[ViewVC] Diff of: 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 1536 by gezelter, Wed Jan 5 14:49:05 2011 UTC

#	Line 54 \| Line 54
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56		#include "primitives/StuntDouble.hpp"
57	–	#include "UseTheForce/fCutoffPolicy.h"
58	–	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
59	–	#include "UseTheForce/doForces_interface.h"
57		#include "UseTheForce/DarkSide/neighborLists_interface.h"
58	<	#include "UseTheForce/DarkSide/switcheroo_interface.h"
58	>	#include "UseTheForce/doForces_interface.h"
59		#include "utils/MemoryUtils.hpp"
60		#include "utils/simError.h"
61		#include "selection/SelectionManager.hpp"
62		#include "io/ForceFieldOptions.hpp"
63		#include "UseTheForce/ForceField.hpp"
64	+	#include "nonbonded/SwitchingFunction.hpp"
65
68	–
66		#ifdef IS_MPI
67		#include "UseTheForce/mpiComponentPlan.h"
68		#include "UseTheForce/DarkSide/simParallel_interface.h"
69		#endif
70
71	+	using namespace std;
72		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	–	}
73
74		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
75		forceField_(ff), simParams_(simParams),
#	Line 90 \| Line 79 \| namespace OpenMD {
79		nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0),
80		nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
81		nConstraints_(0), sman_(NULL), fortranInitialized_(false),
82	<	calcBoxDipole_(false), useAtomicVirial_(true) {
83	<
84	<
85	<	MoleculeStamp* molStamp;
86	<	int nMolWithSameStamp;
87	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
88	<	int nGroups = 0; //total cutoff groups defined in meta-data file
89	<	CutoffGroupStamp* cgStamp;
90	<	RigidBodyStamp* rbStamp;
91	<	int nRigidAtoms = 0;
92	<
93	<	std::vector<Component*> components = simParams->getComponents();
82	>	calcBoxDipole_(false), useAtomicVirial_(true) {
83	>
84	>	MoleculeStamp* molStamp;
85	>	int nMolWithSameStamp;
86	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87	>	int nGroups = 0; //total cutoff groups defined in meta-data file
88	>	CutoffGroupStamp* cgStamp;
89	>	RigidBodyStamp* rbStamp;
90	>	int nRigidAtoms = 0;
91	>
92	>	vector<Component*> components = simParams->getComponents();
93	>
94	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
95	>	molStamp = (*i)->getMoleculeStamp();
96	>	nMolWithSameStamp = (*i)->getNMol();
97
98	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
99	<	molStamp = (*i)->getMoleculeStamp();
100	<	nMolWithSameStamp = (*i)->getNMol();
101	<
102	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
103	<
104	<	//calculate atoms in molecules
105	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
106	<
107	<	//calculate atoms in cutoff groups
108	<	int nAtomsInGroups = 0;
109	<	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	<
98	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
99	>
100	>	//calculate atoms in molecules
101	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
102	>
103	>	//calculate atoms in cutoff groups
104	>	int nAtomsInGroups = 0;
105	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
106	>
107	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
108	>	cgStamp = molStamp->getCutoffGroupStamp(j);
109	>	nAtomsInGroups += cgStamp->getNMembers();
110		}
111	<
112	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
113	<	//group therefore the total number of cutoff groups in the system is
114	<	//equal to the total number of atoms minus number of atoms belong to
115	<	//cutoff group defined in meta-data file plus the number of cutoff
116	<	//groups defined in meta-data file
117	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
118	<
119	<	//every free atom (atom does not belong to rigid bodies) is an
120	<	//integrable object therefore the total number of integrable objects
121	<	//in the system is equal to the total number of atoms minus number of
122	<	//atoms belong to rigid body defined in meta-data file plus the number
123	<	//of rigid bodies defined in meta-data file
124	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
125	<	+ nGlobalRigidBodies_;
126	<
127	<	nGlobalMols_ = molStampIds_.size();
128	<	molToProcMap_.resize(nGlobalMols_);
129	<	}
130	<
111	>
112	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
113	>
114	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
115	>
116	>	//calculate atoms in rigid bodies
117	>	int nAtomsInRigidBodies = 0;
118	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
119	>
120	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
121	>	rbStamp = molStamp->getRigidBodyStamp(j);
122	>	nAtomsInRigidBodies += rbStamp->getNMembers();
123	>	}
124	>
125	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
126	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
127	>
128	>	}
129	>
130	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
131	>	//group therefore the total number of cutoff groups in the system is
132	>	//equal to the total number of atoms minus number of atoms belong to
133	>	//cutoff group defined in meta-data file plus the number of cutoff
134	>	//groups defined in meta-data file
135	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
136	>
137	>	//every free atom (atom does not belong to rigid bodies) is an
138	>	//integrable object therefore the total number of integrable objects
139	>	//in the system is equal to the total number of atoms minus number of
140	>	//atoms belong to rigid body defined in meta-data file plus the number
141	>	//of rigid bodies defined in meta-data file
142	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
143	>	+ nGlobalRigidBodies_;
144	>
145	>	nGlobalMols_ = molStampIds_.size();
146	>	molToProcMap_.resize(nGlobalMols_);
147	>	}
148	>
149		SimInfo::~SimInfo() {
150	<	std::map<int, Molecule*>::iterator i;
150	>	map<int, Molecule*>::iterator i;
151		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
152		delete i->second;
153		}
#	Line 170 \| Line 158 \| namespace OpenMD {
158		delete forceField_;
159		}
160
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	–	}
161
162		bool SimInfo::addMolecule(Molecule* mol) {
163		MoleculeIterator i;
164	<
164	>
165		i = molecules_.find(mol->getGlobalIndex());
166		if (i == molecules_.end() ) {
167	<
168	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
169	<
167	>
168	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
169	>
170		nAtoms_ += mol->getNAtoms();
171		nBonds_ += mol->getNBonds();
172		nBends_ += mol->getNBends();
#	Line 198 \| Line 176 \| namespace OpenMD {
176		nIntegrableObjects_ += mol->getNIntegrableObjects();
177		nCutoffGroups_ += mol->getNCutoffGroups();
178		nConstraints_ += mol->getNConstraintPairs();
179	<
179	>
180		addInteractionPairs(mol);
181	<
181	>
182		return true;
183		} else {
184		return false;
185		}
186		}
187	<
187	>
188		bool SimInfo::removeMolecule(Molecule* mol) {
189		MoleculeIterator i;
190		i = molecules_.find(mol->getGlobalIndex());
#	Line 234 \| Line 212 \| namespace OpenMD {
212		} else {
213		return false;
214		}
237	–
238	–
215		}
216
217
#	Line 253 \| Line 229 \| namespace OpenMD {
229		void SimInfo::calcNdf() {
230		int ndf_local;
231		MoleculeIterator i;
232	<	std::vector<StuntDouble*>::iterator j;
232	>	vector<StuntDouble*>::iterator j;
233		Molecule* mol;
234		StuntDouble* integrableObject;
235
#	Line 304 \| Line 280 \| namespace OpenMD {
280		int ndfRaw_local;
281
282		MoleculeIterator i;
283	<	std::vector<StuntDouble*>::iterator j;
283	>	vector<StuntDouble*>::iterator j;
284		Molecule* mol;
285		StuntDouble* integrableObject;
286
#	Line 353 \| Line 329 \| namespace OpenMD {
329
330		void SimInfo::addInteractionPairs(Molecule* mol) {
331		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
332	<	std::vector<Bond*>::iterator bondIter;
333	<	std::vector<Bend*>::iterator bendIter;
334	<	std::vector<Torsion*>::iterator torsionIter;
335	<	std::vector<Inversion*>::iterator inversionIter;
332	>	vector<Bond*>::iterator bondIter;
333	>	vector<Bend*>::iterator bendIter;
334	>	vector<Torsion*>::iterator torsionIter;
335	>	vector<Inversion*>::iterator inversionIter;
336		Bond* bond;
337		Bend* bend;
338		Torsion* torsion;
#	Line 374 \| Line 350 \| namespace OpenMD {
350		// always be excluded. These are done at the bottom of this
351		// function.
352
353	<	std::map<int, std::set<int> > atomGroups;
353	>	map<int, set<int> > atomGroups;
354		Molecule::RigidBodyIterator rbIter;
355		RigidBody* rb;
356		Molecule::IntegrableObjectIterator ii;
#	Line 386 \| Line 362 \| namespace OpenMD {
362
363		if (integrableObject->isRigidBody()) {
364		rb = static_cast<RigidBody*>(integrableObject);
365	<	std::vector<Atom*> atoms = rb->getAtoms();
366	<	std::set<int> rigidAtoms;
365	>	vector<Atom*> atoms = rb->getAtoms();
366	>	set<int> rigidAtoms;
367		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
368		rigidAtoms.insert(atoms[i]->getGlobalIndex());
369		}
370		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
371	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
371	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
372		}
373		} else {
374	<	std::set<int> oneAtomSet;
374	>	set<int> oneAtomSet;
375		oneAtomSet.insert(integrableObject->getGlobalIndex());
376	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
376	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
377		}
378		}
379
#	Line 500 \| Line 476 \| namespace OpenMD {
476
477		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
478		rb = mol->nextRigidBody(rbIter)) {
479	<	std::vector<Atom*> atoms = rb->getAtoms();
479	>	vector<Atom*> atoms = rb->getAtoms();
480		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
481		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
482		a = atoms[i]->getGlobalIndex();
#	Line 514 \| Line 490 \| namespace OpenMD {
490
491		void SimInfo::removeInteractionPairs(Molecule* mol) {
492		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
493	<	std::vector<Bond*>::iterator bondIter;
494	<	std::vector<Bend*>::iterator bendIter;
495	<	std::vector<Torsion*>::iterator torsionIter;
496	<	std::vector<Inversion*>::iterator inversionIter;
493	>	vector<Bond*>::iterator bondIter;
494	>	vector<Bend*>::iterator bendIter;
495	>	vector<Torsion*>::iterator torsionIter;
496	>	vector<Inversion*>::iterator inversionIter;
497		Bond* bond;
498		Bend* bend;
499		Torsion* torsion;
#	Line 527 \| Line 503 \| namespace OpenMD {
503		int c;
504		int d;
505
506	<	std::map<int, std::set<int> > atomGroups;
506	>	map<int, set<int> > atomGroups;
507		Molecule::RigidBodyIterator rbIter;
508		RigidBody* rb;
509		Molecule::IntegrableObjectIterator ii;
#	Line 539 \| Line 515 \| namespace OpenMD {
515
516		if (integrableObject->isRigidBody()) {
517		rb = static_cast<RigidBody*>(integrableObject);
518	<	std::vector<Atom*> atoms = rb->getAtoms();
519	<	std::set<int> rigidAtoms;
518	>	vector<Atom*> atoms = rb->getAtoms();
519	>	set<int> rigidAtoms;
520		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
521		rigidAtoms.insert(atoms[i]->getGlobalIndex());
522		}
523		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
524	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
524	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
525		}
526		} else {
527	<	std::set<int> oneAtomSet;
527	>	set<int> oneAtomSet;
528		oneAtomSet.insert(integrableObject->getGlobalIndex());
529	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
529	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
530		}
531		}
532
#	Line 653 \| Line 629 \| namespace OpenMD {
629
630		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
631		rb = mol->nextRigidBody(rbIter)) {
632	<	std::vector<Atom*> atoms = rb->getAtoms();
632	>	vector<Atom*> atoms = rb->getAtoms();
633		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
634		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
635		a = atoms[i]->getGlobalIndex();
#	Line 676 \| Line 652 \| namespace OpenMD {
652		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
653		}
654
679	–	void SimInfo::update() {
655
656	<	setupSimType();
657	<
658	<	#ifdef IS_MPI
659	<	setupFortranParallel();
660	<	#endif
661	<
662	<	setupFortranSim();
663	<
664	<	//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	<
656	>	/**
657	>	* update
658	>	*
659	>	* Performs the global checks and variable settings after the
660	>	* objects have been created.
661	>	*
662	>	*/
663	>	void SimInfo::update() {
664	>	setupSimVariables();
665		calcNdf();
666		calcNdfRaw();
667		calcNdfTrans();
709	–
710	–	fortranInitialized_ = true;
668		}
669	<
670	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
669	>
670	>	/**
671	>	* getSimulatedAtomTypes
672	>	*
673	>	* Returns an STL set of AtomType* that are actually present in this
674	>	* simulation. Must query all processors to assemble this information.
675	>	*
676	>	*/
677	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
678		SimInfo::MoleculeIterator mi;
679		Molecule* mol;
680		Molecule::AtomIterator ai;
681		Atom* atom;
682	<	std::set<AtomType*> atomTypes;
683	<
684	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
721	<
682	>	set<AtomType*> atomTypes;
683	>
684	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
685		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
686		atomTypes.insert(atom->getAtomType());
687	<	}
688	<
726	<	}
687	>	}
688	>	}
689
690	<	return atomTypes;
729	<	}
690	>	#ifdef IS_MPI
691
692	<	void SimInfo::setupSimType() {
693	<	std::set<AtomType*>::iterator i;
733	<	std::set<AtomType*> atomTypes;
734	<	atomTypes = getUniqueAtomTypes();
735	<
736	<	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;
692	>	// loop over the found atom types on this processor, and add their
693	>	// numerical idents to a vector:
694
695	<	std::string myMethod;
695	>	vector<int> foundTypes;
696	>	set<AtomType*>::iterator i;
697	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
698	>	foundTypes.push_back( (*i)->getIdent() );
699
700	<	// set the useRF logical
701	<	useRF = 0;
761	<	useSF = 0;
762	<	useSP = 0;
763	<	useBoxDipole = 0;
700	>	// count_local holds the number of found types on this processor
701	>	int count_local = foundTypes.size();
702
703	<	if (simParams_->haveElectrostaticSummationMethod()) {
704	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
705	<	toUpper(myMethod);
706	<	if (myMethod == "REACTION_FIELD"){
707	<	useRF = 1;
708	<	} else if (myMethod == "SHIFTED_FORCE"){
709	<	useSF = 1;
710	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
711	<	useSP = 1;
712	<	}
713	<	}
703	>	// count holds the total number of found types on all processors
704	>	// (some will be redundant with the ones found locally):
705	>	int count;
706	>	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
707	>
708	>	// create a vector to hold the globally found types, and resize it:
709	>	vector<int> ftGlobal;
710	>	ftGlobal.resize(count);
711	>	vector<int> counts;
712	>
713	>	int nproc = MPI::COMM_WORLD.Get_size();
714	>	counts.resize(nproc);
715	>	vector<int> disps;
716	>	disps.resize(nproc);
717	>
718	>	// now spray out the foundTypes to all the other processors:
719
720	<	if (simParams_->haveAccumulateBoxDipole())
721	<	if (simParams_->getAccumulateBoxDipole())
779	<	useBoxDipole = 1;
720	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
721	>	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
722
723	+	// foundIdents is a stl set, so inserting an already found ident
724	+	// will have no effect.
725	+	set<int> foundIdents;
726	+	vector<int>::iterator j;
727	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
728	+	foundIdents.insert((*j));
729	+
730	+	// now iterate over the foundIdents and get the actual atom types
731	+	// that correspond to these:
732	+	set<int>::iterator it;
733	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
734	+	atomTypes.insert( forceField_->getAtomType((*it)) );
735	+
736	+	#endif
737	+
738	+	return atomTypes;
739	+	}
740	+
741	+	void SimInfo::setupSimVariables() {
742		useAtomicVirial_ = simParams_->getUseAtomicVirial();
743	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
744	+	calcBoxDipole_ = false;
745	+	if ( simParams_->haveAccumulateBoxDipole() )
746	+	if ( simParams_->getAccumulateBoxDipole() ) {
747	+	calcBoxDipole_ = true;
748	+	}
749
750	+	set<AtomType*>::iterator i;
751	+	set<AtomType*> atomTypes;
752	+	atomTypes = getSimulatedAtomTypes();
753	+	int usesElectrostatic = 0;
754	+	int usesMetallic = 0;
755	+	int usesDirectional = 0;
756		//loop over all of the atom types
757		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
758	<	useLennardJones \|= (*i)->isLennardJones();
759	<	useElectrostatic \|= (*i)->isElectrostatic();
760	<	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();
758	>	usesElectrostatic \|= (*i)->isElectrostatic();
759	>	usesMetallic \|= (*i)->isMetal();
760	>	usesDirectional \|= (*i)->isDirectional();
761		}
762
798	–	if (useSticky \|\| useStickyPower \|\| useDipole \|\| useGayBerne \|\| useShape) {
799	–	useDirectionalAtom = 1;
800	–	}
801	–
802	–	if (useCharge \|\| useDipole) {
803	–	useElectrostatics = 1;
804	–	}
805	–
763		#ifdef IS_MPI
764		int temp;
765	+	temp = usesDirectional;
766	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767
768	<	temp = usePBC;
769	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
811	<
812	<	temp = useDirectionalAtom;
813	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814	<
815	<	temp = useLennardJones;
816	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
817	<
818	<	temp = useElectrostatics;
819	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
820	<
821	<	temp = useCharge;
822	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
768	>	temp = usesMetallic;
769	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770
771	<	temp = useDipole;
772	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
826	<
827	<	temp = useSticky;
828	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
829	<
830	<	temp = useStickyPower;
831	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
832	<
833	<	temp = useGayBerne;
834	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
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);
841	<
842	<	temp = useShape;
843	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
844	<
845	<	temp = useFLARB;
846	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
847	<
848	<	temp = useRF;
849	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
850	<
851	<	temp = useSF;
852	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
853	<
854	<	temp = useSP;
855	<	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
856	<
857	<	temp = useBoxDipole;
858	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
859	<
860	<	temp = useAtomicVirial_;
861	<	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
862	<
771	>	temp = usesElectrostatic;
772	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
773		#endif
774	<	fInfo_.SIM_uses_PBC = usePBC;
775	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
776	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
777	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
778	<	fInfo_.SIM_uses_Charges = useCharge;
779	<	fInfo_.SIM_uses_Dipoles = useDipole;
870	<	fInfo_.SIM_uses_Sticky = useSticky;
871	<	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_;
774	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
775	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
776	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
777	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
778	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
779	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
780		}
781
782	<	void SimInfo::setupFortranSim() {
782	>	void SimInfo::setupFortran() {
783		int isError;
784		int nExclude, nOneTwo, nOneThree, nOneFour;
785	<	std::vector<int> fortranGlobalGroupMembership;
785	>	vector<int> fortranGlobalGroupMembership;
786
787		isError = 0;
788
#	Line 894 \| Line 792 \| namespace OpenMD {
792		}
793
794		//calculate mass ratio of cutoff group
795	<	std::vector<RealType> mfact;
795	>	vector<RealType> mfact;
796		SimInfo::MoleculeIterator mi;
797		Molecule* mol;
798		Molecule::CutoffGroupIterator ci;
#	Line 920 \| Line 818 \| namespace OpenMD {
818		}
819		}
820
821	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
822	<	std::vector<int> identArray;
821	>	//fill ident array of local atoms (it is actually ident of
822	>	//AtomType, it is so confusing !!!)
823	>	vector<int> identArray;
824
825		//to avoid memory reallocation, reserve enough space identArray
826		identArray.reserve(getNAtoms());
#	Line 934 \| Line 833 \| namespace OpenMD {
833
834		//fill molMembershipArray
835		//molMembershipArray is filled by SimCreator
836	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
836	>	vector<int> molMembershipArray(nGlobalAtoms_);
837		for (int i = 0; i < nGlobalAtoms_; i++) {
838		molMembershipArray[i] = globalMolMembership_[i] + 1;
839		}
#	Line 980 \| Line 879 \| namespace OpenMD {
879		setNeighbors(&nlistNeighbors);
880		}
881
983	–
984	–	}
985	–
986	–
987	–	void SimInfo::setupFortranParallel() {
882		#ifdef IS_MPI
883	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
884	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
885	<	std::vector<int> localToGlobalCutoffGroupIndex;
886	<	SimInfo::MoleculeIterator mi;
993	<	Molecule::AtomIterator ai;
994	<	Molecule::CutoffGroupIterator ci;
995	<	Molecule* mol;
996	<	Atom* atom;
997	<	CutoffGroup* cg;
883	>	//SimInfo is responsible for creating localToGlobalAtomIndex and
884	>	//localToGlobalGroupIndex
885	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
886	>	vector<int> localToGlobalCutoffGroupIndex;
887		mpiSimData parallelData;
999	–	int isError;
888
889		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
890
#	Line 1036 \| Line 924 \| namespace OpenMD {
924
925		sprintf(checkPointMsg, " mpiRefresh successful.\n");
926		errorCheckPoint();
1039	–
927		#endif
1041	–	}
928
929	<	void SimInfo::setupCutoff() {
930	<
931	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
932	<
933	<	// Check the cutoff policy
934	<	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();
929	>	initFortranFF(&isError);
930	>	if (isError) {
931	>	sprintf(painCave.errMsg,
932	>	"initFortranFF errror: fortran didn't like something we gave it.\n");
933	>	painCave.isFatal = 1;
934	>	simError();
935		}
936	<
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_);
1130	<
1131	<	} else {
1132	<
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	<	}
936	>	fortranInitialized_ = true;
937		}
938
1191	–	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	–
939		void SimInfo::addProperty(GenericData* genData) {
940		properties_.addProperty(genData);
941		}
942
943	<	void SimInfo::removeProperty(const std::string& propName) {
943	>	void SimInfo::removeProperty(const string& propName) {
944		properties_.removeProperty(propName);
945		}
946
#	Line 1336 \| Line 948 \| namespace OpenMD {
948		properties_.clearProperties();
949		}
950
951	<	std::vector<std::string> SimInfo::getPropertyNames() {
951	>	vector<string> SimInfo::getPropertyNames() {
952		return properties_.getPropertyNames();
953		}
954
955	<	std::vector<GenericData*> SimInfo::getProperties() {
955	>	vector<GenericData*> SimInfo::getProperties() {
956		return properties_.getProperties();
957		}
958
959	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
959	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
960		return properties_.getPropertyByName(propName);
961		}
962
#	Line 1427 \| Line 1039 \| namespace OpenMD {
1039
1040		}
1041
1042	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1042	>	ostream& operator <<(ostream& o, SimInfo& info) {
1043
1044		return o;
1045		}
#	Line 1577 \| Line 1189 \| namespace OpenMD {
1189		return IOIndexToIntegrableObject.at(index);
1190		}
1191
1192	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1192	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1193		IOIndexToIntegrableObject= v;
1194		}
1195
#	Line 1619 \| Line 1231 \| namespace OpenMD {
1231		return;
1232		}
1233		/*
1234	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1234	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1235		assert( v.size() == nAtoms_ + nRigidBodies_);
1236		sdByGlobalIndex_ = v;
1237		}
#	Line 1629 \| Line 1241 \| namespace OpenMD {
1241		return sdByGlobalIndex_.at(index);
1242		}
1243		*/
1244	+	int SimInfo::getNGlobalConstraints() {
1245	+	int nGlobalConstraints;
1246	+	#ifdef IS_MPI
1247	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1248	+	MPI_COMM_WORLD);
1249	+	#else
1250	+	nGlobalConstraints = nConstraints_;
1251	+	#endif
1252	+	return nGlobalConstraints;
1253	+	}
1254	+
1255		}//end namespace OpenMD
1256

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Comparing branches/development/src/brains/SimInfo.cpp (file contents): Revision 1505 by gezelter, Sun Oct 3 22:18:59 2010 UTC vs. Revision 1536 by gezelter, Wed Jan 5 14:49:05 2011 UTC

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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1505 by gezelter, Sun Oct 3 22:18:59 2010 UTC vs.
Revision 1536 by gezelter, Wed Jan 5 14:49:05 2011 UTC