[ViewVC] Diff of: OpenMD/branches/development/src/brains/SimInfo.cpp

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 720 by chrisfen, Tue Nov 8 13:32:06 2005 UTC vs.
Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC

#	Line 48 \| Line 48
48
49		#include <algorithm>
50		#include <set>
51	+	#include <map>
52
53		#include "brains/SimInfo.hpp"
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56	+	#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/notifyCutoffs_interface.h"
64	>	#include "UseTheForce/DarkSide/switcheroo_interface.h"
65		#include "utils/MemoryUtils.hpp"
66		#include "utils/simError.h"
67		#include "selection/SelectionManager.hpp"
68	+	#include "io/ForceFieldOptions.hpp"
69	+	#include "UseTheForce/ForceField.hpp"
70
71	+
72		#ifdef IS_MPI
73		#include "UseTheForce/mpiComponentPlan.h"
74		#include "UseTheForce/DarkSide/simParallel_interface.h"
75		#endif
76
77		namespace oopse {
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	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
86	<	ForceField* ff, Globals* simParams) :
87	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
88	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
85	>	return result;
86	>	}
87	>
88	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
89	>	forceField_(ff), simParams_(simParams),
90	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
91		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
92		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
93		nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
94		nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
95	<	sman_(NULL), fortranInitialized_(false) {
95	>	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false),
96	>	useAtomicVirial_(true) {
97
82	–
83	–	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
98		MoleculeStamp* molStamp;
99		int nMolWithSameStamp;
100		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
#	Line 88 \| Line 102 \| namespace oopse {
102		CutoffGroupStamp* cgStamp;
103		RigidBodyStamp* rbStamp;
104		int nRigidAtoms = 0;
105	<
106	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
107	<	molStamp = i->first;
108	<	nMolWithSameStamp = i->second;
105	>	std::vector<Component*> components = simParams->getComponents();
106	>
107	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
108	>	molStamp = (*i)->getMoleculeStamp();
109	>	nMolWithSameStamp = (*i)->getNMol();
110
111		addMoleculeStamp(molStamp, nMolWithSameStamp);
112
113		//calculate atoms in molecules
114		nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
115
101	–
116		//calculate atoms in cutoff groups
117		int nAtomsInGroups = 0;
118		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
119
120		for (int j=0; j < nCutoffGroupsInStamp; j++) {
121	<	cgStamp = molStamp->getCutoffGroup(j);
121	>	cgStamp = molStamp->getCutoffGroupStamp(j);
122		nAtomsInGroups += cgStamp->getNMembers();
123		}
124
#	Line 117 \| Line 131 \| namespace oopse {
131		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
132
133		for (int j=0; j < nRigidBodiesInStamp; j++) {
134	<	rbStamp = molStamp->getRigidBody(j);
134	>	rbStamp = molStamp->getRigidBodyStamp(j);
135		nAtomsInRigidBodies += rbStamp->getNMembers();
136		}
137
#	Line 142 \| Line 156 \| namespace oopse {
156		+ nGlobalRigidBodies_;
157
158		nGlobalMols_ = molStampIds_.size();
145	–
146	–	#ifdef IS_MPI
159		molToProcMap_.resize(nGlobalMols_);
148	–	#endif
149	–
160		}
161
162		SimInfo::~SimInfo() {
#	Line 156 \| Line 166 \| namespace oopse {
166		}
167		molecules_.clear();
168
159	–	delete stamps_;
169		delete sman_;
170		delete simParams_;
171		delete forceField_;
#	Line 263 \| Line 272 \| namespace oopse {
272		}
273		}
274
275	<	}//end for (integrableObject)
276	<	}// end for (mol)
275	>	}
276	>	}
277
278		// n_constraints is local, so subtract them on each processor
279		ndf_local -= nConstraints_;
#	Line 281 \| Line 290 \| namespace oopse {
290
291		}
292
293	+	int SimInfo::getFdf() {
294	+	#ifdef IS_MPI
295	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
296	+	#else
297	+	fdf_ = fdf_local;
298	+	#endif
299	+	return fdf_;
300	+	}
301	+
302		void SimInfo::calcNdfRaw() {
303		int ndfRaw_local;
304
#	Line 343 \| Line 361 \| namespace oopse {
361		int b;
362		int c;
363		int d;
364	+
365	+	std::map<int, std::set<int> > atomGroups;
366	+
367	+	Molecule::RigidBodyIterator rbIter;
368	+	RigidBody* rb;
369	+	Molecule::IntegrableObjectIterator ii;
370	+	StuntDouble* integrableObject;
371
372	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
373	+	integrableObject = mol->nextIntegrableObject(ii)) {
374	+
375	+	if (integrableObject->isRigidBody()) {
376	+	rb = static_cast<RigidBody*>(integrableObject);
377	+	std::vector<Atom*> atoms = rb->getAtoms();
378	+	std::set<int> rigidAtoms;
379	+	for (int i = 0; i < atoms.size(); ++i) {
380	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
381	+	}
382	+	for (int i = 0; i < atoms.size(); ++i) {
383	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
384	+	}
385	+	} else {
386	+	std::set<int> oneAtomSet;
387	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
388	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
389	+	}
390	+	}
391	+
392	+
393	+
394		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
395		a = bond->getAtomA()->getGlobalIndex();
396		b = bond->getAtomB()->getGlobalIndex();
#	Line 354 \| Line 401 \| namespace oopse {
401		a = bend->getAtomA()->getGlobalIndex();
402		b = bend->getAtomB()->getGlobalIndex();
403		c = bend->getAtomC()->getGlobalIndex();
404	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
405	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
406	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
407
408	<	exclude_.addPair(a, b);
409	<	exclude_.addPair(a, c);
410	<	exclude_.addPair(b, c);
408	>	exclude_.addPairs(rigidSetA, rigidSetB);
409	>	exclude_.addPairs(rigidSetA, rigidSetC);
410	>	exclude_.addPairs(rigidSetB, rigidSetC);
411	>
412	>	//exclude_.addPair(a, b);
413	>	//exclude_.addPair(a, c);
414	>	//exclude_.addPair(b, c);
415		}
416
417		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
#	Line 365 \| Line 419 \| namespace oopse {
419		b = torsion->getAtomB()->getGlobalIndex();
420		c = torsion->getAtomC()->getGlobalIndex();
421		d = torsion->getAtomD()->getGlobalIndex();
422	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
423	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
424	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
425	+	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
426
427	+	exclude_.addPairs(rigidSetA, rigidSetB);
428	+	exclude_.addPairs(rigidSetA, rigidSetC);
429	+	exclude_.addPairs(rigidSetA, rigidSetD);
430	+	exclude_.addPairs(rigidSetB, rigidSetC);
431	+	exclude_.addPairs(rigidSetB, rigidSetD);
432	+	exclude_.addPairs(rigidSetC, rigidSetD);
433	+
434	+	/*
435	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
436	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
437	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
438	+	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
439	+	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
440	+	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
441	+
442	+
443		exclude_.addPair(a, b);
444		exclude_.addPair(a, c);
445		exclude_.addPair(a, d);
446		exclude_.addPair(b, c);
447		exclude_.addPair(b, d);
448		exclude_.addPair(c, d);
449	+	*/
450		}
451
377	–	Molecule::RigidBodyIterator rbIter;
378	–	RigidBody* rb;
452		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
453		std::vector<Atom*> atoms = rb->getAtoms();
454		for (int i = 0; i < atoms.size() -1 ; ++i) {
#	Line 400 \| Line 473 \| namespace oopse {
473		int b;
474		int c;
475		int d;
476	+
477	+	std::map<int, std::set<int> > atomGroups;
478	+
479	+	Molecule::RigidBodyIterator rbIter;
480	+	RigidBody* rb;
481	+	Molecule::IntegrableObjectIterator ii;
482	+	StuntDouble* integrableObject;
483
484	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
485	+	integrableObject = mol->nextIntegrableObject(ii)) {
486	+
487	+	if (integrableObject->isRigidBody()) {
488	+	rb = static_cast<RigidBody*>(integrableObject);
489	+	std::vector<Atom*> atoms = rb->getAtoms();
490	+	std::set<int> rigidAtoms;
491	+	for (int i = 0; i < atoms.size(); ++i) {
492	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
493	+	}
494	+	for (int i = 0; i < atoms.size(); ++i) {
495	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
496	+	}
497	+	} else {
498	+	std::set<int> oneAtomSet;
499	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
500	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
501	+	}
502	+	}
503	+
504	+
505		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
506		a = bond->getAtomA()->getGlobalIndex();
507		b = bond->getAtomB()->getGlobalIndex();
#	Line 412 \| Line 513 \| namespace oopse {
513		b = bend->getAtomB()->getGlobalIndex();
514		c = bend->getAtomC()->getGlobalIndex();
515
516	<	exclude_.removePair(a, b);
517	<	exclude_.removePair(a, c);
518	<	exclude_.removePair(b, c);
516	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
517	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
518	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
519	>
520	>	exclude_.removePairs(rigidSetA, rigidSetB);
521	>	exclude_.removePairs(rigidSetA, rigidSetC);
522	>	exclude_.removePairs(rigidSetB, rigidSetC);
523	>
524	>	//exclude_.removePair(a, b);
525	>	//exclude_.removePair(a, c);
526	>	//exclude_.removePair(b, c);
527		}
528
529		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
#	Line 422 \| Line 531 \| namespace oopse {
531		b = torsion->getAtomB()->getGlobalIndex();
532		c = torsion->getAtomC()->getGlobalIndex();
533		d = torsion->getAtomD()->getGlobalIndex();
534	+
535	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
536	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
537	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
538	+	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
539	+
540	+	exclude_.removePairs(rigidSetA, rigidSetB);
541	+	exclude_.removePairs(rigidSetA, rigidSetC);
542	+	exclude_.removePairs(rigidSetA, rigidSetD);
543	+	exclude_.removePairs(rigidSetB, rigidSetC);
544	+	exclude_.removePairs(rigidSetB, rigidSetD);
545	+	exclude_.removePairs(rigidSetC, rigidSetD);
546	+
547	+	/*
548	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
549	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
550	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
551	+	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
552	+	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
553	+	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
554
555	+
556		exclude_.removePair(a, b);
557		exclude_.removePair(a, c);
558		exclude_.removePair(a, d);
559		exclude_.removePair(b, c);
560		exclude_.removePair(b, d);
561		exclude_.removePair(c, d);
562	+	*/
563		}
564
434	–	Molecule::RigidBodyIterator rbIter;
435	–	RigidBody* rb;
565		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
566		std::vector<Atom*> atoms = rb->getAtoms();
567		for (int i = 0; i < atoms.size() -1 ; ++i) {
#	Line 471 \| Line 600 \| namespace oopse {
600		/** @deprecate */
601		int isError = 0;
602
603	+	setupCutoff();
604	+
605		setupElectrostaticSummationMethod( isError );
606	+	setupSwitchingFunction();
607	+	setupAccumulateBoxDipole();
608
609		if(isError){
610		sprintf( painCave.errMsg,
#	Line 479 \| Line 612 \| namespace oopse {
612		painCave.isFatal = 1;
613		simError();
614		}
482	–
483	–
484	–	setupCutoff();
615
616		calcNdf();
617		calcNdfRaw();
#	Line 516 \| Line 646 \| namespace oopse {
646		int useLennardJones = 0;
647		int useElectrostatic = 0;
648		int useEAM = 0;
649	+	int useSC = 0;
650		int useCharge = 0;
651		int useDirectional = 0;
652		int useDipole = 0;
#	Line 530 \| Line 661 \| namespace oopse {
661		int usePBC = simParams_->getUsePeriodicBoundaryConditions();
662		int useRF;
663		int useSF;
664	+	int useSP;
665	+	int useBoxDipole;
666	+
667		std::string myMethod;
668
669		// set the useRF logical
670		useRF = 0;
671		useSF = 0;
672	+	useSP = 0;
673
674
675		if (simParams_->haveElectrostaticSummationMethod()) {
676		std::string myMethod = simParams_->getElectrostaticSummationMethod();
677		toUpper(myMethod);
678	<	if (myMethod == "REACTION_FIELD") {
679	<	useRF=1;
680	<	} else {
681	<	if (myMethod == "SHIFTED_FORCE") {
682	<	useSF = 1;
683	<	}
678	>	if (myMethod == "REACTION_FIELD"){
679	>	useRF = 1;
680	>	} else if (myMethod == "SHIFTED_FORCE"){
681	>	useSF = 1;
682	>	} else if (myMethod == "SHIFTED_POTENTIAL"){
683	>	useSP = 1;
684		}
685		}
686	+
687	+	if (simParams_->haveAccumulateBoxDipole())
688	+	if (simParams_->getAccumulateBoxDipole())
689	+	useBoxDipole = 1;
690
691	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
692	+
693		//loop over all of the atom types
694		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
695		useLennardJones \|= (*i)->isLennardJones();
696		useElectrostatic \|= (*i)->isElectrostatic();
697		useEAM \|= (*i)->isEAM();
698	+	useSC \|= (*i)->isSC();
699		useCharge \|= (*i)->isCharge();
700		useDirectional \|= (*i)->isDirectional();
701		useDipole \|= (*i)->isDipole();
#	Line 604 \| Line 746 \| namespace oopse {
746		temp = useEAM;
747		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
748
749	+	temp = useSC;
750	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
751	+
752		temp = useShape;
753		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
754
#	Line 614 \| Line 759 \| namespace oopse {
759		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
760
761		temp = useSF;
762	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
762	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
763
764	+	temp = useSP;
765	+	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766	+
767	+	temp = useBoxDipole;
768	+	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769	+
770	+	temp = useAtomicVirial_;
771	+	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
772	+
773		#endif
774
775		fInfo_.SIM_uses_PBC = usePBC;
#	Line 628 \| Line 782 \| namespace oopse {
782		fInfo_.SIM_uses_StickyPower = useStickyPower;
783		fInfo_.SIM_uses_GayBerne = useGayBerne;
784		fInfo_.SIM_uses_EAM = useEAM;
785	+	fInfo_.SIM_uses_SC = useSC;
786		fInfo_.SIM_uses_Shapes = useShape;
787		fInfo_.SIM_uses_FLARB = useFLARB;
788		fInfo_.SIM_uses_RF = useRF;
789		fInfo_.SIM_uses_SF = useSF;
790	<
791	<	if( myMethod == "REACTION_FIELD") {
792	<
638	<	if (simParams_->haveDielectric()) {
639	<	fInfo_.dielect = simParams_->getDielectric();
640	<	} else {
641	<	sprintf(painCave.errMsg,
642	<	"SimSetup Error: No Dielectric constant was set.\n"
643	<	"\tYou are trying to use Reaction Field without"
644	<	"\tsetting a dielectric constant!\n");
645	<	painCave.isFatal = 1;
646	<	simError();
647	<	}
648	<	}
649	<
790	>	fInfo_.SIM_uses_SP = useSP;
791	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
792	>	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
793		}
794
795		void SimInfo::setupFortranSim() {
#	Line 663 \| Line 806 \| namespace oopse {
806		}
807
808		//calculate mass ratio of cutoff group
809	<	std::vector<double> mfact;
809	>	std::vector<RealType> mfact;
810		SimInfo::MoleculeIterator mi;
811		Molecule* mol;
812		Molecule::CutoffGroupIterator ci;
813		CutoffGroup* cg;
814		Molecule::AtomIterator ai;
815		Atom* atom;
816	<	double totalMass;
816	>	RealType totalMass;
817
818		//to avoid memory reallocation, reserve enough space for mfact
819		mfact.reserve(getNCutoffGroups());
#	Line 713 \| Line 856 \| namespace oopse {
856		int nGlobalExcludes = 0;
857		int* globalExcludes = NULL;
858		int* excludeList = exclude_.getExcludeList();
859	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
860	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
861	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
862	<
859	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
860	>	&nExclude, excludeList , &nGlobalExcludes, globalExcludes,
861	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
862	>	&fortranGlobalGroupMembership[0], &isError);
863	>
864		if( isError ){
865	<
865	>
866		sprintf( painCave.errMsg,
867		"There was an error setting the simulation information in fortran.\n" );
868		painCave.isFatal = 1;
869		painCave.severity = OOPSE_ERROR;
870		simError();
871		}
872	<
873	<	#ifdef IS_MPI
872	>
873	>
874		sprintf( checkPointMsg,
875		"succesfully sent the simulation information to fortran.\n");
876	<	MPIcheckPoint();
877	<	#endif // is_mpi
876	>
877	>	errorCheckPoint();
878	>
879	>	// Setup number of neighbors in neighbor list if present
880	>	if (simParams_->haveNeighborListNeighbors()) {
881	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
882	>	setNeighbors(&nlistNeighbors);
883	>	}
884	>
885	>
886		}
887
888
737	–	#ifdef IS_MPI
889		void SimInfo::setupFortranParallel() {
890	<
890	>	#ifdef IS_MPI
891		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
892		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
893		std::vector<int> localToGlobalCutoffGroupIndex;
#	Line 786 \| Line 937 \| namespace oopse {
937		}
938
939		sprintf(checkPointMsg, " mpiRefresh successful.\n");
940	<	MPIcheckPoint();
940	>	errorCheckPoint();
941
942	<
942	>	#endif
943		}
944
945	<	#endif
945	>	void SimInfo::setupCutoff() {
946	>
947	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
948
949	<	double SimInfo::calcMaxCutoffRadius() {
949	>	// Check the cutoff policy
950	>	int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
951
952	+	// Set LJ shifting bools to false
953	+	ljsp_ = false;
954	+	ljsf_ = false;
955
956	<	std::set<AtomType*> atomTypes;
957	<	std::set<AtomType*>::iterator i;
958	<	std::vector<double> cutoffRadius;
959	<
960	<	//get the unique atom types
804	<	atomTypes = getUniqueAtomTypes();
805	<
806	<	//query the max cutoff radius among these atom types
807	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
808	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
956	>	std::string myPolicy;
957	>	if (forceFieldOptions_.haveCutoffPolicy()){
958	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
959	>	}else if (simParams_->haveCutoffPolicy()) {
960	>	myPolicy = simParams_->getCutoffPolicy();
961		}
962
963	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
812	<	#ifdef IS_MPI
813	<	//pick the max cutoff radius among the processors
814	<	#endif
815	<
816	<	return maxCutoffRadius;
817	<	}
818	<
819	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
820	<
821	<	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
822	<
823	<	if (!simParams_->haveCutoffRadius()){
824	<	sprintf(painCave.errMsg,
825	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
826	<	"\tOOPSE will use a default value of 15.0 angstroms"
827	<	"\tfor the cutoffRadius.\n");
828	<	painCave.isFatal = 0;
829	<	simError();
830	<	rcut = 15.0;
831	<	} else{
832	<	rcut = simParams_->getCutoffRadius();
833	<	}
834	<
835	<	if (!simParams_->haveSwitchingRadius()){
836	<	sprintf(painCave.errMsg,
837	<	"SimCreator Warning: No value was set for switchingRadius.\n"
838	<	"\tOOPSE will use a default value of\n"
839	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
840	<	painCave.isFatal = 0;
841	<	simError();
842	<	rsw = 0.85 * rcut;
843	<	} else{
844	<	rsw = simParams_->getSwitchingRadius();
845	<	}
846	<
847	<	} else {
848	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
849	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
850	<
851	<	if (simParams_->haveCutoffRadius()) {
852	<	rcut = simParams_->getCutoffRadius();
853	<	} else {
854	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
855	<	rcut = calcMaxCutoffRadius();
856	<	}
857	<
858	<	if (simParams_->haveSwitchingRadius()) {
859	<	rsw = simParams_->getSwitchingRadius();
860	<	} else {
861	<	rsw = rcut;
862	<	}
863	<
864	<	}
865	<	}
866	<
867	<	void SimInfo::setupCutoff() {
868	<	getCutoff(rcut_, rsw_);
869	<	double rnblist = rcut_ + 1; // skin of neighbor list
870	<
871	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
872	<
873	<	int cp = TRADITIONAL_CUTOFF_POLICY;
874	<	if (simParams_->haveCutoffPolicy()) {
875	<	std::string myPolicy = simParams_->getCutoffPolicy();
963	>	if (!myPolicy.empty()){
964		toUpper(myPolicy);
965		if (myPolicy == "MIX") {
966		cp = MIX_CUTOFF_POLICY;
#	Line 891 \| Line 979 \| namespace oopse {
979		}
980		}
981		}
982	<	}
982	>	}
983	>	notifyFortranCutoffPolicy(&cp);
984
985	<
985	>	// Check the Skin Thickness for neighborlists
986	>	RealType skin;
987		if (simParams_->haveSkinThickness()) {
988	<	double skinThickness = simParams_->getSkinThickness();
989	<	}
988	>	skin = simParams_->getSkinThickness();
989	>	notifyFortranSkinThickness(&skin);
990	>	}
991	>
992	>	// Check if the cutoff was set explicitly:
993	>	if (simParams_->haveCutoffRadius()) {
994	>	rcut_ = simParams_->getCutoffRadius();
995	>	if (simParams_->haveSwitchingRadius()) {
996	>	rsw_ = simParams_->getSwitchingRadius();
997	>	} else {
998	>	if (fInfo_.SIM_uses_Charges \|
999	>	fInfo_.SIM_uses_Dipoles \|
1000	>	fInfo_.SIM_uses_RF) {
1001	>
1002	>	rsw_ = 0.85 * rcut_;
1003	>	sprintf(painCave.errMsg,
1004	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1005	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1006	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1007	>	painCave.isFatal = 0;
1008	>	simError();
1009	>	} else {
1010	>	rsw_ = rcut_;
1011	>	sprintf(painCave.errMsg,
1012	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1013	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
1014	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1015	>	painCave.isFatal = 0;
1016	>	simError();
1017	>	}
1018	>	}
1019
1020	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1021	<	// also send cutoff notification to electrostatics
1022	<	setElectrostaticCutoffRadius(&rcut_, &rsw_);
1020	>	if (simParams_->haveElectrostaticSummationMethod()) {
1021	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1022	>	toUpper(myMethod);
1023	>
1024	>	if (myMethod == "SHIFTED_POTENTIAL") {
1025	>	ljsp_ = true;
1026	>	} else if (myMethod == "SHIFTED_FORCE") {
1027	>	ljsf_ = true;
1028	>	}
1029	>	}
1030	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1031	>
1032	>	} else {
1033	>
1034	>	// For electrostatic atoms, we'll assume a large safe value:
1035	>	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
1036	>	sprintf(painCave.errMsg,
1037	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1038	>	"\tOOPSE will use a default value of 15.0 angstroms"
1039	>	"\tfor the cutoffRadius.\n");
1040	>	painCave.isFatal = 0;
1041	>	simError();
1042	>	rcut_ = 15.0;
1043	>
1044	>	if (simParams_->haveElectrostaticSummationMethod()) {
1045	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1046	>	toUpper(myMethod);
1047	>
1048	>	// For the time being, we're tethering the LJ shifted behavior to the
1049	>	// electrostaticSummationMethod keyword options
1050	>	if (myMethod == "SHIFTED_POTENTIAL") {
1051	>	ljsp_ = true;
1052	>	} else if (myMethod == "SHIFTED_FORCE") {
1053	>	ljsf_ = true;
1054	>	}
1055	>	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
1056	>	if (simParams_->haveSwitchingRadius()){
1057	>	sprintf(painCave.errMsg,
1058	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1059	>	"\teven though the electrostaticSummationMethod was\n"
1060	>	"\tset to %s\n", myMethod.c_str());
1061	>	painCave.isFatal = 1;
1062	>	simError();
1063	>	}
1064	>	}
1065	>	}
1066	>
1067	>	if (simParams_->haveSwitchingRadius()){
1068	>	rsw_ = simParams_->getSwitchingRadius();
1069	>	} else {
1070	>	sprintf(painCave.errMsg,
1071	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1072	>	"\tOOPSE will use a default value of\n"
1073	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1074	>	painCave.isFatal = 0;
1075	>	simError();
1076	>	rsw_ = 0.85 * rcut_;
1077	>	}
1078	>
1079	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1080	>
1081	>	} else {
1082	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1083	>	// We'll punt and let fortran figure out the cutoffs later.
1084	>
1085	>	notifyFortranYouAreOnYourOwn();
1086	>
1087	>	}
1088	>	}
1089		}
1090
1091		void SimInfo::setupElectrostaticSummationMethod( int isError ) {
#	Line 908 \| Line 1093 \| namespace oopse {
1093		int errorOut;
1094		int esm = NONE;
1095		int sm = UNDAMPED;
1096	<	double alphaVal;
1097	<	double dielectric;
1098	<
1096	>	RealType alphaVal;
1097	>	RealType dielectric;
1098	>
1099		errorOut = isError;
915	–	alphaVal = simParams_->getDampingAlpha();
916	–	dielectric = simParams_->getDielectric();
1100
1101		if (simParams_->haveElectrostaticSummationMethod()) {
1102		std::string myMethod = simParams_->getElectrostaticSummationMethod();
#	Line 930 \| Line 1113 \| namespace oopse {
1113		if (myMethod == "SHIFTED_FORCE") {
1114		esm = SHIFTED_FORCE;
1115		} else {
1116	<	if (myMethod == "REACTION_FIELD") {
1116	>	if (myMethod == "REACTION_FIELD") {
1117		esm = REACTION_FIELD;
1118	+	dielectric = simParams_->getDielectric();
1119	+	if (!simParams_->haveDielectric()) {
1120	+	// throw warning
1121	+	sprintf( painCave.errMsg,
1122	+	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1123	+	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1124	+	painCave.isFatal = 0;
1125	+	simError();
1126	+	}
1127		} else {
1128		// throw error
1129		sprintf( painCave.errMsg,
1130	<	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() );
1130	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1131	>	"\t(Input file specified %s .)\n"
1132	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1133	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1134	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1135		painCave.isFatal = 1;
1136		simError();
1137		}
#	Line 954 \| Line 1150 \| namespace oopse {
1150		if (myScreen == "DAMPED") {
1151		sm = DAMPED;
1152		if (!simParams_->haveDampingAlpha()) {
1153	<	//throw error
1153	>	// first set a cutoff dependent alpha value
1154	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1155	>	alphaVal = 0.5125 - rcut_* 0.025;
1156	>	// for values rcut > 20.5, alpha is zero
1157	>	if (alphaVal < 0) alphaVal = 0;
1158	>
1159	>	// throw warning
1160		sprintf( painCave.errMsg,
1161	<	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
1161	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1162	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1163		painCave.isFatal = 0;
1164		simError();
1165	+	} else {
1166	+	alphaVal = simParams_->getDampingAlpha();
1167		}
1168	+
1169		} else {
1170		// throw error
1171		sprintf( painCave.errMsg,
1172	<	"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
1172	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1173	>	"\t(Input file specified %s .)\n"
1174	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1175	>	"or \"damped\".\n", myScreen.c_str() );
1176		painCave.isFatal = 1;
1177		simError();
1178		}
#	Line 972 \| Line 1181 \| namespace oopse {
1181
1182		// let's pass some summation method variables to fortran
1183		setElectrostaticSummationMethod( &esm );
1184	+	setFortranElectrostaticMethod( &esm );
1185		setScreeningMethod( &sm );
1186		setDampingAlpha( &alphaVal );
1187		setReactionFieldDielectric( &dielectric );
1188	<	initFortranFF( &esm, &errorOut );
1188	>	initFortranFF( &errorOut );
1189		}
1190
1191	+	void SimInfo::setupSwitchingFunction() {
1192	+	int ft = CUBIC;
1193	+
1194	+	if (simParams_->haveSwitchingFunctionType()) {
1195	+	std::string funcType = simParams_->getSwitchingFunctionType();
1196	+	toUpper(funcType);
1197	+	if (funcType == "CUBIC") {
1198	+	ft = CUBIC;
1199	+	} else {
1200	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1201	+	ft = FIFTH_ORDER_POLY;
1202	+	} else {
1203	+	// throw error
1204	+	sprintf( painCave.errMsg,
1205	+	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1206	+	painCave.isFatal = 1;
1207	+	simError();
1208	+	}
1209	+	}
1210	+	}
1211	+
1212	+	// send switching function notification to switcheroo
1213	+	setFunctionType(&ft);
1214	+
1215	+	}
1216	+
1217	+	void SimInfo::setupAccumulateBoxDipole() {
1218	+
1219	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1220	+	if ( simParams_->haveAccumulateBoxDipole() )
1221	+	if ( simParams_->getAccumulateBoxDipole() ) {
1222	+	setAccumulateBoxDipole();
1223	+	calcBoxDipole_ = true;
1224	+	}
1225	+
1226	+	}
1227	+
1228		void SimInfo::addProperty(GenericData* genData) {
1229		properties_.addProperty(genData);
1230		}
#	Line 1034 \| Line 1281 \| namespace oopse {
1281		Molecule* mol;
1282
1283		Vector3d comVel(0.0);
1284	<	double totalMass = 0.0;
1284	>	RealType totalMass = 0.0;
1285
1286
1287		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1288	<	double mass = mol->getMass();
1288	>	RealType mass = mol->getMass();
1289		totalMass += mass;
1290		comVel += mass * mol->getComVel();
1291		}
1292
1293		#ifdef IS_MPI
1294	<	double tmpMass = totalMass;
1294	>	RealType tmpMass = totalMass;
1295		Vector3d tmpComVel(comVel);
1296	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1297	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1296	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1297	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1298		#endif
1299
1300		comVel /= totalMass;
#	Line 1060 \| Line 1307 \| namespace oopse {
1307		Molecule* mol;
1308
1309		Vector3d com(0.0);
1310	<	double totalMass = 0.0;
1310	>	RealType totalMass = 0.0;
1311
1312		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1313	<	double mass = mol->getMass();
1313	>	RealType mass = mol->getMass();
1314		totalMass += mass;
1315		com += mass * mol->getCom();
1316		}
1317
1318		#ifdef IS_MPI
1319	<	double tmpMass = totalMass;
1319	>	RealType tmpMass = totalMass;
1320		Vector3d tmpCom(com);
1321	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1322	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1321	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1322	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1323		#endif
1324
1325		com /= totalMass;
#	Line 1096 \| Line 1343 \| namespace oopse {
1343		Molecule* mol;
1344
1345
1346	<	double totalMass = 0.0;
1346	>	RealType totalMass = 0.0;
1347
1348
1349		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1350	<	double mass = mol->getMass();
1350	>	RealType mass = mol->getMass();
1351		totalMass += mass;
1352		com += mass * mol->getCom();
1353		comVel += mass * mol->getComVel();
1354		}
1355
1356		#ifdef IS_MPI
1357	<	double tmpMass = totalMass;
1357	>	RealType tmpMass = totalMass;
1358		Vector3d tmpCom(com);
1359		Vector3d tmpComVel(comVel);
1360	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1361	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1362	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1360	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1361	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1362	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1363		#endif
1364
1365		com /= totalMass;
#	Line 1131 \| Line 1378 \| namespace oopse {
1378		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1379
1380
1381	<	double xx = 0.0;
1382	<	double yy = 0.0;
1383	<	double zz = 0.0;
1384	<	double xy = 0.0;
1385	<	double xz = 0.0;
1386	<	double yz = 0.0;
1381	>	RealType xx = 0.0;
1382	>	RealType yy = 0.0;
1383	>	RealType zz = 0.0;
1384	>	RealType xy = 0.0;
1385	>	RealType xz = 0.0;
1386	>	RealType yz = 0.0;
1387		Vector3d com(0.0);
1388		Vector3d comVel(0.0);
1389
#	Line 1148 \| Line 1395 \| namespace oopse {
1395		Vector3d thisq(0.0);
1396		Vector3d thisv(0.0);
1397
1398	<	double thisMass = 0.0;
1398	>	RealType thisMass = 0.0;
1399
1400
1401
#	Line 1186 \| Line 1433 \| namespace oopse {
1433		#ifdef IS_MPI
1434		Mat3x3d tmpI(inertiaTensor);
1435		Vector3d tmpAngMom;
1436	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1437	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1436	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1437	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1438		#endif
1439
1440		return;
#	Line 1208 \| Line 1455 \| namespace oopse {
1455		Vector3d thisr(0.0);
1456		Vector3d thisp(0.0);
1457
1458	<	double thisMass;
1458	>	RealType thisMass;
1459
1460		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1461		thisMass = mol->getMass();
#	Line 1221 \| Line 1468 \| namespace oopse {
1468
1469		#ifdef IS_MPI
1470		Vector3d tmpAngMom;
1471	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1471	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1472		#endif
1473
1474		return angularMomentum;
1475		}
1476
1477	<
1477	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1478	>	return IOIndexToIntegrableObject.at(index);
1479	>	}
1480	>
1481	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1482	>	IOIndexToIntegrableObject= v;
1483	>	}
1484	>
1485	>	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1486	>	based on the radius of gyration V=4/3PiR_1R_2R_3
1487	>	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1488	>	V = 4/3Pi(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1489	>	*/
1490	>	void SimInfo::getGyrationalVolume(RealType &volume){
1491	>	Mat3x3d intTensor;
1492	>	RealType det;
1493	>	Vector3d dummyAngMom;
1494	>	RealType sysconstants;
1495	>	RealType geomCnst;
1496	>
1497	>	geomCnst = 3.0/2.0;
1498	>	/* Get the inertial tensor and angular momentum for free*/
1499	>	getInertiaTensor(intTensor,dummyAngMom);
1500	>
1501	>	det = intTensor.determinant();
1502	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1503	>	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(det);
1504	>	return;
1505	>	}
1506	>
1507	>	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1508	>	Mat3x3d intTensor;
1509	>	Vector3d dummyAngMom;
1510	>	RealType sysconstants;
1511	>	RealType geomCnst;
1512	>
1513	>	geomCnst = 3.0/2.0;
1514	>	/* Get the inertial tensor and angular momentum for free*/
1515	>	getInertiaTensor(intTensor,dummyAngMom);
1516	>
1517	>	detI = intTensor.determinant();
1518	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1519	>	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(detI);
1520	>	return;
1521	>	}
1522	>	/*
1523	>	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1524	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1525	>	sdByGlobalIndex_ = v;
1526	>	}
1527	>
1528	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1529	>	//assert(index < nAtoms_ + nRigidBodies_);
1530	>	return sdByGlobalIndex_.at(index);
1531	>	}
1532	>	*/
1533		}//end namespace oopse
1534

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Comparing trunk/src/brains/SimInfo.cpp (file contents): Revision 720 by chrisfen, Tue Nov 8 13:32:06 2005 UTC vs. Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC

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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 720 by chrisfen, Tue Nov 8 13:32:06 2005 UTC vs.
Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC