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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 586 by gezelter, Wed Sep 7 20:46:46 2005 UTC vs.
Revision 878 by chrisfen, Wed Feb 1 20:54:46 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 65 \| 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 76 \| Line 91 \| namespace oopse {
91		nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
92		sman_(NULL), fortranInitialized_(false) {
93
79	–
80	–	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
98	–
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 113 \| 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 122 \| 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 149 \| Line 166 \| namespace oopse {
166		}
167		molecules_.clear();
168
152	–	delete stamps_;
169		delete sman_;
170		delete simParams_;
171		delete forceField_;
#	Line 256 \| 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 336 \| 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 347 \| 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 358 \| 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
370	–	Molecule::RigidBodyIterator rbIter;
371	–	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 393 \| 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 405 \| 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 416 \| 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
427	–	Molecule::RigidBodyIterator rbIter;
428	–	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 463 \| Line 590 \| namespace oopse {
590		//setup fortran force field
591		/** @deprecate */
592		int isError = 0;
593	<	initFortranFF( &fInfo_.SIM_uses_RF, &fInfo_.SIM_uses_UW,
594	<	&fInfo_.SIM_uses_DW, &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 508 \| 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 519 \| 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();
654	<	int useUW = simParams_->getUseUndampedWolf();
655	<	int useDW = simParams_->getUseDampedWolf();
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 579 \| 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 588 \| Line 739 \| namespace oopse {
739		temp = useRF;
740		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
741
742	<	temp = useUW;
743	<	MPI_Allreduce(&temp, &useUW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
742	>	temp = useSF;
743	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
744
594	–	temp = useDW;
595	–	MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
596	–
745		#endif
746
747		fInfo_.SIM_uses_PBC = usePBC;
#	Line 606 \| 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_UW = useUW;
613	<	fInfo_.SIM_uses_DW = useDW;
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 623 \| Line 771 \| namespace oopse {
771		"\tsetting a dielectric constant!\n");
772		painCave.isFatal = 1;
773		simError();
774	<	}
627	<
628	<	} else {
629	<	fInfo_.dielect = 0.0;
774	>	}
775		}
776
777		}
#	Line 662 \| 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 771 \| Line 920 \| namespace oopse {
920
921		#endif
922
923	<	double SimInfo::calcMaxCutoffRadius() {
923	>	void SimInfo::setupCutoff() {
924	>
925	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
926
927	<
928	<	std::set<AtomType*> atomTypes;
778	<	std::set<AtomType*>::iterator i;
779	<	std::vector<double> cutoffRadius;
780	<
781	<	//get the unique atom types
782	<	atomTypes = getUniqueAtomTypes();
927	>	// Check the cutoff policy
928	>	int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
929
930	<	//query the max cutoff radius among these atom types
931	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
932	<	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
791	<	//pick the max cutoff radius among the processors
792	<	#endif
793	<
794	<	return maxCutoffRadius;
795	<	}
796	<
797	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
798	<
799	<	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
800	<
801	<	if (!simParams_->haveRcut()){
802	<	sprintf(painCave.errMsg,
803	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
804	<	"\tOOPSE will use a default value of 15.0 angstroms"
805	<	"\tfor the cutoffRadius.\n");
806	<	painCave.isFatal = 0;
807	<	simError();
808	<	rcut = 15.0;
809	<	} else{
810	<	rcut = simParams_->getRcut();
811	<	}
812	<
813	<	if (!simParams_->haveRsw()){
814	<	sprintf(painCave.errMsg,
815	<	"SimCreator Warning: No value was set for switchingRadius.\n"
816	<	"\tOOPSE will use a default value of\n"
817	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
818	<	painCave.isFatal = 0;
819	<	simError();
820	<	rsw = 0.95 * rcut;
821	<	} else{
822	<	rsw = simParams_->getRsw();
823	<	}
824	<
825	<	} else {
826	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
827	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
828	<
829	<	if (simParams_->haveRcut()) {
830	<	rcut = simParams_->getRcut();
831	<	} else {
832	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
833	<	rcut = calcMaxCutoffRadius();
834	<	}
835	<
836	<	if (simParams_->haveRsw()) {
837	<	rsw = simParams_->getRsw();
838	<	} else {
839	<	rsw = rcut;
840	<	}
841	<
842	<	}
843	<	}
844	<
845	<	void SimInfo::setupCutoff() {
846	<	getCutoff(rcut_, rsw_);
847	<	double rnblist = rcut_ + 1; // skin of neighbor list
848	<
849	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
850	<
851	<	int cp = TRADITIONAL_CUTOFF_POLICY;
852	<	if (simParams_->haveCutoffPolicy()) {
853	<	std::string myPolicy = simParams_->getCutoffPolicy();
937	>	if (!myPolicy.empty()){
938	>	toUpper(myPolicy);
939		if (myPolicy == "MIX") {
940		cp = MIX_CUTOFF_POLICY;
941		} else {
#	Line 868 \| Line 953 \| namespace oopse {
953		}
954		}
955		}
956	+	}
957	+	notifyFortranCutoffPolicy(&cp);
958	+
959	+	// Check the Skin Thickness for neighborlists
960	+	double skin;
961	+	if (simParams_->haveSkinThickness()) {
962	+	skin = simParams_->getSkinThickness();
963	+	notifyFortranSkinThickness(&skin);
964	+	}
965	+
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	+	if (fInfo_.SIM_uses_Charges \|
973	+	fInfo_.SIM_uses_Dipoles \|
974	+	fInfo_.SIM_uses_RF) {
975	+
976	+	rsw_ = 0.85 * rcut_;
977	+	sprintf(painCave.errMsg,
978	+	"SimCreator Warning: No value was set for the switchingRadius.\n"
979	+	"\tOOPSE will use a default value of 85\% of the cutoffRadius"
980	+	"\tswitchingRadius = %f. for this simulation\n", rsw_);
981	+	painCave.isFatal = 0;
982	+	simError();
983	+	} else {
984	+	rsw_ = rcut_;
985	+	sprintf(painCave.errMsg,
986	+	"SimCreator Warning: No value was set for the switchingRadius.\n"
987	+	"\tOOPSE will use the same value as the cutoffRadius.\n"
988	+	"\tswitchingRadius = %f. for this simulation\n", rsw_);
989	+	painCave.isFatal = 0;
990	+	simError();
991	+	}
992	+
993	+	notifyFortranCutoffs(&rcut_, &rsw_);
994	+
995	+	} else {
996	+
997	+	// For electrostatic atoms, we'll assume a large safe value:
998	+	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
999	+	sprintf(painCave.errMsg,
1000	+	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1001	+	"\tOOPSE will use a default value of 15.0 angstroms"
1002	+	"\tfor the cutoffRadius.\n");
1003	+	painCave.isFatal = 0;
1004	+	simError();
1005	+	rcut_ = 15.0;
1006	+
1007	+	if (simParams_->haveElectrostaticSummationMethod()) {
1008	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1009	+	toUpper(myMethod);
1010	+	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
1011	+	if (simParams_->haveSwitchingRadius()){
1012	+	sprintf(painCave.errMsg,
1013	+	"SimInfo Warning: A value was set for the switchingRadius\n"
1014	+	"\teven though the electrostaticSummationMethod was\n"
1015	+	"\tset to %s\n", myMethod.c_str());
1016	+	painCave.isFatal = 1;
1017	+	simError();
1018	+	}
1019	+	}
1020	+	}
1021	+
1022	+	if (simParams_->haveSwitchingRadius()){
1023	+	rsw_ = simParams_->getSwitchingRadius();
1024	+	} else {
1025	+	sprintf(painCave.errMsg,
1026	+	"SimCreator Warning: No value was set for switchingRadius.\n"
1027	+	"\tOOPSE will use a default value of\n"
1028	+	"\t0.85 * cutoffRadius for the switchingRadius\n");
1029	+	painCave.isFatal = 0;
1030	+	simError();
1031	+	rsw_ = 0.85 * rcut_;
1032	+	}
1033	+	notifyFortranCutoffs(&rcut_, &rsw_);
1034	+	} else {
1035	+	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1036	+	// We'll punt and let fortran figure out the cutoffs later.
1037	+
1038	+	notifyFortranYouAreOnYourOwn();
1039	+
1040	+	}
1041		}
1042	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1042	>	}
1043	>
1044	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1045	>
1046	>	int errorOut;
1047	>	int esm = NONE;
1048	>	int sm = UNDAMPED;
1049	>	double alphaVal;
1050	>	double dielectric;
1051	>
1052	>	errorOut = isError;
1053	>	alphaVal = simParams_->getDampingAlpha();
1054	>	dielectric = simParams_->getDielectric();
1055	>
1056	>	if (simParams_->haveElectrostaticSummationMethod()) {
1057	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1058	>	toUpper(myMethod);
1059	>	if (myMethod == "NONE") {
1060	>	esm = NONE;
1061	>	} else {
1062	>	if (myMethod == "SWITCHING_FUNCTION") {
1063	>	esm = SWITCHING_FUNCTION;
1064	>	} else {
1065	>	if (myMethod == "SHIFTED_POTENTIAL") {
1066	>	esm = SHIFTED_POTENTIAL;
1067	>	} else {
1068	>	if (myMethod == "SHIFTED_FORCE") {
1069	>	esm = SHIFTED_FORCE;
1070	>	} else {
1071	>	if (myMethod == "REACTION_FIELD") {
1072	>	esm = REACTION_FIELD;
1073	>	} else {
1074	>	// throw error
1075	>	sprintf( painCave.errMsg,
1076	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1077	>	"\t(Input file specified %s .)\n"
1078	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1079	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1080	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1081	>	painCave.isFatal = 1;
1082	>	simError();
1083	>	}
1084	>	}
1085	>	}
1086	>	}
1087	>	}
1088	>	}
1089	>
1090	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1091	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1092	>	toUpper(myScreen);
1093	>	if (myScreen == "UNDAMPED") {
1094	>	sm = UNDAMPED;
1095	>	} else {
1096	>	if (myScreen == "DAMPED") {
1097	>	sm = DAMPED;
1098	>	if (!simParams_->haveDampingAlpha()) {
1099	>	//throw error
1100	>	sprintf( painCave.errMsg,
1101	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1102	>	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1103	>	painCave.isFatal = 0;
1104	>	simError();
1105	>	}
1106	>	} else {
1107	>	// throw error
1108	>	sprintf( painCave.errMsg,
1109	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1110	>	"\t(Input file specified %s .)\n"
1111	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1112	>	"or \"damped\".\n", myScreen.c_str() );
1113	>	painCave.isFatal = 1;
1114	>	simError();
1115	>	}
1116	>	}
1117	>	}
1118	>
1119	>	// let's pass some summation method variables to fortran
1120	>	setElectrostaticSummationMethod( &esm );
1121	>	setFortranElectrostaticMethod( &esm );
1122	>	setScreeningMethod( &sm );
1123	>	setDampingAlpha( &alphaVal );
1124	>	setReactionFieldDielectric( &dielectric );
1125	>	initFortranFF( &errorOut );
1126		}
1127
1128	+	void SimInfo::setupSwitchingFunction() {
1129	+	int ft = CUBIC;
1130	+
1131	+	if (simParams_->haveSwitchingFunctionType()) {
1132	+	std::string funcType = simParams_->getSwitchingFunctionType();
1133	+	toUpper(funcType);
1134	+	if (funcType == "CUBIC") {
1135	+	ft = CUBIC;
1136	+	} else {
1137	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1138	+	ft = FIFTH_ORDER_POLY;
1139	+	} else {
1140	+	// throw error
1141	+	sprintf( painCave.errMsg,
1142	+	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1143	+	painCave.isFatal = 1;
1144	+	simError();
1145	+	}
1146	+	}
1147	+	}
1148	+
1149	+	// send switching function notification to switcheroo
1150	+	setFunctionType(&ft);
1151	+
1152	+	}
1153	+
1154		void SimInfo::addProperty(GenericData* genData) {
1155		properties_.addProperty(genData);
1156		}

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Comparing trunk/src/brains/SimInfo.cpp (file contents): Revision 586 by gezelter, Wed Sep 7 20:46:46 2005 UTC vs. Revision 878 by chrisfen, Wed Feb 1 20:54:46 2006 UTC

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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 586 by gezelter, Wed Sep 7 20:46:46 2005 UTC vs.
Revision 878 by chrisfen, Wed Feb 1 20:54:46 2006 UTC