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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 555 by chuckv, Mon May 30 14:01:52 2005 UTC vs.
Revision 853 by chrisfen, Thu Jan 12 16:47:25 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),
82	>	return result;
83	>	}
84	>
85	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
86	>	forceField_(ff), simParams_(simParams),
87		ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
88		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
89		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
#	Line 75 \| Line 91 \| namespace oopse {
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 335 \| Line 352 \| namespace oopse {
352		int b;
353		int c;
354		int d;
355	+
356	+	std::map<int, std::set<int> > atomGroups;
357	+
358	+	Molecule::RigidBodyIterator rbIter;
359	+	RigidBody* rb;
360	+	Molecule::IntegrableObjectIterator ii;
361	+	StuntDouble* integrableObject;
362
363	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
364	+	integrableObject = mol->nextIntegrableObject(ii)) {
365	+
366	+	if (integrableObject->isRigidBody()) {
367	+	rb = static_cast<RigidBody*>(integrableObject);
368	+	std::vector<Atom*> atoms = rb->getAtoms();
369	+	std::set<int> rigidAtoms;
370	+	for (int i = 0; i < atoms.size(); ++i) {
371	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
372	+	}
373	+	for (int i = 0; i < atoms.size(); ++i) {
374	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
375	+	}
376	+	} else {
377	+	std::set<int> oneAtomSet;
378	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
379	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
380	+	}
381	+	}
382	+
383	+
384	+
385		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
386		a = bond->getAtomA()->getGlobalIndex();
387		b = bond->getAtomB()->getGlobalIndex();
#	Line 346 \| Line 392 \| namespace oopse {
392		a = bend->getAtomA()->getGlobalIndex();
393		b = bend->getAtomB()->getGlobalIndex();
394		c = bend->getAtomC()->getGlobalIndex();
395	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
396	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
397	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
398
399	<	exclude_.addPair(a, b);
400	<	exclude_.addPair(a, c);
401	<	exclude_.addPair(b, c);
399	>	exclude_.addPairs(rigidSetA, rigidSetB);
400	>	exclude_.addPairs(rigidSetA, rigidSetC);
401	>	exclude_.addPairs(rigidSetB, rigidSetC);
402	>
403	>	//exclude_.addPair(a, b);
404	>	//exclude_.addPair(a, c);
405	>	//exclude_.addPair(b, c);
406		}
407
408		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
#	Line 357 \| Line 410 \| namespace oopse {
410		b = torsion->getAtomB()->getGlobalIndex();
411		c = torsion->getAtomC()->getGlobalIndex();
412		d = torsion->getAtomD()->getGlobalIndex();
413	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
414	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
415	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
416	+	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
417
418	+	exclude_.addPairs(rigidSetA, rigidSetB);
419	+	exclude_.addPairs(rigidSetA, rigidSetC);
420	+	exclude_.addPairs(rigidSetA, rigidSetD);
421	+	exclude_.addPairs(rigidSetB, rigidSetC);
422	+	exclude_.addPairs(rigidSetB, rigidSetD);
423	+	exclude_.addPairs(rigidSetC, rigidSetD);
424	+
425	+	/*
426	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
427	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
428	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
429	+	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
430	+	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
431	+	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
432	+
433	+
434		exclude_.addPair(a, b);
435		exclude_.addPair(a, c);
436		exclude_.addPair(a, d);
437		exclude_.addPair(b, c);
438		exclude_.addPair(b, d);
439		exclude_.addPair(c, d);
440	+	*/
441		}
442
369	–	Molecule::RigidBodyIterator rbIter;
370	–	RigidBody* rb;
443		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
444		std::vector<Atom*> atoms = rb->getAtoms();
445		for (int i = 0; i < atoms.size() -1 ; ++i) {
#	Line 392 \| Line 464 \| namespace oopse {
464		int b;
465		int c;
466		int d;
467	+
468	+	std::map<int, std::set<int> > atomGroups;
469	+
470	+	Molecule::RigidBodyIterator rbIter;
471	+	RigidBody* rb;
472	+	Molecule::IntegrableObjectIterator ii;
473	+	StuntDouble* integrableObject;
474
475	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
476	+	integrableObject = mol->nextIntegrableObject(ii)) {
477	+
478	+	if (integrableObject->isRigidBody()) {
479	+	rb = static_cast<RigidBody*>(integrableObject);
480	+	std::vector<Atom*> atoms = rb->getAtoms();
481	+	std::set<int> rigidAtoms;
482	+	for (int i = 0; i < atoms.size(); ++i) {
483	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
484	+	}
485	+	for (int i = 0; i < atoms.size(); ++i) {
486	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
487	+	}
488	+	} else {
489	+	std::set<int> oneAtomSet;
490	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
491	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
492	+	}
493	+	}
494	+
495	+
496		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
497		a = bond->getAtomA()->getGlobalIndex();
498		b = bond->getAtomB()->getGlobalIndex();
#	Line 404 \| Line 504 \| namespace oopse {
504		b = bend->getAtomB()->getGlobalIndex();
505		c = bend->getAtomC()->getGlobalIndex();
506
507	<	exclude_.removePair(a, b);
508	<	exclude_.removePair(a, c);
509	<	exclude_.removePair(b, c);
507	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
508	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
509	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
510	>
511	>	exclude_.removePairs(rigidSetA, rigidSetB);
512	>	exclude_.removePairs(rigidSetA, rigidSetC);
513	>	exclude_.removePairs(rigidSetB, rigidSetC);
514	>
515	>	//exclude_.removePair(a, b);
516	>	//exclude_.removePair(a, c);
517	>	//exclude_.removePair(b, c);
518		}
519
520		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
#	Line 415 \| Line 523 \| namespace oopse {
523		c = torsion->getAtomC()->getGlobalIndex();
524		d = torsion->getAtomD()->getGlobalIndex();
525
526	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
527	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
528	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
529	+	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
530	+
531	+	exclude_.removePairs(rigidSetA, rigidSetB);
532	+	exclude_.removePairs(rigidSetA, rigidSetC);
533	+	exclude_.removePairs(rigidSetA, rigidSetD);
534	+	exclude_.removePairs(rigidSetB, rigidSetC);
535	+	exclude_.removePairs(rigidSetB, rigidSetD);
536	+	exclude_.removePairs(rigidSetC, rigidSetD);
537	+
538	+	/*
539	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
540	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
541	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
542	+	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
543	+	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
544	+	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
545	+
546	+
547		exclude_.removePair(a, b);
548		exclude_.removePair(a, c);
549		exclude_.removePair(a, d);
550		exclude_.removePair(b, c);
551		exclude_.removePair(b, d);
552		exclude_.removePair(c, d);
553	+	*/
554		}
555
426	–	Molecule::RigidBodyIterator rbIter;
427	–	RigidBody* rb;
556		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
557		std::vector<Atom*> atoms = rb->getAtoms();
558		for (int i = 0; i < atoms.size() -1 ; ++i) {
#	Line 462 \| Line 590 \| namespace oopse {
590		//setup fortran force field
591		/** @deprecate */
592		int isError = 0;
593	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
593	>
594	>	setupElectrostaticSummationMethod( isError );
595	>	setupSwitchingFunction();
596	>
597		if(isError){
598		sprintf( painCave.errMsg,
599		"ForceField error: There was an error initializing the forceField in fortran.\n" );
#	Line 506 \| Line 637 \| namespace oopse {
637		int useLennardJones = 0;
638		int useElectrostatic = 0;
639		int useEAM = 0;
640	+	int useSC = 0;
641		int useCharge = 0;
642		int useDirectional = 0;
643		int useDipole = 0;
#	Line 517 \| Line 649 \| namespace oopse {
649		int useDirectionalAtom = 0;
650		int useElectrostatics = 0;
651		//usePBC and useRF are from simParams
652	<	int usePBC = simParams_->getPBC();
653	<	int useRF = simParams_->getUseRF();
652	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
653	>	int useRF;
654	>	int useSF;
655	>	std::string myMethod;
656
657	+	// set the useRF logical
658	+	useRF = 0;
659	+	useSF = 0;
660	+
661	+
662	+	if (simParams_->haveElectrostaticSummationMethod()) {
663	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
664	+	toUpper(myMethod);
665	+	if (myMethod == "REACTION_FIELD") {
666	+	useRF=1;
667	+	} else {
668	+	if (myMethod == "SHIFTED_FORCE") {
669	+	useSF = 1;
670	+	}
671	+	}
672	+	}
673	+
674		//loop over all of the atom types
675		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
676		useLennardJones \|= (*i)->isLennardJones();
677		useElectrostatic \|= (*i)->isElectrostatic();
678		useEAM \|= (*i)->isEAM();
679	+	useSC \|= (*i)->isSC();
680		useCharge \|= (*i)->isCharge();
681		useDirectional \|= (*i)->isDirectional();
682		useDipole \|= (*i)->isDipole();
#	Line 575 \| Line 727 \| namespace oopse {
727		temp = useEAM;
728		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
729
730	+	temp = useSC;
731	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
732	+
733		temp = useShape;
734		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
735
#	Line 583 \| Line 738 \| namespace oopse {
738
739		temp = useRF;
740		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
741	<
741	>
742	>	temp = useSF;
743	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
744	>
745		#endif
746
747		fInfo_.SIM_uses_PBC = usePBC;
#	Line 596 \| Line 754 \| namespace oopse {
754		fInfo_.SIM_uses_StickyPower = useStickyPower;
755		fInfo_.SIM_uses_GayBerne = useGayBerne;
756		fInfo_.SIM_uses_EAM = useEAM;
757	+	fInfo_.SIM_uses_SC = useSC;
758		fInfo_.SIM_uses_Shapes = useShape;
759		fInfo_.SIM_uses_FLARB = useFLARB;
760		fInfo_.SIM_uses_RF = useRF;
761	+	fInfo_.SIM_uses_SF = useSF;
762
763	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
764	<
763	>	if( myMethod == "REACTION_FIELD") {
764	>
765		if (simParams_->haveDielectric()) {
766		fInfo_.dielect = simParams_->getDielectric();
767		} else {
#	Line 611 \| Line 771 \| namespace oopse {
771		"\tsetting a dielectric constant!\n");
772		painCave.isFatal = 1;
773		simError();
774	<	}
615	<
616	<	} else {
617	<	fInfo_.dielect = 0.0;
774	>	}
775		}
776
777		}
#	Line 650 \| Line 807 \| namespace oopse {
807
808		totalMass = cg->getMass();
809		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
810	<	mfact.push_back(atom->getMass()/totalMass);
810	>	// Check for massless groups - set mfact to 1 if true
811	>	if (totalMass != 0)
812	>	mfact.push_back(atom->getMass()/totalMass);
813	>	else
814	>	mfact.push_back( 1.0 );
815		}
816
817		}
#	Line 759 \| Line 920 \| namespace oopse {
920
921		#endif
922
923	<	double SimInfo::calcMaxCutoffRadius() {
923	>	void SimInfo::setupCutoff() {
924	>
925	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
926
927	+	// Check the cutoff policy
928	+	int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
929
930	<	std::set<AtomType*> atomTypes;
931	<	std::set<AtomType*>::iterator i;
932	<	std::vector<double> cutoffRadius;
933	<
934	<	//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));
930	>	std::string myPolicy;
931	>	if (forceFieldOptions_.haveCutoffPolicy()){
932	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
933	>	}else if (simParams_->haveCutoffPolicy()) {
934	>	myPolicy = simParams_->getCutoffPolicy();
935		}
936
937	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
938	<	#ifdef IS_MPI
939	<	//pick the max cutoff radius among the processors
940	<	#endif
937	>	if (!myPolicy.empty()){
938	>	toUpper(myPolicy);
939	>	if (myPolicy == "MIX") {
940	>	cp = MIX_CUTOFF_POLICY;
941	>	} else {
942	>	if (myPolicy == "MAX") {
943	>	cp = MAX_CUTOFF_POLICY;
944	>	} else {
945	>	if (myPolicy == "TRADITIONAL") {
946	>	cp = TRADITIONAL_CUTOFF_POLICY;
947	>	} else {
948	>	// throw error
949	>	sprintf( painCave.errMsg,
950	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
951	>	painCave.isFatal = 1;
952	>	simError();
953	>	}
954	>	}
955	>	}
956	>	}
957	>	notifyFortranCutoffPolicy(&cp);
958
959	<	return maxCutoffRadius;
960	<	}
961	<
962	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
963	<
964	<	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
959	>	// Check the Skin Thickness for neighborlists
960	>	double skin;
961	>	if (simParams_->haveSkinThickness()) {
962	>	skin = simParams_->getSkinThickness();
963	>	notifyFortranSkinThickness(&skin);
964	>	}
965
966	<	if (!simParams_->haveRcut()){
967	<	sprintf(painCave.errMsg,
966	>	// Check if the cutoff was set explicitly:
967	>	if (simParams_->haveCutoffRadius()) {
968	>	rcut_ = simParams_->getCutoffRadius();
969	>	if (simParams_->haveSwitchingRadius()) {
970	>	rsw_ = simParams_->getSwitchingRadius();
971	>	} else {
972	>	rsw_ = rcut_;
973	>	}
974	>	notifyFortranCutoffs(&rcut_, &rsw_);
975	>
976	>	} else {
977	>
978	>	// For electrostatic atoms, we'll assume a large safe value:
979	>	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
980	>	sprintf(painCave.errMsg,
981		"SimCreator Warning: No value was set for the cutoffRadius.\n"
982		"\tOOPSE will use a default value of 15.0 angstroms"
983		"\tfor the cutoffRadius.\n");
984	<	painCave.isFatal = 0;
984	>	painCave.isFatal = 0;
985		simError();
986	<	rcut = 15.0;
987	<	} else{
988	<	rcut = simParams_->getRcut();
989	<	}
986	>	rcut_ = 15.0;
987	>
988	>	if (simParams_->haveElectrostaticSummationMethod()) {
989	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
990	>	toUpper(myMethod);
991	>	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
992	>	if (simParams_->haveSwitchingRadius()){
993	>	sprintf(painCave.errMsg,
994	>	"SimInfo Warning: A value was set for the switchingRadius\n"
995	>	"\teven though the electrostaticSummationMethod was\n"
996	>	"\tset to %s\n", myMethod.c_str());
997	>	painCave.isFatal = 1;
998	>	simError();
999	>	}
1000	>	}
1001	>	}
1002	>
1003	>	if (simParams_->haveSwitchingRadius()){
1004	>	rsw_ = simParams_->getSwitchingRadius();
1005	>	} else {
1006	>	sprintf(painCave.errMsg,
1007	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1008	>	"\tOOPSE will use a default value of\n"
1009	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1010	>	painCave.isFatal = 0;
1011	>	simError();
1012	>	rsw_ = 0.85 * rcut_;
1013	>	}
1014	>	notifyFortranCutoffs(&rcut_, &rsw_);
1015	>	} else {
1016	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1017	>	// We'll punt and let fortran figure out the cutoffs later.
1018	>
1019	>	notifyFortranYouAreOnYourOwn();
1020
801	–	if (!simParams_->haveRsw()){
802	–	sprintf(painCave.errMsg,
803	–	"SimCreator Warning: No value was set for switchingRadius.\n"
804	–	"\tOOPSE will use a default value of\n"
805	–	"\t0.95 * cutoffRadius for the switchingRadius\n");
806	–	painCave.isFatal = 0;
807	–	simError();
808	–	rsw = 0.95 * rcut;
809	–	} else{
810	–	rsw = simParams_->getRsw();
1021		}
1022	+	}
1023	+	}
1024
1025	<	} else {
1026	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
1027	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
1028	<
1029	<	if (simParams_->haveRcut()) {
1030	<	rcut = simParams_->getRcut();
1031	<	} else {
1032	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
1033	<	rcut = calcMaxCutoffRadius();
1034	<	}
1035	<
1036	<	if (simParams_->haveRsw()) {
1037	<	rsw = simParams_->getRsw();
1038	<	} else {
1039	<	rsw = rcut;
1025	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1026	>
1027	>	int errorOut;
1028	>	int esm = NONE;
1029	>	int sm = UNDAMPED;
1030	>	double alphaVal;
1031	>	double dielectric;
1032	>
1033	>	errorOut = isError;
1034	>	alphaVal = simParams_->getDampingAlpha();
1035	>	dielectric = simParams_->getDielectric();
1036	>
1037	>	if (simParams_->haveElectrostaticSummationMethod()) {
1038	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1039	>	toUpper(myMethod);
1040	>	if (myMethod == "NONE") {
1041	>	esm = NONE;
1042	>	} else {
1043	>	if (myMethod == "SWITCHING_FUNCTION") {
1044	>	esm = SWITCHING_FUNCTION;
1045	>	} else {
1046	>	if (myMethod == "SHIFTED_POTENTIAL") {
1047	>	esm = SHIFTED_POTENTIAL;
1048	>	} else {
1049	>	if (myMethod == "SHIFTED_FORCE") {
1050	>	esm = SHIFTED_FORCE;
1051	>	} else {
1052	>	if (myMethod == "REACTION_FIELD") {
1053	>	esm = REACTION_FIELD;
1054	>	} else {
1055	>	// throw error
1056	>	sprintf( painCave.errMsg,
1057	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1058	>	"\t(Input file specified %s .)\n"
1059	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1060	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1061	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1062	>	painCave.isFatal = 1;
1063	>	simError();
1064	>	}
1065	>	}
1066	>	}
1067	>	}
1068		}
1069	+	}
1070
1071	+	if (simParams_->haveElectrostaticScreeningMethod()) {
1072	+	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1073	+	toUpper(myScreen);
1074	+	if (myScreen == "UNDAMPED") {
1075	+	sm = UNDAMPED;
1076	+	} else {
1077	+	if (myScreen == "DAMPED") {
1078	+	sm = DAMPED;
1079	+	if (!simParams_->haveDampingAlpha()) {
1080	+	//throw error
1081	+	sprintf( painCave.errMsg,
1082	+	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1083	+	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1084	+	painCave.isFatal = 0;
1085	+	simError();
1086	+	}
1087	+	} else {
1088	+	// throw error
1089	+	sprintf( painCave.errMsg,
1090	+	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1091	+	"\t(Input file specified %s .)\n"
1092	+	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1093	+	"or \"damped\".\n", myScreen.c_str() );
1094	+	painCave.isFatal = 1;
1095	+	simError();
1096	+	}
1097	+	}
1098		}
1099	+
1100	+	// let's pass some summation method variables to fortran
1101	+	setElectrostaticSummationMethod( &esm );
1102	+	setFortranElectrostaticMethod( &esm );
1103	+	setScreeningMethod( &sm );
1104	+	setDampingAlpha( &alphaVal );
1105	+	setReactionFieldDielectric( &dielectric );
1106	+	initFortranFF( &errorOut );
1107		}
1108
1109	<	void SimInfo::setupCutoff() {
1110	<	getCutoff(rcut_, rsw_);
835	<	double rnblist = rcut_ + 1; // skin of neighbor list
1109	>	void SimInfo::setupSwitchingFunction() {
1110	>	int ft = CUBIC;
1111
1112	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1113	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
1112	>	if (simParams_->haveSwitchingFunctionType()) {
1113	>	std::string funcType = simParams_->getSwitchingFunctionType();
1114	>	toUpper(funcType);
1115	>	if (funcType == "CUBIC") {
1116	>	ft = CUBIC;
1117	>	} else {
1118	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1119	>	ft = FIFTH_ORDER_POLY;
1120	>	} else {
1121	>	// throw error
1122	>	sprintf( painCave.errMsg,
1123	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1124	>	painCave.isFatal = 1;
1125	>	simError();
1126	>	}
1127	>	}
1128	>	}
1129	>
1130	>	// send switching function notification to switcheroo
1131	>	setFunctionType(&ft);
1132	>
1133		}
1134
1135		void SimInfo::addProperty(GenericData* genData) {
#	Line 981 \| Line 1275 \| namespace oopse {
1275
1276		/*
1277		Return intertia tensor for entire system and angular momentum Vector.
1278	+
1279	+
1280	+	[ Ixx -Ixy -Ixz ]
1281	+	J =\| -Iyx Iyy -Iyz \|
1282	+	[ -Izx -Iyz Izz ]
1283		*/
1284
1285		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
#	Line 1032 \| Line 1331 \| namespace oopse {
1331		inertiaTensor(0,1) = -xy;
1332		inertiaTensor(0,2) = -xz;
1333		inertiaTensor(1,0) = -xy;
1334	<	inertiaTensor(2,0) = xx + zz;
1334	>	inertiaTensor(1,1) = xx + zz;
1335		inertiaTensor(1,2) = -yz;
1336		inertiaTensor(2,0) = -xz;
1337		inertiaTensor(2,1) = -yz;
#	Line 1060 \| Line 1359 \| namespace oopse {
1359		SimInfo::MoleculeIterator i;
1360		Molecule* mol;
1361
1362	<	Vector3d thisq(0.0);
1363	<	Vector3d thisv(0.0);
1362	>	Vector3d thisr(0.0);
1363	>	Vector3d thisp(0.0);
1364
1365	<	double thisMass = 0.0;
1365	>	double thisMass;
1366
1367		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1368	<	thisq = mol->getCom()-com;
1369	<	thisv = mol->getComVel()-comVel;
1370	<	thisMass = mol->getMass();
1072	<	angularMomentum += cross( thisq, thisv ) * thisMass;
1368	>	thisMass = mol->getMass();
1369	>	thisr = mol->getCom()-com;
1370	>	thisp = (mol->getComVel()-comVel)*thisMass;
1371
1372	+	angularMomentum += cross( thisr, thisp );
1373	+
1374		}
1375
1376		#ifdef IS_MPI

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Comparing trunk/src/brains/SimInfo.cpp (file contents): Revision 555 by chuckv, Mon May 30 14:01:52 2005 UTC vs. Revision 853 by chrisfen, Thu Jan 12 16:47:25 2006 UTC

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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 555 by chuckv, Mon May 30 14:01:52 2005 UTC vs.
Revision 853 by chrisfen, Thu Jan 12 16:47:25 2006 UTC