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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 523 by chrisfen, Thu May 5 14:47:35 2005 UTC vs.
Revision 1024 by tim, Wed Aug 30 18:42:29 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/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/electrostatic_interface.h"
63	>	#include "UseTheForce/DarkSide/switcheroo_interface.h"
64		#include "utils/MemoryUtils.hpp"
65		#include "utils/simError.h"
66		#include "selection/SelectionManager.hpp"
67	+	#include "io/ForceFieldOptions.hpp"
68	+	#include "UseTheForce/ForceField.hpp"
69
70		#ifdef IS_MPI
71		#include "UseTheForce/mpiComponentPlan.h"
#	Line 64 \| Line 73 \| namespace oopse {
73		#endif
74
75		namespace oopse {
76	+	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
77	+	std::map<int, std::set<int> >::iterator i = container.find(index);
78	+	std::set<int> result;
79	+	if (i != container.end()) {
80	+	result = i->second;
81	+	}
82
83	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
84	<	ForceField* ff, Globals* simParams) :
85	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
86	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
83	>	return result;
84	>	}
85	>
86	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
87	>	forceField_(ff), simParams_(simParams),
88	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
89		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
90		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
91		nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
92		nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
93	<	sman_(NULL), fortranInitialized_(false) {
93	>	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) {
94
78	–
79	–	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
95		MoleculeStamp* molStamp;
96		int nMolWithSameStamp;
97		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
98	<	int nGroups = 0; //total cutoff groups defined in meta-data file
98	>	int nGroups = 0; //total cutoff groups defined in meta-data file
99		CutoffGroupStamp* cgStamp;
100		RigidBodyStamp* rbStamp;
101		int nRigidAtoms = 0;
102	<
103	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
104	<	molStamp = i->first;
105	<	nMolWithSameStamp = i->second;
102	>	std::vector<Component*> components = simParams->getComponents();
103	>
104	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
105	>	molStamp = (*i)->getMoleculeStamp();
106	>	nMolWithSameStamp = (*i)->getNMol();
107
108		addMoleculeStamp(molStamp, nMolWithSameStamp);
109
110		//calculate atoms in molecules
111		nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
112
97	–
113		//calculate atoms in cutoff groups
114		int nAtomsInGroups = 0;
115		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
116
117		for (int j=0; j < nCutoffGroupsInStamp; j++) {
118	<	cgStamp = molStamp->getCutoffGroup(j);
118	>	cgStamp = molStamp->getCutoffGroupStamp(j);
119		nAtomsInGroups += cgStamp->getNMembers();
120		}
121
122		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
123	+
124		nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
125
126		//calculate atoms in rigid bodies
#	Line 112 \| Line 128 \| namespace oopse {
128		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
129
130		for (int j=0; j < nRigidBodiesInStamp; j++) {
131	<	rbStamp = molStamp->getRigidBody(j);
131	>	rbStamp = molStamp->getRigidBodyStamp(j);
132		nAtomsInRigidBodies += rbStamp->getNMembers();
133		}
134
#	Line 121 \| Line 137 \| namespace oopse {
137
138		}
139
140	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
141	<	//therefore the total number of cutoff groups in the system is equal to
142	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
143	<	//file plus the number of cutoff groups defined in meta-data file
140	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
141	>	//group therefore the total number of cutoff groups in the system is
142	>	//equal to the total number of atoms minus number of atoms belong to
143	>	//cutoff group defined in meta-data file plus the number of cutoff
144	>	//groups defined in meta-data file
145		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
146
147	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
148	<	//therefore the total number of integrable objects in the system is equal to
149	<	//the total number of atoms minus number of atoms belong to rigid body defined in meta-data
150	<	//file plus the number of rigid bodies defined in meta-data file
151	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
152	<
147	>	//every free atom (atom does not belong to rigid bodies) is an
148	>	//integrable object therefore the total number of integrable objects
149	>	//in the system is equal to the total number of atoms minus number of
150	>	//atoms belong to rigid body defined in meta-data file plus the number
151	>	//of rigid bodies defined in meta-data file
152	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
153	>	+ nGlobalRigidBodies_;
154	>
155		nGlobalMols_ = molStampIds_.size();
156
157		#ifdef IS_MPI
#	Line 148 \| Line 167 \| namespace oopse {
167		}
168		molecules_.clear();
169
151	–	delete stamps_;
170		delete sman_;
171		delete simParams_;
172		delete forceField_;
#	Line 255 \| Line 273 \| namespace oopse {
273		}
274		}
275
276	<	}//end for (integrableObject)
277	<	}// end for (mol)
276	>	}
277	>	}
278
279		// n_constraints is local, so subtract them on each processor
280		ndf_local -= nConstraints_;
#	Line 273 \| Line 291 \| namespace oopse {
291
292		}
293
294	+	int SimInfo::getFdf() {
295	+	#ifdef IS_MPI
296	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
297	+	#else
298	+	fdf_ = fdf_local;
299	+	#endif
300	+	return fdf_;
301	+	}
302	+
303		void SimInfo::calcNdfRaw() {
304		int ndfRaw_local;
305
#	Line 335 \| Line 362 \| namespace oopse {
362		int b;
363		int c;
364		int d;
365	+
366	+	std::map<int, std::set<int> > atomGroups;
367	+
368	+	Molecule::RigidBodyIterator rbIter;
369	+	RigidBody* rb;
370	+	Molecule::IntegrableObjectIterator ii;
371	+	StuntDouble* integrableObject;
372
373	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
374	+	integrableObject = mol->nextIntegrableObject(ii)) {
375	+
376	+	if (integrableObject->isRigidBody()) {
377	+	rb = static_cast<RigidBody*>(integrableObject);
378	+	std::vector<Atom*> atoms = rb->getAtoms();
379	+	std::set<int> rigidAtoms;
380	+	for (int i = 0; i < atoms.size(); ++i) {
381	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
382	+	}
383	+	for (int i = 0; i < atoms.size(); ++i) {
384	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
385	+	}
386	+	} else {
387	+	std::set<int> oneAtomSet;
388	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
389	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
390	+	}
391	+	}
392	+
393	+
394	+
395		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
396		a = bond->getAtomA()->getGlobalIndex();
397		b = bond->getAtomB()->getGlobalIndex();
#	Line 346 \| Line 402 \| namespace oopse {
402		a = bend->getAtomA()->getGlobalIndex();
403		b = bend->getAtomB()->getGlobalIndex();
404		c = bend->getAtomC()->getGlobalIndex();
405	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
406	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
407	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
408
409	<	exclude_.addPair(a, b);
410	<	exclude_.addPair(a, c);
411	<	exclude_.addPair(b, c);
409	>	exclude_.addPairs(rigidSetA, rigidSetB);
410	>	exclude_.addPairs(rigidSetA, rigidSetC);
411	>	exclude_.addPairs(rigidSetB, rigidSetC);
412	>
413	>	//exclude_.addPair(a, b);
414	>	//exclude_.addPair(a, c);
415	>	//exclude_.addPair(b, c);
416		}
417
418		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
#	Line 357 \| Line 420 \| namespace oopse {
420		b = torsion->getAtomB()->getGlobalIndex();
421		c = torsion->getAtomC()->getGlobalIndex();
422		d = torsion->getAtomD()->getGlobalIndex();
423	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
424	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
425	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
426	+	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
427
428	+	exclude_.addPairs(rigidSetA, rigidSetB);
429	+	exclude_.addPairs(rigidSetA, rigidSetC);
430	+	exclude_.addPairs(rigidSetA, rigidSetD);
431	+	exclude_.addPairs(rigidSetB, rigidSetC);
432	+	exclude_.addPairs(rigidSetB, rigidSetD);
433	+	exclude_.addPairs(rigidSetC, rigidSetD);
434	+
435	+	/*
436	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
437	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
438	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
439	+	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
440	+	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
441	+	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
442	+
443	+
444		exclude_.addPair(a, b);
445		exclude_.addPair(a, c);
446		exclude_.addPair(a, d);
447		exclude_.addPair(b, c);
448		exclude_.addPair(b, d);
449		exclude_.addPair(c, d);
450	+	*/
451		}
452
369	–	Molecule::RigidBodyIterator rbIter;
370	–	RigidBody* rb;
453		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
454		std::vector<Atom*> atoms = rb->getAtoms();
455		for (int i = 0; i < atoms.size() -1 ; ++i) {
#	Line 392 \| Line 474 \| namespace oopse {
474		int b;
475		int c;
476		int d;
477	+
478	+	std::map<int, std::set<int> > atomGroups;
479	+
480	+	Molecule::RigidBodyIterator rbIter;
481	+	RigidBody* rb;
482	+	Molecule::IntegrableObjectIterator ii;
483	+	StuntDouble* integrableObject;
484
485	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
486	+	integrableObject = mol->nextIntegrableObject(ii)) {
487	+
488	+	if (integrableObject->isRigidBody()) {
489	+	rb = static_cast<RigidBody*>(integrableObject);
490	+	std::vector<Atom*> atoms = rb->getAtoms();
491	+	std::set<int> rigidAtoms;
492	+	for (int i = 0; i < atoms.size(); ++i) {
493	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
494	+	}
495	+	for (int i = 0; i < atoms.size(); ++i) {
496	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
497	+	}
498	+	} else {
499	+	std::set<int> oneAtomSet;
500	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
501	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
502	+	}
503	+	}
504	+
505	+
506		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
507		a = bond->getAtomA()->getGlobalIndex();
508		b = bond->getAtomB()->getGlobalIndex();
#	Line 404 \| Line 514 \| namespace oopse {
514		b = bend->getAtomB()->getGlobalIndex();
515		c = bend->getAtomC()->getGlobalIndex();
516
517	<	exclude_.removePair(a, b);
518	<	exclude_.removePair(a, c);
519	<	exclude_.removePair(b, c);
517	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
518	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
519	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
520	>
521	>	exclude_.removePairs(rigidSetA, rigidSetB);
522	>	exclude_.removePairs(rigidSetA, rigidSetC);
523	>	exclude_.removePairs(rigidSetB, rigidSetC);
524	>
525	>	//exclude_.removePair(a, b);
526	>	//exclude_.removePair(a, c);
527	>	//exclude_.removePair(b, c);
528		}
529
530		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
#	Line 415 \| Line 533 \| namespace oopse {
533		c = torsion->getAtomC()->getGlobalIndex();
534		d = torsion->getAtomD()->getGlobalIndex();
535
536	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
537	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
538	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
539	+	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
540	+
541	+	exclude_.removePairs(rigidSetA, rigidSetB);
542	+	exclude_.removePairs(rigidSetA, rigidSetC);
543	+	exclude_.removePairs(rigidSetA, rigidSetD);
544	+	exclude_.removePairs(rigidSetB, rigidSetC);
545	+	exclude_.removePairs(rigidSetB, rigidSetD);
546	+	exclude_.removePairs(rigidSetC, rigidSetD);
547	+
548	+	/*
549	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
550	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
551	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
552	+	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
553	+	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
554	+	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
555	+
556	+
557		exclude_.removePair(a, b);
558		exclude_.removePair(a, c);
559		exclude_.removePair(a, d);
560		exclude_.removePair(b, c);
561		exclude_.removePair(b, d);
562		exclude_.removePair(c, d);
563	+	*/
564		}
565
426	–	Molecule::RigidBodyIterator rbIter;
427	–	RigidBody* rb;
566		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
567		std::vector<Atom*> atoms = rb->getAtoms();
568		for (int i = 0; i < atoms.size() -1 ; ++i) {
#	Line 462 \| Line 600 \| namespace oopse {
600		//setup fortran force field
601		/** @deprecate */
602		int isError = 0;
603	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
603	>
604	>	setupElectrostaticSummationMethod( isError );
605	>	setupSwitchingFunction();
606	>	setupAccumulateBoxDipole();
607	>
608		if(isError){
609		sprintf( painCave.errMsg,
610		"ForceField error: There was an error initializing the forceField in fortran.\n" );
#	Line 506 \| Line 648 \| namespace oopse {
648		int useLennardJones = 0;
649		int useElectrostatic = 0;
650		int useEAM = 0;
651	+	int useSC = 0;
652		int useCharge = 0;
653		int useDirectional = 0;
654		int useDipole = 0;
#	Line 517 \| Line 660 \| namespace oopse {
660		int useDirectionalAtom = 0;
661		int useElectrostatics = 0;
662		//usePBC and useRF are from simParams
663	<	int usePBC = simParams_->getPBC();
664	<	int useRF = simParams_->getUseRF();
663	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
664	>	int useRF;
665	>	int useSF;
666	>	int useSP;
667	>	int useBoxDipole;
668	>	std::string myMethod;
669	>
670	>	// set the useRF logical
671	>	useRF = 0;
672	>	useSF = 0;
673	>
674	>
675	>	if (simParams_->haveElectrostaticSummationMethod()) {
676	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
677	>	toUpper(myMethod);
678	>	if (myMethod == "REACTION_FIELD"){
679	>	useRF=1;
680	>	} else if (myMethod == "SHIFTED_FORCE"){
681	>	useSF = 1;
682	>	} else if (myMethod == "SHIFTED_POTENTIAL"){
683	>	useSP = 1;
684	>	}
685	>	}
686	>
687	>	if (simParams_->haveAccumulateBoxDipole())
688	>	if (simParams_->getAccumulateBoxDipole())
689	>	useBoxDipole = 1;
690
691		//loop over all of the atom types
692		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
693		useLennardJones \|= (*i)->isLennardJones();
694		useElectrostatic \|= (*i)->isElectrostatic();
695		useEAM \|= (*i)->isEAM();
696	+	useSC \|= (*i)->isSC();
697		useCharge \|= (*i)->isCharge();
698		useDirectional \|= (*i)->isDirectional();
699		useDipole \|= (*i)->isDipole();
#	Line 575 \| Line 744 \| namespace oopse {
744		temp = useEAM;
745		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
746
747	+	temp = useSC;
748	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
749	+
750		temp = useShape;
751		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
752
#	Line 583 \| Line 755 \| namespace oopse {
755
756		temp = useRF;
757		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
758	<
758	>
759	>	temp = useSF;
760	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
761	>
762	>	temp = useSP;
763	>	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
764	>
765	>	temp = useBoxDipole;
766	>	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767	>
768		#endif
769
770		fInfo_.SIM_uses_PBC = usePBC;
#	Line 596 \| Line 777 \| namespace oopse {
777		fInfo_.SIM_uses_StickyPower = useStickyPower;
778		fInfo_.SIM_uses_GayBerne = useGayBerne;
779		fInfo_.SIM_uses_EAM = useEAM;
780	+	fInfo_.SIM_uses_SC = useSC;
781		fInfo_.SIM_uses_Shapes = useShape;
782		fInfo_.SIM_uses_FLARB = useFLARB;
783		fInfo_.SIM_uses_RF = useRF;
784	+	fInfo_.SIM_uses_SF = useSF;
785	+	fInfo_.SIM_uses_SP = useSP;
786	+	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
787
788	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
789	<
788	>	if( myMethod == "REACTION_FIELD") {
789	>
790		if (simParams_->haveDielectric()) {
791		fInfo_.dielect = simParams_->getDielectric();
792		} else {
#	Line 611 \| Line 796 \| namespace oopse {
796		"\tsetting a dielectric constant!\n");
797		painCave.isFatal = 1;
798		simError();
799	<	}
615	<
616	<	} else {
617	<	fInfo_.dielect = 0.0;
799	>	}
800		}
801
802		}
#	Line 633 \| Line 815 \| namespace oopse {
815		}
816
817		//calculate mass ratio of cutoff group
818	<	std::vector<double> mfact;
818	>	std::vector<RealType> mfact;
819		SimInfo::MoleculeIterator mi;
820		Molecule* mol;
821		Molecule::CutoffGroupIterator ci;
822		CutoffGroup* cg;
823		Molecule::AtomIterator ai;
824		Atom* atom;
825	<	double totalMass;
825	>	RealType totalMass;
826
827		//to avoid memory reallocation, reserve enough space for mfact
828		mfact.reserve(getNCutoffGroups());
#	Line 650 \| Line 832 \| namespace oopse {
832
833		totalMass = cg->getMass();
834		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
835	<	mfact.push_back(atom->getMass()/totalMass);
835	>	// Check for massless groups - set mfact to 1 if true
836	>	if (totalMass != 0)
837	>	mfact.push_back(atom->getMass()/totalMass);
838	>	else
839	>	mfact.push_back( 1.0 );
840		}
841
842		}
#	Line 759 \| Line 945 \| namespace oopse {
945
946		#endif
947
948	<	double SimInfo::calcMaxCutoffRadius() {
948	>	void SimInfo::setupCutoff() {
949	>
950	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
951
952	+	// Check the cutoff policy
953	+	int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
954
955	<	std::set<AtomType*> atomTypes;
956	<	std::set<AtomType*>::iterator i;
957	<	std::vector<double> cutoffRadius;
958	<
959	<	//get the unique atom types
770	<	atomTypes = getUniqueAtomTypes();
771	<
772	<	//query the max cutoff radius among these atom types
773	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
774	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
955	>	std::string myPolicy;
956	>	if (forceFieldOptions_.haveCutoffPolicy()){
957	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
958	>	}else if (simParams_->haveCutoffPolicy()) {
959	>	myPolicy = simParams_->getCutoffPolicy();
960		}
961
962	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
963	<	#ifdef IS_MPI
964	<	//pick the max cutoff radius among the processors
965	<	#endif
962	>	if (!myPolicy.empty()){
963	>	toUpper(myPolicy);
964	>	if (myPolicy == "MIX") {
965	>	cp = MIX_CUTOFF_POLICY;
966	>	} else {
967	>	if (myPolicy == "MAX") {
968	>	cp = MAX_CUTOFF_POLICY;
969	>	} else {
970	>	if (myPolicy == "TRADITIONAL") {
971	>	cp = TRADITIONAL_CUTOFF_POLICY;
972	>	} else {
973	>	// throw error
974	>	sprintf( painCave.errMsg,
975	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
976	>	painCave.isFatal = 1;
977	>	simError();
978	>	}
979	>	}
980	>	}
981	>	}
982	>	notifyFortranCutoffPolicy(&cp);
983
984	<	return maxCutoffRadius;
985	<	}
986	<
987	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
988	<
989	<	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
984	>	// Check the Skin Thickness for neighborlists
985	>	RealType skin;
986	>	if (simParams_->haveSkinThickness()) {
987	>	skin = simParams_->getSkinThickness();
988	>	notifyFortranSkinThickness(&skin);
989	>	}
990
991	<	if (!simParams_->haveRcut()){
992	<	sprintf(painCave.errMsg,
993	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
994	<	"\tOOPSE will use a default value of 15.0 angstroms"
995	<	"\tfor the cutoffRadius.\n");
996	<	painCave.isFatal = 0;
991	>	// Check if the cutoff was set explicitly:
992	>	if (simParams_->haveCutoffRadius()) {
993	>	rcut_ = simParams_->getCutoffRadius();
994	>	if (simParams_->haveSwitchingRadius()) {
995	>	rsw_ = simParams_->getSwitchingRadius();
996	>	} else {
997	>	if (fInfo_.SIM_uses_Charges \|
998	>	fInfo_.SIM_uses_Dipoles \|
999	>	fInfo_.SIM_uses_RF) {
1000	>
1001	>	rsw_ = 0.85 * rcut_;
1002	>	sprintf(painCave.errMsg,
1003	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1004	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1005	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1006	>	painCave.isFatal = 0;
1007		simError();
1008	<	rcut = 15.0;
1009	<	} else{
1010	<	rcut = simParams_->getRcut();
1008	>	} else {
1009	>	rsw_ = rcut_;
1010	>	sprintf(painCave.errMsg,
1011	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1012	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
1013	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1014	>	painCave.isFatal = 0;
1015	>	simError();
1016	>	}
1017		}
1018	<
1019	<	if (!simParams_->haveRsw()){
1020	<	sprintf(painCave.errMsg,
1021	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1022	<	"\tOOPSE will use a default value of\n"
1023	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
1024	<	painCave.isFatal = 0;
1018	>
1019	>	notifyFortranCutoffs(&rcut_, &rsw_);
1020	>
1021	>	} else {
1022	>
1023	>	// For electrostatic atoms, we'll assume a large safe value:
1024	>	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
1025	>	sprintf(painCave.errMsg,
1026	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1027	>	"\tOOPSE will use a default value of 15.0 angstroms"
1028	>	"\tfor the cutoffRadius.\n");
1029	>	painCave.isFatal = 0;
1030		simError();
1031	<	rsw = 0.95 * rcut;
1032	<	} else{
1033	<	rsw = simParams_->getRsw();
1031	>	rcut_ = 15.0;
1032	>
1033	>	if (simParams_->haveElectrostaticSummationMethod()) {
1034	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1035	>	toUpper(myMethod);
1036	>	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
1037	>	if (simParams_->haveSwitchingRadius()){
1038	>	sprintf(painCave.errMsg,
1039	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1040	>	"\teven though the electrostaticSummationMethod was\n"
1041	>	"\tset to %s\n", myMethod.c_str());
1042	>	painCave.isFatal = 1;
1043	>	simError();
1044	>	}
1045	>	}
1046	>	}
1047	>
1048	>	if (simParams_->haveSwitchingRadius()){
1049	>	rsw_ = simParams_->getSwitchingRadius();
1050	>	} else {
1051	>	sprintf(painCave.errMsg,
1052	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1053	>	"\tOOPSE will use a default value of\n"
1054	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1055	>	painCave.isFatal = 0;
1056	>	simError();
1057	>	rsw_ = 0.85 * rcut_;
1058	>	}
1059	>	notifyFortranCutoffs(&rcut_, &rsw_);
1060	>	} else {
1061	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1062	>	// We'll punt and let fortran figure out the cutoffs later.
1063	>
1064	>	notifyFortranYouAreOnYourOwn();
1065	>
1066		}
1067	+	}
1068	+	}
1069
1070	<	} else {
1071	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
1072	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
1073	<
1074	<	if (simParams_->haveRcut()) {
1075	<	rcut = simParams_->getRcut();
1070	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1071	>
1072	>	int errorOut;
1073	>	int esm = NONE;
1074	>	int sm = UNDAMPED;
1075	>	RealType alphaVal;
1076	>	RealType dielectric;
1077	>
1078	>	errorOut = isError;
1079	>	alphaVal = simParams_->getDampingAlpha();
1080	>	dielectric = simParams_->getDielectric();
1081	>
1082	>	if (simParams_->haveElectrostaticSummationMethod()) {
1083	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1084	>	toUpper(myMethod);
1085	>	if (myMethod == "NONE") {
1086	>	esm = NONE;
1087		} else {
1088	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
1089	<	rcut = calcMaxCutoffRadius();
1088	>	if (myMethod == "SWITCHING_FUNCTION") {
1089	>	esm = SWITCHING_FUNCTION;
1090	>	} else {
1091	>	if (myMethod == "SHIFTED_POTENTIAL") {
1092	>	esm = SHIFTED_POTENTIAL;
1093	>	} else {
1094	>	if (myMethod == "SHIFTED_FORCE") {
1095	>	esm = SHIFTED_FORCE;
1096	>	} else {
1097	>	if (myMethod == "REACTION_FIELD") {
1098	>	esm = REACTION_FIELD;
1099	>	} else {
1100	>	// throw error
1101	>	sprintf( painCave.errMsg,
1102	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1103	>	"\t(Input file specified %s .)\n"
1104	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1105	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1106	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1107	>	painCave.isFatal = 1;
1108	>	simError();
1109	>	}
1110	>	}
1111	>	}
1112	>	}
1113		}
1114	<
1115	<	if (simParams_->haveRsw()) {
1116	<	rsw = simParams_->getRsw();
1114	>	}
1115	>
1116	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1117	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1118	>	toUpper(myScreen);
1119	>	if (myScreen == "UNDAMPED") {
1120	>	sm = UNDAMPED;
1121		} else {
1122	<	rsw = rcut;
1122	>	if (myScreen == "DAMPED") {
1123	>	sm = DAMPED;
1124	>	if (!simParams_->haveDampingAlpha()) {
1125	>	//throw error
1126	>	sprintf( painCave.errMsg,
1127	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1128	>	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1129	>	painCave.isFatal = 0;
1130	>	simError();
1131	>	}
1132	>	} else {
1133	>	// throw error
1134	>	sprintf( painCave.errMsg,
1135	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1136	>	"\t(Input file specified %s .)\n"
1137	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1138	>	"or \"damped\".\n", myScreen.c_str() );
1139	>	painCave.isFatal = 1;
1140	>	simError();
1141	>	}
1142		}
1143	+	}
1144
1145	+	// let's pass some summation method variables to fortran
1146	+	setElectrostaticSummationMethod( &esm );
1147	+	setFortranElectrostaticMethod( &esm );
1148	+	setScreeningMethod( &sm );
1149	+	setDampingAlpha( &alphaVal );
1150	+	setReactionFieldDielectric( &dielectric );
1151	+	initFortranFF( &errorOut );
1152	+	}
1153	+
1154	+	void SimInfo::setupSwitchingFunction() {
1155	+	int ft = CUBIC;
1156	+
1157	+	if (simParams_->haveSwitchingFunctionType()) {
1158	+	std::string funcType = simParams_->getSwitchingFunctionType();
1159	+	toUpper(funcType);
1160	+	if (funcType == "CUBIC") {
1161	+	ft = CUBIC;
1162	+	} else {
1163	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1164	+	ft = FIFTH_ORDER_POLY;
1165	+	} else {
1166	+	// throw error
1167	+	sprintf( painCave.errMsg,
1168	+	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1169	+	painCave.isFatal = 1;
1170	+	simError();
1171	+	}
1172	+	}
1173		}
1174	+
1175	+	// send switching function notification to switcheroo
1176	+	setFunctionType(&ft);
1177	+
1178		}
1179
1180	<	void SimInfo::setupCutoff() {
834	<	getCutoff(rcut_, rsw_);
835	<	double rnblist = rcut_ + 1; // skin of neighbor list
1180	>	void SimInfo::setupAccumulateBoxDipole() {
1181
1182	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1183	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
1182	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1183	>	if ( simParams_->haveAccumulateBoxDipole() )
1184	>	if ( simParams_->getAccumulateBoxDipole() ) {
1185	>	setAccumulateBoxDipole();
1186	>	calcBoxDipole_ = true;
1187	>	}
1188	>
1189		}
1190
1191		void SimInfo::addProperty(GenericData* genData) {
#	Line 894 \| Line 1244 \| namespace oopse {
1244		Molecule* mol;
1245
1246		Vector3d comVel(0.0);
1247	<	double totalMass = 0.0;
1247	>	RealType totalMass = 0.0;
1248
1249
1250		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1251	<	double mass = mol->getMass();
1251	>	RealType mass = mol->getMass();
1252		totalMass += mass;
1253		comVel += mass * mol->getComVel();
1254		}
1255
1256		#ifdef IS_MPI
1257	<	double tmpMass = totalMass;
1257	>	RealType tmpMass = totalMass;
1258		Vector3d tmpComVel(comVel);
1259	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1260	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1259	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1260	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1261		#endif
1262
1263		comVel /= totalMass;
#	Line 920 \| Line 1270 \| namespace oopse {
1270		Molecule* mol;
1271
1272		Vector3d com(0.0);
1273	<	double totalMass = 0.0;
1273	>	RealType totalMass = 0.0;
1274
1275		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1276	<	double mass = mol->getMass();
1276	>	RealType mass = mol->getMass();
1277		totalMass += mass;
1278		com += mass * mol->getCom();
1279		}
1280
1281		#ifdef IS_MPI
1282	<	double tmpMass = totalMass;
1282	>	RealType tmpMass = totalMass;
1283		Vector3d tmpCom(com);
1284	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1285	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1284	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1285	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1286		#endif
1287
1288		com /= totalMass;
#	Line 945 \| Line 1295 \| namespace oopse {
1295
1296		return o;
1297		}
1298	+
1299	+
1300	+	/*
1301	+	Returns center of mass and center of mass velocity in one function call.
1302	+	*/
1303	+
1304	+	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1305	+	SimInfo::MoleculeIterator i;
1306	+	Molecule* mol;
1307	+
1308	+
1309	+	RealType totalMass = 0.0;
1310	+
1311
1312	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1313	+	RealType mass = mol->getMass();
1314	+	totalMass += mass;
1315	+	com += mass * mol->getCom();
1316	+	comVel += mass * mol->getComVel();
1317	+	}
1318	+
1319	+	#ifdef IS_MPI
1320	+	RealType tmpMass = totalMass;
1321	+	Vector3d tmpCom(com);
1322	+	Vector3d tmpComVel(comVel);
1323	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1324	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1325	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1326	+	#endif
1327	+
1328	+	com /= totalMass;
1329	+	comVel /= totalMass;
1330	+	}
1331	+
1332	+	/*
1333	+	Return intertia tensor for entire system and angular momentum Vector.
1334	+
1335	+
1336	+	[ Ixx -Ixy -Ixz ]
1337	+	J =\| -Iyx Iyy -Iyz \|
1338	+	[ -Izx -Iyz Izz ]
1339	+	*/
1340	+
1341	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1342	+
1343	+
1344	+	RealType xx = 0.0;
1345	+	RealType yy = 0.0;
1346	+	RealType zz = 0.0;
1347	+	RealType xy = 0.0;
1348	+	RealType xz = 0.0;
1349	+	RealType yz = 0.0;
1350	+	Vector3d com(0.0);
1351	+	Vector3d comVel(0.0);
1352	+
1353	+	getComAll(com, comVel);
1354	+
1355	+	SimInfo::MoleculeIterator i;
1356	+	Molecule* mol;
1357	+
1358	+	Vector3d thisq(0.0);
1359	+	Vector3d thisv(0.0);
1360	+
1361	+	RealType thisMass = 0.0;
1362	+
1363	+
1364	+
1365	+
1366	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1367	+
1368	+	thisq = mol->getCom()-com;
1369	+	thisv = mol->getComVel()-comVel;
1370	+	thisMass = mol->getMass();
1371	+	// Compute moment of intertia coefficients.
1372	+	xx += thisq[0]thisq[0]thisMass;
1373	+	yy += thisq[1]thisq[1]thisMass;
1374	+	zz += thisq[2]thisq[2]thisMass;
1375	+
1376	+	// compute products of intertia
1377	+	xy += thisq[0]thisq[1]thisMass;
1378	+	xz += thisq[0]thisq[2]thisMass;
1379	+	yz += thisq[1]thisq[2]thisMass;
1380	+
1381	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1382	+
1383	+	}
1384	+
1385	+
1386	+	inertiaTensor(0,0) = yy + zz;
1387	+	inertiaTensor(0,1) = -xy;
1388	+	inertiaTensor(0,2) = -xz;
1389	+	inertiaTensor(1,0) = -xy;
1390	+	inertiaTensor(1,1) = xx + zz;
1391	+	inertiaTensor(1,2) = -yz;
1392	+	inertiaTensor(2,0) = -xz;
1393	+	inertiaTensor(2,1) = -yz;
1394	+	inertiaTensor(2,2) = xx + yy;
1395	+
1396	+	#ifdef IS_MPI
1397	+	Mat3x3d tmpI(inertiaTensor);
1398	+	Vector3d tmpAngMom;
1399	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1400	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1401	+	#endif
1402	+
1403	+	return;
1404	+	}
1405	+
1406	+	//Returns the angular momentum of the system
1407	+	Vector3d SimInfo::getAngularMomentum(){
1408	+
1409	+	Vector3d com(0.0);
1410	+	Vector3d comVel(0.0);
1411	+	Vector3d angularMomentum(0.0);
1412	+
1413	+	getComAll(com,comVel);
1414	+
1415	+	SimInfo::MoleculeIterator i;
1416	+	Molecule* mol;
1417	+
1418	+	Vector3d thisr(0.0);
1419	+	Vector3d thisp(0.0);
1420	+
1421	+	RealType thisMass;
1422	+
1423	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1424	+	thisMass = mol->getMass();
1425	+	thisr = mol->getCom()-com;
1426	+	thisp = (mol->getComVel()-comVel)*thisMass;
1427	+
1428	+	angularMomentum += cross( thisr, thisp );
1429	+
1430	+	}
1431	+
1432	+	#ifdef IS_MPI
1433	+	Vector3d tmpAngMom;
1434	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1435	+	#endif
1436	+
1437	+	return angularMomentum;
1438	+	}
1439	+
1440	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1441	+	return IOIndexToIntegrableObject.at(index);
1442	+	}
1443	+
1444	+	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1445	+	IOIndexToIntegrableObject= v;
1446	+	}
1447	+
1448	+	/*
1449	+	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1450	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1451	+	sdByGlobalIndex_ = v;
1452	+	}
1453	+
1454	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1455	+	//assert(index < nAtoms_ + nRigidBodies_);
1456	+	return sdByGlobalIndex_.at(index);
1457	+	}
1458	+	*/
1459		}//end namespace oopse
1460

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Comparing trunk/src/brains/SimInfo.cpp (file contents): Revision 523 by chrisfen, Thu May 5 14:47:35 2005 UTC vs. Revision 1024 by tim, Wed Aug 30 18:42:29 2006 UTC

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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 523 by chrisfen, Thu May 5 14:47:35 2005 UTC vs.
Revision 1024 by tim, Wed Aug 30 18:42:29 2006 UTC