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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 963 by tim, Wed May 17 21:51:42 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 "UseTheForce/fCutoffPolicy.h"
57	+	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
58	+	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
59	+	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
60		#include "UseTheForce/doForces_interface.h"
61	<	#include "UseTheForce/notifyCutoffs_interface.h"
61	>	#include "UseTheForce/DarkSide/electrostatic_interface.h"
62	>	#include "UseTheForce/DarkSide/switcheroo_interface.h"
63		#include "utils/MemoryUtils.hpp"
64		#include "utils/simError.h"
65		#include "selection/SelectionManager.hpp"
66	+	#include "io/ForceFieldOptions.hpp"
67	+	#include "UseTheForce/ForceField.hpp"
68
69		#ifdef IS_MPI
70		#include "UseTheForce/mpiComponentPlan.h"
#	Line 64 \| Line 72 \| namespace oopse {
72		#endif
73
74		namespace oopse {
75	+	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
76	+	std::map<int, std::set<int> >::iterator i = container.find(index);
77	+	std::set<int> result;
78	+	if (i != container.end()) {
79	+	result = i->second;
80	+	}
81
82	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
83	<	ForceField* ff, Globals* simParams) :
84	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
85	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
82	>	return result;
83	>	}
84	>
85	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
86	>	forceField_(ff), simParams_(simParams),
87	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
88		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
89		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
90		nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
91		nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
92		sman_(NULL), fortranInitialized_(false) {
93
78	–
79	–	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
94		MoleculeStamp* molStamp;
95		int nMolWithSameStamp;
96		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
97	<	int nGroups = 0; //total cutoff groups defined in meta-data file
97	>	int nGroups = 0; //total cutoff groups defined in meta-data file
98		CutoffGroupStamp* cgStamp;
99		RigidBodyStamp* rbStamp;
100		int nRigidAtoms = 0;
101	<
102	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
103	<	molStamp = i->first;
104	<	nMolWithSameStamp = i->second;
101	>	std::vector<Component*> components = simParams->getComponents();
102	>
103	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
104	>	molStamp = (*i)->getMoleculeStamp();
105	>	nMolWithSameStamp = (*i)->getNMol();
106
107		addMoleculeStamp(molStamp, nMolWithSameStamp);
108
109		//calculate atoms in molecules
110		nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
111
97	–
112		//calculate atoms in cutoff groups
113		int nAtomsInGroups = 0;
114		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
115
116		for (int j=0; j < nCutoffGroupsInStamp; j++) {
117	<	cgStamp = molStamp->getCutoffGroup(j);
117	>	cgStamp = molStamp->getCutoffGroupStamp(j);
118		nAtomsInGroups += cgStamp->getNMembers();
119		}
120
121		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
122	+
123		nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
124
125		//calculate atoms in rigid bodies
#	Line 112 \| Line 127 \| namespace oopse {
127		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
128
129		for (int j=0; j < nRigidBodiesInStamp; j++) {
130	<	rbStamp = molStamp->getRigidBody(j);
130	>	rbStamp = molStamp->getRigidBodyStamp(j);
131		nAtomsInRigidBodies += rbStamp->getNMembers();
132		}
133
#	Line 121 \| Line 136 \| namespace oopse {
136
137		}
138
139	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
140	<	//therefore the total number of cutoff groups in the system is equal to
141	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
142	<	//file plus the number of cutoff groups defined in meta-data file
139	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
140	>	//group therefore the total number of cutoff groups in the system is
141	>	//equal to the total number of atoms minus number of atoms belong to
142	>	//cutoff group defined in meta-data file plus the number of cutoff
143	>	//groups defined in meta-data file
144		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
145
146	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
147	<	//therefore the total number of integrable objects in the system is equal to
148	<	//the total number of atoms minus number of atoms belong to rigid body defined in meta-data
149	<	//file plus the number of rigid bodies defined in meta-data file
150	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
151	<
146	>	//every free atom (atom does not belong to rigid bodies) is an
147	>	//integrable object therefore the total number of integrable objects
148	>	//in the system is equal to the total number of atoms minus number of
149	>	//atoms belong to rigid body defined in meta-data file plus the number
150	>	//of rigid bodies defined in meta-data file
151	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
152	>	+ nGlobalRigidBodies_;
153	>
154		nGlobalMols_ = molStampIds_.size();
155
156		#ifdef IS_MPI
#	Line 148 \| Line 166 \| namespace oopse {
166		}
167		molecules_.clear();
168
151	–	delete stamps_;
169		delete sman_;
170		delete simParams_;
171		delete forceField_;
#	Line 255 \| Line 272 \| namespace oopse {
272		}
273		}
274
275	<	}//end for (integrableObject)
276	<	}// end for (mol)
275	>	}
276	>	}
277
278		// n_constraints is local, so subtract them on each processor
279		ndf_local -= nConstraints_;
#	Line 273 \| Line 290 \| namespace oopse {
290
291		}
292
293	+	int SimInfo::getFdf() {
294	+	#ifdef IS_MPI
295	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
296	+	#else
297	+	fdf_ = fdf_local;
298	+	#endif
299	+	return fdf_;
300	+	}
301	+
302		void SimInfo::calcNdfRaw() {
303		int ndfRaw_local;
304
#	Line 335 \| Line 361 \| namespace oopse {
361		int b;
362		int c;
363		int d;
364	+
365	+	std::map<int, std::set<int> > atomGroups;
366	+
367	+	Molecule::RigidBodyIterator rbIter;
368	+	RigidBody* rb;
369	+	Molecule::IntegrableObjectIterator ii;
370	+	StuntDouble* integrableObject;
371
372	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
373	+	integrableObject = mol->nextIntegrableObject(ii)) {
374	+
375	+	if (integrableObject->isRigidBody()) {
376	+	rb = static_cast<RigidBody*>(integrableObject);
377	+	std::vector<Atom*> atoms = rb->getAtoms();
378	+	std::set<int> rigidAtoms;
379	+	for (int i = 0; i < atoms.size(); ++i) {
380	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
381	+	}
382	+	for (int i = 0; i < atoms.size(); ++i) {
383	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
384	+	}
385	+	} else {
386	+	std::set<int> oneAtomSet;
387	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
388	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
389	+	}
390	+	}
391	+
392	+
393	+
394		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
395		a = bond->getAtomA()->getGlobalIndex();
396		b = bond->getAtomB()->getGlobalIndex();
#	Line 346 \| Line 401 \| namespace oopse {
401		a = bend->getAtomA()->getGlobalIndex();
402		b = bend->getAtomB()->getGlobalIndex();
403		c = bend->getAtomC()->getGlobalIndex();
404	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
405	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
406	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
407
408	<	exclude_.addPair(a, b);
409	<	exclude_.addPair(a, c);
410	<	exclude_.addPair(b, c);
408	>	exclude_.addPairs(rigidSetA, rigidSetB);
409	>	exclude_.addPairs(rigidSetA, rigidSetC);
410	>	exclude_.addPairs(rigidSetB, rigidSetC);
411	>
412	>	//exclude_.addPair(a, b);
413	>	//exclude_.addPair(a, c);
414	>	//exclude_.addPair(b, c);
415		}
416
417		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
#	Line 357 \| Line 419 \| namespace oopse {
419		b = torsion->getAtomB()->getGlobalIndex();
420		c = torsion->getAtomC()->getGlobalIndex();
421		d = torsion->getAtomD()->getGlobalIndex();
422	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
423	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
424	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
425	+	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
426
427	+	exclude_.addPairs(rigidSetA, rigidSetB);
428	+	exclude_.addPairs(rigidSetA, rigidSetC);
429	+	exclude_.addPairs(rigidSetA, rigidSetD);
430	+	exclude_.addPairs(rigidSetB, rigidSetC);
431	+	exclude_.addPairs(rigidSetB, rigidSetD);
432	+	exclude_.addPairs(rigidSetC, rigidSetD);
433	+
434	+	/*
435	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
436	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
437	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
438	+	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
439	+	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
440	+	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
441	+
442	+
443		exclude_.addPair(a, b);
444		exclude_.addPair(a, c);
445		exclude_.addPair(a, d);
446		exclude_.addPair(b, c);
447		exclude_.addPair(b, d);
448		exclude_.addPair(c, d);
449	+	*/
450		}
451
369	–	Molecule::RigidBodyIterator rbIter;
370	–	RigidBody* rb;
452		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
453		std::vector<Atom*> atoms = rb->getAtoms();
454		for (int i = 0; i < atoms.size() -1 ; ++i) {
#	Line 392 \| Line 473 \| namespace oopse {
473		int b;
474		int c;
475		int d;
476	+
477	+	std::map<int, std::set<int> > atomGroups;
478	+
479	+	Molecule::RigidBodyIterator rbIter;
480	+	RigidBody* rb;
481	+	Molecule::IntegrableObjectIterator ii;
482	+	StuntDouble* integrableObject;
483
484	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
485	+	integrableObject = mol->nextIntegrableObject(ii)) {
486	+
487	+	if (integrableObject->isRigidBody()) {
488	+	rb = static_cast<RigidBody*>(integrableObject);
489	+	std::vector<Atom*> atoms = rb->getAtoms();
490	+	std::set<int> rigidAtoms;
491	+	for (int i = 0; i < atoms.size(); ++i) {
492	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
493	+	}
494	+	for (int i = 0; i < atoms.size(); ++i) {
495	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
496	+	}
497	+	} else {
498	+	std::set<int> oneAtomSet;
499	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
500	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
501	+	}
502	+	}
503	+
504	+
505		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
506		a = bond->getAtomA()->getGlobalIndex();
507		b = bond->getAtomB()->getGlobalIndex();
#	Line 404 \| Line 513 \| namespace oopse {
513		b = bend->getAtomB()->getGlobalIndex();
514		c = bend->getAtomC()->getGlobalIndex();
515
516	<	exclude_.removePair(a, b);
517	<	exclude_.removePair(a, c);
518	<	exclude_.removePair(b, c);
516	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
517	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
518	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
519	>
520	>	exclude_.removePairs(rigidSetA, rigidSetB);
521	>	exclude_.removePairs(rigidSetA, rigidSetC);
522	>	exclude_.removePairs(rigidSetB, rigidSetC);
523	>
524	>	//exclude_.removePair(a, b);
525	>	//exclude_.removePair(a, c);
526	>	//exclude_.removePair(b, c);
527		}
528
529		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
#	Line 415 \| Line 532 \| namespace oopse {
532		c = torsion->getAtomC()->getGlobalIndex();
533		d = torsion->getAtomD()->getGlobalIndex();
534
535	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
536	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
537	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
538	+	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
539	+
540	+	exclude_.removePairs(rigidSetA, rigidSetB);
541	+	exclude_.removePairs(rigidSetA, rigidSetC);
542	+	exclude_.removePairs(rigidSetA, rigidSetD);
543	+	exclude_.removePairs(rigidSetB, rigidSetC);
544	+	exclude_.removePairs(rigidSetB, rigidSetD);
545	+	exclude_.removePairs(rigidSetC, rigidSetD);
546	+
547	+	/*
548	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
549	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
550	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
551	+	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
552	+	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
553	+	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
554	+
555	+
556		exclude_.removePair(a, b);
557		exclude_.removePair(a, c);
558		exclude_.removePair(a, d);
559		exclude_.removePair(b, c);
560		exclude_.removePair(b, d);
561		exclude_.removePair(c, d);
562	+	*/
563		}
564
426	–	Molecule::RigidBodyIterator rbIter;
427	–	RigidBody* rb;
565		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
566		std::vector<Atom*> atoms = rb->getAtoms();
567		for (int i = 0; i < atoms.size() -1 ; ++i) {
#	Line 462 \| Line 599 \| namespace oopse {
599		//setup fortran force field
600		/** @deprecate */
601		int isError = 0;
602	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
602	>
603	>	setupElectrostaticSummationMethod( isError );
604	>	setupSwitchingFunction();
605	>
606		if(isError){
607		sprintf( painCave.errMsg,
608		"ForceField error: There was an error initializing the forceField in fortran.\n" );
#	Line 506 \| Line 646 \| namespace oopse {
646		int useLennardJones = 0;
647		int useElectrostatic = 0;
648		int useEAM = 0;
649	+	int useSC = 0;
650		int useCharge = 0;
651		int useDirectional = 0;
652		int useDipole = 0;
653		int useGayBerne = 0;
654		int useSticky = 0;
655	+	int useStickyPower = 0;
656		int useShape = 0;
657		int useFLARB = 0; //it is not in AtomType yet
658		int useDirectionalAtom = 0;
659		int useElectrostatics = 0;
660		//usePBC and useRF are from simParams
661	<	int usePBC = simParams_->getPBC();
662	<	int useRF = simParams_->getUseRF();
661	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
662	>	int useRF;
663	>	int useSF;
664	>	std::string myMethod;
665
666	+	// set the useRF logical
667	+	useRF = 0;
668	+	useSF = 0;
669	+
670	+
671	+	if (simParams_->haveElectrostaticSummationMethod()) {
672	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
673	+	toUpper(myMethod);
674	+	if (myMethod == "REACTION_FIELD") {
675	+	useRF=1;
676	+	} else {
677	+	if (myMethod == "SHIFTED_FORCE") {
678	+	useSF = 1;
679	+	}
680	+	}
681	+	}
682	+
683		//loop over all of the atom types
684		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
685		useLennardJones \|= (*i)->isLennardJones();
686		useElectrostatic \|= (*i)->isElectrostatic();
687		useEAM \|= (*i)->isEAM();
688	+	useSC \|= (*i)->isSC();
689		useCharge \|= (*i)->isCharge();
690		useDirectional \|= (*i)->isDirectional();
691		useDipole \|= (*i)->isDipole();
692		useGayBerne \|= (*i)->isGayBerne();
693		useSticky \|= (*i)->isSticky();
694	+	useStickyPower \|= (*i)->isStickyPower();
695		useShape \|= (*i)->isShape();
696		}
697
698	<	if (useSticky \|\| useDipole \|\| useGayBerne \|\| useShape) {
698	>	if (useSticky \|\| useStickyPower \|\| useDipole \|\| useGayBerne \|\| useShape) {
699		useDirectionalAtom = 1;
700		}
701
#	Line 564 \| Line 727 \| namespace oopse {
727		temp = useSticky;
728		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
729
730	+	temp = useStickyPower;
731	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
732	+
733		temp = useGayBerne;
734		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
735
736		temp = useEAM;
737		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
738
739	+	temp = useSC;
740	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
741	+
742		temp = useShape;
743		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
744
#	Line 578 \| Line 747 \| namespace oopse {
747
748		temp = useRF;
749		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
750	<
750	>
751	>	temp = useSF;
752	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
753	>
754		#endif
755
756		fInfo_.SIM_uses_PBC = usePBC;
#	Line 588 \| Line 760 \| namespace oopse {
760		fInfo_.SIM_uses_Charges = useCharge;
761		fInfo_.SIM_uses_Dipoles = useDipole;
762		fInfo_.SIM_uses_Sticky = useSticky;
763	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
764		fInfo_.SIM_uses_GayBerne = useGayBerne;
765		fInfo_.SIM_uses_EAM = useEAM;
766	+	fInfo_.SIM_uses_SC = useSC;
767		fInfo_.SIM_uses_Shapes = useShape;
768		fInfo_.SIM_uses_FLARB = useFLARB;
769		fInfo_.SIM_uses_RF = useRF;
770	+	fInfo_.SIM_uses_SF = useSF;
771
772	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
773	<
772	>	if( myMethod == "REACTION_FIELD") {
773	>
774		if (simParams_->haveDielectric()) {
775		fInfo_.dielect = simParams_->getDielectric();
776		} else {
#	Line 605 \| Line 780 \| namespace oopse {
780		"\tsetting a dielectric constant!\n");
781		painCave.isFatal = 1;
782		simError();
783	<	}
609	<
610	<	} else {
611	<	fInfo_.dielect = 0.0;
783	>	}
784		}
785
786		}
#	Line 627 \| Line 799 \| namespace oopse {
799		}
800
801		//calculate mass ratio of cutoff group
802	<	std::vector<double> mfact;
802	>	std::vector<RealType> mfact;
803		SimInfo::MoleculeIterator mi;
804		Molecule* mol;
805		Molecule::CutoffGroupIterator ci;
806		CutoffGroup* cg;
807		Molecule::AtomIterator ai;
808		Atom* atom;
809	<	double totalMass;
809	>	RealType totalMass;
810
811		//to avoid memory reallocation, reserve enough space for mfact
812		mfact.reserve(getNCutoffGroups());
#	Line 644 \| Line 816 \| namespace oopse {
816
817		totalMass = cg->getMass();
818		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
819	<	mfact.push_back(atom->getMass()/totalMass);
819	>	// Check for massless groups - set mfact to 1 if true
820	>	if (totalMass != 0)
821	>	mfact.push_back(atom->getMass()/totalMass);
822	>	else
823	>	mfact.push_back( 1.0 );
824		}
825
826		}
#	Line 753 \| Line 929 \| namespace oopse {
929
930		#endif
931
932	<	double SimInfo::calcMaxCutoffRadius() {
932	>	void SimInfo::setupCutoff() {
933	>
934	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
935
936	+	// Check the cutoff policy
937	+	int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
938
939	<	std::set<AtomType*> atomTypes;
940	<	std::set<AtomType*>::iterator i;
941	<	std::vector<double> cutoffRadius;
942	<
943	<	//get the unique atom types
764	<	atomTypes = getUniqueAtomTypes();
765	<
766	<	//query the max cutoff radius among these atom types
767	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
768	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
939	>	std::string myPolicy;
940	>	if (forceFieldOptions_.haveCutoffPolicy()){
941	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
942	>	}else if (simParams_->haveCutoffPolicy()) {
943	>	myPolicy = simParams_->getCutoffPolicy();
944		}
945
946	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
947	<	#ifdef IS_MPI
948	<	//pick the max cutoff radius among the processors
949	<	#endif
946	>	if (!myPolicy.empty()){
947	>	toUpper(myPolicy);
948	>	if (myPolicy == "MIX") {
949	>	cp = MIX_CUTOFF_POLICY;
950	>	} else {
951	>	if (myPolicy == "MAX") {
952	>	cp = MAX_CUTOFF_POLICY;
953	>	} else {
954	>	if (myPolicy == "TRADITIONAL") {
955	>	cp = TRADITIONAL_CUTOFF_POLICY;
956	>	} else {
957	>	// throw error
958	>	sprintf( painCave.errMsg,
959	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
960	>	painCave.isFatal = 1;
961	>	simError();
962	>	}
963	>	}
964	>	}
965	>	}
966	>	notifyFortranCutoffPolicy(&cp);
967
968	<	return maxCutoffRadius;
969	<	}
970	<
971	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
972	<
973	<	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
968	>	// Check the Skin Thickness for neighborlists
969	>	RealType skin;
970	>	if (simParams_->haveSkinThickness()) {
971	>	skin = simParams_->getSkinThickness();
972	>	notifyFortranSkinThickness(&skin);
973	>	}
974
975	<	if (!simParams_->haveRcut()){
976	<	sprintf(painCave.errMsg,
977	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
978	<	"\tOOPSE will use a default value of 15.0 angstroms"
979	<	"\tfor the cutoffRadius.\n");
980	<	painCave.isFatal = 0;
975	>	// Check if the cutoff was set explicitly:
976	>	if (simParams_->haveCutoffRadius()) {
977	>	rcut_ = simParams_->getCutoffRadius();
978	>	if (simParams_->haveSwitchingRadius()) {
979	>	rsw_ = simParams_->getSwitchingRadius();
980	>	} else {
981	>	if (fInfo_.SIM_uses_Charges \|
982	>	fInfo_.SIM_uses_Dipoles \|
983	>	fInfo_.SIM_uses_RF) {
984	>
985	>	rsw_ = 0.85 * rcut_;
986	>	sprintf(painCave.errMsg,
987	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
988	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
989	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
990	>	painCave.isFatal = 0;
991		simError();
992	<	rcut = 15.0;
993	<	} else{
994	<	rcut = simParams_->getRcut();
992	>	} else {
993	>	rsw_ = rcut_;
994	>	sprintf(painCave.errMsg,
995	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
996	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
997	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
998	>	painCave.isFatal = 0;
999	>	simError();
1000	>	}
1001		}
1002	<
1003	<	if (!simParams_->haveRsw()){
1004	<	sprintf(painCave.errMsg,
797	<	"SimCreator Warning: No value was set for switchingRadius.\n"
798	<	"\tOOPSE will use a default value of\n"
799	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
800	<	painCave.isFatal = 0;
801	<	simError();
802	<	rsw = 0.95 * rcut;
803	<	} else{
804	<	rsw = simParams_->getRsw();
805	<	}
806	<
1002	>
1003	>	notifyFortranCutoffs(&rcut_, &rsw_);
1004	>
1005		} else {
1006	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
1007	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
1008	<
1009	<	if (simParams_->haveRcut()) {
1010	<	rcut = simParams_->getRcut();
1006	>
1007	>	// For electrostatic atoms, we'll assume a large safe value:
1008	>	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
1009	>	sprintf(painCave.errMsg,
1010	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1011	>	"\tOOPSE will use a default value of 15.0 angstroms"
1012	>	"\tfor the cutoffRadius.\n");
1013	>	painCave.isFatal = 0;
1014	>	simError();
1015	>	rcut_ = 15.0;
1016	>
1017	>	if (simParams_->haveElectrostaticSummationMethod()) {
1018	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1019	>	toUpper(myMethod);
1020	>	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
1021	>	if (simParams_->haveSwitchingRadius()){
1022	>	sprintf(painCave.errMsg,
1023	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1024	>	"\teven though the electrostaticSummationMethod was\n"
1025	>	"\tset to %s\n", myMethod.c_str());
1026	>	painCave.isFatal = 1;
1027	>	simError();
1028	>	}
1029	>	}
1030	>	}
1031	>
1032	>	if (simParams_->haveSwitchingRadius()){
1033	>	rsw_ = simParams_->getSwitchingRadius();
1034	>	} else {
1035	>	sprintf(painCave.errMsg,
1036	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1037	>	"\tOOPSE will use a default value of\n"
1038	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1039	>	painCave.isFatal = 0;
1040	>	simError();
1041	>	rsw_ = 0.85 * rcut_;
1042	>	}
1043	>	notifyFortranCutoffs(&rcut_, &rsw_);
1044		} else {
1045	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
1046	<	rcut = calcMaxCutoffRadius();
1045	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1046	>	// We'll punt and let fortran figure out the cutoffs later.
1047	>
1048	>	notifyFortranYouAreOnYourOwn();
1049	>
1050		}
1051	+	}
1052	+	}
1053
1054	<	if (simParams_->haveRsw()) {
1055	<	rsw = simParams_->getRsw();
1054	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1055	>
1056	>	int errorOut;
1057	>	int esm = NONE;
1058	>	int sm = UNDAMPED;
1059	>	RealType alphaVal;
1060	>	RealType dielectric;
1061	>
1062	>	errorOut = isError;
1063	>	alphaVal = simParams_->getDampingAlpha();
1064	>	dielectric = simParams_->getDielectric();
1065	>
1066	>	if (simParams_->haveElectrostaticSummationMethod()) {
1067	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1068	>	toUpper(myMethod);
1069	>	if (myMethod == "NONE") {
1070	>	esm = NONE;
1071		} else {
1072	<	rsw = rcut;
1072	>	if (myMethod == "SWITCHING_FUNCTION") {
1073	>	esm = SWITCHING_FUNCTION;
1074	>	} else {
1075	>	if (myMethod == "SHIFTED_POTENTIAL") {
1076	>	esm = SHIFTED_POTENTIAL;
1077	>	} else {
1078	>	if (myMethod == "SHIFTED_FORCE") {
1079	>	esm = SHIFTED_FORCE;
1080	>	} else {
1081	>	if (myMethod == "REACTION_FIELD") {
1082	>	esm = REACTION_FIELD;
1083	>	} else {
1084	>	// throw error
1085	>	sprintf( painCave.errMsg,
1086	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1087	>	"\t(Input file specified %s .)\n"
1088	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1089	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1090	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1091	>	painCave.isFatal = 1;
1092	>	simError();
1093	>	}
1094	>	}
1095	>	}
1096	>	}
1097		}
1098	+	}
1099
1100	+	if (simParams_->haveElectrostaticScreeningMethod()) {
1101	+	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1102	+	toUpper(myScreen);
1103	+	if (myScreen == "UNDAMPED") {
1104	+	sm = UNDAMPED;
1105	+	} else {
1106	+	if (myScreen == "DAMPED") {
1107	+	sm = DAMPED;
1108	+	if (!simParams_->haveDampingAlpha()) {
1109	+	//throw error
1110	+	sprintf( painCave.errMsg,
1111	+	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1112	+	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1113	+	painCave.isFatal = 0;
1114	+	simError();
1115	+	}
1116	+	} else {
1117	+	// throw error
1118	+	sprintf( painCave.errMsg,
1119	+	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1120	+	"\t(Input file specified %s .)\n"
1121	+	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1122	+	"or \"damped\".\n", myScreen.c_str() );
1123	+	painCave.isFatal = 1;
1124	+	simError();
1125	+	}
1126	+	}
1127		}
1128	+
1129	+	// let's pass some summation method variables to fortran
1130	+	setElectrostaticSummationMethod( &esm );
1131	+	setFortranElectrostaticMethod( &esm );
1132	+	setScreeningMethod( &sm );
1133	+	setDampingAlpha( &alphaVal );
1134	+	setReactionFieldDielectric( &dielectric );
1135	+	initFortranFF( &errorOut );
1136		}
1137
1138	<	void SimInfo::setupCutoff() {
1139	<	getCutoff(rcut_, rsw_);
829	<	double rnblist = rcut_ + 1; // skin of neighbor list
1138	>	void SimInfo::setupSwitchingFunction() {
1139	>	int ft = CUBIC;
1140
1141	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1142	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
1141	>	if (simParams_->haveSwitchingFunctionType()) {
1142	>	std::string funcType = simParams_->getSwitchingFunctionType();
1143	>	toUpper(funcType);
1144	>	if (funcType == "CUBIC") {
1145	>	ft = CUBIC;
1146	>	} else {
1147	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1148	>	ft = FIFTH_ORDER_POLY;
1149	>	} else {
1150	>	// throw error
1151	>	sprintf( painCave.errMsg,
1152	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1153	>	painCave.isFatal = 1;
1154	>	simError();
1155	>	}
1156	>	}
1157	>	}
1158	>
1159	>	// send switching function notification to switcheroo
1160	>	setFunctionType(&ft);
1161	>
1162		}
1163
1164		void SimInfo::addProperty(GenericData* genData) {
#	Line 888 \| Line 1217 \| namespace oopse {
1217		Molecule* mol;
1218
1219		Vector3d comVel(0.0);
1220	<	double totalMass = 0.0;
1220	>	RealType totalMass = 0.0;
1221
1222
1223		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1224	<	double mass = mol->getMass();
1224	>	RealType mass = mol->getMass();
1225		totalMass += mass;
1226		comVel += mass * mol->getComVel();
1227		}
1228
1229		#ifdef IS_MPI
1230	<	double tmpMass = totalMass;
1230	>	RealType tmpMass = totalMass;
1231		Vector3d tmpComVel(comVel);
1232	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1233	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1232	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1233	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1234		#endif
1235
1236		comVel /= totalMass;
#	Line 914 \| Line 1243 \| namespace oopse {
1243		Molecule* mol;
1244
1245		Vector3d com(0.0);
1246	<	double totalMass = 0.0;
1246	>	RealType totalMass = 0.0;
1247
1248		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1249	<	double mass = mol->getMass();
1249	>	RealType mass = mol->getMass();
1250		totalMass += mass;
1251		com += mass * mol->getCom();
1252		}
1253
1254		#ifdef IS_MPI
1255	<	double tmpMass = totalMass;
1255	>	RealType tmpMass = totalMass;
1256		Vector3d tmpCom(com);
1257	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1258	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1257	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1258	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1259		#endif
1260
1261		com /= totalMass;
#	Line 939 \| Line 1268 \| namespace oopse {
1268
1269		return o;
1270		}
1271	+
1272	+
1273	+	/*
1274	+	Returns center of mass and center of mass velocity in one function call.
1275	+	*/
1276	+
1277	+	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1278	+	SimInfo::MoleculeIterator i;
1279	+	Molecule* mol;
1280	+
1281	+
1282	+	RealType totalMass = 0.0;
1283	+
1284
1285	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1286	+	RealType mass = mol->getMass();
1287	+	totalMass += mass;
1288	+	com += mass * mol->getCom();
1289	+	comVel += mass * mol->getComVel();
1290	+	}
1291	+
1292	+	#ifdef IS_MPI
1293	+	RealType tmpMass = totalMass;
1294	+	Vector3d tmpCom(com);
1295	+	Vector3d tmpComVel(comVel);
1296	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1297	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1298	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1299	+	#endif
1300	+
1301	+	com /= totalMass;
1302	+	comVel /= totalMass;
1303	+	}
1304	+
1305	+	/*
1306	+	Return intertia tensor for entire system and angular momentum Vector.
1307	+
1308	+
1309	+	[ Ixx -Ixy -Ixz ]
1310	+	J =\| -Iyx Iyy -Iyz \|
1311	+	[ -Izx -Iyz Izz ]
1312	+	*/
1313	+
1314	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1315	+
1316	+
1317	+	RealType xx = 0.0;
1318	+	RealType yy = 0.0;
1319	+	RealType zz = 0.0;
1320	+	RealType xy = 0.0;
1321	+	RealType xz = 0.0;
1322	+	RealType yz = 0.0;
1323	+	Vector3d com(0.0);
1324	+	Vector3d comVel(0.0);
1325	+
1326	+	getComAll(com, comVel);
1327	+
1328	+	SimInfo::MoleculeIterator i;
1329	+	Molecule* mol;
1330	+
1331	+	Vector3d thisq(0.0);
1332	+	Vector3d thisv(0.0);
1333	+
1334	+	RealType thisMass = 0.0;
1335	+
1336	+
1337	+
1338	+
1339	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1340	+
1341	+	thisq = mol->getCom()-com;
1342	+	thisv = mol->getComVel()-comVel;
1343	+	thisMass = mol->getMass();
1344	+	// Compute moment of intertia coefficients.
1345	+	xx += thisq[0]thisq[0]thisMass;
1346	+	yy += thisq[1]thisq[1]thisMass;
1347	+	zz += thisq[2]thisq[2]thisMass;
1348	+
1349	+	// compute products of intertia
1350	+	xy += thisq[0]thisq[1]thisMass;
1351	+	xz += thisq[0]thisq[2]thisMass;
1352	+	yz += thisq[1]thisq[2]thisMass;
1353	+
1354	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1355	+
1356	+	}
1357	+
1358	+
1359	+	inertiaTensor(0,0) = yy + zz;
1360	+	inertiaTensor(0,1) = -xy;
1361	+	inertiaTensor(0,2) = -xz;
1362	+	inertiaTensor(1,0) = -xy;
1363	+	inertiaTensor(1,1) = xx + zz;
1364	+	inertiaTensor(1,2) = -yz;
1365	+	inertiaTensor(2,0) = -xz;
1366	+	inertiaTensor(2,1) = -yz;
1367	+	inertiaTensor(2,2) = xx + yy;
1368	+
1369	+	#ifdef IS_MPI
1370	+	Mat3x3d tmpI(inertiaTensor);
1371	+	Vector3d tmpAngMom;
1372	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1373	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1374	+	#endif
1375	+
1376	+	return;
1377	+	}
1378	+
1379	+	//Returns the angular momentum of the system
1380	+	Vector3d SimInfo::getAngularMomentum(){
1381	+
1382	+	Vector3d com(0.0);
1383	+	Vector3d comVel(0.0);
1384	+	Vector3d angularMomentum(0.0);
1385	+
1386	+	getComAll(com,comVel);
1387	+
1388	+	SimInfo::MoleculeIterator i;
1389	+	Molecule* mol;
1390	+
1391	+	Vector3d thisr(0.0);
1392	+	Vector3d thisp(0.0);
1393	+
1394	+	RealType thisMass;
1395	+
1396	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1397	+	thisMass = mol->getMass();
1398	+	thisr = mol->getCom()-com;
1399	+	thisp = (mol->getComVel()-comVel)*thisMass;
1400	+
1401	+	angularMomentum += cross( thisr, thisp );
1402	+
1403	+	}
1404	+
1405	+	#ifdef IS_MPI
1406	+	Vector3d tmpAngMom;
1407	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1408	+	#endif
1409	+
1410	+	return angularMomentum;
1411	+	}
1412	+
1413	+
1414		}//end namespace oopse
1415

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Comparing trunk/src/brains/SimInfo.cpp (file contents): Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs. Revision 963 by tim, Wed May 17 21:51:42 2006 UTC

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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC