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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC vs.
Revision 1930 by gezelter, Mon Aug 19 13:51:04 2013 UTC

#	Line 35 | Line 35
35		*
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	<	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 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) {
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	>	if ( (*i)->haveRegion() ) {
95	>	molStamp->setRegion( (*i)->getRegion() );
96	>	} else {
97	>	// set the region to a disallowed value:
98	>	molStamp->setRegion( -1 );
99	>	}
100
101	<
99	<	MoleculeStamp* molStamp;
100	<	int nMolWithSameStamp;
101	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
102	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
103	<	CutoffGroupStamp* cgStamp;
104	<	RigidBodyStamp* rbStamp;
105	<	int nRigidAtoms = 0;
106	<
107	<	std::vector<Component*> components = simParams->getComponents();
101	>	nMolWithSameStamp = (*i)->getNMol();
102
103	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
104	<	molStamp = (*i)->getMoleculeStamp();
105	<	nMolWithSameStamp = (*i)->getNMol();
106	<
107	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
108	<
109	<	//calculate atoms in molecules
110	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
111	<
112	<	//calculate atoms in cutoff groups
113	<	int nAtomsInGroups = 0;
114	<	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	<
103	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
104	>
105	>	//calculate atoms in molecules
106	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
107	>
108	>	//calculate atoms in cutoff groups
109	>	int nAtomsInGroups = 0;
110	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
111	>
112	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
113	>	cgStamp = molStamp->getCutoffGroupStamp(j);
114	>	nAtomsInGroups += cgStamp->getNMembers();
115		}
116	<
117	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
118	<	//group therefore the total number of cutoff groups in the system is
119	<	//equal to the total number of atoms minus number of atoms belong to
120	<	//cutoff group defined in meta-data file plus the number of cutoff
121	<	//groups defined in meta-data file
122	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
123	<
124	<	//every free atom (atom does not belong to rigid bodies) is an
125	<	//integrable object therefore the total number of integrable objects
126	<	//in the system is equal to the total number of atoms minus number of
127	<	//atoms belong to rigid body defined in meta-data file plus the number
128	<	//of rigid bodies defined in meta-data file
129	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
130	<	+ nGlobalRigidBodies_;
131	<
132	<	nGlobalMols_ = molStampIds_.size();
161	<	molToProcMap_.resize(nGlobalMols_);
116	>
117	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
118	>
119	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
120	>
121	>	//calculate atoms in rigid bodies
122	>	int nAtomsInRigidBodies = 0;
123	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
124	>
125	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
126	>	rbStamp = molStamp->getRigidBodyStamp(j);
127	>	nAtomsInRigidBodies += rbStamp->getNMembers();
128	>	}
129	>
130	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
131	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
132	>
133		}
134	+
135	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
136	+	//group therefore the total number of cutoff groups in the system is
137	+	//equal to the total number of atoms minus number of atoms belong to
138	+	//cutoff group defined in meta-data file plus the number of cutoff
139	+	//groups defined in meta-data file
140
141	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
142	+
143	+	//every free atom (atom does not belong to rigid bodies) is an
144	+	//integrable object therefore the total number of integrable objects
145	+	//in the system is equal to the total number of atoms minus number of
146	+	//atoms belong to rigid body defined in meta-data file plus the number
147	+	//of rigid bodies defined in meta-data file
148	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
149	+	+ nGlobalRigidBodies_;
150	+
151	+	nGlobalMols_ = molStampIds_.size();
152	+	molToProcMap_.resize(nGlobalMols_);
153	+	}
154	+
155		SimInfo::~SimInfo() {
156	<	std::map<int, Molecule*>::iterator i;
156	>	map<int, Molecule*>::iterator i;
157		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
158		delete i->second;
159		}
#	Line 173 | Line 164 | namespace OpenMD {
164		delete forceField_;
165		}
166
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	–	}
167
168		bool SimInfo::addMolecule(Molecule* mol) {
169		MoleculeIterator i;
170	<
170	>
171		i = molecules_.find(mol->getGlobalIndex());
172		if (i == molecules_.end() ) {
173	<
174	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
175	<
173	>
174	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
175	>
176		nAtoms_ += mol->getNAtoms();
177		nBonds_ += mol->getNBonds();
178		nBends_ += mol->getNBends();
#	Line 201 | Line 182 | namespace OpenMD {
182		nIntegrableObjects_ += mol->getNIntegrableObjects();
183		nCutoffGroups_ += mol->getNCutoffGroups();
184		nConstraints_ += mol->getNConstraintPairs();
185	<
185	>
186		addInteractionPairs(mol);
187	<
187	>
188		return true;
189		} else {
190		return false;
191		}
192		}
193	<
193	>
194		bool SimInfo::removeMolecule(Molecule* mol) {
195		MoleculeIterator i;
196		i = molecules_.find(mol->getGlobalIndex());
#	Line 237 | Line 218 | namespace OpenMD {
218		} else {
219		return false;
220		}
240	–
241	–
221		}
222
223
#	Line 254 | Line 233 | namespace OpenMD {
233
234
235		void SimInfo::calcNdf() {
236	<	int ndf_local;
236	>	int ndf_local, nfq_local;
237		MoleculeIterator i;
238	<	std::vector<StuntDouble*>::iterator j;
238	>	vector<StuntDouble*>::iterator j;
239	>	vector<Atom*>::iterator k;
240	>
241		Molecule* mol;
242	<	StuntDouble* integrableObject;
242	>	StuntDouble* sd;
243	>	Atom* atom;
244
245		ndf_local = 0;
246	+	nfq_local = 0;
247
248		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
266	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
267	–	integrableObject = mol->nextIntegrableObject(j)) {
249
250	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
251	+	sd = mol->nextIntegrableObject(j)) {
252	+
253		ndf_local += 3;
254
255	<	if (integrableObject->isDirectional()) {
256	<	if (integrableObject->isLinear()) {
255	>	if (sd->isDirectional()) {
256	>	if (sd->isLinear()) {
257		ndf_local += 2;
258		} else {
259		ndf_local += 3;
260		}
261		}
278	–
262		}
263	+
264	+	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
265	+	atom = mol->nextFluctuatingCharge(k)) {
266	+	if (atom->isFluctuatingCharge()) {
267	+	nfq_local++;
268	+	}
269	+	}
270		}
271
272	+	ndfLocal_ = ndf_local;
273	+
274		// n_constraints is local, so subtract them on each processor
275		ndf_local -= nConstraints_;
276
277		#ifdef IS_MPI
278	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
278	>	MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
279	>	MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
280	>	MPI::INT, MPI::SUM);
281		#else
282		ndf_ = ndf_local;
283	+	nGlobalFluctuatingCharges_ = nfq_local;
284		#endif
285
286		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 296 | Line 291 | namespace OpenMD {
291
292		int SimInfo::getFdf() {
293		#ifdef IS_MPI
294	<	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
294	>	MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
295		#else
296		fdf_ = fdf_local;
297		#endif
298		return fdf_;
299		}
300	+
301	+	unsigned int SimInfo::getNLocalCutoffGroups(){
302	+	int nLocalCutoffAtoms = 0;
303	+	Molecule* mol;
304	+	MoleculeIterator mi;
305	+	CutoffGroup* cg;
306	+	Molecule::CutoffGroupIterator ci;
307
308	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
309	+
310	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
311	+	cg = mol->nextCutoffGroup(ci)) {
312	+	nLocalCutoffAtoms += cg->getNumAtom();
313	+
314	+	}
315	+	}
316	+
317	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
318	+	}
319	+
320		void SimInfo::calcNdfRaw() {
321		int ndfRaw_local;
322
323		MoleculeIterator i;
324	<	std::vector<StuntDouble*>::iterator j;
324	>	vector<StuntDouble*>::iterator j;
325		Molecule* mol;
326	<	StuntDouble* integrableObject;
326	>	StuntDouble* sd;
327
328		// Raw degrees of freedom that we have to set
329		ndfRaw_local = 0;
330
331		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
318	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
319	–	integrableObject = mol->nextIntegrableObject(j)) {
332
333	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
334	+	sd = mol->nextIntegrableObject(j)) {
335	+
336		ndfRaw_local += 3;
337
338	<	if (integrableObject->isDirectional()) {
339	<	if (integrableObject->isLinear()) {
338	>	if (sd->isDirectional()) {
339	>	if (sd->isLinear()) {
340		ndfRaw_local += 2;
341		} else {
342		ndfRaw_local += 3;
#	Line 332 | Line 347 | namespace OpenMD {
347		}
348
349		#ifdef IS_MPI
350	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
350	>	MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
351		#else
352		ndfRaw_ = ndfRaw_local;
353		#endif
#	Line 345 | Line 360 | namespace OpenMD {
360
361
362		#ifdef IS_MPI
363	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
363	>	MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
364	>	MPI::INT, MPI::SUM);
365		#else
366		ndfTrans_ = ndfTrans_local;
367		#endif
#	Line 356 | Line 372 | namespace OpenMD {
372
373		void SimInfo::addInteractionPairs(Molecule* mol) {
374		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
375	<	std::vector<Bond*>::iterator bondIter;
376	<	std::vector<Bend*>::iterator bendIter;
377	<	std::vector<Torsion*>::iterator torsionIter;
378	<	std::vector<Inversion*>::iterator inversionIter;
375	>	vector<Atom*>::iterator atomIter;
376	>	vector<Bond*>::iterator bondIter;
377	>	vector<Bend*>::iterator bendIter;
378	>	vector<Torsion*>::iterator torsionIter;
379	>	vector<Inversion*>::iterator inversionIter;
380	>	Atom* atom;
381		Bond* bond;
382		Bend* bend;
383		Torsion* torsion;
#	Line 377 | Line 395 | namespace OpenMD {
395		// always be excluded.  These are done at the bottom of this
396		// function.
397
398	<	std::map<int, std::set<int> > atomGroups;
398	>	map<int, set<int> > atomGroups;
399		Molecule::RigidBodyIterator rbIter;
400		RigidBody* rb;
401		Molecule::IntegrableObjectIterator ii;
402	<	StuntDouble* integrableObject;
402	>	StuntDouble* sd;
403
404	<	for (integrableObject = mol->beginIntegrableObject(ii);
405	<	integrableObject != NULL;
388	<	integrableObject = mol->nextIntegrableObject(ii)) {
404	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
405	>	sd = mol->nextIntegrableObject(ii)) {
406
407	<	if (integrableObject->isRigidBody()) {
408	<	rb = static_cast<RigidBody*>(integrableObject);
409	<	std::vector<Atom*> atoms = rb->getAtoms();
410	<	std::set<int> rigidAtoms;
407	>	if (sd->isRigidBody()) {
408	>	rb = static_cast<RigidBody*>(sd);
409	>	vector<Atom*> atoms = rb->getAtoms();
410	>	set<int> rigidAtoms;
411		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
412		rigidAtoms.insert(atoms[i]->getGlobalIndex());
413		}
414		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
415	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
415	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
416		}
417		} else {
418	<	std::set<int> oneAtomSet;
419	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
420	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
418	>	set<int> oneAtomSet;
419	>	oneAtomSet.insert(sd->getGlobalIndex());
420	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
421		}
422		}
423	+
424
425		for (bond= mol->beginBond(bondIter); bond != NULL;
426		bond = mol->nextBond(bondIter)) {
427
428		a = bond->getAtomA()->getGlobalIndex();
429		b = bond->getAtomB()->getGlobalIndex();
430	<
430	>
431		if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
432		oneTwoInteractions_.addPair(a, b);
433		} else {
#	Line 503 | Line 521 | namespace OpenMD {
521
522		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
523		rb = mol->nextRigidBody(rbIter)) {
524	<	std::vector<Atom*> atoms = rb->getAtoms();
524	>	vector<Atom*> atoms = rb->getAtoms();
525		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
526		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
527		a = atoms[i]->getGlobalIndex();
#	Line 517 | Line 535 | namespace OpenMD {
535
536		void SimInfo::removeInteractionPairs(Molecule* mol) {
537		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
538	<	std::vector<Bond*>::iterator bondIter;
539	<	std::vector<Bend*>::iterator bendIter;
540	<	std::vector<Torsion*>::iterator torsionIter;
541	<	std::vector<Inversion*>::iterator inversionIter;
538	>	vector<Bond*>::iterator bondIter;
539	>	vector<Bend*>::iterator bendIter;
540	>	vector<Torsion*>::iterator torsionIter;
541	>	vector<Inversion*>::iterator inversionIter;
542		Bond* bond;
543		Bend* bend;
544		Torsion* torsion;
#	Line 530 | Line 548 | namespace OpenMD {
548		int c;
549		int d;
550
551	<	std::map<int, std::set<int> > atomGroups;
551	>	map<int, set<int> > atomGroups;
552		Molecule::RigidBodyIterator rbIter;
553		RigidBody* rb;
554		Molecule::IntegrableObjectIterator ii;
555	<	StuntDouble* integrableObject;
555	>	StuntDouble* sd;
556
557	<	for (integrableObject = mol->beginIntegrableObject(ii);
558	<	integrableObject != NULL;
541	<	integrableObject = mol->nextIntegrableObject(ii)) {
557	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
558	>	sd = mol->nextIntegrableObject(ii)) {
559
560	<	if (integrableObject->isRigidBody()) {
561	<	rb = static_cast<RigidBody*>(integrableObject);
562	<	std::vector<Atom*> atoms = rb->getAtoms();
563	<	std::set<int> rigidAtoms;
560	>	if (sd->isRigidBody()) {
561	>	rb = static_cast<RigidBody*>(sd);
562	>	vector<Atom*> atoms = rb->getAtoms();
563	>	set<int> rigidAtoms;
564		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
565		rigidAtoms.insert(atoms[i]->getGlobalIndex());
566		}
567		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
568	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
568	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
569		}
570		} else {
571	<	std::set<int> oneAtomSet;
572	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
573	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
571	>	set<int> oneAtomSet;
572	>	oneAtomSet.insert(sd->getGlobalIndex());
573	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
574		}
575		}
576
#	Line 656 | Line 673 | namespace OpenMD {
673
674		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
675		rb = mol->nextRigidBody(rbIter)) {
676	<	std::vector<Atom*> atoms = rb->getAtoms();
676	>	vector<Atom*> atoms = rb->getAtoms();
677		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
678		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
679		a = atoms[i]->getGlobalIndex();
#	Line 679 | Line 696 | namespace OpenMD {
696		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
697		}
698
682	–	void SimInfo::update() {
699
700	<	setupSimType();
701	<
702	<	#ifdef IS_MPI
703	<	setupFortranParallel();
704	<	#endif
705	<
706	<	setupFortranSim();
707	<
708	<	//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	<
700	>	/**
701	>	* update
702	>	*
703	>	*  Performs the global checks and variable settings after the
704	>	*  objects have been created.
705	>	*
706	>	*/
707	>	void SimInfo::update() {
708	>	setupSimVariables();
709		calcNdf();
710		calcNdfRaw();
711		calcNdfTrans();
712	–
713	–	fortranInitialized_ = true;
712		}
713	<
714	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
713	>
714	>	/**
715	>	* getSimulatedAtomTypes
716	>	*
717	>	* Returns an STL set of AtomType* that are actually present in this
718	>	* simulation.  Must query all processors to assemble this information.
719	>	*
720	>	*/
721	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
722		SimInfo::MoleculeIterator mi;
723		Molecule* mol;
724		Molecule::AtomIterator ai;
725		Atom* atom;
726	<	std::set<AtomType*> atomTypes;
727	<
726	>	set<AtomType*> atomTypes;
727	>
728		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
729	<
730	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
729	>	for(atom = mol->beginAtom(ai); atom != NULL;
730	>	atom = mol->nextAtom(ai)) {
731		atomTypes.insert(atom->getAtomType());
732	<	}
733	<
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();
732	>	}
733	>	}
734
735	<	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;
735	>	#ifdef IS_MPI
736
737	<	std::string myMethod;
738	<
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	<	}
737	>	// loop over the found atom types on this processor, and add their
738	>	// numerical idents to a vector:
739
740	<	if (simParams_->haveAccumulateBoxDipole())
741	<	if (simParams_->getAccumulateBoxDipole())
742	<	useBoxDipole = 1;
740	>	vector<int> foundTypes;
741	>	set<AtomType*>::iterator i;
742	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
743	>	foundTypes.push_back( (*i)->getIdent() );
744
745	<	useAtomicVirial_ = simParams_->getUseAtomicVirial();
745	>	// count_local holds the number of found types on this processor
746	>	int count_local = foundTypes.size();
747
748	<	//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	<	}
748	>	int nproc = MPI::COMM_WORLD.Get_size();
749
750	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
751	<	useDirectionalAtom = 1;
752	<	}
750	>	// we need arrays to hold the counts and displacement vectors for
751	>	// all processors
752	>	vector<int> counts(nproc, 0);
753	>	vector<int> disps(nproc, 0);
754
755	<	if (useCharge || useDipole) {
756	<	useElectrostatics = 1;
755	>	// fill the counts array
756	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
757	>	1, MPI::INT);
758	>
759	>	// use the processor counts to compute the displacement array
760	>	disps[0] = 0;
761	>	int totalCount = counts[0];
762	>	for (int iproc = 1; iproc < nproc; iproc++) {
763	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
764	>	totalCount += counts[iproc];
765		}
766
767	<	#ifdef IS_MPI
768	<	int temp;
767	>	// we need a (possibly redundant) set of all found types:
768	>	vector<int> ftGlobal(totalCount);
769	>
770	>	// now spray out the foundTypes to all the other processors:
771	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
772	>	&ftGlobal[0], &counts[0], &disps[0],
773	>	MPI::INT);
774
775	<	temp = usePBC;
814	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
775	>	vector<int>::iterator j;
776
777	<	temp = useDirectionalAtom;
778	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
777	>	// foundIdents is a stl set, so inserting an already found ident
778	>	// will have no effect.
779	>	set<int> foundIdents;
780
781	<	temp = useLennardJones;
782	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
781	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
782	>	foundIdents.insert((*j));
783	>
784	>	// now iterate over the foundIdents and get the actual atom types
785	>	// that correspond to these:
786	>	set<int>::iterator it;
787	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
788	>	atomTypes.insert( forceField_->getAtomType((*it)) );
789	>
790	>	#endif
791
792	<	temp = useElectrostatics;
793	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
792	>	return atomTypes;
793	>	}
794
825	–	temp = useCharge;
826	–	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
795
796	<	temp = useDipole;
797	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
796	>	int getGlobalCountOfType(AtomType* atype) {
797	>	/*
798	>	set<AtomType*> atypes = getSimulatedAtomTypes();
799	>	map<AtomType*, int> counts_;
800
801	<	temp = useSticky;
802	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
801	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
802	>	for(atom = mol->beginAtom(ai); atom != NULL;
803	>	atom = mol->nextAtom(ai)) {
804	>	atom->getAtomType();
805	>	}
806	>	}
807	>	*/
808	>	return 0;
809	>	}
810
811	<	temp = useStickyPower;
812	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
811	>	void SimInfo::setupSimVariables() {
812	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
813	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
814	>	// parameter is true
815	>	calcBoxDipole_ = false;
816	>	if ( simParams_->haveAccumulateBoxDipole() )
817	>	if ( simParams_->getAccumulateBoxDipole() ) {
818	>	calcBoxDipole_ = true;
819	>	}
820
821	<	temp = useGayBerne;
822	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
821	>	set<AtomType*>::iterator i;
822	>	set<AtomType*> atomTypes;
823	>	atomTypes = getSimulatedAtomTypes();
824	>	bool usesElectrostatic = false;
825	>	bool usesMetallic = false;
826	>	bool usesDirectional = false;
827	>	bool usesFluctuatingCharges =  false;
828	>	//loop over all of the atom types
829	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
830	>	usesElectrostatic |= (*i)->isElectrostatic();
831	>	usesMetallic |= (*i)->isMetal();
832	>	usesDirectional |= (*i)->isDirectional();
833	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
834	>	}
835
836	<	temp = useEAM;
837	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
838	<
839	<	temp = useSC;
840	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
836	>	#ifdef IS_MPI
837	>	bool temp;
838	>	temp = usesDirectional;
839	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
840	>	MPI::LOR);
841	>
842	>	temp = usesMetallic;
843	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
844	>	MPI::LOR);
845
846	<	temp = useShape;
847	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
846	>	temp = usesElectrostatic;
847	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
848	>	MPI::LOR);
849
850	<	temp = useFLARB;
851	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
850	>	temp = usesFluctuatingCharges;
851	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
852	>	MPI::LOR);
853	>	#else
854
855	<	temp = useRF;
856	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
855	>	usesDirectionalAtoms_ = usesDirectional;
856	>	usesMetallicAtoms_ = usesMetallic;
857	>	usesElectrostaticAtoms_ = usesElectrostatic;
858	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
859
860	<	temp = useSF;
861	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860	>	#endif
861	>
862	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
863	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
864	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
865	>	}
866
858	–	temp = useSP;
859	–	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
867
868	<	temp = useBoxDipole;
869	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
868	>	vector<int> SimInfo::getGlobalAtomIndices() {
869	>	SimInfo::MoleculeIterator mi;
870	>	Molecule* mol;
871	>	Molecule::AtomIterator ai;
872	>	Atom* atom;
873
874	<	temp = useAtomicVirial_;
875	<	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
874	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
875	>
876	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
877	>
878	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
879	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
880	>	}
881	>	}
882	>	return GlobalAtomIndices;
883	>	}
884
867	–	#endif
885
886	<	fInfo_.SIM_uses_PBC = usePBC;
887	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
888	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
889	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
890	<	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	<	}
886	>	vector<int> SimInfo::getGlobalGroupIndices() {
887	>	SimInfo::MoleculeIterator mi;
888	>	Molecule* mol;
889	>	Molecule::CutoffGroupIterator ci;
890	>	CutoffGroup* cg;
891
892	<	void SimInfo::setupFortranSim() {
890	<	int isError;
891	<	int nExclude, nOneTwo, nOneThree, nOneFour;
892	<	std::vector<int> fortranGlobalGroupMembership;
892	>	vector<int> GlobalGroupIndices;
893
894	<	isError = 0;
895	<
896	<	//globalGroupMembership_ is filled by SimCreator
897	<	for (int i = 0; i < nGlobalAtoms_; i++) {
898	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
894	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
895	>
896	>	//local index of cutoff group is trivial, it only depends on the
897	>	//order of travesing
898	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
899	>	cg = mol->nextCutoffGroup(ci)) {
900	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
901	>	}
902		}
903	+	return GlobalGroupIndices;
904	+	}
905
906	+
907	+	void SimInfo::prepareTopology() {
908	+
909		//calculate mass ratio of cutoff group
902	–	std::vector<RealType> mfact;
910		SimInfo::MoleculeIterator mi;
911		Molecule* mol;
912		Molecule::CutoffGroupIterator ci;
#	Line 908 | Line 915 | namespace OpenMD {
915		Atom* atom;
916		RealType totalMass;
917
918	<	//to avoid memory reallocation, reserve enough space for mfact
919	<	mfact.reserve(getNCutoffGroups());
918	>	/**
919	>	* The mass factor is the relative mass of an atom to the total
920	>	* mass of the cutoff group it belongs to.  By default, all atoms
921	>	* are their own cutoff groups, and therefore have mass factors of
922	>	* 1.  We need some special handling for massless atoms, which
923	>	* will be treated as carrying the entire mass of the cutoff
924	>	* group.
925	>	*/
926	>	massFactors_.clear();
927	>	massFactors_.resize(getNAtoms(), 1.0);
928
929		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
930	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
930	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
931	>	cg = mol->nextCutoffGroup(ci)) {
932
933		totalMass = cg->getMass();
934		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
935		// Check for massless groups - set mfact to 1 if true
936	<	if (totalMass != 0)
937	<	mfact.push_back(atom->getMass()/totalMass);
936	>	if (totalMass != 0)
937	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
938		else
939	<	mfact.push_back( 1.0 );
939	>	massFactors_[atom->getLocalIndex()] = 1.0;
940		}
941		}
942		}
943
944	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
929	<	std::vector<int> identArray;
944	>	// Build the identArray_ and regions_
945
946	<	//to avoid memory reallocation, reserve enough space identArray
947	<	identArray.reserve(getNAtoms());
948	<
949	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
946	>	identArray_.clear();
947	>	identArray_.reserve(getNAtoms());
948	>	regions_.clear();
949	>	regions_.reserve(getNAtoms());
950	>
951	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
952	>	int reg = mol->getRegion();
953		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
954	<	identArray.push_back(atom->getIdent());
954	>	identArray_.push_back(atom->getIdent());
955	>	regions_.push_back(reg);
956		}
957		}
958	+
959	+	topologyDone_ = true;
960	+	}
961
962	<	//fill molMembershipArray
963	<	//molMembershipArray is filled by SimCreator
964	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
943	<	for (int i = 0; i < nGlobalAtoms_; i++) {
944	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
945	<	}
946	<
947	<	//setup fortran simulation
962	>	void SimInfo::addProperty(GenericData* genData) {
963	>	properties_.addProperty(genData);
964	>	}
965
966	<	nExclude = excludedInteractions_.getSize();
967	<	nOneTwo = oneTwoInteractions_.getSize();
968	<	nOneThree = oneThreeInteractions_.getSize();
952	<	nOneFour = oneFourInteractions_.getSize();
966	>	void SimInfo::removeProperty(const string& propName) {
967	>	properties_.removeProperty(propName);
968	>	}
969
970	<	int* excludeList = excludedInteractions_.getPairList();
971	<	int* oneTwoList = oneTwoInteractions_.getPairList();
972	<	int* oneThreeList = oneThreeInteractions_.getPairList();
957	<	int* oneFourList = oneFourInteractions_.getPairList();
970	>	void SimInfo::clearProperties() {
971	>	properties_.clearProperties();
972	>	}
973
974	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
975	<	&nExclude, excludeList,
976	<	&nOneTwo, oneTwoList,
962	<	&nOneThree, oneThreeList,
963	<	&nOneFour, oneFourList,
964	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
965	<	&fortranGlobalGroupMembership[0], &isError);
966	<
967	<	if( isError ){
974	>	vector<string> SimInfo::getPropertyNames() {
975	>	return properties_.getPropertyNames();
976	>	}
977
978	<	sprintf( painCave.errMsg,
979	<	"There was an error setting the simulation information in fortran.\n" );
980	<	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	<
978	>	vector<GenericData*> SimInfo::getProperties() {
979	>	return properties_.getProperties();
980	>	}
981
982	+	GenericData* SimInfo::getPropertyByName(const string& propName) {
983	+	return properties_.getPropertyByName(propName);
984		}
985
986	+	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
987	+	if (sman_ == sman) {
988	+	return;
989	+	}
990	+	delete sman_;
991	+	sman_ = sman;
992
992	–	void SimInfo::setupFortranParallel() {
993	–	#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;
993		Molecule* mol;
994	+	RigidBody* rb;
995		Atom* atom;
996		CutoffGroup* cg;
997	<	mpiSimData parallelData;
998	<	int isError;
999	<
1000	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1001	<
1002	<	//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	<	}
997	>	SimInfo::MoleculeIterator mi;
998	>	Molecule::RigidBodyIterator rbIter;
999	>	Molecule::AtomIterator atomIter;
1000	>	Molecule::CutoffGroupIterator cgIter;
1001	>
1002	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1003
1004	<	}
1005	<
1006	<	//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
1046	<	}
1047	<
1048	<	void SimInfo::setupCutoff() {
1049	<
1050	<	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	<	}
1004	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
1005	>	atom = mol->nextAtom(atomIter)) {
1006	>	atom->setSnapshotManager(sman_);
1007		}
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	–	}
1008
1009	<	// Check if the cutoff was set explicitly:
1010	<	if (simParams_->haveCutoffRadius()) {
1011	<	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	<	}
1009	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1010	>	rb = mol->nextRigidBody(rbIter)) {
1011	>	rb->setSnapshotManager(sman_);
1012		}
1013
1014	<	if (simParams_->haveElectrostaticSummationMethod()) {
1015	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1016	<	toUpper(myMethod);
1126	<
1127	<	if (myMethod == "SHIFTED_POTENTIAL") {
1128	<	ljsp_ = 1;
1129	<	} else if (myMethod == "SHIFTED_FORCE") {
1130	<	ljsf_ = 1;
1131	<	}
1014	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1015	>	cg = mol->nextCutoffGroup(cgIter)) {
1016	>	cg->setSnapshotManager(sman_);
1017		}
1018	<
1019	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1135	<
1136	<	} else {
1137	<
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	<	}
1018	>	}
1019	>
1020		}
1021
1195	–	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;
1022
1023	<	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;
1023	>	ostream& operator <<(ostream& o, SimInfo& info) {
1024
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) {
1353	–	return properties_.getPropertyByName(propName);
1354	–	}
1355	–
1356	–	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1357	–	if (sman_ == sman) {
1358	–	return;
1359	–	}
1360	–	delete sman_;
1361	–	sman_ = sman;
1362	–
1363	–	Molecule* mol;
1364	–	RigidBody* rb;
1365	–	Atom* atom;
1366	–	SimInfo::MoleculeIterator mi;
1367	–	Molecule::RigidBodyIterator rbIter;
1368	–	Molecule::AtomIterator atomIter;;
1369	–
1370	–	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1371	–
1372	–	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1373	–	atom->setSnapshotManager(sman_);
1374	–	}
1375	–
1376	–	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1377	–	rb->setSnapshotManager(sman_);
1378	–	}
1379	–	}
1380	–
1381	–	}
1382	–
1383	–	Vector3d SimInfo::getComVel(){
1384	–	SimInfo::MoleculeIterator i;
1385	–	Molecule* mol;
1386	–
1387	–	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	–	}
1396	–
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	–
1025		return o;
1026		}
1027
1028	<
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	<
1028	>
1029		StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1030	<	return IOIndexToIntegrableObject.at(index);
1030	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1031	>	sprintf(painCave.errMsg,
1032	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1033	>	"\tindex exceeds number of known objects!\n");
1034	>	painCave.isFatal = 1;
1035	>	simError();
1036	>	return NULL;
1037	>	} else
1038	>	return IOIndexToIntegrableObject.at(index);
1039		}
1040
1041	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1041	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1042		IOIndexToIntegrableObject= v;
1043		}
1044
1045	<	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1046	<	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1047	<	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1048	<	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1049	<	*/
1050	<	void SimInfo::getGyrationalVolume(RealType &volume){
1051	<	Mat3x3d intTensor;
1052	<	RealType det;
1053	<	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;
1045	>	int SimInfo::getNGlobalConstraints() {
1046	>	int nGlobalConstraints;
1047	>	#ifdef IS_MPI
1048	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1049	>	MPI::INT, MPI::SUM);
1050	>	#else
1051	>	nGlobalConstraints =  nConstraints_;
1052	>	#endif
1053	>	return nGlobalConstraints;
1054		}
1055
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	–	}
1626	–	/*
1627	–	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1628	–	assert( v.size() == nAtoms_ + nRigidBodies_);
1629	–	sdByGlobalIndex_ = v;
1630	–	}
1631	–
1632	–	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1633	–	//assert(index < nAtoms_ + nRigidBodies_);
1634	–	return sdByGlobalIndex_.at(index);
1635	–	}
1636	–	*/
1056		}//end namespace OpenMD
1057

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