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

Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1550 by gezelter, Wed Apr 27 21:49:59 2011 UTC

#	Line 54 \| Line 54
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56		#include "primitives/StuntDouble.hpp"
57	–	#include "UseTheForce/fCutoffPolicy.h"
58	–	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	–	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60	–	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61	–	#include "UseTheForce/doForces_interface.h"
62	–	#include "UseTheForce/DarkSide/neighborLists_interface.h"
63	–	#include "UseTheForce/DarkSide/electrostatic_interface.h"
64	–	#include "UseTheForce/DarkSide/switcheroo_interface.h"
57		#include "utils/MemoryUtils.hpp"
58		#include "utils/simError.h"
59		#include "selection/SelectionManager.hpp"
60		#include "io/ForceFieldOptions.hpp"
61		#include "UseTheForce/ForceField.hpp"
62	+	#include "nonbonded/SwitchingFunction.hpp"
63
64	<
72	<	#ifdef IS_MPI
73	<	#include "UseTheForce/mpiComponentPlan.h"
74	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
75	<	#endif
76	<
64	>	using namespace std;
65		namespace OpenMD {
78	–	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79	–	std::map<int, std::set<int> >::iterator i = container.find(index);
80	–	std::set<int> result;
81	–	if (i != container.end()) {
82	–	result = i->second;
83	–	}
84	–
85	–	return result;
86	–	}
66
67		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
68		forceField_(ff), simParams_(simParams),
#	Line 93 \| Line 72 \| namespace OpenMD {
72		nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0),
73		nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
74		nConstraints_(0), sman_(NULL), fortranInitialized_(false),
75	<	calcBoxDipole_(false), useAtomicVirial_(true) {
76	<
77	<
78	<	MoleculeStamp* molStamp;
79	<	int nMolWithSameStamp;
80	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
81	<	int nGroups = 0; //total cutoff groups defined in meta-data file
82	<	CutoffGroupStamp* cgStamp;
83	<	RigidBodyStamp* rbStamp;
84	<	int nRigidAtoms = 0;
85	<
86	<	std::vector<Component*> components = simParams->getComponents();
75	>	calcBoxDipole_(false), useAtomicVirial_(true) {
76	>
77	>	MoleculeStamp* molStamp;
78	>	int nMolWithSameStamp;
79	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
80	>	int nGroups = 0; //total cutoff groups defined in meta-data file
81	>	CutoffGroupStamp* cgStamp;
82	>	RigidBodyStamp* rbStamp;
83	>	int nRigidAtoms = 0;
84	>
85	>	vector<Component*> components = simParams->getComponents();
86	>
87	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
88	>	molStamp = (*i)->getMoleculeStamp();
89	>	nMolWithSameStamp = (*i)->getNMol();
90
91	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
92	<	molStamp = (*i)->getMoleculeStamp();
93	<	nMolWithSameStamp = (*i)->getNMol();
94	<
95	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
96	<
97	<	//calculate atoms in molecules
98	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
99	<
100	<	//calculate atoms in cutoff groups
101	<	int nAtomsInGroups = 0;
102	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
121	<
122	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
123	<	cgStamp = molStamp->getCutoffGroupStamp(j);
124	<	nAtomsInGroups += cgStamp->getNMembers();
125	<	}
126	<
127	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
128	<
129	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
130	<
131	<	//calculate atoms in rigid bodies
132	<	int nAtomsInRigidBodies = 0;
133	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
134	<
135	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
136	<	rbStamp = molStamp->getRigidBodyStamp(j);
137	<	nAtomsInRigidBodies += rbStamp->getNMembers();
138	<	}
139	<
140	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
141	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
142	<
91	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
92	>
93	>	//calculate atoms in molecules
94	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
95	>
96	>	//calculate atoms in cutoff groups
97	>	int nAtomsInGroups = 0;
98	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
99	>
100	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
101	>	cgStamp = molStamp->getCutoffGroupStamp(j);
102	>	nAtomsInGroups += cgStamp->getNMembers();
103		}
104	<
105	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
106	<	//group therefore the total number of cutoff groups in the system is
107	<	//equal to the total number of atoms minus number of atoms belong to
108	<	//cutoff group defined in meta-data file plus the number of cutoff
109	<	//groups defined in meta-data file
110	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
111	<
112	<	//every free atom (atom does not belong to rigid bodies) is an
113	<	//integrable object therefore the total number of integrable objects
114	<	//in the system is equal to the total number of atoms minus number of
115	<	//atoms belong to rigid body defined in meta-data file plus the number
116	<	//of rigid bodies defined in meta-data file
117	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
118	<	+ nGlobalRigidBodies_;
119	<
120	<	nGlobalMols_ = molStampIds_.size();
161	<	molToProcMap_.resize(nGlobalMols_);
104	>
105	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
106	>
107	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
108	>
109	>	//calculate atoms in rigid bodies
110	>	int nAtomsInRigidBodies = 0;
111	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
112	>
113	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
114	>	rbStamp = molStamp->getRigidBodyStamp(j);
115	>	nAtomsInRigidBodies += rbStamp->getNMembers();
116	>	}
117	>
118	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
119	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
120	>
121		}
122	+
123	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
124	+	//group therefore the total number of cutoff groups in the system is
125	+	//equal to the total number of atoms minus number of atoms belong to
126	+	//cutoff group defined in meta-data file plus the number of cutoff
127	+	//groups defined in meta-data file
128	+	std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
129	+	std::cerr << "nCA = " << nCutoffAtoms << "\n";
130	+	std::cerr << "nG = " << nGroups << "\n";
131
132	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
133	+
134	+	std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
135	+
136	+	//every free atom (atom does not belong to rigid bodies) is an
137	+	//integrable object therefore the total number of integrable objects
138	+	//in the system is equal to the total number of atoms minus number of
139	+	//atoms belong to rigid body defined in meta-data file plus the number
140	+	//of rigid bodies defined in meta-data file
141	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
142	+	+ nGlobalRigidBodies_;
143	+
144	+	nGlobalMols_ = molStampIds_.size();
145	+	molToProcMap_.resize(nGlobalMols_);
146	+	}
147	+
148		SimInfo::~SimInfo() {
149	<	std::map<int, Molecule*>::iterator i;
149	>	map<int, Molecule*>::iterator i;
150		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
151		delete i->second;
152		}
#	Line 173 \| Line 157 \| namespace OpenMD {
157		delete forceField_;
158		}
159
176	–	int SimInfo::getNGlobalConstraints() {
177	–	int nGlobalConstraints;
178	–	#ifdef IS_MPI
179	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
180	–	MPI_COMM_WORLD);
181	–	#else
182	–	nGlobalConstraints = nConstraints_;
183	–	#endif
184	–	return nGlobalConstraints;
185	–	}
160
161		bool SimInfo::addMolecule(Molecule* mol) {
162		MoleculeIterator i;
163	<
163	>
164		i = molecules_.find(mol->getGlobalIndex());
165		if (i == molecules_.end() ) {
166	<
167	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
168	<
166	>
167	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
168	>
169		nAtoms_ += mol->getNAtoms();
170		nBonds_ += mol->getNBonds();
171		nBends_ += mol->getNBends();
#	Line 201 \| Line 175 \| namespace OpenMD {
175		nIntegrableObjects_ += mol->getNIntegrableObjects();
176		nCutoffGroups_ += mol->getNCutoffGroups();
177		nConstraints_ += mol->getNConstraintPairs();
178	<
178	>
179		addInteractionPairs(mol);
180	<
180	>
181		return true;
182		} else {
183		return false;
184		}
185		}
186	<
186	>
187		bool SimInfo::removeMolecule(Molecule* mol) {
188		MoleculeIterator i;
189		i = molecules_.find(mol->getGlobalIndex());
#	Line 237 \| Line 211 \| namespace OpenMD {
211		} else {
212		return false;
213		}
240	–
241	–
214		}
215
216
#	Line 256 \| Line 228 \| namespace OpenMD {
228		void SimInfo::calcNdf() {
229		int ndf_local;
230		MoleculeIterator i;
231	<	std::vector<StuntDouble*>::iterator j;
231	>	vector<StuntDouble*>::iterator j;
232		Molecule* mol;
233		StuntDouble* integrableObject;
234
#	Line 307 \| Line 279 \| namespace OpenMD {
279		int ndfRaw_local;
280
281		MoleculeIterator i;
282	<	std::vector<StuntDouble*>::iterator j;
282	>	vector<StuntDouble*>::iterator j;
283		Molecule* mol;
284		StuntDouble* integrableObject;
285
#	Line 356 \| Line 328 \| namespace OpenMD {
328
329		void SimInfo::addInteractionPairs(Molecule* mol) {
330		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
331	<	std::vector<Bond*>::iterator bondIter;
332	<	std::vector<Bend*>::iterator bendIter;
333	<	std::vector<Torsion*>::iterator torsionIter;
334	<	std::vector<Inversion*>::iterator inversionIter;
331	>	vector<Bond*>::iterator bondIter;
332	>	vector<Bend*>::iterator bendIter;
333	>	vector<Torsion*>::iterator torsionIter;
334	>	vector<Inversion*>::iterator inversionIter;
335		Bond* bond;
336		Bend* bend;
337		Torsion* torsion;
#	Line 377 \| Line 349 \| namespace OpenMD {
349		// always be excluded. These are done at the bottom of this
350		// function.
351
352	<	std::map<int, std::set<int> > atomGroups;
352	>	map<int, set<int> > atomGroups;
353		Molecule::RigidBodyIterator rbIter;
354		RigidBody* rb;
355		Molecule::IntegrableObjectIterator ii;
#	Line 389 \| Line 361 \| namespace OpenMD {
361
362		if (integrableObject->isRigidBody()) {
363		rb = static_cast<RigidBody*>(integrableObject);
364	<	std::vector<Atom*> atoms = rb->getAtoms();
365	<	std::set<int> rigidAtoms;
364	>	vector<Atom*> atoms = rb->getAtoms();
365	>	set<int> rigidAtoms;
366		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
367		rigidAtoms.insert(atoms[i]->getGlobalIndex());
368		}
369		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
370	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
370	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
371		}
372		} else {
373	<	std::set<int> oneAtomSet;
373	>	set<int> oneAtomSet;
374		oneAtomSet.insert(integrableObject->getGlobalIndex());
375	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
375	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
376		}
377		}
378
#	Line 503 \| Line 475 \| namespace OpenMD {
475
476		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
477		rb = mol->nextRigidBody(rbIter)) {
478	<	std::vector<Atom*> atoms = rb->getAtoms();
478	>	vector<Atom*> atoms = rb->getAtoms();
479		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
480		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
481		a = atoms[i]->getGlobalIndex();
#	Line 517 \| Line 489 \| namespace OpenMD {
489
490		void SimInfo::removeInteractionPairs(Molecule* mol) {
491		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
492	<	std::vector<Bond*>::iterator bondIter;
493	<	std::vector<Bend*>::iterator bendIter;
494	<	std::vector<Torsion*>::iterator torsionIter;
495	<	std::vector<Inversion*>::iterator inversionIter;
492	>	vector<Bond*>::iterator bondIter;
493	>	vector<Bend*>::iterator bendIter;
494	>	vector<Torsion*>::iterator torsionIter;
495	>	vector<Inversion*>::iterator inversionIter;
496		Bond* bond;
497		Bend* bend;
498		Torsion* torsion;
#	Line 530 \| Line 502 \| namespace OpenMD {
502		int c;
503		int d;
504
505	<	std::map<int, std::set<int> > atomGroups;
505	>	map<int, set<int> > atomGroups;
506		Molecule::RigidBodyIterator rbIter;
507		RigidBody* rb;
508		Molecule::IntegrableObjectIterator ii;
#	Line 542 \| Line 514 \| namespace OpenMD {
514
515		if (integrableObject->isRigidBody()) {
516		rb = static_cast<RigidBody*>(integrableObject);
517	<	std::vector<Atom*> atoms = rb->getAtoms();
518	<	std::set<int> rigidAtoms;
517	>	vector<Atom*> atoms = rb->getAtoms();
518	>	set<int> rigidAtoms;
519		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
520		rigidAtoms.insert(atoms[i]->getGlobalIndex());
521		}
522		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
523	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
523	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
524		}
525		} else {
526	<	std::set<int> oneAtomSet;
526	>	set<int> oneAtomSet;
527		oneAtomSet.insert(integrableObject->getGlobalIndex());
528	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
528	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
529		}
530		}
531
#	Line 656 \| Line 628 \| namespace OpenMD {
628
629		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
630		rb = mol->nextRigidBody(rbIter)) {
631	<	std::vector<Atom*> atoms = rb->getAtoms();
631	>	vector<Atom*> atoms = rb->getAtoms();
632		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
633		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
634		a = atoms[i]->getGlobalIndex();
#	Line 679 \| Line 651 \| namespace OpenMD {
651		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
652		}
653
682	–	void SimInfo::update() {
654
655	<	setupSimType();
656	<
657	<	#ifdef IS_MPI
658	<	setupFortranParallel();
659	<	#endif
660	<
661	<	setupFortranSim();
662	<
663	<	//setup fortran force field
693	<	/** @deprecate */
694	<	int isError = 0;
695	<
696	<	setupCutoff();
697	<
698	<	setupElectrostaticSummationMethod( isError );
699	<	setupSwitchingFunction();
700	<	setupAccumulateBoxDipole();
701	<
702	<	if(isError){
703	<	sprintf( painCave.errMsg,
704	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
705	<	painCave.isFatal = 1;
706	<	simError();
707	<	}
708	<
655	>	/**
656	>	* update
657	>	*
658	>	* Performs the global checks and variable settings after the
659	>	* objects have been created.
660	>	*
661	>	*/
662	>	void SimInfo::update() {
663	>	setupSimVariables();
664		calcNdf();
665		calcNdfRaw();
666		calcNdfTrans();
712	–
713	–	fortranInitialized_ = true;
667		}
668	<
669	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
668	>
669	>	/**
670	>	* getSimulatedAtomTypes
671	>	*
672	>	* Returns an STL set of AtomType* that are actually present in this
673	>	* simulation. Must query all processors to assemble this information.
674	>	*
675	>	*/
676	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
677		SimInfo::MoleculeIterator mi;
678		Molecule* mol;
679		Molecule::AtomIterator ai;
680		Atom* atom;
681	<	std::set<AtomType*> atomTypes;
682	<
683	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
724	<
681	>	set<AtomType*> atomTypes;
682	>
683	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
684		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
685		atomTypes.insert(atom->getAtomType());
686	<	}
687	<
729	<	}
686	>	}
687	>	}
688
689	<	return atomTypes;
732	<	}
689	>	#ifdef IS_MPI
690
691	<	void SimInfo::setupSimType() {
692	<	std::set<AtomType*>::iterator i;
736	<	std::set<AtomType*> atomTypes;
737	<	atomTypes = getUniqueAtomTypes();
738	<
739	<	int useLennardJones = 0;
740	<	int useElectrostatic = 0;
741	<	int useEAM = 0;
742	<	int useSC = 0;
743	<	int useCharge = 0;
744	<	int useDirectional = 0;
745	<	int useDipole = 0;
746	<	int useGayBerne = 0;
747	<	int useSticky = 0;
748	<	int useStickyPower = 0;
749	<	int useShape = 0;
750	<	int useFLARB = 0; //it is not in AtomType yet
751	<	int useDirectionalAtom = 0;
752	<	int useElectrostatics = 0;
753	<	//usePBC and useRF are from simParams
754	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
755	<	int useRF;
756	<	int useSF;
757	<	int useSP;
758	<	int useBoxDipole;
691	>	// loop over the found atom types on this processor, and add their
692	>	// numerical idents to a vector:
693
694	<	std::string myMethod;
694	>	vector<int> foundTypes;
695	>	set<AtomType*>::iterator i;
696	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
697	>	foundTypes.push_back( (*i)->getIdent() );
698
699	<	// set the useRF logical
700	<	useRF = 0;
764	<	useSF = 0;
765	<	useSP = 0;
766	<	useBoxDipole = 0;
699	>	// count_local holds the number of found types on this processor
700	>	int count_local = foundTypes.size();
701
702	+	// count holds the total number of found types on all processors
703	+	// (some will be redundant with the ones found locally):
704	+	int count;
705	+	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
706
707	<	if (simParams_->haveElectrostaticSummationMethod()) {
708	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
709	<	toUpper(myMethod);
710	<	if (myMethod == "REACTION_FIELD"){
711	<	useRF = 1;
712	<	} else if (myMethod == "SHIFTED_FORCE"){
713	<	useSF = 1;
714	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
715	<	useSP = 1;
716	<	}
717	<	}
707	>	// create a vector to hold the globally found types, and resize it:
708	>	vector<int> ftGlobal;
709	>	ftGlobal.resize(count);
710	>	vector<int> counts;
711	>
712	>	int nproc = MPI::COMM_WORLD.Get_size();
713	>	counts.resize(nproc);
714	>	vector<int> disps;
715	>	disps.resize(nproc);
716	>
717	>	// now spray out the foundTypes to all the other processors:
718
719	<	if (simParams_->haveAccumulateBoxDipole())
720	<	if (simParams_->getAccumulateBoxDipole())
783	<	useBoxDipole = 1;
719	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
720	>	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
721
722	+	// foundIdents is a stl set, so inserting an already found ident
723	+	// will have no effect.
724	+	set<int> foundIdents;
725	+	vector<int>::iterator j;
726	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
727	+	foundIdents.insert((*j));
728	+
729	+	// now iterate over the foundIdents and get the actual atom types
730	+	// that correspond to these:
731	+	set<int>::iterator it;
732	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
733	+	atomTypes.insert( forceField_->getAtomType((*it)) );
734	+
735	+	#endif
736	+
737	+	return atomTypes;
738	+	}
739	+
740	+	void SimInfo::setupSimVariables() {
741		useAtomicVirial_ = simParams_->getUseAtomicVirial();
742	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
743	+	calcBoxDipole_ = false;
744	+	if ( simParams_->haveAccumulateBoxDipole() )
745	+	if ( simParams_->getAccumulateBoxDipole() ) {
746	+	calcBoxDipole_ = true;
747	+	}
748
749	+	set<AtomType*>::iterator i;
750	+	set<AtomType*> atomTypes;
751	+	atomTypes = getSimulatedAtomTypes();
752	+	int usesElectrostatic = 0;
753	+	int usesMetallic = 0;
754	+	int usesDirectional = 0;
755		//loop over all of the atom types
756		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
757	<	useLennardJones \|= (*i)->isLennardJones();
758	<	useElectrostatic \|= (*i)->isElectrostatic();
759	<	useEAM \|= (*i)->isEAM();
792	<	useSC \|= (*i)->isSC();
793	<	useCharge \|= (*i)->isCharge();
794	<	useDirectional \|= (*i)->isDirectional();
795	<	useDipole \|= (*i)->isDipole();
796	<	useGayBerne \|= (*i)->isGayBerne();
797	<	useSticky \|= (*i)->isSticky();
798	<	useStickyPower \|= (*i)->isStickyPower();
799	<	useShape \|= (*i)->isShape();
757	>	usesElectrostatic \|= (*i)->isElectrostatic();
758	>	usesMetallic \|= (*i)->isMetal();
759	>	usesDirectional \|= (*i)->isDirectional();
760		}
761
802	–	if (useSticky \|\| useStickyPower \|\| useDipole \|\| useGayBerne \|\| useShape) {
803	–	useDirectionalAtom = 1;
804	–	}
805	–
806	–	if (useCharge \|\| useDipole) {
807	–	useElectrostatics = 1;
808	–	}
809	–
762		#ifdef IS_MPI
763		int temp;
764	+	temp = usesDirectional;
765	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766
767	<	temp = usePBC;
768	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767	>	temp = usesMetallic;
768	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769
770	<	temp = useDirectionalAtom;
771	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770	>	temp = usesElectrostatic;
771	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
772	>	#endif
773	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
774	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
775	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
776	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
777	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
778	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
779	>	}
780
819	–	temp = useLennardJones;
820	–	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
781
782	<	temp = useElectrostatics;
783	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
782	>	vector<int> SimInfo::getGlobalAtomIndices() {
783	>	SimInfo::MoleculeIterator mi;
784	>	Molecule* mol;
785	>	Molecule::AtomIterator ai;
786	>	Atom* atom;
787
788	<	temp = useCharge;
826	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
827	<
828	<	temp = useDipole;
829	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
830	<
831	<	temp = useSticky;
832	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
833	<
834	<	temp = useStickyPower;
835	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
788	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
789
790	<	temp = useGayBerne;
791	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
790	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
791	>
792	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
793	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
794	>	}
795	>	}
796	>	return GlobalAtomIndices;
797	>	}
798
840	–	temp = useEAM;
841	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
799
800	<	temp = useSC;
801	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
802	<
803	<	temp = useShape;
804	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
800	>	vector<int> SimInfo::getGlobalGroupIndices() {
801	>	SimInfo::MoleculeIterator mi;
802	>	Molecule* mol;
803	>	Molecule::CutoffGroupIterator ci;
804	>	CutoffGroup* cg;
805
806	<	temp = useFLARB;
807	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
808	<
809	<	temp = useRF;
810	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
811	<
812	<	temp = useSF;
813	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814	<
815	<	temp = useSP;
816	<	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
817	<
861	<	temp = useBoxDipole;
862	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
863	<
864	<	temp = useAtomicVirial_;
865	<	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
866	<
867	<	#endif
868	<
869	<	fInfo_.SIM_uses_PBC = usePBC;
870	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
871	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
872	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
873	<	fInfo_.SIM_uses_Charges = useCharge;
874	<	fInfo_.SIM_uses_Dipoles = useDipole;
875	<	fInfo_.SIM_uses_Sticky = useSticky;
876	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
877	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
878	<	fInfo_.SIM_uses_EAM = useEAM;
879	<	fInfo_.SIM_uses_SC = useSC;
880	<	fInfo_.SIM_uses_Shapes = useShape;
881	<	fInfo_.SIM_uses_FLARB = useFLARB;
882	<	fInfo_.SIM_uses_RF = useRF;
883	<	fInfo_.SIM_uses_SF = useSF;
884	<	fInfo_.SIM_uses_SP = useSP;
885	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
886	<	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
806	>	vector<int> GlobalGroupIndices;
807	>
808	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
809	>
810	>	//local index of cutoff group is trivial, it only depends on the
811	>	//order of travesing
812	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
813	>	cg = mol->nextCutoffGroup(ci)) {
814	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
815	>	}
816	>	}
817	>	return GlobalGroupIndices;
818		}
819
820	<	void SimInfo::setupFortranSim() {
820	>
821	>	void SimInfo::setupFortran() {
822		int isError;
823		int nExclude, nOneTwo, nOneThree, nOneFour;
824	<	std::vector<int> fortranGlobalGroupMembership;
824	>	vector<int> fortranGlobalGroupMembership;
825
826		isError = 0;
827
#	Line 899 \| Line 831 \| namespace OpenMD {
831		}
832
833		//calculate mass ratio of cutoff group
834	<	std::vector<RealType> mfact;
834	>	vector<RealType> mfact;
835		SimInfo::MoleculeIterator mi;
836		Molecule* mol;
837		Molecule::CutoffGroupIterator ci;
#	Line 925 \| Line 857 \| namespace OpenMD {
857		}
858		}
859
860	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
929	<	std::vector<int> identArray;
860	>	// Build the identArray_
861
862	<	//to avoid memory reallocation, reserve enough space identArray
863	<	identArray.reserve(getNAtoms());
933	<
862	>	identArray_.clear();
863	>	identArray_.reserve(getNAtoms());
864		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
865		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
866	<	identArray.push_back(atom->getIdent());
866	>	identArray_.push_back(atom->getIdent());
867		}
868		}
869
870		//fill molMembershipArray
871		//molMembershipArray is filled by SimCreator
872	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
872	>	vector<int> molMembershipArray(nGlobalAtoms_);
873		for (int i = 0; i < nGlobalAtoms_; i++) {
874		molMembershipArray[i] = globalMolMembership_[i] + 1;
875		}
#	Line 956 \| Line 886 \| namespace OpenMD {
886		int* oneThreeList = oneThreeInteractions_.getPairList();
887		int* oneFourList = oneFourInteractions_.getPairList();
888
889	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
890	<	&nExclude, excludeList,
891	<	&nOneTwo, oneTwoList,
892	<	&nOneThree, oneThreeList,
893	<	&nOneFour, oneFourList,
894	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
895	<	&fortranGlobalGroupMembership[0], &isError);
889	>	//setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0],
890	>	// &nExclude, excludeList,
891	>	// &nOneTwo, oneTwoList,
892	>	// &nOneThree, oneThreeList,
893	>	// &nOneFour, oneFourList,
894	>	// &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
895	>	// &fortranGlobalGroupMembership[0], &isError);
896
897	<	if( isError ){
898	<
899	<	sprintf( painCave.errMsg,
900	<	"There was an error setting the simulation information in fortran.\n" );
901	<	painCave.isFatal = 1;
902	<	painCave.severity = OPENMD_ERROR;
903	<	simError();
904	<	}
897	>	// if( isError ){
898	>	//
899	>	// sprintf( painCave.errMsg,
900	>	// "There was an error setting the simulation information in fortran.\n" );
901	>	// painCave.isFatal = 1;
902	>	// painCave.severity = OPENMD_ERROR;
903	>	// simError();
904	>	//}
905
906
907	<	sprintf( checkPointMsg,
908	<	"succesfully sent the simulation information to fortran.\n");
907	>	// sprintf( checkPointMsg,
908	>	// "succesfully sent the simulation information to fortran.\n");
909
910	<	errorCheckPoint();
910	>	// errorCheckPoint();
911
912		// Setup number of neighbors in neighbor list if present
913	<	if (simParams_->haveNeighborListNeighbors()) {
914	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
915	<	setNeighbors(&nlistNeighbors);
916	<	}
913	>	//if (simParams_->haveNeighborListNeighbors()) {
914	>	// int nlistNeighbors = simParams_->getNeighborListNeighbors();
915	>	// setNeighbors(&nlistNeighbors);
916	>	//}
917
988	–
989	–	}
990	–
991	–
992	–	void SimInfo::setupFortranParallel() {
918		#ifdef IS_MPI
919	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
995	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
996	<	std::vector<int> localToGlobalCutoffGroupIndex;
997	<	SimInfo::MoleculeIterator mi;
998	<	Molecule::AtomIterator ai;
999	<	Molecule::CutoffGroupIterator ci;
1000	<	Molecule* mol;
1001	<	Atom* atom;
1002	<	CutoffGroup* cg;
1003	<	mpiSimData parallelData;
1004	<	int isError;
919	>	// mpiSimData parallelData;
920
1006	–	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1007	–
1008	–	//local index(index in DataStorge) of atom is important
1009	–	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1010	–	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1011	–	}
1012	–
1013	–	//local index of cutoff group is trivial, it only depends on the order of travesing
1014	–	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1015	–	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1016	–	}
1017	–
1018	–	}
1019	–
921		//fill up mpiSimData struct
922	<	parallelData.nMolGlobal = getNGlobalMolecules();
923	<	parallelData.nMolLocal = getNMolecules();
924	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
925	<	parallelData.nAtomsLocal = getNAtoms();
926	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
927	<	parallelData.nGroupsLocal = getNCutoffGroups();
928	<	parallelData.myNode = worldRank;
929	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
922	>	// parallelData.nMolGlobal = getNGlobalMolecules();
923	>	// parallelData.nMolLocal = getNMolecules();
924	>	// parallelData.nAtomsGlobal = getNGlobalAtoms();
925	>	// parallelData.nAtomsLocal = getNAtoms();
926	>	// parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
927	>	// parallelData.nGroupsLocal = getNCutoffGroups();
928	>	// parallelData.myNode = worldRank;
929	>	// MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
930
931		//pass mpiSimData struct and index arrays to fortran
932	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
933	<	&localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal),
934	<	&localToGlobalCutoffGroupIndex[0], &isError);
932	>	//setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
933	>	// &localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal),
934	>	// &localToGlobalCutoffGroupIndex[0], &isError);
935
936	<	if (isError) {
937	<	sprintf(painCave.errMsg,
938	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
939	<	painCave.isFatal = 1;
940	<	simError();
941	<	}
936	>	// if (isError) {
937	>	// sprintf(painCave.errMsg,
938	>	// "mpiRefresh errror: fortran didn't like something we gave it.\n");
939	>	// painCave.isFatal = 1;
940	>	// simError();
941	>	// }
942
943	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
944	<	errorCheckPoint();
1044	<
943	>	// sprintf(checkPointMsg, " mpiRefresh successful.\n");
944	>	// errorCheckPoint();
945		#endif
1046	–	}
946
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	<	// Set LJ shifting bools to false
1056	<	ljsp_ = 0;
1057	<	ljsf_ = 0;
1058	<
1059	<	std::string myPolicy;
1060	<	if (forceFieldOptions_.haveCutoffPolicy()){
1061	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
1062	<	}else if (simParams_->haveCutoffPolicy()) {
1063	<	myPolicy = simParams_->getCutoffPolicy();
1064	<	}
1065	<
1066	<	if (!myPolicy.empty()){
1067	<	toUpper(myPolicy);
1068	<	if (myPolicy == "MIX") {
1069	<	cp = MIX_CUTOFF_POLICY;
1070	<	} else {
1071	<	if (myPolicy == "MAX") {
1072	<	cp = MAX_CUTOFF_POLICY;
1073	<	} else {
1074	<	if (myPolicy == "TRADITIONAL") {
1075	<	cp = TRADITIONAL_CUTOFF_POLICY;
1076	<	} else {
1077	<	// throw error
1078	<	sprintf( painCave.errMsg,
1079	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1080	<	painCave.isFatal = 1;
1081	<	simError();
1082	<	}
1083	<	}
1084	<	}
1085	<	}
1086	<	notifyFortranCutoffPolicy(&cp);
1087	<
1088	<	// Check the Skin Thickness for neighborlists
1089	<	RealType skin;
1090	<	if (simParams_->haveSkinThickness()) {
1091	<	skin = simParams_->getSkinThickness();
1092	<	notifyFortranSkinThickness(&skin);
1093	<	}
1094	<
1095	<	// Check if the cutoff was set explicitly:
1096	<	if (simParams_->haveCutoffRadius()) {
1097	<	rcut_ = simParams_->getCutoffRadius();
1098	<	if (simParams_->haveSwitchingRadius()) {
1099	<	rsw_ = simParams_->getSwitchingRadius();
1100	<	} else {
1101	<	if (fInfo_.SIM_uses_Charges \|
1102	<	fInfo_.SIM_uses_Dipoles \|
1103	<	fInfo_.SIM_uses_RF) {
1104	<
1105	<	rsw_ = 0.85 * rcut_;
1106	<	sprintf(painCave.errMsg,
1107	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1108	<	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1109	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1110	<	painCave.isFatal = 0;
1111	<	simError();
1112	<	} else {
1113	<	rsw_ = rcut_;
1114	<	sprintf(painCave.errMsg,
1115	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1116	<	"\tOpenMD will use the same value as the cutoffRadius.\n"
1117	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1118	<	painCave.isFatal = 0;
1119	<	simError();
1120	<	}
1121	<	}
1122	<
1123	<	if (simParams_->haveElectrostaticSummationMethod()) {
1124	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1125	<	toUpper(myMethod);
1126	<
1127	<	if (myMethod == "SHIFTED_POTENTIAL") {
1128	<	ljsp_ = 1;
1129	<	} else if (myMethod == "SHIFTED_FORCE") {
1130	<	ljsf_ = 1;
1131	<	}
1132	<	}
1133	<
1134	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1135	<
1136	<	} else {
1137	<
1138	<	// For electrostatic atoms, we'll assume a large safe value:
1139	<	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
1140	<	sprintf(painCave.errMsg,
1141	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1142	<	"\tOpenMD will use a default value of 15.0 angstroms"
1143	<	"\tfor the cutoffRadius.\n");
1144	<	painCave.isFatal = 0;
1145	<	simError();
1146	<	rcut_ = 15.0;
1147	<
1148	<	if (simParams_->haveElectrostaticSummationMethod()) {
1149	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1150	<	toUpper(myMethod);
1151	<
1152	<	// For the time being, we're tethering the LJ shifted behavior to the
1153	<	// electrostaticSummationMethod keyword options
1154	<	if (myMethod == "SHIFTED_POTENTIAL") {
1155	<	ljsp_ = 1;
1156	<	} else if (myMethod == "SHIFTED_FORCE") {
1157	<	ljsf_ = 1;
1158	<	}
1159	<	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
1160	<	if (simParams_->haveSwitchingRadius()){
1161	<	sprintf(painCave.errMsg,
1162	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1163	<	"\teven though the electrostaticSummationMethod was\n"
1164	<	"\tset to %s\n", myMethod.c_str());
1165	<	painCave.isFatal = 1;
1166	<	simError();
1167	<	}
1168	<	}
1169	<	}
1170	<
1171	<	if (simParams_->haveSwitchingRadius()){
1172	<	rsw_ = simParams_->getSwitchingRadius();
1173	<	} else {
1174	<	sprintf(painCave.errMsg,
1175	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1176	<	"\tOpenMD will use a default value of\n"
1177	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1178	<	painCave.isFatal = 0;
1179	<	simError();
1180	<	rsw_ = 0.85 * rcut_;
1181	<	}
1182	<
1183	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1184	<
1185	<	} else {
1186	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1187	<	// We'll punt and let fortran figure out the cutoffs later.
1188	<
1189	<	notifyFortranYouAreOnYourOwn();
1190	<
1191	<	}
1192	<	}
1193	<	}
1194	<
1195	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1196	<
1197	<	int errorOut;
1198	<	int esm = NONE;
1199	<	int sm = UNDAMPED;
1200	<	RealType alphaVal;
1201	<	RealType dielectric;
1202	<
1203	<	errorOut = isError;
1204	<
1205	<	if (simParams_->haveElectrostaticSummationMethod()) {
1206	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1207	<	toUpper(myMethod);
1208	<	if (myMethod == "NONE") {
1209	<	esm = NONE;
1210	<	} else {
1211	<	if (myMethod == "SWITCHING_FUNCTION") {
1212	<	esm = SWITCHING_FUNCTION;
1213	<	} else {
1214	<	if (myMethod == "SHIFTED_POTENTIAL") {
1215	<	esm = SHIFTED_POTENTIAL;
1216	<	} else {
1217	<	if (myMethod == "SHIFTED_FORCE") {
1218	<	esm = SHIFTED_FORCE;
1219	<	} else {
1220	<	if (myMethod == "REACTION_FIELD") {
1221	<	esm = REACTION_FIELD;
1222	<	dielectric = simParams_->getDielectric();
1223	<	if (!simParams_->haveDielectric()) {
1224	<	// throw warning
1225	<	sprintf( painCave.errMsg,
1226	<	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1227	<	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1228	<	painCave.isFatal = 0;
1229	<	simError();
1230	<	}
1231	<	} else {
1232	<	// throw error
1233	<	sprintf( painCave.errMsg,
1234	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1235	<	"\t(Input file specified %s .)\n"
1236	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1237	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1238	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1239	<	painCave.isFatal = 1;
1240	<	simError();
1241	<	}
1242	<	}
1243	<	}
1244	<	}
1245	<	}
1246	<	}
1247	<
1248	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1249	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1250	<	toUpper(myScreen);
1251	<	if (myScreen == "UNDAMPED") {
1252	<	sm = UNDAMPED;
1253	<	} else {
1254	<	if (myScreen == "DAMPED") {
1255	<	sm = DAMPED;
1256	<	if (!simParams_->haveDampingAlpha()) {
1257	<	// first set a cutoff dependent alpha value
1258	<	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1259	<	alphaVal = 0.5125 - rcut_* 0.025;
1260	<	// for values rcut > 20.5, alpha is zero
1261	<	if (alphaVal < 0) alphaVal = 0;
1262	<
1263	<	// throw warning
1264	<	sprintf( painCave.errMsg,
1265	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1266	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1267	<	painCave.isFatal = 0;
1268	<	simError();
1269	<	} else {
1270	<	alphaVal = simParams_->getDampingAlpha();
1271	<	}
1272	<
1273	<	} else {
1274	<	// throw error
1275	<	sprintf( painCave.errMsg,
1276	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1277	<	"\t(Input file specified %s .)\n"
1278	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1279	<	"or \"damped\".\n", myScreen.c_str() );
1280	<	painCave.isFatal = 1;
1281	<	simError();
1282	<	}
1283	<	}
1284	<	}
1285	<
1286	<	// let's pass some summation method variables to fortran
1287	<	setElectrostaticSummationMethod( &esm );
1288	<	setFortranElectrostaticMethod( &esm );
1289	<	setScreeningMethod( &sm );
1290	<	setDampingAlpha( &alphaVal );
1291	<	setReactionFieldDielectric( &dielectric );
1292	<	initFortranFF( &errorOut );
1293	<	}
1294	<
1295	<	void SimInfo::setupSwitchingFunction() {
1296	<	int ft = CUBIC;
1297	<
1298	<	if (simParams_->haveSwitchingFunctionType()) {
1299	<	std::string funcType = simParams_->getSwitchingFunctionType();
1300	<	toUpper(funcType);
1301	<	if (funcType == "CUBIC") {
1302	<	ft = CUBIC;
1303	<	} else {
1304	<	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1305	<	ft = FIFTH_ORDER_POLY;
1306	<	} else {
1307	<	// throw error
1308	<	sprintf( painCave.errMsg,
1309	<	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1310	<	painCave.isFatal = 1;
1311	<	simError();
1312	<	}
1313	<	}
1314	<	}
1315	<
1316	<	// send switching function notification to switcheroo
1317	<	setFunctionType(&ft);
1318	<
947	>	// initFortranFF(&isError);
948	>	// if (isError) {
949	>	// sprintf(painCave.errMsg,
950	>	// "initFortranFF errror: fortran didn't like something we gave it.\n");
951	>	// painCave.isFatal = 1;
952	>	// simError();
953	>	// }
954	>	// fortranInitialized_ = true;
955		}
956
1321	–	void SimInfo::setupAccumulateBoxDipole() {
1322	–
1323	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1324	–	if ( simParams_->haveAccumulateBoxDipole() )
1325	–	if ( simParams_->getAccumulateBoxDipole() ) {
1326	–	setAccumulateBoxDipole();
1327	–	calcBoxDipole_ = true;
1328	–	}
1329	–
1330	–	}
1331	–
957		void SimInfo::addProperty(GenericData* genData) {
958		properties_.addProperty(genData);
959		}
960
961	<	void SimInfo::removeProperty(const std::string& propName) {
961	>	void SimInfo::removeProperty(const string& propName) {
962		properties_.removeProperty(propName);
963		}
964
#	Line 1341 \| Line 966 \| namespace OpenMD {
966		properties_.clearProperties();
967		}
968
969	<	std::vector<std::string> SimInfo::getPropertyNames() {
969	>	vector<string> SimInfo::getPropertyNames() {
970		return properties_.getPropertyNames();
971		}
972
973	<	std::vector<GenericData*> SimInfo::getProperties() {
973	>	vector<GenericData*> SimInfo::getProperties() {
974		return properties_.getProperties();
975		}
976
977	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
977	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
978		return properties_.getPropertyByName(propName);
979		}
980
#	Line 1363 \| Line 988 \| namespace OpenMD {
988		Molecule* mol;
989		RigidBody* rb;
990		Atom* atom;
991	+	CutoffGroup* cg;
992		SimInfo::MoleculeIterator mi;
993		Molecule::RigidBodyIterator rbIter;
994	<	Molecule::AtomIterator atomIter;;
994	>	Molecule::AtomIterator atomIter;
995	>	Molecule::CutoffGroupIterator cgIter;
996
997		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
998
#	Line 1376 \| Line 1003 \| namespace OpenMD {
1003		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1004		rb->setSnapshotManager(sman_);
1005		}
1006	+
1007	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
1008	+	cg->setSnapshotManager(sman_);
1009	+	}
1010		}
1011
1012		}
#	Line 1432 \| Line 1063 \| namespace OpenMD {
1063
1064		}
1065
1066	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1066	>	ostream& operator <<(ostream& o, SimInfo& info) {
1067
1068		return o;
1069		}
#	Line 1475 \| Line 1106 \| namespace OpenMD {
1106
1107
1108		[ Ixx -Ixy -Ixz ]
1109	<	J =\| -Iyx Iyy -Iyz \|
1109	>	J =\| -Iyx Iyy -Iyz \|
1110		[ -Izx -Iyz Izz ]
1111		*/
1112
#	Line 1582 \| Line 1213 \| namespace OpenMD {
1213		return IOIndexToIntegrableObject.at(index);
1214		}
1215
1216	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1216	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1217		IOIndexToIntegrableObject= v;
1218		}
1219
#	Line 1624 \| Line 1255 \| namespace OpenMD {
1255		return;
1256		}
1257		/*
1258	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1258	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1259		assert( v.size() == nAtoms_ + nRigidBodies_);
1260		sdByGlobalIndex_ = v;
1261		}
#	Line 1634 \| Line 1265 \| namespace OpenMD {
1265		return sdByGlobalIndex_.at(index);
1266		}
1267		*/
1268	+	int SimInfo::getNGlobalConstraints() {
1269	+	int nGlobalConstraints;
1270	+	#ifdef IS_MPI
1271	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1272	+	MPI_COMM_WORLD);
1273	+	#else
1274	+	nGlobalConstraints = nConstraints_;
1275	+	#endif
1276	+	return nGlobalConstraints;
1277	+	}
1278	+
1279		}//end namespace OpenMD
1280

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Comparing branches/development/src/brains/SimInfo.cpp (file contents): Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs. Revision 1550 by gezelter, Wed Apr 27 21:49:59 2011 UTC

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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1550 by gezelter, Wed Apr 27 21:49:59 2011 UTC