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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 598 by chrisfen, Thu Sep 15 00:14:35 2005 UTC vs.
Revision 1095 by chuckv, Tue Dec 5 00:17:24 2006 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/fCoulombicCorrection.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
80	–
81	–	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
97		MoleculeStamp* molStamp;
98		int nMolWithSameStamp;
99		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
100	<	int nGroups = 0; //total cutoff groups defined in meta-data file
100	>	int nGroups = 0; //total cutoff groups defined in meta-data file
101		CutoffGroupStamp* cgStamp;
102		RigidBodyStamp* rbStamp;
103		int nRigidAtoms = 0;
104	<
105	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
106	<	molStamp = i->first;
107	<	nMolWithSameStamp = i->second;
104	>	std::vector<Component*> components = simParams->getComponents();
105	>
106	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
107	>	molStamp = (*i)->getMoleculeStamp();
108	>	nMolWithSameStamp = (*i)->getNMol();
109
110		addMoleculeStamp(molStamp, nMolWithSameStamp);
111
112		//calculate atoms in molecules
113		nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
114
99	–
115		//calculate atoms in cutoff groups
116		int nAtomsInGroups = 0;
117		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
118
119		for (int j=0; j < nCutoffGroupsInStamp; j++) {
120	<	cgStamp = molStamp->getCutoffGroup(j);
120	>	cgStamp = molStamp->getCutoffGroupStamp(j);
121		nAtomsInGroups += cgStamp->getNMembers();
122		}
123
124		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
125	+
126		nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
127
128		//calculate atoms in rigid bodies
#	Line 114 \| Line 130 \| namespace oopse {
130		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
131
132		for (int j=0; j < nRigidBodiesInStamp; j++) {
133	<	rbStamp = molStamp->getRigidBody(j);
133	>	rbStamp = molStamp->getRigidBodyStamp(j);
134		nAtomsInRigidBodies += rbStamp->getNMembers();
135		}
136
#	Line 123 \| Line 139 \| namespace oopse {
139
140		}
141
142	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
143	<	//therefore the total number of cutoff groups in the system is equal to
144	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
145	<	//file plus the number of cutoff groups defined in meta-data file
142	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
143	>	//group therefore the total number of cutoff groups in the system is
144	>	//equal to the total number of atoms minus number of atoms belong to
145	>	//cutoff group defined in meta-data file plus the number of cutoff
146	>	//groups defined in meta-data file
147		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
148
149	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
150	<	//therefore the total number of integrable objects in the system is equal to
151	<	//the total number of atoms minus number of atoms belong to rigid body defined in meta-data
152	<	//file plus the number of rigid bodies defined in meta-data file
153	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
154	<
149	>	//every free atom (atom does not belong to rigid bodies) is an
150	>	//integrable object therefore the total number of integrable objects
151	>	//in the system is equal to the total number of atoms minus number of
152	>	//atoms belong to rigid body defined in meta-data file plus the number
153	>	//of rigid bodies defined in meta-data file
154	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
155	>	+ nGlobalRigidBodies_;
156	>
157		nGlobalMols_ = molStampIds_.size();
158
159		#ifdef IS_MPI
#	Line 150 \| Line 169 \| namespace oopse {
169		}
170		molecules_.clear();
171
153	–	delete stamps_;
172		delete sman_;
173		delete simParams_;
174		delete forceField_;
#	Line 257 \| Line 275 \| namespace oopse {
275		}
276		}
277
278	<	}//end for (integrableObject)
279	<	}// end for (mol)
278	>	}
279	>	}
280
281		// n_constraints is local, so subtract them on each processor
282		ndf_local -= nConstraints_;
#	Line 275 \| Line 293 \| namespace oopse {
293
294		}
295
296	+	int SimInfo::getFdf() {
297	+	#ifdef IS_MPI
298	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
299	+	#else
300	+	fdf_ = fdf_local;
301	+	#endif
302	+	return fdf_;
303	+	}
304	+
305		void SimInfo::calcNdfRaw() {
306		int ndfRaw_local;
307
#	Line 337 \| Line 364 \| namespace oopse {
364		int b;
365		int c;
366		int d;
367	+
368	+	std::map<int, std::set<int> > atomGroups;
369	+
370	+	Molecule::RigidBodyIterator rbIter;
371	+	RigidBody* rb;
372	+	Molecule::IntegrableObjectIterator ii;
373	+	StuntDouble* integrableObject;
374
375	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
376	+	integrableObject = mol->nextIntegrableObject(ii)) {
377	+
378	+	if (integrableObject->isRigidBody()) {
379	+	rb = static_cast<RigidBody*>(integrableObject);
380	+	std::vector<Atom*> atoms = rb->getAtoms();
381	+	std::set<int> rigidAtoms;
382	+	for (int i = 0; i < atoms.size(); ++i) {
383	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
384	+	}
385	+	for (int i = 0; i < atoms.size(); ++i) {
386	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
387	+	}
388	+	} else {
389	+	std::set<int> oneAtomSet;
390	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
391	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
392	+	}
393	+	}
394	+
395	+
396	+
397		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
398		a = bond->getAtomA()->getGlobalIndex();
399		b = bond->getAtomB()->getGlobalIndex();
#	Line 348 \| Line 404 \| namespace oopse {
404		a = bend->getAtomA()->getGlobalIndex();
405		b = bend->getAtomB()->getGlobalIndex();
406		c = bend->getAtomC()->getGlobalIndex();
407	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
408	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
409	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
410
411	<	exclude_.addPair(a, b);
412	<	exclude_.addPair(a, c);
413	<	exclude_.addPair(b, c);
411	>	exclude_.addPairs(rigidSetA, rigidSetB);
412	>	exclude_.addPairs(rigidSetA, rigidSetC);
413	>	exclude_.addPairs(rigidSetB, rigidSetC);
414	>
415	>	//exclude_.addPair(a, b);
416	>	//exclude_.addPair(a, c);
417	>	//exclude_.addPair(b, c);
418		}
419
420		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
#	Line 359 \| Line 422 \| namespace oopse {
422		b = torsion->getAtomB()->getGlobalIndex();
423		c = torsion->getAtomC()->getGlobalIndex();
424		d = torsion->getAtomD()->getGlobalIndex();
425	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
426	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
427	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
428	+	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
429
430	+	exclude_.addPairs(rigidSetA, rigidSetB);
431	+	exclude_.addPairs(rigidSetA, rigidSetC);
432	+	exclude_.addPairs(rigidSetA, rigidSetD);
433	+	exclude_.addPairs(rigidSetB, rigidSetC);
434	+	exclude_.addPairs(rigidSetB, rigidSetD);
435	+	exclude_.addPairs(rigidSetC, rigidSetD);
436	+
437	+	/*
438	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
439	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
440	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
441	+	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
442	+	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
443	+	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
444	+
445	+
446		exclude_.addPair(a, b);
447		exclude_.addPair(a, c);
448		exclude_.addPair(a, d);
449		exclude_.addPair(b, c);
450		exclude_.addPair(b, d);
451		exclude_.addPair(c, d);
452	+	*/
453		}
454
371	–	Molecule::RigidBodyIterator rbIter;
372	–	RigidBody* rb;
455		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
456		std::vector<Atom*> atoms = rb->getAtoms();
457		for (int i = 0; i < atoms.size() -1 ; ++i) {
#	Line 394 \| Line 476 \| namespace oopse {
476		int b;
477		int c;
478		int d;
479	+
480	+	std::map<int, std::set<int> > atomGroups;
481	+
482	+	Molecule::RigidBodyIterator rbIter;
483	+	RigidBody* rb;
484	+	Molecule::IntegrableObjectIterator ii;
485	+	StuntDouble* integrableObject;
486
487	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
488	+	integrableObject = mol->nextIntegrableObject(ii)) {
489	+
490	+	if (integrableObject->isRigidBody()) {
491	+	rb = static_cast<RigidBody*>(integrableObject);
492	+	std::vector<Atom*> atoms = rb->getAtoms();
493	+	std::set<int> rigidAtoms;
494	+	for (int i = 0; i < atoms.size(); ++i) {
495	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
496	+	}
497	+	for (int i = 0; i < atoms.size(); ++i) {
498	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
499	+	}
500	+	} else {
501	+	std::set<int> oneAtomSet;
502	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
503	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
504	+	}
505	+	}
506	+
507	+
508		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
509		a = bond->getAtomA()->getGlobalIndex();
510		b = bond->getAtomB()->getGlobalIndex();
#	Line 406 \| Line 516 \| namespace oopse {
516		b = bend->getAtomB()->getGlobalIndex();
517		c = bend->getAtomC()->getGlobalIndex();
518
519	<	exclude_.removePair(a, b);
520	<	exclude_.removePair(a, c);
521	<	exclude_.removePair(b, c);
519	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
520	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
521	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
522	>
523	>	exclude_.removePairs(rigidSetA, rigidSetB);
524	>	exclude_.removePairs(rigidSetA, rigidSetC);
525	>	exclude_.removePairs(rigidSetB, rigidSetC);
526	>
527	>	//exclude_.removePair(a, b);
528	>	//exclude_.removePair(a, c);
529	>	//exclude_.removePair(b, c);
530		}
531
532		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
#	Line 417 \| Line 535 \| namespace oopse {
535		c = torsion->getAtomC()->getGlobalIndex();
536		d = torsion->getAtomD()->getGlobalIndex();
537
538	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
539	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
540	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
541	+	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
542	+
543	+	exclude_.removePairs(rigidSetA, rigidSetB);
544	+	exclude_.removePairs(rigidSetA, rigidSetC);
545	+	exclude_.removePairs(rigidSetA, rigidSetD);
546	+	exclude_.removePairs(rigidSetB, rigidSetC);
547	+	exclude_.removePairs(rigidSetB, rigidSetD);
548	+	exclude_.removePairs(rigidSetC, rigidSetD);
549	+
550	+	/*
551	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
552	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
553	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
554	+	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
555	+	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
556	+	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
557	+
558	+
559		exclude_.removePair(a, b);
560		exclude_.removePair(a, c);
561		exclude_.removePair(a, d);
562		exclude_.removePair(b, c);
563		exclude_.removePair(b, d);
564		exclude_.removePair(c, d);
565	+	*/
566		}
567
428	–	Molecule::RigidBodyIterator rbIter;
429	–	RigidBody* rb;
568		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
569		std::vector<Atom*> atoms = rb->getAtoms();
570		for (int i = 0; i < atoms.size() -1 ; ++i) {
#	Line 465 \| Line 603 \| namespace oopse {
603		/** @deprecate */
604		int isError = 0;
605
606	<	setupCoulombicCorrection( isError );
606	>	setupCutoff();
607	>
608	>	setupElectrostaticSummationMethod( isError );
609	>	setupSwitchingFunction();
610	>	setupAccumulateBoxDipole();
611
612		if(isError){
613		sprintf( painCave.errMsg,
#	Line 473 \| Line 615 \| namespace oopse {
615		painCave.isFatal = 1;
616		simError();
617		}
476	–
477	–
478	–	setupCutoff();
618
619		calcNdf();
620		calcNdfRaw();
#	Line 510 \| Line 649 \| namespace oopse {
649		int useLennardJones = 0;
650		int useElectrostatic = 0;
651		int useEAM = 0;
652	+	int useSC = 0;
653		int useCharge = 0;
654		int useDirectional = 0;
655		int useDipole = 0;
#	Line 521 \| Line 661 \| namespace oopse {
661		int useDirectionalAtom = 0;
662		int useElectrostatics = 0;
663		//usePBC and useRF are from simParams
664	<	int usePBC = simParams_->getPBC();
665	<	int useRF = simParams_->getUseRF();
664	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
665	>	int useRF;
666	>	int useSF;
667	>	int useSP;
668	>	int useBoxDipole;
669	>	std::string myMethod;
670
671	+	// set the useRF logical
672	+	useRF = 0;
673	+	useSF = 0;
674	+	useSP = 0;
675	+
676	+
677	+	if (simParams_->haveElectrostaticSummationMethod()) {
678	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
679	+	toUpper(myMethod);
680	+	if (myMethod == "REACTION_FIELD"){
681	+	useRF = 1;
682	+	} else if (myMethod == "SHIFTED_FORCE"){
683	+	useSF = 1;
684	+	} else if (myMethod == "SHIFTED_POTENTIAL"){
685	+	useSP = 1;
686	+	}
687	+	}
688	+
689	+	if (simParams_->haveAccumulateBoxDipole())
690	+	if (simParams_->getAccumulateBoxDipole())
691	+	useBoxDipole = 1;
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 579 \| 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 588 \| Line 758 \| namespace oopse {
758		temp = useRF;
759		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
760
761	<	temp = useUW;
762	<	MPI_Allreduce(&temp, &useUW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
761	>	temp = useSF;
762	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
763
764	<	temp = useDW;
765	<	MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766	<
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		#endif
771
772		fInfo_.SIM_uses_PBC = usePBC;
#	Line 606 \| Line 779 \| namespace oopse {
779		fInfo_.SIM_uses_StickyPower = useStickyPower;
780		fInfo_.SIM_uses_GayBerne = useGayBerne;
781		fInfo_.SIM_uses_EAM = useEAM;
782	+	fInfo_.SIM_uses_SC = useSC;
783		fInfo_.SIM_uses_Shapes = useShape;
784		fInfo_.SIM_uses_FLARB = useFLARB;
785		fInfo_.SIM_uses_RF = useRF;
786	<
787	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
788	<
615	<	if (simParams_->haveDielectric()) {
616	<	fInfo_.dielect = simParams_->getDielectric();
617	<	} else {
618	<	sprintf(painCave.errMsg,
619	<	"SimSetup Error: No Dielectric constant was set.\n"
620	<	"\tYou are trying to use Reaction Field without"
621	<	"\tsetting a dielectric constant!\n");
622	<	painCave.isFatal = 1;
623	<	simError();
624	<	}
625	<
626	<	} else {
627	<	fInfo_.dielect = 0.0;
628	<	}
629	<
786	>	fInfo_.SIM_uses_SF = useSF;
787	>	fInfo_.SIM_uses_SP = useSP;
788	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
789		}
790
791		void SimInfo::setupFortranSim() {
#	Line 643 \| Line 802 \| namespace oopse {
802		}
803
804		//calculate mass ratio of cutoff group
805	<	std::vector<double> mfact;
805	>	std::vector<RealType> mfact;
806		SimInfo::MoleculeIterator mi;
807		Molecule* mol;
808		Molecule::CutoffGroupIterator ci;
809		CutoffGroup* cg;
810		Molecule::AtomIterator ai;
811		Atom* atom;
812	<	double totalMass;
812	>	RealType totalMass;
813
814		//to avoid memory reallocation, reserve enough space for mfact
815		mfact.reserve(getNCutoffGroups());
#	Line 660 \| Line 819 \| namespace oopse {
819
820		totalMass = cg->getMass();
821		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
822	<	mfact.push_back(atom->getMass()/totalMass);
822	>	// Check for massless groups - set mfact to 1 if true
823	>	if (totalMass != 0)
824	>	mfact.push_back(atom->getMass()/totalMass);
825	>	else
826	>	mfact.push_back( 1.0 );
827		}
828
829		}
#	Line 707 \| Line 870 \| namespace oopse {
870		"succesfully sent the simulation information to fortran.\n");
871		MPIcheckPoint();
872		#endif // is_mpi
873	+
874	+	// Setup number of neighbors in neighbor list if present
875	+	if (simParams_->haveNeighborListNeighbors()) {
876	+	setNeighbors(simParams_->getNeighborListNeighbors());
877	+	}
878	+
879	+
880		}
881
882
#	Line 769 \| Line 939 \| namespace oopse {
939
940		#endif
941
942	<	double SimInfo::calcMaxCutoffRadius() {
942	>	void SimInfo::setupCutoff() {
943	>
944	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
945
946	+	// Check the cutoff policy
947	+	int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
948
949	<	std::set<AtomType*> atomTypes;
950	<	std::set<AtomType*>::iterator i;
951	<	std::vector<double> cutoffRadius;
952	<
953	<	//get the unique atom types
780	<	atomTypes = getUniqueAtomTypes();
781	<
782	<	//query the max cutoff radius among these atom types
783	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
784	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
949	>	std::string myPolicy;
950	>	if (forceFieldOptions_.haveCutoffPolicy()){
951	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
952	>	}else if (simParams_->haveCutoffPolicy()) {
953	>	myPolicy = simParams_->getCutoffPolicy();
954		}
955
956	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
957	<	#ifdef IS_MPI
789	<	//pick the max cutoff radius among the processors
790	<	#endif
791	<
792	<	return maxCutoffRadius;
793	<	}
794	<
795	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
796	<
797	<	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
798	<
799	<	if (!simParams_->haveRcut()){
800	<	sprintf(painCave.errMsg,
801	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
802	<	"\tOOPSE will use a default value of 15.0 angstroms"
803	<	"\tfor the cutoffRadius.\n");
804	<	painCave.isFatal = 0;
805	<	simError();
806	<	rcut = 15.0;
807	<	} else{
808	<	rcut = simParams_->getRcut();
809	<	}
810	<
811	<	if (!simParams_->haveRsw()){
812	<	sprintf(painCave.errMsg,
813	<	"SimCreator Warning: No value was set for switchingRadius.\n"
814	<	"\tOOPSE will use a default value of\n"
815	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
816	<	painCave.isFatal = 0;
817	<	simError();
818	<	rsw = 0.95 * rcut;
819	<	} else{
820	<	rsw = simParams_->getRsw();
821	<	}
822	<
823	<	} else {
824	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
825	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
826	<
827	<	if (simParams_->haveRcut()) {
828	<	rcut = simParams_->getRcut();
829	<	} else {
830	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
831	<	rcut = calcMaxCutoffRadius();
832	<	}
833	<
834	<	if (simParams_->haveRsw()) {
835	<	rsw = simParams_->getRsw();
836	<	} else {
837	<	rsw = rcut;
838	<	}
839	<
840	<	}
841	<	}
842	<
843	<	void SimInfo::setupCutoff() {
844	<	getCutoff(rcut_, rsw_);
845	<	double rnblist = rcut_ + 1; // skin of neighbor list
846	<
847	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
848	<
849	<	int cp = TRADITIONAL_CUTOFF_POLICY;
850	<	if (simParams_->haveCutoffPolicy()) {
851	<	std::string myPolicy = simParams_->getCutoffPolicy();
956	>	if (!myPolicy.empty()){
957	>	toUpper(myPolicy);
958		if (myPolicy == "MIX") {
959		cp = MIX_CUTOFF_POLICY;
960		} else {
#	Line 866 \| Line 972 \| namespace oopse {
972		}
973		}
974		}
975	+	}
976	+	notifyFortranCutoffPolicy(&cp);
977	+
978	+	// Check the Skin Thickness for neighborlists
979	+	RealType skin;
980	+	if (simParams_->haveSkinThickness()) {
981	+	skin = simParams_->getSkinThickness();
982	+	notifyFortranSkinThickness(&skin);
983	+	}
984	+
985	+	// Check if the cutoff was set explicitly:
986	+	if (simParams_->haveCutoffRadius()) {
987	+	rcut_ = simParams_->getCutoffRadius();
988	+	if (simParams_->haveSwitchingRadius()) {
989	+	rsw_ = simParams_->getSwitchingRadius();
990	+	} else {
991	+	if (fInfo_.SIM_uses_Charges \|
992	+	fInfo_.SIM_uses_Dipoles \|
993	+	fInfo_.SIM_uses_RF) {
994	+
995	+	rsw_ = 0.85 * rcut_;
996	+	sprintf(painCave.errMsg,
997	+	"SimCreator Warning: No value was set for the switchingRadius.\n"
998	+	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
999	+	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1000	+	painCave.isFatal = 0;
1001	+	simError();
1002	+	} else {
1003	+	rsw_ = rcut_;
1004	+	sprintf(painCave.errMsg,
1005	+	"SimCreator Warning: No value was set for the switchingRadius.\n"
1006	+	"\tOOPSE will use the same value as the cutoffRadius.\n"
1007	+	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1008	+	painCave.isFatal = 0;
1009	+	simError();
1010	+	}
1011	+	}
1012	+
1013	+	notifyFortranCutoffs(&rcut_, &rsw_);
1014	+
1015	+	} else {
1016	+
1017	+	// For electrostatic atoms, we'll assume a large safe value:
1018	+	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
1019	+	sprintf(painCave.errMsg,
1020	+	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1021	+	"\tOOPSE will use a default value of 15.0 angstroms"
1022	+	"\tfor the cutoffRadius.\n");
1023	+	painCave.isFatal = 0;
1024	+	simError();
1025	+	rcut_ = 15.0;
1026	+
1027	+	if (simParams_->haveElectrostaticSummationMethod()) {
1028	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1029	+	toUpper(myMethod);
1030	+	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
1031	+	if (simParams_->haveSwitchingRadius()){
1032	+	sprintf(painCave.errMsg,
1033	+	"SimInfo Warning: A value was set for the switchingRadius\n"
1034	+	"\teven though the electrostaticSummationMethod was\n"
1035	+	"\tset to %s\n", myMethod.c_str());
1036	+	painCave.isFatal = 1;
1037	+	simError();
1038	+	}
1039	+	}
1040	+	}
1041	+
1042	+	if (simParams_->haveSwitchingRadius()){
1043	+	rsw_ = simParams_->getSwitchingRadius();
1044	+	} else {
1045	+	sprintf(painCave.errMsg,
1046	+	"SimCreator Warning: No value was set for switchingRadius.\n"
1047	+	"\tOOPSE will use a default value of\n"
1048	+	"\t0.85 * cutoffRadius for the switchingRadius\n");
1049	+	painCave.isFatal = 0;
1050	+	simError();
1051	+	rsw_ = 0.85 * rcut_;
1052	+	}
1053	+	notifyFortranCutoffs(&rcut_, &rsw_);
1054	+	} else {
1055	+	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1056	+	// We'll punt and let fortran figure out the cutoffs later.
1057	+
1058	+	notifyFortranYouAreOnYourOwn();
1059	+
1060	+	}
1061		}
870	–	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1062		}
1063
1064	<	void SimInfo::setupCoulombicCorrection( int isError ) {
1064	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1065
1066		int errorOut;
1067	<	int cc = NONE;
1068	<	double alphaVal;
1069	<
1067	>	int esm = NONE;
1068	>	int sm = UNDAMPED;
1069	>	RealType alphaVal;
1070	>	RealType dielectric;
1071	>
1072		errorOut = isError;
1073
1074	<	if (simParams_->haveCoulombicCorrection()) {
1075	<	std::string myCorrection = simParams_->getCoulombicCorrection();
1076	<	if (myCorrection == "NONE") {
1077	<	cc = NONE;
1074	>	if (simParams_->haveElectrostaticSummationMethod()) {
1075	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1076	>	toUpper(myMethod);
1077	>	if (myMethod == "NONE") {
1078	>	esm = NONE;
1079		} else {
1080	<	if (myCorrection == "UNDAMPED_WOLF") {
1081	<	cc = UNDAMPED_WOLF;
1080	>	if (myMethod == "SWITCHING_FUNCTION") {
1081	>	esm = SWITCHING_FUNCTION;
1082		} else {
1083	<	if (myCorrection == "WOLF") {
1084	<	cc = WOLF;
1085	<	if (!simParams_->haveDampingAlpha()) {
1086	<	//throw error
1087	<	sprintf( painCave.errMsg,
894	<	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Wolf Coulombic Correction.", simParams_->getDampingAlpha());
895	<	painCave.isFatal = 0;
896	<	simError();
897	<	}
898	<	alphaVal = simParams_->getDampingAlpha();
899	<	} else {
900	<	if (myCorrection == "REACTION_FIELD") {
901	<	cc = REACTION_FIELD;
1083	>	if (myMethod == "SHIFTED_POTENTIAL") {
1084	>	esm = SHIFTED_POTENTIAL;
1085	>	} else {
1086	>	if (myMethod == "SHIFTED_FORCE") {
1087	>	esm = SHIFTED_FORCE;
1088		} else {
1089	<	// throw error
1090	<	sprintf( painCave.errMsg,
1091	<	"SimInfo error: Unknown coulombicCorrection. (Input file specified %s .)\n\tcoulombicCorrection must be one of: \"none\", \"undamped_wolf\", \"wolf\", or \"reaction_field\".", myCorrection.c_str() );
1092	<	painCave.isFatal = 1;
1093	<	simError();
1094	<	}
1095	<	}
1089	>	if (myMethod == "REACTION_FIELD") {
1090	>	esm = REACTION_FIELD;
1091	>	dielectric = simParams_->getDielectric();
1092	>	if (!simParams_->haveDielectric()) {
1093	>	// throw warning
1094	>	sprintf( painCave.errMsg,
1095	>	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1096	>	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1097	>	painCave.isFatal = 0;
1098	>	simError();
1099	>	}
1100	>	} else {
1101	>	// throw error
1102	>	sprintf( painCave.errMsg,
1103	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1104	>	"\t(Input file specified %s .)\n"
1105	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1106	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1107	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1108	>	painCave.isFatal = 1;
1109	>	simError();
1110	>	}
1111	>	}
1112	>	}
1113		}
1114		}
1115		}
1116	<	initFortranFF( &fInfo_.SIM_uses_RF, &cc, &alphaVal, &errorOut );
1116	>
1117	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1118	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1119	>	toUpper(myScreen);
1120	>	if (myScreen == "UNDAMPED") {
1121	>	sm = UNDAMPED;
1122	>	} else {
1123	>	if (myScreen == "DAMPED") {
1124	>	sm = DAMPED;
1125	>	if (!simParams_->haveDampingAlpha()) {
1126	>	// first set a cutoff dependent alpha value
1127	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1128	>	alphaVal = 0.5125 - rcut_* 0.025;
1129	>	// for values rcut > 20.5, alpha is zero
1130	>	if (alphaVal < 0) alphaVal = 0;
1131	>
1132	>	// throw warning
1133	>	sprintf( painCave.errMsg,
1134	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1135	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1136	>	painCave.isFatal = 0;
1137	>	simError();
1138	>	} else {
1139	>	alphaVal = simParams_->getDampingAlpha();
1140	>	}
1141	>
1142	>	} else {
1143	>	// throw error
1144	>	sprintf( painCave.errMsg,
1145	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1146	>	"\t(Input file specified %s .)\n"
1147	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1148	>	"or \"damped\".\n", myScreen.c_str() );
1149	>	painCave.isFatal = 1;
1150	>	simError();
1151	>	}
1152	>	}
1153	>	}
1154	>
1155	>	// let's pass some summation method variables to fortran
1156	>	setElectrostaticSummationMethod( &esm );
1157	>	setFortranElectrostaticMethod( &esm );
1158	>	setScreeningMethod( &sm );
1159	>	setDampingAlpha( &alphaVal );
1160	>	setReactionFieldDielectric( &dielectric );
1161	>	initFortranFF( &errorOut );
1162	>	}
1163	>
1164	>	void SimInfo::setupSwitchingFunction() {
1165	>	int ft = CUBIC;
1166	>
1167	>	if (simParams_->haveSwitchingFunctionType()) {
1168	>	std::string funcType = simParams_->getSwitchingFunctionType();
1169	>	toUpper(funcType);
1170	>	if (funcType == "CUBIC") {
1171	>	ft = CUBIC;
1172	>	} else {
1173	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1174	>	ft = FIFTH_ORDER_POLY;
1175	>	} else {
1176	>	// throw error
1177	>	sprintf( painCave.errMsg,
1178	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1179	>	painCave.isFatal = 1;
1180	>	simError();
1181	>	}
1182	>	}
1183	>	}
1184	>
1185	>	// send switching function notification to switcheroo
1186	>	setFunctionType(&ft);
1187	>
1188	>	}
1189	>
1190	>	void SimInfo::setupAccumulateBoxDipole() {
1191	>
1192	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1193	>	if ( simParams_->haveAccumulateBoxDipole() )
1194	>	if ( simParams_->getAccumulateBoxDipole() ) {
1195	>	setAccumulateBoxDipole();
1196	>	calcBoxDipole_ = true;
1197	>	}
1198	>
1199		}
1200
1201		void SimInfo::addProperty(GenericData* genData) {
#	Line 969 \| Line 1254 \| namespace oopse {
1254		Molecule* mol;
1255
1256		Vector3d comVel(0.0);
1257	<	double totalMass = 0.0;
1257	>	RealType totalMass = 0.0;
1258
1259
1260		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1261	<	double mass = mol->getMass();
1261	>	RealType mass = mol->getMass();
1262		totalMass += mass;
1263		comVel += mass * mol->getComVel();
1264		}
1265
1266		#ifdef IS_MPI
1267	<	double tmpMass = totalMass;
1267	>	RealType tmpMass = totalMass;
1268		Vector3d tmpComVel(comVel);
1269	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1270	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1269	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1270	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1271		#endif
1272
1273		comVel /= totalMass;
#	Line 995 \| Line 1280 \| namespace oopse {
1280		Molecule* mol;
1281
1282		Vector3d com(0.0);
1283	<	double totalMass = 0.0;
1283	>	RealType totalMass = 0.0;
1284
1285		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1286	<	double mass = mol->getMass();
1286	>	RealType mass = mol->getMass();
1287		totalMass += mass;
1288		com += mass * mol->getCom();
1289		}
1290
1291		#ifdef IS_MPI
1292	<	double tmpMass = totalMass;
1292	>	RealType tmpMass = totalMass;
1293		Vector3d tmpCom(com);
1294	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1295	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1294	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1295	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1296		#endif
1297
1298		com /= totalMass;
#	Line 1031 \| Line 1316 \| namespace oopse {
1316		Molecule* mol;
1317
1318
1319	<	double totalMass = 0.0;
1319	>	RealType totalMass = 0.0;
1320
1321
1322		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1323	<	double mass = mol->getMass();
1323	>	RealType mass = mol->getMass();
1324		totalMass += mass;
1325		com += mass * mol->getCom();
1326		comVel += mass * mol->getComVel();
1327		}
1328
1329		#ifdef IS_MPI
1330	<	double tmpMass = totalMass;
1330	>	RealType tmpMass = totalMass;
1331		Vector3d tmpCom(com);
1332		Vector3d tmpComVel(comVel);
1333	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1334	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1335	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1333	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1334	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1335	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1336		#endif
1337
1338		com /= totalMass;
#	Line 1066 \| Line 1351 \| namespace oopse {
1351		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1352
1353
1354	<	double xx = 0.0;
1355	<	double yy = 0.0;
1356	<	double zz = 0.0;
1357	<	double xy = 0.0;
1358	<	double xz = 0.0;
1359	<	double yz = 0.0;
1354	>	RealType xx = 0.0;
1355	>	RealType yy = 0.0;
1356	>	RealType zz = 0.0;
1357	>	RealType xy = 0.0;
1358	>	RealType xz = 0.0;
1359	>	RealType yz = 0.0;
1360		Vector3d com(0.0);
1361		Vector3d comVel(0.0);
1362
#	Line 1083 \| Line 1368 \| namespace oopse {
1368		Vector3d thisq(0.0);
1369		Vector3d thisv(0.0);
1370
1371	<	double thisMass = 0.0;
1371	>	RealType thisMass = 0.0;
1372
1373
1374
#	Line 1121 \| Line 1406 \| namespace oopse {
1406		#ifdef IS_MPI
1407		Mat3x3d tmpI(inertiaTensor);
1408		Vector3d tmpAngMom;
1409	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1410	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1409	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1410	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1411		#endif
1412
1413		return;
#	Line 1143 \| Line 1428 \| namespace oopse {
1428		Vector3d thisr(0.0);
1429		Vector3d thisp(0.0);
1430
1431	<	double thisMass;
1431	>	RealType thisMass;
1432
1433		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1434		thisMass = mol->getMass();
#	Line 1156 \| Line 1441 \| namespace oopse {
1441
1442		#ifdef IS_MPI
1443		Vector3d tmpAngMom;
1444	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1444	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1445		#endif
1446
1447		return angularMomentum;
1448		}
1449
1450	<
1450	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1451	>	return IOIndexToIntegrableObject.at(index);
1452	>	}
1453	>
1454	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1455	>	IOIndexToIntegrableObject= v;
1456	>	}
1457	>
1458	>	/*
1459	>	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1460	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1461	>	sdByGlobalIndex_ = v;
1462	>	}
1463	>
1464	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1465	>	//assert(index < nAtoms_ + nRigidBodies_);
1466	>	return sdByGlobalIndex_.at(index);
1467	>	}
1468	>	*/
1469		}//end namespace oopse
1470

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Comparing trunk/src/brains/SimInfo.cpp (file contents): Revision 598 by chrisfen, Thu Sep 15 00:14:35 2005 UTC vs. Revision 1095 by chuckv, Tue Dec 5 00:17:24 2006 UTC

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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 598 by chrisfen, Thu Sep 15 00:14:35 2005 UTC vs.
Revision 1095 by chuckv, Tue Dec 5 00:17:24 2006 UTC