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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 734 by chuckv, Tue Nov 15 16:05:38 2005 UTC vs.
Revision 1129 by chrisfen, Fri Apr 20 18:15:48 2007 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/fElectrostaticScreeningMethod.h"
60		#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61		#include "UseTheForce/doForces_interface.h"
62	+	#include "UseTheForce/DarkSide/neighborLists_interface.h"
63		#include "UseTheForce/DarkSide/electrostatic_interface.h"
61	–	#include "UseTheForce/notifyCutoffs_interface.h"
64		#include "UseTheForce/DarkSide/switcheroo_interface.h"
65		#include "utils/MemoryUtils.hpp"
66		#include "utils/simError.h"
67		#include "selection/SelectionManager.hpp"
68	+	#include "io/ForceFieldOptions.hpp"
69	+	#include "UseTheForce/ForceField.hpp"
70
71	+
72		#ifdef IS_MPI
73		#include "UseTheForce/mpiComponentPlan.h"
74		#include "UseTheForce/DarkSide/simParallel_interface.h"
75		#endif
76
77		namespace oopse {
78	+	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79	+	std::map<int, std::set<int> >::iterator i = container.find(index);
80	+	std::set<int> result;
81	+	if (i != container.end()) {
82	+	result = i->second;
83	+	}
84
85	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
86	<	ForceField* ff, Globals* simParams) :
87	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
88	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
85	>	return result;
86	>	}
87	>
88	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
89	>	forceField_(ff), simParams_(simParams),
90	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
91		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
92		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
93		nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
94		nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
95	<	sman_(NULL), fortranInitialized_(false) {
95	>	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false),
96	>	useAtomicVirial_(true) {
97
84	–
85	–	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
98		MoleculeStamp* molStamp;
99		int nMolWithSameStamp;
100		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
#	Line 90 \| Line 102 \| namespace oopse {
102		CutoffGroupStamp* cgStamp;
103		RigidBodyStamp* rbStamp;
104		int nRigidAtoms = 0;
105	<
106	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
107	<	molStamp = i->first;
108	<	nMolWithSameStamp = i->second;
105	>	std::vector<Component*> components = simParams->getComponents();
106	>
107	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
108	>	molStamp = (*i)->getMoleculeStamp();
109	>	nMolWithSameStamp = (*i)->getNMol();
110
111		addMoleculeStamp(molStamp, nMolWithSameStamp);
112
113		//calculate atoms in molecules
114		nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
115
103	–
116		//calculate atoms in cutoff groups
117		int nAtomsInGroups = 0;
118		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
119
120		for (int j=0; j < nCutoffGroupsInStamp; j++) {
121	<	cgStamp = molStamp->getCutoffGroup(j);
121	>	cgStamp = molStamp->getCutoffGroupStamp(j);
122		nAtomsInGroups += cgStamp->getNMembers();
123		}
124
#	Line 119 \| Line 131 \| namespace oopse {
131		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
132
133		for (int j=0; j < nRigidBodiesInStamp; j++) {
134	<	rbStamp = molStamp->getRigidBody(j);
134	>	rbStamp = molStamp->getRigidBodyStamp(j);
135		nAtomsInRigidBodies += rbStamp->getNMembers();
136		}
137
#	Line 158 \| Line 170 \| namespace oopse {
170		}
171		molecules_.clear();
172
161	–	delete stamps_;
173		delete sman_;
174		delete simParams_;
175		delete forceField_;
#	Line 265 \| Line 276 \| namespace oopse {
276		}
277		}
278
279	<	}//end for (integrableObject)
280	<	}// end for (mol)
279	>	}
280	>	}
281
282		// n_constraints is local, so subtract them on each processor
283		ndf_local -= nConstraints_;
#	Line 283 \| Line 294 \| namespace oopse {
294
295		}
296
297	+	int SimInfo::getFdf() {
298	+	#ifdef IS_MPI
299	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
300	+	#else
301	+	fdf_ = fdf_local;
302	+	#endif
303	+	return fdf_;
304	+	}
305	+
306		void SimInfo::calcNdfRaw() {
307		int ndfRaw_local;
308
#	Line 345 \| Line 365 \| namespace oopse {
365		int b;
366		int c;
367		int d;
368	+
369	+	std::map<int, std::set<int> > atomGroups;
370	+
371	+	Molecule::RigidBodyIterator rbIter;
372	+	RigidBody* rb;
373	+	Molecule::IntegrableObjectIterator ii;
374	+	StuntDouble* integrableObject;
375	+
376	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
377	+	integrableObject = mol->nextIntegrableObject(ii)) {
378	+
379	+	if (integrableObject->isRigidBody()) {
380	+	rb = static_cast<RigidBody*>(integrableObject);
381	+	std::vector<Atom*> atoms = rb->getAtoms();
382	+	std::set<int> rigidAtoms;
383	+	for (int i = 0; i < atoms.size(); ++i) {
384	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
385	+	}
386	+	for (int i = 0; i < atoms.size(); ++i) {
387	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
388	+	}
389	+	} else {
390	+	std::set<int> oneAtomSet;
391	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
392	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
393	+	}
394	+	}
395	+
396
397	+
398		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
399		a = bond->getAtomA()->getGlobalIndex();
400		b = bond->getAtomB()->getGlobalIndex();
#	Line 356 \| Line 405 \| namespace oopse {
405		a = bend->getAtomA()->getGlobalIndex();
406		b = bend->getAtomB()->getGlobalIndex();
407		c = bend->getAtomC()->getGlobalIndex();
408	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
409	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
410	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
411
412	<	exclude_.addPair(a, b);
413	<	exclude_.addPair(a, c);
414	<	exclude_.addPair(b, c);
412	>	exclude_.addPairs(rigidSetA, rigidSetB);
413	>	exclude_.addPairs(rigidSetA, rigidSetC);
414	>	exclude_.addPairs(rigidSetB, rigidSetC);
415	>
416	>	//exclude_.addPair(a, b);
417	>	//exclude_.addPair(a, c);
418	>	//exclude_.addPair(b, c);
419		}
420
421		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
#	Line 367 \| Line 423 \| namespace oopse {
423		b = torsion->getAtomB()->getGlobalIndex();
424		c = torsion->getAtomC()->getGlobalIndex();
425		d = torsion->getAtomD()->getGlobalIndex();
426	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
427	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
428	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
429	+	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
430
431	+	exclude_.addPairs(rigidSetA, rigidSetB);
432	+	exclude_.addPairs(rigidSetA, rigidSetC);
433	+	exclude_.addPairs(rigidSetA, rigidSetD);
434	+	exclude_.addPairs(rigidSetB, rigidSetC);
435	+	exclude_.addPairs(rigidSetB, rigidSetD);
436	+	exclude_.addPairs(rigidSetC, rigidSetD);
437	+
438	+	/*
439	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
440	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
441	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
442	+	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
443	+	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
444	+	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
445	+
446	+
447		exclude_.addPair(a, b);
448		exclude_.addPair(a, c);
449		exclude_.addPair(a, d);
450		exclude_.addPair(b, c);
451		exclude_.addPair(b, d);
452		exclude_.addPair(c, d);
453	+	*/
454		}
455
379	–	Molecule::RigidBodyIterator rbIter;
380	–	RigidBody* rb;
456		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
457		std::vector<Atom*> atoms = rb->getAtoms();
458		for (int i = 0; i < atoms.size() -1 ; ++i) {
#	Line 402 \| Line 477 \| namespace oopse {
477		int b;
478		int c;
479		int d;
480	+
481	+	std::map<int, std::set<int> > atomGroups;
482	+
483	+	Molecule::RigidBodyIterator rbIter;
484	+	RigidBody* rb;
485	+	Molecule::IntegrableObjectIterator ii;
486	+	StuntDouble* integrableObject;
487
488	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
489	+	integrableObject = mol->nextIntegrableObject(ii)) {
490	+
491	+	if (integrableObject->isRigidBody()) {
492	+	rb = static_cast<RigidBody*>(integrableObject);
493	+	std::vector<Atom*> atoms = rb->getAtoms();
494	+	std::set<int> rigidAtoms;
495	+	for (int i = 0; i < atoms.size(); ++i) {
496	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
497	+	}
498	+	for (int i = 0; i < atoms.size(); ++i) {
499	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
500	+	}
501	+	} else {
502	+	std::set<int> oneAtomSet;
503	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
504	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
505	+	}
506	+	}
507	+
508	+
509		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
510		a = bond->getAtomA()->getGlobalIndex();
511		b = bond->getAtomB()->getGlobalIndex();
#	Line 414 \| Line 517 \| namespace oopse {
517		b = bend->getAtomB()->getGlobalIndex();
518		c = bend->getAtomC()->getGlobalIndex();
519
520	<	exclude_.removePair(a, b);
521	<	exclude_.removePair(a, c);
522	<	exclude_.removePair(b, c);
520	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
521	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
522	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
523	>
524	>	exclude_.removePairs(rigidSetA, rigidSetB);
525	>	exclude_.removePairs(rigidSetA, rigidSetC);
526	>	exclude_.removePairs(rigidSetB, rigidSetC);
527	>
528	>	//exclude_.removePair(a, b);
529	>	//exclude_.removePair(a, c);
530	>	//exclude_.removePair(b, c);
531		}
532
533		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
#	Line 425 \| Line 536 \| namespace oopse {
536		c = torsion->getAtomC()->getGlobalIndex();
537		d = torsion->getAtomD()->getGlobalIndex();
538
539	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
540	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
541	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
542	+	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
543	+
544	+	exclude_.removePairs(rigidSetA, rigidSetB);
545	+	exclude_.removePairs(rigidSetA, rigidSetC);
546	+	exclude_.removePairs(rigidSetA, rigidSetD);
547	+	exclude_.removePairs(rigidSetB, rigidSetC);
548	+	exclude_.removePairs(rigidSetB, rigidSetD);
549	+	exclude_.removePairs(rigidSetC, rigidSetD);
550	+
551	+	/*
552	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
553	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
554	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
555	+	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
556	+	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
557	+	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
558	+
559	+
560		exclude_.removePair(a, b);
561		exclude_.removePair(a, c);
562		exclude_.removePair(a, d);
563		exclude_.removePair(b, c);
564		exclude_.removePair(b, d);
565		exclude_.removePair(c, d);
566	+	*/
567		}
568
436	–	Molecule::RigidBodyIterator rbIter;
437	–	RigidBody* rb;
569		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
570		std::vector<Atom*> atoms = rb->getAtoms();
571		for (int i = 0; i < atoms.size() -1 ; ++i) {
#	Line 473 \| Line 604 \| namespace oopse {
604		/** @deprecate */
605		int isError = 0;
606
607	+	setupCutoff();
608	+
609		setupElectrostaticSummationMethod( isError );
610		setupSwitchingFunction();
611	+	setupAccumulateBoxDipole();
612
613		if(isError){
614		sprintf( painCave.errMsg,
#	Line 482 \| Line 616 \| namespace oopse {
616		painCave.isFatal = 1;
617		simError();
618		}
485	–
486	–
487	–	setupCutoff();
619
620		calcNdf();
621		calcNdfRaw();
#	Line 534 \| Line 665 \| namespace oopse {
665		int usePBC = simParams_->getUsePeriodicBoundaryConditions();
666		int useRF;
667		int useSF;
668	+	int useSP;
669	+	int useBoxDipole;
670	+
671		std::string myMethod;
672
673		// set the useRF logical
674		useRF = 0;
675		useSF = 0;
676	+	useSP = 0;
677
678
679		if (simParams_->haveElectrostaticSummationMethod()) {
680		std::string myMethod = simParams_->getElectrostaticSummationMethod();
681		toUpper(myMethod);
682	<	if (myMethod == "REACTION_FIELD") {
683	<	useRF=1;
684	<	} else {
685	<	if (myMethod == "SHIFTED_FORCE") {
686	<	useSF = 1;
687	<	}
682	>	if (myMethod == "REACTION_FIELD"){
683	>	useRF = 1;
684	>	} else if (myMethod == "SHIFTED_FORCE"){
685	>	useSF = 1;
686	>	} else if (myMethod == "SHIFTED_POTENTIAL"){
687	>	useSP = 1;
688		}
689		}
690	+
691	+	if (simParams_->haveAccumulateBoxDipole())
692	+	if (simParams_->getAccumulateBoxDipole())
693	+	useBoxDipole = 1;
694
695	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
696	+
697		//loop over all of the atom types
698		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
699		useLennardJones \|= (*i)->isLennardJones();
#	Line 622 \| Line 763 \| namespace oopse {
763		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
764
765		temp = useSF;
766	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767
768	+	temp = useSP;
769	+	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770	+
771	+	temp = useBoxDipole;
772	+	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
773	+
774	+	temp = useAtomicVirial_;
775	+	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776	+
777		#endif
778
779		fInfo_.SIM_uses_PBC = usePBC;
#	Line 641 \| Line 791 \| namespace oopse {
791		fInfo_.SIM_uses_FLARB = useFLARB;
792		fInfo_.SIM_uses_RF = useRF;
793		fInfo_.SIM_uses_SF = useSF;
794	<
795	<	if( myMethod == "REACTION_FIELD") {
796	<
647	<	if (simParams_->haveDielectric()) {
648	<	fInfo_.dielect = simParams_->getDielectric();
649	<	} else {
650	<	sprintf(painCave.errMsg,
651	<	"SimSetup Error: No Dielectric constant was set.\n"
652	<	"\tYou are trying to use Reaction Field without"
653	<	"\tsetting a dielectric constant!\n");
654	<	painCave.isFatal = 1;
655	<	simError();
656	<	}
657	<	}
658	<
794	>	fInfo_.SIM_uses_SP = useSP;
795	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
796	>	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
797		}
798
799		void SimInfo::setupFortranSim() {
#	Line 672 \| Line 810 \| namespace oopse {
810		}
811
812		//calculate mass ratio of cutoff group
813	<	std::vector<double> mfact;
813	>	std::vector<RealType> mfact;
814		SimInfo::MoleculeIterator mi;
815		Molecule* mol;
816		Molecule::CutoffGroupIterator ci;
817		CutoffGroup* cg;
818		Molecule::AtomIterator ai;
819		Atom* atom;
820	<	double totalMass;
820	>	RealType totalMass;
821
822		//to avoid memory reallocation, reserve enough space for mfact
823		mfact.reserve(getNCutoffGroups());
#	Line 740 \| Line 878 \| namespace oopse {
878		"succesfully sent the simulation information to fortran.\n");
879		MPIcheckPoint();
880		#endif // is_mpi
881	+
882	+	// Setup number of neighbors in neighbor list if present
883	+	if (simParams_->haveNeighborListNeighbors()) {
884	+	int nlistNeighbors = simParams_->getNeighborListNeighbors();
885	+	setNeighbors(&nlistNeighbors);
886	+	}
887	+
888	+
889		}
890
891
#	Line 802 \| Line 948 \| namespace oopse {
948
949		#endif
950
951	<	double SimInfo::calcMaxCutoffRadius() {
951	>	void SimInfo::setupCutoff() {
952	>
953	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
954
955	+	// Check the cutoff policy
956	+	int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
957
958	<	std::set<AtomType*> atomTypes;
959	<	std::set<AtomType*>::iterator i;
960	<	std::vector<double> cutoffRadius;
958	>	// Set LJ shifting bools to false
959	>	ljsp_ = false;
960	>	ljsf_ = false;
961
962	<	//get the unique atom types
963	<	atomTypes = getUniqueAtomTypes();
964	<
965	<	//query the max cutoff radius among these atom types
966	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
817	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
962	>	std::string myPolicy;
963	>	if (forceFieldOptions_.haveCutoffPolicy()){
964	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
965	>	}else if (simParams_->haveCutoffPolicy()) {
966	>	myPolicy = simParams_->getCutoffPolicy();
967		}
968
969	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
821	<	#ifdef IS_MPI
822	<	//pick the max cutoff radius among the processors
823	<	#endif
824	<
825	<	return maxCutoffRadius;
826	<	}
827	<
828	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
829	<
830	<	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
831	<
832	<	if (!simParams_->haveCutoffRadius()){
833	<	sprintf(painCave.errMsg,
834	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
835	<	"\tOOPSE will use a default value of 15.0 angstroms"
836	<	"\tfor the cutoffRadius.\n");
837	<	painCave.isFatal = 0;
838	<	simError();
839	<	rcut = 15.0;
840	<	} else{
841	<	rcut = simParams_->getCutoffRadius();
842	<	}
843	<
844	<	if (!simParams_->haveSwitchingRadius()){
845	<	sprintf(painCave.errMsg,
846	<	"SimCreator Warning: No value was set for switchingRadius.\n"
847	<	"\tOOPSE will use a default value of\n"
848	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
849	<	painCave.isFatal = 0;
850	<	simError();
851	<	rsw = 0.85 * rcut;
852	<	} else{
853	<	rsw = simParams_->getSwitchingRadius();
854	<	}
855	<
856	<	} else {
857	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
858	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
859	<
860	<	if (simParams_->haveCutoffRadius()) {
861	<	rcut = simParams_->getCutoffRadius();
862	<	} else {
863	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
864	<	rcut = calcMaxCutoffRadius();
865	<	}
866	<
867	<	if (simParams_->haveSwitchingRadius()) {
868	<	rsw = simParams_->getSwitchingRadius();
869	<	} else {
870	<	rsw = rcut;
871	<	}
872	<
873	<	}
874	<	}
875	<
876	<	void SimInfo::setupCutoff() {
877	<	getCutoff(rcut_, rsw_);
878	<	double rnblist = rcut_ + 1; // skin of neighbor list
879	<
880	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
881	<
882	<	int cp = TRADITIONAL_CUTOFF_POLICY;
883	<	if (simParams_->haveCutoffPolicy()) {
884	<	std::string myPolicy = simParams_->getCutoffPolicy();
969	>	if (!myPolicy.empty()){
970		toUpper(myPolicy);
971		if (myPolicy == "MIX") {
972		cp = MIX_CUTOFF_POLICY;
#	Line 900 \| Line 985 \| namespace oopse {
985		}
986		}
987		}
988	<	}
988	>	}
989	>	notifyFortranCutoffPolicy(&cp);
990
991	<
991	>	// Check the Skin Thickness for neighborlists
992	>	RealType skin;
993		if (simParams_->haveSkinThickness()) {
994	<	double skinThickness = simParams_->getSkinThickness();
995	<	}
994	>	skin = simParams_->getSkinThickness();
995	>	notifyFortranSkinThickness(&skin);
996	>	}
997	>
998	>	// Check if the cutoff was set explicitly:
999	>	if (simParams_->haveCutoffRadius()) {
1000	>	rcut_ = simParams_->getCutoffRadius();
1001	>	if (simParams_->haveSwitchingRadius()) {
1002	>	rsw_ = simParams_->getSwitchingRadius();
1003	>	} else {
1004	>	if (fInfo_.SIM_uses_Charges \|
1005	>	fInfo_.SIM_uses_Dipoles \|
1006	>	fInfo_.SIM_uses_RF) {
1007	>
1008	>	rsw_ = 0.85 * rcut_;
1009	>	sprintf(painCave.errMsg,
1010	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1011	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1012	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1013	>	painCave.isFatal = 0;
1014	>	simError();
1015	>	} else {
1016	>	rsw_ = rcut_;
1017	>	sprintf(painCave.errMsg,
1018	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1019	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
1020	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1021	>	painCave.isFatal = 0;
1022	>	simError();
1023	>	}
1024	>	}
1025
1026	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1027	<	// also send cutoff notification to electrostatics
1028	<	setElectrostaticCutoffRadius(&rcut_, &rsw_);
1026	>	if (simParams_->haveElectrostaticSummationMethod()) {
1027	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1028	>	toUpper(myMethod);
1029	>
1030	>	if (myMethod == "SHIFTED_POTENTIAL") {
1031	>	ljsp_ = true;
1032	>	} else if (myMethod == "SHIFTED_FORCE") {
1033	>	ljsf_ = true;
1034	>	}
1035	>	}
1036	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1037	>
1038	>	} else {
1039	>
1040	>	// For electrostatic atoms, we'll assume a large safe value:
1041	>	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
1042	>	sprintf(painCave.errMsg,
1043	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1044	>	"\tOOPSE will use a default value of 15.0 angstroms"
1045	>	"\tfor the cutoffRadius.\n");
1046	>	painCave.isFatal = 0;
1047	>	simError();
1048	>	rcut_ = 15.0;
1049	>
1050	>	if (simParams_->haveElectrostaticSummationMethod()) {
1051	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1052	>	toUpper(myMethod);
1053	>
1054	>	// For the time being, we're tethering the LJ shifted behavior to the
1055	>	// electrostaticSummationMethod keyword options
1056	>	if (myMethod == "SHIFTED_POTENTIAL") {
1057	>	ljsp_ = true;
1058	>	} else if (myMethod == "SHIFTED_FORCE") {
1059	>	ljsf_ = true;
1060	>	}
1061	>	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
1062	>	if (simParams_->haveSwitchingRadius()){
1063	>	sprintf(painCave.errMsg,
1064	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1065	>	"\teven though the electrostaticSummationMethod was\n"
1066	>	"\tset to %s\n", myMethod.c_str());
1067	>	painCave.isFatal = 1;
1068	>	simError();
1069	>	}
1070	>	}
1071	>	}
1072	>
1073	>	if (simParams_->haveSwitchingRadius()){
1074	>	rsw_ = simParams_->getSwitchingRadius();
1075	>	} else {
1076	>	sprintf(painCave.errMsg,
1077	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1078	>	"\tOOPSE will use a default value of\n"
1079	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1080	>	painCave.isFatal = 0;
1081	>	simError();
1082	>	rsw_ = 0.85 * rcut_;
1083	>	}
1084	>
1085	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1086	>
1087	>	} else {
1088	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1089	>	// We'll punt and let fortran figure out the cutoffs later.
1090	>
1091	>	notifyFortranYouAreOnYourOwn();
1092	>
1093	>	}
1094	>	}
1095		}
1096
1097		void SimInfo::setupElectrostaticSummationMethod( int isError ) {
#	Line 917 \| Line 1099 \| namespace oopse {
1099		int errorOut;
1100		int esm = NONE;
1101		int sm = UNDAMPED;
1102	<	double alphaVal;
1103	<	double dielectric;
1104	<
1102	>	RealType alphaVal;
1103	>	RealType dielectric;
1104	>
1105		errorOut = isError;
924	–	alphaVal = simParams_->getDampingAlpha();
925	–	dielectric = simParams_->getDielectric();
1106
1107		if (simParams_->haveElectrostaticSummationMethod()) {
1108		std::string myMethod = simParams_->getElectrostaticSummationMethod();
#	Line 939 \| Line 1119 \| namespace oopse {
1119		if (myMethod == "SHIFTED_FORCE") {
1120		esm = SHIFTED_FORCE;
1121		} else {
1122	<	if (myMethod == "REACTION_FIELD") {
1122	>	if (myMethod == "REACTION_FIELD") {
1123		esm = REACTION_FIELD;
1124	+	dielectric = simParams_->getDielectric();
1125	+	if (!simParams_->haveDielectric()) {
1126	+	// throw warning
1127	+	sprintf( painCave.errMsg,
1128	+	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1129	+	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1130	+	painCave.isFatal = 0;
1131	+	simError();
1132	+	}
1133		} else {
1134		// throw error
1135		sprintf( painCave.errMsg,
1136	<	"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() );
1136	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1137	>	"\t(Input file specified %s .)\n"
1138	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1139	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1140	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1141		painCave.isFatal = 1;
1142		simError();
1143		}
#	Line 963 \| Line 1156 \| namespace oopse {
1156		if (myScreen == "DAMPED") {
1157		sm = DAMPED;
1158		if (!simParams_->haveDampingAlpha()) {
1159	<	//throw error
1159	>	// first set a cutoff dependent alpha value
1160	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1161	>	alphaVal = 0.5125 - rcut_* 0.025;
1162	>	// for values rcut > 20.5, alpha is zero
1163	>	if (alphaVal < 0) alphaVal = 0;
1164	>
1165	>	// throw warning
1166		sprintf( painCave.errMsg,
1167	<	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
1167	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1168	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1169		painCave.isFatal = 0;
1170		simError();
1171	+	} else {
1172	+	alphaVal = simParams_->getDampingAlpha();
1173		}
1174	+
1175		} else {
1176		// throw error
1177		sprintf( painCave.errMsg,
1178	<	"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
1178	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1179	>	"\t(Input file specified %s .)\n"
1180	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1181	>	"or \"damped\".\n", myScreen.c_str() );
1182		painCave.isFatal = 1;
1183		simError();
1184		}
#	Line 981 \| Line 1187 \| namespace oopse {
1187
1188		// let's pass some summation method variables to fortran
1189		setElectrostaticSummationMethod( &esm );
1190	+	setFortranElectrostaticMethod( &esm );
1191		setScreeningMethod( &sm );
1192		setDampingAlpha( &alphaVal );
1193		setReactionFieldDielectric( &dielectric );
1194	<	initFortranFF( &esm, &errorOut );
1194	>	initFortranFF( &errorOut );
1195		}
1196
1197		void SimInfo::setupSwitchingFunction() {
#	Line 1013 \| Line 1220 \| namespace oopse {
1220
1221		}
1222
1223	+	void SimInfo::setupAccumulateBoxDipole() {
1224	+
1225	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1226	+	if ( simParams_->haveAccumulateBoxDipole() )
1227	+	if ( simParams_->getAccumulateBoxDipole() ) {
1228	+	setAccumulateBoxDipole();
1229	+	calcBoxDipole_ = true;
1230	+	}
1231	+
1232	+	}
1233	+
1234		void SimInfo::addProperty(GenericData* genData) {
1235		properties_.addProperty(genData);
1236		}
#	Line 1069 \| Line 1287 \| namespace oopse {
1287		Molecule* mol;
1288
1289		Vector3d comVel(0.0);
1290	<	double totalMass = 0.0;
1290	>	RealType totalMass = 0.0;
1291
1292
1293		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1294	<	double mass = mol->getMass();
1294	>	RealType mass = mol->getMass();
1295		totalMass += mass;
1296		comVel += mass * mol->getComVel();
1297		}
1298
1299		#ifdef IS_MPI
1300	<	double tmpMass = totalMass;
1300	>	RealType tmpMass = totalMass;
1301		Vector3d tmpComVel(comVel);
1302	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1303	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1302	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1303	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1304		#endif
1305
1306		comVel /= totalMass;
#	Line 1095 \| Line 1313 \| namespace oopse {
1313		Molecule* mol;
1314
1315		Vector3d com(0.0);
1316	<	double totalMass = 0.0;
1316	>	RealType totalMass = 0.0;
1317
1318		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1319	<	double mass = mol->getMass();
1319	>	RealType mass = mol->getMass();
1320		totalMass += mass;
1321		com += mass * mol->getCom();
1322		}
1323
1324		#ifdef IS_MPI
1325	<	double tmpMass = totalMass;
1325	>	RealType tmpMass = totalMass;
1326		Vector3d tmpCom(com);
1327	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1328	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1327	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1328	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1329		#endif
1330
1331		com /= totalMass;
#	Line 1131 \| Line 1349 \| namespace oopse {
1349		Molecule* mol;
1350
1351
1352	<	double totalMass = 0.0;
1352	>	RealType totalMass = 0.0;
1353
1354
1355		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1356	<	double mass = mol->getMass();
1356	>	RealType mass = mol->getMass();
1357		totalMass += mass;
1358		com += mass * mol->getCom();
1359		comVel += mass * mol->getComVel();
1360		}
1361
1362		#ifdef IS_MPI
1363	<	double tmpMass = totalMass;
1363	>	RealType tmpMass = totalMass;
1364		Vector3d tmpCom(com);
1365		Vector3d tmpComVel(comVel);
1366	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1367	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1368	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1366	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1367	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1368	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1369		#endif
1370
1371		com /= totalMass;
#	Line 1166 \| Line 1384 \| namespace oopse {
1384		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1385
1386
1387	<	double xx = 0.0;
1388	<	double yy = 0.0;
1389	<	double zz = 0.0;
1390	<	double xy = 0.0;
1391	<	double xz = 0.0;
1392	<	double yz = 0.0;
1387	>	RealType xx = 0.0;
1388	>	RealType yy = 0.0;
1389	>	RealType zz = 0.0;
1390	>	RealType xy = 0.0;
1391	>	RealType xz = 0.0;
1392	>	RealType yz = 0.0;
1393		Vector3d com(0.0);
1394		Vector3d comVel(0.0);
1395
#	Line 1183 \| Line 1401 \| namespace oopse {
1401		Vector3d thisq(0.0);
1402		Vector3d thisv(0.0);
1403
1404	<	double thisMass = 0.0;
1404	>	RealType thisMass = 0.0;
1405
1406
1407
#	Line 1221 \| Line 1439 \| namespace oopse {
1439		#ifdef IS_MPI
1440		Mat3x3d tmpI(inertiaTensor);
1441		Vector3d tmpAngMom;
1442	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1443	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1442	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1443	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1444		#endif
1445
1446		return;
#	Line 1243 \| Line 1461 \| namespace oopse {
1461		Vector3d thisr(0.0);
1462		Vector3d thisp(0.0);
1463
1464	<	double thisMass;
1464	>	RealType thisMass;
1465
1466		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1467		thisMass = mol->getMass();
#	Line 1256 \| Line 1474 \| namespace oopse {
1474
1475		#ifdef IS_MPI
1476		Vector3d tmpAngMom;
1477	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1477	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1478		#endif
1479
1480		return angularMomentum;
1481		}
1482
1483	<
1483	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1484	>	return IOIndexToIntegrableObject.at(index);
1485	>	}
1486	>
1487	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1488	>	IOIndexToIntegrableObject= v;
1489	>	}
1490	>
1491	>	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1492	>	based on the radius of gyration V=4/3PiR_1R_2R_3
1493	>	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1494	>	V = 4/3Pi(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1495	>	*/
1496	>	void SimInfo::getGyrationalVolume(RealType &volume){
1497	>	Mat3x3d intTensor;
1498	>	RealType det;
1499	>	Vector3d dummyAngMom;
1500	>	RealType sysconstants;
1501	>	RealType geomCnst;
1502	>
1503	>	geomCnst = 3.0/2.0;
1504	>	/* Get the inertial tensor and angular momentum for free*/
1505	>	getInertiaTensor(intTensor,dummyAngMom);
1506	>
1507	>	det = intTensor.determinant();
1508	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1509	>	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(det);
1510	>	return;
1511	>	}
1512	>
1513	>	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1514	>	Mat3x3d intTensor;
1515	>	Vector3d dummyAngMom;
1516	>	RealType sysconstants;
1517	>	RealType geomCnst;
1518	>
1519	>	geomCnst = 3.0/2.0;
1520	>	/* Get the inertial tensor and angular momentum for free*/
1521	>	getInertiaTensor(intTensor,dummyAngMom);
1522	>
1523	>	detI = intTensor.determinant();
1524	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1525	>	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(detI);
1526	>	return;
1527	>	}
1528	>	/*
1529	>	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1530	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1531	>	sdByGlobalIndex_ = v;
1532	>	}
1533	>
1534	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1535	>	//assert(index < nAtoms_ + nRigidBodies_);
1536	>	return sdByGlobalIndex_.at(index);
1537	>	}
1538	>	*/
1539		}//end namespace oopse
1540

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Comparing trunk/src/brains/SimInfo.cpp (file contents): Revision 734 by chuckv, Tue Nov 15 16:05:38 2005 UTC vs. Revision 1129 by chrisfen, Fri Apr 20 18:15:48 2007 UTC

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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 734 by chuckv, Tue Nov 15 16:05:38 2005 UTC vs.
Revision 1129 by chrisfen, Fri Apr 20 18:15:48 2007 UTC