local = 0;
322
323		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
315	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
316	–	integrableObject = mol->nextIntegrableObject(j)) {
324
325	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
326	+	sd = mol->nextIntegrableObject(j)) {
327	+
328		ndfRaw_local += 3;
329
330	<	if (integrableObject->isDirectional()) {
331	<	if (integrableObject->isLinear()) {
330	>	if (sd->isDirectional()) {
331	>	if (sd->isLinear()) {
332		ndfRaw_local += 2;
333		} else {
334		ndfRaw_local += 3;
#	Line 353 | Line 363 | namespace OpenMD {
363
364		void SimInfo::addInteractionPairs(Molecule* mol) {
365		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
366	<	std::vector<Bond*>::iterator bondIter;
367	<	std::vector<Bend*>::iterator bendIter;
368	<	std::vector<Torsion*>::iterator torsionIter;
369	<	std::vector<Inversion*>::iterator inversionIter;
366	>	vector<Bond*>::iterator bondIter;
367	>	vector<Bend*>::iterator bendIter;
368	>	vector<Torsion*>::iterator torsionIter;
369	>	vector<Inversion*>::iterator inversionIter;
370		Bond* bond;
371		Bend* bend;
372		Torsion* torsion;
#	Line 374 | Line 384 | namespace OpenMD {
384		// always be excluded.  These are done at the bottom of this
385		// function.
386
387	<	std::map<int, std::set<int> > atomGroups;
387	>	map<int, set<int> > atomGroups;
388		Molecule::RigidBodyIterator rbIter;
389		RigidBody* rb;
390		Molecule::IntegrableObjectIterator ii;
391	<	StuntDouble* integrableObject;
391	>	StuntDouble* sd;
392
393	<	for (integrableObject = mol->beginIntegrableObject(ii);
394	<	integrableObject != NULL;
385	<	integrableObject = mol->nextIntegrableObject(ii)) {
393	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
394	>	sd = mol->nextIntegrableObject(ii)) {
395
396	<	if (integrableObject->isRigidBody()) {
397	<	rb = static_cast<RigidBody*>(integrableObject);
398	<	std::vector<Atom*> atoms = rb->getAtoms();
399	<	std::set<int> rigidAtoms;
396	>	if (sd->isRigidBody()) {
397	>	rb = static_cast<RigidBody*>(sd);
398	>	vector<Atom*> atoms = rb->getAtoms();
399	>	set<int> rigidAtoms;
400		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
401		rigidAtoms.insert(atoms[i]->getGlobalIndex());
402		}
403		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
404	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
404	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
405		}
406		} else {
407	<	std::set<int> oneAtomSet;
408	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
409	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
407	>	set<int> oneAtomSet;
408	>	oneAtomSet.insert(sd->getGlobalIndex());
409	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
410		}
411		}
412
#	Line 500 | Line 509 | namespace OpenMD {
509
510		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
511		rb = mol->nextRigidBody(rbIter)) {
512	<	std::vector<Atom*> atoms = rb->getAtoms();
512	>	vector<Atom*> atoms = rb->getAtoms();
513		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
514		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
515		a = atoms[i]->getGlobalIndex();
#	Line 514 | Line 523 | namespace OpenMD {
523
524		void SimInfo::removeInteractionPairs(Molecule* mol) {
525		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
526	<	std::vector<Bond*>::iterator bondIter;
527	<	std::vector<Bend*>::iterator bendIter;
528	<	std::vector<Torsion*>::iterator torsionIter;
529	<	std::vector<Inversion*>::iterator inversionIter;
526	>	vector<Bond*>::iterator bondIter;
527	>	vector<Bend*>::iterator bendIter;
528	>	vector<Torsion*>::iterator torsionIter;
529	>	vector<Inversion*>::iterator inversionIter;
530		Bond* bond;
531		Bend* bend;
532		Torsion* torsion;
#	Line 527 | Line 536 | namespace OpenMD {
536		int c;
537		int d;
538
539	<	std::map<int, std::set<int> > atomGroups;
539	>	map<int, set<int> > atomGroups;
540		Molecule::RigidBodyIterator rbIter;
541		RigidBody* rb;
542		Molecule::IntegrableObjectIterator ii;
543	<	StuntDouble* integrableObject;
543	>	StuntDouble* sd;
544
545	<	for (integrableObject = mol->beginIntegrableObject(ii);
546	<	integrableObject != NULL;
538	<	integrableObject = mol->nextIntegrableObject(ii)) {
545	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
546	>	sd = mol->nextIntegrableObject(ii)) {
547
548	<	if (integrableObject->isRigidBody()) {
549	<	rb = static_cast<RigidBody*>(integrableObject);
550	<	std::vector<Atom*> atoms = rb->getAtoms();
551	<	std::set<int> rigidAtoms;
548	>	if (sd->isRigidBody()) {
549	>	rb = static_cast<RigidBody*>(sd);
550	>	vector<Atom*> atoms = rb->getAtoms();
551	>	set<int> rigidAtoms;
552		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
553		rigidAtoms.insert(atoms[i]->getGlobalIndex());
554		}
555		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
556	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
556	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
557		}
558		} else {
559	<	std::set<int> oneAtomSet;
560	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
561	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
559	>	set<int> oneAtomSet;
560	>	oneAtomSet.insert(sd->getGlobalIndex());
561	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
562		}
563		}
564
#	Line 653 | Line 661 | namespace OpenMD {
661
662		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
663		rb = mol->nextRigidBody(rbIter)) {
664	<	std::vector<Atom*> atoms = rb->getAtoms();
664	>	vector<Atom*> atoms = rb->getAtoms();
665		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
666		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
667		a = atoms[i]->getGlobalIndex();
#	Line 676 | Line 684 | namespace OpenMD {
684		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
685		}
686
679	–	void SimInfo::update() {
687
688	<	setupSimType();
689	<
690	<	#ifdef IS_MPI
691	<	setupFortranParallel();
692	<	#endif
693	<
694	<	setupFortranSim();
695	<
696	<	//setup fortran force field
690	<	/** @deprecate */
691	<	int isError = 0;
692	<
693	<	setupCutoff();
694	<
695	<	setupElectrostaticSummationMethod( isError );
696	<	setupSwitchingFunction();
697	<	setupAccumulateBoxDipole();
698	<
699	<	if(isError){
700	<	sprintf( painCave.errMsg,
701	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
702	<	painCave.isFatal = 1;
703	<	simError();
704	<	}
705	<
688	>	/**
689	>	* update
690	>	*
691	>	*  Performs the global checks and variable settings after the
692	>	*  objects have been created.
693	>	*
694	>	*/
695	>	void SimInfo::update() {
696	>	setupSimVariables();
697		calcNdf();
698		calcNdfRaw();
699		calcNdfTrans();
709	–
710	–	fortranInitialized_ = true;
700		}
701	<
702	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
701	>
702	>	/**
703	>	* getSimulatedAtomTypes
704	>	*
705	>	* Returns an STL set of AtomType* that are actually present in this
706	>	* simulation.  Must query all processors to assemble this information.
707	>	*
708	>	*/
709	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
710		SimInfo::MoleculeIterator mi;
711		Molecule* mol;
712		Molecule::AtomIterator ai;
713		Atom* atom;
714	<	std::set<AtomType*> atomTypes;
715	<
714	>	set<AtomType*> atomTypes;
715	>
716		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
717	<
718	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
717	>	for(atom = mol->beginAtom(ai); atom != NULL;
718	>	atom = mol->nextAtom(ai)) {
719		atomTypes.insert(atom->getAtomType());
720	<	}
721	<
726	<	}
727	<
728	<	return atomTypes;
729	<	}
730	<
731	<	void SimInfo::setupSimType() {
732	<	std::set<AtomType*>::iterator i;
733	<	std::set<AtomType*> atomTypes;
734	<	atomTypes = getUniqueAtomTypes();
720	>	}
721	>	}
722
723	<	int useLennardJones = 0;
737	<	int useElectrostatic = 0;
738	<	int useEAM = 0;
739	<	int useSC = 0;
740	<	int useCharge = 0;
741	<	int useDirectional = 0;
742	<	int useDipole = 0;
743	<	int useGayBerne = 0;
744	<	int useSticky = 0;
745	<	int useStickyPower = 0;
746	<	int useShape = 0;
747	<	int useFLARB = 0; //it is not in AtomType yet
748	<	int useDirectionalAtom = 0;
749	<	int useElectrostatics = 0;
750	<	//usePBC and useRF are from simParams
751	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
752	<	int useRF;
753	<	int useSF;
754	<	int useSP;
755	<	int useBoxDipole;
723	>	#ifdef IS_MPI
724
725	<	std::string myMethod;
726	<
759	<	// set the useRF logical
760	<	useRF = 0;
761	<	useSF = 0;
762	<	useSP = 0;
763	<	useBoxDipole = 0;
764	<
765	<	if (simParams_->haveElectrostaticSummationMethod()) {
766	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
767	<	toUpper(myMethod);
768	<	if (myMethod == "REACTION_FIELD"){
769	<	useRF = 1;
770	<	} else if (myMethod == "SHIFTED_FORCE"){
771	<	useSF = 1;
772	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
773	<	useSP = 1;
774	<	}
775	<	}
725	>	// loop over the found atom types on this processor, and add their
726	>	// numerical idents to a vector:
727
728	<	if (simParams_->haveAccumulateBoxDipole())
729	<	if (simParams_->getAccumulateBoxDipole())
730	<	useBoxDipole = 1;
728	>	vector<int> foundTypes;
729	>	set<AtomType*>::iterator i;
730	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
731	>	foundTypes.push_back( (*i)->getIdent() );
732
733	<	useAtomicVirial_ = simParams_->getUseAtomicVirial();
733	>	// count_local holds the number of found types on this processor
734	>	int count_local = foundTypes.size();
735
736	<	//loop over all of the atom types
784	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
785	<	useLennardJones |= (*i)->isLennardJones();
786	<	useElectrostatic |= (*i)->isElectrostatic();
787	<	useEAM |= (*i)->isEAM();
788	<	useSC |= (*i)->isSC();
789	<	useCharge |= (*i)->isCharge();
790	<	useDirectional |= (*i)->isDirectional();
791	<	useDipole |= (*i)->isDipole();
792	<	useGayBerne |= (*i)->isGayBerne();
793	<	useSticky |= (*i)->isSticky();
794	<	useStickyPower |= (*i)->isStickyPower();
795	<	useShape |= (*i)->isShape();
796	<	}
736	>	int nproc = MPI::COMM_WORLD.Get_size();
737
738	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
739	<	useDirectionalAtom = 1;
740	<	}
738	>	// we need arrays to hold the counts and displacement vectors for
739	>	// all processors
740	>	vector<int> counts(nproc, 0);
741	>	vector<int> disps(nproc, 0);
742
743	<	if (useCharge || useDipole) {
744	<	useElectrostatics = 1;
743	>	// fill the counts array
744	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
745	>	1, MPI::INT);
746	>
747	>	// use the processor counts to compute the displacement array
748	>	disps[0] = 0;
749	>	int totalCount = counts[0];
750	>	for (int iproc = 1; iproc < nproc; iproc++) {
751	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
752	>	totalCount += counts[iproc];
753		}
754
755	<	#ifdef IS_MPI
756	<	int temp;
755	>	// we need a (possibly redundant) set of all found types:
756	>	vector<int> ftGlobal(totalCount);
757	>
758	>	// now spray out the foundTypes to all the other processors:
759	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
760	>	&ftGlobal[0], &counts[0], &disps[0],
761	>	MPI::INT);
762
763	<	temp = usePBC;
810	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
763	>	vector<int>::iterator j;
764
765	<	temp = useDirectionalAtom;
766	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
765	>	// foundIdents is a stl set, so inserting an already found ident
766	>	// will have no effect.
767	>	set<int> foundIdents;
768
769	<	temp = useLennardJones;
770	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
770	>	foundIdents.insert((*j));
771	>
772	>	// now iterate over the foundIdents and get the actual atom types
773	>	// that correspond to these:
774	>	set<int>::iterator it;
775	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
776	>	atomTypes.insert( forceField_->getAtomType((*it)) );
777	>
778	>	#endif
779
780	<	temp = useElectrostatics;
781	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
780	>	return atomTypes;
781	>	}
782
783	<	temp = useCharge;
784	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
783	>	void SimInfo::setupSimVariables() {
784	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
785	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
786	>	// parameter is true
787	>	calcBoxDipole_ = false;
788	>	if ( simParams_->haveAccumulateBoxDipole() )
789	>	if ( simParams_->getAccumulateBoxDipole() ) {
790	>	calcBoxDipole_ = true;
791	>	}
792	>
793	>	set<AtomType*>::iterator i;
794	>	set<AtomType*> atomTypes;
795	>	atomTypes = getSimulatedAtomTypes();
796	>	bool usesElectrostatic = false;
797	>	bool usesMetallic = false;
798	>	bool usesDirectional = false;
799	>	bool usesFluctuatingCharges =  false;
800	>	//loop over all of the atom types
801	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
802	>	usesElectrostatic |= (*i)->isElectrostatic();
803	>	usesMetallic |= (*i)->isMetal();
804	>	usesDirectional |= (*i)->isDirectional();
805	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
806	>	}
807
808	<	temp = useDipole;
809	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810	<
811	<	temp = useSticky;
812	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813	<
814	<	temp = useStickyPower;
815	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
808	>	#ifdef IS_MPI
809	>	bool temp;
810	>	temp = usesDirectional;
811	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
812	>	MPI::LOR);
813	>
814	>	temp = usesMetallic;
815	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
816	>	MPI::LOR);
817
818	<	temp = useGayBerne;
819	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
818	>	temp = usesElectrostatic;
819	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
820	>	MPI::LOR);
821
822	<	temp = useEAM;
823	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
822	>	temp = usesFluctuatingCharges;
823	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
824	>	MPI::LOR);
825	>	#else
826
827	<	temp = useSC;
828	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
827	>	usesDirectionalAtoms_ = usesDirectional;
828	>	usesMetallicAtoms_ = usesMetallic;
829	>	usesElectrostaticAtoms_ = usesElectrostatic;
830	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
831	>
832	>	#endif
833
834	<	temp = useShape;
835	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
834	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
835	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
836	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
837	>	}
838
845	–	temp = useFLARB;
846	–	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
839
840	<	temp = useRF;
841	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
840	>	vector<int> SimInfo::getGlobalAtomIndices() {
841	>	SimInfo::MoleculeIterator mi;
842	>	Molecule* mol;
843	>	Molecule::AtomIterator ai;
844	>	Atom* atom;
845
846	<	temp = useSF;
847	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
846	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
847	>
848	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
849	>
850	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
851	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
852	>	}
853	>	}
854	>	return GlobalAtomIndices;
855	>	}
856
854	–	temp = useSP;
855	–	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
857
858	<	temp = useBoxDipole;
859	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
858	>	vector<int> SimInfo::getGlobalGroupIndices() {
859	>	SimInfo::MoleculeIterator mi;
860	>	Molecule* mol;
861	>	Molecule::CutoffGroupIterator ci;
862	>	CutoffGroup* cg;
863
864	<	temp = useAtomicVirial_;
865	<	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
866	<
867	<	#endif
868	<	fInfo_.SIM_uses_PBC = usePBC;
869	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
870	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
871	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
872	<	fInfo_.SIM_uses_Charges = useCharge;
873	<	fInfo_.SIM_uses_Dipoles = useDipole;
874	<	fInfo_.SIM_uses_Sticky = useSticky;
875	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
872	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
873	<	fInfo_.SIM_uses_EAM = useEAM;
874	<	fInfo_.SIM_uses_SC = useSC;
875	<	fInfo_.SIM_uses_Shapes = useShape;
876	<	fInfo_.SIM_uses_FLARB = useFLARB;
877	<	fInfo_.SIM_uses_RF = useRF;
878	<	fInfo_.SIM_uses_SF = useSF;
879	<	fInfo_.SIM_uses_SP = useSP;
880	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
881	<	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
864	>	vector<int> GlobalGroupIndices;
865	>
866	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
867	>
868	>	//local index of cutoff group is trivial, it only depends on the
869	>	//order of travesing
870	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
871	>	cg = mol->nextCutoffGroup(ci)) {
872	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
873	>	}
874	>	}
875	>	return GlobalGroupIndices;
876		}
877
878	<	void SimInfo::setupFortranSim() {
879	<	int isError;
878	>
879	>	void SimInfo::prepareTopology() {
880		int nExclude, nOneTwo, nOneThree, nOneFour;
887	–	std::vector<int> fortranGlobalGroupMembership;
888	–
889	–	isError = 0;
881
891	–	//globalGroupMembership_ is filled by SimCreator
892	–	for (int i = 0; i < nGlobalAtoms_; i++) {
893	–	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
894	–	}
895	–
882		//calculate mass ratio of cutoff group
897	–	std::vector<RealType> mfact;
883		SimInfo::MoleculeIterator mi;
884		Molecule* mol;
885		Molecule::CutoffGroupIterator ci;
#	Line 903 | Line 888 | namespace OpenMD {
888		Atom* atom;
889		RealType totalMass;
890
891	<	//to avoid memory reallocation, reserve enough space for mfact
892	<	mfact.reserve(getNCutoffGroups());
891	>	/**
892	>	* The mass factor is the relative mass of an atom to the total
893	>	* mass of the cutoff group it belongs to.  By default, all atoms
894	>	* are their own cutoff groups, and therefore have mass factors of
895	>	* 1.  We need some special handling for massless atoms, which
896	>	* will be treated as carrying the entire mass of the cutoff
897	>	* group.
898	>	*/
899	>	massFactors_.clear();
900	>	massFactors_.resize(getNAtoms(), 1.0);
901
902		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
903	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
903	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
904	>	cg = mol->nextCutoffGroup(ci)) {
905
906		totalMass = cg->getMass();
907		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
908		// Check for massless groups - set mfact to 1 if true
909	<	if (totalMass != 0)
910	<	mfact.push_back(atom->getMass()/totalMass);
909	>	if (totalMass != 0)
910	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
911		else
912	<	mfact.push_back( 1.0 );
912	>	massFactors_[atom->getLocalIndex()] = 1.0;
913		}
914		}
915		}
916
917	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
924	<	std::vector<int> identArray;
917	>	// Build the identArray_
918
919	<	//to avoid memory reallocation, reserve enough space identArray
920	<	identArray.reserve(getNAtoms());
928	<
919	>	identArray_.clear();
920	>	identArray_.reserve(getNAtoms());
921		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
922		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
923	<	identArray.push_back(atom->getIdent());
923	>	identArray_.push_back(atom->getIdent());
924		}
925		}
934	–
935	–	//fill molMembershipArray
936	–	//molMembershipArray is filled by SimCreator
937	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
938	–	for (int i = 0; i < nGlobalAtoms_; i++) {
939	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
940	–	}
926
927	<	//setup fortran simulation
927	>	//scan topology
928
929		nExclude = excludedInteractions_.getSize();
930		nOneTwo = oneTwoInteractions_.getSize();
#	Line 951 | Line 936 | namespace OpenMD {
936		int* oneThreeList = oneThreeInteractions_.getPairList();
937		int* oneFourList = oneFourInteractions_.getPairList();
938
939	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
940	<	&nExclude, excludeList,
956	<	&nOneTwo, oneTwoList,
957	<	&nOneThree, oneThreeList,
958	<	&nOneFour, oneFourList,
959	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
960	<	&fortranGlobalGroupMembership[0], &isError);
961	<
962	<	if( isError ){
963	<
964	<	sprintf( painCave.errMsg,
965	<	"There was an error setting the simulation information in fortran.\n" );
966	<	painCave.isFatal = 1;
967	<	painCave.severity = OPENMD_ERROR;
968	<	simError();
969	<	}
970	<
971	<
972	<	sprintf( checkPointMsg,
973	<	"succesfully sent the simulation information to fortran.\n");
974	<
975	<	errorCheckPoint();
976	<
977	<	// Setup number of neighbors in neighbor list if present
978	<	if (simParams_->haveNeighborListNeighbors()) {
979	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
980	<	setNeighbors(&nlistNeighbors);
981	<	}
982	<
939	>	topologyDone_ = true;
940	>	}
941
942	+	void SimInfo::addProperty(GenericData* genData) {
943	+	properties_.addProperty(genData);
944		}
945
946	+	void SimInfo::removeProperty(const string& propName) {
947	+	properties_.removeProperty(propName);
948	+	}
949
950	<	void SimInfo::setupFortranParallel() {
951	<	#ifdef IS_MPI
989	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
990	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
991	<	std::vector<int> localToGlobalCutoffGroupIndex;
992	<	SimInfo::MoleculeIterator mi;
993	<	Molecule::AtomIterator ai;
994	<	Molecule::CutoffGroupIterator ci;
995	<	Molecule* mol;
996	<	Atom* atom;
997	<	CutoffGroup* cg;
998	<	mpiSimData parallelData;
999	<	int isError;
1000	<
1001	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1002	<
1003	<	//local index(index in DataStorge) of atom is important
1004	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1005	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1006	<	}
1007	<
1008	<	//local index of cutoff group is trivial, it only depends on the order of travesing
1009	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1010	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1011	<	}
1012	<
1013	<	}
1014	<
1015	<	//fill up mpiSimData struct
1016	<	parallelData.nMolGlobal = getNGlobalMolecules();
1017	<	parallelData.nMolLocal = getNMolecules();
1018	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
1019	<	parallelData.nAtomsLocal = getNAtoms();
1020	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1021	<	parallelData.nGroupsLocal = getNCutoffGroups();
1022	<	parallelData.myNode = worldRank;
1023	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1024	<
1025	<	//pass mpiSimData struct and index arrays to fortran
1026	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1027	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1028	<	&localToGlobalCutoffGroupIndex[0], &isError);
1029	<
1030	<	if (isError) {
1031	<	sprintf(painCave.errMsg,
1032	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1033	<	painCave.isFatal = 1;
1034	<	simError();
1035	<	}
1036	<
1037	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
1038	<	errorCheckPoint();
1039	<
1040	<	#endif
950	>	void SimInfo::clearProperties() {
951	>	properties_.clearProperties();
952		}
953
954	<	void SimInfo::setupCutoff() {
955	<
956	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1046	<
1047	<	// Check the cutoff policy
1048	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1049	<
1050	<	// Set LJ shifting bools to false
1051	<	ljsp_ = 0;
1052	<	ljsf_ = 0;
1053	<
1054	<	std::string myPolicy;
1055	<	if (forceFieldOptions_.haveCutoffPolicy()){
1056	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
1057	<	}else if (simParams_->haveCutoffPolicy()) {
1058	<	myPolicy = simParams_->getCutoffPolicy();
1059	<	}
1060	<
1061	<	if (!myPolicy.empty()){
1062	<	toUpper(myPolicy);
1063	<	if (myPolicy == "MIX") {
1064	<	cp = MIX_CUTOFF_POLICY;
1065	<	} else {
1066	<	if (myPolicy == "MAX") {
1067	<	cp = MAX_CUTOFF_POLICY;
1068	<	} else {
1069	<	if (myPolicy == "TRADITIONAL") {
1070	<	cp = TRADITIONAL_CUTOFF_POLICY;
1071	<	} else {
1072	<	// throw error
1073	<	sprintf( painCave.errMsg,
1074	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1075	<	painCave.isFatal = 1;
1076	<	simError();
1077	<	}
1078	<	}
1079	<	}
1080	<	}
1081	<	notifyFortranCutoffPolicy(&cp);
1082	<
1083	<	// Check the Skin Thickness for neighborlists
1084	<	RealType skin;
1085	<	if (simParams_->haveSkinThickness()) {
1086	<	skin = simParams_->getSkinThickness();
1087	<	notifyFortranSkinThickness(&skin);
1088	<	}
1089	<
1090	<	// Check if the cutoff was set explicitly:
1091	<	if (simParams_->haveCutoffRadius()) {
1092	<	rcut_ = simParams_->getCutoffRadius();
1093	<	if (simParams_->haveSwitchingRadius()) {
1094	<	rsw_  = simParams_->getSwitchingRadius();
1095	<	} else {
1096	<	if (fInfo_.SIM_uses_Charges |
1097	<	fInfo_.SIM_uses_Dipoles |
1098	<	fInfo_.SIM_uses_RF) {
1099	<
1100	<	rsw_ = 0.85 * rcut_;
1101	<	sprintf(painCave.errMsg,
1102	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1103	<	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1104	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1105	<	painCave.isFatal = 0;
1106	<	simError();
1107	<	} else {
1108	<	rsw_ = rcut_;
1109	<	sprintf(painCave.errMsg,
1110	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1111	<	"\tOpenMD will use the same value as the cutoffRadius.\n"
1112	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1113	<	painCave.isFatal = 0;
1114	<	simError();
1115	<	}
1116	<	}
1117	<
1118	<	if (simParams_->haveElectrostaticSummationMethod()) {
1119	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1120	<	toUpper(myMethod);
1121	<
1122	<	if (myMethod == "SHIFTED_POTENTIAL") {
1123	<	ljsp_ = 1;
1124	<	} else if (myMethod == "SHIFTED_FORCE") {
1125	<	ljsf_ = 1;
1126	<	}
1127	<	}
1128	<
1129	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
954	>	vector<string> SimInfo::getPropertyNames() {
955	>	return properties_.getPropertyNames();
956	>	}
957
958	<	} else {
959	<
1133	<	// For electrostatic atoms, we'll assume a large safe value:
1134	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1135	<	sprintf(painCave.errMsg,
1136	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1137	<	"\tOpenMD will use a default value of 15.0 angstroms"
1138	<	"\tfor the cutoffRadius.\n");
1139	<	painCave.isFatal = 0;
1140	<	simError();
1141	<	rcut_ = 15.0;
1142	<
1143	<	if (simParams_->haveElectrostaticSummationMethod()) {
1144	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1145	<	toUpper(myMethod);
1146	<
1147	<	// For the time being, we're tethering the LJ shifted behavior to the
1148	<	// electrostaticSummationMethod keyword options
1149	<	if (myMethod == "SHIFTED_POTENTIAL") {
1150	<	ljsp_ = 1;
1151	<	} else if (myMethod == "SHIFTED_FORCE") {
1152	<	ljsf_ = 1;
1153	<	}
1154	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1155	<	if (simParams_->haveSwitchingRadius()){
1156	<	sprintf(painCave.errMsg,
1157	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1158	<	"\teven though the electrostaticSummationMethod was\n"
1159	<	"\tset to %s\n", myMethod.c_str());
1160	<	painCave.isFatal = 1;
1161	<	simError();
1162	<	}
1163	<	}
1164	<	}
1165	<
1166	<	if (simParams_->haveSwitchingRadius()){
1167	<	rsw_ = simParams_->getSwitchingRadius();
1168	<	} else {
1169	<	sprintf(painCave.errMsg,
1170	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1171	<	"\tOpenMD will use a default value of\n"
1172	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1173	<	painCave.isFatal = 0;
1174	<	simError();
1175	<	rsw_ = 0.85 * rcut_;
1176	<	}
1177	<
1178	<	Electrostatic::setElectrostaticCutoffRadius(rcut_, rsw_);
1179	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1180	<
1181	<	} else {
1182	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1183	<	// We'll punt and let fortran figure out the cutoffs later.
1184	<
1185	<	notifyFortranYouAreOnYourOwn();
1186	<
1187	<	}
1188	<	}
958	>	vector<GenericData*> SimInfo::getProperties() {
959	>	return properties_.getProperties();
960		}
961
962	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1192	<
1193	<	int errorOut;
1194	<	ElectrostaticSummationMethod esm = NONE;
1195	<	ElectrostaticScreeningMethod sm = UNDAMPED;
1196	<	RealType alphaVal;
1197	<	RealType dielectric;
1198	<
1199	<	errorOut = isError;
1200	<
1201	<	if (simParams_->haveElectrostaticSummationMethod()) {
1202	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1203	<	toUpper(myMethod);
1204	<	if (myMethod == "NONE") {
1205	<	esm = NONE;
1206	<	} else {
1207	<	if (myMethod == "SWITCHING_FUNCTION") {
1208	<	esm = SWITCHING_FUNCTION;
1209	<	} else {
1210	<	if (myMethod == "SHIFTED_POTENTIAL") {
1211	<	esm = SHIFTED_POTENTIAL;
1212	<	} else {
1213	<	if (myMethod == "SHIFTED_FORCE") {
1214	<	esm = SHIFTED_FORCE;
1215	<	} else {
1216	<	if (myMethod == "REACTION_FIELD") {
1217	<	esm = REACTION_FIELD;
1218	<	dielectric = simParams_->getDielectric();
1219	<	if (!simParams_->haveDielectric()) {
1220	<	// throw warning
1221	<	sprintf( painCave.errMsg,
1222	<	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1223	<	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1224	<	painCave.isFatal = 0;
1225	<	simError();
1226	<	}
1227	<	} else {
1228	<	// throw error
1229	<	sprintf( painCave.errMsg,
1230	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1231	<	"\t(Input file specified %s .)\n"
1232	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1233	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1234	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1235	<	painCave.isFatal = 1;
1236	<	simError();
1237	<	}
1238	<	}
1239	<	}
1240	<	}
1241	<	}
1242	<	}
1243	<
1244	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1245	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1246	<	toUpper(myScreen);
1247	<	if (myScreen == "UNDAMPED") {
1248	<	sm = UNDAMPED;
1249	<	} else {
1250	<	if (myScreen == "DAMPED") {
1251	<	sm = DAMPED;
1252	<	if (!simParams_->haveDampingAlpha()) {
1253	<	// first set a cutoff dependent alpha value
1254	<	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1255	<	alphaVal = 0.5125 - rcut_* 0.025;
1256	<	// for values rcut > 20.5, alpha is zero
1257	<	if (alphaVal < 0) alphaVal = 0;
1258	<
1259	<	// throw warning
1260	<	sprintf( painCave.errMsg,
1261	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1262	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1263	<	painCave.isFatal = 0;
1264	<	simError();
1265	<	} else {
1266	<	alphaVal = simParams_->getDampingAlpha();
1267	<	}
1268	<
1269	<	} else {
1270	<	// throw error
1271	<	sprintf( painCave.errMsg,
1272	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1273	<	"\t(Input file specified %s .)\n"
1274	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1275	<	"or \"damped\".\n", myScreen.c_str() );
1276	<	painCave.isFatal = 1;
1277	<	simError();
1278	<	}
1279	<	}
1280	<	}
1281	<
1282	<
1283	<	Electrostatic::setElectrostaticSummationMethod( esm );
1284	<	Electrostatic::setElectrostaticScreeningMethod( sm );
1285	<	Electrostatic::setDampingAlpha( alphaVal );
1286	<	Electrostatic::setReactionFieldDielectric( dielectric );
1287	<	initFortranFF( &errorOut );
1288	<	}
1289	<
1290	<	void SimInfo::setupSwitchingFunction() {
1291	<	int ft = CUBIC;
1292	<
1293	<	if (simParams_->haveSwitchingFunctionType()) {
1294	<	std::string funcType = simParams_->getSwitchingFunctionType();
1295	<	toUpper(funcType);
1296	<	if (funcType == "CUBIC") {
1297	<	ft = CUBIC;
1298	<	} else {
1299	<	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1300	<	ft = FIFTH_ORDER_POLY;
1301	<	} else {
1302	<	// throw error
1303	<	sprintf( painCave.errMsg,
1304	<	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1305	<	painCave.isFatal = 1;
1306	<	simError();
1307	<	}
1308	<	}
1309	<	}
1310	<
1311	<	// send switching function notification to switcheroo
1312	<	setFunctionType(&ft);
1313	<
1314	<	}
1315	<
1316	<	void SimInfo::setupAccumulateBoxDipole() {
1317	<
1318	<	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1319	<	if ( simParams_->haveAccumulateBoxDipole() )
1320	<	if ( simParams_->getAccumulateBoxDipole() ) {
1321	<	setAccumulateBoxDipole();
1322	<	calcBoxDipole_ = true;
1323	<	}
1324	<
1325	<	}
1326	<
1327	<	void SimInfo::addProperty(GenericData* genData) {
1328	<	properties_.addProperty(genData);
1329	<	}
1330	<
1331	<	void SimInfo::removeProperty(const std::string& propName) {
1332	<	properties_.removeProperty(propName);
1333	<	}
1334	<
1335	<	void SimInfo::clearProperties() {
1336	<	properties_.clearProperties();
1337	<	}
1338	<
1339	<	std::vector<std::string> SimInfo::getPropertyNames() {
1340	<	return properties_.getPropertyNames();
1341	<	}
1342	<
1343	<	std::vector<GenericData*> SimInfo::getProperties() {
1344	<	return properties_.getProperties();
1345	<	}
1346	<
1347	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
962	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
963		return properties_.getPropertyByName(propName);
964		}
965
#	Line 1358 | Line 973 | namespace OpenMD {
973		Molecule* mol;
974		RigidBody* rb;
975		Atom* atom;
976	+	CutoffGroup* cg;
977		SimInfo::MoleculeIterator mi;
978		Molecule::RigidBodyIterator rbIter;
979	<	Molecule::AtomIterator atomIter;;
979	>	Molecule::AtomIterator atomIter;
980	>	Molecule::CutoffGroupIterator cgIter;
981
982		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
983
984	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
984	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
985	>	atom = mol->nextAtom(atomIter)) {
986		atom->setSnapshotManager(sman_);
987		}
988
989	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
989	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
990	>	rb = mol->nextRigidBody(rbIter)) {
991		rb->setSnapshotManager(sman_);
992		}
993	+
994	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
995	+	cg = mol->nextCutoffGroup(cgIter)) {
996	+	cg->setSnapshotManager(sman_);
997	+	}
998		}
999
1000		}
1001
1378	–	Vector3d SimInfo::getComVel(){
1379	–	SimInfo::MoleculeIterator i;
1380	–	Molecule* mol;
1002
1003	<	Vector3d comVel(0.0);
1383	<	RealType totalMass = 0.0;
1384	<
1385	<
1386	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1387	<	RealType mass = mol->getMass();
1388	<	totalMass += mass;
1389	<	comVel += mass * mol->getComVel();
1390	<	}
1003	>	ostream& operator <<(ostream& o, SimInfo& info) {
1004
1392	–	#ifdef IS_MPI
1393	–	RealType tmpMass = totalMass;
1394	–	Vector3d tmpComVel(comVel);
1395	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1396	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1397	–	#endif
1398	–
1399	–	comVel /= totalMass;
1400	–
1401	–	return comVel;
1402	–	}
1403	–
1404	–	Vector3d SimInfo::getCom(){
1405	–	SimInfo::MoleculeIterator i;
1406	–	Molecule* mol;
1407	–
1408	–	Vector3d com(0.0);
1409	–	RealType totalMass = 0.0;
1410	–
1411	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1412	–	RealType mass = mol->getMass();
1413	–	totalMass += mass;
1414	–	com += mass * mol->getCom();
1415	–	}
1416	–
1417	–	#ifdef IS_MPI
1418	–	RealType tmpMass = totalMass;
1419	–	Vector3d tmpCom(com);
1420	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1421	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1422	–	#endif
1423	–
1424	–	com /= totalMass;
1425	–
1426	–	return com;
1427	–
1428	–	}
1429	–
1430	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1431	–
1005		return o;
1006		}
1007
1008	<
1436	<	/*
1437	<	Returns center of mass and center of mass velocity in one function call.
1438	<	*/
1439	<
1440	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1441	<	SimInfo::MoleculeIterator i;
1442	<	Molecule* mol;
1443	<
1444	<
1445	<	RealType totalMass = 0.0;
1446	<
1447	<
1448	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1449	<	RealType mass = mol->getMass();
1450	<	totalMass += mass;
1451	<	com += mass * mol->getCom();
1452	<	comVel += mass * mol->getComVel();
1453	<	}
1454	<
1455	<	#ifdef IS_MPI
1456	<	RealType tmpMass = totalMass;
1457	<	Vector3d tmpCom(com);
1458	<	Vector3d tmpComVel(comVel);
1459	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1460	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1461	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1462	<	#endif
1463	<
1464	<	com /= totalMass;
1465	<	comVel /= totalMass;
1466	<	}
1467	<
1468	<	/*
1469	<	Return intertia tensor for entire system and angular momentum Vector.
1470	<
1471	<
1472	<	[  Ixx -Ixy  -Ixz ]
1473	<	J =| -Iyx  Iyy  -Iyz |
1474	<	[ -Izx -Iyz   Izz ]
1475	<	*/
1476	<
1477	<	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1478	<
1479	<
1480	<	RealType xx = 0.0;
1481	<	RealType yy = 0.0;
1482	<	RealType zz = 0.0;
1483	<	RealType xy = 0.0;
1484	<	RealType xz = 0.0;
1485	<	RealType yz = 0.0;
1486	<	Vector3d com(0.0);
1487	<	Vector3d comVel(0.0);
1488	<
1489	<	getComAll(com, comVel);
1490	<
1491	<	SimInfo::MoleculeIterator i;
1492	<	Molecule* mol;
1493	<
1494	<	Vector3d thisq(0.0);
1495	<	Vector3d thisv(0.0);
1496	<
1497	<	RealType thisMass = 0.0;
1498	<
1499	<
1500	<
1501	<
1502	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1503	<
1504	<	thisq = mol->getCom()-com;
1505	<	thisv = mol->getComVel()-comVel;
1506	<	thisMass = mol->getMass();
1507	<	// Compute moment of intertia coefficients.
1508	<	xx += thisq[0]*thisq[0]*thisMass;
1509	<	yy += thisq[1]*thisq[1]*thisMass;
1510	<	zz += thisq[2]*thisq[2]*thisMass;
1511	<
1512	<	// compute products of intertia
1513	<	xy += thisq[0]*thisq[1]*thisMass;
1514	<	xz += thisq[0]*thisq[2]*thisMass;
1515	<	yz += thisq[1]*thisq[2]*thisMass;
1516	<
1517	<	angularMomentum += cross( thisq, thisv ) * thisMass;
1518	<
1519	<	}
1520	<
1521	<
1522	<	inertiaTensor(0,0) = yy + zz;
1523	<	inertiaTensor(0,1) = -xy;
1524	<	inertiaTensor(0,2) = -xz;
1525	<	inertiaTensor(1,0) = -xy;
1526	<	inertiaTensor(1,1) = xx + zz;
1527	<	inertiaTensor(1,2) = -yz;
1528	<	inertiaTensor(2,0) = -xz;
1529	<	inertiaTensor(2,1) = -yz;
1530	<	inertiaTensor(2,2) = xx + yy;
1531	<
1532	<	#ifdef IS_MPI
1533	<	Mat3x3d tmpI(inertiaTensor);
1534	<	Vector3d tmpAngMom;
1535	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1536	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1537	<	#endif
1538	<
1539	<	return;
1540	<	}
1541	<
1542	<	//Returns the angular momentum of the system
1543	<	Vector3d SimInfo::getAngularMomentum(){
1544	<
1545	<	Vector3d com(0.0);
1546	<	Vector3d comVel(0.0);
1547	<	Vector3d angularMomentum(0.0);
1548	<
1549	<	getComAll(com,comVel);
1550	<
1551	<	SimInfo::MoleculeIterator i;
1552	<	Molecule* mol;
1553	<
1554	<	Vector3d thisr(0.0);
1555	<	Vector3d thisp(0.0);
1556	<
1557	<	RealType thisMass;
1558	<
1559	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1560	<	thisMass = mol->getMass();
1561	<	thisr = mol->getCom()-com;
1562	<	thisp = (mol->getComVel()-comVel)*thisMass;
1563	<
1564	<	angularMomentum += cross( thisr, thisp );
1565	<
1566	<	}
1567	<
1568	<	#ifdef IS_MPI
1569	<	Vector3d tmpAngMom;
1570	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1571	<	#endif
1572	<
1573	<	return angularMomentum;
1574	<	}
1575	<
1008	>
1009		StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1010	<	return IOIndexToIntegrableObject.at(index);
1010	>	if (index >= IOIndexToIntegrableObject.size()) {
1011	>	sprintf(painCave.errMsg,
1012	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1013	>	"\tindex exceeds number of known objects!\n");
1014	>	painCave.isFatal = 1;
1015	>	simError();
1016	>	return NULL;
1017	>	} else
1018	>	return IOIndexToIntegrableObject.at(index);
1019		}
1020
1021	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1021	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1022		IOIndexToIntegrableObject= v;
1023		}
1024
1025	<	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1026	<	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1027	<	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1028	<	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1029	<	*/
1030	<	void SimInfo::getGyrationalVolume(RealType &volume){
1031	<	Mat3x3d intTensor;
1032	<	RealType det;
1033	<	Vector3d dummyAngMom;
1593	<	RealType sysconstants;
1594	<	RealType geomCnst;
1595	<
1596	<	geomCnst = 3.0/2.0;
1597	<	/* Get the inertial tensor and angular momentum for free*/
1598	<	getInertiaTensor(intTensor,dummyAngMom);
1599	<
1600	<	det = intTensor.determinant();
1601	<	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1602	<	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1603	<	return;
1025	>	int SimInfo::getNGlobalConstraints() {
1026	>	int nGlobalConstraints;
1027	>	#ifdef IS_MPI
1028	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1029	>	MPI_COMM_WORLD);
1030	>	#else
1031	>	nGlobalConstraints =  nConstraints_;
1032	>	#endif
1033	>	return nGlobalConstraints;
1034		}
1035
1606	–	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1607	–	Mat3x3d intTensor;
1608	–	Vector3d dummyAngMom;
1609	–	RealType sysconstants;
1610	–	RealType geomCnst;
1611	–
1612	–	geomCnst = 3.0/2.0;
1613	–	/* Get the inertial tensor and angular momentum for free*/
1614	–	getInertiaTensor(intTensor,dummyAngMom);
1615	–
1616	–	detI = intTensor.determinant();
1617	–	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1618	–	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1619	–	return;
1620	–	}
1621	–	/*
1622	–	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1623	–	assert( v.size() == nAtoms_ + nRigidBodies_);
1624	–	sdByGlobalIndex_ = v;
1625	–	}
1626	–
1627	–	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1628	–	//assert(index < nAtoms_ + nRigidBodies_);
1629	–	return sdByGlobalIndex_.at(index);
1630	–	}
1631	–	*/
1036		}//end namespace OpenMD
1037

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