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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 1287 by gezelter, Wed Sep 10 18:11:32 2008 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1529 by gezelter, Mon Dec 27 18:35:59 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 55 | Line 55
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"
58		#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
59		#include "UseTheForce/doForces_interface.h"
60		#include "UseTheForce/DarkSide/neighborLists_interface.h"
63	–	#include "UseTheForce/DarkSide/electrostatic_interface.h"
61		#include "UseTheForce/DarkSide/switcheroo_interface.h"
62		#include "utils/MemoryUtils.hpp"
63		#include "utils/simError.h"
64		#include "selection/SelectionManager.hpp"
65		#include "io/ForceFieldOptions.hpp"
66		#include "UseTheForce/ForceField.hpp"
67	+	#include "nonbonded/InteractionManager.hpp"
68
69
70		#ifdef IS_MPI
#	Line 74 | Line 72
72		#include "UseTheForce/DarkSide/simParallel_interface.h"
73		#endif
74
75	<	namespace oopse {
76	<	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	<	}
75	>	using namespace std;
76	>	namespace OpenMD {
77
78		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
79		forceField_(ff), simParams_(simParams),
#	Line 93 | Line 83 | namespace oopse {
83		nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
84		nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
85		nConstraints_(0), sman_(NULL), fortranInitialized_(false),
86	<	calcBoxDipole_(false), useAtomicVirial_(true) {
87	<
88	<
89	<	MoleculeStamp* molStamp;
90	<	int nMolWithSameStamp;
91	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
92	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
93	<	CutoffGroupStamp* cgStamp;
94	<	RigidBodyStamp* rbStamp;
95	<	int nRigidAtoms = 0;
96	<
97	<	std::vector<Component*> components = simParams->getComponents();
86	>	calcBoxDipole_(false), useAtomicVirial_(true) {
87	>
88	>	MoleculeStamp* molStamp;
89	>	int nMolWithSameStamp;
90	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
91	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
92	>	CutoffGroupStamp* cgStamp;
93	>	RigidBodyStamp* rbStamp;
94	>	int nRigidAtoms = 0;
95	>
96	>	vector<Component*> components = simParams->getComponents();
97	>
98	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
99	>	molStamp = (*i)->getMoleculeStamp();
100	>	nMolWithSameStamp = (*i)->getNMol();
101
102	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
103	<	molStamp = (*i)->getMoleculeStamp();
104	<	nMolWithSameStamp = (*i)->getNMol();
105	<
106	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
107	<
108	<	//calculate atoms in molecules
109	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
110	<
111	<	//calculate atoms in cutoff groups
112	<	int nAtomsInGroups = 0;
113	<	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	<
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();
110	>
111	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
112	>	cgStamp = molStamp->getCutoffGroupStamp(j);
113	>	nAtomsInGroups += cgStamp->getNMembers();
114		}
115	<
116	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
117	<	//group therefore the total number of cutoff groups in the system is
118	<	//equal to the total number of atoms minus number of atoms belong to
119	<	//cutoff group defined in meta-data file plus the number of cutoff
120	<	//groups defined in meta-data file
121	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
122	<
123	<	//every free atom (atom does not belong to rigid bodies) is an
124	<	//integrable object therefore the total number of integrable objects
125	<	//in the system is equal to the total number of atoms minus number of
126	<	//atoms belong to rigid body defined in meta-data file plus the number
127	<	//of rigid bodies defined in meta-data file
128	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
129	<	+ nGlobalRigidBodies_;
130	<
131	<	nGlobalMols_ = molStampIds_.size();
161	<	molToProcMap_.resize(nGlobalMols_);
115	>
116	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
117	>
118	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
119	>
120	>	//calculate atoms in rigid bodies
121	>	int nAtomsInRigidBodies = 0;
122	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
123	>
124	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
125	>	rbStamp = molStamp->getRigidBodyStamp(j);
126	>	nAtomsInRigidBodies += rbStamp->getNMembers();
127	>	}
128	>
129	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
130	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
131	>
132		}
133	<
133	>
134	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
135	>	//group therefore the total number of cutoff groups in the system is
136	>	//equal to the total number of atoms minus number of atoms belong to
137	>	//cutoff group defined in meta-data file plus the number of cutoff
138	>	//groups defined in meta-data file
139	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
140	>
141	>	//every free atom (atom does not belong to rigid bodies) is an
142	>	//integrable object therefore the total number of integrable objects
143	>	//in the system is equal to the total number of atoms minus number of
144	>	//atoms belong to rigid body defined in meta-data file plus the number
145	>	//of rigid bodies defined in meta-data file
146	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
147	>	+ nGlobalRigidBodies_;
148	>
149	>	nGlobalMols_ = molStampIds_.size();
150	>	molToProcMap_.resize(nGlobalMols_);
151	>	}
152	>
153		SimInfo::~SimInfo() {
154	<	std::map<int, Molecule*>::iterator i;
154	>	map<int, Molecule*>::iterator i;
155		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
156		delete i->second;
157		}
#	Line 173 | Line 162 | namespace oopse {
162		delete forceField_;
163		}
164
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	–	}
165
166		bool SimInfo::addMolecule(Molecule* mol) {
167		MoleculeIterator i;
168	<
168	>
169		i = molecules_.find(mol->getGlobalIndex());
170		if (i == molecules_.end() ) {
171	<
172	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
173	<
171	>
172	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
173	>
174		nAtoms_ += mol->getNAtoms();
175		nBonds_ += mol->getNBonds();
176		nBends_ += mol->getNBends();
#	Line 201 | Line 180 | namespace oopse {
180		nIntegrableObjects_ += mol->getNIntegrableObjects();
181		nCutoffGroups_ += mol->getNCutoffGroups();
182		nConstraints_ += mol->getNConstraintPairs();
183	<
183	>
184		addInteractionPairs(mol);
185	<
185	>
186		return true;
187		} else {
188		return false;
189		}
190		}
191	<
191	>
192		bool SimInfo::removeMolecule(Molecule* mol) {
193		MoleculeIterator i;
194		i = molecules_.find(mol->getGlobalIndex());
#	Line 237 | Line 216 | namespace oopse {
216		} else {
217		return false;
218		}
240	–
241	–
219		}
220
221
#	Line 256 | Line 233 | namespace oopse {
233		void SimInfo::calcNdf() {
234		int ndf_local;
235		MoleculeIterator i;
236	<	std::vector<StuntDouble*>::iterator j;
236	>	vector<StuntDouble*>::iterator j;
237		Molecule* mol;
238		StuntDouble* integrableObject;
239
#	Line 307 | Line 284 | namespace oopse {
284		int ndfRaw_local;
285
286		MoleculeIterator i;
287	<	std::vector<StuntDouble*>::iterator j;
287	>	vector<StuntDouble*>::iterator j;
288		Molecule* mol;
289		StuntDouble* integrableObject;
290
#	Line 356 | Line 333 | namespace oopse {
333
334		void SimInfo::addInteractionPairs(Molecule* mol) {
335		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
336	<	std::vector<Bond*>::iterator bondIter;
337	<	std::vector<Bend*>::iterator bendIter;
338	<	std::vector<Torsion*>::iterator torsionIter;
339	<	std::vector<Inversion*>::iterator inversionIter;
336	>	vector<Bond*>::iterator bondIter;
337	>	vector<Bend*>::iterator bendIter;
338	>	vector<Torsion*>::iterator torsionIter;
339	>	vector<Inversion*>::iterator inversionIter;
340		Bond* bond;
341		Bend* bend;
342		Torsion* torsion;
#	Line 377 | Line 354 | namespace oopse {
354		// always be excluded.  These are done at the bottom of this
355		// function.
356
357	<	std::map<int, std::set<int> > atomGroups;
357	>	map<int, set<int> > atomGroups;
358		Molecule::RigidBodyIterator rbIter;
359		RigidBody* rb;
360		Molecule::IntegrableObjectIterator ii;
#	Line 389 | Line 366 | namespace oopse {
366
367		if (integrableObject->isRigidBody()) {
368		rb = static_cast<RigidBody*>(integrableObject);
369	<	std::vector<Atom*> atoms = rb->getAtoms();
370	<	std::set<int> rigidAtoms;
369	>	vector<Atom*> atoms = rb->getAtoms();
370	>	set<int> rigidAtoms;
371		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
372		rigidAtoms.insert(atoms[i]->getGlobalIndex());
373		}
374		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
375	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
375	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
376		}
377		} else {
378	<	std::set<int> oneAtomSet;
378	>	set<int> oneAtomSet;
379		oneAtomSet.insert(integrableObject->getGlobalIndex());
380	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
380	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
381		}
382		}
383
#	Line 446 | Line 423 | namespace oopse {
423		b = torsion->getAtomB()->getGlobalIndex();
424		c = torsion->getAtomC()->getGlobalIndex();
425		d = torsion->getAtomD()->getGlobalIndex();
426	<
426	>
427		if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
428		oneTwoInteractions_.addPair(a, b);
429		oneTwoInteractions_.addPair(b, c);
#	Line 503 | Line 480 | namespace oopse {
480
481		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
482		rb = mol->nextRigidBody(rbIter)) {
483	<	std::vector<Atom*> atoms = rb->getAtoms();
483	>	vector<Atom*> atoms = rb->getAtoms();
484		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
485		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
486		a = atoms[i]->getGlobalIndex();
#	Line 517 | Line 494 | namespace oopse {
494
495		void SimInfo::removeInteractionPairs(Molecule* mol) {
496		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
497	<	std::vector<Bond*>::iterator bondIter;
498	<	std::vector<Bend*>::iterator bendIter;
499	<	std::vector<Torsion*>::iterator torsionIter;
500	<	std::vector<Inversion*>::iterator inversionIter;
497	>	vector<Bond*>::iterator bondIter;
498	>	vector<Bend*>::iterator bendIter;
499	>	vector<Torsion*>::iterator torsionIter;
500	>	vector<Inversion*>::iterator inversionIter;
501		Bond* bond;
502		Bend* bend;
503		Torsion* torsion;
#	Line 530 | Line 507 | namespace oopse {
507		int c;
508		int d;
509
510	<	std::map<int, std::set<int> > atomGroups;
510	>	map<int, set<int> > atomGroups;
511		Molecule::RigidBodyIterator rbIter;
512		RigidBody* rb;
513		Molecule::IntegrableObjectIterator ii;
#	Line 542 | Line 519 | namespace oopse {
519
520		if (integrableObject->isRigidBody()) {
521		rb = static_cast<RigidBody*>(integrableObject);
522	<	std::vector<Atom*> atoms = rb->getAtoms();
523	<	std::set<int> rigidAtoms;
522	>	vector<Atom*> atoms = rb->getAtoms();
523	>	set<int> rigidAtoms;
524		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
525		rigidAtoms.insert(atoms[i]->getGlobalIndex());
526		}
527		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
528	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
528	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
529		}
530		} else {
531	<	std::set<int> oneAtomSet;
531	>	set<int> oneAtomSet;
532		oneAtomSet.insert(integrableObject->getGlobalIndex());
533	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
533	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
534		}
535		}
536
#	Line 656 | Line 633 | namespace oopse {
633
634		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
635		rb = mol->nextRigidBody(rbIter)) {
636	<	std::vector<Atom*> atoms = rb->getAtoms();
636	>	vector<Atom*> atoms = rb->getAtoms();
637		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
638		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
639		a = atoms[i]->getGlobalIndex();
#	Line 682 | Line 659 | namespace oopse {
659		void SimInfo::update() {
660
661		setupSimType();
662	+	setupCutoffRadius();
663	+	setupSwitchingRadius();
664	+	setupCutoffMethod();
665	+	setupSkinThickness();
666	+	setupSwitchingFunction();
667	+	setupAccumulateBoxDipole();
668
669		#ifdef IS_MPI
670		setupFortranParallel();
671		#endif
689	–
672		setupFortranSim();
673	+	fortranInitialized_ = true;
674
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	–
675		calcNdf();
676		calcNdfRaw();
677		calcNdfTrans();
712	–
713	–	fortranInitialized_ = true;
678		}
679	<
680	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
679	>
680	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
681		SimInfo::MoleculeIterator mi;
682		Molecule* mol;
683		Molecule::AtomIterator ai;
684		Atom* atom;
685	<	std::set<AtomType*> atomTypes;
686	<
687	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
724	<
685	>	set<AtomType*> atomTypes;
686	>
687	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
688		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
689		atomTypes.insert(atom->getAtomType());
690	<	}
691	<
729	<	}
730	<
690	>	}
691	>	}
692		return atomTypes;
693		}
694
695	<	void SimInfo::setupSimType() {
696	<	std::set<AtomType*>::iterator i;
697	<	std::set<AtomType*> atomTypes;
698	<	atomTypes = getUniqueAtomTypes();
699	<
700	<	int useLennardJones = 0;
701	<	int useElectrostatic = 0;
702	<	int useEAM = 0;
703	<	int useSC = 0;
704	<	int useCharge = 0;
705	<	int useDirectional = 0;
706	<	int useDipole = 0;
707	<	int useGayBerne = 0;
708	<	int useSticky = 0;
709	<	int useStickyPower = 0;
710	<	int useShape = 0;
711	<	int useFLARB = 0; //it is not in AtomType yet
712	<	int useDirectionalAtom = 0;
713	<	int useElectrostatics = 0;
714	<	//usePBC and useRF are from simParams
715	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
716	<	int useRF;
717	<	int useSF;
718	<	int useSP;
719	<	int useBoxDipole;
720	<
721	<	std::string myMethod;
722	<
723	<	// set the useRF logical
724	<	useRF = 0;
725	<	useSF = 0;
726	<	useSP = 0;
695	>	/**
696	>	* setupCutoffRadius
697	>	*
698	>	*  If the cutoffRadius was explicitly set, use that value.
699	>	*  If the cutoffRadius was not explicitly set:
700	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
701	>	*      No electrostatic atoms?  Poll the atom types present in the
702	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
703	>	*      Use the maximum suggested value that was found.
704	>	*/
705	>	void SimInfo::setupCutoffRadius() {
706	>
707	>	if (simParams_->haveCutoffRadius()) {
708	>	cutoffRadius_ = simParams_->getCutoffRadius();
709	>	} else {
710	>	if (usesElectrostaticAtoms_) {
711	>	sprintf(painCave.errMsg,
712	>	"SimInfo Warning: No value was set for the cutoffRadius.\n"
713	>	"\tOpenMD will use a default value of 12.0 angstroms"
714	>	"\tfor the cutoffRadius.\n");
715	>	painCave.isFatal = 0;
716	>	simError();
717	>	cutoffRadius_ = 12.0;
718	>	} else {
719	>	RealType thisCut;
720	>	set<AtomType*>::iterator i;
721	>	set<AtomType*> atomTypes;
722	>	atomTypes = getSimulatedAtomTypes();
723	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
724	>	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
725	>	cutoffRadius_ = max(thisCut, cutoffRadius_);
726	>	}
727	>	sprintf(painCave.errMsg,
728	>	"SimInfo Warning: No value was set for the cutoffRadius.\n"
729	>	"\tOpenMD will use %lf angstroms.\n",
730	>	cutoffRadius_);
731	>	painCave.isFatal = 0;
732	>	simError();
733	>	}
734	>	}
735
736	+	InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
737	+	}
738	+
739	+	/**
740	+	* setupSwitchingRadius
741	+	*
742	+	*  If the switchingRadius was explicitly set, use that value (but check it)
743	+	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
744	+	*/
745	+	void SimInfo::setupSwitchingRadius() {
746	+
747	+	if (simParams_->haveSwitchingRadius()) {
748	+	switchingRadius_ = simParams_->getSwitchingRadius();
749	+	if (switchingRadius_ > cutoffRadius_) {
750	+	sprintf(painCave.errMsg,
751	+	"SimInfo Error: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
752	+	switchingRadius_, cutoffRadius_);
753	+	painCave.isFatal = 1;
754	+	simError();
755
768	–	if (simParams_->haveElectrostaticSummationMethod()) {
769	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
770	–	toUpper(myMethod);
771	–	if (myMethod == "REACTION_FIELD"){
772	–	useRF = 1;
773	–	} else if (myMethod == "SHIFTED_FORCE"){
774	–	useSF = 1;
775	–	} else if (myMethod == "SHIFTED_POTENTIAL"){
776	–	useSP = 1;
756		}
757	<	}
758	<
759	<	if (simParams_->haveAccumulateBoxDipole())
760	<	if (simParams_->getAccumulateBoxDipole())
761	<	useBoxDipole = 1;
757	>	} else {
758	>	switchingRadius_ = 0.85 * cutoffRadius_;
759	>	sprintf(painCave.errMsg,
760	>	"SimInfo Warning: No value was set for the switchingRadius.\n"
761	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
762	>	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
763	>	painCave.isFatal = 0;
764	>	simError();
765	>	}
766	>	InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
767	>	}
768	>
769	>	/**
770	>	* setupSkinThickness
771	>	*
772	>	*  If the skinThickness was explicitly set, use that value (but check it)
773	>	*  If the skinThickness was not explicitly set: use 1.0 angstroms
774	>	*/
775	>	void SimInfo::setupSkinThickness() {
776	>	if (simParams_->haveSkinThickness()) {
777	>	skinThickness_ = simParams_->getSkinThickness();
778	>	} else {
779	>	skinThickness_ = 1.0;
780	>	sprintf(painCave.errMsg,
781	>	"SimInfo Warning: No value was set for the skinThickness.\n"
782	>	"\tOpenMD will use a default value of %f Angstroms\n"
783	>	"\tfor this simulation\n", skinThickness_);
784	>	painCave.isFatal = 0;
785	>	simError();
786	>	}
787	>	}
788	>
789	>	void SimInfo::setupSimType() {
790	>	set<AtomType*>::iterator i;
791	>	set<AtomType*> atomTypes;
792	>	atomTypes = getSimulatedAtomTypes();
793
794		useAtomicVirial_ = simParams_->getUseAtomicVirial();
795
796	+	int usesElectrostatic = 0;
797	+	int usesMetallic = 0;
798	+	int usesDirectional = 0;
799		//loop over all of the atom types
800		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
801	<	useLennardJones |= (*i)->isLennardJones();
802	<	useElectrostatic |= (*i)->isElectrostatic();
803	<	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();
801	>	usesElectrostatic |= (*i)->isElectrostatic();
802	>	usesMetallic |= (*i)->isMetal();
803	>	usesDirectional |= (*i)->isDirectional();
804		}
805
801	–	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
802	–	useDirectionalAtom = 1;
803	–	}
804	–
805	–	if (useCharge || useDipole) {
806	–	useElectrostatics = 1;
807	–	}
808	–
806		#ifdef IS_MPI
807		int temp;
808	+	temp = usesDirectional;
809	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810
811	<	temp = usePBC;
812	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
811	>	temp = usesMetallic;
812	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813
814	<	temp = useDirectionalAtom;
815	<	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	<
814	>	temp = usesElectrostatic;
815	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816		#endif
817	<
818	<	fInfo_.SIM_uses_PBC = usePBC;
819	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
820	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
821	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
822	<	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_;
817	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
818	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
819	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
820	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
821	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
822	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
823		}
824
825		void SimInfo::setupFortranSim() {
826		int isError;
827		int nExclude, nOneTwo, nOneThree, nOneFour;
828	<	std::vector<int> fortranGlobalGroupMembership;
828	>	vector<int> fortranGlobalGroupMembership;
829
830	+	notifyFortranSkinThickness(&skinThickness_);
831	+
832	+	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
833	+	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
834	+	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
835	+
836		isError = 0;
837
838		//globalGroupMembership_ is filled by SimCreator
#	Line 898 | Line 841 | namespace oopse {
841		}
842
843		//calculate mass ratio of cutoff group
844	<	std::vector<RealType> mfact;
844	>	vector<RealType> mfact;
845		SimInfo::MoleculeIterator mi;
846		Molecule* mol;
847		Molecule::CutoffGroupIterator ci;
#	Line 925 | Line 868 | namespace oopse {
868		}
869
870		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
871	<	std::vector<int> identArray;
871	>	vector<int> identArray;
872
873		//to avoid memory reallocation, reserve enough space identArray
874		identArray.reserve(getNAtoms());
#	Line 938 | Line 881 | namespace oopse {
881
882		//fill molMembershipArray
883		//molMembershipArray is filled by SimCreator
884	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
884	>	vector<int> molMembershipArray(nGlobalAtoms_);
885		for (int i = 0; i < nGlobalAtoms_; i++) {
886		molMembershipArray[i] = globalMolMembership_[i] + 1;
887		}
#	Line 950 | Line 893 | namespace oopse {
893		nOneThree = oneThreeInteractions_.getSize();
894		nOneFour = oneFourInteractions_.getSize();
895
953	–	std::cerr << "exculdes:\n";
954	–	std::cerr << excludedInteractions_;
955	–	std::cerr << "\noneTwo:\n";
956	–	std::cerr << oneTwoInteractions_;
957	–	std::cerr << "\noneThree:\n";
958	–	std::cerr << oneThreeInteractions_;
959	–	std::cerr << "\noneFour:\n";
960	–	std::cerr << oneFourInteractions_;
961	–
896		int* excludeList = excludedInteractions_.getPairList();
897		int* oneTwoList = oneTwoInteractions_.getPairList();
898		int* oneThreeList = oneThreeInteractions_.getPairList();
#	Line 977 | Line 911 | namespace oopse {
911		sprintf( painCave.errMsg,
912		"There was an error setting the simulation information in fortran.\n" );
913		painCave.isFatal = 1;
914	<	painCave.severity = OOPSE_ERROR;
914	>	painCave.severity = OPENMD_ERROR;
915		simError();
916		}
917
#	Line 1000 | Line 934 | namespace oopse {
934		void SimInfo::setupFortranParallel() {
935		#ifdef IS_MPI
936		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
937	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
938	<	std::vector<int> localToGlobalCutoffGroupIndex;
937	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
938	>	vector<int> localToGlobalCutoffGroupIndex;
939		SimInfo::MoleculeIterator mi;
940		Molecule::AtomIterator ai;
941		Molecule::CutoffGroupIterator ci;
#	Line 1053 | Line 987 | namespace oopse {
987		#endif
988		}
989
1056	–	void SimInfo::setupCutoff() {
1057	–
1058	–	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
990
991	<	// Check the cutoff policy
992	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1062	<
1063	<	// Set LJ shifting bools to false
1064	<	ljsp_ = false;
1065	<	ljsf_ = false;
1066	<
1067	<	std::string myPolicy;
1068	<	if (forceFieldOptions_.haveCutoffPolicy()){
1069	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
1070	<	}else if (simParams_->haveCutoffPolicy()) {
1071	<	myPolicy = simParams_->getCutoffPolicy();
1072	<	}
1073	<
1074	<	if (!myPolicy.empty()){
1075	<	toUpper(myPolicy);
1076	<	if (myPolicy == "MIX") {
1077	<	cp = MIX_CUTOFF_POLICY;
1078	<	} else {
1079	<	if (myPolicy == "MAX") {
1080	<	cp = MAX_CUTOFF_POLICY;
1081	<	} else {
1082	<	if (myPolicy == "TRADITIONAL") {
1083	<	cp = TRADITIONAL_CUTOFF_POLICY;
1084	<	} else {
1085	<	// throw error
1086	<	sprintf( painCave.errMsg,
1087	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1088	<	painCave.isFatal = 1;
1089	<	simError();
1090	<	}
1091	<	}
1092	<	}
1093	<	}
1094	<	notifyFortranCutoffPolicy(&cp);
1095	<
1096	<	// Check the Skin Thickness for neighborlists
1097	<	RealType skin;
1098	<	if (simParams_->haveSkinThickness()) {
1099	<	skin = simParams_->getSkinThickness();
1100	<	notifyFortranSkinThickness(&skin);
1101	<	}
1102	<
1103	<	// Check if the cutoff was set explicitly:
1104	<	if (simParams_->haveCutoffRadius()) {
1105	<	rcut_ = simParams_->getCutoffRadius();
1106	<	if (simParams_->haveSwitchingRadius()) {
1107	<	rsw_  = simParams_->getSwitchingRadius();
1108	<	} else {
1109	<	if (fInfo_.SIM_uses_Charges |
1110	<	fInfo_.SIM_uses_Dipoles |
1111	<	fInfo_.SIM_uses_RF) {
1112	<
1113	<	rsw_ = 0.85 * rcut_;
1114	<	sprintf(painCave.errMsg,
1115	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1116	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1117	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1118	<	painCave.isFatal = 0;
1119	<	simError();
1120	<	} else {
1121	<	rsw_ = rcut_;
1122	<	sprintf(painCave.errMsg,
1123	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1124	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
1125	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1126	<	painCave.isFatal = 0;
1127	<	simError();
1128	<	}
1129	<	}
1130	<
1131	<	if (simParams_->haveElectrostaticSummationMethod()) {
1132	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1133	<	toUpper(myMethod);
1134	<
1135	<	if (myMethod == "SHIFTED_POTENTIAL") {
1136	<	ljsp_ = true;
1137	<	} else if (myMethod == "SHIFTED_FORCE") {
1138	<	ljsf_ = true;
1139	<	}
1140	<	}
1141	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1142	<
1143	<	} else {
1144	<
1145	<	// For electrostatic atoms, we'll assume a large safe value:
1146	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1147	<	sprintf(painCave.errMsg,
1148	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1149	<	"\tOOPSE will use a default value of 15.0 angstroms"
1150	<	"\tfor the cutoffRadius.\n");
1151	<	painCave.isFatal = 0;
1152	<	simError();
1153	<	rcut_ = 15.0;
1154	<
1155	<	if (simParams_->haveElectrostaticSummationMethod()) {
1156	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1157	<	toUpper(myMethod);
1158	<
1159	<	// For the time being, we're tethering the LJ shifted behavior to the
1160	<	// electrostaticSummationMethod keyword options
1161	<	if (myMethod == "SHIFTED_POTENTIAL") {
1162	<	ljsp_ = true;
1163	<	} else if (myMethod == "SHIFTED_FORCE") {
1164	<	ljsf_ = true;
1165	<	}
1166	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1167	<	if (simParams_->haveSwitchingRadius()){
1168	<	sprintf(painCave.errMsg,
1169	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1170	<	"\teven though the electrostaticSummationMethod was\n"
1171	<	"\tset to %s\n", myMethod.c_str());
1172	<	painCave.isFatal = 1;
1173	<	simError();
1174	<	}
1175	<	}
1176	<	}
1177	<
1178	<	if (simParams_->haveSwitchingRadius()){
1179	<	rsw_ = simParams_->getSwitchingRadius();
1180	<	} else {
1181	<	sprintf(painCave.errMsg,
1182	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1183	<	"\tOOPSE will use a default value of\n"
1184	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1185	<	painCave.isFatal = 0;
1186	<	simError();
1187	<	rsw_ = 0.85 * rcut_;
1188	<	}
1189	<
1190	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1191	<
1192	<	} else {
1193	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1194	<	// We'll punt and let fortran figure out the cutoffs later.
1195	<
1196	<	notifyFortranYouAreOnYourOwn();
1197	<
1198	<	}
1199	<	}
1200	<	}
1201	<
1202	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1203	<
1204	<	int errorOut;
1205	<	int esm =  NONE;
1206	<	int sm = UNDAMPED;
1207	<	RealType alphaVal;
1208	<	RealType dielectric;
991	>	void SimInfo::setupSwitchingFunction() {
992	>	int ft = CUBIC;
993
994	<	errorOut = isError;
995	<
1212	<	if (simParams_->haveElectrostaticSummationMethod()) {
1213	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1214	<	toUpper(myMethod);
1215	<	if (myMethod == "NONE") {
1216	<	esm = NONE;
1217	<	} else {
1218	<	if (myMethod == "SWITCHING_FUNCTION") {
1219	<	esm = SWITCHING_FUNCTION;
1220	<	} else {
1221	<	if (myMethod == "SHIFTED_POTENTIAL") {
1222	<	esm = SHIFTED_POTENTIAL;
1223	<	} else {
1224	<	if (myMethod == "SHIFTED_FORCE") {
1225	<	esm = SHIFTED_FORCE;
1226	<	} else {
1227	<	if (myMethod == "REACTION_FIELD") {
1228	<	esm = REACTION_FIELD;
1229	<	dielectric = simParams_->getDielectric();
1230	<	if (!simParams_->haveDielectric()) {
1231	<	// throw warning
1232	<	sprintf( painCave.errMsg,
1233	<	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1234	<	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1235	<	painCave.isFatal = 0;
1236	<	simError();
1237	<	}
1238	<	} else {
1239	<	// throw error
1240	<	sprintf( painCave.errMsg,
1241	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1242	<	"\t(Input file specified %s .)\n"
1243	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1244	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1245	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1246	<	painCave.isFatal = 1;
1247	<	simError();
1248	<	}
1249	<	}
1250	<	}
1251	<	}
1252	<	}
1253	<	}
1254	<
1255	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1256	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1257	<	toUpper(myScreen);
1258	<	if (myScreen == "UNDAMPED") {
1259	<	sm = UNDAMPED;
1260	<	} else {
1261	<	if (myScreen == "DAMPED") {
1262	<	sm = DAMPED;
1263	<	if (!simParams_->haveDampingAlpha()) {
1264	<	// first set a cutoff dependent alpha value
1265	<	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1266	<	alphaVal = 0.5125 - rcut_* 0.025;
1267	<	// for values rcut > 20.5, alpha is zero
1268	<	if (alphaVal < 0) alphaVal = 0;
1269	<
1270	<	// throw warning
1271	<	sprintf( painCave.errMsg,
1272	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1273	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1274	<	painCave.isFatal = 0;
1275	<	simError();
1276	<	} else {
1277	<	alphaVal = simParams_->getDampingAlpha();
1278	<	}
1279	<
1280	<	} else {
1281	<	// throw error
1282	<	sprintf( painCave.errMsg,
1283	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1284	<	"\t(Input file specified %s .)\n"
1285	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1286	<	"or \"damped\".\n", myScreen.c_str() );
1287	<	painCave.isFatal = 1;
1288	<	simError();
1289	<	}
1290	<	}
1291	<	}
1292	<
1293	<	// let's pass some summation method variables to fortran
1294	<	setElectrostaticSummationMethod( &esm );
1295	<	setFortranElectrostaticMethod( &esm );
1296	<	setScreeningMethod( &sm );
1297	<	setDampingAlpha( &alphaVal );
1298	<	setReactionFieldDielectric( &dielectric );
1299	<	initFortranFF( &errorOut );
1300	<	}
1301	<
1302	<	void SimInfo::setupSwitchingFunction() {
1303	<	int ft = CUBIC;
1304	<
1305	<	if (simParams_->haveSwitchingFunctionType()) {
1306	<	std::string funcType = simParams_->getSwitchingFunctionType();
994	>	if (simParams_->haveSwitchingFunctionType()) {
995	>	string funcType = simParams_->getSwitchingFunctionType();
996		toUpper(funcType);
997		if (funcType == "CUBIC") {
998		ft = CUBIC;
#	Line 1313 | Line 1002 | namespace oopse {
1002		} else {
1003		// throw error
1004		sprintf( painCave.errMsg,
1005	<	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1005	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n"
1006	>	"\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".",
1007	>	funcType.c_str() );
1008		painCave.isFatal = 1;
1009		simError();
1010		}
#	Line 1330 | Line 1021 | namespace oopse {
1021		// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1022		if ( simParams_->haveAccumulateBoxDipole() )
1023		if ( simParams_->getAccumulateBoxDipole() ) {
1333	–	setAccumulateBoxDipole();
1024		calcBoxDipole_ = true;
1025		}
1026
#	Line 1340 | Line 1030 | namespace oopse {
1030		properties_.addProperty(genData);
1031		}
1032
1033	<	void SimInfo::removeProperty(const std::string& propName) {
1033	>	void SimInfo::removeProperty(const string& propName) {
1034		properties_.removeProperty(propName);
1035		}
1036
#	Line 1348 | Line 1038 | namespace oopse {
1038		properties_.clearProperties();
1039		}
1040
1041	<	std::vector<std::string> SimInfo::getPropertyNames() {
1041	>	vector<string> SimInfo::getPropertyNames() {
1042		return properties_.getPropertyNames();
1043		}
1044
1045	<	std::vector<GenericData*> SimInfo::getProperties() {
1045	>	vector<GenericData*> SimInfo::getProperties() {
1046		return properties_.getProperties();
1047		}
1048
1049	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1049	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1050		return properties_.getPropertyByName(propName);
1051		}
1052
#	Line 1439 | Line 1129 | namespace oopse {
1129
1130		}
1131
1132	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1132	>	ostream& operator <<(ostream& o, SimInfo& info) {
1133
1134		return o;
1135		}
#	Line 1482 | Line 1172 | namespace oopse {
1172
1173
1174		[  Ixx -Ixy  -Ixz ]
1175	<	J =| -Iyx  Iyy  -Iyz |
1175	>	J =| -Iyx  Iyy  -Iyz |
1176		[ -Izx -Iyz   Izz ]
1177		*/
1178
#	Line 1589 | Line 1279 | namespace oopse {
1279		return IOIndexToIntegrableObject.at(index);
1280		}
1281
1282	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1282	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1283		IOIndexToIntegrableObject= v;
1284		}
1285
#	Line 1631 | Line 1321 | namespace oopse {
1321		return;
1322		}
1323		/*
1324	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1324	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1325		assert( v.size() == nAtoms_ + nRigidBodies_);
1326		sdByGlobalIndex_ = v;
1327		}
#	Line 1641 | Line 1331 | namespace oopse {
1331		return sdByGlobalIndex_.at(index);
1332		}
1333		*/
1334	<	}//end namespace oopse
1334	>	int SimInfo::getNGlobalConstraints() {
1335	>	int nGlobalConstraints;
1336	>	#ifdef IS_MPI
1337	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1338	>	MPI_COMM_WORLD);
1339	>	#else
1340	>	nGlobalConstraints =  nConstraints_;
1341	>	#endif
1342	>	return nGlobalConstraints;
1343	>	}
1344
1345	+	}//end namespace OpenMD
1346	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 1287 by gezelter, Wed Sep 10 18:11:32 2008 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1529 by gezelter, Mon Dec 27 18:35:59 2010 UTC

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