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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 1313 by gezelter, Wed Oct 22 20:01:49 2008 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1528 by gezelter, Fri Dec 17 20:11:05 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 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	<
685	>	set<AtomType*> atomTypes;
686	>
687		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
688	<
688	>
689		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
690		atomTypes.insert(atom->getAtomType());
691		}
692	<
692	>
693		}
694	<
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	>	* setupCutoffRadius
700	>	*
701	>	*  If the cutoffRadius was explicitly set, use that value.
702	>	*  If the cutoffRadius was not explicitly set:
703	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
704	>	*      No electrostatic atoms?  Poll the atom types present in the
705	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
706	>	*      Use the maximum suggested value that was found.
707	>	*/
708	>	void SimInfo::setupCutoffRadius() {
709
710	<	int useLennardJones = 0;
711	<	int useElectrostatic = 0;
712	<	int useEAM = 0;
713	<	int useSC = 0;
714	<	int useCharge = 0;
715	<	int useDirectional = 0;
716	<	int useDipole = 0;
717	<	int useGayBerne = 0;
718	<	int useSticky = 0;
719	<	int useStickyPower = 0;
720	<	int useShape = 0;
721	<	int useFLARB = 0; //it is not in AtomType yet
722	<	int useDirectionalAtom = 0;
723	<	int useElectrostatics = 0;
724	<	//usePBC and useRF are from simParams
725	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
726	<	int useRF;
727	<	int useSF;
728	<	int useSP;
729	<	int useBoxDipole;
710	>	if (simParams_->haveCutoffRadius()) {
711	>	cutoffRadius_ = simParams_->getCutoffRadius();
712	>	} else {
713	>	if (usesElectrostaticAtoms_) {
714	>	sprintf(painCave.errMsg,
715	>	"SimInfo Warning: No value was set for the cutoffRadius.\n"
716	>	"\tOpenMD will use a default value of 12.0 angstroms"
717	>	"\tfor the cutoffRadius.\n");
718	>	painCave.isFatal = 0;
719	>	simError();
720	>	cutoffRadius_ = 12.0;
721	>	} else {
722	>	RealType thisCut;
723	>	set<AtomType*>::iterator i;
724	>	set<AtomType*> atomTypes;
725	>	atomTypes = getSimulatedAtomTypes();
726	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
727	>	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
728	>	cutoffRadius_ = max(thisCut, cutoffRadius_);
729	>	}
730	>	sprintf(painCave.errMsg,
731	>	"SimInfo Warning: No value was set for the cutoffRadius.\n"
732	>	"\tOpenMD will use %lf angstroms.\n",
733	>	cutoffRadius_);
734	>	painCave.isFatal = 0;
735	>	simError();
736	>	}
737	>	}
738
739	<	std::string myMethod;
739	>	InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
740	>	}
741	>
742	>	/**
743	>	* setupSwitchingRadius
744	>	*
745	>	*  If the switchingRadius was explicitly set, use that value (but check it)
746	>	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
747	>	*/
748	>	void SimInfo::setupSwitchingRadius() {
749	>
750	>	if (simParams_->haveSwitchingRadius()) {
751	>	switchingRadius_ = simParams_->getSwitchingRadius();
752	>	if (switchingRadius_ > cutoffRadius_) {
753	>	sprintf(painCave.errMsg,
754	>	"SimInfo Error: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
755	>	switchingRadius_, cutoffRadius_);
756	>	painCave.isFatal = 1;
757	>	simError();
758
759	<	// set the useRF logical
760	<	useRF = 0;
761	<	useSF = 0;
762	<	useSP = 0;
763	<	useBoxDipole = 0;
759	>	}
760	>	} else {
761	>	switchingRadius_ = 0.85 * cutoffRadius_;
762	>	sprintf(painCave.errMsg,
763	>	"SimInfo Warning: No value was set for the switchingRadius.\n"
764	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
765	>	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
766	>	painCave.isFatal = 0;
767	>	simError();
768	>	}
769	>	InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
770	>	}
771
772	+	/**
773	+	* setupSkinThickness
774	+	*
775	+	*  If the skinThickness was explicitly set, use that value (but check it)
776	+	*  If the skinThickness was not explicitly set: use 1.0 angstroms
777	+	*/
778	+	void SimInfo::setupSkinThickness() {
779	+	if (simParams_->haveSkinThickness()) {
780	+	skinThickness_ = simParams_->getSkinThickness();
781	+	} else {
782	+	skinThickness_ = 1.0;
783	+	sprintf(painCave.errMsg,
784	+	"SimInfo Warning: No value was set for the skinThickness.\n"
785	+	"\tOpenMD will use a default value of %f Angstroms\n"
786	+	"\tfor this simulation\n", skinThickness_);
787	+	painCave.isFatal = 0;
788	+	simError();
789	+	}
790	+	}
791
792	<	if (simParams_->haveElectrostaticSummationMethod()) {
793	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
794	<	toUpper(myMethod);
795	<	if (myMethod == "REACTION_FIELD"){
773	<	useRF = 1;
774	<	} else if (myMethod == "SHIFTED_FORCE"){
775	<	useSF = 1;
776	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
777	<	useSP = 1;
778	<	}
779	<	}
780	<
781	<	if (simParams_->haveAccumulateBoxDipole())
782	<	if (simParams_->getAccumulateBoxDipole())
783	<	useBoxDipole = 1;
792	>	void SimInfo::setupSimType() {
793	>	set<AtomType*>::iterator i;
794	>	set<AtomType*> atomTypes;
795	>	atomTypes = getSimulatedAtomTypes();
796
797		useAtomicVirial_ = simParams_->getUseAtomicVirial();
798
799	+	int usesElectrostatic = 0;
800	+	int usesMetallic = 0;
801	+	int usesDirectional = 0;
802		//loop over all of the atom types
803		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
804	<	useLennardJones |= (*i)->isLennardJones();
805	<	useElectrostatic |= (*i)->isElectrostatic();
806	<	useEAM |= (*i)->isEAM();
792	<	useSC |= (*i)->isSC();
793	<	useCharge |= (*i)->isCharge();
794	<	useDirectional |= (*i)->isDirectional();
795	<	useDipole |= (*i)->isDipole();
796	<	useGayBerne |= (*i)->isGayBerne();
797	<	useSticky |= (*i)->isSticky();
798	<	useStickyPower |= (*i)->isStickyPower();
799	<	useShape |= (*i)->isShape();
804	>	usesElectrostatic |= (*i)->isElectrostatic();
805	>	usesMetallic |= (*i)->isMetal();
806	>	usesDirectional |= (*i)->isDirectional();
807		}
808
802	–	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
803	–	useDirectionalAtom = 1;
804	–	}
805	–
806	–	if (useCharge || useDipole) {
807	–	useElectrostatics = 1;
808	–	}
809	–
809		#ifdef IS_MPI
810		int temp;
811	+	temp = usesDirectional;
812	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813
814	<	temp = usePBC;
815	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814	>	temp = usesMetallic;
815	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816
817	<	temp = useDirectionalAtom;
818	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
818	<
819	<	temp = useLennardJones;
820	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
821	<
822	<	temp = useElectrostatics;
823	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
824	<
825	<	temp = useCharge;
826	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
827	<
828	<	temp = useDipole;
829	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
830	<
831	<	temp = useSticky;
832	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
833	<
834	<	temp = useStickyPower;
835	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
836	<
837	<	temp = useGayBerne;
838	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
839	<
840	<	temp = useEAM;
841	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
842	<
843	<	temp = useSC;
844	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
845	<
846	<	temp = useShape;
847	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
848	<
849	<	temp = useFLARB;
850	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
851	<
852	<	temp = useRF;
853	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
854	<
855	<	temp = useSF;
856	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
857	<
858	<	temp = useSP;
859	<	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860	<
861	<	temp = useBoxDipole;
862	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
863	<
864	<	temp = useAtomicVirial_;
865	<	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
866	<
817	>	temp = usesElectrostatic;
818	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819		#endif
820	<
821	<	fInfo_.SIM_uses_PBC = usePBC;
822	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
823	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
824	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
825	<	fInfo_.SIM_uses_Charges = useCharge;
874	<	fInfo_.SIM_uses_Dipoles = useDipole;
875	<	fInfo_.SIM_uses_Sticky = useSticky;
876	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
877	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
878	<	fInfo_.SIM_uses_EAM = useEAM;
879	<	fInfo_.SIM_uses_SC = useSC;
880	<	fInfo_.SIM_uses_Shapes = useShape;
881	<	fInfo_.SIM_uses_FLARB = useFLARB;
882	<	fInfo_.SIM_uses_RF = useRF;
883	<	fInfo_.SIM_uses_SF = useSF;
884	<	fInfo_.SIM_uses_SP = useSP;
885	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
886	<	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
820	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
821	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
822	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
823	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
824	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
825	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
826		}
827
828		void SimInfo::setupFortranSim() {
829		int isError;
830		int nExclude, nOneTwo, nOneThree, nOneFour;
831	<	std::vector<int> fortranGlobalGroupMembership;
831	>	vector<int> fortranGlobalGroupMembership;
832
833	+	notifyFortranSkinThickness(&skinThickness_);
834	+
835	+	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
836	+	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
837	+	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
838	+
839		isError = 0;
840
841		//globalGroupMembership_ is filled by SimCreator
#	Line 899 | Line 844 | namespace oopse {
844		}
845
846		//calculate mass ratio of cutoff group
847	<	std::vector<RealType> mfact;
847	>	vector<RealType> mfact;
848		SimInfo::MoleculeIterator mi;
849		Molecule* mol;
850		Molecule::CutoffGroupIterator ci;
#	Line 926 | Line 871 | namespace oopse {
871		}
872
873		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
874	<	std::vector<int> identArray;
874	>	vector<int> identArray;
875
876		//to avoid memory reallocation, reserve enough space identArray
877		identArray.reserve(getNAtoms());
#	Line 939 | Line 884 | namespace oopse {
884
885		//fill molMembershipArray
886		//molMembershipArray is filled by SimCreator
887	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
887	>	vector<int> molMembershipArray(nGlobalAtoms_);
888		for (int i = 0; i < nGlobalAtoms_; i++) {
889		molMembershipArray[i] = globalMolMembership_[i] + 1;
890		}
#	Line 969 | Line 914 | namespace oopse {
914		sprintf( painCave.errMsg,
915		"There was an error setting the simulation information in fortran.\n" );
916		painCave.isFatal = 1;
917	<	painCave.severity = OOPSE_ERROR;
917	>	painCave.severity = OPENMD_ERROR;
918		simError();
919		}
920
#	Line 992 | Line 937 | namespace oopse {
937		void SimInfo::setupFortranParallel() {
938		#ifdef IS_MPI
939		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
940	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
941	<	std::vector<int> localToGlobalCutoffGroupIndex;
940	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
941	>	vector<int> localToGlobalCutoffGroupIndex;
942		SimInfo::MoleculeIterator mi;
943		Molecule::AtomIterator ai;
944		Molecule::CutoffGroupIterator ci;
#	Line 1043 | Line 988 | namespace oopse {
988		errorCheckPoint();
989
990		#endif
1046	–	}
1047	–
1048	–	void SimInfo::setupCutoff() {
1049	–
1050	–	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1051	–
1052	–	// Check the cutoff policy
1053	–	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1054	–
1055	–	// Set LJ shifting bools to false
1056	–	ljsp_ = false;
1057	–	ljsf_ = false;
1058	–
1059	–	std::string myPolicy;
1060	–	if (forceFieldOptions_.haveCutoffPolicy()){
1061	–	myPolicy = forceFieldOptions_.getCutoffPolicy();
1062	–	}else if (simParams_->haveCutoffPolicy()) {
1063	–	myPolicy = simParams_->getCutoffPolicy();
1064	–	}
1065	–
1066	–	if (!myPolicy.empty()){
1067	–	toUpper(myPolicy);
1068	–	if (myPolicy == "MIX") {
1069	–	cp = MIX_CUTOFF_POLICY;
1070	–	} else {
1071	–	if (myPolicy == "MAX") {
1072	–	cp = MAX_CUTOFF_POLICY;
1073	–	} else {
1074	–	if (myPolicy == "TRADITIONAL") {
1075	–	cp = TRADITIONAL_CUTOFF_POLICY;
1076	–	} else {
1077	–	// throw error
1078	–	sprintf( painCave.errMsg,
1079	–	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1080	–	painCave.isFatal = 1;
1081	–	simError();
1082	–	}
1083	–	}
1084	–	}
1085	–	}
1086	–	notifyFortranCutoffPolicy(&cp);
1087	–
1088	–	// Check the Skin Thickness for neighborlists
1089	–	RealType skin;
1090	–	if (simParams_->haveSkinThickness()) {
1091	–	skin = simParams_->getSkinThickness();
1092	–	notifyFortranSkinThickness(&skin);
1093	–	}
1094	–
1095	–	// Check if the cutoff was set explicitly:
1096	–	if (simParams_->haveCutoffRadius()) {
1097	–	rcut_ = simParams_->getCutoffRadius();
1098	–	if (simParams_->haveSwitchingRadius()) {
1099	–	rsw_  = simParams_->getSwitchingRadius();
1100	–	} else {
1101	–	if (fInfo_.SIM_uses_Charges |
1102	–	fInfo_.SIM_uses_Dipoles |
1103	–	fInfo_.SIM_uses_RF) {
1104	–
1105	–	rsw_ = 0.85 * rcut_;
1106	–	sprintf(painCave.errMsg,
1107	–	"SimCreator Warning: No value was set for the switchingRadius.\n"
1108	–	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1109	–	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1110	–	painCave.isFatal = 0;
1111	–	simError();
1112	–	} else {
1113	–	rsw_ = rcut_;
1114	–	sprintf(painCave.errMsg,
1115	–	"SimCreator Warning: No value was set for the switchingRadius.\n"
1116	–	"\tOOPSE will use the same value as the cutoffRadius.\n"
1117	–	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1118	–	painCave.isFatal = 0;
1119	–	simError();
1120	–	}
1121	–	}
1122	–
1123	–	if (simParams_->haveElectrostaticSummationMethod()) {
1124	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1125	–	toUpper(myMethod);
1126	–
1127	–	if (myMethod == "SHIFTED_POTENTIAL") {
1128	–	ljsp_ = true;
1129	–	} else if (myMethod == "SHIFTED_FORCE") {
1130	–	ljsf_ = true;
1131	–	}
1132	–	}
1133	–	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1134	–
1135	–	} else {
1136	–
1137	–	// For electrostatic atoms, we'll assume a large safe value:
1138	–	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1139	–	sprintf(painCave.errMsg,
1140	–	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1141	–	"\tOOPSE will use a default value of 15.0 angstroms"
1142	–	"\tfor the cutoffRadius.\n");
1143	–	painCave.isFatal = 0;
1144	–	simError();
1145	–	rcut_ = 15.0;
1146	–
1147	–	if (simParams_->haveElectrostaticSummationMethod()) {
1148	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1149	–	toUpper(myMethod);
1150	–
1151	–	// For the time being, we're tethering the LJ shifted behavior to the
1152	–	// electrostaticSummationMethod keyword options
1153	–	if (myMethod == "SHIFTED_POTENTIAL") {
1154	–	ljsp_ = true;
1155	–	} else if (myMethod == "SHIFTED_FORCE") {
1156	–	ljsf_ = true;
1157	–	}
1158	–	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1159	–	if (simParams_->haveSwitchingRadius()){
1160	–	sprintf(painCave.errMsg,
1161	–	"SimInfo Warning: A value was set for the switchingRadius\n"
1162	–	"\teven though the electrostaticSummationMethod was\n"
1163	–	"\tset to %s\n", myMethod.c_str());
1164	–	painCave.isFatal = 1;
1165	–	simError();
1166	–	}
1167	–	}
1168	–	}
1169	–
1170	–	if (simParams_->haveSwitchingRadius()){
1171	–	rsw_ = simParams_->getSwitchingRadius();
1172	–	} else {
1173	–	sprintf(painCave.errMsg,
1174	–	"SimCreator Warning: No value was set for switchingRadius.\n"
1175	–	"\tOOPSE will use a default value of\n"
1176	–	"\t0.85 * cutoffRadius for the switchingRadius\n");
1177	–	painCave.isFatal = 0;
1178	–	simError();
1179	–	rsw_ = 0.85 * rcut_;
1180	–	}
1181	–
1182	–	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1183	–
1184	–	} else {
1185	–	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1186	–	// We'll punt and let fortran figure out the cutoffs later.
1187	–
1188	–	notifyFortranYouAreOnYourOwn();
1189	–
1190	–	}
1191	–	}
991		}
1193	–
1194	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1195	–
1196	–	int errorOut;
1197	–	int esm =  NONE;
1198	–	int sm = UNDAMPED;
1199	–	RealType alphaVal;
1200	–	RealType dielectric;
1201	–
1202	–	errorOut = isError;
1203	–
1204	–	if (simParams_->haveElectrostaticSummationMethod()) {
1205	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1206	–	toUpper(myMethod);
1207	–	if (myMethod == "NONE") {
1208	–	esm = NONE;
1209	–	} else {
1210	–	if (myMethod == "SWITCHING_FUNCTION") {
1211	–	esm = SWITCHING_FUNCTION;
1212	–	} else {
1213	–	if (myMethod == "SHIFTED_POTENTIAL") {
1214	–	esm = SHIFTED_POTENTIAL;
1215	–	} else {
1216	–	if (myMethod == "SHIFTED_FORCE") {
1217	–	esm = SHIFTED_FORCE;
1218	–	} else {
1219	–	if (myMethod == "REACTION_FIELD") {
1220	–	esm = REACTION_FIELD;
1221	–	dielectric = simParams_->getDielectric();
1222	–	if (!simParams_->haveDielectric()) {
1223	–	// throw warning
1224	–	sprintf( painCave.errMsg,
1225	–	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1226	–	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1227	–	painCave.isFatal = 0;
1228	–	simError();
1229	–	}
1230	–	} else {
1231	–	// throw error
1232	–	sprintf( painCave.errMsg,
1233	–	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1234	–	"\t(Input file specified %s .)\n"
1235	–	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1236	–	"\t\"shifted_potential\", \"shifted_force\", or \n"
1237	–	"\t\"reaction_field\".\n", myMethod.c_str() );
1238	–	painCave.isFatal = 1;
1239	–	simError();
1240	–	}
1241	–	}
1242	–	}
1243	–	}
1244	–	}
1245	–	}
1246	–
1247	–	if (simParams_->haveElectrostaticScreeningMethod()) {
1248	–	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1249	–	toUpper(myScreen);
1250	–	if (myScreen == "UNDAMPED") {
1251	–	sm = UNDAMPED;
1252	–	} else {
1253	–	if (myScreen == "DAMPED") {
1254	–	sm = DAMPED;
1255	–	if (!simParams_->haveDampingAlpha()) {
1256	–	// first set a cutoff dependent alpha value
1257	–	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1258	–	alphaVal = 0.5125 - rcut_* 0.025;
1259	–	// for values rcut > 20.5, alpha is zero
1260	–	if (alphaVal < 0) alphaVal = 0;
992
1262	–	// throw warning
1263	–	sprintf( painCave.errMsg,
1264	–	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1265	–	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1266	–	painCave.isFatal = 0;
1267	–	simError();
1268	–	} else {
1269	–	alphaVal = simParams_->getDampingAlpha();
1270	–	}
1271	–
1272	–	} else {
1273	–	// throw error
1274	–	sprintf( painCave.errMsg,
1275	–	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1276	–	"\t(Input file specified %s .)\n"
1277	–	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1278	–	"or \"damped\".\n", myScreen.c_str() );
1279	–	painCave.isFatal = 1;
1280	–	simError();
1281	–	}
1282	–	}
1283	–	}
1284	–
1285	–	// let's pass some summation method variables to fortran
1286	–	setElectrostaticSummationMethod( &esm );
1287	–	setFortranElectrostaticMethod( &esm );
1288	–	setScreeningMethod( &sm );
1289	–	setDampingAlpha( &alphaVal );
1290	–	setReactionFieldDielectric( &dielectric );
1291	–	initFortranFF( &errorOut );
1292	–	}
993
994		void SimInfo::setupSwitchingFunction() {
995		int ft = CUBIC;
996	<
996	>
997		if (simParams_->haveSwitchingFunctionType()) {
998	<	std::string funcType = simParams_->getSwitchingFunctionType();
998	>	string funcType = simParams_->getSwitchingFunctionType();
999		toUpper(funcType);
1000		if (funcType == "CUBIC") {
1001		ft = CUBIC;
#	Line 1322 | Line 1022 | namespace oopse {
1022		// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1023		if ( simParams_->haveAccumulateBoxDipole() )
1024		if ( simParams_->getAccumulateBoxDipole() ) {
1325	–	setAccumulateBoxDipole();
1025		calcBoxDipole_ = true;
1026		}
1027
#	Line 1332 | Line 1031 | namespace oopse {
1031		properties_.addProperty(genData);
1032		}
1033
1034	<	void SimInfo::removeProperty(const std::string& propName) {
1034	>	void SimInfo::removeProperty(const string& propName) {
1035		properties_.removeProperty(propName);
1036		}
1037
#	Line 1340 | Line 1039 | namespace oopse {
1039		properties_.clearProperties();
1040		}
1041
1042	<	std::vector<std::string> SimInfo::getPropertyNames() {
1042	>	vector<string> SimInfo::getPropertyNames() {
1043		return properties_.getPropertyNames();
1044		}
1045
1046	<	std::vector<GenericData*> SimInfo::getProperties() {
1046	>	vector<GenericData*> SimInfo::getProperties() {
1047		return properties_.getProperties();
1048		}
1049
1050	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1050	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1051		return properties_.getPropertyByName(propName);
1052		}
1053
#	Line 1431 | Line 1130 | namespace oopse {
1130
1131		}
1132
1133	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1133	>	ostream& operator <<(ostream& o, SimInfo& info) {
1134
1135		return o;
1136		}
#	Line 1474 | Line 1173 | namespace oopse {
1173
1174
1175		[  Ixx -Ixy  -Ixz ]
1176	<	J =| -Iyx  Iyy  -Iyz |
1176	>	J =| -Iyx  Iyy  -Iyz |
1177		[ -Izx -Iyz   Izz ]
1178		*/
1179
#	Line 1581 | Line 1280 | namespace oopse {
1280		return IOIndexToIntegrableObject.at(index);
1281		}
1282
1283	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1283	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1284		IOIndexToIntegrableObject= v;
1285		}
1286
#	Line 1623 | Line 1322 | namespace oopse {
1322		return;
1323		}
1324		/*
1325	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1325	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1326		assert( v.size() == nAtoms_ + nRigidBodies_);
1327		sdByGlobalIndex_ = v;
1328		}
#	Line 1633 | Line 1332 | namespace oopse {
1332		return sdByGlobalIndex_.at(index);
1333		}
1334		*/
1335	<	}//end namespace oopse
1335	>	int SimInfo::getNGlobalConstraints() {
1336	>	int nGlobalConstraints;
1337	>	#ifdef IS_MPI
1338	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1339	>	MPI_COMM_WORLD);
1340	>	#else
1341	>	nGlobalConstraints =  nConstraints_;
1342	>	#endif
1343	>	return nGlobalConstraints;
1344	>	}
1345
1346	+	}//end namespace OpenMD
1347	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 1313 by gezelter, Wed Oct 22 20:01:49 2008 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1528 by gezelter, Fri Dec 17 20:11:05 2010 UTC

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