[ViewVC] Diff of: group/trunk/OOPSE-2.0/src/brains/SimInfo.cpp

Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 2204 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 2463 by gezelter, Mon Nov 21 22:59:21 2005 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"
#	Line 64 \| Line 70 \| namespace oopse {
70		#endif
71
72		namespace oopse {
73	+	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
74	+	std::map<int, std::set<int> >::iterator i = container.find(index);
75	+	std::set<int> result;
76	+	if (i != container.end()) {
77	+	result = i->second;
78	+	}
79
80	+	return result;
81	+	}
82	+
83		SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
84		ForceField* ff, Globals* simParams) :
85		stamps_(stamps), forceField_(ff), simParams_(simParams),
#	Line 80 \| Line 95 \| namespace oopse {
95		MoleculeStamp* molStamp;
96		int nMolWithSameStamp;
97		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
98	<	int nGroups = 0; //total cutoff groups defined in meta-data file
98	>	int nGroups = 0; //total cutoff groups defined in meta-data file
99		CutoffGroupStamp* cgStamp;
100		RigidBodyStamp* rbStamp;
101		int nRigidAtoms = 0;
#	Line 105 \| Line 120 \| namespace oopse {
120		}
121
122		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
123	+
124		nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
125
126		//calculate atoms in rigid bodies
#	Line 121 \| Line 137 \| namespace oopse {
137
138		}
139
140	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
141	<	//therefore the total number of cutoff groups in the system is equal to
142	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
143	<	//file plus the number of cutoff groups defined in meta-data file
140	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
141	>	//group therefore the total number of cutoff groups in the system is
142	>	//equal to the total number of atoms minus number of atoms belong to
143	>	//cutoff group defined in meta-data file plus the number of cutoff
144	>	//groups defined in meta-data file
145		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
146
147	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
148	<	//therefore the total number of integrable objects in the system is equal to
149	<	//the total number of atoms minus number of atoms belong to rigid body defined in meta-data
150	<	//file plus the number of rigid bodies defined in meta-data file
151	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
152	<
147	>	//every free atom (atom does not belong to rigid bodies) is an
148	>	//integrable object therefore the total number of integrable objects
149	>	//in the system is equal to the total number of atoms minus number of
150	>	//atoms belong to rigid body defined in meta-data file plus the number
151	>	//of rigid bodies defined in meta-data file
152	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
153	>	+ nGlobalRigidBodies_;
154	>
155		nGlobalMols_ = molStampIds_.size();
156
157		#ifdef IS_MPI
#	Line 335 \| Line 354 \| namespace oopse {
354		int b;
355		int c;
356		int d;
357	+
358	+	std::map<int, std::set<int> > atomGroups;
359	+
360	+	Molecule::RigidBodyIterator rbIter;
361	+	RigidBody* rb;
362	+	Molecule::IntegrableObjectIterator ii;
363	+	StuntDouble* integrableObject;
364
365	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
366	+	integrableObject = mol->nextIntegrableObject(ii)) {
367	+
368	+	if (integrableObject->isRigidBody()) {
369	+	rb = static_cast<RigidBody*>(integrableObject);
370	+	std::vector<Atom*> atoms = rb->getAtoms();
371	+	std::set<int> rigidAtoms;
372	+	for (int i = 0; i < atoms.size(); ++i) {
373	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
374	+	}
375	+	for (int i = 0; i < atoms.size(); ++i) {
376	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
377	+	}
378	+	} else {
379	+	std::set<int> oneAtomSet;
380	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
381	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
382	+	}
383	+	}
384	+
385	+
386	+
387		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
388		a = bond->getAtomA()->getGlobalIndex();
389		b = bond->getAtomB()->getGlobalIndex();
#	Line 346 \| Line 394 \| namespace oopse {
394		a = bend->getAtomA()->getGlobalIndex();
395		b = bend->getAtomB()->getGlobalIndex();
396		c = bend->getAtomC()->getGlobalIndex();
397	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
398	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
399	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
400
401	<	exclude_.addPair(a, b);
402	<	exclude_.addPair(a, c);
403	<	exclude_.addPair(b, c);
401	>	exclude_.addPairs(rigidSetA, rigidSetB);
402	>	exclude_.addPairs(rigidSetA, rigidSetC);
403	>	exclude_.addPairs(rigidSetB, rigidSetC);
404	>
405	>	//exclude_.addPair(a, b);
406	>	//exclude_.addPair(a, c);
407	>	//exclude_.addPair(b, c);
408		}
409
410		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
#	Line 357 \| Line 412 \| namespace oopse {
412		b = torsion->getAtomB()->getGlobalIndex();
413		c = torsion->getAtomC()->getGlobalIndex();
414		d = torsion->getAtomD()->getGlobalIndex();
415	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
416	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
417	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
418	+	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
419
420	+	exclude_.addPairs(rigidSetA, rigidSetB);
421	+	exclude_.addPairs(rigidSetA, rigidSetC);
422	+	exclude_.addPairs(rigidSetA, rigidSetD);
423	+	exclude_.addPairs(rigidSetB, rigidSetC);
424	+	exclude_.addPairs(rigidSetB, rigidSetD);
425	+	exclude_.addPairs(rigidSetC, rigidSetD);
426	+
427	+	/*
428	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
429	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
430	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
431	+	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
432	+	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
433	+	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
434	+
435	+
436		exclude_.addPair(a, b);
437		exclude_.addPair(a, c);
438		exclude_.addPair(a, d);
439		exclude_.addPair(b, c);
440		exclude_.addPair(b, d);
441		exclude_.addPair(c, d);
442	+	*/
443		}
444
369	–	Molecule::RigidBodyIterator rbIter;
370	–	RigidBody* rb;
445		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
446		std::vector<Atom*> atoms = rb->getAtoms();
447		for (int i = 0; i < atoms.size() -1 ; ++i) {
#	Line 392 \| Line 466 \| namespace oopse {
466		int b;
467		int c;
468		int d;
469	+
470	+	std::map<int, std::set<int> > atomGroups;
471	+
472	+	Molecule::RigidBodyIterator rbIter;
473	+	RigidBody* rb;
474	+	Molecule::IntegrableObjectIterator ii;
475	+	StuntDouble* integrableObject;
476
477	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
478	+	integrableObject = mol->nextIntegrableObject(ii)) {
479	+
480	+	if (integrableObject->isRigidBody()) {
481	+	rb = static_cast<RigidBody*>(integrableObject);
482	+	std::vector<Atom*> atoms = rb->getAtoms();
483	+	std::set<int> rigidAtoms;
484	+	for (int i = 0; i < atoms.size(); ++i) {
485	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
486	+	}
487	+	for (int i = 0; i < atoms.size(); ++i) {
488	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
489	+	}
490	+	} else {
491	+	std::set<int> oneAtomSet;
492	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
493	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
494	+	}
495	+	}
496	+
497	+
498		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
499		a = bond->getAtomA()->getGlobalIndex();
500		b = bond->getAtomB()->getGlobalIndex();
#	Line 404 \| Line 506 \| namespace oopse {
506		b = bend->getAtomB()->getGlobalIndex();
507		c = bend->getAtomC()->getGlobalIndex();
508
509	<	exclude_.removePair(a, b);
510	<	exclude_.removePair(a, c);
511	<	exclude_.removePair(b, c);
509	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
510	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
511	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
512	>
513	>	exclude_.removePairs(rigidSetA, rigidSetB);
514	>	exclude_.removePairs(rigidSetA, rigidSetC);
515	>	exclude_.removePairs(rigidSetB, rigidSetC);
516	>
517	>	//exclude_.removePair(a, b);
518	>	//exclude_.removePair(a, c);
519	>	//exclude_.removePair(b, c);
520		}
521
522		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
#	Line 415 \| Line 525 \| namespace oopse {
525		c = torsion->getAtomC()->getGlobalIndex();
526		d = torsion->getAtomD()->getGlobalIndex();
527
528	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
529	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
530	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
531	+	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
532	+
533	+	exclude_.removePairs(rigidSetA, rigidSetB);
534	+	exclude_.removePairs(rigidSetA, rigidSetC);
535	+	exclude_.removePairs(rigidSetA, rigidSetD);
536	+	exclude_.removePairs(rigidSetB, rigidSetC);
537	+	exclude_.removePairs(rigidSetB, rigidSetD);
538	+	exclude_.removePairs(rigidSetC, rigidSetD);
539	+
540	+	/*
541	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
542	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
543	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
544	+	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
545	+	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
546	+	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
547	+
548	+
549		exclude_.removePair(a, b);
550		exclude_.removePair(a, c);
551		exclude_.removePair(a, d);
552		exclude_.removePair(b, c);
553		exclude_.removePair(b, d);
554		exclude_.removePair(c, d);
555	+	*/
556		}
557
426	–	Molecule::RigidBodyIterator rbIter;
427	–	RigidBody* rb;
558		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
559		std::vector<Atom*> atoms = rb->getAtoms();
560		for (int i = 0; i < atoms.size() -1 ; ++i) {
#	Line 462 \| Line 592 \| namespace oopse {
592		//setup fortran force field
593		/** @deprecate */
594		int isError = 0;
595	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
595	>
596	>	setupElectrostaticSummationMethod( isError );
597	>	setupSwitchingFunction();
598	>
599		if(isError){
600		sprintf( painCave.errMsg,
601		"ForceField error: There was an error initializing the forceField in fortran.\n" );
#	Line 506 \| Line 639 \| namespace oopse {
639		int useLennardJones = 0;
640		int useElectrostatic = 0;
641		int useEAM = 0;
642	+	int useSC = 0;
643		int useCharge = 0;
644		int useDirectional = 0;
645		int useDipole = 0;
646		int useGayBerne = 0;
647		int useSticky = 0;
648	+	int useStickyPower = 0;
649		int useShape = 0;
650		int useFLARB = 0; //it is not in AtomType yet
651		int useDirectionalAtom = 0;
652		int useElectrostatics = 0;
653		//usePBC and useRF are from simParams
654	<	int usePBC = simParams_->getPBC();
655	<	int useRF = simParams_->getUseRF();
654	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
655	>	int useRF;
656	>	int useSF;
657	>	std::string myMethod;
658	>
659	>	// set the useRF logical
660	>	useRF = 0;
661	>	useSF = 0;
662	>
663	>
664	>	if (simParams_->haveElectrostaticSummationMethod()) {
665	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
666	>	toUpper(myMethod);
667	>	if (myMethod == "REACTION_FIELD") {
668	>	useRF=1;
669	>	} else {
670	>	if (myMethod == "SHIFTED_FORCE") {
671	>	useSF = 1;
672	>	}
673	>	}
674	>	}
675
676		//loop over all of the atom types
677		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
678		useLennardJones \|= (*i)->isLennardJones();
679		useElectrostatic \|= (*i)->isElectrostatic();
680		useEAM \|= (*i)->isEAM();
681	+	useSC \|= (*i)->isSC();
682		useCharge \|= (*i)->isCharge();
683		useDirectional \|= (*i)->isDirectional();
684		useDipole \|= (*i)->isDipole();
685		useGayBerne \|= (*i)->isGayBerne();
686		useSticky \|= (*i)->isSticky();
687	+	useStickyPower \|= (*i)->isStickyPower();
688		useShape \|= (*i)->isShape();
689		}
690
691	<	if (useSticky \|\| useDipole \|\| useGayBerne \|\| useShape) {
691	>	if (useSticky \|\| useStickyPower \|\| useDipole \|\| useGayBerne \|\| useShape) {
692		useDirectionalAtom = 1;
693		}
694
#	Line 564 \| Line 720 \| namespace oopse {
720		temp = useSticky;
721		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
722
723	+	temp = useStickyPower;
724	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
725	+
726		temp = useGayBerne;
727		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
728
729		temp = useEAM;
730		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
731
732	+	temp = useSC;
733	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
734	+
735		temp = useShape;
736		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
737
#	Line 578 \| Line 740 \| namespace oopse {
740
741		temp = useRF;
742		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
743	<
743	>
744	>	temp = useSF;
745	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
746	>
747		#endif
748
749		fInfo_.SIM_uses_PBC = usePBC;
#	Line 588 \| Line 753 \| namespace oopse {
753		fInfo_.SIM_uses_Charges = useCharge;
754		fInfo_.SIM_uses_Dipoles = useDipole;
755		fInfo_.SIM_uses_Sticky = useSticky;
756	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
757		fInfo_.SIM_uses_GayBerne = useGayBerne;
758		fInfo_.SIM_uses_EAM = useEAM;
759	+	fInfo_.SIM_uses_SC = useSC;
760		fInfo_.SIM_uses_Shapes = useShape;
761		fInfo_.SIM_uses_FLARB = useFLARB;
762		fInfo_.SIM_uses_RF = useRF;
763	+	fInfo_.SIM_uses_SF = useSF;
764
765	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
766	<
765	>	if( myMethod == "REACTION_FIELD") {
766	>
767		if (simParams_->haveDielectric()) {
768		fInfo_.dielect = simParams_->getDielectric();
769		} else {
#	Line 605 \| Line 773 \| namespace oopse {
773		"\tsetting a dielectric constant!\n");
774		painCave.isFatal = 1;
775		simError();
776	<	}
609	<
610	<	} else {
611	<	fInfo_.dielect = 0.0;
776	>	}
777		}
778
779		}
#	Line 644 \| Line 809 \| namespace oopse {
809
810		totalMass = cg->getMass();
811		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
812	<	mfact.push_back(atom->getMass()/totalMass);
812	>	// Check for massless groups - set mfact to 1 if true
813	>	if (totalMass != 0)
814	>	mfact.push_back(atom->getMass()/totalMass);
815	>	else
816	>	mfact.push_back( 1.0 );
817		}
818
819		}
#	Line 753 \| Line 922 \| namespace oopse {
922
923		#endif
924
925	<	double SimInfo::calcMaxCutoffRadius() {
757	<
758	<
759	<	std::set<AtomType*> atomTypes;
760	<	std::set<AtomType*>::iterator i;
761	<	std::vector<double> cutoffRadius;
762	<
763	<	//get the unique atom types
764	<	atomTypes = getUniqueAtomTypes();
765	<
766	<	//query the max cutoff radius among these atom types
767	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
768	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
769	<	}
770	<
771	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
772	<	#ifdef IS_MPI
773	<	//pick the max cutoff radius among the processors
774	<	#endif
775	<
776	<	return maxCutoffRadius;
777	<	}
778	<
779	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
925	>	void SimInfo::setupCutoff() {
926
927	<	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
927	>	// Check the cutoff policy
928	>	int cp = TRADITIONAL_CUTOFF_POLICY;
929	>	if (simParams_->haveCutoffPolicy()) {
930	>	std::string myPolicy = simParams_->getCutoffPolicy();
931	>	toUpper(myPolicy);
932	>	if (myPolicy == "MIX") {
933	>	cp = MIX_CUTOFF_POLICY;
934	>	} else {
935	>	if (myPolicy == "MAX") {
936	>	cp = MAX_CUTOFF_POLICY;
937	>	} else {
938	>	if (myPolicy == "TRADITIONAL") {
939	>	cp = TRADITIONAL_CUTOFF_POLICY;
940	>	} else {
941	>	// throw error
942	>	sprintf( painCave.errMsg,
943	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
944	>	painCave.isFatal = 1;
945	>	simError();
946	>	}
947	>	}
948	>	}
949	>	}
950	>	notifyFortranCutoffPolicy(&cp);
951	>
952	>	// Check the Skin Thickness for neighborlists
953	>	double skin;
954	>	if (simParams_->haveSkinThickness()) {
955	>	skin = simParams_->getSkinThickness();
956	>	notifyFortranSkinThickness(&skin);
957	>	}
958
959	<	if (!simParams_->haveRcut()){
960	<	sprintf(painCave.errMsg,
959	>	// Check if the cutoff was set explicitly:
960	>	if (simParams_->haveCutoffRadius()) {
961	>	rcut_ = simParams_->getCutoffRadius();
962	>	if (simParams_->haveSwitchingRadius()) {
963	>	rsw_ = simParams_->getSwitchingRadius();
964	>	} else {
965	>	rsw_ = rcut_;
966	>	}
967	>	notifyFortranCutoffs(&rcut_, &rsw_);
968	>
969	>	} else {
970	>
971	>	// For electrostatic atoms, we'll assume a large safe value:
972	>	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
973	>	sprintf(painCave.errMsg,
974		"SimCreator Warning: No value was set for the cutoffRadius.\n"
975		"\tOOPSE will use a default value of 15.0 angstroms"
976		"\tfor the cutoffRadius.\n");
977	<	painCave.isFatal = 0;
977	>	painCave.isFatal = 0;
978		simError();
979	<	rcut = 15.0;
980	<	} else{
981	<	rcut = simParams_->getRcut();
982	<	}
979	>	rcut_ = 15.0;
980	>
981	>	if (simParams_->haveElectrostaticSummationMethod()) {
982	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
983	>	toUpper(myMethod);
984	>	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
985	>	if (simParams_->haveSwitchingRadius()){
986	>	sprintf(painCave.errMsg,
987	>	"SimInfo Warning: A value was set for the switchingRadius\n"
988	>	"\teven though the electrostaticSummationMethod was\n"
989	>	"\tset to %s\n", myMethod.c_str());
990	>	painCave.isFatal = 1;
991	>	simError();
992	>	}
993	>	}
994	>	}
995	>
996	>	if (simParams_->haveSwitchingRadius()){
997	>	rsw_ = simParams_->getSwitchingRadius();
998	>	} else {
999	>	sprintf(painCave.errMsg,
1000	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1001	>	"\tOOPSE will use a default value of\n"
1002	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1003	>	painCave.isFatal = 0;
1004	>	simError();
1005	>	rsw_ = 0.85 * rcut_;
1006	>	}
1007	>	notifyFortranCutoffs(&rcut_, &rsw_);
1008	>	} else {
1009	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1010	>	// We'll punt and let fortran figure out the cutoffs later.
1011	>
1012	>	notifyFortranYouAreOnYourOwn();
1013
795	–	if (!simParams_->haveRsw()){
796	–	sprintf(painCave.errMsg,
797	–	"SimCreator Warning: No value was set for switchingRadius.\n"
798	–	"\tOOPSE will use a default value of\n"
799	–	"\t0.95 * cutoffRadius for the switchingRadius\n");
800	–	painCave.isFatal = 0;
801	–	simError();
802	–	rsw = 0.95 * rcut;
803	–	} else{
804	–	rsw = simParams_->getRsw();
1014		}
1015	+	}
1016	+	}
1017
1018	<	} else {
1019	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
1020	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
1021	<
1022	<	if (simParams_->haveRcut()) {
1023	<	rcut = simParams_->getRcut();
1024	<	} else {
814	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
815	<	rcut = calcMaxCutoffRadius();
816	<	}
1018	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1019	>
1020	>	int errorOut;
1021	>	int esm = NONE;
1022	>	int sm = UNDAMPED;
1023	>	double alphaVal;
1024	>	double dielectric;
1025
1026	<	if (simParams_->haveRsw()) {
1027	<	rsw = simParams_->getRsw();
1026	>	errorOut = isError;
1027	>	alphaVal = simParams_->getDampingAlpha();
1028	>	dielectric = simParams_->getDielectric();
1029	>
1030	>	if (simParams_->haveElectrostaticSummationMethod()) {
1031	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1032	>	toUpper(myMethod);
1033	>	if (myMethod == "NONE") {
1034	>	esm = NONE;
1035		} else {
1036	<	rsw = rcut;
1036	>	if (myMethod == "SWITCHING_FUNCTION") {
1037	>	esm = SWITCHING_FUNCTION;
1038	>	} else {
1039	>	if (myMethod == "SHIFTED_POTENTIAL") {
1040	>	esm = SHIFTED_POTENTIAL;
1041	>	} else {
1042	>	if (myMethod == "SHIFTED_FORCE") {
1043	>	esm = SHIFTED_FORCE;
1044	>	} else {
1045	>	if (myMethod == "REACTION_FIELD") {
1046	>	esm = REACTION_FIELD;
1047	>	} else {
1048	>	// throw error
1049	>	sprintf( painCave.errMsg,
1050	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1051	>	"\t(Input file specified %s .)\n"
1052	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1053	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1054	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1055	>	painCave.isFatal = 1;
1056	>	simError();
1057	>	}
1058	>	}
1059	>	}
1060	>	}
1061		}
1062	+	}
1063
1064	+	if (simParams_->haveElectrostaticScreeningMethod()) {
1065	+	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1066	+	toUpper(myScreen);
1067	+	if (myScreen == "UNDAMPED") {
1068	+	sm = UNDAMPED;
1069	+	} else {
1070	+	if (myScreen == "DAMPED") {
1071	+	sm = DAMPED;
1072	+	if (!simParams_->haveDampingAlpha()) {
1073	+	//throw error
1074	+	sprintf( painCave.errMsg,
1075	+	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1076	+	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1077	+	painCave.isFatal = 0;
1078	+	simError();
1079	+	}
1080	+	} else {
1081	+	// throw error
1082	+	sprintf( painCave.errMsg,
1083	+	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1084	+	"\t(Input file specified %s .)\n"
1085	+	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1086	+	"or \"damped\".\n", myScreen.c_str() );
1087	+	painCave.isFatal = 1;
1088	+	simError();
1089	+	}
1090	+	}
1091		}
1092	+
1093	+	// let's pass some summation method variables to fortran
1094	+	setElectrostaticSummationMethod( &esm );
1095	+	notifyFortranElectrostaticMethod( &esm );
1096	+	setScreeningMethod( &sm );
1097	+	setDampingAlpha( &alphaVal );
1098	+	setReactionFieldDielectric( &dielectric );
1099	+	initFortranFF( &errorOut );
1100		}
1101
1102	<	void SimInfo::setupCutoff() {
1103	<	getCutoff(rcut_, rsw_);
829	<	double rnblist = rcut_ + 1; // skin of neighbor list
1102	>	void SimInfo::setupSwitchingFunction() {
1103	>	int ft = CUBIC;
1104
1105	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1106	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
1105	>	if (simParams_->haveSwitchingFunctionType()) {
1106	>	std::string funcType = simParams_->getSwitchingFunctionType();
1107	>	toUpper(funcType);
1108	>	if (funcType == "CUBIC") {
1109	>	ft = CUBIC;
1110	>	} else {
1111	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1112	>	ft = FIFTH_ORDER_POLY;
1113	>	} else {
1114	>	// throw error
1115	>	sprintf( painCave.errMsg,
1116	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1117	>	painCave.isFatal = 1;
1118	>	simError();
1119	>	}
1120	>	}
1121	>	}
1122	>
1123	>	// send switching function notification to switcheroo
1124	>	setFunctionType(&ft);
1125	>
1126		}
1127
1128		void SimInfo::addProperty(GenericData* genData) {
#	Line 939 \| Line 1232 \| namespace oopse {
1232
1233		return o;
1234		}
1235	+
1236	+
1237	+	/*
1238	+	Returns center of mass and center of mass velocity in one function call.
1239	+	*/
1240	+
1241	+	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1242	+	SimInfo::MoleculeIterator i;
1243	+	Molecule* mol;
1244	+
1245	+
1246	+	double totalMass = 0.0;
1247	+
1248
1249	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1250	+	double mass = mol->getMass();
1251	+	totalMass += mass;
1252	+	com += mass * mol->getCom();
1253	+	comVel += mass * mol->getComVel();
1254	+	}
1255	+
1256	+	#ifdef IS_MPI
1257	+	double tmpMass = totalMass;
1258	+	Vector3d tmpCom(com);
1259	+	Vector3d tmpComVel(comVel);
1260	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1261	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1262	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1263	+	#endif
1264	+
1265	+	com /= totalMass;
1266	+	comVel /= totalMass;
1267	+	}
1268	+
1269	+	/*
1270	+	Return intertia tensor for entire system and angular momentum Vector.
1271	+
1272	+
1273	+	[ Ixx -Ixy -Ixz ]
1274	+	J =\| -Iyx Iyy -Iyz \|
1275	+	[ -Izx -Iyz Izz ]
1276	+	*/
1277	+
1278	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1279	+
1280	+
1281	+	double xx = 0.0;
1282	+	double yy = 0.0;
1283	+	double zz = 0.0;
1284	+	double xy = 0.0;
1285	+	double xz = 0.0;
1286	+	double yz = 0.0;
1287	+	Vector3d com(0.0);
1288	+	Vector3d comVel(0.0);
1289	+
1290	+	getComAll(com, comVel);
1291	+
1292	+	SimInfo::MoleculeIterator i;
1293	+	Molecule* mol;
1294	+
1295	+	Vector3d thisq(0.0);
1296	+	Vector3d thisv(0.0);
1297	+
1298	+	double thisMass = 0.0;
1299	+
1300	+
1301	+
1302	+
1303	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1304	+
1305	+	thisq = mol->getCom()-com;
1306	+	thisv = mol->getComVel()-comVel;
1307	+	thisMass = mol->getMass();
1308	+	// Compute moment of intertia coefficients.
1309	+	xx += thisq[0]thisq[0]thisMass;
1310	+	yy += thisq[1]thisq[1]thisMass;
1311	+	zz += thisq[2]thisq[2]thisMass;
1312	+
1313	+	// compute products of intertia
1314	+	xy += thisq[0]thisq[1]thisMass;
1315	+	xz += thisq[0]thisq[2]thisMass;
1316	+	yz += thisq[1]thisq[2]thisMass;
1317	+
1318	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1319	+
1320	+	}
1321	+
1322	+
1323	+	inertiaTensor(0,0) = yy + zz;
1324	+	inertiaTensor(0,1) = -xy;
1325	+	inertiaTensor(0,2) = -xz;
1326	+	inertiaTensor(1,0) = -xy;
1327	+	inertiaTensor(1,1) = xx + zz;
1328	+	inertiaTensor(1,2) = -yz;
1329	+	inertiaTensor(2,0) = -xz;
1330	+	inertiaTensor(2,1) = -yz;
1331	+	inertiaTensor(2,2) = xx + yy;
1332	+
1333	+	#ifdef IS_MPI
1334	+	Mat3x3d tmpI(inertiaTensor);
1335	+	Vector3d tmpAngMom;
1336	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1337	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1338	+	#endif
1339	+
1340	+	return;
1341	+	}
1342	+
1343	+	//Returns the angular momentum of the system
1344	+	Vector3d SimInfo::getAngularMomentum(){
1345	+
1346	+	Vector3d com(0.0);
1347	+	Vector3d comVel(0.0);
1348	+	Vector3d angularMomentum(0.0);
1349	+
1350	+	getComAll(com,comVel);
1351	+
1352	+	SimInfo::MoleculeIterator i;
1353	+	Molecule* mol;
1354	+
1355	+	Vector3d thisr(0.0);
1356	+	Vector3d thisp(0.0);
1357	+
1358	+	double thisMass;
1359	+
1360	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1361	+	thisMass = mol->getMass();
1362	+	thisr = mol->getCom()-com;
1363	+	thisp = (mol->getComVel()-comVel)*thisMass;
1364	+
1365	+	angularMomentum += cross( thisr, thisp );
1366	+
1367	+	}
1368	+
1369	+	#ifdef IS_MPI
1370	+	Vector3d tmpAngMom;
1371	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1372	+	#endif
1373	+
1374	+	return angularMomentum;
1375	+	}
1376	+
1377	+
1378		}//end namespace oopse
1379

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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents): Revision 2204 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs. Revision 2463 by gezelter, Mon Nov 21 22:59:21 2005 UTC

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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 2204 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 2463 by gezelter, Mon Nov 21 22:59:21 2005 UTC