[ViewVC] Diff of: OpenMD/trunk/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 998 by chrisfen, Mon Jul 3 13:18:43 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) {
92	>	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(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	>	setupAccumulateBoxDipole();
606	>
607		if(isError){
608		sprintf( painCave.errMsg,
609		"ForceField error: There was an error initializing the forceField in fortran.\n" );
#	Line 506 \| Line 647 \| namespace oopse {
647		int useLennardJones = 0;
648		int useElectrostatic = 0;
649		int useEAM = 0;
650	+	int useSC = 0;
651		int useCharge = 0;
652		int useDirectional = 0;
653		int useDipole = 0;
#	Line 517 \| Line 659 \| namespace oopse {
659		int useDirectionalAtom = 0;
660		int useElectrostatics = 0;
661		//usePBC and useRF are from simParams
662	<	int usePBC = simParams_->getPBC();
663	<	int useRF = simParams_->getUseRF();
662	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
663	>	int useRF;
664	>	int useSF;
665	>	int useSP;
666	>	int useBoxDipole;
667	>	std::string myMethod;
668
669	+	// set the useRF logical
670	+	useRF = 0;
671	+	useSF = 0;
672	+
673	+
674	+	if (simParams_->haveElectrostaticSummationMethod()) {
675	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
676	+	toUpper(myMethod);
677	+	if (myMethod == "REACTION_FIELD"){
678	+	useRF=1;
679	+	} else if (myMethod == "SHIFTED_FORCE"){
680	+	useSF = 1;
681	+	} else if (myMethod == "SHIFTED_POTENTIAL"){
682	+	useSP = 1;
683	+	}
684	+	}
685	+
686	+	if (simParams_->haveAccumulateBoxDipole())
687	+	if (simParams_->getAccumulateBoxDipole())
688	+	useBoxDipole = 1;
689	+
690		//loop over all of the atom types
691		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
692		useLennardJones \|= (*i)->isLennardJones();
693		useElectrostatic \|= (*i)->isElectrostatic();
694		useEAM \|= (*i)->isEAM();
695	+	useSC \|= (*i)->isSC();
696		useCharge \|= (*i)->isCharge();
697		useDirectional \|= (*i)->isDirectional();
698		useDipole \|= (*i)->isDipole();
#	Line 575 \| Line 743 \| namespace oopse {
743		temp = useEAM;
744		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
745
746	+	temp = useSC;
747	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
748	+
749		temp = useShape;
750		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
751
#	Line 583 \| Line 754 \| namespace oopse {
754
755		temp = useRF;
756		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
757	<
757	>
758	>	temp = useSF;
759	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
760	>
761	>	temp = useSP;
762	>	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
763	>
764	>	temp = useBoxDipole;
765	>	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766	>
767		#endif
768
769		fInfo_.SIM_uses_PBC = usePBC;
#	Line 596 \| Line 776 \| namespace oopse {
776		fInfo_.SIM_uses_StickyPower = useStickyPower;
777		fInfo_.SIM_uses_GayBerne = useGayBerne;
778		fInfo_.SIM_uses_EAM = useEAM;
779	+	fInfo_.SIM_uses_SC = useSC;
780		fInfo_.SIM_uses_Shapes = useShape;
781		fInfo_.SIM_uses_FLARB = useFLARB;
782		fInfo_.SIM_uses_RF = useRF;
783	+	fInfo_.SIM_uses_SF = useSF;
784	+	fInfo_.SIM_uses_SP = useSP;
785	+	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
786
787	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
788	<
787	>	if( myMethod == "REACTION_FIELD") {
788	>
789		if (simParams_->haveDielectric()) {
790		fInfo_.dielect = simParams_->getDielectric();
791		} else {
#	Line 611 \| Line 795 \| namespace oopse {
795		"\tsetting a dielectric constant!\n");
796		painCave.isFatal = 1;
797		simError();
798	<	}
615	<
616	<	} else {
617	<	fInfo_.dielect = 0.0;
798	>	}
799		}
800
801		}
#	Line 633 \| Line 814 \| namespace oopse {
814		}
815
816		//calculate mass ratio of cutoff group
817	<	std::vector<double> mfact;
817	>	std::vector<RealType> mfact;
818		SimInfo::MoleculeIterator mi;
819		Molecule* mol;
820		Molecule::CutoffGroupIterator ci;
821		CutoffGroup* cg;
822		Molecule::AtomIterator ai;
823		Atom* atom;
824	<	double totalMass;
824	>	RealType totalMass;
825
826		//to avoid memory reallocation, reserve enough space for mfact
827		mfact.reserve(getNCutoffGroups());
#	Line 650 \| Line 831 \| namespace oopse {
831
832		totalMass = cg->getMass();
833		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
834	<	mfact.push_back(atom->getMass()/totalMass);
834	>	// Check for massless groups - set mfact to 1 if true
835	>	if (totalMass != 0)
836	>	mfact.push_back(atom->getMass()/totalMass);
837	>	else
838	>	mfact.push_back( 1.0 );
839		}
840
841		}
#	Line 759 \| Line 944 \| namespace oopse {
944
945		#endif
946
947	<	double SimInfo::calcMaxCutoffRadius() {
947	>	void SimInfo::setupCutoff() {
948	>
949	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
950
951	+	// Check the cutoff policy
952	+	int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
953
954	<	std::set<AtomType*> atomTypes;
955	<	std::set<AtomType*>::iterator i;
956	<	std::vector<double> cutoffRadius;
957	<
958	<	//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));
954	>	std::string myPolicy;
955	>	if (forceFieldOptions_.haveCutoffPolicy()){
956	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
957	>	}else if (simParams_->haveCutoffPolicy()) {
958	>	myPolicy = simParams_->getCutoffPolicy();
959		}
960
961	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
962	<	#ifdef IS_MPI
963	<	//pick the max cutoff radius among the processors
964	<	#endif
961	>	if (!myPolicy.empty()){
962	>	toUpper(myPolicy);
963	>	if (myPolicy == "MIX") {
964	>	cp = MIX_CUTOFF_POLICY;
965	>	} else {
966	>	if (myPolicy == "MAX") {
967	>	cp = MAX_CUTOFF_POLICY;
968	>	} else {
969	>	if (myPolicy == "TRADITIONAL") {
970	>	cp = TRADITIONAL_CUTOFF_POLICY;
971	>	} else {
972	>	// throw error
973	>	sprintf( painCave.errMsg,
974	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
975	>	painCave.isFatal = 1;
976	>	simError();
977	>	}
978	>	}
979	>	}
980	>	}
981	>	notifyFortranCutoffPolicy(&cp);
982
983	<	return maxCutoffRadius;
984	<	}
985	<
986	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
987	<
988	<	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
983	>	// Check the Skin Thickness for neighborlists
984	>	RealType skin;
985	>	if (simParams_->haveSkinThickness()) {
986	>	skin = simParams_->getSkinThickness();
987	>	notifyFortranSkinThickness(&skin);
988	>	}
989
990	<	if (!simParams_->haveRcut()){
991	<	sprintf(painCave.errMsg,
992	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
993	<	"\tOOPSE will use a default value of 15.0 angstroms"
994	<	"\tfor the cutoffRadius.\n");
995	<	painCave.isFatal = 0;
990	>	// Check if the cutoff was set explicitly:
991	>	if (simParams_->haveCutoffRadius()) {
992	>	rcut_ = simParams_->getCutoffRadius();
993	>	if (simParams_->haveSwitchingRadius()) {
994	>	rsw_ = simParams_->getSwitchingRadius();
995	>	} else {
996	>	if (fInfo_.SIM_uses_Charges \|
997	>	fInfo_.SIM_uses_Dipoles \|
998	>	fInfo_.SIM_uses_RF) {
999	>
1000	>	rsw_ = 0.85 * rcut_;
1001	>	sprintf(painCave.errMsg,
1002	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1003	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1004	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1005	>	painCave.isFatal = 0;
1006		simError();
1007	<	rcut = 15.0;
1008	<	} else{
1009	<	rcut = simParams_->getRcut();
1007	>	} else {
1008	>	rsw_ = rcut_;
1009	>	sprintf(painCave.errMsg,
1010	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1011	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
1012	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1013	>	painCave.isFatal = 0;
1014	>	simError();
1015	>	}
1016		}
1017	<
1018	<	if (!simParams_->haveRsw()){
1019	<	sprintf(painCave.errMsg,
1020	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1021	<	"\tOOPSE will use a default value of\n"
1022	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
1023	<	painCave.isFatal = 0;
1017	>
1018	>	notifyFortranCutoffs(&rcut_, &rsw_);
1019	>
1020	>	} else {
1021	>
1022	>	// For electrostatic atoms, we'll assume a large safe value:
1023	>	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
1024	>	sprintf(painCave.errMsg,
1025	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1026	>	"\tOOPSE will use a default value of 15.0 angstroms"
1027	>	"\tfor the cutoffRadius.\n");
1028	>	painCave.isFatal = 0;
1029		simError();
1030	<	rsw = 0.95 * rcut;
1031	<	} else{
1032	<	rsw = simParams_->getRsw();
1030	>	rcut_ = 15.0;
1031	>
1032	>	if (simParams_->haveElectrostaticSummationMethod()) {
1033	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1034	>	toUpper(myMethod);
1035	>	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
1036	>	if (simParams_->haveSwitchingRadius()){
1037	>	sprintf(painCave.errMsg,
1038	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1039	>	"\teven though the electrostaticSummationMethod was\n"
1040	>	"\tset to %s\n", myMethod.c_str());
1041	>	painCave.isFatal = 1;
1042	>	simError();
1043	>	}
1044	>	}
1045	>	}
1046	>
1047	>	if (simParams_->haveSwitchingRadius()){
1048	>	rsw_ = simParams_->getSwitchingRadius();
1049	>	} else {
1050	>	sprintf(painCave.errMsg,
1051	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1052	>	"\tOOPSE will use a default value of\n"
1053	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1054	>	painCave.isFatal = 0;
1055	>	simError();
1056	>	rsw_ = 0.85 * rcut_;
1057	>	}
1058	>	notifyFortranCutoffs(&rcut_, &rsw_);
1059	>	} else {
1060	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1061	>	// We'll punt and let fortran figure out the cutoffs later.
1062	>
1063	>	notifyFortranYouAreOnYourOwn();
1064	>
1065		}
1066	+	}
1067	+	}
1068
1069	<	} else {
1070	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
1071	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
1072	<
1073	<	if (simParams_->haveRcut()) {
1074	<	rcut = simParams_->getRcut();
1069	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1070	>
1071	>	int errorOut;
1072	>	int esm = NONE;
1073	>	int sm = UNDAMPED;
1074	>	RealType alphaVal;
1075	>	RealType dielectric;
1076	>
1077	>	errorOut = isError;
1078	>	alphaVal = simParams_->getDampingAlpha();
1079	>	dielectric = simParams_->getDielectric();
1080	>
1081	>	if (simParams_->haveElectrostaticSummationMethod()) {
1082	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1083	>	toUpper(myMethod);
1084	>	if (myMethod == "NONE") {
1085	>	esm = NONE;
1086		} else {
1087	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
1088	<	rcut = calcMaxCutoffRadius();
1087	>	if (myMethod == "SWITCHING_FUNCTION") {
1088	>	esm = SWITCHING_FUNCTION;
1089	>	} else {
1090	>	if (myMethod == "SHIFTED_POTENTIAL") {
1091	>	esm = SHIFTED_POTENTIAL;
1092	>	} else {
1093	>	if (myMethod == "SHIFTED_FORCE") {
1094	>	esm = SHIFTED_FORCE;
1095	>	} else {
1096	>	if (myMethod == "REACTION_FIELD") {
1097	>	esm = REACTION_FIELD;
1098	>	} else {
1099	>	// throw error
1100	>	sprintf( painCave.errMsg,
1101	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1102	>	"\t(Input file specified %s .)\n"
1103	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1104	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1105	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1106	>	painCave.isFatal = 1;
1107	>	simError();
1108	>	}
1109	>	}
1110	>	}
1111	>	}
1112		}
1113	<
1114	<	if (simParams_->haveRsw()) {
1115	<	rsw = simParams_->getRsw();
1113	>	}
1114	>
1115	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1116	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1117	>	toUpper(myScreen);
1118	>	if (myScreen == "UNDAMPED") {
1119	>	sm = UNDAMPED;
1120		} else {
1121	<	rsw = rcut;
1121	>	if (myScreen == "DAMPED") {
1122	>	sm = DAMPED;
1123	>	if (!simParams_->haveDampingAlpha()) {
1124	>	//throw error
1125	>	sprintf( painCave.errMsg,
1126	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1127	>	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1128	>	painCave.isFatal = 0;
1129	>	simError();
1130	>	}
1131	>	} else {
1132	>	// throw error
1133	>	sprintf( painCave.errMsg,
1134	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1135	>	"\t(Input file specified %s .)\n"
1136	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1137	>	"or \"damped\".\n", myScreen.c_str() );
1138	>	painCave.isFatal = 1;
1139	>	simError();
1140	>	}
1141		}
1142	+	}
1143
1144	+	// let's pass some summation method variables to fortran
1145	+	setElectrostaticSummationMethod( &esm );
1146	+	setFortranElectrostaticMethod( &esm );
1147	+	setScreeningMethod( &sm );
1148	+	setDampingAlpha( &alphaVal );
1149	+	setReactionFieldDielectric( &dielectric );
1150	+	initFortranFF( &errorOut );
1151	+	}
1152	+
1153	+	void SimInfo::setupSwitchingFunction() {
1154	+	int ft = CUBIC;
1155	+
1156	+	if (simParams_->haveSwitchingFunctionType()) {
1157	+	std::string funcType = simParams_->getSwitchingFunctionType();
1158	+	toUpper(funcType);
1159	+	if (funcType == "CUBIC") {
1160	+	ft = CUBIC;
1161	+	} else {
1162	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1163	+	ft = FIFTH_ORDER_POLY;
1164	+	} else {
1165	+	// throw error
1166	+	sprintf( painCave.errMsg,
1167	+	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1168	+	painCave.isFatal = 1;
1169	+	simError();
1170	+	}
1171	+	}
1172		}
1173	+
1174	+	// send switching function notification to switcheroo
1175	+	setFunctionType(&ft);
1176	+
1177		}
1178
1179	<	void SimInfo::setupCutoff() {
834	<	getCutoff(rcut_, rsw_);
835	<	double rnblist = rcut_ + 1; // skin of neighbor list
1179	>	void SimInfo::setupAccumulateBoxDipole() {
1180
1181	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1182	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
1181	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1182	>	if ( simParams_->haveAccumulateBoxDipole() )
1183	>	if ( simParams_->getAccumulateBoxDipole() ) {
1184	>	setAccumulateBoxDipole();
1185	>	calcBoxDipole_ = true;
1186	>	}
1187	>
1188		}
1189
1190		void SimInfo::addProperty(GenericData* genData) {
#	Line 894 \| Line 1243 \| namespace oopse {
1243		Molecule* mol;
1244
1245		Vector3d comVel(0.0);
1246	<	double totalMass = 0.0;
1246	>	RealType totalMass = 0.0;
1247
1248
1249		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1250	<	double mass = mol->getMass();
1250	>	RealType mass = mol->getMass();
1251		totalMass += mass;
1252		comVel += mass * mol->getComVel();
1253		}
1254
1255		#ifdef IS_MPI
1256	<	double tmpMass = totalMass;
1256	>	RealType tmpMass = totalMass;
1257		Vector3d tmpComVel(comVel);
1258	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1259	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1258	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1259	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1260		#endif
1261
1262		comVel /= totalMass;
#	Line 920 \| Line 1269 \| namespace oopse {
1269		Molecule* mol;
1270
1271		Vector3d com(0.0);
1272	<	double totalMass = 0.0;
1272	>	RealType totalMass = 0.0;
1273
1274		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1275	<	double mass = mol->getMass();
1275	>	RealType mass = mol->getMass();
1276		totalMass += mass;
1277		com += mass * mol->getCom();
1278		}
1279
1280		#ifdef IS_MPI
1281	<	double tmpMass = totalMass;
1281	>	RealType tmpMass = totalMass;
1282		Vector3d tmpCom(com);
1283	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1284	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1283	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1284	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1285		#endif
1286
1287		com /= totalMass;
#	Line 945 \| Line 1294 \| namespace oopse {
1294
1295		return o;
1296		}
1297	+
1298	+
1299	+	/*
1300	+	Returns center of mass and center of mass velocity in one function call.
1301	+	*/
1302	+
1303	+	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1304	+	SimInfo::MoleculeIterator i;
1305	+	Molecule* mol;
1306	+
1307	+
1308	+	RealType totalMass = 0.0;
1309	+
1310
1311	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1312	+	RealType mass = mol->getMass();
1313	+	totalMass += mass;
1314	+	com += mass * mol->getCom();
1315	+	comVel += mass * mol->getComVel();
1316	+	}
1317	+
1318	+	#ifdef IS_MPI
1319	+	RealType tmpMass = totalMass;
1320	+	Vector3d tmpCom(com);
1321	+	Vector3d tmpComVel(comVel);
1322	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1323	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1324	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1325	+	#endif
1326	+
1327	+	com /= totalMass;
1328	+	comVel /= totalMass;
1329	+	}
1330	+
1331	+	/*
1332	+	Return intertia tensor for entire system and angular momentum Vector.
1333	+
1334	+
1335	+	[ Ixx -Ixy -Ixz ]
1336	+	J =\| -Iyx Iyy -Iyz \|
1337	+	[ -Izx -Iyz Izz ]
1338	+	*/
1339	+
1340	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1341	+
1342	+
1343	+	RealType xx = 0.0;
1344	+	RealType yy = 0.0;
1345	+	RealType zz = 0.0;
1346	+	RealType xy = 0.0;
1347	+	RealType xz = 0.0;
1348	+	RealType yz = 0.0;
1349	+	Vector3d com(0.0);
1350	+	Vector3d comVel(0.0);
1351	+
1352	+	getComAll(com, comVel);
1353	+
1354	+	SimInfo::MoleculeIterator i;
1355	+	Molecule* mol;
1356	+
1357	+	Vector3d thisq(0.0);
1358	+	Vector3d thisv(0.0);
1359	+
1360	+	RealType thisMass = 0.0;
1361	+
1362	+
1363	+
1364	+
1365	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1366	+
1367	+	thisq = mol->getCom()-com;
1368	+	thisv = mol->getComVel()-comVel;
1369	+	thisMass = mol->getMass();
1370	+	// Compute moment of intertia coefficients.
1371	+	xx += thisq[0]thisq[0]thisMass;
1372	+	yy += thisq[1]thisq[1]thisMass;
1373	+	zz += thisq[2]thisq[2]thisMass;
1374	+
1375	+	// compute products of intertia
1376	+	xy += thisq[0]thisq[1]thisMass;
1377	+	xz += thisq[0]thisq[2]thisMass;
1378	+	yz += thisq[1]thisq[2]thisMass;
1379	+
1380	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1381	+
1382	+	}
1383	+
1384	+
1385	+	inertiaTensor(0,0) = yy + zz;
1386	+	inertiaTensor(0,1) = -xy;
1387	+	inertiaTensor(0,2) = -xz;
1388	+	inertiaTensor(1,0) = -xy;
1389	+	inertiaTensor(1,1) = xx + zz;
1390	+	inertiaTensor(1,2) = -yz;
1391	+	inertiaTensor(2,0) = -xz;
1392	+	inertiaTensor(2,1) = -yz;
1393	+	inertiaTensor(2,2) = xx + yy;
1394	+
1395	+	#ifdef IS_MPI
1396	+	Mat3x3d tmpI(inertiaTensor);
1397	+	Vector3d tmpAngMom;
1398	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1399	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1400	+	#endif
1401	+
1402	+	return;
1403	+	}
1404	+
1405	+	//Returns the angular momentum of the system
1406	+	Vector3d SimInfo::getAngularMomentum(){
1407	+
1408	+	Vector3d com(0.0);
1409	+	Vector3d comVel(0.0);
1410	+	Vector3d angularMomentum(0.0);
1411	+
1412	+	getComAll(com,comVel);
1413	+
1414	+	SimInfo::MoleculeIterator i;
1415	+	Molecule* mol;
1416	+
1417	+	Vector3d thisr(0.0);
1418	+	Vector3d thisp(0.0);
1419	+
1420	+	RealType thisMass;
1421	+
1422	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1423	+	thisMass = mol->getMass();
1424	+	thisr = mol->getCom()-com;
1425	+	thisp = (mol->getComVel()-comVel)*thisMass;
1426	+
1427	+	angularMomentum += cross( thisr, thisp );
1428	+
1429	+	}
1430	+
1431	+	#ifdef IS_MPI
1432	+	Vector3d tmpAngMom;
1433	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1434	+	#endif
1435	+
1436	+	return angularMomentum;
1437	+	}
1438	+
1439	+
1440		}//end namespace oopse
1441

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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 998 by chrisfen, Mon Jul 3 13:18:43 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 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC