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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 523 by chrisfen, Thu May 5 14:47:35 2005 UTC vs.
Revision 1129 by chrisfen, Fri Apr 20 18:15:48 2007 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/notifyCutoffs_interface.h"
62	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
63	>	#include "UseTheForce/DarkSide/electrostatic_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
78	–
79	–	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
101	<	int nGroups = 0; //total cutoff groups defined in meta-data file
101	>	int nGroups = 0; //total cutoff groups defined in meta-data file
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
97	–
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
125		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
126	+
127		nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
128
129		//calculate atoms in rigid bodies
#	Line 112 \| 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 121 \| Line 140 \| namespace oopse {
140
141		}
142
143	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
144	<	//therefore the total number of cutoff groups in the system is equal to
145	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
146	<	//file plus the number of cutoff groups defined in meta-data file
143	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
144	>	//group therefore the total number of cutoff groups in the system is
145	>	//equal to the total number of atoms minus number of atoms belong to
146	>	//cutoff group defined in meta-data file plus the number of cutoff
147	>	//groups defined in meta-data file
148		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
149
150	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
151	<	//therefore the total number of integrable objects in the system is equal to
152	<	//the total number of atoms minus number of atoms belong to rigid body defined in meta-data
153	<	//file plus the number of rigid bodies defined in meta-data file
154	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
155	<
150	>	//every free atom (atom does not belong to rigid bodies) is an
151	>	//integrable object therefore the total number of integrable objects
152	>	//in the system is equal to the total number of atoms minus number of
153	>	//atoms belong to rigid body defined in meta-data file plus the number
154	>	//of rigid bodies defined in meta-data file
155	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
156	>	+ nGlobalRigidBodies_;
157	>
158		nGlobalMols_ = molStampIds_.size();
159
160		#ifdef IS_MPI
#	Line 148 \| Line 170 \| namespace oopse {
170		}
171		molecules_.clear();
172
151	–	delete stamps_;
173		delete sman_;
174		delete simParams_;
175		delete forceField_;
#	Line 255 \| Line 276 \| namespace oopse {
276		}
277		}
278
279	<	}//end for (integrableObject)
280	<	}// end for (mol)
279	>	}
280	>	}
281
282		// n_constraints is local, so subtract them on each processor
283		ndf_local -= nConstraints_;
#	Line 273 \| Line 294 \| namespace oopse {
294
295		}
296
297	+	int SimInfo::getFdf() {
298	+	#ifdef IS_MPI
299	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
300	+	#else
301	+	fdf_ = fdf_local;
302	+	#endif
303	+	return fdf_;
304	+	}
305	+
306		void SimInfo::calcNdfRaw() {
307		int ndfRaw_local;
308
#	Line 335 \| Line 365 \| namespace oopse {
365		int b;
366		int c;
367		int d;
368	+
369	+	std::map<int, std::set<int> > atomGroups;
370	+
371	+	Molecule::RigidBodyIterator rbIter;
372	+	RigidBody* rb;
373	+	Molecule::IntegrableObjectIterator ii;
374	+	StuntDouble* integrableObject;
375
376	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
377	+	integrableObject = mol->nextIntegrableObject(ii)) {
378	+
379	+	if (integrableObject->isRigidBody()) {
380	+	rb = static_cast<RigidBody*>(integrableObject);
381	+	std::vector<Atom*> atoms = rb->getAtoms();
382	+	std::set<int> rigidAtoms;
383	+	for (int i = 0; i < atoms.size(); ++i) {
384	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
385	+	}
386	+	for (int i = 0; i < atoms.size(); ++i) {
387	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
388	+	}
389	+	} else {
390	+	std::set<int> oneAtomSet;
391	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
392	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
393	+	}
394	+	}
395	+
396	+
397	+
398		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
399		a = bond->getAtomA()->getGlobalIndex();
400		b = bond->getAtomB()->getGlobalIndex();
#	Line 346 \| Line 405 \| namespace oopse {
405		a = bend->getAtomA()->getGlobalIndex();
406		b = bend->getAtomB()->getGlobalIndex();
407		c = bend->getAtomC()->getGlobalIndex();
408	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
409	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
410	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
411
412	<	exclude_.addPair(a, b);
413	<	exclude_.addPair(a, c);
414	<	exclude_.addPair(b, c);
412	>	exclude_.addPairs(rigidSetA, rigidSetB);
413	>	exclude_.addPairs(rigidSetA, rigidSetC);
414	>	exclude_.addPairs(rigidSetB, rigidSetC);
415	>
416	>	//exclude_.addPair(a, b);
417	>	//exclude_.addPair(a, c);
418	>	//exclude_.addPair(b, c);
419		}
420
421		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
#	Line 357 \| Line 423 \| namespace oopse {
423		b = torsion->getAtomB()->getGlobalIndex();
424		c = torsion->getAtomC()->getGlobalIndex();
425		d = torsion->getAtomD()->getGlobalIndex();
426	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
427	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
428	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
429	+	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
430
431	+	exclude_.addPairs(rigidSetA, rigidSetB);
432	+	exclude_.addPairs(rigidSetA, rigidSetC);
433	+	exclude_.addPairs(rigidSetA, rigidSetD);
434	+	exclude_.addPairs(rigidSetB, rigidSetC);
435	+	exclude_.addPairs(rigidSetB, rigidSetD);
436	+	exclude_.addPairs(rigidSetC, rigidSetD);
437	+
438	+	/*
439	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
440	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
441	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
442	+	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
443	+	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
444	+	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
445	+
446	+
447		exclude_.addPair(a, b);
448		exclude_.addPair(a, c);
449		exclude_.addPair(a, d);
450		exclude_.addPair(b, c);
451		exclude_.addPair(b, d);
452		exclude_.addPair(c, d);
453	+	*/
454		}
455
369	–	Molecule::RigidBodyIterator rbIter;
370	–	RigidBody* rb;
456		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
457		std::vector<Atom*> atoms = rb->getAtoms();
458		for (int i = 0; i < atoms.size() -1 ; ++i) {
#	Line 392 \| Line 477 \| namespace oopse {
477		int b;
478		int c;
479		int d;
480	+
481	+	std::map<int, std::set<int> > atomGroups;
482	+
483	+	Molecule::RigidBodyIterator rbIter;
484	+	RigidBody* rb;
485	+	Molecule::IntegrableObjectIterator ii;
486	+	StuntDouble* integrableObject;
487
488	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
489	+	integrableObject = mol->nextIntegrableObject(ii)) {
490	+
491	+	if (integrableObject->isRigidBody()) {
492	+	rb = static_cast<RigidBody*>(integrableObject);
493	+	std::vector<Atom*> atoms = rb->getAtoms();
494	+	std::set<int> rigidAtoms;
495	+	for (int i = 0; i < atoms.size(); ++i) {
496	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
497	+	}
498	+	for (int i = 0; i < atoms.size(); ++i) {
499	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
500	+	}
501	+	} else {
502	+	std::set<int> oneAtomSet;
503	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
504	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
505	+	}
506	+	}
507	+
508	+
509		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
510		a = bond->getAtomA()->getGlobalIndex();
511		b = bond->getAtomB()->getGlobalIndex();
#	Line 404 \| Line 517 \| namespace oopse {
517		b = bend->getAtomB()->getGlobalIndex();
518		c = bend->getAtomC()->getGlobalIndex();
519
520	<	exclude_.removePair(a, b);
521	<	exclude_.removePair(a, c);
522	<	exclude_.removePair(b, c);
520	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
521	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
522	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
523	>
524	>	exclude_.removePairs(rigidSetA, rigidSetB);
525	>	exclude_.removePairs(rigidSetA, rigidSetC);
526	>	exclude_.removePairs(rigidSetB, rigidSetC);
527	>
528	>	//exclude_.removePair(a, b);
529	>	//exclude_.removePair(a, c);
530	>	//exclude_.removePair(b, c);
531		}
532
533		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
#	Line 415 \| Line 536 \| namespace oopse {
536		c = torsion->getAtomC()->getGlobalIndex();
537		d = torsion->getAtomD()->getGlobalIndex();
538
539	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
540	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
541	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
542	+	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
543	+
544	+	exclude_.removePairs(rigidSetA, rigidSetB);
545	+	exclude_.removePairs(rigidSetA, rigidSetC);
546	+	exclude_.removePairs(rigidSetA, rigidSetD);
547	+	exclude_.removePairs(rigidSetB, rigidSetC);
548	+	exclude_.removePairs(rigidSetB, rigidSetD);
549	+	exclude_.removePairs(rigidSetC, rigidSetD);
550	+
551	+	/*
552	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
553	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
554	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
555	+	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
556	+	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
557	+	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
558	+
559	+
560		exclude_.removePair(a, b);
561		exclude_.removePair(a, c);
562		exclude_.removePair(a, d);
563		exclude_.removePair(b, c);
564		exclude_.removePair(b, d);
565		exclude_.removePair(c, d);
566	+	*/
567		}
568
426	–	Molecule::RigidBodyIterator rbIter;
427	–	RigidBody* rb;
569		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
570		std::vector<Atom*> atoms = rb->getAtoms();
571		for (int i = 0; i < atoms.size() -1 ; ++i) {
#	Line 462 \| Line 603 \| namespace oopse {
603		//setup fortran force field
604		/** @deprecate */
605		int isError = 0;
606	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
606	>
607	>	setupCutoff();
608	>
609	>	setupElectrostaticSummationMethod( isError );
610	>	setupSwitchingFunction();
611	>	setupAccumulateBoxDipole();
612	>
613		if(isError){
614		sprintf( painCave.errMsg,
615		"ForceField error: There was an error initializing the forceField in fortran.\n" );
616		painCave.isFatal = 1;
617		simError();
618		}
472	–
473	–
474	–	setupCutoff();
619
620		calcNdf();
621		calcNdfRaw();
#	Line 506 \| Line 650 \| namespace oopse {
650		int useLennardJones = 0;
651		int useElectrostatic = 0;
652		int useEAM = 0;
653	+	int useSC = 0;
654		int useCharge = 0;
655		int useDirectional = 0;
656		int useDipole = 0;
#	Line 517 \| Line 662 \| namespace oopse {
662		int useDirectionalAtom = 0;
663		int useElectrostatics = 0;
664		//usePBC and useRF are from simParams
665	<	int usePBC = simParams_->getPBC();
666	<	int useRF = simParams_->getUseRF();
665	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
666	>	int useRF;
667	>	int useSF;
668	>	int useSP;
669	>	int useBoxDipole;
670
671	+	std::string myMethod;
672	+
673	+	// set the useRF logical
674	+	useRF = 0;
675	+	useSF = 0;
676	+	useSP = 0;
677	+
678	+
679	+	if (simParams_->haveElectrostaticSummationMethod()) {
680	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
681	+	toUpper(myMethod);
682	+	if (myMethod == "REACTION_FIELD"){
683	+	useRF = 1;
684	+	} else if (myMethod == "SHIFTED_FORCE"){
685	+	useSF = 1;
686	+	} else if (myMethod == "SHIFTED_POTENTIAL"){
687	+	useSP = 1;
688	+	}
689	+	}
690	+
691	+	if (simParams_->haveAccumulateBoxDipole())
692	+	if (simParams_->getAccumulateBoxDipole())
693	+	useBoxDipole = 1;
694	+
695	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
696	+
697		//loop over all of the atom types
698		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
699		useLennardJones \|= (*i)->isLennardJones();
700		useElectrostatic \|= (*i)->isElectrostatic();
701		useEAM \|= (*i)->isEAM();
702	+	useSC \|= (*i)->isSC();
703		useCharge \|= (*i)->isCharge();
704		useDirectional \|= (*i)->isDirectional();
705		useDipole \|= (*i)->isDipole();
#	Line 575 \| Line 750 \| namespace oopse {
750		temp = useEAM;
751		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
752
753	+	temp = useSC;
754	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
755	+
756		temp = useShape;
757		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
758
#	Line 583 \| Line 761 \| namespace oopse {
761
762		temp = useRF;
763		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
764	<
764	>
765	>	temp = useSF;
766	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767	>
768	>	temp = useSP;
769	>	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770	>
771	>	temp = useBoxDipole;
772	>	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
773	>
774	>	temp = useAtomicVirial_;
775	>	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776	>
777		#endif
778
779		fInfo_.SIM_uses_PBC = usePBC;
#	Line 596 \| Line 786 \| namespace oopse {
786		fInfo_.SIM_uses_StickyPower = useStickyPower;
787		fInfo_.SIM_uses_GayBerne = useGayBerne;
788		fInfo_.SIM_uses_EAM = useEAM;
789	+	fInfo_.SIM_uses_SC = useSC;
790		fInfo_.SIM_uses_Shapes = useShape;
791		fInfo_.SIM_uses_FLARB = useFLARB;
792		fInfo_.SIM_uses_RF = useRF;
793	<
794	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
795	<
796	<	if (simParams_->haveDielectric()) {
606	<	fInfo_.dielect = simParams_->getDielectric();
607	<	} else {
608	<	sprintf(painCave.errMsg,
609	<	"SimSetup Error: No Dielectric constant was set.\n"
610	<	"\tYou are trying to use Reaction Field without"
611	<	"\tsetting a dielectric constant!\n");
612	<	painCave.isFatal = 1;
613	<	simError();
614	<	}
615	<
616	<	} else {
617	<	fInfo_.dielect = 0.0;
618	<	}
619	<
793	>	fInfo_.SIM_uses_SF = useSF;
794	>	fInfo_.SIM_uses_SP = useSP;
795	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
796	>	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
797		}
798
799		void SimInfo::setupFortranSim() {
#	Line 633 \| Line 810 \| namespace oopse {
810		}
811
812		//calculate mass ratio of cutoff group
813	<	std::vector<double> mfact;
813	>	std::vector<RealType> mfact;
814		SimInfo::MoleculeIterator mi;
815		Molecule* mol;
816		Molecule::CutoffGroupIterator ci;
817		CutoffGroup* cg;
818		Molecule::AtomIterator ai;
819		Atom* atom;
820	<	double totalMass;
820	>	RealType totalMass;
821
822		//to avoid memory reallocation, reserve enough space for mfact
823		mfact.reserve(getNCutoffGroups());
#	Line 650 \| Line 827 \| namespace oopse {
827
828		totalMass = cg->getMass();
829		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
830	<	mfact.push_back(atom->getMass()/totalMass);
830	>	// Check for massless groups - set mfact to 1 if true
831	>	if (totalMass != 0)
832	>	mfact.push_back(atom->getMass()/totalMass);
833	>	else
834	>	mfact.push_back( 1.0 );
835		}
836
837		}
#	Line 697 \| Line 878 \| namespace oopse {
878		"succesfully sent the simulation information to fortran.\n");
879		MPIcheckPoint();
880		#endif // is_mpi
881	+
882	+	// Setup number of neighbors in neighbor list if present
883	+	if (simParams_->haveNeighborListNeighbors()) {
884	+	int nlistNeighbors = simParams_->getNeighborListNeighbors();
885	+	setNeighbors(&nlistNeighbors);
886	+	}
887	+
888	+
889		}
890
891
#	Line 759 \| Line 948 \| namespace oopse {
948
949		#endif
950
951	<	double SimInfo::calcMaxCutoffRadius() {
952	<
953	<
765	<	std::set<AtomType*> atomTypes;
766	<	std::set<AtomType*>::iterator i;
767	<	std::vector<double> cutoffRadius;
768	<
769	<	//get the unique atom types
770	<	atomTypes = getUniqueAtomTypes();
951	>	void SimInfo::setupCutoff() {
952	>
953	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
954
955	<	//query the max cutoff radius among these atom types
956	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
957	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
955	>	// Check the cutoff policy
956	>	int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
957	>
958	>	// Set LJ shifting bools to false
959	>	ljsp_ = false;
960	>	ljsf_ = false;
961	>
962	>	std::string myPolicy;
963	>	if (forceFieldOptions_.haveCutoffPolicy()){
964	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
965	>	}else if (simParams_->haveCutoffPolicy()) {
966	>	myPolicy = simParams_->getCutoffPolicy();
967		}
968
969	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
970	<	#ifdef IS_MPI
971	<	//pick the max cutoff radius among the processors
972	<	#endif
969	>	if (!myPolicy.empty()){
970	>	toUpper(myPolicy);
971	>	if (myPolicy == "MIX") {
972	>	cp = MIX_CUTOFF_POLICY;
973	>	} else {
974	>	if (myPolicy == "MAX") {
975	>	cp = MAX_CUTOFF_POLICY;
976	>	} else {
977	>	if (myPolicy == "TRADITIONAL") {
978	>	cp = TRADITIONAL_CUTOFF_POLICY;
979	>	} else {
980	>	// throw error
981	>	sprintf( painCave.errMsg,
982	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
983	>	painCave.isFatal = 1;
984	>	simError();
985	>	}
986	>	}
987	>	}
988	>	}
989	>	notifyFortranCutoffPolicy(&cp);
990
991	<	return maxCutoffRadius;
992	<	}
991	>	// Check the Skin Thickness for neighborlists
992	>	RealType skin;
993	>	if (simParams_->haveSkinThickness()) {
994	>	skin = simParams_->getSkinThickness();
995	>	notifyFortranSkinThickness(&skin);
996	>	}
997	>
998	>	// Check if the cutoff was set explicitly:
999	>	if (simParams_->haveCutoffRadius()) {
1000	>	rcut_ = simParams_->getCutoffRadius();
1001	>	if (simParams_->haveSwitchingRadius()) {
1002	>	rsw_ = simParams_->getSwitchingRadius();
1003	>	} else {
1004	>	if (fInfo_.SIM_uses_Charges \|
1005	>	fInfo_.SIM_uses_Dipoles \|
1006	>	fInfo_.SIM_uses_RF) {
1007	>
1008	>	rsw_ = 0.85 * rcut_;
1009	>	sprintf(painCave.errMsg,
1010	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1011	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1012	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1013	>	painCave.isFatal = 0;
1014	>	simError();
1015	>	} else {
1016	>	rsw_ = rcut_;
1017	>	sprintf(painCave.errMsg,
1018	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1019	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
1020	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1021	>	painCave.isFatal = 0;
1022	>	simError();
1023	>	}
1024	>	}
1025
1026	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
1027	<
1028	<	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
1026	>	if (simParams_->haveElectrostaticSummationMethod()) {
1027	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1028	>	toUpper(myMethod);
1029
1030	<	if (!simParams_->haveRcut()){
1031	<	sprintf(painCave.errMsg,
1030	>	if (myMethod == "SHIFTED_POTENTIAL") {
1031	>	ljsp_ = true;
1032	>	} else if (myMethod == "SHIFTED_FORCE") {
1033	>	ljsf_ = true;
1034	>	}
1035	>	}
1036	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1037	>
1038	>	} else {
1039	>
1040	>	// For electrostatic atoms, we'll assume a large safe value:
1041	>	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
1042	>	sprintf(painCave.errMsg,
1043		"SimCreator Warning: No value was set for the cutoffRadius.\n"
1044		"\tOOPSE will use a default value of 15.0 angstroms"
1045		"\tfor the cutoffRadius.\n");
1046	<	painCave.isFatal = 0;
1046	>	painCave.isFatal = 0;
1047		simError();
1048	<	rcut = 15.0;
1049	<	} else{
1050	<	rcut = simParams_->getRcut();
1051	<	}
1048	>	rcut_ = 15.0;
1049	>
1050	>	if (simParams_->haveElectrostaticSummationMethod()) {
1051	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1052	>	toUpper(myMethod);
1053	>
1054	>	// For the time being, we're tethering the LJ shifted behavior to the
1055	>	// electrostaticSummationMethod keyword options
1056	>	if (myMethod == "SHIFTED_POTENTIAL") {
1057	>	ljsp_ = true;
1058	>	} else if (myMethod == "SHIFTED_FORCE") {
1059	>	ljsf_ = true;
1060	>	}
1061	>	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
1062	>	if (simParams_->haveSwitchingRadius()){
1063	>	sprintf(painCave.errMsg,
1064	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1065	>	"\teven though the electrostaticSummationMethod was\n"
1066	>	"\tset to %s\n", myMethod.c_str());
1067	>	painCave.isFatal = 1;
1068	>	simError();
1069	>	}
1070	>	}
1071	>	}
1072	>
1073	>	if (simParams_->haveSwitchingRadius()){
1074	>	rsw_ = simParams_->getSwitchingRadius();
1075	>	} else {
1076	>	sprintf(painCave.errMsg,
1077	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1078	>	"\tOOPSE will use a default value of\n"
1079	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1080	>	painCave.isFatal = 0;
1081	>	simError();
1082	>	rsw_ = 0.85 * rcut_;
1083	>	}
1084
1085	<	if (!simParams_->haveRsw()){
802	<	sprintf(painCave.errMsg,
803	<	"SimCreator Warning: No value was set for switchingRadius.\n"
804	<	"\tOOPSE will use a default value of\n"
805	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
806	<	painCave.isFatal = 0;
807	<	simError();
808	<	rsw = 0.95 * rcut;
809	<	} else{
810	<	rsw = simParams_->getRsw();
811	<	}
1085	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1086
813	–	} else {
814	–	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
815	–	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
816	–
817	–	if (simParams_->haveRcut()) {
818	–	rcut = simParams_->getRcut();
1087		} else {
1088	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
1089	<	rcut = calcMaxCutoffRadius();
1088	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1089	>	// We'll punt and let fortran figure out the cutoffs later.
1090	>
1091	>	notifyFortranYouAreOnYourOwn();
1092	>
1093		}
1094	+	}
1095	+	}
1096
1097	<	if (simParams_->haveRsw()) {
1098	<	rsw = simParams_->getRsw();
1097	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1098	>
1099	>	int errorOut;
1100	>	int esm = NONE;
1101	>	int sm = UNDAMPED;
1102	>	RealType alphaVal;
1103	>	RealType dielectric;
1104	>
1105	>	errorOut = isError;
1106	>
1107	>	if (simParams_->haveElectrostaticSummationMethod()) {
1108	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1109	>	toUpper(myMethod);
1110	>	if (myMethod == "NONE") {
1111	>	esm = NONE;
1112		} else {
1113	<	rsw = rcut;
1113	>	if (myMethod == "SWITCHING_FUNCTION") {
1114	>	esm = SWITCHING_FUNCTION;
1115	>	} else {
1116	>	if (myMethod == "SHIFTED_POTENTIAL") {
1117	>	esm = SHIFTED_POTENTIAL;
1118	>	} else {
1119	>	if (myMethod == "SHIFTED_FORCE") {
1120	>	esm = SHIFTED_FORCE;
1121	>	} else {
1122	>	if (myMethod == "REACTION_FIELD") {
1123	>	esm = REACTION_FIELD;
1124	>	dielectric = simParams_->getDielectric();
1125	>	if (!simParams_->haveDielectric()) {
1126	>	// throw warning
1127	>	sprintf( painCave.errMsg,
1128	>	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1129	>	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1130	>	painCave.isFatal = 0;
1131	>	simError();
1132	>	}
1133	>	} else {
1134	>	// throw error
1135	>	sprintf( painCave.errMsg,
1136	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1137	>	"\t(Input file specified %s .)\n"
1138	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1139	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1140	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1141	>	painCave.isFatal = 1;
1142	>	simError();
1143	>	}
1144	>	}
1145	>	}
1146	>	}
1147		}
1148	+	}
1149
1150	+	if (simParams_->haveElectrostaticScreeningMethod()) {
1151	+	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1152	+	toUpper(myScreen);
1153	+	if (myScreen == "UNDAMPED") {
1154	+	sm = UNDAMPED;
1155	+	} else {
1156	+	if (myScreen == "DAMPED") {
1157	+	sm = DAMPED;
1158	+	if (!simParams_->haveDampingAlpha()) {
1159	+	// first set a cutoff dependent alpha value
1160	+	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1161	+	alphaVal = 0.5125 - rcut_* 0.025;
1162	+	// for values rcut > 20.5, alpha is zero
1163	+	if (alphaVal < 0) alphaVal = 0;
1164	+
1165	+	// throw warning
1166	+	sprintf( painCave.errMsg,
1167	+	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1168	+	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1169	+	painCave.isFatal = 0;
1170	+	simError();
1171	+	} else {
1172	+	alphaVal = simParams_->getDampingAlpha();
1173	+	}
1174	+
1175	+	} else {
1176	+	// throw error
1177	+	sprintf( painCave.errMsg,
1178	+	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1179	+	"\t(Input file specified %s .)\n"
1180	+	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1181	+	"or \"damped\".\n", myScreen.c_str() );
1182	+	painCave.isFatal = 1;
1183	+	simError();
1184	+	}
1185	+	}
1186		}
1187	+
1188	+	// let's pass some summation method variables to fortran
1189	+	setElectrostaticSummationMethod( &esm );
1190	+	setFortranElectrostaticMethod( &esm );
1191	+	setScreeningMethod( &sm );
1192	+	setDampingAlpha( &alphaVal );
1193	+	setReactionFieldDielectric( &dielectric );
1194	+	initFortranFF( &errorOut );
1195		}
1196
1197	<	void SimInfo::setupCutoff() {
1198	<	getCutoff(rcut_, rsw_);
835	<	double rnblist = rcut_ + 1; // skin of neighbor list
1197	>	void SimInfo::setupSwitchingFunction() {
1198	>	int ft = CUBIC;
1199
1200	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1201	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
1200	>	if (simParams_->haveSwitchingFunctionType()) {
1201	>	std::string funcType = simParams_->getSwitchingFunctionType();
1202	>	toUpper(funcType);
1203	>	if (funcType == "CUBIC") {
1204	>	ft = CUBIC;
1205	>	} else {
1206	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1207	>	ft = FIFTH_ORDER_POLY;
1208	>	} else {
1209	>	// throw error
1210	>	sprintf( painCave.errMsg,
1211	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1212	>	painCave.isFatal = 1;
1213	>	simError();
1214	>	}
1215	>	}
1216	>	}
1217	>
1218	>	// send switching function notification to switcheroo
1219	>	setFunctionType(&ft);
1220	>
1221		}
1222
1223	+	void SimInfo::setupAccumulateBoxDipole() {
1224	+
1225	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1226	+	if ( simParams_->haveAccumulateBoxDipole() )
1227	+	if ( simParams_->getAccumulateBoxDipole() ) {
1228	+	setAccumulateBoxDipole();
1229	+	calcBoxDipole_ = true;
1230	+	}
1231	+
1232	+	}
1233	+
1234		void SimInfo::addProperty(GenericData* genData) {
1235		properties_.addProperty(genData);
1236		}
#	Line 894 \| Line 1287 \| namespace oopse {
1287		Molecule* mol;
1288
1289		Vector3d comVel(0.0);
1290	<	double totalMass = 0.0;
1290	>	RealType totalMass = 0.0;
1291
1292
1293		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1294	<	double mass = mol->getMass();
1294	>	RealType mass = mol->getMass();
1295		totalMass += mass;
1296		comVel += mass * mol->getComVel();
1297		}
1298
1299		#ifdef IS_MPI
1300	<	double tmpMass = totalMass;
1300	>	RealType tmpMass = totalMass;
1301		Vector3d tmpComVel(comVel);
1302	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1303	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1302	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1303	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1304		#endif
1305
1306		comVel /= totalMass;
#	Line 920 \| Line 1313 \| namespace oopse {
1313		Molecule* mol;
1314
1315		Vector3d com(0.0);
1316	<	double totalMass = 0.0;
1316	>	RealType totalMass = 0.0;
1317
1318		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1319	<	double mass = mol->getMass();
1319	>	RealType mass = mol->getMass();
1320		totalMass += mass;
1321		com += mass * mol->getCom();
1322		}
1323
1324		#ifdef IS_MPI
1325	<	double tmpMass = totalMass;
1325	>	RealType tmpMass = totalMass;
1326		Vector3d tmpCom(com);
1327	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1328	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1327	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1328	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1329		#endif
1330
1331		com /= totalMass;
#	Line 945 \| Line 1338 \| namespace oopse {
1338
1339		return o;
1340		}
1341	+
1342	+
1343	+	/*
1344	+	Returns center of mass and center of mass velocity in one function call.
1345	+	*/
1346	+
1347	+	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1348	+	SimInfo::MoleculeIterator i;
1349	+	Molecule* mol;
1350	+
1351	+
1352	+	RealType totalMass = 0.0;
1353	+
1354
1355	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1356	+	RealType mass = mol->getMass();
1357	+	totalMass += mass;
1358	+	com += mass * mol->getCom();
1359	+	comVel += mass * mol->getComVel();
1360	+	}
1361	+
1362	+	#ifdef IS_MPI
1363	+	RealType tmpMass = totalMass;
1364	+	Vector3d tmpCom(com);
1365	+	Vector3d tmpComVel(comVel);
1366	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1367	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1368	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1369	+	#endif
1370	+
1371	+	com /= totalMass;
1372	+	comVel /= totalMass;
1373	+	}
1374	+
1375	+	/*
1376	+	Return intertia tensor for entire system and angular momentum Vector.
1377	+
1378	+
1379	+	[ Ixx -Ixy -Ixz ]
1380	+	J =\| -Iyx Iyy -Iyz \|
1381	+	[ -Izx -Iyz Izz ]
1382	+	*/
1383	+
1384	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1385	+
1386	+
1387	+	RealType xx = 0.0;
1388	+	RealType yy = 0.0;
1389	+	RealType zz = 0.0;
1390	+	RealType xy = 0.0;
1391	+	RealType xz = 0.0;
1392	+	RealType yz = 0.0;
1393	+	Vector3d com(0.0);
1394	+	Vector3d comVel(0.0);
1395	+
1396	+	getComAll(com, comVel);
1397	+
1398	+	SimInfo::MoleculeIterator i;
1399	+	Molecule* mol;
1400	+
1401	+	Vector3d thisq(0.0);
1402	+	Vector3d thisv(0.0);
1403	+
1404	+	RealType thisMass = 0.0;
1405	+
1406	+
1407	+
1408	+
1409	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1410	+
1411	+	thisq = mol->getCom()-com;
1412	+	thisv = mol->getComVel()-comVel;
1413	+	thisMass = mol->getMass();
1414	+	// Compute moment of intertia coefficients.
1415	+	xx += thisq[0]thisq[0]thisMass;
1416	+	yy += thisq[1]thisq[1]thisMass;
1417	+	zz += thisq[2]thisq[2]thisMass;
1418	+
1419	+	// compute products of intertia
1420	+	xy += thisq[0]thisq[1]thisMass;
1421	+	xz += thisq[0]thisq[2]thisMass;
1422	+	yz += thisq[1]thisq[2]thisMass;
1423	+
1424	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1425	+
1426	+	}
1427	+
1428	+
1429	+	inertiaTensor(0,0) = yy + zz;
1430	+	inertiaTensor(0,1) = -xy;
1431	+	inertiaTensor(0,2) = -xz;
1432	+	inertiaTensor(1,0) = -xy;
1433	+	inertiaTensor(1,1) = xx + zz;
1434	+	inertiaTensor(1,2) = -yz;
1435	+	inertiaTensor(2,0) = -xz;
1436	+	inertiaTensor(2,1) = -yz;
1437	+	inertiaTensor(2,2) = xx + yy;
1438	+
1439	+	#ifdef IS_MPI
1440	+	Mat3x3d tmpI(inertiaTensor);
1441	+	Vector3d tmpAngMom;
1442	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1443	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1444	+	#endif
1445	+
1446	+	return;
1447	+	}
1448	+
1449	+	//Returns the angular momentum of the system
1450	+	Vector3d SimInfo::getAngularMomentum(){
1451	+
1452	+	Vector3d com(0.0);
1453	+	Vector3d comVel(0.0);
1454	+	Vector3d angularMomentum(0.0);
1455	+
1456	+	getComAll(com,comVel);
1457	+
1458	+	SimInfo::MoleculeIterator i;
1459	+	Molecule* mol;
1460	+
1461	+	Vector3d thisr(0.0);
1462	+	Vector3d thisp(0.0);
1463	+
1464	+	RealType thisMass;
1465	+
1466	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1467	+	thisMass = mol->getMass();
1468	+	thisr = mol->getCom()-com;
1469	+	thisp = (mol->getComVel()-comVel)*thisMass;
1470	+
1471	+	angularMomentum += cross( thisr, thisp );
1472	+
1473	+	}
1474	+
1475	+	#ifdef IS_MPI
1476	+	Vector3d tmpAngMom;
1477	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1478	+	#endif
1479	+
1480	+	return angularMomentum;
1481	+	}
1482	+
1483	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1484	+	return IOIndexToIntegrableObject.at(index);
1485	+	}
1486	+
1487	+	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1488	+	IOIndexToIntegrableObject= v;
1489	+	}
1490	+
1491	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1492	+	based on the radius of gyration V=4/3PiR_1R_2R_3
1493	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1494	+	V = 4/3Pi(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1495	+	*/
1496	+	void SimInfo::getGyrationalVolume(RealType &volume){
1497	+	Mat3x3d intTensor;
1498	+	RealType det;
1499	+	Vector3d dummyAngMom;
1500	+	RealType sysconstants;
1501	+	RealType geomCnst;
1502	+
1503	+	geomCnst = 3.0/2.0;
1504	+	/* Get the inertial tensor and angular momentum for free*/
1505	+	getInertiaTensor(intTensor,dummyAngMom);
1506	+
1507	+	det = intTensor.determinant();
1508	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1509	+	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(det);
1510	+	return;
1511	+	}
1512	+
1513	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1514	+	Mat3x3d intTensor;
1515	+	Vector3d dummyAngMom;
1516	+	RealType sysconstants;
1517	+	RealType geomCnst;
1518	+
1519	+	geomCnst = 3.0/2.0;
1520	+	/* Get the inertial tensor and angular momentum for free*/
1521	+	getInertiaTensor(intTensor,dummyAngMom);
1522	+
1523	+	detI = intTensor.determinant();
1524	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1525	+	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(detI);
1526	+	return;
1527	+	}
1528	+	/*
1529	+	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1530	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1531	+	sdByGlobalIndex_ = v;
1532	+	}
1533	+
1534	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1535	+	//assert(index < nAtoms_ + nRigidBodies_);
1536	+	return sdByGlobalIndex_.at(index);
1537	+	}
1538	+	*/
1539		}//end namespace oopse
1540

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Comparing trunk/src/brains/SimInfo.cpp (file contents): Revision 523 by chrisfen, Thu May 5 14:47:35 2005 UTC vs. Revision 1129 by chrisfen, Fri Apr 20 18:15:48 2007 UTC

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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 523 by chrisfen, Thu May 5 14:47:35 2005 UTC vs.
Revision 1129 by chrisfen, Fri Apr 20 18:15:48 2007 UTC