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

Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1503 by gezelter, Sat Oct 2 19:54:41 2010 UTC vs.
Revision 1534 by gezelter, Wed Dec 29 21:53:28 2010 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/fSwitchingFunctionType.h"
57		#include "UseTheForce/doForces_interface.h"
58		#include "UseTheForce/DarkSide/neighborLists_interface.h"
61	–	#include "UseTheForce/DarkSide/switcheroo_interface.h"
59		#include "utils/MemoryUtils.hpp"
60		#include "utils/simError.h"
61		#include "selection/SelectionManager.hpp"
62		#include "io/ForceFieldOptions.hpp"
63		#include "UseTheForce/ForceField.hpp"
64	+	#include "nonbonded/SwitchingFunction.hpp"
65
68	–
66		#ifdef IS_MPI
67		#include "UseTheForce/mpiComponentPlan.h"
68		#include "UseTheForce/DarkSide/simParallel_interface.h"
69		#endif
70
71	+	using namespace std;
72		namespace OpenMD {
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	–	return result;
83	–	}
73
74		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
75		forceField_(ff), simParams_(simParams),
#	Line 90 \| Line 79 \| namespace OpenMD {
79		nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0),
80		nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
81		nConstraints_(0), sman_(NULL), fortranInitialized_(false),
82	<	calcBoxDipole_(false), useAtomicVirial_(true) {
83	<
84	<
85	<	MoleculeStamp* molStamp;
86	<	int nMolWithSameStamp;
87	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
88	<	int nGroups = 0; //total cutoff groups defined in meta-data file
89	<	CutoffGroupStamp* cgStamp;
90	<	RigidBodyStamp* rbStamp;
91	<	int nRigidAtoms = 0;
92	<
93	<	std::vector<Component*> components = simParams->getComponents();
82	>	calcBoxDipole_(false), useAtomicVirial_(true) {
83	>
84	>	MoleculeStamp* molStamp;
85	>	int nMolWithSameStamp;
86	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87	>	int nGroups = 0; //total cutoff groups defined in meta-data file
88	>	CutoffGroupStamp* cgStamp;
89	>	RigidBodyStamp* rbStamp;
90	>	int nRigidAtoms = 0;
91	>
92	>	vector<Component*> components = simParams->getComponents();
93	>
94	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
95	>	molStamp = (*i)->getMoleculeStamp();
96	>	nMolWithSameStamp = (*i)->getNMol();
97
98	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
99	<	molStamp = (*i)->getMoleculeStamp();
100	<	nMolWithSameStamp = (*i)->getNMol();
101	<
102	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
103	<
104	<	//calculate atoms in molecules
105	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
106	<
107	<	//calculate atoms in cutoff groups
108	<	int nAtomsInGroups = 0;
109	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
118	<
119	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
120	<	cgStamp = molStamp->getCutoffGroupStamp(j);
121	<	nAtomsInGroups += cgStamp->getNMembers();
122	<	}
123	<
124	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
125	<
126	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
127	<
128	<	//calculate atoms in rigid bodies
129	<	int nAtomsInRigidBodies = 0;
130	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
131	<
132	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
133	<	rbStamp = molStamp->getRigidBodyStamp(j);
134	<	nAtomsInRigidBodies += rbStamp->getNMembers();
135	<	}
136	<
137	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
138	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
139	<
98	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
99	>
100	>	//calculate atoms in molecules
101	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
102	>
103	>	//calculate atoms in cutoff groups
104	>	int nAtomsInGroups = 0;
105	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
106	>
107	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
108	>	cgStamp = molStamp->getCutoffGroupStamp(j);
109	>	nAtomsInGroups += cgStamp->getNMembers();
110		}
111	<
112	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
113	<	//group therefore the total number of cutoff groups in the system is
114	<	//equal to the total number of atoms minus number of atoms belong to
115	<	//cutoff group defined in meta-data file plus the number of cutoff
116	<	//groups defined in meta-data file
117	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
118	<
119	<	//every free atom (atom does not belong to rigid bodies) is an
120	<	//integrable object therefore the total number of integrable objects
121	<	//in the system is equal to the total number of atoms minus number of
122	<	//atoms belong to rigid body defined in meta-data file plus the number
123	<	//of rigid bodies defined in meta-data file
124	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
125	<	+ nGlobalRigidBodies_;
126	<
127	<	nGlobalMols_ = molStampIds_.size();
128	<	molToProcMap_.resize(nGlobalMols_);
129	<	}
130	<
111	>
112	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
113	>
114	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
115	>
116	>	//calculate atoms in rigid bodies
117	>	int nAtomsInRigidBodies = 0;
118	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
119	>
120	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
121	>	rbStamp = molStamp->getRigidBodyStamp(j);
122	>	nAtomsInRigidBodies += rbStamp->getNMembers();
123	>	}
124	>
125	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
126	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
127	>
128	>	}
129	>
130	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
131	>	//group therefore the total number of cutoff groups in the system is
132	>	//equal to the total number of atoms minus number of atoms belong to
133	>	//cutoff group defined in meta-data file plus the number of cutoff
134	>	//groups defined in meta-data file
135	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
136	>
137	>	//every free atom (atom does not belong to rigid bodies) is an
138	>	//integrable object therefore the total number of integrable objects
139	>	//in the system is equal to the total number of atoms minus number of
140	>	//atoms belong to rigid body defined in meta-data file plus the number
141	>	//of rigid bodies defined in meta-data file
142	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
143	>	+ nGlobalRigidBodies_;
144	>
145	>	nGlobalMols_ = molStampIds_.size();
146	>	molToProcMap_.resize(nGlobalMols_);
147	>	}
148	>
149		SimInfo::~SimInfo() {
150	<	std::map<int, Molecule*>::iterator i;
150	>	map<int, Molecule*>::iterator i;
151		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
152		delete i->second;
153		}
#	Line 170 \| Line 158 \| namespace OpenMD {
158		delete forceField_;
159		}
160
173	–	int SimInfo::getNGlobalConstraints() {
174	–	int nGlobalConstraints;
175	–	#ifdef IS_MPI
176	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
177	–	MPI_COMM_WORLD);
178	–	#else
179	–	nGlobalConstraints = nConstraints_;
180	–	#endif
181	–	return nGlobalConstraints;
182	–	}
161
162		bool SimInfo::addMolecule(Molecule* mol) {
163		MoleculeIterator i;
164	<
164	>
165		i = molecules_.find(mol->getGlobalIndex());
166		if (i == molecules_.end() ) {
167	<
168	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
169	<
167	>
168	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
169	>
170		nAtoms_ += mol->getNAtoms();
171		nBonds_ += mol->getNBonds();
172		nBends_ += mol->getNBends();
#	Line 198 \| Line 176 \| namespace OpenMD {
176		nIntegrableObjects_ += mol->getNIntegrableObjects();
177		nCutoffGroups_ += mol->getNCutoffGroups();
178		nConstraints_ += mol->getNConstraintPairs();
179	<
179	>
180		addInteractionPairs(mol);
181	<
181	>
182		return true;
183		} else {
184		return false;
185		}
186		}
187	<
187	>
188		bool SimInfo::removeMolecule(Molecule* mol) {
189		MoleculeIterator i;
190		i = molecules_.find(mol->getGlobalIndex());
#	Line 234 \| Line 212 \| namespace OpenMD {
212		} else {
213		return false;
214		}
237	–
238	–
215		}
216
217
#	Line 253 \| Line 229 \| namespace OpenMD {
229		void SimInfo::calcNdf() {
230		int ndf_local;
231		MoleculeIterator i;
232	<	std::vector<StuntDouble*>::iterator j;
232	>	vector<StuntDouble*>::iterator j;
233		Molecule* mol;
234		StuntDouble* integrableObject;
235
#	Line 304 \| Line 280 \| namespace OpenMD {
280		int ndfRaw_local;
281
282		MoleculeIterator i;
283	<	std::vector<StuntDouble*>::iterator j;
283	>	vector<StuntDouble*>::iterator j;
284		Molecule* mol;
285		StuntDouble* integrableObject;
286
#	Line 353 \| Line 329 \| namespace OpenMD {
329
330		void SimInfo::addInteractionPairs(Molecule* mol) {
331		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
332	<	std::vector<Bond*>::iterator bondIter;
333	<	std::vector<Bend*>::iterator bendIter;
334	<	std::vector<Torsion*>::iterator torsionIter;
335	<	std::vector<Inversion*>::iterator inversionIter;
332	>	vector<Bond*>::iterator bondIter;
333	>	vector<Bend*>::iterator bendIter;
334	>	vector<Torsion*>::iterator torsionIter;
335	>	vector<Inversion*>::iterator inversionIter;
336		Bond* bond;
337		Bend* bend;
338		Torsion* torsion;
#	Line 374 \| Line 350 \| namespace OpenMD {
350		// always be excluded. These are done at the bottom of this
351		// function.
352
353	<	std::map<int, std::set<int> > atomGroups;
353	>	map<int, set<int> > atomGroups;
354		Molecule::RigidBodyIterator rbIter;
355		RigidBody* rb;
356		Molecule::IntegrableObjectIterator ii;
#	Line 386 \| Line 362 \| namespace OpenMD {
362
363		if (integrableObject->isRigidBody()) {
364		rb = static_cast<RigidBody*>(integrableObject);
365	<	std::vector<Atom*> atoms = rb->getAtoms();
366	<	std::set<int> rigidAtoms;
365	>	vector<Atom*> atoms = rb->getAtoms();
366	>	set<int> rigidAtoms;
367		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
368		rigidAtoms.insert(atoms[i]->getGlobalIndex());
369		}
370		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
371	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
371	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
372		}
373		} else {
374	<	std::set<int> oneAtomSet;
374	>	set<int> oneAtomSet;
375		oneAtomSet.insert(integrableObject->getGlobalIndex());
376	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
376	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
377		}
378		}
379
#	Line 500 \| Line 476 \| namespace OpenMD {
476
477		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
478		rb = mol->nextRigidBody(rbIter)) {
479	<	std::vector<Atom*> atoms = rb->getAtoms();
479	>	vector<Atom*> atoms = rb->getAtoms();
480		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
481		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
482		a = atoms[i]->getGlobalIndex();
#	Line 514 \| Line 490 \| namespace OpenMD {
490
491		void SimInfo::removeInteractionPairs(Molecule* mol) {
492		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
493	<	std::vector<Bond*>::iterator bondIter;
494	<	std::vector<Bend*>::iterator bendIter;
495	<	std::vector<Torsion*>::iterator torsionIter;
496	<	std::vector<Inversion*>::iterator inversionIter;
493	>	vector<Bond*>::iterator bondIter;
494	>	vector<Bend*>::iterator bendIter;
495	>	vector<Torsion*>::iterator torsionIter;
496	>	vector<Inversion*>::iterator inversionIter;
497		Bond* bond;
498		Bend* bend;
499		Torsion* torsion;
#	Line 527 \| Line 503 \| namespace OpenMD {
503		int c;
504		int d;
505
506	<	std::map<int, std::set<int> > atomGroups;
506	>	map<int, set<int> > atomGroups;
507		Molecule::RigidBodyIterator rbIter;
508		RigidBody* rb;
509		Molecule::IntegrableObjectIterator ii;
#	Line 539 \| Line 515 \| namespace OpenMD {
515
516		if (integrableObject->isRigidBody()) {
517		rb = static_cast<RigidBody*>(integrableObject);
518	<	std::vector<Atom*> atoms = rb->getAtoms();
519	<	std::set<int> rigidAtoms;
518	>	vector<Atom*> atoms = rb->getAtoms();
519	>	set<int> rigidAtoms;
520		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
521		rigidAtoms.insert(atoms[i]->getGlobalIndex());
522		}
523		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
524	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
524	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
525		}
526		} else {
527	<	std::set<int> oneAtomSet;
527	>	set<int> oneAtomSet;
528		oneAtomSet.insert(integrableObject->getGlobalIndex());
529	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
529	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
530		}
531		}
532
#	Line 653 \| Line 629 \| namespace OpenMD {
629
630		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
631		rb = mol->nextRigidBody(rbIter)) {
632	<	std::vector<Atom*> atoms = rb->getAtoms();
632	>	vector<Atom*> atoms = rb->getAtoms();
633		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
634		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
635		a = atoms[i]->getGlobalIndex();
#	Line 676 \| Line 652 \| namespace OpenMD {
652		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
653		}
654
679	–	void SimInfo::update() {
655
656	<	setupSimType();
656	>	/**
657	>	* update
658	>	*
659	>	* Performs the global checks and variable settings after the objects have been
660	>	* created.
661	>	*
662	>	*/
663	>	void SimInfo::update() {
664	>
665	>	setupSimVariables();
666	>	setupCutoffs();
667	>	setupSwitching();
668	>	setupElectrostatics();
669	>	setupNeighborlists();
670
671		#ifdef IS_MPI
672		setupFortranParallel();
673		#endif
686	–
674		setupFortranSim();
675	+	fortranInitialized_ = true;
676
689	–	//setup fortran force field
690	–	/** @deprecate */
691	–	int isError = 0;
692	–
693	–	setupCutoff();
694	–
695	–	setupElectrostaticSummationMethod( isError );
696	–	setupSwitchingFunction();
697	–	setupAccumulateBoxDipole();
698	–
699	–	if(isError){
700	–	sprintf( painCave.errMsg,
701	–	"ForceField error: There was an error initializing the forceField in fortran.\n" );
702	–	painCave.isFatal = 1;
703	–	simError();
704	–	}
705	–
677		calcNdf();
678		calcNdfRaw();
679		calcNdfTrans();
709	–
710	–	fortranInitialized_ = true;
680		}
681	<
682	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
681	>
682	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
683		SimInfo::MoleculeIterator mi;
684		Molecule* mol;
685		Molecule::AtomIterator ai;
686		Atom* atom;
687	<	std::set<AtomType*> atomTypes;
688	<
689	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
721	<
687	>	set<AtomType*> atomTypes;
688	>
689	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
690		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
691		atomTypes.insert(atom->getAtomType());
692	<	}
693	<
726	<	}
727	<
692	>	}
693	>	}
694		return atomTypes;
695		}
696
697	<	void SimInfo::setupSimType() {
698	<	std::set<AtomType*>::iterator i;
699	<	std::set<AtomType*> atomTypes;
700	<	atomTypes = getUniqueAtomTypes();
697	>	/**
698	>	* setupCutoffs
699	>	*
700	>	* Sets the values of cutoffRadius and cutoffMethod
701	>	*
702	>	* cutoffRadius : realType
703	>	* If the cutoffRadius was explicitly set, use that value.
704	>	* If the cutoffRadius was not explicitly set:
705	>	* Are there electrostatic atoms? Use 12.0 Angstroms.
706	>	* No electrostatic atoms? Poll the atom types present in the
707	>	* simulation for suggested cutoff values (e.g. 2.5 * sigma).
708	>	* Use the maximum suggested value that was found.
709	>	*
710	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
711	>	* If cutoffMethod was explicitly set, use that choice.
712	>	* If cutoffMethod was not explicitly set, use SHIFTED_FORCE
713	>	*/
714	>	void SimInfo::setupCutoffs() {
715
716	<	int useLennardJones = 0;
717	<	int useElectrostatic = 0;
718	<	int useEAM = 0;
719	<	int useSC = 0;
720	<	int useCharge = 0;
721	<	int useDirectional = 0;
722	<	int useDipole = 0;
723	<	int useGayBerne = 0;
724	<	int useSticky = 0;
725	<	int useStickyPower = 0;
726	<	int useShape = 0;
727	<	int useFLARB = 0; //it is not in AtomType yet
728	<	int useDirectionalAtom = 0;
729	<	int useElectrostatics = 0;
730	<	//usePBC and useRF are from simParams
731	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
732	<	int useRF;
733	<	int useSF;
734	<	int useSP;
735	<	int useBoxDipole;
716	>	if (simParams_->haveCutoffRadius()) {
717	>	cutoffRadius_ = simParams_->getCutoffRadius();
718	>	} else {
719	>	if (usesElectrostaticAtoms_) {
720	>	sprintf(painCave.errMsg,
721	>	"SimInfo: No value was set for the cutoffRadius.\n"
722	>	"\tOpenMD will use a default value of 12.0 angstroms"
723	>	"\tfor the cutoffRadius.\n");
724	>	painCave.isFatal = 0;
725	>	painCave.severity = OPENMD_INFO;
726	>	simError();
727	>	cutoffRadius_ = 12.0;
728	>	} else {
729	>	RealType thisCut;
730	>	set<AtomType*>::iterator i;
731	>	set<AtomType*> atomTypes;
732	>	atomTypes = getSimulatedAtomTypes();
733	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
734	>	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
735	>	cutoffRadius_ = max(thisCut, cutoffRadius_);
736	>	}
737	>	sprintf(painCave.errMsg,
738	>	"SimInfo: No value was set for the cutoffRadius.\n"
739	>	"\tOpenMD will use %lf angstroms.\n",
740	>	cutoffRadius_);
741	>	painCave.isFatal = 0;
742	>	painCave.severity = OPENMD_INFO;
743	>	simError();
744	>	}
745	>	}
746
747	<	std::string myMethod;
748	<
749	<	// set the useRF logical
750	<	useRF = 0;
751	<	useSF = 0;
752	<	useSP = 0;
753	<	useBoxDipole = 0;
754	<
755	<
756	<	if (simParams_->haveElectrostaticSummationMethod()) {
757	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
758	<	toUpper(myMethod);
759	<	if (myMethod == "REACTION_FIELD"){
760	<	useRF = 1;
761	<	} else if (myMethod == "SHIFTED_FORCE"){
762	<	useSF = 1;
763	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
764	<	useSP = 1;
747	>	map<string, CutoffMethod> stringToCutoffMethod;
748	>	stringToCutoffMethod["HARD"] = HARD;
749	>	stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
750	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
751	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
752	>
753	>	if (simParams_->haveCutoffMethod()) {
754	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
755	>	map<string, CutoffMethod>::iterator i;
756	>	i = stringToCutoffMethod.find(cutMeth);
757	>	if (i == stringToCutoffMethod.end()) {
758	>	sprintf(painCave.errMsg,
759	>	"SimInfo: Could not find chosen cutoffMethod %s\n"
760	>	"\tShould be one of: "
761	>	"HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
762	>	cutMeth.c_str());
763	>	painCave.isFatal = 1;
764	>	painCave.severity = OPENMD_ERROR;
765	>	simError();
766	>	} else {
767	>	cutoffMethod_ = i->second;
768		}
769	+	} else {
770	+	sprintf(painCave.errMsg,
771	+	"SimInfo: No value was set for the cutoffMethod.\n"
772	+	"\tOpenMD will use SHIFTED_FORCE.\n");
773	+	painCave.isFatal = 0;
774	+	painCave.severity = OPENMD_INFO;
775	+	simError();
776	+	cutoffMethod_ = SHIFTED_FORCE;
777		}
778	+	}
779	+
780	+	/**
781	+	* setupSwitching
782	+	*
783	+	* Sets the values of switchingRadius and
784	+	* If the switchingRadius was explicitly set, use that value (but check it)
785	+	* If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
786	+	*/
787	+	void SimInfo::setupSwitching() {
788
789	<	if (simParams_->haveAccumulateBoxDipole())
790	<	if (simParams_->getAccumulateBoxDipole())
791	<	useBoxDipole = 1;
789	>	if (simParams_->haveSwitchingRadius()) {
790	>	switchingRadius_ = simParams_->getSwitchingRadius();
791	>	if (switchingRadius_ > cutoffRadius_) {
792	>	sprintf(painCave.errMsg,
793	>	"SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
794	>	switchingRadius_, cutoffRadius_);
795	>	painCave.isFatal = 1;
796	>	painCave.severity = OPENMD_ERROR;
797	>	simError();
798	>	}
799	>	} else {
800	>	switchingRadius_ = 0.85 * cutoffRadius_;
801	>	sprintf(painCave.errMsg,
802	>	"SimInfo: No value was set for the switchingRadius.\n"
803	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
804	>	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
805	>	painCave.isFatal = 0;
806	>	painCave.severity = OPENMD_WARNING;
807	>	simError();
808	>	}
809	>
810	>	if (simParams_->haveSwitchingFunctionType()) {
811	>	string funcType = simParams_->getSwitchingFunctionType();
812	>	toUpper(funcType);
813	>	if (funcType == "CUBIC") {
814	>	sft_ = cubic;
815	>	} else {
816	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
817	>	sft_ = fifth_order_poly;
818	>	} else {
819	>	// throw error
820	>	sprintf( painCave.errMsg,
821	>	"SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
822	>	"\tswitchingFunctionType must be one of: "
823	>	"\"cubic\" or \"fifth_order_polynomial\".",
824	>	funcType.c_str() );
825	>	painCave.isFatal = 1;
826	>	painCave.severity = OPENMD_ERROR;
827	>	simError();
828	>	}
829	>	}
830	>	}
831	>	}
832	>
833	>	/**
834	>	* setupNeighborlists
835	>	*
836	>	* If the skinThickness was explicitly set, use that value (but check it)
837	>	* If the skinThickness was not explicitly set: use 1.0 angstroms
838	>	*/
839	>	void SimInfo::setupNeighborlists() {
840	>	if (simParams_->haveSkinThickness()) {
841	>	skinThickness_ = simParams_->getSkinThickness();
842	>	} else {
843	>	skinThickness_ = 1.0;
844	>	sprintf(painCave.errMsg,
845	>	"SimInfo: No value was set for the skinThickness.\n"
846	>	"\tOpenMD will use a default value of %f Angstroms\n"
847	>	"\tfor this simulation\n", skinThickness_);
848	>	painCave.severity = OPENMD_INFO;
849	>	painCave.isFatal = 0;
850	>	simError();
851	>	}
852	>	}
853
854	+	void SimInfo::setupSimVariables() {
855		useAtomicVirial_ = simParams_->getUseAtomicVirial();
856	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
857	+	calcBoxDipole_ = false;
858	+	if ( simParams_->haveAccumulateBoxDipole() )
859	+	if ( simParams_->getAccumulateBoxDipole() ) {
860	+	calcBoxDipole_ = true;
861	+	}
862
863	+	set<AtomType*>::iterator i;
864	+	set<AtomType*> atomTypes;
865	+	atomTypes = getSimulatedAtomTypes();
866	+	int usesElectrostatic = 0;
867	+	int usesMetallic = 0;
868	+	int usesDirectional = 0;
869		//loop over all of the atom types
870		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
871	<	useLennardJones \|= (*i)->isLennardJones();
872	<	useElectrostatic \|= (*i)->isElectrostatic();
873	<	useEAM \|= (*i)->isEAM();
789	<	useSC \|= (*i)->isSC();
790	<	useCharge \|= (*i)->isCharge();
791	<	useDirectional \|= (*i)->isDirectional();
792	<	useDipole \|= (*i)->isDipole();
793	<	useGayBerne \|= (*i)->isGayBerne();
794	<	useSticky \|= (*i)->isSticky();
795	<	useStickyPower \|= (*i)->isStickyPower();
796	<	useShape \|= (*i)->isShape();
871	>	usesElectrostatic \|= (*i)->isElectrostatic();
872	>	usesMetallic \|= (*i)->isMetal();
873	>	usesDirectional \|= (*i)->isDirectional();
874		}
875
799	–	if (useSticky \|\| useStickyPower \|\| useDipole \|\| useGayBerne \|\| useShape) {
800	–	useDirectionalAtom = 1;
801	–	}
802	–
803	–	if (useCharge \|\| useDipole) {
804	–	useElectrostatics = 1;
805	–	}
806	–
876		#ifdef IS_MPI
877		int temp;
878	+	temp = usesDirectional;
879	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
880
881	<	temp = usePBC;
882	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
881	>	temp = usesMetallic;
882	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
883
884	<	temp = useDirectionalAtom;
885	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
815	<
816	<	temp = useLennardJones;
817	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
818	<
819	<	temp = useElectrostatics;
820	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
821	<
822	<	temp = useCharge;
823	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
824	<
825	<	temp = useDipole;
826	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
827	<
828	<	temp = useSticky;
829	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
830	<
831	<	temp = useStickyPower;
832	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
833	<
834	<	temp = useGayBerne;
835	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
836	<
837	<	temp = useEAM;
838	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
839	<
840	<	temp = useSC;
841	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
842	<
843	<	temp = useShape;
844	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
845	<
846	<	temp = useFLARB;
847	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
848	<
849	<	temp = useRF;
850	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
851	<
852	<	temp = useSF;
853	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
854	<
855	<	temp = useSP;
856	<	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
857	<
858	<	temp = useBoxDipole;
859	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860	<
861	<	temp = useAtomicVirial_;
862	<	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
863	<
884	>	temp = usesElectrostatic;
885	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
886		#endif
887	<
888	<	fInfo_.SIM_uses_PBC = usePBC;
889	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
890	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
891	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
892	<	fInfo_.SIM_uses_Charges = useCharge;
871	<	fInfo_.SIM_uses_Dipoles = useDipole;
872	<	fInfo_.SIM_uses_Sticky = useSticky;
873	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
874	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
875	<	fInfo_.SIM_uses_EAM = useEAM;
876	<	fInfo_.SIM_uses_SC = useSC;
877	<	fInfo_.SIM_uses_Shapes = useShape;
878	<	fInfo_.SIM_uses_FLARB = useFLARB;
879	<	fInfo_.SIM_uses_RF = useRF;
880	<	fInfo_.SIM_uses_SF = useSF;
881	<	fInfo_.SIM_uses_SP = useSP;
882	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
883	<	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
887	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
888	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
889	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
890	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
891	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
892	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
893		}
894
895		void SimInfo::setupFortranSim() {
896		int isError;
897		int nExclude, nOneTwo, nOneThree, nOneFour;
898	<	std::vector<int> fortranGlobalGroupMembership;
898	>	vector<int> fortranGlobalGroupMembership;
899
900	+	notifyFortranSkinThickness(&skinThickness_);
901	+
902	+	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
903	+	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
904	+	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
905	+
906		isError = 0;
907
908		//globalGroupMembership_ is filled by SimCreator
#	Line 896 \| Line 911 \| namespace OpenMD {
911		}
912
913		//calculate mass ratio of cutoff group
914	<	std::vector<RealType> mfact;
914	>	vector<RealType> mfact;
915		SimInfo::MoleculeIterator mi;
916		Molecule* mol;
917		Molecule::CutoffGroupIterator ci;
#	Line 923 \| Line 938 \| namespace OpenMD {
938		}
939
940		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
941	<	std::vector<int> identArray;
941	>	vector<int> identArray;
942
943		//to avoid memory reallocation, reserve enough space identArray
944		identArray.reserve(getNAtoms());
#	Line 936 \| Line 951 \| namespace OpenMD {
951
952		//fill molMembershipArray
953		//molMembershipArray is filled by SimCreator
954	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
954	>	vector<int> molMembershipArray(nGlobalAtoms_);
955		for (int i = 0; i < nGlobalAtoms_; i++) {
956		molMembershipArray[i] = globalMolMembership_[i] + 1;
957		}
#	Line 989 \| Line 1004 \| namespace OpenMD {
1004		void SimInfo::setupFortranParallel() {
1005		#ifdef IS_MPI
1006		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1007	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1008	<	std::vector<int> localToGlobalCutoffGroupIndex;
1007	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1008	>	vector<int> localToGlobalCutoffGroupIndex;
1009		SimInfo::MoleculeIterator mi;
1010		Molecule::AtomIterator ai;
1011		Molecule::CutoffGroupIterator ci;
#	Line 1040 \| Line 1055 \| namespace OpenMD {
1055		errorCheckPoint();
1056
1057		#endif
1043	–	}
1044	–
1045	–	void SimInfo::setupCutoff() {
1046	–
1047	–	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1048	–
1049	–	// Check the cutoff policy
1050	–	int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1051	–
1052	–	// Set LJ shifting bools to false
1053	–	ljsp_ = 0;
1054	–	ljsf_ = 0;
1055	–
1056	–	std::string myPolicy;
1057	–	if (forceFieldOptions_.haveCutoffPolicy()){
1058	–	myPolicy = forceFieldOptions_.getCutoffPolicy();
1059	–	}else if (simParams_->haveCutoffPolicy()) {
1060	–	myPolicy = simParams_->getCutoffPolicy();
1061	–	}
1062	–
1063	–	if (!myPolicy.empty()){
1064	–	toUpper(myPolicy);
1065	–	if (myPolicy == "MIX") {
1066	–	cp = MIX_CUTOFF_POLICY;
1067	–	} else {
1068	–	if (myPolicy == "MAX") {
1069	–	cp = MAX_CUTOFF_POLICY;
1070	–	} else {
1071	–	if (myPolicy == "TRADITIONAL") {
1072	–	cp = TRADITIONAL_CUTOFF_POLICY;
1073	–	} else {
1074	–	// throw error
1075	–	sprintf( painCave.errMsg,
1076	–	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1077	–	painCave.isFatal = 1;
1078	–	simError();
1079	–	}
1080	–	}
1081	–	}
1082	–	}
1083	–	notifyFortranCutoffPolicy(&cp);
1084	–
1085	–	// Check the Skin Thickness for neighborlists
1086	–	RealType skin;
1087	–	if (simParams_->haveSkinThickness()) {
1088	–	skin = simParams_->getSkinThickness();
1089	–	notifyFortranSkinThickness(&skin);
1090	–	}
1091	–
1092	–	// Check if the cutoff was set explicitly:
1093	–	if (simParams_->haveCutoffRadius()) {
1094	–	rcut_ = simParams_->getCutoffRadius();
1095	–	if (simParams_->haveSwitchingRadius()) {
1096	–	rsw_ = simParams_->getSwitchingRadius();
1097	–	} else {
1098	–	if (fInfo_.SIM_uses_Charges \|
1099	–	fInfo_.SIM_uses_Dipoles \|
1100	–	fInfo_.SIM_uses_RF) {
1101	–
1102	–	rsw_ = 0.85 * rcut_;
1103	–	sprintf(painCave.errMsg,
1104	–	"SimCreator Warning: No value was set for the switchingRadius.\n"
1105	–	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1106	–	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1107	–	painCave.isFatal = 0;
1108	–	simError();
1109	–	} else {
1110	–	rsw_ = rcut_;
1111	–	sprintf(painCave.errMsg,
1112	–	"SimCreator Warning: No value was set for the switchingRadius.\n"
1113	–	"\tOpenMD will use the same value as the cutoffRadius.\n"
1114	–	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1115	–	painCave.isFatal = 0;
1116	–	simError();
1117	–	}
1118	–	}
1119	–
1120	–	if (simParams_->haveElectrostaticSummationMethod()) {
1121	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1122	–	toUpper(myMethod);
1123	–
1124	–	if (myMethod == "SHIFTED_POTENTIAL") {
1125	–	ljsp_ = 1;
1126	–	} else if (myMethod == "SHIFTED_FORCE") {
1127	–	ljsf_ = 1;
1128	–	}
1129	–	}
1130	–
1131	–	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1132	–
1133	–	} else {
1134	–
1135	–	// For electrostatic atoms, we'll assume a large safe value:
1136	–	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
1137	–	sprintf(painCave.errMsg,
1138	–	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1139	–	"\tOpenMD will use a default value of 15.0 angstroms"
1140	–	"\tfor the cutoffRadius.\n");
1141	–	painCave.isFatal = 0;
1142	–	simError();
1143	–	rcut_ = 15.0;
1144	–
1145	–	if (simParams_->haveElectrostaticSummationMethod()) {
1146	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1147	–	toUpper(myMethod);
1148	–
1149	–	// For the time being, we're tethering the LJ shifted behavior to the
1150	–	// electrostaticSummationMethod keyword options
1151	–	if (myMethod == "SHIFTED_POTENTIAL") {
1152	–	ljsp_ = 1;
1153	–	} else if (myMethod == "SHIFTED_FORCE") {
1154	–	ljsf_ = 1;
1155	–	}
1156	–	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
1157	–	if (simParams_->haveSwitchingRadius()){
1158	–	sprintf(painCave.errMsg,
1159	–	"SimInfo Warning: A value was set for the switchingRadius\n"
1160	–	"\teven though the electrostaticSummationMethod was\n"
1161	–	"\tset to %s\n", myMethod.c_str());
1162	–	painCave.isFatal = 1;
1163	–	simError();
1164	–	}
1165	–	}
1166	–	}
1167	–
1168	–	if (simParams_->haveSwitchingRadius()){
1169	–	rsw_ = simParams_->getSwitchingRadius();
1170	–	} else {
1171	–	sprintf(painCave.errMsg,
1172	–	"SimCreator Warning: No value was set for switchingRadius.\n"
1173	–	"\tOpenMD will use a default value of\n"
1174	–	"\t0.85 * cutoffRadius for the switchingRadius\n");
1175	–	painCave.isFatal = 0;
1176	–	simError();
1177	–	rsw_ = 0.85 * rcut_;
1178	–	}
1179	–
1180	–	Electrostatic::setElectrostaticCutoffRadius(rcut_, rsw_);
1181	–	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1182	–
1183	–	} else {
1184	–	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1185	–	// We'll punt and let fortran figure out the cutoffs later.
1186	–
1187	–	notifyFortranYouAreOnYourOwn();
1188	–
1189	–	}
1190	–	}
1191	–	}
1192	–
1193	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1194	–
1195	–	int errorOut;
1196	–	ElectrostaticSummationMethod esm = NONE;
1197	–	ElectrostaticScreeningMethod sm = UNDAMPED;
1198	–	RealType alphaVal;
1199	–	RealType dielectric;
1200	–
1201	–	errorOut = isError;
1202	–
1203	–	if (simParams_->haveElectrostaticSummationMethod()) {
1204	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1205	–	toUpper(myMethod);
1206	–	if (myMethod == "NONE") {
1207	–	esm = NONE;
1208	–	} else {
1209	–	if (myMethod == "SWITCHING_FUNCTION") {
1210	–	esm = SWITCHING_FUNCTION;
1211	–	} else {
1212	–	if (myMethod == "SHIFTED_POTENTIAL") {
1213	–	esm = SHIFTED_POTENTIAL;
1214	–	} else {
1215	–	if (myMethod == "SHIFTED_FORCE") {
1216	–	esm = SHIFTED_FORCE;
1217	–	} else {
1218	–	if (myMethod == "REACTION_FIELD") {
1219	–	esm = REACTION_FIELD;
1220	–	dielectric = simParams_->getDielectric();
1221	–	if (!simParams_->haveDielectric()) {
1222	–	// throw warning
1223	–	sprintf( painCave.errMsg,
1224	–	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1225	–	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1226	–	painCave.isFatal = 0;
1227	–	simError();
1228	–	}
1229	–	} else {
1230	–	// throw error
1231	–	sprintf( painCave.errMsg,
1232	–	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1233	–	"\t(Input file specified %s .)\n"
1234	–	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1235	–	"\t\"shifted_potential\", \"shifted_force\", or \n"
1236	–	"\t\"reaction_field\".\n", myMethod.c_str() );
1237	–	painCave.isFatal = 1;
1238	–	simError();
1239	–	}
1240	–	}
1241	–	}
1242	–	}
1243	–	}
1244	–	}
1245	–
1246	–	if (simParams_->haveElectrostaticScreeningMethod()) {
1247	–	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1248	–	toUpper(myScreen);
1249	–	if (myScreen == "UNDAMPED") {
1250	–	sm = UNDAMPED;
1251	–	} else {
1252	–	if (myScreen == "DAMPED") {
1253	–	sm = DAMPED;
1254	–	if (!simParams_->haveDampingAlpha()) {
1255	–	// first set a cutoff dependent alpha value
1256	–	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1257	–	alphaVal = 0.5125 - rcut_* 0.025;
1258	–	// for values rcut > 20.5, alpha is zero
1259	–	if (alphaVal < 0) alphaVal = 0;
1260	–
1261	–	// throw warning
1262	–	sprintf( painCave.errMsg,
1263	–	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1264	–	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1265	–	painCave.isFatal = 0;
1266	–	simError();
1267	–	} else {
1268	–	alphaVal = simParams_->getDampingAlpha();
1269	–	}
1270	–
1271	–	} else {
1272	–	// throw error
1273	–	sprintf( painCave.errMsg,
1274	–	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1275	–	"\t(Input file specified %s .)\n"
1276	–	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1277	–	"or \"damped\".\n", myScreen.c_str() );
1278	–	painCave.isFatal = 1;
1279	–	simError();
1280	–	}
1281	–	}
1282	–	}
1283	–
1284	–
1285	–	Electrostatic::setElectrostaticSummationMethod( esm );
1286	–	Electrostatic::setElectrostaticScreeningMethod( sm );
1287	–	Electrostatic::setDampingAlpha( alphaVal );
1288	–	Electrostatic::setReactionFieldDielectric( dielectric );
1289	–	initFortranFF( &errorOut );
1058		}
1291	–
1292	–	void SimInfo::setupSwitchingFunction() {
1293	–	int ft = CUBIC;
1059
1295	–	if (simParams_->haveSwitchingFunctionType()) {
1296	–	std::string funcType = simParams_->getSwitchingFunctionType();
1297	–	toUpper(funcType);
1298	–	if (funcType == "CUBIC") {
1299	–	ft = CUBIC;
1300	–	} else {
1301	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1302	–	ft = FIFTH_ORDER_POLY;
1303	–	} else {
1304	–	// throw error
1305	–	sprintf( painCave.errMsg,
1306	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1307	–	painCave.isFatal = 1;
1308	–	simError();
1309	–	}
1310	–	}
1311	–	}
1060
1313	–	// send switching function notification to switcheroo
1314	–	setFunctionType(&ft);
1315	–
1316	–	}
1317	–
1061		void SimInfo::setupAccumulateBoxDipole() {
1062
1320	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1321	–	if ( simParams_->haveAccumulateBoxDipole() )
1322	–	if ( simParams_->getAccumulateBoxDipole() ) {
1323	–	setAccumulateBoxDipole();
1324	–	calcBoxDipole_ = true;
1325	–	}
1063
1064		}
1065
#	Line 1330 \| Line 1067 \| namespace OpenMD {
1067		properties_.addProperty(genData);
1068		}
1069
1070	<	void SimInfo::removeProperty(const std::string& propName) {
1070	>	void SimInfo::removeProperty(const string& propName) {
1071		properties_.removeProperty(propName);
1072		}
1073
#	Line 1338 \| Line 1075 \| namespace OpenMD {
1075		properties_.clearProperties();
1076		}
1077
1078	<	std::vector<std::string> SimInfo::getPropertyNames() {
1078	>	vector<string> SimInfo::getPropertyNames() {
1079		return properties_.getPropertyNames();
1080		}
1081
1082	<	std::vector<GenericData*> SimInfo::getProperties() {
1082	>	vector<GenericData*> SimInfo::getProperties() {
1083		return properties_.getProperties();
1084		}
1085
1086	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1086	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1087		return properties_.getPropertyByName(propName);
1088		}
1089
#	Line 1429 \| Line 1166 \| namespace OpenMD {
1166
1167		}
1168
1169	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1169	>	ostream& operator <<(ostream& o, SimInfo& info) {
1170
1171		return o;
1172		}
#	Line 1472 \| Line 1209 \| namespace OpenMD {
1209
1210
1211		[ Ixx -Ixy -Ixz ]
1212	<	J =\| -Iyx Iyy -Iyz \|
1212	>	J =\| -Iyx Iyy -Iyz \|
1213		[ -Izx -Iyz Izz ]
1214		*/
1215
#	Line 1579 \| Line 1316 \| namespace OpenMD {
1316		return IOIndexToIntegrableObject.at(index);
1317		}
1318
1319	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1319	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1320		IOIndexToIntegrableObject= v;
1321		}
1322
#	Line 1621 \| Line 1358 \| namespace OpenMD {
1358		return;
1359		}
1360		/*
1361	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1361	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1362		assert( v.size() == nAtoms_ + nRigidBodies_);
1363		sdByGlobalIndex_ = v;
1364		}
#	Line 1631 \| Line 1368 \| namespace OpenMD {
1368		return sdByGlobalIndex_.at(index);
1369		}
1370		*/
1371	+	int SimInfo::getNGlobalConstraints() {
1372	+	int nGlobalConstraints;
1373	+	#ifdef IS_MPI
1374	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1375	+	MPI_COMM_WORLD);
1376	+	#else
1377	+	nGlobalConstraints = nConstraints_;
1378	+	#endif
1379	+	return nGlobalConstraints;
1380	+	}
1381	+
1382		}//end namespace OpenMD
1383

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Comparing branches/development/src/brains/SimInfo.cpp (file contents): Revision 1503 by gezelter, Sat Oct 2 19:54:41 2010 UTC vs. Revision 1534 by gezelter, Wed Dec 29 21:53:28 2010 UTC

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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1503 by gezelter, Sat Oct 2 19:54:41 2010 UTC vs.
Revision 1534 by gezelter, Wed Dec 29 21:53:28 2010 UTC