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

Comparing:
trunk/src/brains/SimInfo.cpp (file contents), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1549 by gezelter, Wed Apr 27 18:38:15 2011 UTC

#	Line 54 | Line 54
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56		#include "primitives/StuntDouble.hpp"
57	–	#include "UseTheForce/fCutoffPolicy.h"
58	–	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	–	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60	–	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61	–	#include "UseTheForce/doForces_interface.h"
57		#include "UseTheForce/DarkSide/neighborLists_interface.h"
58	<	#include "UseTheForce/DarkSide/electrostatic_interface.h"
64	<	#include "UseTheForce/DarkSide/switcheroo_interface.h"
58	>	#include "UseTheForce/doForces_interface.h"
59		#include "utils/MemoryUtils.hpp"
60		#include "utils/simError.h"
61		#include "selection/SelectionManager.hpp"
62		#include "io/ForceFieldOptions.hpp"
63		#include "UseTheForce/ForceField.hpp"
64	+	#include "nonbonded/SwitchingFunction.hpp"
65
71	–
66		#ifdef IS_MPI
67		#include "UseTheForce/mpiComponentPlan.h"
68		#include "UseTheForce/DarkSide/simParallel_interface.h"
69		#endif
70
71	+	using namespace std;
72		namespace OpenMD {
78	–	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
74		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
75		forceField_(ff), simParams_(simParams),
#	Line 93 | Line 79 | namespace OpenMD {
79		nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
80		nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
81		nConstraints_(0), sman_(NULL), fortranInitialized_(false),
82	<	calcBoxDipole_(false), useAtomicVirial_(true) {
83	<
84	<
85	<	MoleculeStamp* molStamp;
86	<	int nMolWithSameStamp;
87	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
88	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
89	<	CutoffGroupStamp* cgStamp;
90	<	RigidBodyStamp* rbStamp;
91	<	int nRigidAtoms = 0;
92	<
93	<	std::vector<Component*> components = simParams->getComponents();
82	>	calcBoxDipole_(false), useAtomicVirial_(true) {
83	>
84	>	MoleculeStamp* molStamp;
85	>	int nMolWithSameStamp;
86	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
88	>	CutoffGroupStamp* cgStamp;
89	>	RigidBodyStamp* rbStamp;
90	>	int nRigidAtoms = 0;
91	>
92	>	vector<Component*> components = simParams->getComponents();
93	>
94	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
95	>	molStamp = (*i)->getMoleculeStamp();
96	>	nMolWithSameStamp = (*i)->getNMol();
97
98	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
99	<	molStamp = (*i)->getMoleculeStamp();
100	<	nMolWithSameStamp = (*i)->getNMol();
101	<
102	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
103	<
104	<	//calculate atoms in molecules
105	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
106	<
107	<	//calculate atoms in cutoff groups
108	<	int nAtomsInGroups = 0;
109	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
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	<
98	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
99	>
100	>	//calculate atoms in molecules
101	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
102	>
103	>	//calculate atoms in cutoff groups
104	>	int nAtomsInGroups = 0;
105	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
106	>
107	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
108	>	cgStamp = molStamp->getCutoffGroupStamp(j);
109	>	nAtomsInGroups += cgStamp->getNMembers();
110		}
111	<
112	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
113	<	//group therefore the total number of cutoff groups in the system is
114	<	//equal to the total number of atoms minus number of atoms belong to
115	<	//cutoff group defined in meta-data file plus the number of cutoff
116	<	//groups defined in meta-data file
117	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
118	<
119	<	//every free atom (atom does not belong to rigid bodies) is an
120	<	//integrable object therefore the total number of integrable objects
121	<	//in the system is equal to the total number of atoms minus number of
122	<	//atoms belong to rigid body defined in meta-data file plus the number
123	<	//of rigid bodies defined in meta-data file
124	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
125	<	+ nGlobalRigidBodies_;
126	<
127	<	nGlobalMols_ = molStampIds_.size();
161	<	molToProcMap_.resize(nGlobalMols_);
111	>
112	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
113	>
114	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
115	>
116	>	//calculate atoms in rigid bodies
117	>	int nAtomsInRigidBodies = 0;
118	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
119	>
120	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
121	>	rbStamp = molStamp->getRigidBodyStamp(j);
122	>	nAtomsInRigidBodies += rbStamp->getNMembers();
123	>	}
124	>
125	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
126	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
127	>
128		}
129	+
130	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
131	+	//group therefore the total number of cutoff groups in the system is
132	+	//equal to the total number of atoms minus number of atoms belong to
133	+	//cutoff group defined in meta-data file plus the number of cutoff
134	+	//groups defined in meta-data file
135	+	std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
136	+	std::cerr << "nCA = " << nCutoffAtoms << "\n";
137	+	std::cerr << "nG = " << nGroups << "\n";
138
139	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
140	+
141	+	std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
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	+
151	+	nGlobalMols_ = molStampIds_.size();
152	+	molToProcMap_.resize(nGlobalMols_);
153	+	}
154	+
155		SimInfo::~SimInfo() {
156	<	std::map<int, Molecule*>::iterator i;
156	>	map<int, Molecule*>::iterator i;
157		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
158		delete i->second;
159		}
#	Line 173 | Line 164 | namespace OpenMD {
164		delete forceField_;
165		}
166
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	–	}
167
168		bool SimInfo::addMolecule(Molecule* mol) {
169		MoleculeIterator i;
170	<
170	>
171		i = molecules_.find(mol->getGlobalIndex());
172		if (i == molecules_.end() ) {
173	<
174	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
175	<
173	>
174	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
175	>
176		nAtoms_ += mol->getNAtoms();
177		nBonds_ += mol->getNBonds();
178		nBends_ += mol->getNBends();
#	Line 201 | Line 182 | namespace OpenMD {
182		nIntegrableObjects_ += mol->getNIntegrableObjects();
183		nCutoffGroups_ += mol->getNCutoffGroups();
184		nConstraints_ += mol->getNConstraintPairs();
185	<
185	>
186		addInteractionPairs(mol);
187	<
187	>
188		return true;
189		} else {
190		return false;
191		}
192		}
193	<
193	>
194		bool SimInfo::removeMolecule(Molecule* mol) {
195		MoleculeIterator i;
196		i = molecules_.find(mol->getGlobalIndex());
#	Line 237 | Line 218 | namespace OpenMD {
218		} else {
219		return false;
220		}
240	–
241	–
221		}
222
223
#	Line 256 | Line 235 | namespace OpenMD {
235		void SimInfo::calcNdf() {
236		int ndf_local;
237		MoleculeIterator i;
238	<	std::vector<StuntDouble*>::iterator j;
238	>	vector<StuntDouble*>::iterator j;
239		Molecule* mol;
240		StuntDouble* integrableObject;
241
#	Line 307 | Line 286 | namespace OpenMD {
286		int ndfRaw_local;
287
288		MoleculeIterator i;
289	<	std::vector<StuntDouble*>::iterator j;
289	>	vector<StuntDouble*>::iterator j;
290		Molecule* mol;
291		StuntDouble* integrableObject;
292
#	Line 356 | Line 335 | namespace OpenMD {
335
336		void SimInfo::addInteractionPairs(Molecule* mol) {
337		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
338	<	std::vector<Bond*>::iterator bondIter;
339	<	std::vector<Bend*>::iterator bendIter;
340	<	std::vector<Torsion*>::iterator torsionIter;
341	<	std::vector<Inversion*>::iterator inversionIter;
338	>	vector<Bond*>::iterator bondIter;
339	>	vector<Bend*>::iterator bendIter;
340	>	vector<Torsion*>::iterator torsionIter;
341	>	vector<Inversion*>::iterator inversionIter;
342		Bond* bond;
343		Bend* bend;
344		Torsion* torsion;
#	Line 377 | Line 356 | namespace OpenMD {
356		// always be excluded.  These are done at the bottom of this
357		// function.
358
359	<	std::map<int, std::set<int> > atomGroups;
359	>	map<int, set<int> > atomGroups;
360		Molecule::RigidBodyIterator rbIter;
361		RigidBody* rb;
362		Molecule::IntegrableObjectIterator ii;
#	Line 389 | Line 368 | namespace OpenMD {
368
369		if (integrableObject->isRigidBody()) {
370		rb = static_cast<RigidBody*>(integrableObject);
371	<	std::vector<Atom*> atoms = rb->getAtoms();
372	<	std::set<int> rigidAtoms;
371	>	vector<Atom*> atoms = rb->getAtoms();
372	>	set<int> rigidAtoms;
373		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
374		rigidAtoms.insert(atoms[i]->getGlobalIndex());
375		}
376		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
377	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
377	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
378		}
379		} else {
380	<	std::set<int> oneAtomSet;
380	>	set<int> oneAtomSet;
381		oneAtomSet.insert(integrableObject->getGlobalIndex());
382	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
382	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
383		}
384		}
385
#	Line 503 | Line 482 | namespace OpenMD {
482
483		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
484		rb = mol->nextRigidBody(rbIter)) {
485	<	std::vector<Atom*> atoms = rb->getAtoms();
485	>	vector<Atom*> atoms = rb->getAtoms();
486		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
487		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
488		a = atoms[i]->getGlobalIndex();
#	Line 517 | Line 496 | namespace OpenMD {
496
497		void SimInfo::removeInteractionPairs(Molecule* mol) {
498		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
499	<	std::vector<Bond*>::iterator bondIter;
500	<	std::vector<Bend*>::iterator bendIter;
501	<	std::vector<Torsion*>::iterator torsionIter;
502	<	std::vector<Inversion*>::iterator inversionIter;
499	>	vector<Bond*>::iterator bondIter;
500	>	vector<Bend*>::iterator bendIter;
501	>	vector<Torsion*>::iterator torsionIter;
502	>	vector<Inversion*>::iterator inversionIter;
503		Bond* bond;
504		Bend* bend;
505		Torsion* torsion;
#	Line 530 | Line 509 | namespace OpenMD {
509		int c;
510		int d;
511
512	<	std::map<int, std::set<int> > atomGroups;
512	>	map<int, set<int> > atomGroups;
513		Molecule::RigidBodyIterator rbIter;
514		RigidBody* rb;
515		Molecule::IntegrableObjectIterator ii;
#	Line 542 | Line 521 | namespace OpenMD {
521
522		if (integrableObject->isRigidBody()) {
523		rb = static_cast<RigidBody*>(integrableObject);
524	<	std::vector<Atom*> atoms = rb->getAtoms();
525	<	std::set<int> rigidAtoms;
524	>	vector<Atom*> atoms = rb->getAtoms();
525	>	set<int> rigidAtoms;
526		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
527		rigidAtoms.insert(atoms[i]->getGlobalIndex());
528		}
529		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
530	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
530	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
531		}
532		} else {
533	<	std::set<int> oneAtomSet;
533	>	set<int> oneAtomSet;
534		oneAtomSet.insert(integrableObject->getGlobalIndex());
535	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
535	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
536		}
537		}
538
#	Line 656 | Line 635 | namespace OpenMD {
635
636		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
637		rb = mol->nextRigidBody(rbIter)) {
638	<	std::vector<Atom*> atoms = rb->getAtoms();
638	>	vector<Atom*> atoms = rb->getAtoms();
639		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
640		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
641		a = atoms[i]->getGlobalIndex();
#	Line 679 | Line 658 | namespace OpenMD {
658		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
659		}
660
682	–	void SimInfo::update() {
661
662	<	setupSimType();
663	<
664	<	#ifdef IS_MPI
665	<	setupFortranParallel();
666	<	#endif
667	<
668	<	setupFortranSim();
669	<
670	<	//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	<
662	>	/**
663	>	* update
664	>	*
665	>	*  Performs the global checks and variable settings after the
666	>	*  objects have been created.
667	>	*
668	>	*/
669	>	void SimInfo::update() {
670	>	setupSimVariables();
671		calcNdf();
672		calcNdfRaw();
673		calcNdfTrans();
712	–
713	–	fortranInitialized_ = true;
674		}
675	<
676	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
675	>
676	>	/**
677	>	* getSimulatedAtomTypes
678	>	*
679	>	* Returns an STL set of AtomType* that are actually present in this
680	>	* simulation.  Must query all processors to assemble this information.
681	>	*
682	>	*/
683	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
684		SimInfo::MoleculeIterator mi;
685		Molecule* mol;
686		Molecule::AtomIterator ai;
687		Atom* atom;
688	<	std::set<AtomType*> atomTypes;
689	<
690	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
724	<
688	>	set<AtomType*> atomTypes;
689	>
690	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
691		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
692		atomTypes.insert(atom->getAtomType());
693	<	}
694	<
729	<	}
693	>	}
694	>	}
695
696	<	return atomTypes;
732	<	}
696	>	#ifdef IS_MPI
697
698	<	void SimInfo::setupSimType() {
699	<	std::set<AtomType*>::iterator i;
736	<	std::set<AtomType*> atomTypes;
737	<	atomTypes = getUniqueAtomTypes();
738	<
739	<	int useLennardJones = 0;
740	<	int useElectrostatic = 0;
741	<	int useEAM = 0;
742	<	int useSC = 0;
743	<	int useCharge = 0;
744	<	int useDirectional = 0;
745	<	int useDipole = 0;
746	<	int useGayBerne = 0;
747	<	int useSticky = 0;
748	<	int useStickyPower = 0;
749	<	int useShape = 0;
750	<	int useFLARB = 0; //it is not in AtomType yet
751	<	int useDirectionalAtom = 0;
752	<	int useElectrostatics = 0;
753	<	//usePBC and useRF are from simParams
754	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
755	<	int useRF;
756	<	int useSF;
757	<	int useSP;
758	<	int useBoxDipole;
698	>	// loop over the found atom types on this processor, and add their
699	>	// numerical idents to a vector:
700
701	<	std::string myMethod;
701	>	vector<int> foundTypes;
702	>	set<AtomType*>::iterator i;
703	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
704	>	foundTypes.push_back( (*i)->getIdent() );
705
706	<	// set the useRF logical
707	<	useRF = 0;
764	<	useSF = 0;
765	<	useSP = 0;
766	<	useBoxDipole = 0;
706	>	// count_local holds the number of found types on this processor
707	>	int count_local = foundTypes.size();
708
709	+	// count holds the total number of found types on all processors
710	+	// (some will be redundant with the ones found locally):
711	+	int count;
712	+	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
713
714	<	if (simParams_->haveElectrostaticSummationMethod()) {
715	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
716	<	toUpper(myMethod);
717	<	if (myMethod == "REACTION_FIELD"){
718	<	useRF = 1;
719	<	} else if (myMethod == "SHIFTED_FORCE"){
720	<	useSF = 1;
721	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
722	<	useSP = 1;
723	<	}
724	<	}
714	>	// create a vector to hold the globally found types, and resize it:
715	>	vector<int> ftGlobal;
716	>	ftGlobal.resize(count);
717	>	vector<int> counts;
718	>
719	>	int nproc = MPI::COMM_WORLD.Get_size();
720	>	counts.resize(nproc);
721	>	vector<int> disps;
722	>	disps.resize(nproc);
723	>
724	>	// now spray out the foundTypes to all the other processors:
725
726	<	if (simParams_->haveAccumulateBoxDipole())
727	<	if (simParams_->getAccumulateBoxDipole())
783	<	useBoxDipole = 1;
726	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
727	>	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
728
729	+	// foundIdents is a stl set, so inserting an already found ident
730	+	// will have no effect.
731	+	set<int> foundIdents;
732	+	vector<int>::iterator j;
733	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
734	+	foundIdents.insert((*j));
735	+
736	+	// now iterate over the foundIdents and get the actual atom types
737	+	// that correspond to these:
738	+	set<int>::iterator it;
739	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
740	+	atomTypes.insert( forceField_->getAtomType((*it)) );
741	+
742	+	#endif
743	+
744	+	return atomTypes;
745	+	}
746	+
747	+	void SimInfo::setupSimVariables() {
748		useAtomicVirial_ = simParams_->getUseAtomicVirial();
749	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
750	+	calcBoxDipole_ = false;
751	+	if ( simParams_->haveAccumulateBoxDipole() )
752	+	if ( simParams_->getAccumulateBoxDipole() ) {
753	+	calcBoxDipole_ = true;
754	+	}
755
756	+	set<AtomType*>::iterator i;
757	+	set<AtomType*> atomTypes;
758	+	atomTypes = getSimulatedAtomTypes();
759	+	int usesElectrostatic = 0;
760	+	int usesMetallic = 0;
761	+	int usesDirectional = 0;
762		//loop over all of the atom types
763		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
764	<	useLennardJones |= (*i)->isLennardJones();
765	<	useElectrostatic |= (*i)->isElectrostatic();
766	<	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();
764	>	usesElectrostatic |= (*i)->isElectrostatic();
765	>	usesMetallic |= (*i)->isMetal();
766	>	usesDirectional |= (*i)->isDirectional();
767		}
768
802	–	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
803	–	useDirectionalAtom = 1;
804	–	}
805	–
806	–	if (useCharge || useDipole) {
807	–	useElectrostatics = 1;
808	–	}
809	–
769		#ifdef IS_MPI
770		int temp;
771	+	temp = usesDirectional;
772	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
773
774	<	temp = usePBC;
775	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
774	>	temp = usesMetallic;
775	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776
777	<	temp = useDirectionalAtom;
778	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
777	>	temp = usesElectrostatic;
778	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
779	>	#endif
780	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
781	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
782	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
783	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
784	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
785	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
786	>	}
787
819	–	temp = useLennardJones;
820	–	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
788
789	<	temp = useElectrostatics;
790	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
789	>	vector<int> SimInfo::getGlobalAtomIndices() {
790	>	SimInfo::MoleculeIterator mi;
791	>	Molecule* mol;
792	>	Molecule::AtomIterator ai;
793	>	Atom* atom;
794
795	<	temp = useCharge;
796	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
795	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
796	>
797	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
798	>
799	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
800	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
801	>	}
802	>	}
803	>	return GlobalAtomIndices;
804	>	}
805
828	–	temp = useDipole;
829	–	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
806
807	<	temp = useSticky;
808	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
809	<
810	<	temp = useStickyPower;
811	<	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);
807	>	vector<int> SimInfo::getGlobalGroupIndices() {
808	>	SimInfo::MoleculeIterator mi;
809	>	Molecule* mol;
810	>	Molecule::CutoffGroupIterator ci;
811	>	CutoffGroup* cg;
812
813	<	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);
813	>	vector<int> GlobalGroupIndices;
814
815	<	temp = useShape;
816	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
817	<
818	<	temp = useFLARB;
819	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
820	<
821	<	temp = useRF;
822	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
823	<
824	<	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	<
867	<	#endif
868	<
869	<	fInfo_.SIM_uses_PBC = usePBC;
870	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
871	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
872	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
873	<	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_;
815	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
816	>
817	>	//local index of cutoff group is trivial, it only depends on the
818	>	//order of travesing
819	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
820	>	cg = mol->nextCutoffGroup(ci)) {
821	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
822	>	}
823	>	}
824	>	return GlobalGroupIndices;
825		}
826
827	<	void SimInfo::setupFortranSim() {
827	>
828	>	void SimInfo::setupFortran() {
829		int isError;
830		int nExclude, nOneTwo, nOneThree, nOneFour;
831	<	std::vector<int> fortranGlobalGroupMembership;
831	>	vector<int> fortranGlobalGroupMembership;
832
833		isError = 0;
834
#	Line 899 | Line 838 | namespace OpenMD {
838		}
839
840		//calculate mass ratio of cutoff group
841	<	std::vector<RealType> mfact;
841	>	vector<RealType> mfact;
842		SimInfo::MoleculeIterator mi;
843		Molecule* mol;
844		Molecule::CutoffGroupIterator ci;
#	Line 925 | Line 864 | namespace OpenMD {
864		}
865		}
866
867	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
929	<	std::vector<int> identArray;
867	>	// Build the identArray_
868
869	<	//to avoid memory reallocation, reserve enough space identArray
870	<	identArray.reserve(getNAtoms());
933	<
869	>	identArray_.clear();
870	>	identArray_.reserve(getNAtoms());
871		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
872		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
873	<	identArray.push_back(atom->getIdent());
873	>	identArray_.push_back(atom->getIdent());
874		}
875		}
876
877		//fill molMembershipArray
878		//molMembershipArray is filled by SimCreator
879	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
879	>	vector<int> molMembershipArray(nGlobalAtoms_);
880		for (int i = 0; i < nGlobalAtoms_; i++) {
881		molMembershipArray[i] = globalMolMembership_[i] + 1;
882		}
#	Line 956 | Line 893 | namespace OpenMD {
893		int* oneThreeList = oneThreeInteractions_.getPairList();
894		int* oneFourList = oneFourInteractions_.getPairList();
895
896	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
896	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0],
897		&nExclude, excludeList,
898		&nOneTwo, oneTwoList,
899		&nOneThree, oneThreeList,
#	Line 985 | Line 922 | namespace OpenMD {
922		setNeighbors(&nlistNeighbors);
923		}
924
988	–
989	–	}
990	–
991	–
992	–	void SimInfo::setupFortranParallel() {
925		#ifdef IS_MPI
994	–	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
995	–	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
996	–	std::vector<int> localToGlobalCutoffGroupIndex;
997	–	SimInfo::MoleculeIterator mi;
998	–	Molecule::AtomIterator ai;
999	–	Molecule::CutoffGroupIterator ci;
1000	–	Molecule* mol;
1001	–	Atom* atom;
1002	–	CutoffGroup* cg;
926		mpiSimData parallelData;
1004	–	int isError;
927
1006	–	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1007	–
1008	–	//local index(index in DataStorge) of atom is important
1009	–	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1010	–	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1011	–	}
1012	–
1013	–	//local index of cutoff group is trivial, it only depends on the order of travesing
1014	–	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1015	–	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1016	–	}
1017	–
1018	–	}
1019	–
928		//fill up mpiSimData struct
929		parallelData.nMolGlobal = getNGlobalMolecules();
930		parallelData.nMolLocal = getNMolecules();
#	Line 1028 | Line 936 | namespace OpenMD {
936		MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
937
938		//pass mpiSimData struct and index arrays to fortran
939	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
940	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
941	<	&localToGlobalCutoffGroupIndex[0], &isError);
939	>	//setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
940	>	//                &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
941	>	//                &localToGlobalCutoffGroupIndex[0], &isError);
942
943		if (isError) {
944		sprintf(painCave.errMsg,
#	Line 1041 | Line 949 | namespace OpenMD {
949
950		sprintf(checkPointMsg, " mpiRefresh successful.\n");
951		errorCheckPoint();
1044	–
952		#endif
1046	–	}
953
954	<	void SimInfo::setupCutoff() {
955	<
956	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
957	<
958	<	// Check the cutoff policy
959	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1054	<
1055	<	// Set LJ shifting bools to false
1056	<	ljsp_ = 0;
1057	<	ljsf_ = 0;
1058	<
1059	<	std::string myPolicy;
1060	<	if (forceFieldOptions_.haveCutoffPolicy()){
1061	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
1062	<	}else if (simParams_->haveCutoffPolicy()) {
1063	<	myPolicy = simParams_->getCutoffPolicy();
954	>	initFortranFF(&isError);
955	>	if (isError) {
956	>	sprintf(painCave.errMsg,
957	>	"initFortranFF errror: fortran didn't like something we gave it.\n");
958	>	painCave.isFatal = 1;
959	>	simError();
960		}
961	<
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	<	"\tOpenMD 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	<	"\tOpenMD 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_ = 1;
1129	<	} else if (myMethod == "SHIFTED_FORCE") {
1130	<	ljsf_ = 1;
1131	<	}
1132	<	}
1133	<
1134	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1135	<
1136	<	} else {
1137	<
1138	<	// For electrostatic atoms, we'll assume a large safe value:
1139	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1140	<	sprintf(painCave.errMsg,
1141	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1142	<	"\tOpenMD will use a default value of 15.0 angstroms"
1143	<	"\tfor the cutoffRadius.\n");
1144	<	painCave.isFatal = 0;
1145	<	simError();
1146	<	rcut_ = 15.0;
1147	<
1148	<	if (simParams_->haveElectrostaticSummationMethod()) {
1149	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1150	<	toUpper(myMethod);
1151	<
1152	<	// For the time being, we're tethering the LJ shifted behavior to the
1153	<	// electrostaticSummationMethod keyword options
1154	<	if (myMethod == "SHIFTED_POTENTIAL") {
1155	<	ljsp_ = 1;
1156	<	} else if (myMethod == "SHIFTED_FORCE") {
1157	<	ljsf_ = 1;
1158	<	}
1159	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1160	<	if (simParams_->haveSwitchingRadius()){
1161	<	sprintf(painCave.errMsg,
1162	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1163	<	"\teven though the electrostaticSummationMethod was\n"
1164	<	"\tset to %s\n", myMethod.c_str());
1165	<	painCave.isFatal = 1;
1166	<	simError();
1167	<	}
1168	<	}
1169	<	}
1170	<
1171	<	if (simParams_->haveSwitchingRadius()){
1172	<	rsw_ = simParams_->getSwitchingRadius();
1173	<	} else {
1174	<	sprintf(painCave.errMsg,
1175	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1176	<	"\tOpenMD will use a default value of\n"
1177	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1178	<	painCave.isFatal = 0;
1179	<	simError();
1180	<	rsw_ = 0.85 * rcut_;
1181	<	}
1182	<
1183	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1184	<
1185	<	} else {
1186	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1187	<	// We'll punt and let fortran figure out the cutoffs later.
1188	<
1189	<	notifyFortranYouAreOnYourOwn();
1190	<
1191	<	}
1192	<	}
1193	<	}
1194	<
1195	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1196	<
1197	<	int errorOut;
1198	<	int esm =  NONE;
1199	<	int sm = UNDAMPED;
1200	<	RealType alphaVal;
1201	<	RealType dielectric;
1202	<
1203	<	errorOut = isError;
1204	<
1205	<	if (simParams_->haveElectrostaticSummationMethod()) {
1206	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1207	<	toUpper(myMethod);
1208	<	if (myMethod == "NONE") {
1209	<	esm = NONE;
1210	<	} else {
1211	<	if (myMethod == "SWITCHING_FUNCTION") {
1212	<	esm = SWITCHING_FUNCTION;
1213	<	} else {
1214	<	if (myMethod == "SHIFTED_POTENTIAL") {
1215	<	esm = SHIFTED_POTENTIAL;
1216	<	} else {
1217	<	if (myMethod == "SHIFTED_FORCE") {
1218	<	esm = SHIFTED_FORCE;
1219	<	} else {
1220	<	if (myMethod == "REACTION_FIELD") {
1221	<	esm = REACTION_FIELD;
1222	<	dielectric = simParams_->getDielectric();
1223	<	if (!simParams_->haveDielectric()) {
1224	<	// throw warning
1225	<	sprintf( painCave.errMsg,
1226	<	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1227	<	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1228	<	painCave.isFatal = 0;
1229	<	simError();
1230	<	}
1231	<	} else {
1232	<	// throw error
1233	<	sprintf( painCave.errMsg,
1234	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1235	<	"\t(Input file specified %s .)\n"
1236	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1237	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1238	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1239	<	painCave.isFatal = 1;
1240	<	simError();
1241	<	}
1242	<	}
1243	<	}
1244	<	}
1245	<	}
1246	<	}
1247	<
1248	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1249	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1250	<	toUpper(myScreen);
1251	<	if (myScreen == "UNDAMPED") {
1252	<	sm = UNDAMPED;
1253	<	} else {
1254	<	if (myScreen == "DAMPED") {
1255	<	sm = DAMPED;
1256	<	if (!simParams_->haveDampingAlpha()) {
1257	<	// first set a cutoff dependent alpha value
1258	<	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1259	<	alphaVal = 0.5125 - rcut_* 0.025;
1260	<	// for values rcut > 20.5, alpha is zero
1261	<	if (alphaVal < 0) alphaVal = 0;
1262	<
1263	<	// throw warning
1264	<	sprintf( painCave.errMsg,
1265	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1266	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1267	<	painCave.isFatal = 0;
1268	<	simError();
1269	<	} else {
1270	<	alphaVal = simParams_->getDampingAlpha();
1271	<	}
1272	<
1273	<	} else {
1274	<	// throw error
1275	<	sprintf( painCave.errMsg,
1276	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1277	<	"\t(Input file specified %s .)\n"
1278	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1279	<	"or \"damped\".\n", myScreen.c_str() );
1280	<	painCave.isFatal = 1;
1281	<	simError();
1282	<	}
1283	<	}
1284	<	}
1285	<
1286	<	// let's pass some summation method variables to fortran
1287	<	setElectrostaticSummationMethod( &esm );
1288	<	setFortranElectrostaticMethod( &esm );
1289	<	setScreeningMethod( &sm );
1290	<	setDampingAlpha( &alphaVal );
1291	<	setReactionFieldDielectric( &dielectric );
1292	<	initFortranFF( &errorOut );
1293	<	}
1294	<
1295	<	void SimInfo::setupSwitchingFunction() {
1296	<	int ft = CUBIC;
1297	<
1298	<	if (simParams_->haveSwitchingFunctionType()) {
1299	<	std::string funcType = simParams_->getSwitchingFunctionType();
1300	<	toUpper(funcType);
1301	<	if (funcType == "CUBIC") {
1302	<	ft = CUBIC;
1303	<	} else {
1304	<	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1305	<	ft = FIFTH_ORDER_POLY;
1306	<	} else {
1307	<	// throw error
1308	<	sprintf( painCave.errMsg,
1309	<	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1310	<	painCave.isFatal = 1;
1311	<	simError();
1312	<	}
1313	<	}
1314	<	}
1315	<
1316	<	// send switching function notification to switcheroo
1317	<	setFunctionType(&ft);
1318	<
961	>	fortranInitialized_ = true;
962		}
963
1321	–	void SimInfo::setupAccumulateBoxDipole() {
1322	–
1323	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1324	–	if ( simParams_->haveAccumulateBoxDipole() )
1325	–	if ( simParams_->getAccumulateBoxDipole() ) {
1326	–	setAccumulateBoxDipole();
1327	–	calcBoxDipole_ = true;
1328	–	}
1329	–
1330	–	}
1331	–
964		void SimInfo::addProperty(GenericData* genData) {
965		properties_.addProperty(genData);
966		}
967
968	<	void SimInfo::removeProperty(const std::string& propName) {
968	>	void SimInfo::removeProperty(const string& propName) {
969		properties_.removeProperty(propName);
970		}
971
#	Line 1341 | Line 973 | namespace OpenMD {
973		properties_.clearProperties();
974		}
975
976	<	std::vector<std::string> SimInfo::getPropertyNames() {
976	>	vector<string> SimInfo::getPropertyNames() {
977		return properties_.getPropertyNames();
978		}
979
980	<	std::vector<GenericData*> SimInfo::getProperties() {
980	>	vector<GenericData*> SimInfo::getProperties() {
981		return properties_.getProperties();
982		}
983
984	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
984	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
985		return properties_.getPropertyByName(propName);
986		}
987
#	Line 1363 | Line 995 | namespace OpenMD {
995		Molecule* mol;
996		RigidBody* rb;
997		Atom* atom;
998	+	CutoffGroup* cg;
999		SimInfo::MoleculeIterator mi;
1000		Molecule::RigidBodyIterator rbIter;
1001	<	Molecule::AtomIterator atomIter;;
1001	>	Molecule::AtomIterator atomIter;
1002	>	Molecule::CutoffGroupIterator cgIter;
1003
1004		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1005
#	Line 1376 | Line 1010 | namespace OpenMD {
1010		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1011		rb->setSnapshotManager(sman_);
1012		}
1013	+
1014	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
1015	+	cg->setSnapshotManager(sman_);
1016	+	}
1017		}
1018
1019		}
#	Line 1432 | Line 1070 | namespace OpenMD {
1070
1071		}
1072
1073	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1073	>	ostream& operator <<(ostream& o, SimInfo& info) {
1074
1075		return o;
1076		}
#	Line 1475 | Line 1113 | namespace OpenMD {
1113
1114
1115		[  Ixx -Ixy  -Ixz ]
1116	<	J =| -Iyx  Iyy  -Iyz |
1116	>	J =| -Iyx  Iyy  -Iyz |
1117		[ -Izx -Iyz   Izz ]
1118		*/
1119
#	Line 1582 | Line 1220 | namespace OpenMD {
1220		return IOIndexToIntegrableObject.at(index);
1221		}
1222
1223	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1223	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1224		IOIndexToIntegrableObject= v;
1225		}
1226
#	Line 1624 | Line 1262 | namespace OpenMD {
1262		return;
1263		}
1264		/*
1265	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1265	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1266		assert( v.size() == nAtoms_ + nRigidBodies_);
1267		sdByGlobalIndex_ = v;
1268		}
#	Line 1634 | Line 1272 | namespace OpenMD {
1272		return sdByGlobalIndex_.at(index);
1273		}
1274		*/
1275	+	int SimInfo::getNGlobalConstraints() {
1276	+	int nGlobalConstraints;
1277	+	#ifdef IS_MPI
1278	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1279	+	MPI_COMM_WORLD);
1280	+	#else
1281	+	nGlobalConstraints =  nConstraints_;
1282	+	#endif
1283	+	return nGlobalConstraints;
1284	+	}
1285	+
1286		}//end namespace OpenMD
1287

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1549 by gezelter, Wed Apr 27 18:38:15 2011 UTC

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