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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 1530 by gezelter, Tue Dec 28 21:47:55 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"
60	–	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
58		#include "UseTheForce/doForces_interface.h"
59		#include "UseTheForce/DarkSide/neighborLists_interface.h"
63	–	#include "UseTheForce/DarkSide/electrostatic_interface.h"
64	–	#include "UseTheForce/DarkSide/switcheroo_interface.h"
60		#include "utils/MemoryUtils.hpp"
61		#include "utils/simError.h"
62		#include "selection/SelectionManager.hpp"
63		#include "io/ForceFieldOptions.hpp"
64		#include "UseTheForce/ForceField.hpp"
65	+	#include "nonbonded/SwitchingFunction.hpp"
66
67
68		#ifdef IS_MPI
#	Line 74 | Line 70
70		#include "UseTheForce/DarkSide/simParallel_interface.h"
71		#endif
72
73	<	namespace oopse {
74	<	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	<	}
73	>	using namespace std;
74	>	namespace OpenMD {
75
76		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
77		forceField_(ff), simParams_(simParams),
#	Line 93 | Line 81 | namespace oopse {
81		nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
82		nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
83		nConstraints_(0), sman_(NULL), fortranInitialized_(false),
84	<	calcBoxDipole_(false), useAtomicVirial_(true) {
85	<
86	<
87	<	MoleculeStamp* molStamp;
88	<	int nMolWithSameStamp;
89	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
90	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
91	<	CutoffGroupStamp* cgStamp;
92	<	RigidBodyStamp* rbStamp;
93	<	int nRigidAtoms = 0;
94	<
95	<	std::vector<Component*> components = simParams->getComponents();
84	>	calcBoxDipole_(false), useAtomicVirial_(true) {
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	>	vector<Component*> components = simParams->getComponents();
95	>
96	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
97	>	molStamp = (*i)->getMoleculeStamp();
98	>	nMolWithSameStamp = (*i)->getNMol();
99
100	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
101	<	molStamp = (*i)->getMoleculeStamp();
102	<	nMolWithSameStamp = (*i)->getNMol();
103	<
104	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
105	<
106	<	//calculate atoms in molecules
107	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
108	<
109	<	//calculate atoms in cutoff groups
110	<	int nAtomsInGroups = 0;
111	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
112	<
113	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
114	<	cgStamp = molStamp->getCutoffGroupStamp(j);
115	<	nAtomsInGroups += cgStamp->getNMembers();
116	<	}
117	<
118	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
119	<
120	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
121	<
122	<	//calculate atoms in rigid bodies
123	<	int nAtomsInRigidBodies = 0;
124	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
125	<
126	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
127	<	rbStamp = molStamp->getRigidBodyStamp(j);
128	<	nAtomsInRigidBodies += rbStamp->getNMembers();
129	<	}
130	<
131	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
132	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
133	<
134	<	}
135	<
136	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
137	<	//group therefore the total number of cutoff groups in the system is
138	<	//equal to the total number of atoms minus number of atoms belong to
139	<	//cutoff group defined in meta-data file plus the number of cutoff
140	<	//groups defined in meta-data file
141	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
142	<
143	<	//every free atom (atom does not belong to rigid bodies) is an
144	<	//integrable object therefore the total number of integrable objects
145	<	//in the system is equal to the total number of atoms minus number of
146	<	//atoms belong to rigid body defined in meta-data file plus the number
147	<	//of rigid bodies defined in meta-data file
148	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
149	<	+ nGlobalRigidBodies_;
150	<
160	<	nGlobalMols_ = molStampIds_.size();
161	<	molToProcMap_.resize(nGlobalMols_);
162	<	}
163	<
100	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
101	>
102	>	//calculate atoms in molecules
103	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
104	>
105	>	//calculate atoms in cutoff groups
106	>	int nAtomsInGroups = 0;
107	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
108	>
109	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
110	>	cgStamp = molStamp->getCutoffGroupStamp(j);
111	>	nAtomsInGroups += cgStamp->getNMembers();
112	>	}
113	>
114	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
115	>
116	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
117	>
118	>	//calculate atoms in rigid bodies
119	>	int nAtomsInRigidBodies = 0;
120	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
121	>
122	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
123	>	rbStamp = molStamp->getRigidBodyStamp(j);
124	>	nAtomsInRigidBodies += rbStamp->getNMembers();
125	>	}
126	>
127	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
128	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
129	>
130	>	}
131	>
132	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
133	>	//group therefore the total number of cutoff groups in the system is
134	>	//equal to the total number of atoms minus number of atoms belong to
135	>	//cutoff group defined in meta-data file plus the number of cutoff
136	>	//groups defined in meta-data file
137	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
138	>
139	>	//every free atom (atom does not belong to rigid bodies) is an
140	>	//integrable object therefore the total number of integrable objects
141	>	//in the system is equal to the total number of atoms minus number of
142	>	//atoms belong to rigid body defined in meta-data file plus the number
143	>	//of rigid bodies defined in meta-data file
144	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
145	>	+ nGlobalRigidBodies_;
146	>
147	>	nGlobalMols_ = molStampIds_.size();
148	>	molToProcMap_.resize(nGlobalMols_);
149	>	}
150	>
151		SimInfo::~SimInfo() {
152	<	std::map<int, Molecule*>::iterator i;
152	>	map<int, Molecule*>::iterator i;
153		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
154		delete i->second;
155		}
#	Line 173 | Line 160 | namespace oopse {
160		delete forceField_;
161		}
162
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	–	}
163
164		bool SimInfo::addMolecule(Molecule* mol) {
165		MoleculeIterator i;
166	<
166	>
167		i = molecules_.find(mol->getGlobalIndex());
168		if (i == molecules_.end() ) {
169	<
170	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
171	<
169	>
170	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
171	>
172		nAtoms_ += mol->getNAtoms();
173		nBonds_ += mol->getNBonds();
174		nBends_ += mol->getNBends();
#	Line 201 | Line 178 | namespace oopse {
178		nIntegrableObjects_ += mol->getNIntegrableObjects();
179		nCutoffGroups_ += mol->getNCutoffGroups();
180		nConstraints_ += mol->getNConstraintPairs();
181	<
181	>
182		addInteractionPairs(mol);
183	<
183	>
184		return true;
185		} else {
186		return false;
187		}
188		}
189	<
189	>
190		bool SimInfo::removeMolecule(Molecule* mol) {
191		MoleculeIterator i;
192		i = molecules_.find(mol->getGlobalIndex());
#	Line 237 | Line 214 | namespace oopse {
214		} else {
215		return false;
216		}
240	–
241	–
217		}
218
219
#	Line 256 | Line 231 | namespace oopse {
231		void SimInfo::calcNdf() {
232		int ndf_local;
233		MoleculeIterator i;
234	<	std::vector<StuntDouble*>::iterator j;
234	>	vector<StuntDouble*>::iterator j;
235		Molecule* mol;
236		StuntDouble* integrableObject;
237
#	Line 307 | Line 282 | namespace oopse {
282		int ndfRaw_local;
283
284		MoleculeIterator i;
285	<	std::vector<StuntDouble*>::iterator j;
285	>	vector<StuntDouble*>::iterator j;
286		Molecule* mol;
287		StuntDouble* integrableObject;
288
#	Line 356 | Line 331 | namespace oopse {
331
332		void SimInfo::addInteractionPairs(Molecule* mol) {
333		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
334	<	std::vector<Bond*>::iterator bondIter;
335	<	std::vector<Bend*>::iterator bendIter;
336	<	std::vector<Torsion*>::iterator torsionIter;
337	<	std::vector<Inversion*>::iterator inversionIter;
334	>	vector<Bond*>::iterator bondIter;
335	>	vector<Bend*>::iterator bendIter;
336	>	vector<Torsion*>::iterator torsionIter;
337	>	vector<Inversion*>::iterator inversionIter;
338		Bond* bond;
339		Bend* bend;
340		Torsion* torsion;
#	Line 377 | Line 352 | namespace oopse {
352		// always be excluded.  These are done at the bottom of this
353		// function.
354
355	<	std::map<int, std::set<int> > atomGroups;
355	>	map<int, set<int> > atomGroups;
356		Molecule::RigidBodyIterator rbIter;
357		RigidBody* rb;
358		Molecule::IntegrableObjectIterator ii;
#	Line 389 | Line 364 | namespace oopse {
364
365		if (integrableObject->isRigidBody()) {
366		rb = static_cast<RigidBody*>(integrableObject);
367	<	std::vector<Atom*> atoms = rb->getAtoms();
368	<	std::set<int> rigidAtoms;
367	>	vector<Atom*> atoms = rb->getAtoms();
368	>	set<int> rigidAtoms;
369		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
370		rigidAtoms.insert(atoms[i]->getGlobalIndex());
371		}
372		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
373	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
373	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
374		}
375		} else {
376	<	std::set<int> oneAtomSet;
376	>	set<int> oneAtomSet;
377		oneAtomSet.insert(integrableObject->getGlobalIndex());
378	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
378	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
379		}
380		}
381
#	Line 503 | Line 478 | namespace oopse {
478
479		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
480		rb = mol->nextRigidBody(rbIter)) {
481	<	std::vector<Atom*> atoms = rb->getAtoms();
481	>	vector<Atom*> atoms = rb->getAtoms();
482		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
483		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
484		a = atoms[i]->getGlobalIndex();
#	Line 517 | Line 492 | namespace oopse {
492
493		void SimInfo::removeInteractionPairs(Molecule* mol) {
494		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
495	<	std::vector<Bond*>::iterator bondIter;
496	<	std::vector<Bend*>::iterator bendIter;
497	<	std::vector<Torsion*>::iterator torsionIter;
498	<	std::vector<Inversion*>::iterator inversionIter;
495	>	vector<Bond*>::iterator bondIter;
496	>	vector<Bend*>::iterator bendIter;
497	>	vector<Torsion*>::iterator torsionIter;
498	>	vector<Inversion*>::iterator inversionIter;
499		Bond* bond;
500		Bend* bend;
501		Torsion* torsion;
#	Line 530 | Line 505 | namespace oopse {
505		int c;
506		int d;
507
508	<	std::map<int, std::set<int> > atomGroups;
508	>	map<int, set<int> > atomGroups;
509		Molecule::RigidBodyIterator rbIter;
510		RigidBody* rb;
511		Molecule::IntegrableObjectIterator ii;
#	Line 542 | Line 517 | namespace oopse {
517
518		if (integrableObject->isRigidBody()) {
519		rb = static_cast<RigidBody*>(integrableObject);
520	<	std::vector<Atom*> atoms = rb->getAtoms();
521	<	std::set<int> rigidAtoms;
520	>	vector<Atom*> atoms = rb->getAtoms();
521	>	set<int> rigidAtoms;
522		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
523		rigidAtoms.insert(atoms[i]->getGlobalIndex());
524		}
525		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
526	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
526	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
527		}
528		} else {
529	<	std::set<int> oneAtomSet;
529	>	set<int> oneAtomSet;
530		oneAtomSet.insert(integrableObject->getGlobalIndex());
531	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
531	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
532		}
533		}
534
#	Line 656 | Line 631 | namespace oopse {
631
632		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
633		rb = mol->nextRigidBody(rbIter)) {
634	<	std::vector<Atom*> atoms = rb->getAtoms();
634	>	vector<Atom*> atoms = rb->getAtoms();
635		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
636		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
637		a = atoms[i]->getGlobalIndex();
#	Line 679 | Line 654 | namespace oopse {
654		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
655		}
656
657	+
658	+	/**
659	+	* update
660	+	*
661	+	*  Performs the global checks and variable settings after the objects have been
662	+	*  created.
663	+	*
664	+	*/
665		void SimInfo::update() {
666	+
667	+	setupSimVariables();
668	+	setupCutoffs();
669	+	setupSwitching();
670	+	setupElectrostatics();
671	+	setupNeighborlists();
672
684	–	setupSimType();
685	–
673		#ifdef IS_MPI
674		setupFortranParallel();
675		#endif
689	–
676		setupFortranSim();
677	+	fortranInitialized_ = true;
678
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	–
679		calcNdf();
680		calcNdfRaw();
681		calcNdfTrans();
712	–
713	–	fortranInitialized_ = true;
682		}
683	<
684	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
683	>
684	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
685		SimInfo::MoleculeIterator mi;
686		Molecule* mol;
687		Molecule::AtomIterator ai;
688		Atom* atom;
689	<	std::set<AtomType*> atomTypes;
690	<
691	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
724	<
689	>	set<AtomType*> atomTypes;
690	>
691	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
692		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
693		atomTypes.insert(atom->getAtomType());
694	<	}
695	<
729	<	}
730	<
694	>	}
695	>	}
696		return atomTypes;
697		}
698
699	<	void SimInfo::setupSimType() {
700	<	std::set<AtomType*>::iterator i;
701	<	std::set<AtomType*> atomTypes;
702	<	atomTypes = getUniqueAtomTypes();
699	>	/**
700	>	* setupCutoffs
701	>	*
702	>	* Sets the values of cutoffRadius and cutoffMethod
703	>	*
704	>	* cutoffRadius : realType
705	>	*  If the cutoffRadius was explicitly set, use that value.
706	>	*  If the cutoffRadius was not explicitly set:
707	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
708	>	*      No electrostatic atoms?  Poll the atom types present in the
709	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
710	>	*      Use the maximum suggested value that was found.
711	>	*
712	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
713	>	*      If cutoffMethod was explicitly set, use that choice.
714	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
715	>	*/
716	>	void SimInfo::setupCutoffs() {
717
718	<	int useLennardJones = 0;
719	<	int useElectrostatic = 0;
720	<	int useEAM = 0;
721	<	int useSC = 0;
722	<	int useCharge = 0;
723	<	int useDirectional = 0;
724	<	int useDipole = 0;
725	<	int useGayBerne = 0;
726	<	int useSticky = 0;
727	<	int useStickyPower = 0;
728	<	int useShape = 0;
729	<	int useFLARB = 0; //it is not in AtomType yet
730	<	int useDirectionalAtom = 0;
731	<	int useElectrostatics = 0;
732	<	//usePBC and useRF are from simParams
733	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
734	<	int useRF;
735	<	int useSF;
736	<	int useSP;
737	<	int useBoxDipole;
738	<
739	<	std::string myMethod;
740	<
741	<	// set the useRF logical
742	<	useRF = 0;
743	<	useSF = 0;
744	<	useSP = 0;
718	>	if (simParams_->haveCutoffRadius()) {
719	>	cutoffRadius_ = simParams_->getCutoffRadius();
720	>	} else {
721	>	if (usesElectrostaticAtoms_) {
722	>	sprintf(painCave.errMsg,
723	>	"SimInfo: No value was set for the cutoffRadius.\n"
724	>	"\tOpenMD will use a default value of 12.0 angstroms"
725	>	"\tfor the cutoffRadius.\n");
726	>	painCave.isFatal = 0;
727	>	painCave.severity = OPENMD_INFO;
728	>	simError();
729	>	cutoffRadius_ = 12.0;
730	>	} else {
731	>	RealType thisCut;
732	>	set<AtomType*>::iterator i;
733	>	set<AtomType*> atomTypes;
734	>	atomTypes = getSimulatedAtomTypes();
735	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
736	>	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
737	>	cutoffRadius_ = max(thisCut, cutoffRadius_);
738	>	}
739	>	sprintf(painCave.errMsg,
740	>	"SimInfo: No value was set for the cutoffRadius.\n"
741	>	"\tOpenMD will use %lf angstroms.\n",
742	>	cutoffRadius_);
743	>	painCave.isFatal = 0;
744	>	painCave.severity = OPENMD_INFO;
745	>	simError();
746	>	}
747	>	}
748
749	+	InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
750
751	<	if (simParams_->haveElectrostaticSummationMethod()) {
752	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
753	<	toUpper(myMethod);
754	<	if (myMethod == "REACTION_FIELD"){
755	<	useRF = 1;
756	<	} else if (myMethod == "SHIFTED_FORCE"){
757	<	useSF = 1;
758	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
759	<	useSP = 1;
751	>	map<string, CutoffMethod> stringToCutoffMethod;
752	>	stringToCutoffMethod["HARD"] = HARD;
753	>	stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
754	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
755	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
756	>
757	>	if (simParams_->haveCutoffMethod()) {
758	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
759	>	map<string, CutoffMethod>::iterator i;
760	>	i = stringToCutoffMethod.find(cutMeth);
761	>	if (i == stringToCutoffMethod.end()) {
762	>	sprintf(painCave.errMsg,
763	>	"SimInfo: Could not find chosen cutoffMethod %s\n"
764	>	"\tShould be one of: "
765	>	"HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
766	>	cutMeth.c_str());
767	>	painCave.isFatal = 1;
768	>	painCave.severity = OPENMD_ERROR;
769	>	simError();
770	>	} else {
771	>	cutoffMethod_ = i->second;
772	>	}
773	>	} else {
774	>	sprintf(painCave.errMsg,
775	>	"SimInfo: No value was set for the cutoffMethod.\n"
776	>	"\tOpenMD will use SHIFTED_FORCE.\n");
777	>	painCave.isFatal = 0;
778	>	painCave.severity = OPENMD_INFO;
779	>	simError();
780	>	cutoffMethod_ = SHIFTED_FORCE;
781	>	}
782	>
783	>	InteractionManager::Instance()->setCutoffMethod(cutoffMethod_);
784	>	}
785	>
786	>	/**
787	>	* setupSwitching
788	>	*
789	>	* Sets the values of switchingRadius and
790	>	*  If the switchingRadius was explicitly set, use that value (but check it)
791	>	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
792	>	*/
793	>	void SimInfo::setupSwitching() {
794	>
795	>	if (simParams_->haveSwitchingRadius()) {
796	>	switchingRadius_ = simParams_->getSwitchingRadius();
797	>	if (switchingRadius_ > cutoffRadius_) {
798	>	sprintf(painCave.errMsg,
799	>	"SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
800	>	switchingRadius_, cutoffRadius_);
801	>	painCave.isFatal = 1;
802	>	painCave.severity = OPENMD_ERROR;
803	>	simError();
804	>	}
805	>	} else {
806	>	switchingRadius_ = 0.85 * cutoffRadius_;
807	>	sprintf(painCave.errMsg,
808	>	"SimInfo: No value was set for the switchingRadius.\n"
809	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
810	>	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
811	>	painCave.isFatal = 0;
812	>	painCave.severity = OPENMD_WARNING;
813	>	simError();
814	>	}
815	>
816	>	InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
817	>
818	>	SwitchingFunctionType ft;
819	>
820	>	if (simParams_->haveSwitchingFunctionType()) {
821	>	string funcType = simParams_->getSwitchingFunctionType();
822	>	toUpper(funcType);
823	>	if (funcType == "CUBIC") {
824	>	ft = cubic;
825	>	} else {
826	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
827	>	ft = fifth_order_poly;
828	>	} else {
829	>	// throw error
830	>	sprintf( painCave.errMsg,
831	>	"SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
832	>	"\tswitchingFunctionType must be one of: "
833	>	"\"cubic\" or \"fifth_order_polynomial\".",
834	>	funcType.c_str() );
835	>	painCave.isFatal = 1;
836	>	painCave.severity = OPENMD_ERROR;
837	>	simError();
838	>	}
839		}
840		}
779	–
780	–	if (simParams_->haveAccumulateBoxDipole())
781	–	if (simParams_->getAccumulateBoxDipole())
782	–	useBoxDipole = 1;
841
842	+	InteractionManager::Instance()->setSwitchingFunctionType(ft);
843	+	}
844	+
845	+	/**
846	+	* setupSkinThickness
847	+	*
848	+	*  If the skinThickness was explicitly set, use that value (but check it)
849	+	*  If the skinThickness was not explicitly set: use 1.0 angstroms
850	+	*/
851	+	void SimInfo::setupSkinThickness() {
852	+	if (simParams_->haveSkinThickness()) {
853	+	skinThickness_ = simParams_->getSkinThickness();
854	+	} else {
855	+	skinThickness_ = 1.0;
856	+	sprintf(painCave.errMsg,
857	+	"SimInfo Warning: No value was set for the skinThickness.\n"
858	+	"\tOpenMD will use a default value of %f Angstroms\n"
859	+	"\tfor this simulation\n", skinThickness_);
860	+	painCave.isFatal = 0;
861	+	simError();
862	+	}
863	+	}
864	+
865	+	void SimInfo::setupSimType() {
866	+	set<AtomType*>::iterator i;
867	+	set<AtomType*> atomTypes;
868	+	atomTypes = getSimulatedAtomTypes();
869	+
870		useAtomicVirial_ = simParams_->getUseAtomicVirial();
871
872	+	int usesElectrostatic = 0;
873	+	int usesMetallic = 0;
874	+	int usesDirectional = 0;
875		//loop over all of the atom types
876		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
877	<	useLennardJones |= (*i)->isLennardJones();
878	<	useElectrostatic |= (*i)->isElectrostatic();
879	<	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();
877	>	usesElectrostatic |= (*i)->isElectrostatic();
878	>	usesMetallic |= (*i)->isMetal();
879	>	usesDirectional |= (*i)->isDirectional();
880		}
881
801	–	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
802	–	useDirectionalAtom = 1;
803	–	}
804	–
805	–	if (useCharge || useDipole) {
806	–	useElectrostatics = 1;
807	–	}
808	–
882		#ifdef IS_MPI
883		int temp;
884	+	temp = usesDirectional;
885	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
886
887	<	temp = usePBC;
888	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
887	>	temp = usesMetallic;
888	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
889
890	<	temp = useDirectionalAtom;
891	<	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	<
890	>	temp = usesElectrostatic;
891	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
892		#endif
893	<
894	<	fInfo_.SIM_uses_PBC = usePBC;
895	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
896	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
897	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
898	<	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_;
893	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
894	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
895	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
896	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
897	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
898	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
899		}
900
901		void SimInfo::setupFortranSim() {
902		int isError;
903		int nExclude, nOneTwo, nOneThree, nOneFour;
904	<	std::vector<int> fortranGlobalGroupMembership;
904	>	vector<int> fortranGlobalGroupMembership;
905
906	+	notifyFortranSkinThickness(&skinThickness_);
907	+
908	+	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
909	+	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
910	+	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
911	+
912		isError = 0;
913
914		//globalGroupMembership_ is filled by SimCreator
#	Line 898 | Line 917 | namespace oopse {
917		}
918
919		//calculate mass ratio of cutoff group
920	<	std::vector<RealType> mfact;
920	>	vector<RealType> mfact;
921		SimInfo::MoleculeIterator mi;
922		Molecule* mol;
923		Molecule::CutoffGroupIterator ci;
#	Line 925 | Line 944 | namespace oopse {
944		}
945
946		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
947	<	std::vector<int> identArray;
947	>	vector<int> identArray;
948
949		//to avoid memory reallocation, reserve enough space identArray
950		identArray.reserve(getNAtoms());
#	Line 938 | Line 957 | namespace oopse {
957
958		//fill molMembershipArray
959		//molMembershipArray is filled by SimCreator
960	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
960	>	vector<int> molMembershipArray(nGlobalAtoms_);
961		for (int i = 0; i < nGlobalAtoms_; i++) {
962		molMembershipArray[i] = globalMolMembership_[i] + 1;
963		}
#	Line 950 | Line 969 | namespace oopse {
969		nOneThree = oneThreeInteractions_.getSize();
970		nOneFour = oneFourInteractions_.getSize();
971
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	–
972		int* excludeList = excludedInteractions_.getPairList();
973		int* oneTwoList = oneTwoInteractions_.getPairList();
974		int* oneThreeList = oneThreeInteractions_.getPairList();
#	Line 973 | Line 987 | namespace oopse {
987		sprintf( painCave.errMsg,
988		"There was an error setting the simulation information in fortran.\n" );
989		painCave.isFatal = 1;
990	<	painCave.severity = OOPSE_ERROR;
990	>	painCave.severity = OPENMD_ERROR;
991		simError();
992		}
993
#	Line 996 | Line 1010 | namespace oopse {
1010		void SimInfo::setupFortranParallel() {
1011		#ifdef IS_MPI
1012		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1013	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1014	<	std::vector<int> localToGlobalCutoffGroupIndex;
1013	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1014	>	vector<int> localToGlobalCutoffGroupIndex;
1015		SimInfo::MoleculeIterator mi;
1016		Molecule::AtomIterator ai;
1017		Molecule::CutoffGroupIterator ci;
#	Line 1047 | Line 1061 | namespace oopse {
1061		errorCheckPoint();
1062
1063		#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	–	}
1064		}
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;
1065
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	–	}
1066
1067		void SimInfo::setupSwitchingFunction() {
1299	–	int ft = CUBIC;
1068
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	–
1069		}
1070
1071		void SimInfo::setupAccumulateBoxDipole() {
#	Line 1326 | Line 1073 | namespace oopse {
1073		// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1074		if ( simParams_->haveAccumulateBoxDipole() )
1075		if ( simParams_->getAccumulateBoxDipole() ) {
1329	–	setAccumulateBoxDipole();
1076		calcBoxDipole_ = true;
1077		}
1078
#	Line 1336 | Line 1082 | namespace oopse {
1082		properties_.addProperty(genData);
1083		}
1084
1085	<	void SimInfo::removeProperty(const std::string& propName) {
1085	>	void SimInfo::removeProperty(const string& propName) {
1086		properties_.removeProperty(propName);
1087		}
1088
#	Line 1344 | Line 1090 | namespace oopse {
1090		properties_.clearProperties();
1091		}
1092
1093	<	std::vector<std::string> SimInfo::getPropertyNames() {
1093	>	vector<string> SimInfo::getPropertyNames() {
1094		return properties_.getPropertyNames();
1095		}
1096
1097	<	std::vector<GenericData*> SimInfo::getProperties() {
1097	>	vector<GenericData*> SimInfo::getProperties() {
1098		return properties_.getProperties();
1099		}
1100
1101	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1101	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1102		return properties_.getPropertyByName(propName);
1103		}
1104
#	Line 1435 | Line 1181 | namespace oopse {
1181
1182		}
1183
1184	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1184	>	ostream& operator <<(ostream& o, SimInfo& info) {
1185
1186		return o;
1187		}
#	Line 1478 | Line 1224 | namespace oopse {
1224
1225
1226		[  Ixx -Ixy  -Ixz ]
1227	<	J =| -Iyx  Iyy  -Iyz |
1227	>	J =| -Iyx  Iyy  -Iyz |
1228		[ -Izx -Iyz   Izz ]
1229		*/
1230
#	Line 1585 | Line 1331 | namespace oopse {
1331		return IOIndexToIntegrableObject.at(index);
1332		}
1333
1334	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1334	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1335		IOIndexToIntegrableObject= v;
1336		}
1337
#	Line 1627 | Line 1373 | namespace oopse {
1373		return;
1374		}
1375		/*
1376	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1376	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1377		assert( v.size() == nAtoms_ + nRigidBodies_);
1378		sdByGlobalIndex_ = v;
1379		}
#	Line 1637 | Line 1383 | namespace oopse {
1383		return sdByGlobalIndex_.at(index);
1384		}
1385		*/
1386	<	}//end namespace oopse
1386	>	int SimInfo::getNGlobalConstraints() {
1387	>	int nGlobalConstraints;
1388	>	#ifdef IS_MPI
1389	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1390	>	MPI_COMM_WORLD);
1391	>	#else
1392	>	nGlobalConstraints =  nConstraints_;
1393	>	#endif
1394	>	return nGlobalConstraints;
1395	>	}
1396
1397	+	}//end namespace OpenMD
1398	+

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 1530 by gezelter, Tue Dec 28 21:47:55 2010 UTC

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