[ViewVC] Diff of: OpenMD/trunk/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 1078 by gezelter, Wed Oct 18 21:58:48 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/fElectrostaticScreeningMethod.h"
60		#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61		#include "UseTheForce/doForces_interface.h"
62		#include "UseTheForce/DarkSide/electrostatic_interface.h"
61	–	#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 70 \| 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
84	–
85	–	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 90 \| 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;
102	–
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 119 \| 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 158 \| Line 167 \| namespace oopse {
167		}
168		molecules_.clear();
169
161	–	delete stamps_;
170		delete sman_;
171		delete simParams_;
172		delete forceField_;
#	Line 265 \| 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 283 \| 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 345 \| 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 356 \| 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 367 \| 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
379	–	Molecule::RigidBodyIterator rbIter;
380	–	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 402 \| 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();
#	Line 414 \| 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 425 \| 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
436	–	Molecule::RigidBodyIterator rbIter;
437	–	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 473 \| 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 482 \| Line 613 \| namespace oopse {
613		painCave.isFatal = 1;
614		simError();
615		}
485	–
486	–
487	–	setupCutoff();
616
617		calcNdf();
618		calcNdfRaw();
#	Line 534 \| Line 662 \| namespace oopse {
662		int usePBC = simParams_->getUsePeriodicBoundaryConditions();
663		int useRF;
664		int useSF;
665	+	int useSP;
666	+	int useBoxDipole;
667		std::string myMethod;
668
669		// set the useRF logical
670		useRF = 0;
671		useSF = 0;
672	+	useSP = 0;
673
674
675		if (simParams_->haveElectrostaticSummationMethod()) {
676		std::string myMethod = simParams_->getElectrostaticSummationMethod();
677		toUpper(myMethod);
678	<	if (myMethod == "REACTION_FIELD") {
679	<	useRF=1;
680	<	} else {
681	<	if (myMethod == "SHIFTED_FORCE") {
682	<	useSF = 1;
683	<	}
678	>	if (myMethod == "REACTION_FIELD"){
679	>	useRF = 1;
680	>	} else if (myMethod == "SHIFTED_FORCE"){
681	>	useSF = 1;
682	>	} else if (myMethod == "SHIFTED_POTENTIAL"){
683	>	useSP = 1;
684		}
685		}
686	+
687	+	if (simParams_->haveAccumulateBoxDipole())
688	+	if (simParams_->getAccumulateBoxDipole())
689	+	useBoxDipole = 1;
690
691		//loop over all of the atom types
692		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
#	Line 622 \| Line 757 \| namespace oopse {
757		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
758
759		temp = useSF;
760	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
760	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
761	>
762	>	temp = useSP;
763	>	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
764
765	+	temp = useBoxDipole;
766	+	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767	+
768		#endif
769
770		fInfo_.SIM_uses_PBC = usePBC;
#	Line 641 \| Line 782 \| namespace oopse {
782		fInfo_.SIM_uses_FLARB = useFLARB;
783		fInfo_.SIM_uses_RF = useRF;
784		fInfo_.SIM_uses_SF = useSF;
785	<
786	<	if( myMethod == "REACTION_FIELD") {
646	<
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	<
785	>	fInfo_.SIM_uses_SP = useSP;
786	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
787		}
788
789		void SimInfo::setupFortranSim() {
#	Line 672 \| Line 800 \| namespace oopse {
800		}
801
802		//calculate mass ratio of cutoff group
803	<	std::vector<double> mfact;
803	>	std::vector<RealType> mfact;
804		SimInfo::MoleculeIterator mi;
805		Molecule* mol;
806		Molecule::CutoffGroupIterator ci;
807		CutoffGroup* cg;
808		Molecule::AtomIterator ai;
809		Atom* atom;
810	<	double totalMass;
810	>	RealType totalMass;
811
812		//to avoid memory reallocation, reserve enough space for mfact
813		mfact.reserve(getNCutoffGroups());
#	Line 802 \| Line 930 \| namespace oopse {
930
931		#endif
932
933	<	double SimInfo::calcMaxCutoffRadius() {
933	>	void SimInfo::setupCutoff() {
934	>
935	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
936
937	+	// Check the cutoff policy
938	+	int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
939
940	<	std::set<AtomType*> atomTypes;
941	<	std::set<AtomType*>::iterator i;
942	<	std::vector<double> cutoffRadius;
943	<
944	<	//get the unique atom types
813	<	atomTypes = getUniqueAtomTypes();
814	<
815	<	//query the max cutoff radius among these atom types
816	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
817	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
940	>	std::string myPolicy;
941	>	if (forceFieldOptions_.haveCutoffPolicy()){
942	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
943	>	}else if (simParams_->haveCutoffPolicy()) {
944	>	myPolicy = simParams_->getCutoffPolicy();
945		}
946
947	<	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();
947	>	if (!myPolicy.empty()){
948		toUpper(myPolicy);
949		if (myPolicy == "MIX") {
950		cp = MIX_CUTOFF_POLICY;
#	Line 900 \| Line 963 \| namespace oopse {
963		}
964		}
965		}
966	<	}
966	>	}
967	>	notifyFortranCutoffPolicy(&cp);
968
969	<
969	>	// Check the Skin Thickness for neighborlists
970	>	RealType skin;
971		if (simParams_->haveSkinThickness()) {
972	<	double skinThickness = simParams_->getSkinThickness();
973	<	}
972	>	skin = simParams_->getSkinThickness();
973	>	notifyFortranSkinThickness(&skin);
974	>	}
975	>
976	>	// Check if the cutoff was set explicitly:
977	>	if (simParams_->haveCutoffRadius()) {
978	>	rcut_ = simParams_->getCutoffRadius();
979	>	if (simParams_->haveSwitchingRadius()) {
980	>	rsw_ = simParams_->getSwitchingRadius();
981	>	} else {
982	>	if (fInfo_.SIM_uses_Charges \|
983	>	fInfo_.SIM_uses_Dipoles \|
984	>	fInfo_.SIM_uses_RF) {
985	>
986	>	rsw_ = 0.85 * rcut_;
987	>	sprintf(painCave.errMsg,
988	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
989	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
990	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
991	>	painCave.isFatal = 0;
992	>	simError();
993	>	} else {
994	>	rsw_ = rcut_;
995	>	sprintf(painCave.errMsg,
996	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
997	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
998	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
999	>	painCave.isFatal = 0;
1000	>	simError();
1001	>	}
1002	>	}
1003	>
1004	>	notifyFortranCutoffs(&rcut_, &rsw_);
1005	>
1006	>	} else {
1007	>
1008	>	// For electrostatic atoms, we'll assume a large safe value:
1009	>	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
1010	>	sprintf(painCave.errMsg,
1011	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1012	>	"\tOOPSE will use a default value of 15.0 angstroms"
1013	>	"\tfor the cutoffRadius.\n");
1014	>	painCave.isFatal = 0;
1015	>	simError();
1016	>	rcut_ = 15.0;
1017	>
1018	>	if (simParams_->haveElectrostaticSummationMethod()) {
1019	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1020	>	toUpper(myMethod);
1021	>	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
1022	>	if (simParams_->haveSwitchingRadius()){
1023	>	sprintf(painCave.errMsg,
1024	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1025	>	"\teven though the electrostaticSummationMethod was\n"
1026	>	"\tset to %s\n", myMethod.c_str());
1027	>	painCave.isFatal = 1;
1028	>	simError();
1029	>	}
1030	>	}
1031	>	}
1032	>
1033	>	if (simParams_->haveSwitchingRadius()){
1034	>	rsw_ = simParams_->getSwitchingRadius();
1035	>	} else {
1036	>	sprintf(painCave.errMsg,
1037	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1038	>	"\tOOPSE will use a default value of\n"
1039	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1040	>	painCave.isFatal = 0;
1041	>	simError();
1042	>	rsw_ = 0.85 * rcut_;
1043	>	}
1044	>	notifyFortranCutoffs(&rcut_, &rsw_);
1045	>	} else {
1046	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1047	>	// We'll punt and let fortran figure out the cutoffs later.
1048	>
1049	>	notifyFortranYouAreOnYourOwn();
1050
1051	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1052	<	// also send cutoff notification to electrostatics
912	<	setElectrostaticCutoffRadius(&rcut_, &rsw_);
1051	>	}
1052	>	}
1053		}
1054
1055		void SimInfo::setupElectrostaticSummationMethod( int isError ) {
#	Line 917 \| Line 1057 \| namespace oopse {
1057		int errorOut;
1058		int esm = NONE;
1059		int sm = UNDAMPED;
1060	<	double alphaVal;
1061	<	double dielectric;
1062	<
1060	>	RealType alphaVal;
1061	>	RealType dielectric;
1062	>
1063		errorOut = isError;
924	–	alphaVal = simParams_->getDampingAlpha();
925	–	dielectric = simParams_->getDielectric();
1064
1065		if (simParams_->haveElectrostaticSummationMethod()) {
1066		std::string myMethod = simParams_->getElectrostaticSummationMethod();
#	Line 939 \| Line 1077 \| namespace oopse {
1077		if (myMethod == "SHIFTED_FORCE") {
1078		esm = SHIFTED_FORCE;
1079		} else {
1080	<	if (myMethod == "REACTION_FIELD") {
1080	>	if (myMethod == "REACTION_FIELD") {
1081		esm = REACTION_FIELD;
1082	+	dielectric = simParams_->getDielectric();
1083	+	if (!simParams_->haveDielectric()) {
1084	+	// throw warning
1085	+	sprintf( painCave.errMsg,
1086	+	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1087	+	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1088	+	painCave.isFatal = 0;
1089	+	simError();
1090	+	}
1091		} else {
1092		// throw error
1093		sprintf( painCave.errMsg,
1094	<	"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() );
1094	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1095	>	"\t(Input file specified %s .)\n"
1096	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1097	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1098	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1099		painCave.isFatal = 1;
1100		simError();
1101		}
#	Line 963 \| Line 1114 \| namespace oopse {
1114		if (myScreen == "DAMPED") {
1115		sm = DAMPED;
1116		if (!simParams_->haveDampingAlpha()) {
1117	<	//throw error
1117	>	// first set a cutoff dependent alpha value
1118	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1119	>	alphaVal = 0.5125 - rcut_* 0.025;
1120	>	// for values rcut > 20.5, alpha is zero
1121	>	if (alphaVal < 0) alphaVal = 0;
1122	>
1123	>	// throw warning
1124		sprintf( painCave.errMsg,
1125	<	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
1125	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1126	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1127		painCave.isFatal = 0;
1128		simError();
1129		}
1130		} else {
1131		// throw error
1132		sprintf( painCave.errMsg,
1133	<	"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
1133	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1134	>	"\t(Input file specified %s .)\n"
1135	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1136	>	"or \"damped\".\n", myScreen.c_str() );
1137		painCave.isFatal = 1;
1138		simError();
1139		}
#	Line 981 \| Line 1142 \| namespace oopse {
1142
1143		// let's pass some summation method variables to fortran
1144		setElectrostaticSummationMethod( &esm );
1145	+	setFortranElectrostaticMethod( &esm );
1146		setScreeningMethod( &sm );
1147		setDampingAlpha( &alphaVal );
1148		setReactionFieldDielectric( &dielectric );
1149	<	initFortranFF( &esm, &errorOut );
1149	>	initFortranFF( &errorOut );
1150		}
1151
1152		void SimInfo::setupSwitchingFunction() {
#	Line 1013 \| Line 1175 \| namespace oopse {
1175
1176		}
1177
1178	+	void SimInfo::setupAccumulateBoxDipole() {
1179	+
1180	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1181	+	if ( simParams_->haveAccumulateBoxDipole() )
1182	+	if ( simParams_->getAccumulateBoxDipole() ) {
1183	+	setAccumulateBoxDipole();
1184	+	calcBoxDipole_ = true;
1185	+	}
1186	+
1187	+	}
1188	+
1189		void SimInfo::addProperty(GenericData* genData) {
1190		properties_.addProperty(genData);
1191		}
#	Line 1069 \| Line 1242 \| namespace oopse {
1242		Molecule* mol;
1243
1244		Vector3d comVel(0.0);
1245	<	double totalMass = 0.0;
1245	>	RealType totalMass = 0.0;
1246
1247
1248		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1249	<	double mass = mol->getMass();
1249	>	RealType mass = mol->getMass();
1250		totalMass += mass;
1251		comVel += mass * mol->getComVel();
1252		}
1253
1254		#ifdef IS_MPI
1255	<	double tmpMass = totalMass;
1255	>	RealType tmpMass = totalMass;
1256		Vector3d tmpComVel(comVel);
1257	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1258	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1257	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1258	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1259		#endif
1260
1261		comVel /= totalMass;
#	Line 1095 \| Line 1268 \| namespace oopse {
1268		Molecule* mol;
1269
1270		Vector3d com(0.0);
1271	<	double totalMass = 0.0;
1271	>	RealType totalMass = 0.0;
1272
1273		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1274	<	double mass = mol->getMass();
1274	>	RealType mass = mol->getMass();
1275		totalMass += mass;
1276		com += mass * mol->getCom();
1277		}
1278
1279		#ifdef IS_MPI
1280	<	double tmpMass = totalMass;
1280	>	RealType tmpMass = totalMass;
1281		Vector3d tmpCom(com);
1282	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1283	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1282	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1283	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1284		#endif
1285
1286		com /= totalMass;
#	Line 1131 \| Line 1304 \| namespace oopse {
1304		Molecule* mol;
1305
1306
1307	<	double totalMass = 0.0;
1307	>	RealType totalMass = 0.0;
1308
1309
1310		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1311	<	double mass = mol->getMass();
1311	>	RealType mass = mol->getMass();
1312		totalMass += mass;
1313		com += mass * mol->getCom();
1314		comVel += mass * mol->getComVel();
1315		}
1316
1317		#ifdef IS_MPI
1318	<	double tmpMass = totalMass;
1318	>	RealType tmpMass = totalMass;
1319		Vector3d tmpCom(com);
1320		Vector3d tmpComVel(comVel);
1321	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1322	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1323	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1321	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1322	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1323	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1324		#endif
1325
1326		com /= totalMass;
#	Line 1166 \| Line 1339 \| namespace oopse {
1339		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1340
1341
1342	<	double xx = 0.0;
1343	<	double yy = 0.0;
1344	<	double zz = 0.0;
1345	<	double xy = 0.0;
1346	<	double xz = 0.0;
1347	<	double yz = 0.0;
1342	>	RealType xx = 0.0;
1343	>	RealType yy = 0.0;
1344	>	RealType zz = 0.0;
1345	>	RealType xy = 0.0;
1346	>	RealType xz = 0.0;
1347	>	RealType yz = 0.0;
1348		Vector3d com(0.0);
1349		Vector3d comVel(0.0);
1350
#	Line 1183 \| Line 1356 \| namespace oopse {
1356		Vector3d thisq(0.0);
1357		Vector3d thisv(0.0);
1358
1359	<	double thisMass = 0.0;
1359	>	RealType thisMass = 0.0;
1360
1361
1362
#	Line 1221 \| Line 1394 \| namespace oopse {
1394		#ifdef IS_MPI
1395		Mat3x3d tmpI(inertiaTensor);
1396		Vector3d tmpAngMom;
1397	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1398	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1397	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1398	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1399		#endif
1400
1401		return;
#	Line 1243 \| Line 1416 \| namespace oopse {
1416		Vector3d thisr(0.0);
1417		Vector3d thisp(0.0);
1418
1419	<	double thisMass;
1419	>	RealType thisMass;
1420
1421		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1422		thisMass = mol->getMass();
#	Line 1256 \| Line 1429 \| namespace oopse {
1429
1430		#ifdef IS_MPI
1431		Vector3d tmpAngMom;
1432	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1432	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1433		#endif
1434
1435		return angularMomentum;
1436		}
1437
1438	<
1438	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1439	>	return IOIndexToIntegrableObject.at(index);
1440	>	}
1441	>
1442	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1443	>	IOIndexToIntegrableObject= v;
1444	>	}
1445	>
1446	>	/*
1447	>	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1448	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1449	>	sdByGlobalIndex_ = v;
1450	>	}
1451	>
1452	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1453	>	//assert(index < nAtoms_ + nRigidBodies_);
1454	>	return sdByGlobalIndex_.at(index);
1455	>	}
1456	>	*/
1457		}//end namespace oopse
1458

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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 1078 by gezelter, Wed Oct 18 21:58:48 2006 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 1078 by gezelter, Wed Oct 18 21:58:48 2006 UTC