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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 726 by chrisfen, Fri Nov 11 15:22:11 2005 UTC vs.
Revision 998 by chrisfen, Mon Jul 3 13:18:43 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"
#	Line 58 \| Line 59
59		#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
60		#include "UseTheForce/doForces_interface.h"
61		#include "UseTheForce/DarkSide/electrostatic_interface.h"
61	–	#include "UseTheForce/notifyCutoffs_interface.h"
62		#include "UseTheForce/DarkSide/switcheroo_interface.h"
63		#include "utils/MemoryUtils.hpp"
64		#include "utils/simError.h"
65		#include "selection/SelectionManager.hpp"
66	+	#include "io/ForceFieldOptions.hpp"
67	+	#include "UseTheForce/ForceField.hpp"
68
69		#ifdef IS_MPI
70		#include "UseTheForce/mpiComponentPlan.h"
#	Line 70 \| Line 72 \| namespace oopse {
72		#endif
73
74		namespace oopse {
75	+	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
76	+	std::map<int, std::set<int> >::iterator i = container.find(index);
77	+	std::set<int> result;
78	+	if (i != container.end()) {
79	+	result = i->second;
80	+	}
81
82	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
83	<	ForceField* ff, Globals* simParams) :
84	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
85	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
82	>	return result;
83	>	}
84	>
85	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
86	>	forceField_(ff), simParams_(simParams),
87	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
88		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
89		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
90		nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
91		nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
92	<	sman_(NULL), fortranInitialized_(false) {
92	>	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) {
93
84	–
85	–	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
94		MoleculeStamp* molStamp;
95		int nMolWithSameStamp;
96		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
#	Line 90 \| Line 98 \| namespace oopse {
98		CutoffGroupStamp* cgStamp;
99		RigidBodyStamp* rbStamp;
100		int nRigidAtoms = 0;
101	<
102	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
103	<	molStamp = i->first;
104	<	nMolWithSameStamp = i->second;
101	>	std::vector<Component*> components = simParams->getComponents();
102	>
103	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
104	>	molStamp = (*i)->getMoleculeStamp();
105	>	nMolWithSameStamp = (*i)->getNMol();
106
107		addMoleculeStamp(molStamp, nMolWithSameStamp);
108
109		//calculate atoms in molecules
110		nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
111
103	–
112		//calculate atoms in cutoff groups
113		int nAtomsInGroups = 0;
114		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
115
116		for (int j=0; j < nCutoffGroupsInStamp; j++) {
117	<	cgStamp = molStamp->getCutoffGroup(j);
117	>	cgStamp = molStamp->getCutoffGroupStamp(j);
118		nAtomsInGroups += cgStamp->getNMembers();
119		}
120
#	Line 119 \| Line 127 \| namespace oopse {
127		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
128
129		for (int j=0; j < nRigidBodiesInStamp; j++) {
130	<	rbStamp = molStamp->getRigidBody(j);
130	>	rbStamp = molStamp->getRigidBodyStamp(j);
131		nAtomsInRigidBodies += rbStamp->getNMembers();
132		}
133
#	Line 158 \| Line 166 \| namespace oopse {
166		}
167		molecules_.clear();
168
161	–	delete stamps_;
169		delete sman_;
170		delete simParams_;
171		delete forceField_;
#	Line 265 \| Line 272 \| namespace oopse {
272		}
273		}
274
275	<	}//end for (integrableObject)
276	<	}// end for (mol)
275	>	}
276	>	}
277
278		// n_constraints is local, so subtract them on each processor
279		ndf_local -= nConstraints_;
#	Line 283 \| Line 290 \| namespace oopse {
290
291		}
292
293	+	int SimInfo::getFdf() {
294	+	#ifdef IS_MPI
295	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
296	+	#else
297	+	fdf_ = fdf_local;
298	+	#endif
299	+	return fdf_;
300	+	}
301	+
302		void SimInfo::calcNdfRaw() {
303		int ndfRaw_local;
304
#	Line 345 \| Line 361 \| namespace oopse {
361		int b;
362		int c;
363		int d;
364	+
365	+	std::map<int, std::set<int> > atomGroups;
366	+
367	+	Molecule::RigidBodyIterator rbIter;
368	+	RigidBody* rb;
369	+	Molecule::IntegrableObjectIterator ii;
370	+	StuntDouble* integrableObject;
371	+
372	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
373	+	integrableObject = mol->nextIntegrableObject(ii)) {
374	+
375	+	if (integrableObject->isRigidBody()) {
376	+	rb = static_cast<RigidBody*>(integrableObject);
377	+	std::vector<Atom*> atoms = rb->getAtoms();
378	+	std::set<int> rigidAtoms;
379	+	for (int i = 0; i < atoms.size(); ++i) {
380	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
381	+	}
382	+	for (int i = 0; i < atoms.size(); ++i) {
383	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
384	+	}
385	+	} else {
386	+	std::set<int> oneAtomSet;
387	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
388	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
389	+	}
390	+	}
391	+
392
393	+
394		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
395		a = bond->getAtomA()->getGlobalIndex();
396		b = bond->getAtomB()->getGlobalIndex();
#	Line 356 \| Line 401 \| namespace oopse {
401		a = bend->getAtomA()->getGlobalIndex();
402		b = bend->getAtomB()->getGlobalIndex();
403		c = bend->getAtomC()->getGlobalIndex();
404	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
405	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
406	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
407
408	<	exclude_.addPair(a, b);
409	<	exclude_.addPair(a, c);
410	<	exclude_.addPair(b, c);
408	>	exclude_.addPairs(rigidSetA, rigidSetB);
409	>	exclude_.addPairs(rigidSetA, rigidSetC);
410	>	exclude_.addPairs(rigidSetB, rigidSetC);
411	>
412	>	//exclude_.addPair(a, b);
413	>	//exclude_.addPair(a, c);
414	>	//exclude_.addPair(b, c);
415		}
416
417		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
#	Line 367 \| Line 419 \| namespace oopse {
419		b = torsion->getAtomB()->getGlobalIndex();
420		c = torsion->getAtomC()->getGlobalIndex();
421		d = torsion->getAtomD()->getGlobalIndex();
422	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
423	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
424	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
425	+	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
426
427	+	exclude_.addPairs(rigidSetA, rigidSetB);
428	+	exclude_.addPairs(rigidSetA, rigidSetC);
429	+	exclude_.addPairs(rigidSetA, rigidSetD);
430	+	exclude_.addPairs(rigidSetB, rigidSetC);
431	+	exclude_.addPairs(rigidSetB, rigidSetD);
432	+	exclude_.addPairs(rigidSetC, rigidSetD);
433	+
434	+	/*
435	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
436	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
437	+	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
438	+	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
439	+	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
440	+	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
441	+
442	+
443		exclude_.addPair(a, b);
444		exclude_.addPair(a, c);
445		exclude_.addPair(a, d);
446		exclude_.addPair(b, c);
447		exclude_.addPair(b, d);
448		exclude_.addPair(c, d);
449	+	*/
450		}
451
379	–	Molecule::RigidBodyIterator rbIter;
380	–	RigidBody* rb;
452		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
453		std::vector<Atom*> atoms = rb->getAtoms();
454		for (int i = 0; i < atoms.size() -1 ; ++i) {
#	Line 402 \| Line 473 \| namespace oopse {
473		int b;
474		int c;
475		int d;
476	+
477	+	std::map<int, std::set<int> > atomGroups;
478	+
479	+	Molecule::RigidBodyIterator rbIter;
480	+	RigidBody* rb;
481	+	Molecule::IntegrableObjectIterator ii;
482	+	StuntDouble* integrableObject;
483	+
484	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
485	+	integrableObject = mol->nextIntegrableObject(ii)) {
486	+
487	+	if (integrableObject->isRigidBody()) {
488	+	rb = static_cast<RigidBody*>(integrableObject);
489	+	std::vector<Atom*> atoms = rb->getAtoms();
490	+	std::set<int> rigidAtoms;
491	+	for (int i = 0; i < atoms.size(); ++i) {
492	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
493	+	}
494	+	for (int i = 0; i < atoms.size(); ++i) {
495	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
496	+	}
497	+	} else {
498	+	std::set<int> oneAtomSet;
499	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
500	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
501	+	}
502	+	}
503	+
504
505		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
506		a = bond->getAtomA()->getGlobalIndex();
#	Line 414 \| Line 513 \| namespace oopse {
513		b = bend->getAtomB()->getGlobalIndex();
514		c = bend->getAtomC()->getGlobalIndex();
515
516	<	exclude_.removePair(a, b);
517	<	exclude_.removePair(a, c);
518	<	exclude_.removePair(b, c);
516	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
517	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
518	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
519	>
520	>	exclude_.removePairs(rigidSetA, rigidSetB);
521	>	exclude_.removePairs(rigidSetA, rigidSetC);
522	>	exclude_.removePairs(rigidSetB, rigidSetC);
523	>
524	>	//exclude_.removePair(a, b);
525	>	//exclude_.removePair(a, c);
526	>	//exclude_.removePair(b, c);
527		}
528
529		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
#	Line 425 \| Line 532 \| namespace oopse {
532		c = torsion->getAtomC()->getGlobalIndex();
533		d = torsion->getAtomD()->getGlobalIndex();
534
535	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
536	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
537	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
538	+	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
539	+
540	+	exclude_.removePairs(rigidSetA, rigidSetB);
541	+	exclude_.removePairs(rigidSetA, rigidSetC);
542	+	exclude_.removePairs(rigidSetA, rigidSetD);
543	+	exclude_.removePairs(rigidSetB, rigidSetC);
544	+	exclude_.removePairs(rigidSetB, rigidSetD);
545	+	exclude_.removePairs(rigidSetC, rigidSetD);
546	+
547	+	/*
548	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
549	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
550	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
551	+	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
552	+	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
553	+	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
554	+
555	+
556		exclude_.removePair(a, b);
557		exclude_.removePair(a, c);
558		exclude_.removePair(a, d);
559		exclude_.removePair(b, c);
560		exclude_.removePair(b, d);
561		exclude_.removePair(c, d);
562	+	*/
563		}
564
436	–	Molecule::RigidBodyIterator rbIter;
437	–	RigidBody* rb;
565		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
566		std::vector<Atom*> atoms = rb->getAtoms();
567		for (int i = 0; i < atoms.size() -1 ; ++i) {
#	Line 475 \| Line 602 \| namespace oopse {
602
603		setupElectrostaticSummationMethod( isError );
604		setupSwitchingFunction();
605	+	setupAccumulateBoxDipole();
606
607		if(isError){
608		sprintf( painCave.errMsg,
#	Line 519 \| 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 533 \| 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
#	Line 543 \| Line 674 \| namespace oopse {
674		if (simParams_->haveElectrostaticSummationMethod()) {
675		std::string myMethod = simParams_->getElectrostaticSummationMethod();
676		toUpper(myMethod);
677	<	if (myMethod == "REACTION_FIELD") {
677	>	if (myMethod == "REACTION_FIELD"){
678		useRF=1;
679	<	} else {
680	<	if (myMethod == "SHIFTED_FORCE") {
681	<	useSF = 1;
682	<	}
679	>	} else if (myMethod == "SHIFTED_FORCE"){
680	>	useSF = 1;
681	>	} else if (myMethod == "SHIFTED_POTENTIAL"){
682	>	useSP = 1;
683		}
684		}
685	+
686	+	if (simParams_->haveAccumulateBoxDipole())
687	+	if (simParams_->getAccumulateBoxDipole())
688	+	useBoxDipole = 1;
689
690		//loop over all of the atom types
691		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
692		useLennardJones \|= (*i)->isLennardJones();
693		useElectrostatic \|= (*i)->isElectrostatic();
694		useEAM \|= (*i)->isEAM();
695	+	useSC \|= (*i)->isSC();
696		useCharge \|= (*i)->isCharge();
697		useDirectional \|= (*i)->isDirectional();
698		useDipole \|= (*i)->isDipole();
#	Line 607 \| Line 743 \| namespace oopse {
743		temp = useEAM;
744		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
745
746	+	temp = useSC;
747	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
748	+
749		temp = useShape;
750		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
751
#	Line 617 \| Line 756 \| namespace oopse {
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);
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 631 \| 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( myMethod == "REACTION_FIELD") {
788
#	Line 666 \| 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 796 \| 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
807	<	atomTypes = getUniqueAtomTypes();
808	<
809	<	//query the max cutoff radius among these atom types
810	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
811	<	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		}
813	–
814	–	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
815	–	#ifdef IS_MPI
816	–	//pick the max cutoff radius among the processors
817	–	#endif
960
961	<	return maxCutoffRadius;
820	<	}
821	<
822	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
823	<
824	<	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
825	<
826	<	if (!simParams_->haveCutoffRadius()){
827	<	sprintf(painCave.errMsg,
828	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
829	<	"\tOOPSE will use a default value of 15.0 angstroms"
830	<	"\tfor the cutoffRadius.\n");
831	<	painCave.isFatal = 0;
832	<	simError();
833	<	rcut = 15.0;
834	<	} else{
835	<	rcut = simParams_->getCutoffRadius();
836	<	}
837	<
838	<	if (!simParams_->haveSwitchingRadius()){
839	<	sprintf(painCave.errMsg,
840	<	"SimCreator Warning: No value was set for switchingRadius.\n"
841	<	"\tOOPSE will use a default value of\n"
842	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
843	<	painCave.isFatal = 0;
844	<	simError();
845	<	rsw = 0.85 * rcut;
846	<	} else{
847	<	rsw = simParams_->getSwitchingRadius();
848	<	}
849	<
850	<	} else {
851	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
852	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
853	<
854	<	if (simParams_->haveCutoffRadius()) {
855	<	rcut = simParams_->getCutoffRadius();
856	<	} else {
857	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
858	<	rcut = calcMaxCutoffRadius();
859	<	}
860	<
861	<	if (simParams_->haveSwitchingRadius()) {
862	<	rsw = simParams_->getSwitchingRadius();
863	<	} else {
864	<	rsw = rcut;
865	<	}
866	<
867	<	}
868	<	}
869	<
870	<	void SimInfo::setupCutoff() {
871	<	getCutoff(rcut_, rsw_);
872	<	double rnblist = rcut_ + 1; // skin of neighbor list
873	<
874	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
875	<
876	<	int cp = TRADITIONAL_CUTOFF_POLICY;
877	<	if (simParams_->haveCutoffPolicy()) {
878	<	std::string myPolicy = simParams_->getCutoffPolicy();
961	>	if (!myPolicy.empty()){
962		toUpper(myPolicy);
963		if (myPolicy == "MIX") {
964		cp = MIX_CUTOFF_POLICY;
#	Line 894 \| Line 977 \| namespace oopse {
977		}
978		}
979		}
980	<	}
980	>	}
981	>	notifyFortranCutoffPolicy(&cp);
982
983	<
983	>	// Check the Skin Thickness for neighborlists
984	>	RealType skin;
985		if (simParams_->haveSkinThickness()) {
986	<	double skinThickness = simParams_->getSkinThickness();
987	<	}
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	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1066	<	// also send cutoff notification to electrostatics
906	<	setElectrostaticCutoffRadius(&rcut_, &rsw_);
1065	>	}
1066	>	}
1067		}
1068
1069		void SimInfo::setupElectrostaticSummationMethod( int isError ) {
#	Line 911 \| Line 1071 \| namespace oopse {
1071		int errorOut;
1072		int esm = NONE;
1073		int sm = UNDAMPED;
1074	<	double alphaVal;
1075	<	double dielectric;
1074	>	RealType alphaVal;
1075	>	RealType dielectric;
1076
1077		errorOut = isError;
1078		alphaVal = simParams_->getDampingAlpha();
#	Line 938 \| Line 1098 \| namespace oopse {
1098		} else {
1099		// throw error
1100		sprintf( painCave.errMsg,
1101	<	"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() );
1101	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1102	>	"\t(Input file specified %s .)\n"
1103	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1104	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1105	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1106		painCave.isFatal = 1;
1107		simError();
1108		}
#	Line 959 \| Line 1123 \| namespace oopse {
1123		if (!simParams_->haveDampingAlpha()) {
1124		//throw error
1125		sprintf( painCave.errMsg,
1126	<	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
1126	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1127	>	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1128		painCave.isFatal = 0;
1129		simError();
1130		}
1131		} else {
1132		// throw error
1133		sprintf( painCave.errMsg,
1134	<	"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
1134	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1135	>	"\t(Input file specified %s .)\n"
1136	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1137	>	"or \"damped\".\n", myScreen.c_str() );
1138		painCave.isFatal = 1;
1139		simError();
1140		}
#	Line 975 \| Line 1143 \| namespace oopse {
1143
1144		// let's pass some summation method variables to fortran
1145		setElectrostaticSummationMethod( &esm );
1146	+	setFortranElectrostaticMethod( &esm );
1147		setScreeningMethod( &sm );
1148		setDampingAlpha( &alphaVal );
1149		setReactionFieldDielectric( &dielectric );
1150	<	initFortranFF( &esm, &errorOut );
1150	>	initFortranFF( &errorOut );
1151		}
1152
1153		void SimInfo::setupSwitchingFunction() {
#	Line 1004 \| Line 1173 \| namespace oopse {
1173
1174		// send switching function notification to switcheroo
1175		setFunctionType(&ft);
1176	+
1177	+	}
1178	+
1179	+	void SimInfo::setupAccumulateBoxDipole() {
1180	+
1181	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1182	+	if ( simParams_->haveAccumulateBoxDipole() )
1183	+	if ( simParams_->getAccumulateBoxDipole() ) {
1184	+	setAccumulateBoxDipole();
1185	+	calcBoxDipole_ = true;
1186	+	}
1187
1188		}
1189
#	Line 1063 \| Line 1243 \| namespace oopse {
1243		Molecule* mol;
1244
1245		Vector3d comVel(0.0);
1246	<	double totalMass = 0.0;
1246	>	RealType totalMass = 0.0;
1247
1248
1249		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1250	<	double mass = mol->getMass();
1250	>	RealType mass = mol->getMass();
1251		totalMass += mass;
1252		comVel += mass * mol->getComVel();
1253		}
1254
1255		#ifdef IS_MPI
1256	<	double tmpMass = totalMass;
1256	>	RealType tmpMass = totalMass;
1257		Vector3d tmpComVel(comVel);
1258	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1259	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1258	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1259	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1260		#endif
1261
1262		comVel /= totalMass;
#	Line 1089 \| Line 1269 \| namespace oopse {
1269		Molecule* mol;
1270
1271		Vector3d com(0.0);
1272	<	double totalMass = 0.0;
1272	>	RealType totalMass = 0.0;
1273
1274		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1275	<	double mass = mol->getMass();
1275	>	RealType mass = mol->getMass();
1276		totalMass += mass;
1277		com += mass * mol->getCom();
1278		}
1279
1280		#ifdef IS_MPI
1281	<	double tmpMass = totalMass;
1281	>	RealType tmpMass = totalMass;
1282		Vector3d tmpCom(com);
1283	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1284	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1283	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1284	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1285		#endif
1286
1287		com /= totalMass;
#	Line 1125 \| Line 1305 \| namespace oopse {
1305		Molecule* mol;
1306
1307
1308	<	double totalMass = 0.0;
1308	>	RealType totalMass = 0.0;
1309
1310
1311		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1312	<	double mass = mol->getMass();
1312	>	RealType mass = mol->getMass();
1313		totalMass += mass;
1314		com += mass * mol->getCom();
1315		comVel += mass * mol->getComVel();
1316		}
1317
1318		#ifdef IS_MPI
1319	<	double tmpMass = totalMass;
1319	>	RealType tmpMass = totalMass;
1320		Vector3d tmpCom(com);
1321		Vector3d tmpComVel(comVel);
1322	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1323	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1324	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1322	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1323	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1324	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1325		#endif
1326
1327		com /= totalMass;
#	Line 1160 \| Line 1340 \| namespace oopse {
1340		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1341
1342
1343	<	double xx = 0.0;
1344	<	double yy = 0.0;
1345	<	double zz = 0.0;
1346	<	double xy = 0.0;
1347	<	double xz = 0.0;
1348	<	double yz = 0.0;
1343	>	RealType xx = 0.0;
1344	>	RealType yy = 0.0;
1345	>	RealType zz = 0.0;
1346	>	RealType xy = 0.0;
1347	>	RealType xz = 0.0;
1348	>	RealType yz = 0.0;
1349		Vector3d com(0.0);
1350		Vector3d comVel(0.0);
1351
#	Line 1177 \| Line 1357 \| namespace oopse {
1357		Vector3d thisq(0.0);
1358		Vector3d thisv(0.0);
1359
1360	<	double thisMass = 0.0;
1360	>	RealType thisMass = 0.0;
1361
1362
1363
#	Line 1215 \| Line 1395 \| namespace oopse {
1395		#ifdef IS_MPI
1396		Mat3x3d tmpI(inertiaTensor);
1397		Vector3d tmpAngMom;
1398	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1399	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1398	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1399	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1400		#endif
1401
1402		return;
#	Line 1237 \| Line 1417 \| namespace oopse {
1417		Vector3d thisr(0.0);
1418		Vector3d thisp(0.0);
1419
1420	<	double thisMass;
1420	>	RealType thisMass;
1421
1422		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1423		thisMass = mol->getMass();
#	Line 1250 \| Line 1430 \| namespace oopse {
1430
1431		#ifdef IS_MPI
1432		Vector3d tmpAngMom;
1433	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1433	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1434		#endif
1435
1436		return angularMomentum;

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Comparing trunk/src/brains/SimInfo.cpp (file contents): Revision 726 by chrisfen, Fri Nov 11 15:22:11 2005 UTC vs. Revision 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC

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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 726 by chrisfen, Fri Nov 11 15:22:11 2005 UTC vs.
Revision 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC