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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 610 by chrisfen, Sun Sep 18 20:45:38 2005 UTC vs.
Revision 1126 by gezelter, Fri Apr 6 21:53:43 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/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
81	–
82	–	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
100	–
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 115 \| 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 124 \| 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 151 \| Line 170 \| namespace oopse {
170		}
171		molecules_.clear();
172
154	–	delete stamps_;
173		delete sman_;
174		delete simParams_;
175		delete forceField_;
#	Line 258 \| 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 276 \| 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 338 \| 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 349 \| 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 360 \| 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
372	–	Molecule::RigidBodyIterator rbIter;
373	–	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 395 \| 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 407 \| 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 418 \| 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
429	–	Molecule::RigidBodyIterator rbIter;
430	–	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 466 \| Line 604 \| namespace oopse {
604		/** @deprecate */
605		int isError = 0;
606
607	+	setupCutoff();
608	+
609		setupElectrostaticSummationMethod( isError );
610	+	setupSwitchingFunction();
611	+	setupAccumulateBoxDipole();
612
613		if(isError){
614		sprintf( painCave.errMsg,
#	Line 474 \| Line 616 \| namespace oopse {
616		painCave.isFatal = 1;
617		simError();
618		}
477	–
478	–
479	–	setupCutoff();
619
620		calcNdf();
621		calcNdfRaw();
#	Line 511 \| 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 522 \| Line 662 \| namespace oopse {
662		int useDirectionalAtom = 0;
663		int useElectrostatics = 0;
664		//usePBC and useRF are from simParams
665	<	int usePBC = simParams_->getPBC();
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 579 \| 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
759		temp = useFLARB;
760		MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
761
762	+	temp = useRF;
763	+	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
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 597 \| 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	<
793	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
794	<
795	<	if (simParams_->haveDielectric()) {
796	<	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	<
792	>	fInfo_.SIM_uses_RF = useRF;
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() {
763	<
764	<
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();
771	<
772	<	//query the max cutoff radius among these atom types
773	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
774	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
775	<	}
776	<
777	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
778	<	#ifdef IS_MPI
779	<	//pick the max cutoff radius among the processors
780	<	#endif
781	<
782	<	return maxCutoffRadius;
783	<	}
784	<
785	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
951	>	void SimInfo::setupCutoff() {
952
953	<	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
788	<
789	<	if (!simParams_->haveRcut()){
790	<	sprintf(painCave.errMsg,
791	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
792	<	"\tOOPSE will use a default value of 15.0 angstroms"
793	<	"\tfor the cutoffRadius.\n");
794	<	painCave.isFatal = 0;
795	<	simError();
796	<	rcut = 15.0;
797	<	} else{
798	<	rcut = simParams_->getRcut();
799	<	}
953	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
954
955	<	if (!simParams_->haveRsw()){
956	<	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	<	}
955	>	// Check the cutoff policy
956	>	int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
957
958	<	} else {
959	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
960	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
961	<
962	<	if (simParams_->haveRcut()) {
818	<	rcut = simParams_->getRcut();
819	<	} else {
820	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
821	<	rcut = calcMaxCutoffRadius();
822	<	}
823	<
824	<	if (simParams_->haveRsw()) {
825	<	rsw = simParams_->getRsw();
826	<	} else {
827	<	rsw = rcut;
828	<	}
829	<
958	>	std::string myPolicy;
959	>	if (forceFieldOptions_.haveCutoffPolicy()){
960	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
961	>	}else if (simParams_->haveCutoffPolicy()) {
962	>	myPolicy = simParams_->getCutoffPolicy();
963		}
831	–	}
964
965	<	void SimInfo::setupCutoff() {
966	<	getCutoff(rcut_, rsw_);
835	<	double rnblist = rcut_ + 1; // skin of neighbor list
836	<
837	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
838	<
839	<	int cp = TRADITIONAL_CUTOFF_POLICY;
840	<	if (simParams_->haveCutoffPolicy()) {
841	<	std::string myPolicy = simParams_->getCutoffPolicy();
965	>	if (!myPolicy.empty()){
966	>	toUpper(myPolicy);
967		if (myPolicy == "MIX") {
968		cp = MIX_CUTOFF_POLICY;
969		} else {
#	Line 856 \| Line 981 \| namespace oopse {
981		}
982		}
983		}
984	+	}
985	+	notifyFortranCutoffPolicy(&cp);
986	+
987	+	// Check the Skin Thickness for neighborlists
988	+	RealType skin;
989	+	if (simParams_->haveSkinThickness()) {
990	+	skin = simParams_->getSkinThickness();
991	+	notifyFortranSkinThickness(&skin);
992	+	}
993	+
994	+	// Check if the cutoff was set explicitly:
995	+	if (simParams_->haveCutoffRadius()) {
996	+	rcut_ = simParams_->getCutoffRadius();
997	+	if (simParams_->haveSwitchingRadius()) {
998	+	rsw_ = simParams_->getSwitchingRadius();
999	+	} else {
1000	+	if (fInfo_.SIM_uses_Charges \|
1001	+	fInfo_.SIM_uses_Dipoles \|
1002	+	fInfo_.SIM_uses_RF) {
1003	+
1004	+	rsw_ = 0.85 * rcut_;
1005	+	sprintf(painCave.errMsg,
1006	+	"SimCreator Warning: No value was set for the switchingRadius.\n"
1007	+	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1008	+	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1009	+	painCave.isFatal = 0;
1010	+	simError();
1011	+	} else {
1012	+	rsw_ = rcut_;
1013	+	sprintf(painCave.errMsg,
1014	+	"SimCreator Warning: No value was set for the switchingRadius.\n"
1015	+	"\tOOPSE will use the same value as the cutoffRadius.\n"
1016	+	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1017	+	painCave.isFatal = 0;
1018	+	simError();
1019	+	}
1020	+	}
1021	+
1022	+	notifyFortranCutoffs(&rcut_, &rsw_);
1023	+
1024	+	} else {
1025	+
1026	+	// For electrostatic atoms, we'll assume a large safe value:
1027	+	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
1028	+	sprintf(painCave.errMsg,
1029	+	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1030	+	"\tOOPSE will use a default value of 15.0 angstroms"
1031	+	"\tfor the cutoffRadius.\n");
1032	+	painCave.isFatal = 0;
1033	+	simError();
1034	+	rcut_ = 15.0;
1035	+
1036	+	if (simParams_->haveElectrostaticSummationMethod()) {
1037	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1038	+	toUpper(myMethod);
1039	+	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
1040	+	if (simParams_->haveSwitchingRadius()){
1041	+	sprintf(painCave.errMsg,
1042	+	"SimInfo Warning: A value was set for the switchingRadius\n"
1043	+	"\teven though the electrostaticSummationMethod was\n"
1044	+	"\tset to %s\n", myMethod.c_str());
1045	+	painCave.isFatal = 1;
1046	+	simError();
1047	+	}
1048	+	}
1049	+	}
1050	+
1051	+	if (simParams_->haveSwitchingRadius()){
1052	+	rsw_ = simParams_->getSwitchingRadius();
1053	+	} else {
1054	+	sprintf(painCave.errMsg,
1055	+	"SimCreator Warning: No value was set for switchingRadius.\n"
1056	+	"\tOOPSE will use a default value of\n"
1057	+	"\t0.85 * cutoffRadius for the switchingRadius\n");
1058	+	painCave.isFatal = 0;
1059	+	simError();
1060	+	rsw_ = 0.85 * rcut_;
1061	+	}
1062	+	notifyFortranCutoffs(&rcut_, &rsw_);
1063	+	} else {
1064	+	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1065	+	// We'll punt and let fortran figure out the cutoffs later.
1066	+
1067	+	notifyFortranYouAreOnYourOwn();
1068	+
1069	+	}
1070		}
860	–	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
861	–	// also send cutoff notification to electrostatics
862	–	setElectrostaticCutoffRadius(&rcut_);
1071		}
1072
1073		void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1074
1075		int errorOut;
1076		int esm = NONE;
1077	<	double alphaVal;
1078	<	double dielectric;
1079	<
1077	>	int sm = UNDAMPED;
1078	>	RealType alphaVal;
1079	>	RealType dielectric;
1080	>
1081		errorOut = isError;
873	–	alphaVal = simParams_->getDampingAlpha();
874	–	dielectric = simParams_->getDielectric();
1082
1083		if (simParams_->haveElectrostaticSummationMethod()) {
1084		std::string myMethod = simParams_->getElectrostaticSummationMethod();
1085	+	toUpper(myMethod);
1086		if (myMethod == "NONE") {
1087		esm = NONE;
1088		} else {
1089	<	if (myMethod == "UNDAMPED_WOLF") {
1090	<	esm = UNDAMPED_WOLF;
1089	>	if (myMethod == "SWITCHING_FUNCTION") {
1090	>	esm = SWITCHING_FUNCTION;
1091		} else {
1092	<	if (myMethod == "DAMPED_WOLF") {
1093	<	esm = DAMPED_WOLF;
1094	<	if (!simParams_->haveDampingAlpha()) {
1095	<	//throw error
1096	<	sprintf( painCave.errMsg,
889	<	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", alphaVal);
890	<	painCave.isFatal = 0;
891	<	simError();
892	<	}
893	<	} else {
894	<	if (myMethod == "REACTION_FIELD") {
895	<	esm = REACTION_FIELD;
1092	>	if (myMethod == "SHIFTED_POTENTIAL") {
1093	>	esm = SHIFTED_POTENTIAL;
1094	>	} else {
1095	>	if (myMethod == "SHIFTED_FORCE") {
1096	>	esm = SHIFTED_FORCE;
1097		} else {
1098	<	// throw error
1099	<	sprintf( painCave.errMsg,
1100	<	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"undamped_wolf\", \"damped_wolf\", or \"reaction_field\".", myMethod.c_str() );
1101	<	painCave.isFatal = 1;
1102	<	simError();
1103	<	}
1104	<	}
1098	>	if (myMethod == "REACTION_FIELD") {
1099	>	esm = REACTION_FIELD;
1100	>	dielectric = simParams_->getDielectric();
1101	>	if (!simParams_->haveDielectric()) {
1102	>	// throw warning
1103	>	sprintf( painCave.errMsg,
1104	>	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1105	>	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1106	>	painCave.isFatal = 0;
1107	>	simError();
1108	>	}
1109	>	} else {
1110	>	// throw error
1111	>	sprintf( painCave.errMsg,
1112	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1113	>	"\t(Input file specified %s .)\n"
1114	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1115	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1116	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1117	>	painCave.isFatal = 1;
1118	>	simError();
1119	>	}
1120	>	}
1121	>	}
1122		}
1123		}
1124		}
1125	+
1126	+	if (simParams_->haveElectrostaticScreeningMethod()) {
1127	+	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1128	+	toUpper(myScreen);
1129	+	if (myScreen == "UNDAMPED") {
1130	+	sm = UNDAMPED;
1131	+	} else {
1132	+	if (myScreen == "DAMPED") {
1133	+	sm = DAMPED;
1134	+	if (!simParams_->haveDampingAlpha()) {
1135	+	// first set a cutoff dependent alpha value
1136	+	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1137	+	alphaVal = 0.5125 - rcut_* 0.025;
1138	+	// for values rcut > 20.5, alpha is zero
1139	+	if (alphaVal < 0) alphaVal = 0;
1140	+
1141	+	// throw warning
1142	+	sprintf( painCave.errMsg,
1143	+	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1144	+	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1145	+	painCave.isFatal = 0;
1146	+	simError();
1147	+	} else {
1148	+	alphaVal = simParams_->getDampingAlpha();
1149	+	}
1150	+
1151	+	} else {
1152	+	// throw error
1153	+	sprintf( painCave.errMsg,
1154	+	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1155	+	"\t(Input file specified %s .)\n"
1156	+	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1157	+	"or \"damped\".\n", myScreen.c_str() );
1158	+	painCave.isFatal = 1;
1159	+	simError();
1160	+	}
1161	+	}
1162	+	}
1163	+
1164		// let's pass some summation method variables to fortran
1165		setElectrostaticSummationMethod( &esm );
1166	<	setDampedWolfAlpha( &alphaVal );
1166	>	setFortranElectrostaticMethod( &esm );
1167	>	setScreeningMethod( &sm );
1168	>	setDampingAlpha( &alphaVal );
1169		setReactionFieldDielectric( &dielectric );
1170	<	initFortranFF( &esm, &errorOut );
1170	>	initFortranFF( &errorOut );
1171		}
1172
1173	+	void SimInfo::setupSwitchingFunction() {
1174	+	int ft = CUBIC;
1175	+
1176	+	if (simParams_->haveSwitchingFunctionType()) {
1177	+	std::string funcType = simParams_->getSwitchingFunctionType();
1178	+	toUpper(funcType);
1179	+	if (funcType == "CUBIC") {
1180	+	ft = CUBIC;
1181	+	} else {
1182	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1183	+	ft = FIFTH_ORDER_POLY;
1184	+	} else {
1185	+	// throw error
1186	+	sprintf( painCave.errMsg,
1187	+	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1188	+	painCave.isFatal = 1;
1189	+	simError();
1190	+	}
1191	+	}
1192	+	}
1193	+
1194	+	// send switching function notification to switcheroo
1195	+	setFunctionType(&ft);
1196	+
1197	+	}
1198	+
1199	+	void SimInfo::setupAccumulateBoxDipole() {
1200	+
1201	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1202	+	if ( simParams_->haveAccumulateBoxDipole() )
1203	+	if ( simParams_->getAccumulateBoxDipole() ) {
1204	+	setAccumulateBoxDipole();
1205	+	calcBoxDipole_ = true;
1206	+	}
1207	+
1208	+	}
1209	+
1210		void SimInfo::addProperty(GenericData* genData) {
1211		properties_.addProperty(genData);
1212		}
#	Line 967 \| Line 1263 \| namespace oopse {
1263		Molecule* mol;
1264
1265		Vector3d comVel(0.0);
1266	<	double totalMass = 0.0;
1266	>	RealType totalMass = 0.0;
1267
1268
1269		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1270	<	double mass = mol->getMass();
1270	>	RealType mass = mol->getMass();
1271		totalMass += mass;
1272		comVel += mass * mol->getComVel();
1273		}
1274
1275		#ifdef IS_MPI
1276	<	double tmpMass = totalMass;
1276	>	RealType tmpMass = totalMass;
1277		Vector3d tmpComVel(comVel);
1278	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1279	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1278	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1279	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1280		#endif
1281
1282		comVel /= totalMass;
#	Line 993 \| Line 1289 \| namespace oopse {
1289		Molecule* mol;
1290
1291		Vector3d com(0.0);
1292	<	double totalMass = 0.0;
1292	>	RealType totalMass = 0.0;
1293
1294		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1295	<	double mass = mol->getMass();
1295	>	RealType mass = mol->getMass();
1296		totalMass += mass;
1297		com += mass * mol->getCom();
1298		}
1299
1300		#ifdef IS_MPI
1301	<	double tmpMass = totalMass;
1301	>	RealType tmpMass = totalMass;
1302		Vector3d tmpCom(com);
1303	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1304	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1303	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1304	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1305		#endif
1306
1307		com /= totalMass;
#	Line 1029 \| Line 1325 \| namespace oopse {
1325		Molecule* mol;
1326
1327
1328	<	double totalMass = 0.0;
1328	>	RealType totalMass = 0.0;
1329
1330
1331		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1332	<	double mass = mol->getMass();
1332	>	RealType mass = mol->getMass();
1333		totalMass += mass;
1334		com += mass * mol->getCom();
1335		comVel += mass * mol->getComVel();
1336		}
1337
1338		#ifdef IS_MPI
1339	<	double tmpMass = totalMass;
1339	>	RealType tmpMass = totalMass;
1340		Vector3d tmpCom(com);
1341		Vector3d tmpComVel(comVel);
1342	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1343	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1344	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1342	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1343	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1344	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1345		#endif
1346
1347		com /= totalMass;
#	Line 1064 \| Line 1360 \| namespace oopse {
1360		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1361
1362
1363	<	double xx = 0.0;
1364	<	double yy = 0.0;
1365	<	double zz = 0.0;
1366	<	double xy = 0.0;
1367	<	double xz = 0.0;
1368	<	double yz = 0.0;
1363	>	RealType xx = 0.0;
1364	>	RealType yy = 0.0;
1365	>	RealType zz = 0.0;
1366	>	RealType xy = 0.0;
1367	>	RealType xz = 0.0;
1368	>	RealType yz = 0.0;
1369		Vector3d com(0.0);
1370		Vector3d comVel(0.0);
1371
#	Line 1081 \| Line 1377 \| namespace oopse {
1377		Vector3d thisq(0.0);
1378		Vector3d thisv(0.0);
1379
1380	<	double thisMass = 0.0;
1380	>	RealType thisMass = 0.0;
1381
1382
1383
#	Line 1119 \| Line 1415 \| namespace oopse {
1415		#ifdef IS_MPI
1416		Mat3x3d tmpI(inertiaTensor);
1417		Vector3d tmpAngMom;
1418	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1419	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1418	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1419	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1420		#endif
1421
1422		return;
#	Line 1141 \| Line 1437 \| namespace oopse {
1437		Vector3d thisr(0.0);
1438		Vector3d thisp(0.0);
1439
1440	<	double thisMass;
1440	>	RealType thisMass;
1441
1442		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1443		thisMass = mol->getMass();
#	Line 1154 \| Line 1450 \| namespace oopse {
1450
1451		#ifdef IS_MPI
1452		Vector3d tmpAngMom;
1453	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1453	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1454		#endif
1455
1456		return angularMomentum;
1457		}
1458
1459	<
1459	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1460	>	return IOIndexToIntegrableObject.at(index);
1461	>	}
1462	>
1463	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1464	>	IOIndexToIntegrableObject= v;
1465	>	}
1466	>
1467	>	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1468	>	based on the radius of gyration V=4/3PiR_1R_2R_3
1469	>	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1470	>	V = 4/3Pi(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1471	>	*/
1472	>	void SimInfo::getGyrationalVolume(RealType &volume){
1473	>	Mat3x3d intTensor;
1474	>	RealType det;
1475	>	Vector3d dummyAngMom;
1476	>	RealType sysconstants;
1477	>	RealType geomCnst;
1478	>
1479	>	geomCnst = 3.0/2.0;
1480	>	/* Get the inertial tensor and angular momentum for free*/
1481	>	getInertiaTensor(intTensor,dummyAngMom);
1482	>
1483	>	det = intTensor.determinant();
1484	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1485	>	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(det);
1486	>	return;
1487	>	}
1488	>
1489	>	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1490	>	Mat3x3d intTensor;
1491	>	Vector3d dummyAngMom;
1492	>	RealType sysconstants;
1493	>	RealType geomCnst;
1494	>
1495	>	geomCnst = 3.0/2.0;
1496	>	/* Get the inertial tensor and angular momentum for free*/
1497	>	getInertiaTensor(intTensor,dummyAngMom);
1498	>
1499	>	detI = intTensor.determinant();
1500	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1501	>	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(detI);
1502	>	return;
1503	>	}
1504	>	/*
1505	>	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1506	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1507	>	sdByGlobalIndex_ = v;
1508	>	}
1509	>
1510	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1511	>	//assert(index < nAtoms_ + nRigidBodies_);
1512	>	return sdByGlobalIndex_.at(index);
1513	>	}
1514	>	*/
1515		}//end namespace oopse
1516

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Comparing trunk/src/brains/SimInfo.cpp (file contents): Revision 610 by chrisfen, Sun Sep 18 20:45:38 2005 UTC vs. Revision 1126 by gezelter, Fri Apr 6 21:53:43 2007 UTC

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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 610 by chrisfen, Sun Sep 18 20:45:38 2005 UTC vs.
Revision 1126 by gezelter, Fri Apr 6 21:53:43 2007 UTC