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root/OpenMD/branches/development/src/brains/SimInfo.cpp

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trunk/src/brains/SimInfo.cpp (file contents), Revision 1290 by cli2, Wed Sep 10 19:51:45 2008 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	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"
57		#include "UseTheForce/doForces_interface.h"
58		#include "UseTheForce/DarkSide/neighborLists_interface.h"
63	–	#include "UseTheForce/DarkSide/electrostatic_interface.h"
64	–	#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
66
67		#ifdef IS_MPI
#	Line 74 | Line 69
69		#include "UseTheForce/DarkSide/simParallel_interface.h"
70		#endif
71
72	<	namespace oopse {
73	<	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	<	}
72	>	using namespace std;
73	>	namespace OpenMD {
74
75		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
76		forceField_(ff), simParams_(simParams),
#	Line 93 | Line 80 | namespace oopse {
80		nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
81		nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
82		nConstraints_(0), sman_(NULL), fortranInitialized_(false),
83	<	calcBoxDipole_(false), useAtomicVirial_(true) {
84	<
85	<
86	<	MoleculeStamp* molStamp;
87	<	int nMolWithSameStamp;
88	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
89	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
90	<	CutoffGroupStamp* cgStamp;
91	<	RigidBodyStamp* rbStamp;
92	<	int nRigidAtoms = 0;
93	<
94	<	std::vector<Component*> components = simParams->getComponents();
83	>	calcBoxDipole_(false), useAtomicVirial_(true) {
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	>	vector<Component*> components = simParams->getComponents();
94	>
95	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
96	>	molStamp = (*i)->getMoleculeStamp();
97	>	nMolWithSameStamp = (*i)->getNMol();
98
99	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
100	<	molStamp = (*i)->getMoleculeStamp();
101	<	nMolWithSameStamp = (*i)->getNMol();
102	<
103	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
104	<
105	<	//calculate atoms in molecules
106	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
107	<
108	<	//calculate atoms in cutoff groups
109	<	int nAtomsInGroups = 0;
110	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
111	<
112	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
113	<	cgStamp = molStamp->getCutoffGroupStamp(j);
114	<	nAtomsInGroups += cgStamp->getNMembers();
115	<	}
116	<
117	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
118	<
119	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
120	<
121	<	//calculate atoms in rigid bodies
122	<	int nAtomsInRigidBodies = 0;
123	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
124	<
125	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
126	<	rbStamp = molStamp->getRigidBodyStamp(j);
127	<	nAtomsInRigidBodies += rbStamp->getNMembers();
128	<	}
129	<
130	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
131	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
132	<
133	<	}
134	<
135	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
136	<	//group therefore the total number of cutoff groups in the system is
137	<	//equal to the total number of atoms minus number of atoms belong to
138	<	//cutoff group defined in meta-data file plus the number of cutoff
139	<	//groups defined in meta-data file
140	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
141	<
142	<	//every free atom (atom does not belong to rigid bodies) is an
143	<	//integrable object therefore the total number of integrable objects
144	<	//in the system is equal to the total number of atoms minus number of
145	<	//atoms belong to rigid body defined in meta-data file plus the number
146	<	//of rigid bodies defined in meta-data file
147	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
148	<	+ nGlobalRigidBodies_;
149	<
160	<	nGlobalMols_ = molStampIds_.size();
161	<	molToProcMap_.resize(nGlobalMols_);
162	<	}
163	<
99	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
100	>
101	>	//calculate atoms in molecules
102	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
103	>
104	>	//calculate atoms in cutoff groups
105	>	int nAtomsInGroups = 0;
106	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
107	>
108	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
109	>	cgStamp = molStamp->getCutoffGroupStamp(j);
110	>	nAtomsInGroups += cgStamp->getNMembers();
111	>	}
112	>
113	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
114	>
115	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
116	>
117	>	//calculate atoms in rigid bodies
118	>	int nAtomsInRigidBodies = 0;
119	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
120	>
121	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
122	>	rbStamp = molStamp->getRigidBodyStamp(j);
123	>	nAtomsInRigidBodies += rbStamp->getNMembers();
124	>	}
125	>
126	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
127	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
128	>
129	>	}
130	>
131	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
132	>	//group therefore the total number of cutoff groups in the system is
133	>	//equal to the total number of atoms minus number of atoms belong to
134	>	//cutoff group defined in meta-data file plus the number of cutoff
135	>	//groups defined in meta-data file
136	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
137	>
138	>	//every free atom (atom does not belong to rigid bodies) is an
139	>	//integrable object therefore the total number of integrable objects
140	>	//in the system is equal to the total number of atoms minus number of
141	>	//atoms belong to rigid body defined in meta-data file plus the number
142	>	//of rigid bodies defined in meta-data file
143	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
144	>	+ nGlobalRigidBodies_;
145	>
146	>	nGlobalMols_ = molStampIds_.size();
147	>	molToProcMap_.resize(nGlobalMols_);
148	>	}
149	>
150		SimInfo::~SimInfo() {
151	<	std::map<int, Molecule*>::iterator i;
151	>	map<int, Molecule*>::iterator i;
152		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
153		delete i->second;
154		}
#	Line 173 | Line 159 | namespace oopse {
159		delete forceField_;
160		}
161
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	–	}
162
163		bool SimInfo::addMolecule(Molecule* mol) {
164		MoleculeIterator i;
165	<
165	>
166		i = molecules_.find(mol->getGlobalIndex());
167		if (i == molecules_.end() ) {
168	<
169	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
170	<
168	>
169	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
170	>
171		nAtoms_ += mol->getNAtoms();
172		nBonds_ += mol->getNBonds();
173		nBends_ += mol->getNBends();
#	Line 201 | Line 177 | namespace oopse {
177		nIntegrableObjects_ += mol->getNIntegrableObjects();
178		nCutoffGroups_ += mol->getNCutoffGroups();
179		nConstraints_ += mol->getNConstraintPairs();
180	<
180	>
181		addInteractionPairs(mol);
182	<
182	>
183		return true;
184		} else {
185		return false;
186		}
187		}
188	<
188	>
189		bool SimInfo::removeMolecule(Molecule* mol) {
190		MoleculeIterator i;
191		i = molecules_.find(mol->getGlobalIndex());
#	Line 237 | Line 213 | namespace oopse {
213		} else {
214		return false;
215		}
240	–
241	–
216		}
217
218
#	Line 256 | Line 230 | namespace oopse {
230		void SimInfo::calcNdf() {
231		int ndf_local;
232		MoleculeIterator i;
233	<	std::vector<StuntDouble*>::iterator j;
233	>	vector<StuntDouble*>::iterator j;
234		Molecule* mol;
235		StuntDouble* integrableObject;
236
#	Line 307 | Line 281 | namespace oopse {
281		int ndfRaw_local;
282
283		MoleculeIterator i;
284	<	std::vector<StuntDouble*>::iterator j;
284	>	vector<StuntDouble*>::iterator j;
285		Molecule* mol;
286		StuntDouble* integrableObject;
287
#	Line 356 | Line 330 | namespace oopse {
330
331		void SimInfo::addInteractionPairs(Molecule* mol) {
332		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
333	<	std::vector<Bond*>::iterator bondIter;
334	<	std::vector<Bend*>::iterator bendIter;
335	<	std::vector<Torsion*>::iterator torsionIter;
336	<	std::vector<Inversion*>::iterator inversionIter;
333	>	vector<Bond*>::iterator bondIter;
334	>	vector<Bend*>::iterator bendIter;
335	>	vector<Torsion*>::iterator torsionIter;
336	>	vector<Inversion*>::iterator inversionIter;
337		Bond* bond;
338		Bend* bend;
339		Torsion* torsion;
#	Line 377 | Line 351 | namespace oopse {
351		// always be excluded.  These are done at the bottom of this
352		// function.
353
354	<	std::map<int, std::set<int> > atomGroups;
354	>	map<int, set<int> > atomGroups;
355		Molecule::RigidBodyIterator rbIter;
356		RigidBody* rb;
357		Molecule::IntegrableObjectIterator ii;
#	Line 389 | Line 363 | namespace oopse {
363
364		if (integrableObject->isRigidBody()) {
365		rb = static_cast<RigidBody*>(integrableObject);
366	<	std::vector<Atom*> atoms = rb->getAtoms();
367	<	std::set<int> rigidAtoms;
366	>	vector<Atom*> atoms = rb->getAtoms();
367	>	set<int> rigidAtoms;
368		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
369		rigidAtoms.insert(atoms[i]->getGlobalIndex());
370		}
371		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
372	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
372	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
373		}
374		} else {
375	<	std::set<int> oneAtomSet;
375	>	set<int> oneAtomSet;
376		oneAtomSet.insert(integrableObject->getGlobalIndex());
377	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
377	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
378		}
379		}
380
#	Line 503 | Line 477 | namespace oopse {
477
478		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
479		rb = mol->nextRigidBody(rbIter)) {
480	<	std::vector<Atom*> atoms = rb->getAtoms();
480	>	vector<Atom*> atoms = rb->getAtoms();
481		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
482		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
483		a = atoms[i]->getGlobalIndex();
#	Line 517 | Line 491 | namespace oopse {
491
492		void SimInfo::removeInteractionPairs(Molecule* mol) {
493		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
494	<	std::vector<Bond*>::iterator bondIter;
495	<	std::vector<Bend*>::iterator bendIter;
496	<	std::vector<Torsion*>::iterator torsionIter;
497	<	std::vector<Inversion*>::iterator inversionIter;
494	>	vector<Bond*>::iterator bondIter;
495	>	vector<Bend*>::iterator bendIter;
496	>	vector<Torsion*>::iterator torsionIter;
497	>	vector<Inversion*>::iterator inversionIter;
498		Bond* bond;
499		Bend* bend;
500		Torsion* torsion;
#	Line 530 | Line 504 | namespace oopse {
504		int c;
505		int d;
506
507	<	std::map<int, std::set<int> > atomGroups;
507	>	map<int, set<int> > atomGroups;
508		Molecule::RigidBodyIterator rbIter;
509		RigidBody* rb;
510		Molecule::IntegrableObjectIterator ii;
#	Line 542 | Line 516 | namespace oopse {
516
517		if (integrableObject->isRigidBody()) {
518		rb = static_cast<RigidBody*>(integrableObject);
519	<	std::vector<Atom*> atoms = rb->getAtoms();
520	<	std::set<int> rigidAtoms;
519	>	vector<Atom*> atoms = rb->getAtoms();
520	>	set<int> rigidAtoms;
521		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
522		rigidAtoms.insert(atoms[i]->getGlobalIndex());
523		}
524		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
525	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
525	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
526		}
527		} else {
528	<	std::set<int> oneAtomSet;
528	>	set<int> oneAtomSet;
529		oneAtomSet.insert(integrableObject->getGlobalIndex());
530	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
530	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
531		}
532		}
533
#	Line 656 | Line 630 | namespace oopse {
630
631		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
632		rb = mol->nextRigidBody(rbIter)) {
633	<	std::vector<Atom*> atoms = rb->getAtoms();
633	>	vector<Atom*> atoms = rb->getAtoms();
634		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
635		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
636		a = atoms[i]->getGlobalIndex();
#	Line 679 | Line 653 | namespace oopse {
653		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
654		}
655
656	+
657	+	/**
658	+	* update
659	+	*
660	+	*  Performs the global checks and variable settings after the objects have been
661	+	*  created.
662	+	*
663	+	*/
664		void SimInfo::update() {
665	+
666	+	setupSimVariables();
667	+	setupCutoffs();
668	+	setupSwitching();
669	+	setupElectrostatics();
670	+	setupNeighborlists();
671
684	–	setupSimType();
685	–
672		#ifdef IS_MPI
673		setupFortranParallel();
674		#endif
689	–
675		setupFortranSim();
676	+	fortranInitialized_ = true;
677
692	–	//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	–
678		calcNdf();
679		calcNdfRaw();
680		calcNdfTrans();
712	–
713	–	fortranInitialized_ = true;
681		}
682	<
683	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
682	>
683	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
684		SimInfo::MoleculeIterator mi;
685		Molecule* mol;
686		Molecule::AtomIterator ai;
687		Atom* atom;
688	<	std::set<AtomType*> atomTypes;
689	<
690	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
724	<
688	>	set<AtomType*> atomTypes;
689	>
690	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
691		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
692		atomTypes.insert(atom->getAtomType());
693	<	}
694	<
729	<	}
730	<
693	>	}
694	>	}
695		return atomTypes;
696		}
697
698	<	void SimInfo::setupSimType() {
699	<	std::set<AtomType*>::iterator i;
700	<	std::set<AtomType*> atomTypes;
701	<	atomTypes = getUniqueAtomTypes();
698	>	/**
699	>	* setupCutoffs
700	>	*
701	>	* Sets the values of cutoffRadius and cutoffMethod
702	>	*
703	>	* cutoffRadius : realType
704	>	*  If the cutoffRadius was explicitly set, use that value.
705	>	*  If the cutoffRadius was not explicitly set:
706	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
707	>	*      No electrostatic atoms?  Poll the atom types present in the
708	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
709	>	*      Use the maximum suggested value that was found.
710	>	*
711	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
712	>	*      If cutoffMethod was explicitly set, use that choice.
713	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
714	>	*/
715	>	void SimInfo::setupCutoffs() {
716
717	<	int useLennardJones = 0;
718	<	int useElectrostatic = 0;
719	<	int useEAM = 0;
720	<	int useSC = 0;
721	<	int useCharge = 0;
722	<	int useDirectional = 0;
723	<	int useDipole = 0;
724	<	int useGayBerne = 0;
725	<	int useSticky = 0;
726	<	int useStickyPower = 0;
727	<	int useShape = 0;
728	<	int useFLARB = 0; //it is not in AtomType yet
729	<	int useDirectionalAtom = 0;
730	<	int useElectrostatics = 0;
731	<	//usePBC and useRF are from simParams
732	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
733	<	int useRF;
734	<	int useSF;
735	<	int useSP;
736	<	int useBoxDipole;
737	<
738	<	std::string myMethod;
739	<
740	<	// set the useRF logical
741	<	useRF = 0;
742	<	useSF = 0;
743	<	useSP = 0;
717	>	if (simParams_->haveCutoffRadius()) {
718	>	cutoffRadius_ = simParams_->getCutoffRadius();
719	>	} else {
720	>	if (usesElectrostaticAtoms_) {
721	>	sprintf(painCave.errMsg,
722	>	"SimInfo: No value was set for the cutoffRadius.\n"
723	>	"\tOpenMD will use a default value of 12.0 angstroms"
724	>	"\tfor the cutoffRadius.\n");
725	>	painCave.isFatal = 0;
726	>	painCave.severity = OPENMD_INFO;
727	>	simError();
728	>	cutoffRadius_ = 12.0;
729	>	} else {
730	>	RealType thisCut;
731	>	set<AtomType*>::iterator i;
732	>	set<AtomType*> atomTypes;
733	>	atomTypes = getSimulatedAtomTypes();
734	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
735	>	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
736	>	cutoffRadius_ = max(thisCut, cutoffRadius_);
737	>	}
738	>	sprintf(painCave.errMsg,
739	>	"SimInfo: No value was set for the cutoffRadius.\n"
740	>	"\tOpenMD will use %lf angstroms.\n",
741	>	cutoffRadius_);
742	>	painCave.isFatal = 0;
743	>	painCave.severity = OPENMD_INFO;
744	>	simError();
745	>	}
746	>	}
747
748	+	InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
749
750	<	if (simParams_->haveElectrostaticSummationMethod()) {
751	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
752	<	toUpper(myMethod);
753	<	if (myMethod == "REACTION_FIELD"){
754	<	useRF = 1;
755	<	} else if (myMethod == "SHIFTED_FORCE"){
756	<	useSF = 1;
757	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
758	<	useSP = 1;
750	>	map<string, CutoffMethod> stringToCutoffMethod;
751	>	stringToCutoffMethod["HARD"] = HARD;
752	>	stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
753	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
754	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
755	>
756	>	if (simParams_->haveCutoffMethod()) {
757	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
758	>	map<string, CutoffMethod>::iterator i;
759	>	i = stringToCutoffMethod.find(cutMeth);
760	>	if (i == stringToCutoffMethod.end()) {
761	>	sprintf(painCave.errMsg,
762	>	"SimInfo: Could not find chosen cutoffMethod %s\n"
763	>	"\tShould be one of: "
764	>	"HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
765	>	cutMeth.c_str());
766	>	painCave.isFatal = 1;
767	>	painCave.severity = OPENMD_ERROR;
768	>	simError();
769	>	} else {
770	>	cutoffMethod_ = i->second;
771	>	}
772	>	} else {
773	>	sprintf(painCave.errMsg,
774	>	"SimInfo: No value was set for the cutoffMethod.\n"
775	>	"\tOpenMD will use SHIFTED_FORCE.\n");
776	>	painCave.isFatal = 0;
777	>	painCave.severity = OPENMD_INFO;
778	>	simError();
779	>	cutoffMethod_ = SHIFTED_FORCE;
780	>	}
781	>
782	>	InteractionManager::Instance()->setCutoffMethod(cutoffMethod_);
783	>	}
784	>
785	>	/**
786	>	* setupSwitching
787	>	*
788	>	* Sets the values of switchingRadius and
789	>	*  If the switchingRadius was explicitly set, use that value (but check it)
790	>	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
791	>	*/
792	>	void SimInfo::setupSwitching() {
793	>
794	>	if (simParams_->haveSwitchingRadius()) {
795	>	switchingRadius_ = simParams_->getSwitchingRadius();
796	>	if (switchingRadius_ > cutoffRadius_) {
797	>	sprintf(painCave.errMsg,
798	>	"SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
799	>	switchingRadius_, cutoffRadius_);
800	>	painCave.isFatal = 1;
801	>	painCave.severity = OPENMD_ERROR;
802	>	simError();
803	>	}
804	>	} else {
805	>	switchingRadius_ = 0.85 * cutoffRadius_;
806	>	sprintf(painCave.errMsg,
807	>	"SimInfo: No value was set for the switchingRadius.\n"
808	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
809	>	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
810	>	painCave.isFatal = 0;
811	>	painCave.severity = OPENMD_WARNING;
812	>	simError();
813	>	}
814	>
815	>	InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
816	>
817	>	SwitchingFunctionType ft;
818	>
819	>	if (simParams_->haveSwitchingFunctionType()) {
820	>	string funcType = simParams_->getSwitchingFunctionType();
821	>	toUpper(funcType);
822	>	if (funcType == "CUBIC") {
823	>	ft = cubic;
824	>	} else {
825	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
826	>	ft = fifth_order_poly;
827	>	} else {
828	>	// throw error
829	>	sprintf( painCave.errMsg,
830	>	"SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
831	>	"\tswitchingFunctionType must be one of: "
832	>	"\"cubic\" or \"fifth_order_polynomial\".",
833	>	funcType.c_str() );
834	>	painCave.isFatal = 1;
835	>	painCave.severity = OPENMD_ERROR;
836	>	simError();
837	>	}
838		}
839		}
779	–
780	–	if (simParams_->haveAccumulateBoxDipole())
781	–	if (simParams_->getAccumulateBoxDipole())
782	–	useBoxDipole = 1;
840
841	+	InteractionManager::Instance()->setSwitchingFunctionType(ft);
842	+	}
843	+
844	+	/**
845	+	* setupSkinThickness
846	+	*
847	+	*  If the skinThickness was explicitly set, use that value (but check it)
848	+	*  If the skinThickness was not explicitly set: use 1.0 angstroms
849	+	*/
850	+	void SimInfo::setupSkinThickness() {
851	+	if (simParams_->haveSkinThickness()) {
852	+	skinThickness_ = simParams_->getSkinThickness();
853	+	} else {
854	+	skinThickness_ = 1.0;
855	+	sprintf(painCave.errMsg,
856	+	"SimInfo Warning: No value was set for the skinThickness.\n"
857	+	"\tOpenMD will use a default value of %f Angstroms\n"
858	+	"\tfor this simulation\n", skinThickness_);
859	+	painCave.isFatal = 0;
860	+	simError();
861	+	}
862	+	}
863	+
864	+	void SimInfo::setupSimType() {
865	+	set<AtomType*>::iterator i;
866	+	set<AtomType*> atomTypes;
867	+	atomTypes = getSimulatedAtomTypes();
868	+
869		useAtomicVirial_ = simParams_->getUseAtomicVirial();
870
871	+	int usesElectrostatic = 0;
872	+	int usesMetallic = 0;
873	+	int usesDirectional = 0;
874		//loop over all of the atom types
875		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
876	<	useLennardJones |= (*i)->isLennardJones();
877	<	useElectrostatic |= (*i)->isElectrostatic();
878	<	useEAM |= (*i)->isEAM();
791	<	useSC |= (*i)->isSC();
792	<	useCharge |= (*i)->isCharge();
793	<	useDirectional |= (*i)->isDirectional();
794	<	useDipole |= (*i)->isDipole();
795	<	useGayBerne |= (*i)->isGayBerne();
796	<	useSticky |= (*i)->isSticky();
797	<	useStickyPower |= (*i)->isStickyPower();
798	<	useShape |= (*i)->isShape();
876	>	usesElectrostatic |= (*i)->isElectrostatic();
877	>	usesMetallic |= (*i)->isMetal();
878	>	usesDirectional |= (*i)->isDirectional();
879		}
880
801	–	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
802	–	useDirectionalAtom = 1;
803	–	}
804	–
805	–	if (useCharge || useDipole) {
806	–	useElectrostatics = 1;
807	–	}
808	–
881		#ifdef IS_MPI
882		int temp;
883	+	temp = usesDirectional;
884	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
885
886	<	temp = usePBC;
887	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
886	>	temp = usesMetallic;
887	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
888
889	<	temp = useDirectionalAtom;
890	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
817	<
818	<	temp = useLennardJones;
819	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
820	<
821	<	temp = useElectrostatics;
822	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
823	<
824	<	temp = useCharge;
825	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
826	<
827	<	temp = useDipole;
828	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
829	<
830	<	temp = useSticky;
831	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
832	<
833	<	temp = useStickyPower;
834	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
835	<
836	<	temp = useGayBerne;
837	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
838	<
839	<	temp = useEAM;
840	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
841	<
842	<	temp = useSC;
843	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
844	<
845	<	temp = useShape;
846	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
847	<
848	<	temp = useFLARB;
849	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
850	<
851	<	temp = useRF;
852	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
853	<
854	<	temp = useSF;
855	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
856	<
857	<	temp = useSP;
858	<	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
859	<
860	<	temp = useBoxDipole;
861	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
862	<
863	<	temp = useAtomicVirial_;
864	<	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
865	<
889	>	temp = usesElectrostatic;
890	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
891		#endif
892	<
893	<	fInfo_.SIM_uses_PBC = usePBC;
894	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
895	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
896	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
897	<	fInfo_.SIM_uses_Charges = useCharge;
873	<	fInfo_.SIM_uses_Dipoles = useDipole;
874	<	fInfo_.SIM_uses_Sticky = useSticky;
875	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
876	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
877	<	fInfo_.SIM_uses_EAM = useEAM;
878	<	fInfo_.SIM_uses_SC = useSC;
879	<	fInfo_.SIM_uses_Shapes = useShape;
880	<	fInfo_.SIM_uses_FLARB = useFLARB;
881	<	fInfo_.SIM_uses_RF = useRF;
882	<	fInfo_.SIM_uses_SF = useSF;
883	<	fInfo_.SIM_uses_SP = useSP;
884	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
885	<	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
892	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
893	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
894	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
895	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
896	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
897	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
898		}
899
900		void SimInfo::setupFortranSim() {
901		int isError;
902		int nExclude, nOneTwo, nOneThree, nOneFour;
903	<	std::vector<int> fortranGlobalGroupMembership;
903	>	vector<int> fortranGlobalGroupMembership;
904
905	+	notifyFortranSkinThickness(&skinThickness_);
906	+
907	+	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
908	+	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
909	+	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
910	+
911		isError = 0;
912
913		//globalGroupMembership_ is filled by SimCreator
#	Line 898 | Line 916 | namespace oopse {
916		}
917
918		//calculate mass ratio of cutoff group
919	<	std::vector<RealType> mfact;
919	>	vector<RealType> mfact;
920		SimInfo::MoleculeIterator mi;
921		Molecule* mol;
922		Molecule::CutoffGroupIterator ci;
#	Line 925 | Line 943 | namespace oopse {
943		}
944
945		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
946	<	std::vector<int> identArray;
946	>	vector<int> identArray;
947
948		//to avoid memory reallocation, reserve enough space identArray
949		identArray.reserve(getNAtoms());
#	Line 938 | Line 956 | namespace oopse {
956
957		//fill molMembershipArray
958		//molMembershipArray is filled by SimCreator
959	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
959	>	vector<int> molMembershipArray(nGlobalAtoms_);
960		for (int i = 0; i < nGlobalAtoms_; i++) {
961		molMembershipArray[i] = globalMolMembership_[i] + 1;
962		}
#	Line 950 | Line 968 | namespace oopse {
968		nOneThree = oneThreeInteractions_.getSize();
969		nOneFour = oneFourInteractions_.getSize();
970
953	–	std::cerr << "excludedInteractions contains: " << excludedInteractions_.getSize() << " pairs \n";
954	–	std::cerr << "oneTwoInteractions contains: " << oneTwoInteractions_.getSize() << " pairs \n";
955	–	std::cerr << "oneThreeInteractions contains: " << oneThreeInteractions_.getSize() << " pairs \n";
956	–	std::cerr << "oneFourInteractions contains: " << oneFourInteractions_.getSize() << " pairs \n";
957	–
971		int* excludeList = excludedInteractions_.getPairList();
972		int* oneTwoList = oneTwoInteractions_.getPairList();
973		int* oneThreeList = oneThreeInteractions_.getPairList();
#	Line 973 | Line 986 | namespace oopse {
986		sprintf( painCave.errMsg,
987		"There was an error setting the simulation information in fortran.\n" );
988		painCave.isFatal = 1;
989	<	painCave.severity = OOPSE_ERROR;
989	>	painCave.severity = OPENMD_ERROR;
990		simError();
991		}
992
#	Line 996 | Line 1009 | namespace oopse {
1009		void SimInfo::setupFortranParallel() {
1010		#ifdef IS_MPI
1011		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1012	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1013	<	std::vector<int> localToGlobalCutoffGroupIndex;
1012	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1013	>	vector<int> localToGlobalCutoffGroupIndex;
1014		SimInfo::MoleculeIterator mi;
1015		Molecule::AtomIterator ai;
1016		Molecule::CutoffGroupIterator ci;
#	Line 1047 | Line 1060 | namespace oopse {
1060		errorCheckPoint();
1061
1062		#endif
1050	–	}
1051	–
1052	–	void SimInfo::setupCutoff() {
1053	–
1054	–	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1055	–
1056	–	// Check the cutoff policy
1057	–	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1058	–
1059	–	// Set LJ shifting bools to false
1060	–	ljsp_ = false;
1061	–	ljsf_ = false;
1062	–
1063	–	std::string myPolicy;
1064	–	if (forceFieldOptions_.haveCutoffPolicy()){
1065	–	myPolicy = forceFieldOptions_.getCutoffPolicy();
1066	–	}else if (simParams_->haveCutoffPolicy()) {
1067	–	myPolicy = simParams_->getCutoffPolicy();
1068	–	}
1069	–
1070	–	if (!myPolicy.empty()){
1071	–	toUpper(myPolicy);
1072	–	if (myPolicy == "MIX") {
1073	–	cp = MIX_CUTOFF_POLICY;
1074	–	} else {
1075	–	if (myPolicy == "MAX") {
1076	–	cp = MAX_CUTOFF_POLICY;
1077	–	} else {
1078	–	if (myPolicy == "TRADITIONAL") {
1079	–	cp = TRADITIONAL_CUTOFF_POLICY;
1080	–	} else {
1081	–	// throw error
1082	–	sprintf( painCave.errMsg,
1083	–	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1084	–	painCave.isFatal = 1;
1085	–	simError();
1086	–	}
1087	–	}
1088	–	}
1089	–	}
1090	–	notifyFortranCutoffPolicy(&cp);
1091	–
1092	–	// Check the Skin Thickness for neighborlists
1093	–	RealType skin;
1094	–	if (simParams_->haveSkinThickness()) {
1095	–	skin = simParams_->getSkinThickness();
1096	–	notifyFortranSkinThickness(&skin);
1097	–	}
1098	–
1099	–	// Check if the cutoff was set explicitly:
1100	–	if (simParams_->haveCutoffRadius()) {
1101	–	rcut_ = simParams_->getCutoffRadius();
1102	–	if (simParams_->haveSwitchingRadius()) {
1103	–	rsw_  = simParams_->getSwitchingRadius();
1104	–	} else {
1105	–	if (fInfo_.SIM_uses_Charges |
1106	–	fInfo_.SIM_uses_Dipoles |
1107	–	fInfo_.SIM_uses_RF) {
1108	–
1109	–	rsw_ = 0.85 * rcut_;
1110	–	sprintf(painCave.errMsg,
1111	–	"SimCreator Warning: No value was set for the switchingRadius.\n"
1112	–	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1113	–	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1114	–	painCave.isFatal = 0;
1115	–	simError();
1116	–	} else {
1117	–	rsw_ = rcut_;
1118	–	sprintf(painCave.errMsg,
1119	–	"SimCreator Warning: No value was set for the switchingRadius.\n"
1120	–	"\tOOPSE will use the same value as the cutoffRadius.\n"
1121	–	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1122	–	painCave.isFatal = 0;
1123	–	simError();
1124	–	}
1125	–	}
1126	–
1127	–	if (simParams_->haveElectrostaticSummationMethod()) {
1128	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1129	–	toUpper(myMethod);
1130	–
1131	–	if (myMethod == "SHIFTED_POTENTIAL") {
1132	–	ljsp_ = true;
1133	–	} else if (myMethod == "SHIFTED_FORCE") {
1134	–	ljsf_ = true;
1135	–	}
1136	–	}
1137	–	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1138	–
1139	–	} else {
1140	–
1141	–	// For electrostatic atoms, we'll assume a large safe value:
1142	–	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1143	–	sprintf(painCave.errMsg,
1144	–	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1145	–	"\tOOPSE will use a default value of 15.0 angstroms"
1146	–	"\tfor the cutoffRadius.\n");
1147	–	painCave.isFatal = 0;
1148	–	simError();
1149	–	rcut_ = 15.0;
1150	–
1151	–	if (simParams_->haveElectrostaticSummationMethod()) {
1152	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1153	–	toUpper(myMethod);
1154	–
1155	–	// For the time being, we're tethering the LJ shifted behavior to the
1156	–	// electrostaticSummationMethod keyword options
1157	–	if (myMethod == "SHIFTED_POTENTIAL") {
1158	–	ljsp_ = true;
1159	–	} else if (myMethod == "SHIFTED_FORCE") {
1160	–	ljsf_ = true;
1161	–	}
1162	–	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1163	–	if (simParams_->haveSwitchingRadius()){
1164	–	sprintf(painCave.errMsg,
1165	–	"SimInfo Warning: A value was set for the switchingRadius\n"
1166	–	"\teven though the electrostaticSummationMethod was\n"
1167	–	"\tset to %s\n", myMethod.c_str());
1168	–	painCave.isFatal = 1;
1169	–	simError();
1170	–	}
1171	–	}
1172	–	}
1173	–
1174	–	if (simParams_->haveSwitchingRadius()){
1175	–	rsw_ = simParams_->getSwitchingRadius();
1176	–	} else {
1177	–	sprintf(painCave.errMsg,
1178	–	"SimCreator Warning: No value was set for switchingRadius.\n"
1179	–	"\tOOPSE will use a default value of\n"
1180	–	"\t0.85 * cutoffRadius for the switchingRadius\n");
1181	–	painCave.isFatal = 0;
1182	–	simError();
1183	–	rsw_ = 0.85 * rcut_;
1184	–	}
1185	–
1186	–	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1187	–
1188	–	} else {
1189	–	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1190	–	// We'll punt and let fortran figure out the cutoffs later.
1191	–
1192	–	notifyFortranYouAreOnYourOwn();
1193	–
1194	–	}
1195	–	}
1063		}
1197	–
1198	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1199	–
1200	–	int errorOut;
1201	–	int esm =  NONE;
1202	–	int sm = UNDAMPED;
1203	–	RealType alphaVal;
1204	–	RealType dielectric;
1205	–
1206	–	errorOut = isError;
1207	–
1208	–	if (simParams_->haveElectrostaticSummationMethod()) {
1209	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1210	–	toUpper(myMethod);
1211	–	if (myMethod == "NONE") {
1212	–	esm = NONE;
1213	–	} else {
1214	–	if (myMethod == "SWITCHING_FUNCTION") {
1215	–	esm = SWITCHING_FUNCTION;
1216	–	} else {
1217	–	if (myMethod == "SHIFTED_POTENTIAL") {
1218	–	esm = SHIFTED_POTENTIAL;
1219	–	} else {
1220	–	if (myMethod == "SHIFTED_FORCE") {
1221	–	esm = SHIFTED_FORCE;
1222	–	} else {
1223	–	if (myMethod == "REACTION_FIELD") {
1224	–	esm = REACTION_FIELD;
1225	–	dielectric = simParams_->getDielectric();
1226	–	if (!simParams_->haveDielectric()) {
1227	–	// throw warning
1228	–	sprintf( painCave.errMsg,
1229	–	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1230	–	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1231	–	painCave.isFatal = 0;
1232	–	simError();
1233	–	}
1234	–	} else {
1235	–	// throw error
1236	–	sprintf( painCave.errMsg,
1237	–	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1238	–	"\t(Input file specified %s .)\n"
1239	–	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1240	–	"\t\"shifted_potential\", \"shifted_force\", or \n"
1241	–	"\t\"reaction_field\".\n", myMethod.c_str() );
1242	–	painCave.isFatal = 1;
1243	–	simError();
1244	–	}
1245	–	}
1246	–	}
1247	–	}
1248	–	}
1249	–	}
1250	–
1251	–	if (simParams_->haveElectrostaticScreeningMethod()) {
1252	–	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1253	–	toUpper(myScreen);
1254	–	if (myScreen == "UNDAMPED") {
1255	–	sm = UNDAMPED;
1256	–	} else {
1257	–	if (myScreen == "DAMPED") {
1258	–	sm = DAMPED;
1259	–	if (!simParams_->haveDampingAlpha()) {
1260	–	// first set a cutoff dependent alpha value
1261	–	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1262	–	alphaVal = 0.5125 - rcut_* 0.025;
1263	–	// for values rcut > 20.5, alpha is zero
1264	–	if (alphaVal < 0) alphaVal = 0;
1064
1266	–	// throw warning
1267	–	sprintf( painCave.errMsg,
1268	–	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1269	–	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1270	–	painCave.isFatal = 0;
1271	–	simError();
1272	–	} else {
1273	–	alphaVal = simParams_->getDampingAlpha();
1274	–	}
1275	–
1276	–	} else {
1277	–	// throw error
1278	–	sprintf( painCave.errMsg,
1279	–	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1280	–	"\t(Input file specified %s .)\n"
1281	–	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1282	–	"or \"damped\".\n", myScreen.c_str() );
1283	–	painCave.isFatal = 1;
1284	–	simError();
1285	–	}
1286	–	}
1287	–	}
1288	–
1289	–	// let's pass some summation method variables to fortran
1290	–	setElectrostaticSummationMethod( &esm );
1291	–	setFortranElectrostaticMethod( &esm );
1292	–	setScreeningMethod( &sm );
1293	–	setDampingAlpha( &alphaVal );
1294	–	setReactionFieldDielectric( &dielectric );
1295	–	initFortranFF( &errorOut );
1296	–	}
1065
1066		void SimInfo::setupSwitchingFunction() {
1299	–	int ft = CUBIC;
1067
1301	–	if (simParams_->haveSwitchingFunctionType()) {
1302	–	std::string funcType = simParams_->getSwitchingFunctionType();
1303	–	toUpper(funcType);
1304	–	if (funcType == "CUBIC") {
1305	–	ft = CUBIC;
1306	–	} else {
1307	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1308	–	ft = FIFTH_ORDER_POLY;
1309	–	} else {
1310	–	// throw error
1311	–	sprintf( painCave.errMsg,
1312	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1313	–	painCave.isFatal = 1;
1314	–	simError();
1315	–	}
1316	–	}
1317	–	}
1318	–
1319	–	// send switching function notification to switcheroo
1320	–	setFunctionType(&ft);
1321	–
1068		}
1069
1070		void SimInfo::setupAccumulateBoxDipole() {
#	Line 1326 | Line 1072 | namespace oopse {
1072		// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1073		if ( simParams_->haveAccumulateBoxDipole() )
1074		if ( simParams_->getAccumulateBoxDipole() ) {
1329	–	setAccumulateBoxDipole();
1075		calcBoxDipole_ = true;
1076		}
1077
#	Line 1336 | Line 1081 | namespace oopse {
1081		properties_.addProperty(genData);
1082		}
1083
1084	<	void SimInfo::removeProperty(const std::string& propName) {
1084	>	void SimInfo::removeProperty(const string& propName) {
1085		properties_.removeProperty(propName);
1086		}
1087
#	Line 1344 | Line 1089 | namespace oopse {
1089		properties_.clearProperties();
1090		}
1091
1092	<	std::vector<std::string> SimInfo::getPropertyNames() {
1092	>	vector<string> SimInfo::getPropertyNames() {
1093		return properties_.getPropertyNames();
1094		}
1095
1096	<	std::vector<GenericData*> SimInfo::getProperties() {
1096	>	vector<GenericData*> SimInfo::getProperties() {
1097		return properties_.getProperties();
1098		}
1099
1100	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1100	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1101		return properties_.getPropertyByName(propName);
1102		}
1103
#	Line 1435 | Line 1180 | namespace oopse {
1180
1181		}
1182
1183	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1183	>	ostream& operator <<(ostream& o, SimInfo& info) {
1184
1185		return o;
1186		}
#	Line 1478 | Line 1223 | namespace oopse {
1223
1224
1225		[  Ixx -Ixy  -Ixz ]
1226	<	J =| -Iyx  Iyy  -Iyz |
1226	>	J =| -Iyx  Iyy  -Iyz |
1227		[ -Izx -Iyz   Izz ]
1228		*/
1229
#	Line 1585 | Line 1330 | namespace oopse {
1330		return IOIndexToIntegrableObject.at(index);
1331		}
1332
1333	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1333	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1334		IOIndexToIntegrableObject= v;
1335		}
1336
#	Line 1627 | Line 1372 | namespace oopse {
1372		return;
1373		}
1374		/*
1375	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1375	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1376		assert( v.size() == nAtoms_ + nRigidBodies_);
1377		sdByGlobalIndex_ = v;
1378		}
#	Line 1637 | Line 1382 | namespace oopse {
1382		return sdByGlobalIndex_.at(index);
1383		}
1384		*/
1385	<	}//end namespace oopse
1385	>	int SimInfo::getNGlobalConstraints() {
1386	>	int nGlobalConstraints;
1387	>	#ifdef IS_MPI
1388	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1389	>	MPI_COMM_WORLD);
1390	>	#else
1391	>	nGlobalConstraints =  nConstraints_;
1392	>	#endif
1393	>	return nGlobalConstraints;
1394	>	}
1395
1396	+	}//end namespace OpenMD
1397	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 1290 by cli2, Wed Sep 10 19:51:45 2008 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC

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