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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 720 by chrisfen, Tue Nov 8 13:32:06 2005 UTC vs.
Revision 1121 by chuckv, Mon Feb 26 04:45:42 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
82	–
83	–	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
#	Line 88 \| Line 101 \| namespace oopse {
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
101	–
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
#	Line 117 \| 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 156 \| Line 169 \| namespace oopse {
169		}
170		molecules_.clear();
171
159	–	delete stamps_;
172		delete sman_;
173		delete simParams_;
174		delete forceField_;
#	Line 263 \| 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 281 \| 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 343 \| 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 354 \| 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 365 \| 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
377	–	Molecule::RigidBodyIterator rbIter;
378	–	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 400 \| 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 412 \| 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 423 \| 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
434	–	Molecule::RigidBodyIterator rbIter;
435	–	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 471 \| Line 603 \| namespace oopse {
603		/** @deprecate */
604		int isError = 0;
605
606	+	setupCutoff();
607	+
608		setupElectrostaticSummationMethod( isError );
609	+	setupSwitchingFunction();
610	+	setupAccumulateBoxDipole();
611
612		if(isError){
613		sprintf( painCave.errMsg,
#	Line 479 \| Line 615 \| namespace oopse {
615		painCave.isFatal = 1;
616		simError();
617		}
482	–
483	–
484	–	setupCutoff();
618
619		calcNdf();
620		calcNdfRaw();
#	Line 516 \| 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 530 \| Line 664 \| namespace oopse {
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 {
683	<	if (myMethod == "SHIFTED_FORCE") {
684	<	useSF = 1;
685	<	}
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 604 \| Line 746 \| namespace oopse {
746		temp = useEAM;
747		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
748
749	+	temp = useSC;
750	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
751	+
752		temp = useShape;
753		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
754
#	Line 614 \| Line 759 \| namespace oopse {
759		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
760
761		temp = useSF;
762	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
762	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
763
764	+	temp = useSP;
765	+	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766	+
767	+	temp = useBoxDipole;
768	+	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769	+
770		#endif
771
772		fInfo_.SIM_uses_PBC = usePBC;
#	Line 628 \| 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		fInfo_.SIM_uses_SF = useSF;
787	<
788	<	if( myMethod == "REACTION_FIELD") {
637	<
638	<	if (simParams_->haveDielectric()) {
639	<	fInfo_.dielect = simParams_->getDielectric();
640	<	} else {
641	<	sprintf(painCave.errMsg,
642	<	"SimSetup Error: No Dielectric constant was set.\n"
643	<	"\tYou are trying to use Reaction Field without"
644	<	"\tsetting a dielectric constant!\n");
645	<	painCave.isFatal = 1;
646	<	simError();
647	<	}
648	<	}
649	<
787	>	fInfo_.SIM_uses_SP = useSP;
788	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
789		}
790
791		void SimInfo::setupFortranSim() {
#	Line 663 \| 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 731 \| 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	+	int nlistNeighbors = simParams_->getNeighborListNeighbors();
877	+	setNeighbors(&nlistNeighbors);
878	+	}
879	+
880	+
881		}
882
883
#	Line 793 \| Line 940 \| namespace oopse {
940
941		#endif
942
943	<	double SimInfo::calcMaxCutoffRadius() {
797	<
798	<
799	<	std::set<AtomType*> atomTypes;
800	<	std::set<AtomType*>::iterator i;
801	<	std::vector<double> cutoffRadius;
802	<
803	<	//get the unique atom types
804	<	atomTypes = getUniqueAtomTypes();
805	<
806	<	//query the max cutoff radius among these atom types
807	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
808	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
809	<	}
810	<
811	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
812	<	#ifdef IS_MPI
813	<	//pick the max cutoff radius among the processors
814	<	#endif
815	<
816	<	return maxCutoffRadius;
817	<	}
818	<
819	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
943	>	void SimInfo::setupCutoff() {
944
945	<	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
822	<
823	<	if (!simParams_->haveCutoffRadius()){
824	<	sprintf(painCave.errMsg,
825	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
826	<	"\tOOPSE will use a default value of 15.0 angstroms"
827	<	"\tfor the cutoffRadius.\n");
828	<	painCave.isFatal = 0;
829	<	simError();
830	<	rcut = 15.0;
831	<	} else{
832	<	rcut = simParams_->getCutoffRadius();
833	<	}
945	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
946
947	<	if (!simParams_->haveSwitchingRadius()){
948	<	sprintf(painCave.errMsg,
837	<	"SimCreator Warning: No value was set for switchingRadius.\n"
838	<	"\tOOPSE will use a default value of\n"
839	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
840	<	painCave.isFatal = 0;
841	<	simError();
842	<	rsw = 0.85 * rcut;
843	<	} else{
844	<	rsw = simParams_->getSwitchingRadius();
845	<	}
947	>	// Check the cutoff policy
948	>	int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
949
950	<	} else {
951	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
952	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
953	<
954	<	if (simParams_->haveCutoffRadius()) {
852	<	rcut = simParams_->getCutoffRadius();
853	<	} else {
854	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
855	<	rcut = calcMaxCutoffRadius();
856	<	}
857	<
858	<	if (simParams_->haveSwitchingRadius()) {
859	<	rsw = simParams_->getSwitchingRadius();
860	<	} else {
861	<	rsw = rcut;
862	<	}
863	<
950	>	std::string myPolicy;
951	>	if (forceFieldOptions_.haveCutoffPolicy()){
952	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
953	>	}else if (simParams_->haveCutoffPolicy()) {
954	>	myPolicy = simParams_->getCutoffPolicy();
955		}
865	–	}
956
957	<	void SimInfo::setupCutoff() {
868	<	getCutoff(rcut_, rsw_);
869	<	double rnblist = rcut_ + 1; // skin of neighbor list
870	<
871	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
872	<
873	<	int cp = TRADITIONAL_CUTOFF_POLICY;
874	<	if (simParams_->haveCutoffPolicy()) {
875	<	std::string myPolicy = simParams_->getCutoffPolicy();
957	>	if (!myPolicy.empty()){
958		toUpper(myPolicy);
959		if (myPolicy == "MIX") {
960		cp = MIX_CUTOFF_POLICY;
#	Line 891 \| Line 973 \| namespace oopse {
973		}
974		}
975		}
976	<	}
976	>	}
977	>	notifyFortranCutoffPolicy(&cp);
978
979	<
979	>	// Check the Skin Thickness for neighborlists
980	>	RealType skin;
981		if (simParams_->haveSkinThickness()) {
982	<	double skinThickness = simParams_->getSkinThickness();
983	<	}
982	>	skin = simParams_->getSkinThickness();
983	>	notifyFortranSkinThickness(&skin);
984	>	}
985	>
986	>	// Check if the cutoff was set explicitly:
987	>	if (simParams_->haveCutoffRadius()) {
988	>	rcut_ = simParams_->getCutoffRadius();
989	>	if (simParams_->haveSwitchingRadius()) {
990	>	rsw_ = simParams_->getSwitchingRadius();
991	>	} else {
992	>	if (fInfo_.SIM_uses_Charges \|
993	>	fInfo_.SIM_uses_Dipoles \|
994	>	fInfo_.SIM_uses_RF) {
995	>
996	>	rsw_ = 0.85 * rcut_;
997	>	sprintf(painCave.errMsg,
998	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
999	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1000	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1001	>	painCave.isFatal = 0;
1002	>	simError();
1003	>	} else {
1004	>	rsw_ = rcut_;
1005	>	sprintf(painCave.errMsg,
1006	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1007	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
1008	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1009	>	painCave.isFatal = 0;
1010	>	simError();
1011	>	}
1012	>	}
1013	>
1014	>	notifyFortranCutoffs(&rcut_, &rsw_);
1015	>
1016	>	} else {
1017	>
1018	>	// For electrostatic atoms, we'll assume a large safe value:
1019	>	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
1020	>	sprintf(painCave.errMsg,
1021	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1022	>	"\tOOPSE will use a default value of 15.0 angstroms"
1023	>	"\tfor the cutoffRadius.\n");
1024	>	painCave.isFatal = 0;
1025	>	simError();
1026	>	rcut_ = 15.0;
1027	>
1028	>	if (simParams_->haveElectrostaticSummationMethod()) {
1029	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1030	>	toUpper(myMethod);
1031	>	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
1032	>	if (simParams_->haveSwitchingRadius()){
1033	>	sprintf(painCave.errMsg,
1034	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1035	>	"\teven though the electrostaticSummationMethod was\n"
1036	>	"\tset to %s\n", myMethod.c_str());
1037	>	painCave.isFatal = 1;
1038	>	simError();
1039	>	}
1040	>	}
1041	>	}
1042	>
1043	>	if (simParams_->haveSwitchingRadius()){
1044	>	rsw_ = simParams_->getSwitchingRadius();
1045	>	} else {
1046	>	sprintf(painCave.errMsg,
1047	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1048	>	"\tOOPSE will use a default value of\n"
1049	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1050	>	painCave.isFatal = 0;
1051	>	simError();
1052	>	rsw_ = 0.85 * rcut_;
1053	>	}
1054	>	notifyFortranCutoffs(&rcut_, &rsw_);
1055	>	} else {
1056	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1057	>	// We'll punt and let fortran figure out the cutoffs later.
1058	>
1059	>	notifyFortranYouAreOnYourOwn();
1060
1061	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1062	<	// also send cutoff notification to electrostatics
903	<	setElectrostaticCutoffRadius(&rcut_, &rsw_);
1061	>	}
1062	>	}
1063		}
1064
1065		void SimInfo::setupElectrostaticSummationMethod( int isError ) {
#	Line 908 \| Line 1067 \| namespace oopse {
1067		int errorOut;
1068		int esm = NONE;
1069		int sm = UNDAMPED;
1070	<	double alphaVal;
1071	<	double dielectric;
1072	<
1070	>	RealType alphaVal;
1071	>	RealType dielectric;
1072	>
1073		errorOut = isError;
915	–	alphaVal = simParams_->getDampingAlpha();
916	–	dielectric = simParams_->getDielectric();
1074
1075		if (simParams_->haveElectrostaticSummationMethod()) {
1076		std::string myMethod = simParams_->getElectrostaticSummationMethod();
#	Line 930 \| Line 1087 \| namespace oopse {
1087		if (myMethod == "SHIFTED_FORCE") {
1088		esm = SHIFTED_FORCE;
1089		} else {
1090	<	if (myMethod == "REACTION_FIELD") {
1090	>	if (myMethod == "REACTION_FIELD") {
1091		esm = REACTION_FIELD;
1092	+	dielectric = simParams_->getDielectric();
1093	+	if (!simParams_->haveDielectric()) {
1094	+	// throw warning
1095	+	sprintf( painCave.errMsg,
1096	+	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1097	+	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1098	+	painCave.isFatal = 0;
1099	+	simError();
1100	+	}
1101		} else {
1102		// throw error
1103		sprintf( painCave.errMsg,
1104	<	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() );
1104	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1105	>	"\t(Input file specified %s .)\n"
1106	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1107	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1108	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1109		painCave.isFatal = 1;
1110		simError();
1111		}
#	Line 954 \| Line 1124 \| namespace oopse {
1124		if (myScreen == "DAMPED") {
1125		sm = DAMPED;
1126		if (!simParams_->haveDampingAlpha()) {
1127	<	//throw error
1127	>	// first set a cutoff dependent alpha value
1128	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1129	>	alphaVal = 0.5125 - rcut_* 0.025;
1130	>	// for values rcut > 20.5, alpha is zero
1131	>	if (alphaVal < 0) alphaVal = 0;
1132	>
1133	>	// throw warning
1134		sprintf( painCave.errMsg,
1135	<	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
1135	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1136	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1137		painCave.isFatal = 0;
1138		simError();
1139	+	} else {
1140	+	alphaVal = simParams_->getDampingAlpha();
1141		}
1142	+
1143		} else {
1144		// throw error
1145		sprintf( painCave.errMsg,
1146	<	"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
1146	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1147	>	"\t(Input file specified %s .)\n"
1148	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1149	>	"or \"damped\".\n", myScreen.c_str() );
1150		painCave.isFatal = 1;
1151		simError();
1152		}
#	Line 972 \| Line 1155 \| namespace oopse {
1155
1156		// let's pass some summation method variables to fortran
1157		setElectrostaticSummationMethod( &esm );
1158	+	setFortranElectrostaticMethod( &esm );
1159		setScreeningMethod( &sm );
1160		setDampingAlpha( &alphaVal );
1161		setReactionFieldDielectric( &dielectric );
1162	<	initFortranFF( &esm, &errorOut );
1162	>	initFortranFF( &errorOut );
1163		}
1164
1165	+	void SimInfo::setupSwitchingFunction() {
1166	+	int ft = CUBIC;
1167	+
1168	+	if (simParams_->haveSwitchingFunctionType()) {
1169	+	std::string funcType = simParams_->getSwitchingFunctionType();
1170	+	toUpper(funcType);
1171	+	if (funcType == "CUBIC") {
1172	+	ft = CUBIC;
1173	+	} else {
1174	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1175	+	ft = FIFTH_ORDER_POLY;
1176	+	} else {
1177	+	// throw error
1178	+	sprintf( painCave.errMsg,
1179	+	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1180	+	painCave.isFatal = 1;
1181	+	simError();
1182	+	}
1183	+	}
1184	+	}
1185	+
1186	+	// send switching function notification to switcheroo
1187	+	setFunctionType(&ft);
1188	+
1189	+	}
1190	+
1191	+	void SimInfo::setupAccumulateBoxDipole() {
1192	+
1193	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1194	+	if ( simParams_->haveAccumulateBoxDipole() )
1195	+	if ( simParams_->getAccumulateBoxDipole() ) {
1196	+	setAccumulateBoxDipole();
1197	+	calcBoxDipole_ = true;
1198	+	}
1199	+
1200	+	}
1201	+
1202		void SimInfo::addProperty(GenericData* genData) {
1203		properties_.addProperty(genData);
1204		}
#	Line 1034 \| Line 1255 \| namespace oopse {
1255		Molecule* mol;
1256
1257		Vector3d comVel(0.0);
1258	<	double totalMass = 0.0;
1258	>	RealType totalMass = 0.0;
1259
1260
1261		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1262	<	double mass = mol->getMass();
1262	>	RealType mass = mol->getMass();
1263		totalMass += mass;
1264		comVel += mass * mol->getComVel();
1265		}
1266
1267		#ifdef IS_MPI
1268	<	double tmpMass = totalMass;
1268	>	RealType tmpMass = totalMass;
1269		Vector3d tmpComVel(comVel);
1270	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1271	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1270	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1271	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1272		#endif
1273
1274		comVel /= totalMass;
#	Line 1060 \| Line 1281 \| namespace oopse {
1281		Molecule* mol;
1282
1283		Vector3d com(0.0);
1284	<	double totalMass = 0.0;
1284	>	RealType totalMass = 0.0;
1285
1286		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1287	<	double mass = mol->getMass();
1287	>	RealType mass = mol->getMass();
1288		totalMass += mass;
1289		com += mass * mol->getCom();
1290		}
1291
1292		#ifdef IS_MPI
1293	<	double tmpMass = totalMass;
1293	>	RealType tmpMass = totalMass;
1294		Vector3d tmpCom(com);
1295	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1296	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1295	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1296	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1297		#endif
1298
1299		com /= totalMass;
#	Line 1096 \| Line 1317 \| namespace oopse {
1317		Molecule* mol;
1318
1319
1320	<	double totalMass = 0.0;
1320	>	RealType totalMass = 0.0;
1321
1322
1323		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1324	<	double mass = mol->getMass();
1324	>	RealType mass = mol->getMass();
1325		totalMass += mass;
1326		com += mass * mol->getCom();
1327		comVel += mass * mol->getComVel();
1328		}
1329
1330		#ifdef IS_MPI
1331	<	double tmpMass = totalMass;
1331	>	RealType tmpMass = totalMass;
1332		Vector3d tmpCom(com);
1333		Vector3d tmpComVel(comVel);
1334	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1335	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1336	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1334	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1335	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1336	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1337		#endif
1338
1339		com /= totalMass;
#	Line 1131 \| Line 1352 \| namespace oopse {
1352		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1353
1354
1355	<	double xx = 0.0;
1356	<	double yy = 0.0;
1357	<	double zz = 0.0;
1358	<	double xy = 0.0;
1359	<	double xz = 0.0;
1360	<	double yz = 0.0;
1355	>	RealType xx = 0.0;
1356	>	RealType yy = 0.0;
1357	>	RealType zz = 0.0;
1358	>	RealType xy = 0.0;
1359	>	RealType xz = 0.0;
1360	>	RealType yz = 0.0;
1361		Vector3d com(0.0);
1362		Vector3d comVel(0.0);
1363
#	Line 1148 \| Line 1369 \| namespace oopse {
1369		Vector3d thisq(0.0);
1370		Vector3d thisv(0.0);
1371
1372	<	double thisMass = 0.0;
1372	>	RealType thisMass = 0.0;
1373
1374
1375
#	Line 1186 \| Line 1407 \| namespace oopse {
1407		#ifdef IS_MPI
1408		Mat3x3d tmpI(inertiaTensor);
1409		Vector3d tmpAngMom;
1410	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1411	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1410	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1411	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1412		#endif
1413
1414		return;
#	Line 1208 \| Line 1429 \| namespace oopse {
1429		Vector3d thisr(0.0);
1430		Vector3d thisp(0.0);
1431
1432	<	double thisMass;
1432	>	RealType thisMass;
1433
1434		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1435		thisMass = mol->getMass();
#	Line 1221 \| Line 1442 \| namespace oopse {
1442
1443		#ifdef IS_MPI
1444		Vector3d tmpAngMom;
1445	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1445	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1446		#endif
1447
1448		return angularMomentum;
1449		}
1450
1451	<
1451	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1452	>	return IOIndexToIntegrableObject.at(index);
1453	>	}
1454	>
1455	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1456	>	IOIndexToIntegrableObject= v;
1457	>	}
1458	>
1459	>	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1460	>	based on the radius of gyration V=4/3PiR_1R_2R_3
1461	>	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1462	>	V = 4/3Pi(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1463	>	*/
1464	>	void SimInfo::getGyrationalVolume(RealType &volume){
1465	>	Mat3x3d intTensor;
1466	>	RealType det;
1467	>	Vector3d dummyAngMom;
1468	>	RealType sysconstants;
1469	>	RealType geomCnst;
1470	>
1471	>	geomCnst = 3.0/2.0;
1472	>	/* Get the inertial tensor and angular momentum for free*/
1473	>	getInertiaTensor(intTensor,dummyAngMom);
1474	>
1475	>	det = intTensor.determinant();
1476	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1477	>	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(det);
1478	>	return;
1479	>	}
1480	>
1481	>	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1482	>	Mat3x3d intTensor;
1483	>	Vector3d dummyAngMom;
1484	>	RealType sysconstants;
1485	>	RealType geomCnst;
1486	>
1487	>	geomCnst = 3.0/2.0;
1488	>	/* Get the inertial tensor and angular momentum for free*/
1489	>	getInertiaTensor(intTensor,dummyAngMom);
1490	>
1491	>	detI = intTensor.determinant();
1492	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1493	>	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(detI);
1494	>	return;
1495	>	}
1496	>	/*
1497	>	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1498	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1499	>	sdByGlobalIndex_ = v;
1500	>	}
1501	>
1502	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1503	>	//assert(index < nAtoms_ + nRigidBodies_);
1504	>	return sdByGlobalIndex_.at(index);
1505	>	}
1506	>	*/
1507		}//end namespace oopse
1508

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Comparing trunk/src/brains/SimInfo.cpp (file contents): Revision 720 by chrisfen, Tue Nov 8 13:32:06 2005 UTC vs. Revision 1121 by chuckv, Mon Feb 26 04:45:42 2007 UTC

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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 720 by chrisfen, Tue Nov 8 13:32:06 2005 UTC vs.
Revision 1121 by chuckv, Mon Feb 26 04:45:42 2007 UTC