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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 608 by chrisfen, Fri Sep 16 21:07:45 2005 UTC vs.
Revision 1045 by chrisfen, Thu Sep 21 18:25:17 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/notifyCutoffs_interface.h"
62	>	#include "UseTheForce/DarkSide/electrostatic_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 66 \| 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
80	–
81	–	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
98	<	int nGroups = 0; //total cutoff groups defined in meta-data file
98	>	int nGroups = 0; //total cutoff groups defined in meta-data file
99		CutoffGroupStamp* cgStamp;
100		RigidBodyStamp* rbStamp;
101		int nRigidAtoms = 0;
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;
112
99	–
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
122		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
123	+
124		nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
125
126		//calculate atoms in rigid bodies
#	Line 114 \| 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 123 \| Line 137 \| namespace oopse {
137
138		}
139
140	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
141	<	//therefore the total number of cutoff groups in the system is equal to
142	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
143	<	//file plus the number of cutoff groups defined in meta-data file
140	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
141	>	//group therefore the total number of cutoff groups in the system is
142	>	//equal to the total number of atoms minus number of atoms belong to
143	>	//cutoff group defined in meta-data file plus the number of cutoff
144	>	//groups defined in meta-data file
145		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
146
147	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
148	<	//therefore the total number of integrable objects in the system is equal to
149	<	//the total number of atoms minus number of atoms belong to rigid body defined in meta-data
150	<	//file plus the number of rigid bodies defined in meta-data file
151	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
152	<
147	>	//every free atom (atom does not belong to rigid bodies) is an
148	>	//integrable object therefore the total number of integrable objects
149	>	//in the system is equal to the total number of atoms minus number of
150	>	//atoms belong to rigid body defined in meta-data file plus the number
151	>	//of rigid bodies defined in meta-data file
152	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
153	>	+ nGlobalRigidBodies_;
154	>
155		nGlobalMols_ = molStampIds_.size();
156
157		#ifdef IS_MPI
#	Line 150 \| Line 167 \| namespace oopse {
167		}
168		molecules_.clear();
169
153	–	delete stamps_;
170		delete sman_;
171		delete simParams_;
172		delete forceField_;
#	Line 257 \| 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 275 \| 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 337 \| 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 348 \| 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 359 \| 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
371	–	Molecule::RigidBodyIterator rbIter;
372	–	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 394 \| 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 406 \| 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 417 \| 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
428	–	Molecule::RigidBodyIterator rbIter;
429	–	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 465 \| 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 473 \| Line 613 \| namespace oopse {
613		painCave.isFatal = 1;
614		simError();
615		}
476	–
477	–
478	–	setupCutoff();
616
617		calcNdf();
618		calcNdfRaw();
#	Line 510 \| 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 521 \| Line 659 \| namespace oopse {
659		int useDirectionalAtom = 0;
660		int useElectrostatics = 0;
661		//usePBC and useRF are from simParams
662	<	int usePBC = simParams_->getPBC();
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	+
673	+
674	+	if (simParams_->haveElectrostaticSummationMethod()) {
675	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
676	+	toUpper(myMethod);
677	+	if (myMethod == "REACTION_FIELD"){
678	+	useRF=1;
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 578 \| 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
752		temp = useFLARB;
753		MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
754	+
755	+	temp = useRF;
756	+	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
757	+
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 596 \| 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_SF = useSF;
784	+	fInfo_.SIM_uses_SP = useSP;
785	+	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
786
787	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
788	<
787	>	if( myMethod == "REACTION_FIELD") {
788	>
789		if (simParams_->haveDielectric()) {
790		fInfo_.dielect = simParams_->getDielectric();
791		} else {
#	Line 610 \| Line 795 \| namespace oopse {
795		"\tsetting a dielectric constant!\n");
796		painCave.isFatal = 1;
797		simError();
798	<	}
614	<
615	<	} else {
616	<	fInfo_.dielect = 0.0;
798	>	}
799		}
800
801		}
#	Line 632 \| Line 814 \| namespace oopse {
814		}
815
816		//calculate mass ratio of cutoff group
817	<	std::vector<double> mfact;
817	>	std::vector<RealType> mfact;
818		SimInfo::MoleculeIterator mi;
819		Molecule* mol;
820		Molecule::CutoffGroupIterator ci;
821		CutoffGroup* cg;
822		Molecule::AtomIterator ai;
823		Atom* atom;
824	<	double totalMass;
824	>	RealType totalMass;
825
826		//to avoid memory reallocation, reserve enough space for mfact
827		mfact.reserve(getNCutoffGroups());
#	Line 649 \| Line 831 \| namespace oopse {
831
832		totalMass = cg->getMass();
833		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
834	<	mfact.push_back(atom->getMass()/totalMass);
834	>	// Check for massless groups - set mfact to 1 if true
835	>	if (totalMass != 0)
836	>	mfact.push_back(atom->getMass()/totalMass);
837	>	else
838	>	mfact.push_back( 1.0 );
839		}
840
841		}
#	Line 758 \| Line 944 \| namespace oopse {
944
945		#endif
946
947	<	double SimInfo::calcMaxCutoffRadius() {
947	>	void SimInfo::setupCutoff() {
948	>
949	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
950
951	+	// Check the cutoff policy
952	+	int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
953
954	<	std::set<AtomType*> atomTypes;
955	<	std::set<AtomType*>::iterator i;
956	<	std::vector<double> cutoffRadius;
957	<
958	<	//get the unique atom types
769	<	atomTypes = getUniqueAtomTypes();
770	<
771	<	//query the max cutoff radius among these atom types
772	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
773	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
954	>	std::string myPolicy;
955	>	if (forceFieldOptions_.haveCutoffPolicy()){
956	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
957	>	}else if (simParams_->haveCutoffPolicy()) {
958	>	myPolicy = simParams_->getCutoffPolicy();
959		}
960
961	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
962	<	#ifdef IS_MPI
778	<	//pick the max cutoff radius among the processors
779	<	#endif
780	<
781	<	return maxCutoffRadius;
782	<	}
783	<
784	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
785	<
786	<	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
787	<
788	<	if (!simParams_->haveRcut()){
789	<	sprintf(painCave.errMsg,
790	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
791	<	"\tOOPSE will use a default value of 15.0 angstroms"
792	<	"\tfor the cutoffRadius.\n");
793	<	painCave.isFatal = 0;
794	<	simError();
795	<	rcut = 15.0;
796	<	} else{
797	<	rcut = simParams_->getRcut();
798	<	}
799	<
800	<	if (!simParams_->haveRsw()){
801	<	sprintf(painCave.errMsg,
802	<	"SimCreator Warning: No value was set for switchingRadius.\n"
803	<	"\tOOPSE will use a default value of\n"
804	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
805	<	painCave.isFatal = 0;
806	<	simError();
807	<	rsw = 0.95 * rcut;
808	<	} else{
809	<	rsw = simParams_->getRsw();
810	<	}
811	<
812	<	} else {
813	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
814	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
815	<
816	<	if (simParams_->haveRcut()) {
817	<	rcut = simParams_->getRcut();
818	<	} else {
819	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
820	<	rcut = calcMaxCutoffRadius();
821	<	}
822	<
823	<	if (simParams_->haveRsw()) {
824	<	rsw = simParams_->getRsw();
825	<	} else {
826	<	rsw = rcut;
827	<	}
828	<
829	<	}
830	<	}
831	<
832	<	void SimInfo::setupCutoff() {
833	<	getCutoff(rcut_, rsw_);
834	<	double rnblist = rcut_ + 1; // skin of neighbor list
835	<
836	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
837	<
838	<	int cp = TRADITIONAL_CUTOFF_POLICY;
839	<	if (simParams_->haveCutoffPolicy()) {
840	<	std::string myPolicy = simParams_->getCutoffPolicy();
961	>	if (!myPolicy.empty()){
962	>	toUpper(myPolicy);
963		if (myPolicy == "MIX") {
964		cp = MIX_CUTOFF_POLICY;
965		} else {
#	Line 855 \| Line 977 \| namespace oopse {
977		}
978		}
979		}
980	+	}
981	+	notifyFortranCutoffPolicy(&cp);
982	+
983	+	// Check the Skin Thickness for neighborlists
984	+	RealType skin;
985	+	if (simParams_->haveSkinThickness()) {
986	+	skin = simParams_->getSkinThickness();
987	+	notifyFortranSkinThickness(&skin);
988	+	}
989	+
990	+	// Check if the cutoff was set explicitly:
991	+	if (simParams_->haveCutoffRadius()) {
992	+	rcut_ = simParams_->getCutoffRadius();
993	+	if (simParams_->haveSwitchingRadius()) {
994	+	rsw_ = simParams_->getSwitchingRadius();
995	+	} else {
996	+	if (fInfo_.SIM_uses_Charges \|
997	+	fInfo_.SIM_uses_Dipoles \|
998	+	fInfo_.SIM_uses_RF) {
999	+
1000	+	rsw_ = 0.85 * rcut_;
1001	+	sprintf(painCave.errMsg,
1002	+	"SimCreator Warning: No value was set for the switchingRadius.\n"
1003	+	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1004	+	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1005	+	painCave.isFatal = 0;
1006	+	simError();
1007	+	} else {
1008	+	rsw_ = rcut_;
1009	+	sprintf(painCave.errMsg,
1010	+	"SimCreator Warning: No value was set for the switchingRadius.\n"
1011	+	"\tOOPSE will use the same value as the cutoffRadius.\n"
1012	+	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1013	+	painCave.isFatal = 0;
1014	+	simError();
1015	+	}
1016	+	}
1017	+
1018	+	notifyFortranCutoffs(&rcut_, &rsw_);
1019	+
1020	+	} else {
1021	+
1022	+	// For electrostatic atoms, we'll assume a large safe value:
1023	+	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
1024	+	sprintf(painCave.errMsg,
1025	+	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1026	+	"\tOOPSE will use a default value of 15.0 angstroms"
1027	+	"\tfor the cutoffRadius.\n");
1028	+	painCave.isFatal = 0;
1029	+	simError();
1030	+	rcut_ = 15.0;
1031	+
1032	+	if (simParams_->haveElectrostaticSummationMethod()) {
1033	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1034	+	toUpper(myMethod);
1035	+	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
1036	+	if (simParams_->haveSwitchingRadius()){
1037	+	sprintf(painCave.errMsg,
1038	+	"SimInfo Warning: A value was set for the switchingRadius\n"
1039	+	"\teven though the electrostaticSummationMethod was\n"
1040	+	"\tset to %s\n", myMethod.c_str());
1041	+	painCave.isFatal = 1;
1042	+	simError();
1043	+	}
1044	+	}
1045	+	}
1046	+
1047	+	if (simParams_->haveSwitchingRadius()){
1048	+	rsw_ = simParams_->getSwitchingRadius();
1049	+	} else {
1050	+	sprintf(painCave.errMsg,
1051	+	"SimCreator Warning: No value was set for switchingRadius.\n"
1052	+	"\tOOPSE will use a default value of\n"
1053	+	"\t0.85 * cutoffRadius for the switchingRadius\n");
1054	+	painCave.isFatal = 0;
1055	+	simError();
1056	+	rsw_ = 0.85 * rcut_;
1057	+	}
1058	+	notifyFortranCutoffs(&rcut_, &rsw_);
1059	+	} else {
1060	+	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1061	+	// We'll punt and let fortran figure out the cutoffs later.
1062	+
1063	+	notifyFortranYouAreOnYourOwn();
1064	+
1065	+	}
1066		}
859	–	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1067		}
1068
1069		void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1070
1071		int errorOut;
1072		int esm = NONE;
1073	<	double alphaVal;
1074	<
1073	>	int sm = UNDAMPED;
1074	>	RealType alphaVal;
1075	>	RealType dielectric;
1076	>
1077		errorOut = isError;
1078	+	dielectric = simParams_->getDielectric();
1079
1080		if (simParams_->haveElectrostaticSummationMethod()) {
1081		std::string myMethod = simParams_->getElectrostaticSummationMethod();
1082	+	toUpper(myMethod);
1083		if (myMethod == "NONE") {
1084		esm = NONE;
1085		} else {
1086	<	if (myMethod == "UNDAMPED_WOLF") {
1087	<	esm = UNDAMPED_WOLF;
1086	>	if (myMethod == "SWITCHING_FUNCTION") {
1087	>	esm = SWITCHING_FUNCTION;
1088		} else {
1089	<	if (myMethod == "DAMPED_WOLF") {
1090	<	esm = DAMPED_WOLF;
1091	<	if (!simParams_->haveDampingAlpha()) {
1092	<	//throw error
1093	<	sprintf( painCave.errMsg,
883	<	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", simParams_->getDampingAlpha());
884	<	painCave.isFatal = 0;
885	<	simError();
886	<	}
887	<	alphaVal = simParams_->getDampingAlpha();
888	<	} else {
889	<	if (myMethod == "REACTION_FIELD") {
890	<	esm = REACTION_FIELD;
1089	>	if (myMethod == "SHIFTED_POTENTIAL") {
1090	>	esm = SHIFTED_POTENTIAL;
1091	>	} else {
1092	>	if (myMethod == "SHIFTED_FORCE") {
1093	>	esm = SHIFTED_FORCE;
1094		} else {
1095	<	// throw error
1096	<	sprintf( painCave.errMsg,
1097	<	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"undamped_wolf\", \"damped_wolf\", or \"reaction_field\".", myMethod.c_str() );
1098	<	painCave.isFatal = 1;
1099	<	simError();
1100	<	}
1101	<	}
1095	>	if (myMethod == "REACTION_FIELD") {
1096	>	esm = REACTION_FIELD;
1097	>	} else {
1098	>	// throw error
1099	>	sprintf( painCave.errMsg,
1100	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1101	>	"\t(Input file specified %s .)\n"
1102	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1103	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1104	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1105	>	painCave.isFatal = 1;
1106	>	simError();
1107	>	}
1108	>	}
1109	>	}
1110		}
1111		}
1112		}
1113	<	initFortranFF( &esm, &alphaVal, &errorOut );
1113	>
1114	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1115	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1116	>	toUpper(myScreen);
1117	>	if (myScreen == "UNDAMPED") {
1118	>	sm = UNDAMPED;
1119	>	} else {
1120	>	if (myScreen == "DAMPED") {
1121	>	sm = DAMPED;
1122	>	if (!simParams_->haveDampingAlpha()) {
1123	>	// first set a cutoff dependent alpha value
1124	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1125	>	alphaVal = 0.5125 - rcut_* 0.025;
1126	>	// for values rcut > 20.5, alpha is zero
1127	>	if (alphaVal < 0) alphaVal = 0;
1128	>
1129	>	// throw warning
1130	>	sprintf( painCave.errMsg,
1131	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1132	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1133	>	painCave.isFatal = 0;
1134	>	simError();
1135	>	}
1136	>	} else {
1137	>	// throw error
1138	>	sprintf( painCave.errMsg,
1139	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1140	>	"\t(Input file specified %s .)\n"
1141	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1142	>	"or \"damped\".\n", myScreen.c_str() );
1143	>	painCave.isFatal = 1;
1144	>	simError();
1145	>	}
1146	>	}
1147	>	}
1148	>
1149	>	// let's pass some summation method variables to fortran
1150	>	setElectrostaticSummationMethod( &esm );
1151	>	setFortranElectrostaticMethod( &esm );
1152	>	setScreeningMethod( &sm );
1153	>	setDampingAlpha( &alphaVal );
1154	>	setReactionFieldDielectric( &dielectric );
1155	>	initFortranFF( &errorOut );
1156	>	}
1157	>
1158	>	void SimInfo::setupSwitchingFunction() {
1159	>	int ft = CUBIC;
1160	>
1161	>	if (simParams_->haveSwitchingFunctionType()) {
1162	>	std::string funcType = simParams_->getSwitchingFunctionType();
1163	>	toUpper(funcType);
1164	>	if (funcType == "CUBIC") {
1165	>	ft = CUBIC;
1166	>	} else {
1167	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1168	>	ft = FIFTH_ORDER_POLY;
1169	>	} else {
1170	>	// throw error
1171	>	sprintf( painCave.errMsg,
1172	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1173	>	painCave.isFatal = 1;
1174	>	simError();
1175	>	}
1176	>	}
1177	>	}
1178	>
1179	>	// send switching function notification to switcheroo
1180	>	setFunctionType(&ft);
1181	>
1182	>	}
1183	>
1184	>	void SimInfo::setupAccumulateBoxDipole() {
1185	>
1186	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1187	>	if ( simParams_->haveAccumulateBoxDipole() )
1188	>	if ( simParams_->getAccumulateBoxDipole() ) {
1189	>	setAccumulateBoxDipole();
1190	>	calcBoxDipole_ = true;
1191	>	}
1192	>
1193		}
1194
1195		void SimInfo::addProperty(GenericData* genData) {
#	Line 958 \| Line 1248 \| namespace oopse {
1248		Molecule* mol;
1249
1250		Vector3d comVel(0.0);
1251	<	double totalMass = 0.0;
1251	>	RealType totalMass = 0.0;
1252
1253
1254		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1255	<	double mass = mol->getMass();
1255	>	RealType mass = mol->getMass();
1256		totalMass += mass;
1257		comVel += mass * mol->getComVel();
1258		}
1259
1260		#ifdef IS_MPI
1261	<	double tmpMass = totalMass;
1261	>	RealType tmpMass = totalMass;
1262		Vector3d tmpComVel(comVel);
1263	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1264	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1263	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1264	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1265		#endif
1266
1267		comVel /= totalMass;
#	Line 984 \| Line 1274 \| namespace oopse {
1274		Molecule* mol;
1275
1276		Vector3d com(0.0);
1277	<	double totalMass = 0.0;
1277	>	RealType totalMass = 0.0;
1278
1279		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1280	<	double mass = mol->getMass();
1280	>	RealType mass = mol->getMass();
1281		totalMass += mass;
1282		com += mass * mol->getCom();
1283		}
1284
1285		#ifdef IS_MPI
1286	<	double tmpMass = totalMass;
1286	>	RealType tmpMass = totalMass;
1287		Vector3d tmpCom(com);
1288	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1289	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1288	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1289	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1290		#endif
1291
1292		com /= totalMass;
#	Line 1020 \| Line 1310 \| namespace oopse {
1310		Molecule* mol;
1311
1312
1313	<	double totalMass = 0.0;
1313	>	RealType totalMass = 0.0;
1314
1315
1316		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1317	<	double mass = mol->getMass();
1317	>	RealType mass = mol->getMass();
1318		totalMass += mass;
1319		com += mass * mol->getCom();
1320		comVel += mass * mol->getComVel();
1321		}
1322
1323		#ifdef IS_MPI
1324	<	double tmpMass = totalMass;
1324	>	RealType tmpMass = totalMass;
1325		Vector3d tmpCom(com);
1326		Vector3d tmpComVel(comVel);
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);
1329	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.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	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1330		#endif
1331
1332		com /= totalMass;
#	Line 1055 \| Line 1345 \| namespace oopse {
1345		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1346
1347
1348	<	double xx = 0.0;
1349	<	double yy = 0.0;
1350	<	double zz = 0.0;
1351	<	double xy = 0.0;
1352	<	double xz = 0.0;
1353	<	double yz = 0.0;
1348	>	RealType xx = 0.0;
1349	>	RealType yy = 0.0;
1350	>	RealType zz = 0.0;
1351	>	RealType xy = 0.0;
1352	>	RealType xz = 0.0;
1353	>	RealType yz = 0.0;
1354		Vector3d com(0.0);
1355		Vector3d comVel(0.0);
1356
#	Line 1072 \| Line 1362 \| namespace oopse {
1362		Vector3d thisq(0.0);
1363		Vector3d thisv(0.0);
1364
1365	<	double thisMass = 0.0;
1365	>	RealType thisMass = 0.0;
1366
1367
1368
#	Line 1110 \| Line 1400 \| namespace oopse {
1400		#ifdef IS_MPI
1401		Mat3x3d tmpI(inertiaTensor);
1402		Vector3d tmpAngMom;
1403	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1404	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1403	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1404	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1405		#endif
1406
1407		return;
#	Line 1132 \| Line 1422 \| namespace oopse {
1422		Vector3d thisr(0.0);
1423		Vector3d thisp(0.0);
1424
1425	<	double thisMass;
1425	>	RealType thisMass;
1426
1427		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1428		thisMass = mol->getMass();
#	Line 1145 \| Line 1435 \| namespace oopse {
1435
1436		#ifdef IS_MPI
1437		Vector3d tmpAngMom;
1438	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1438	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1439		#endif
1440
1441		return angularMomentum;
1442		}
1443
1444	<
1444	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1445	>	return IOIndexToIntegrableObject.at(index);
1446	>	}
1447	>
1448	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1449	>	IOIndexToIntegrableObject= v;
1450	>	}
1451	>
1452	>	/*
1453	>	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1454	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1455	>	sdByGlobalIndex_ = v;
1456	>	}
1457	>
1458	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1459	>	//assert(index < nAtoms_ + nRigidBodies_);
1460	>	return sdByGlobalIndex_.at(index);
1461	>	}
1462	>	*/
1463		}//end namespace oopse
1464

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Comparing trunk/src/brains/SimInfo.cpp (file contents): Revision 608 by chrisfen, Fri Sep 16 21:07:45 2005 UTC vs. Revision 1045 by chrisfen, Thu Sep 21 18:25:17 2006 UTC

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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 608 by chrisfen, Fri Sep 16 21:07:45 2005 UTC vs.
Revision 1045 by chrisfen, Thu Sep 21 18:25:17 2006 UTC