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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 709 by chrisfen, Wed Nov 2 20:36:15 2005 UTC vs.
Revision 1050 by chrisfen, Fri Sep 22 22:19:59 2006 UTC

#	Line 48 \| Line 48
48
49		#include <algorithm>
50		#include <set>
51	+	#include <map>
52
53		#include "brains/SimInfo.hpp"
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56	+	#include "primitives/StuntDouble.hpp"
57		#include "UseTheForce/fCutoffPolicy.h"
58		#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	<	#include "UseTheForce/DarkSide/fScreeningMethod.h"
59	>	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60	>	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61		#include "UseTheForce/doForces_interface.h"
62		#include "UseTheForce/DarkSide/electrostatic_interface.h"
63	<	#include "UseTheForce/notifyCutoffs_interface.h"
63	>	#include "UseTheForce/DarkSide/switcheroo_interface.h"
64		#include "utils/MemoryUtils.hpp"
65		#include "utils/simError.h"
66		#include "selection/SelectionManager.hpp"
67	+	#include "io/ForceFieldOptions.hpp"
68	+	#include "UseTheForce/ForceField.hpp"
69
70		#ifdef IS_MPI
71		#include "UseTheForce/mpiComponentPlan.h"
#	Line 68 \| Line 73 \| namespace oopse {
73		#endif
74
75		namespace oopse {
76	+	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
77	+	std::map<int, std::set<int> >::iterator i = container.find(index);
78	+	std::set<int> result;
79	+	if (i != container.end()) {
80	+	result = i->second;
81	+	}
82
83	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
84	<	ForceField* ff, Globals* simParams) :
85	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
86	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
83	>	return result;
84	>	}
85	>
86	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
87	>	forceField_(ff), simParams_(simParams),
88	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
89		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
90		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
91		nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
92		nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
93	<	sman_(NULL), fortranInitialized_(false) {
93	>	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) {
94
82	–
83	–	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
95		MoleculeStamp* molStamp;
96		int nMolWithSameStamp;
97		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
#	Line 88 \| Line 99 \| namespace oopse {
99		CutoffGroupStamp* cgStamp;
100		RigidBodyStamp* rbStamp;
101		int nRigidAtoms = 0;
102	<
103	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
104	<	molStamp = i->first;
105	<	nMolWithSameStamp = i->second;
102	>	std::vector<Component*> components = simParams->getComponents();
103	>
104	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
105	>	molStamp = (*i)->getMoleculeStamp();
106	>	nMolWithSameStamp = (*i)->getNMol();
107
108		addMoleculeStamp(molStamp, nMolWithSameStamp);
109
110		//calculate atoms in molecules
111		nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
100	–
112
113		//calculate atoms in cutoff groups
114		int nAtomsInGroups = 0;
115		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
116
117		for (int j=0; j < nCutoffGroupsInStamp; j++) {
118	<	cgStamp = molStamp->getCutoffGroup(j);
118	>	cgStamp = molStamp->getCutoffGroupStamp(j);
119		nAtomsInGroups += cgStamp->getNMembers();
120		}
121
#	Line 117 \| Line 128 \| namespace oopse {
128		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
129
130		for (int j=0; j < nRigidBodiesInStamp; j++) {
131	<	rbStamp = molStamp->getRigidBody(j);
131	>	rbStamp = molStamp->getRigidBodyStamp(j);
132		nAtomsInRigidBodies += rbStamp->getNMembers();
133		}
134
#	Line 156 \| Line 167 \| namespace oopse {
167		}
168		molecules_.clear();
169
159	–	delete stamps_;
170		delete sman_;
171		delete simParams_;
172		delete forceField_;
#	Line 263 \| Line 273 \| namespace oopse {
273		}
274		}
275
276	<	}//end for (integrableObject)
277	<	}// end for (mol)
276	>	}
277	>	}
278
279		// n_constraints is local, so subtract them on each processor
280		ndf_local -= nConstraints_;
#	Line 281 \| Line 291 \| namespace oopse {
291
292		}
293
294	+	int SimInfo::getFdf() {
295	+	#ifdef IS_MPI
296	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
297	+	#else
298	+	fdf_ = fdf_local;
299	+	#endif
300	+	return fdf_;
301	+	}
302	+
303		void SimInfo::calcNdfRaw() {
304		int ndfRaw_local;
305
#	Line 343 \| Line 362 \| namespace oopse {
362		int b;
363		int c;
364		int d;
365	+
366	+	std::map<int, std::set<int> > atomGroups;
367	+
368	+	Molecule::RigidBodyIterator rbIter;
369	+	RigidBody* rb;
370	+	Molecule::IntegrableObjectIterator ii;
371	+	StuntDouble* integrableObject;
372	+
373	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
374	+	integrableObject = mol->nextIntegrableObject(ii)) {
375	+
376	+	if (integrableObject->isRigidBody()) {
377	+	rb = static_cast<RigidBody*>(integrableObject);
378	+	std::vector<Atom*> atoms = rb->getAtoms();
379	+	std::set<int> rigidAtoms;
380	+	for (int i = 0; i < atoms.size(); ++i) {
381	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
382	+	}
383	+	for (int i = 0; i < atoms.size(); ++i) {
384	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
385	+	}
386	+	} else {
387	+	std::set<int> oneAtomSet;
388	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
389	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
390	+	}
391	+	}
392	+
393
394	+
395		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
396		a = bond->getAtomA()->getGlobalIndex();
397		b = bond->getAtomB()->getGlobalIndex();
#	Line 354 \| Line 402 \| namespace oopse {
402		a = bend->getAtomA()->getGlobalIndex();
403		b = bend->getAtomB()->getGlobalIndex();
404		c = bend->getAtomC()->getGlobalIndex();
405	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
406	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
407	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
408
409	<	exclude_.addPair(a, b);
410	<	exclude_.addPair(a, c);
411	<	exclude_.addPair(b, c);
409	>	exclude_.addPairs(rigidSetA, rigidSetB);
410	>	exclude_.addPairs(rigidSetA, rigidSetC);
411	>	exclude_.addPairs(rigidSetB, rigidSetC);
412	>
413	>	//exclude_.addPair(a, b);
414	>	//exclude_.addPair(a, c);
415	>	//exclude_.addPair(b, c);
416		}
417
418		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
#	Line 365 \| Line 420 \| namespace oopse {
420		b = torsion->getAtomB()->getGlobalIndex();
421		c = torsion->getAtomC()->getGlobalIndex();
422		d = torsion->getAtomD()->getGlobalIndex();
423	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
424	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
425	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
426	+	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
427
428	+	exclude_.addPairs(rigidSetA, rigidSetB);
429	+	exclude_.addPairs(rigidSetA, rigidSetC);
430	+	exclude_.addPairs(rigidSetA, rigidSetD);
431	+	exclude_.addPairs(rigidSetB, rigidSetC);
432	+	exclude_.addPairs(rigidSetB, rigidSetD);
433	+	exclude_.addPairs(rigidSetC, rigidSetD);
434	+
435	+	/*
436	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
437	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
438	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
439	+	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
440	+	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
441	+	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
442	+
443	+
444		exclude_.addPair(a, b);
445		exclude_.addPair(a, c);
446		exclude_.addPair(a, d);
447		exclude_.addPair(b, c);
448		exclude_.addPair(b, d);
449		exclude_.addPair(c, d);
450	+	*/
451		}
452
377	–	Molecule::RigidBodyIterator rbIter;
378	–	RigidBody* rb;
453		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
454		std::vector<Atom*> atoms = rb->getAtoms();
455		for (int i = 0; i < atoms.size() -1 ; ++i) {
#	Line 400 \| Line 474 \| namespace oopse {
474		int b;
475		int c;
476		int d;
477	+
478	+	std::map<int, std::set<int> > atomGroups;
479	+
480	+	Molecule::RigidBodyIterator rbIter;
481	+	RigidBody* rb;
482	+	Molecule::IntegrableObjectIterator ii;
483	+	StuntDouble* integrableObject;
484
485	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
486	+	integrableObject = mol->nextIntegrableObject(ii)) {
487	+
488	+	if (integrableObject->isRigidBody()) {
489	+	rb = static_cast<RigidBody*>(integrableObject);
490	+	std::vector<Atom*> atoms = rb->getAtoms();
491	+	std::set<int> rigidAtoms;
492	+	for (int i = 0; i < atoms.size(); ++i) {
493	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
494	+	}
495	+	for (int i = 0; i < atoms.size(); ++i) {
496	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
497	+	}
498	+	} else {
499	+	std::set<int> oneAtomSet;
500	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
501	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
502	+	}
503	+	}
504	+
505	+
506		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
507		a = bond->getAtomA()->getGlobalIndex();
508		b = bond->getAtomB()->getGlobalIndex();
#	Line 412 \| Line 514 \| namespace oopse {
514		b = bend->getAtomB()->getGlobalIndex();
515		c = bend->getAtomC()->getGlobalIndex();
516
517	<	exclude_.removePair(a, b);
518	<	exclude_.removePair(a, c);
519	<	exclude_.removePair(b, c);
517	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
518	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
519	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
520	>
521	>	exclude_.removePairs(rigidSetA, rigidSetB);
522	>	exclude_.removePairs(rigidSetA, rigidSetC);
523	>	exclude_.removePairs(rigidSetB, rigidSetC);
524	>
525	>	//exclude_.removePair(a, b);
526	>	//exclude_.removePair(a, c);
527	>	//exclude_.removePair(b, c);
528		}
529
530		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
#	Line 423 \| Line 533 \| namespace oopse {
533		c = torsion->getAtomC()->getGlobalIndex();
534		d = torsion->getAtomD()->getGlobalIndex();
535
536	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
537	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
538	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
539	+	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
540	+
541	+	exclude_.removePairs(rigidSetA, rigidSetB);
542	+	exclude_.removePairs(rigidSetA, rigidSetC);
543	+	exclude_.removePairs(rigidSetA, rigidSetD);
544	+	exclude_.removePairs(rigidSetB, rigidSetC);
545	+	exclude_.removePairs(rigidSetB, rigidSetD);
546	+	exclude_.removePairs(rigidSetC, rigidSetD);
547	+
548	+	/*
549	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
550	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
551	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
552	+	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
553	+	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
554	+	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
555	+
556	+
557		exclude_.removePair(a, b);
558		exclude_.removePair(a, c);
559		exclude_.removePair(a, d);
560		exclude_.removePair(b, c);
561		exclude_.removePair(b, d);
562		exclude_.removePair(c, d);
563	+	*/
564		}
565
434	–	Molecule::RigidBodyIterator rbIter;
435	–	RigidBody* rb;
566		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
567		std::vector<Atom*> atoms = rb->getAtoms();
568		for (int i = 0; i < atoms.size() -1 ; ++i) {
#	Line 471 \| Line 601 \| namespace oopse {
601		/** @deprecate */
602		int isError = 0;
603
604	+	setupCutoff();
605	+
606		setupElectrostaticSummationMethod( isError );
607	+	setupSwitchingFunction();
608	+	setupAccumulateBoxDipole();
609
610		if(isError){
611		sprintf( painCave.errMsg,
#	Line 479 \| Line 613 \| namespace oopse {
613		painCave.isFatal = 1;
614		simError();
615		}
482	–
483	–
484	–	setupCutoff();
616
617		calcNdf();
618		calcNdfRaw();
#	Line 516 \| 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 529 \| Line 661 \| namespace oopse {
661		//usePBC and useRF are from simParams
662		int usePBC = simParams_->getUsePeriodicBoundaryConditions();
663		int useRF;
664	<	int useDW;
664	>	int useSF;
665	>	int useSP;
666	>	int useBoxDipole;
667		std::string myMethod;
668
669		// set the useRF logical
670		useRF = 0;
671	<	useDW = 0;
671	>	useSF = 0;
672
673
674		if (simParams_->haveElectrostaticSummationMethod()) {
675		std::string myMethod = simParams_->getElectrostaticSummationMethod();
676		toUpper(myMethod);
677	<	if (myMethod == "REACTION_FIELD") {
677	>	if (myMethod == "REACTION_FIELD"){
678		useRF=1;
679	<	} else {
680	<	if (myMethod == "SHIFTED_POTENTIAL") {
681	<	useDW = 1;
682	<	}
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 604 \| 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 613 \| Line 755 \| namespace oopse {
755		temp = useRF;
756		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
757
758	<	temp = useDW;
759	<	MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
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 628 \| 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_DampedWolf = useDW;
784	<
785	<	if( myMethod == "REACTION_FIELD") {
637	<
638	<	if (simParams_->haveDielectric()) {
639	<	fInfo_.dielect = simParams_->getDielectric();
640	<	} else {
641	<	sprintf(painCave.errMsg,
642	<	"SimSetup Error: No Dielectric constant was set.\n"
643	<	"\tYou are trying to use Reaction Field without"
644	<	"\tsetting a dielectric constant!\n");
645	<	painCave.isFatal = 1;
646	<	simError();
647	<	}
648	<	}
649	<
783	>	fInfo_.SIM_uses_SF = useSF;
784	>	fInfo_.SIM_uses_SP = useSP;
785	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
786		}
787
788		void SimInfo::setupFortranSim() {
#	Line 663 \| Line 799 \| namespace oopse {
799		}
800
801		//calculate mass ratio of cutoff group
802	<	std::vector<double> mfact;
802	>	std::vector<RealType> mfact;
803		SimInfo::MoleculeIterator mi;
804		Molecule* mol;
805		Molecule::CutoffGroupIterator ci;
806		CutoffGroup* cg;
807		Molecule::AtomIterator ai;
808		Atom* atom;
809	<	double totalMass;
809	>	RealType totalMass;
810
811		//to avoid memory reallocation, reserve enough space for mfact
812		mfact.reserve(getNCutoffGroups());
#	Line 793 \| Line 929 \| namespace oopse {
929
930		#endif
931
932	<	double SimInfo::calcMaxCutoffRadius() {
932	>	void SimInfo::setupCutoff() {
933	>
934	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
935
936	+	// Check the cutoff policy
937	+	int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
938
939	<	std::set<AtomType*> atomTypes;
940	<	std::set<AtomType*>::iterator i;
941	<	std::vector<double> cutoffRadius;
942	<
943	<	//get the unique atom types
804	<	atomTypes = getUniqueAtomTypes();
805	<
806	<	//query the max cutoff radius among these atom types
807	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
808	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
939	>	std::string myPolicy;
940	>	if (forceFieldOptions_.haveCutoffPolicy()){
941	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
942	>	}else if (simParams_->haveCutoffPolicy()) {
943	>	myPolicy = simParams_->getCutoffPolicy();
944		}
945
946	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
812	<	#ifdef IS_MPI
813	<	//pick the max cutoff radius among the processors
814	<	#endif
815	<
816	<	return maxCutoffRadius;
817	<	}
818	<
819	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
820	<
821	<	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
822	<
823	<	if (!simParams_->haveCutoffRadius()){
824	<	sprintf(painCave.errMsg,
825	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
826	<	"\tOOPSE will use a default value of 15.0 angstroms"
827	<	"\tfor the cutoffRadius.\n");
828	<	painCave.isFatal = 0;
829	<	simError();
830	<	rcut = 15.0;
831	<	} else{
832	<	rcut = simParams_->getCutoffRadius();
833	<	}
834	<
835	<	if (!simParams_->haveSwitchingRadius()){
836	<	sprintf(painCave.errMsg,
837	<	"SimCreator Warning: No value was set for switchingRadius.\n"
838	<	"\tOOPSE will use a default value of\n"
839	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
840	<	painCave.isFatal = 0;
841	<	simError();
842	<	rsw = 0.85 * rcut;
843	<	} else{
844	<	rsw = simParams_->getSwitchingRadius();
845	<	}
846	<
847	<	} else {
848	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
849	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
850	<
851	<	if (simParams_->haveCutoffRadius()) {
852	<	rcut = simParams_->getCutoffRadius();
853	<	} else {
854	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
855	<	rcut = calcMaxCutoffRadius();
856	<	}
857	<
858	<	if (simParams_->haveSwitchingRadius()) {
859	<	rsw = simParams_->getSwitchingRadius();
860	<	} else {
861	<	rsw = rcut;
862	<	}
863	<
864	<	}
865	<	}
866	<
867	<	void SimInfo::setupCutoff() {
868	<	getCutoff(rcut_, rsw_);
869	<	double rnblist = rcut_ + 1; // skin of neighbor list
870	<
871	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
872	<
873	<	int cp = TRADITIONAL_CUTOFF_POLICY;
874	<	if (simParams_->haveCutoffPolicy()) {
875	<	std::string myPolicy = simParams_->getCutoffPolicy();
946	>	if (!myPolicy.empty()){
947		toUpper(myPolicy);
948		if (myPolicy == "MIX") {
949		cp = MIX_CUTOFF_POLICY;
#	Line 891 \| Line 962 \| namespace oopse {
962		}
963		}
964		}
965	<	}
965	>	}
966	>	notifyFortranCutoffPolicy(&cp);
967
968	<
968	>	// Check the Skin Thickness for neighborlists
969	>	RealType skin;
970		if (simParams_->haveSkinThickness()) {
971	<	double skinThickness = simParams_->getSkinThickness();
972	<	}
971	>	skin = simParams_->getSkinThickness();
972	>	notifyFortranSkinThickness(&skin);
973	>	}
974	>
975	>	// Check if the cutoff was set explicitly:
976	>	if (simParams_->haveCutoffRadius()) {
977	>	rcut_ = simParams_->getCutoffRadius();
978	>	if (simParams_->haveSwitchingRadius()) {
979	>	rsw_ = simParams_->getSwitchingRadius();
980	>	} else {
981	>	if (fInfo_.SIM_uses_Charges \|
982	>	fInfo_.SIM_uses_Dipoles \|
983	>	fInfo_.SIM_uses_RF) {
984	>
985	>	rsw_ = 0.85 * rcut_;
986	>	sprintf(painCave.errMsg,
987	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
988	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
989	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
990	>	painCave.isFatal = 0;
991	>	simError();
992	>	} else {
993	>	rsw_ = rcut_;
994	>	sprintf(painCave.errMsg,
995	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
996	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
997	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
998	>	painCave.isFatal = 0;
999	>	simError();
1000	>	}
1001	>	}
1002	>
1003	>	notifyFortranCutoffs(&rcut_, &rsw_);
1004	>
1005	>	} else {
1006	>
1007	>	// For electrostatic atoms, we'll assume a large safe value:
1008	>	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
1009	>	sprintf(painCave.errMsg,
1010	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1011	>	"\tOOPSE will use a default value of 15.0 angstroms"
1012	>	"\tfor the cutoffRadius.\n");
1013	>	painCave.isFatal = 0;
1014	>	simError();
1015	>	rcut_ = 15.0;
1016	>
1017	>	if (simParams_->haveElectrostaticSummationMethod()) {
1018	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1019	>	toUpper(myMethod);
1020	>	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
1021	>	if (simParams_->haveSwitchingRadius()){
1022	>	sprintf(painCave.errMsg,
1023	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1024	>	"\teven though the electrostaticSummationMethod was\n"
1025	>	"\tset to %s\n", myMethod.c_str());
1026	>	painCave.isFatal = 1;
1027	>	simError();
1028	>	}
1029	>	}
1030	>	}
1031	>
1032	>	if (simParams_->haveSwitchingRadius()){
1033	>	rsw_ = simParams_->getSwitchingRadius();
1034	>	} else {
1035	>	sprintf(painCave.errMsg,
1036	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1037	>	"\tOOPSE will use a default value of\n"
1038	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1039	>	painCave.isFatal = 0;
1040	>	simError();
1041	>	rsw_ = 0.85 * rcut_;
1042	>	}
1043	>	notifyFortranCutoffs(&rcut_, &rsw_);
1044	>	} else {
1045	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1046	>	// We'll punt and let fortran figure out the cutoffs later.
1047	>
1048	>	notifyFortranYouAreOnYourOwn();
1049
1050	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1051	<	// also send cutoff notification to electrostatics
903	<	setElectrostaticCutoffRadius(&rcut_, &rsw_);
1050	>	}
1051	>	}
1052		}
1053
1054		void SimInfo::setupElectrostaticSummationMethod( int isError ) {
#	Line 908 \| Line 1056 \| namespace oopse {
1056		int errorOut;
1057		int esm = NONE;
1058		int sm = UNDAMPED;
1059	<	double alphaVal;
1060	<	double dielectric;
1061	<
1059	>	RealType alphaVal;
1060	>	RealType dielectric;
1061	>
1062		errorOut = isError;
915	–	alphaVal = simParams_->getDampingAlpha();
916	–	dielectric = simParams_->getDielectric();
1063
1064		if (simParams_->haveElectrostaticSummationMethod()) {
1065		std::string myMethod = simParams_->getElectrostaticSummationMethod();
#	Line 930 \| Line 1076 \| namespace oopse {
1076		if (myMethod == "SHIFTED_FORCE") {
1077		esm = SHIFTED_FORCE;
1078		} else {
1079	<	if (myMethod == "REACTION_FIELD") {
1079	>	if (myMethod == "REACTION_FIELD") {
1080		esm = REACTION_FIELD;
1081	+	dielectric = simParams_->getDielectric();
1082	+	if (!simParams_->haveDielectric()) {
1083	+	// throw warning
1084	+	sprintf( painCave.errMsg,
1085	+	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1086	+	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1087	+	painCave.isFatal = 0;
1088	+	simError();
1089	+	}
1090		} else {
1091		// throw error
1092		sprintf( painCave.errMsg,
1093	<	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() );
1093	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1094	>	"\t(Input file specified %s .)\n"
1095	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1096	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1097	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1098		painCave.isFatal = 1;
1099		simError();
1100		}
#	Line 945 \| Line 1104 \| namespace oopse {
1104		}
1105		}
1106
1107	<	if (simParams_->haveScreeningMethod()) {
1108	<	std::string myScreen = simParams_->getScreeningMethod();
1107	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1108	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1109		toUpper(myScreen);
1110		if (myScreen == "UNDAMPED") {
1111		sm = UNDAMPED;
#	Line 954 \| Line 1113 \| namespace oopse {
1113		if (myScreen == "DAMPED") {
1114		sm = DAMPED;
1115		if (!simParams_->haveDampingAlpha()) {
1116	<	//throw error
1116	>	// first set a cutoff dependent alpha value
1117	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1118	>	alphaVal = 0.5125 - rcut_* 0.025;
1119	>	// for values rcut > 20.5, alpha is zero
1120	>	if (alphaVal < 0) alphaVal = 0;
1121	>
1122	>	// throw warning
1123		sprintf( painCave.errMsg,
1124	<	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
1124	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1125	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1126		painCave.isFatal = 0;
1127		simError();
962	–	} else {
963	–	// throw error
964	–	sprintf( painCave.errMsg,
965	–	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
966	–	painCave.isFatal = 1;
967	–	simError();
1128		}
1129	+	} else {
1130	+	// throw error
1131	+	sprintf( painCave.errMsg,
1132	+	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1133	+	"\t(Input file specified %s .)\n"
1134	+	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1135	+	"or \"damped\".\n", myScreen.c_str() );
1136	+	painCave.isFatal = 1;
1137	+	simError();
1138		}
1139		}
1140		}
1141	+
1142		// let's pass some summation method variables to fortran
1143		setElectrostaticSummationMethod( &esm );
1144	+	setFortranElectrostaticMethod( &esm );
1145		setScreeningMethod( &sm );
1146		setDampingAlpha( &alphaVal );
1147		setReactionFieldDielectric( &dielectric );
1148	<	initFortranFF( &esm, &errorOut );
1148	>	initFortranFF( &errorOut );
1149		}
1150
1151	+	void SimInfo::setupSwitchingFunction() {
1152	+	int ft = CUBIC;
1153	+
1154	+	if (simParams_->haveSwitchingFunctionType()) {
1155	+	std::string funcType = simParams_->getSwitchingFunctionType();
1156	+	toUpper(funcType);
1157	+	if (funcType == "CUBIC") {
1158	+	ft = CUBIC;
1159	+	} else {
1160	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1161	+	ft = FIFTH_ORDER_POLY;
1162	+	} else {
1163	+	// throw error
1164	+	sprintf( painCave.errMsg,
1165	+	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1166	+	painCave.isFatal = 1;
1167	+	simError();
1168	+	}
1169	+	}
1170	+	}
1171	+
1172	+	// send switching function notification to switcheroo
1173	+	setFunctionType(&ft);
1174	+
1175	+	}
1176	+
1177	+	void SimInfo::setupAccumulateBoxDipole() {
1178	+
1179	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1180	+	if ( simParams_->haveAccumulateBoxDipole() )
1181	+	if ( simParams_->getAccumulateBoxDipole() ) {
1182	+	setAccumulateBoxDipole();
1183	+	calcBoxDipole_ = true;
1184	+	}
1185	+
1186	+	}
1187	+
1188		void SimInfo::addProperty(GenericData* genData) {
1189		properties_.addProperty(genData);
1190		}
#	Line 1033 \| Line 1241 \| namespace oopse {
1241		Molecule* mol;
1242
1243		Vector3d comVel(0.0);
1244	<	double totalMass = 0.0;
1244	>	RealType totalMass = 0.0;
1245
1246
1247		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1248	<	double mass = mol->getMass();
1248	>	RealType mass = mol->getMass();
1249		totalMass += mass;
1250		comVel += mass * mol->getComVel();
1251		}
1252
1253		#ifdef IS_MPI
1254	<	double tmpMass = totalMass;
1254	>	RealType tmpMass = totalMass;
1255		Vector3d tmpComVel(comVel);
1256	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1257	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1256	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1257	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1258		#endif
1259
1260		comVel /= totalMass;
#	Line 1059 \| Line 1267 \| namespace oopse {
1267		Molecule* mol;
1268
1269		Vector3d com(0.0);
1270	<	double totalMass = 0.0;
1270	>	RealType totalMass = 0.0;
1271
1272		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1273	<	double mass = mol->getMass();
1273	>	RealType mass = mol->getMass();
1274		totalMass += mass;
1275		com += mass * mol->getCom();
1276		}
1277
1278		#ifdef IS_MPI
1279	<	double tmpMass = totalMass;
1279	>	RealType tmpMass = totalMass;
1280		Vector3d tmpCom(com);
1281	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1282	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1281	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1282	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1283		#endif
1284
1285		com /= totalMass;
#	Line 1095 \| Line 1303 \| namespace oopse {
1303		Molecule* mol;
1304
1305
1306	<	double totalMass = 0.0;
1306	>	RealType totalMass = 0.0;
1307
1308
1309		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1310	<	double mass = mol->getMass();
1310	>	RealType mass = mol->getMass();
1311		totalMass += mass;
1312		com += mass * mol->getCom();
1313		comVel += mass * mol->getComVel();
1314		}
1315
1316		#ifdef IS_MPI
1317	<	double tmpMass = totalMass;
1317	>	RealType tmpMass = totalMass;
1318		Vector3d tmpCom(com);
1319		Vector3d tmpComVel(comVel);
1320	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1321	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1322	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1320	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1321	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1322	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1323		#endif
1324
1325		com /= totalMass;
#	Line 1130 \| Line 1338 \| namespace oopse {
1338		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1339
1340
1341	<	double xx = 0.0;
1342	<	double yy = 0.0;
1343	<	double zz = 0.0;
1344	<	double xy = 0.0;
1345	<	double xz = 0.0;
1346	<	double yz = 0.0;
1341	>	RealType xx = 0.0;
1342	>	RealType yy = 0.0;
1343	>	RealType zz = 0.0;
1344	>	RealType xy = 0.0;
1345	>	RealType xz = 0.0;
1346	>	RealType yz = 0.0;
1347		Vector3d com(0.0);
1348		Vector3d comVel(0.0);
1349
#	Line 1147 \| Line 1355 \| namespace oopse {
1355		Vector3d thisq(0.0);
1356		Vector3d thisv(0.0);
1357
1358	<	double thisMass = 0.0;
1358	>	RealType thisMass = 0.0;
1359
1360
1361
#	Line 1185 \| Line 1393 \| namespace oopse {
1393		#ifdef IS_MPI
1394		Mat3x3d tmpI(inertiaTensor);
1395		Vector3d tmpAngMom;
1396	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1397	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1396	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1397	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1398		#endif
1399
1400		return;
#	Line 1207 \| Line 1415 \| namespace oopse {
1415		Vector3d thisr(0.0);
1416		Vector3d thisp(0.0);
1417
1418	<	double thisMass;
1418	>	RealType thisMass;
1419
1420		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1421		thisMass = mol->getMass();
#	Line 1220 \| Line 1428 \| namespace oopse {
1428
1429		#ifdef IS_MPI
1430		Vector3d tmpAngMom;
1431	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1431	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1432		#endif
1433
1434		return angularMomentum;
1435		}
1436
1437	<
1437	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1438	>	return IOIndexToIntegrableObject.at(index);
1439	>	}
1440	>
1441	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1442	>	IOIndexToIntegrableObject= v;
1443	>	}
1444	>
1445	>	/*
1446	>	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1447	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1448	>	sdByGlobalIndex_ = v;
1449	>	}
1450	>
1451	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1452	>	//assert(index < nAtoms_ + nRigidBodies_);
1453	>	return sdByGlobalIndex_.at(index);
1454	>	}
1455	>	*/
1456		}//end namespace oopse
1457

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Comparing trunk/src/brains/SimInfo.cpp (file contents): Revision 709 by chrisfen, Wed Nov 2 20:36:15 2005 UTC vs. Revision 1050 by chrisfen, Fri Sep 22 22:19:59 2006 UTC

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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 709 by chrisfen, Wed Nov 2 20:36:15 2005 UTC vs.
Revision 1050 by chrisfen, Fri Sep 22 22:19:59 2006 UTC