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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 1287 by gezelter, Wed Sep 10 18:11:32 2008 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 54 | Line 54
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56		#include "primitives/StuntDouble.hpp"
57	–	#include "UseTheForce/fCutoffPolicy.h"
58	–	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	–	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60	–	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61	–	#include "UseTheForce/doForces_interface.h"
62	–	#include "UseTheForce/DarkSide/neighborLists_interface.h"
63	–	#include "UseTheForce/DarkSide/electrostatic_interface.h"
64	–	#include "UseTheForce/DarkSide/switcheroo_interface.h"
57		#include "utils/MemoryUtils.hpp"
58		#include "utils/simError.h"
59		#include "selection/SelectionManager.hpp"
60		#include "io/ForceFieldOptions.hpp"
61		#include "UseTheForce/ForceField.hpp"
62	+	#include "nonbonded/SwitchingFunction.hpp"
63
64	<
65	<	#ifdef IS_MPI
73	<	#include "UseTheForce/mpiComponentPlan.h"
74	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
75	<	#endif
76	<
77	<	namespace oopse {
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	<	}
64	>	using namespace std;
65	>	namespace OpenMD {
66
67		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
68		forceField_(ff), simParams_(simParams),
#	Line 92 | Line 71 | namespace oopse {
71		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
72		nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
73		nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
74	<	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
75	<	calcBoxDipole_(false), useAtomicVirial_(true) {
76	<
77	<
78	<	MoleculeStamp* molStamp;
79	<	int nMolWithSameStamp;
80	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
81	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
82	<	CutoffGroupStamp* cgStamp;
83	<	RigidBodyStamp* rbStamp;
84	<	int nRigidAtoms = 0;
85	<
86	<	std::vector<Component*> components = simParams->getComponents();
74	>	nConstraints_(0), sman_(NULL), topologyDone_(false),
75	>	calcBoxDipole_(false), useAtomicVirial_(true) {
76	>
77	>	MoleculeStamp* molStamp;
78	>	int nMolWithSameStamp;
79	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
80	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
81	>	CutoffGroupStamp* cgStamp;
82	>	RigidBodyStamp* rbStamp;
83	>	int nRigidAtoms = 0;
84	>
85	>	vector<Component*> components = simParams->getComponents();
86	>
87	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
88	>	molStamp = (*i)->getMoleculeStamp();
89	>	nMolWithSameStamp = (*i)->getNMol();
90
91	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
92	<	molStamp = (*i)->getMoleculeStamp();
93	<	nMolWithSameStamp = (*i)->getNMol();
94	<
95	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
96	<
97	<	//calculate atoms in molecules
98	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
99	<
100	<	//calculate atoms in cutoff groups
101	<	int nAtomsInGroups = 0;
102	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
103	<
104	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
105	<	cgStamp = molStamp->getCutoffGroupStamp(j);
106	<	nAtomsInGroups += cgStamp->getNMembers();
107	<	}
108	<
109	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
110	<
111	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
112	<
113	<	//calculate atoms in rigid bodies
114	<	int nAtomsInRigidBodies = 0;
115	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
116	<
117	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
118	<	rbStamp = molStamp->getRigidBodyStamp(j);
119	<	nAtomsInRigidBodies += rbStamp->getNMembers();
120	<	}
139	<
140	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
141	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
142	<
143	<	}
144	<
145	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
146	<	//group therefore the total number of cutoff groups in the system is
147	<	//equal to the total number of atoms minus number of atoms belong to
148	<	//cutoff group defined in meta-data file plus the number of cutoff
149	<	//groups defined in meta-data file
150	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
151	<
152	<	//every free atom (atom does not belong to rigid bodies) is an
153	<	//integrable object therefore the total number of integrable objects
154	<	//in the system is equal to the total number of atoms minus number of
155	<	//atoms belong to rigid body defined in meta-data file plus the number
156	<	//of rigid bodies defined in meta-data file
157	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
158	<	+ nGlobalRigidBodies_;
159	<
160	<	nGlobalMols_ = molStampIds_.size();
161	<	molToProcMap_.resize(nGlobalMols_);
91	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
92	>
93	>	//calculate atoms in molecules
94	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
95	>
96	>	//calculate atoms in cutoff groups
97	>	int nAtomsInGroups = 0;
98	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
99	>
100	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
101	>	cgStamp = molStamp->getCutoffGroupStamp(j);
102	>	nAtomsInGroups += cgStamp->getNMembers();
103	>	}
104	>
105	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
106	>
107	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
108	>
109	>	//calculate atoms in rigid bodies
110	>	int nAtomsInRigidBodies = 0;
111	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
112	>
113	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
114	>	rbStamp = molStamp->getRigidBodyStamp(j);
115	>	nAtomsInRigidBodies += rbStamp->getNMembers();
116	>	}
117	>
118	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
119	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
120	>
121		}
122	+
123	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
124	+	//group therefore the total number of cutoff groups in the system is
125	+	//equal to the total number of atoms minus number of atoms belong to
126	+	//cutoff group defined in meta-data file plus the number of cutoff
127	+	//groups defined in meta-data file
128	+	std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
129	+	std::cerr << "nCA = " << nCutoffAtoms << "\n";
130	+	std::cerr << "nG = " << nGroups << "\n";
131
132	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
133	+
134	+	std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
135	+
136	+	//every free atom (atom does not belong to rigid bodies) is an
137	+	//integrable object therefore the total number of integrable objects
138	+	//in the system is equal to the total number of atoms minus number of
139	+	//atoms belong to rigid body defined in meta-data file plus the number
140	+	//of rigid bodies defined in meta-data file
141	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
142	+	+ nGlobalRigidBodies_;
143	+
144	+	nGlobalMols_ = molStampIds_.size();
145	+	molToProcMap_.resize(nGlobalMols_);
146	+	}
147	+
148		SimInfo::~SimInfo() {
149	<	std::map<int, Molecule*>::iterator i;
149	>	map<int, Molecule*>::iterator i;
150		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
151		delete i->second;
152		}
#	Line 173 | Line 157 | namespace oopse {
157		delete forceField_;
158		}
159
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	–	}
160
161		bool SimInfo::addMolecule(Molecule* mol) {
162		MoleculeIterator i;
163	<
163	>
164		i = molecules_.find(mol->getGlobalIndex());
165		if (i == molecules_.end() ) {
166	<
167	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
168	<
166	>
167	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
168	>
169		nAtoms_ += mol->getNAtoms();
170		nBonds_ += mol->getNBonds();
171		nBends_ += mol->getNBends();
#	Line 201 | Line 175 | namespace oopse {
175		nIntegrableObjects_ += mol->getNIntegrableObjects();
176		nCutoffGroups_ += mol->getNCutoffGroups();
177		nConstraints_ += mol->getNConstraintPairs();
178	<
178	>
179		addInteractionPairs(mol);
180	<
180	>
181		return true;
182		} else {
183		return false;
184		}
185		}
186	<
186	>
187		bool SimInfo::removeMolecule(Molecule* mol) {
188		MoleculeIterator i;
189		i = molecules_.find(mol->getGlobalIndex());
#	Line 237 | Line 211 | namespace oopse {
211		} else {
212		return false;
213		}
240	–
241	–
214		}
215
216
#	Line 256 | Line 228 | namespace oopse {
228		void SimInfo::calcNdf() {
229		int ndf_local;
230		MoleculeIterator i;
231	<	std::vector<StuntDouble*>::iterator j;
231	>	vector<StuntDouble*>::iterator j;
232		Molecule* mol;
233		StuntDouble* integrableObject;
234
#	Line 307 | Line 279 | namespace oopse {
279		int ndfRaw_local;
280
281		MoleculeIterator i;
282	<	std::vector<StuntDouble*>::iterator j;
282	>	vector<StuntDouble*>::iterator j;
283		Molecule* mol;
284		StuntDouble* integrableObject;
285
#	Line 356 | Line 328 | namespace oopse {
328
329		void SimInfo::addInteractionPairs(Molecule* mol) {
330		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
331	<	std::vector<Bond*>::iterator bondIter;
332	<	std::vector<Bend*>::iterator bendIter;
333	<	std::vector<Torsion*>::iterator torsionIter;
334	<	std::vector<Inversion*>::iterator inversionIter;
331	>	vector<Bond*>::iterator bondIter;
332	>	vector<Bend*>::iterator bendIter;
333	>	vector<Torsion*>::iterator torsionIter;
334	>	vector<Inversion*>::iterator inversionIter;
335		Bond* bond;
336		Bend* bend;
337		Torsion* torsion;
#	Line 377 | Line 349 | namespace oopse {
349		// always be excluded.  These are done at the bottom of this
350		// function.
351
352	<	std::map<int, std::set<int> > atomGroups;
352	>	map<int, set<int> > atomGroups;
353		Molecule::RigidBodyIterator rbIter;
354		RigidBody* rb;
355		Molecule::IntegrableObjectIterator ii;
#	Line 389 | Line 361 | namespace oopse {
361
362		if (integrableObject->isRigidBody()) {
363		rb = static_cast<RigidBody*>(integrableObject);
364	<	std::vector<Atom*> atoms = rb->getAtoms();
365	<	std::set<int> rigidAtoms;
364	>	vector<Atom*> atoms = rb->getAtoms();
365	>	set<int> rigidAtoms;
366		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
367		rigidAtoms.insert(atoms[i]->getGlobalIndex());
368		}
369		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
370	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
370	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
371		}
372		} else {
373	<	std::set<int> oneAtomSet;
373	>	set<int> oneAtomSet;
374		oneAtomSet.insert(integrableObject->getGlobalIndex());
375	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
375	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
376		}
377		}
378
#	Line 446 | Line 418 | namespace oopse {
418		b = torsion->getAtomB()->getGlobalIndex();
419		c = torsion->getAtomC()->getGlobalIndex();
420		d = torsion->getAtomD()->getGlobalIndex();
421	<
421	>
422		if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
423		oneTwoInteractions_.addPair(a, b);
424		oneTwoInteractions_.addPair(b, c);
#	Line 503 | Line 475 | namespace oopse {
475
476		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
477		rb = mol->nextRigidBody(rbIter)) {
478	<	std::vector<Atom*> atoms = rb->getAtoms();
478	>	vector<Atom*> atoms = rb->getAtoms();
479		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
480		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
481		a = atoms[i]->getGlobalIndex();
#	Line 517 | Line 489 | namespace oopse {
489
490		void SimInfo::removeInteractionPairs(Molecule* mol) {
491		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
492	<	std::vector<Bond*>::iterator bondIter;
493	<	std::vector<Bend*>::iterator bendIter;
494	<	std::vector<Torsion*>::iterator torsionIter;
495	<	std::vector<Inversion*>::iterator inversionIter;
492	>	vector<Bond*>::iterator bondIter;
493	>	vector<Bend*>::iterator bendIter;
494	>	vector<Torsion*>::iterator torsionIter;
495	>	vector<Inversion*>::iterator inversionIter;
496		Bond* bond;
497		Bend* bend;
498		Torsion* torsion;
#	Line 530 | Line 502 | namespace oopse {
502		int c;
503		int d;
504
505	<	std::map<int, std::set<int> > atomGroups;
505	>	map<int, set<int> > atomGroups;
506		Molecule::RigidBodyIterator rbIter;
507		RigidBody* rb;
508		Molecule::IntegrableObjectIterator ii;
#	Line 542 | Line 514 | namespace oopse {
514
515		if (integrableObject->isRigidBody()) {
516		rb = static_cast<RigidBody*>(integrableObject);
517	<	std::vector<Atom*> atoms = rb->getAtoms();
518	<	std::set<int> rigidAtoms;
517	>	vector<Atom*> atoms = rb->getAtoms();
518	>	set<int> rigidAtoms;
519		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
520		rigidAtoms.insert(atoms[i]->getGlobalIndex());
521		}
522		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
523	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
523	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
524		}
525		} else {
526	<	std::set<int> oneAtomSet;
526	>	set<int> oneAtomSet;
527		oneAtomSet.insert(integrableObject->getGlobalIndex());
528	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
528	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
529		}
530		}
531
#	Line 656 | Line 628 | namespace oopse {
628
629		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
630		rb = mol->nextRigidBody(rbIter)) {
631	<	std::vector<Atom*> atoms = rb->getAtoms();
631	>	vector<Atom*> atoms = rb->getAtoms();
632		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
633		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
634		a = atoms[i]->getGlobalIndex();
#	Line 679 | Line 651 | namespace oopse {
651		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
652		}
653
682	–	void SimInfo::update() {
654
655	<	setupSimType();
656	<
657	<	#ifdef IS_MPI
658	<	setupFortranParallel();
659	<	#endif
660	<
661	<	setupFortranSim();
662	<
663	<	//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	<
655	>	/**
656	>	* update
657	>	*
658	>	*  Performs the global checks and variable settings after the
659	>	*  objects have been created.
660	>	*
661	>	*/
662	>	void SimInfo::update() {
663	>	setupSimVariables();
664		calcNdf();
665		calcNdfRaw();
666		calcNdfTrans();
712	–
713	–	fortranInitialized_ = true;
667		}
668	<
669	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
668	>
669	>	/**
670	>	* getSimulatedAtomTypes
671	>	*
672	>	* Returns an STL set of AtomType* that are actually present in this
673	>	* simulation.  Must query all processors to assemble this information.
674	>	*
675	>	*/
676	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
677		SimInfo::MoleculeIterator mi;
678		Molecule* mol;
679		Molecule::AtomIterator ai;
680		Atom* atom;
681	<	std::set<AtomType*> atomTypes;
682	<
683	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
724	<
681	>	set<AtomType*> atomTypes;
682	>
683	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
684		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
685		atomTypes.insert(atom->getAtomType());
686	<	}
687	<
729	<	}
686	>	}
687	>	}
688
689	<	return atomTypes;
732	<	}
689	>	#ifdef IS_MPI
690
691	<	void SimInfo::setupSimType() {
692	<	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;
691	>	// loop over the found atom types on this processor, and add their
692	>	// numerical idents to a vector:
693
694	<	std::string myMethod;
694	>	vector<int> foundTypes;
695	>	set<AtomType*>::iterator i;
696	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
697	>	foundTypes.push_back( (*i)->getIdent() );
698
699	<	// set the useRF logical
700	<	useRF = 0;
764	<	useSF = 0;
765	<	useSP = 0;
699	>	// count_local holds the number of found types on this processor
700	>	int count_local = foundTypes.size();
701
702	+	// count holds the total number of found types on all processors
703	+	// (some will be redundant with the ones found locally):
704	+	int count;
705	+	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
706
707	<	if (simParams_->haveElectrostaticSummationMethod()) {
708	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
709	<	toUpper(myMethod);
710	<	if (myMethod == "REACTION_FIELD"){
711	<	useRF = 1;
712	<	} else if (myMethod == "SHIFTED_FORCE"){
713	<	useSF = 1;
714	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
715	<	useSP = 1;
716	<	}
717	<	}
707	>	// create a vector to hold the globally found types, and resize it:
708	>	vector<int> ftGlobal;
709	>	ftGlobal.resize(count);
710	>	vector<int> counts;
711	>
712	>	int nproc = MPI::COMM_WORLD.Get_size();
713	>	counts.resize(nproc);
714	>	vector<int> disps;
715	>	disps.resize(nproc);
716	>
717	>	// now spray out the foundTypes to all the other processors:
718
719	<	if (simParams_->haveAccumulateBoxDipole())
720	<	if (simParams_->getAccumulateBoxDipole())
782	<	useBoxDipole = 1;
719	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
720	>	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
721
722	+	// foundIdents is a stl set, so inserting an already found ident
723	+	// will have no effect.
724	+	set<int> foundIdents;
725	+	vector<int>::iterator j;
726	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
727	+	foundIdents.insert((*j));
728	+
729	+	// now iterate over the foundIdents and get the actual atom types
730	+	// that correspond to these:
731	+	set<int>::iterator it;
732	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
733	+	atomTypes.insert( forceField_->getAtomType((*it)) );
734	+
735	+	#endif
736	+
737	+	return atomTypes;
738	+	}
739	+
740	+	void SimInfo::setupSimVariables() {
741		useAtomicVirial_ = simParams_->getUseAtomicVirial();
742	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
743	+	calcBoxDipole_ = false;
744	+	if ( simParams_->haveAccumulateBoxDipole() )
745	+	if ( simParams_->getAccumulateBoxDipole() ) {
746	+	calcBoxDipole_ = true;
747	+	}
748
749	+	set<AtomType*>::iterator i;
750	+	set<AtomType*> atomTypes;
751	+	atomTypes = getSimulatedAtomTypes();
752	+	int usesElectrostatic = 0;
753	+	int usesMetallic = 0;
754	+	int usesDirectional = 0;
755		//loop over all of the atom types
756		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
757	<	useLennardJones |= (*i)->isLennardJones();
758	<	useElectrostatic |= (*i)->isElectrostatic();
759	<	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();
757	>	usesElectrostatic |= (*i)->isElectrostatic();
758	>	usesMetallic |= (*i)->isMetal();
759	>	usesDirectional |= (*i)->isDirectional();
760		}
761
801	–	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
802	–	useDirectionalAtom = 1;
803	–	}
804	–
805	–	if (useCharge || useDipole) {
806	–	useElectrostatics = 1;
807	–	}
808	–
762		#ifdef IS_MPI
763		int temp;
764	+	temp = usesDirectional;
765	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766
767	<	temp = usePBC;
768	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767	>	temp = usesMetallic;
768	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769
770	<	temp = useDirectionalAtom;
771	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770	>	temp = usesElectrostatic;
771	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
772	>	#endif
773	>	}
774
818	–	temp = useLennardJones;
819	–	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
775
776	<	temp = useElectrostatics;
777	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776	>	vector<int> SimInfo::getGlobalAtomIndices() {
777	>	SimInfo::MoleculeIterator mi;
778	>	Molecule* mol;
779	>	Molecule::AtomIterator ai;
780	>	Atom* atom;
781
782	<	temp = useCharge;
783	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
782	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
783	>
784	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
785	>
786	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
787	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
788	>	}
789	>	}
790	>	return GlobalAtomIndices;
791	>	}
792
827	–	temp = useDipole;
828	–	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
793
794	<	temp = useSticky;
795	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
794	>	vector<int> SimInfo::getGlobalGroupIndices() {
795	>	SimInfo::MoleculeIterator mi;
796	>	Molecule* mol;
797	>	Molecule::CutoffGroupIterator ci;
798	>	CutoffGroup* cg;
799
800	<	temp = useStickyPower;
834	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
800	>	vector<int> GlobalGroupIndices;
801
802	<	temp = useGayBerne;
803	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
802	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
803	>
804	>	//local index of cutoff group is trivial, it only depends on the
805	>	//order of travesing
806	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
807	>	cg = mol->nextCutoffGroup(ci)) {
808	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
809	>	}
810	>	}
811	>	return GlobalGroupIndices;
812	>	}
813
839	–	temp = useEAM;
840	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814
815	<	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	<
866	<	#endif
867	<
868	<	fInfo_.SIM_uses_PBC = usePBC;
869	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
870	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
871	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
872	<	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_;
886	<	}
887	<
888	<	void SimInfo::setupFortranSim() {
889	<	int isError;
815	>	void SimInfo::prepareTopology() {
816		int nExclude, nOneTwo, nOneThree, nOneFour;
891	–	std::vector<int> fortranGlobalGroupMembership;
892	–
893	–	isError = 0;
817
895	–	//globalGroupMembership_ is filled by SimCreator
896	–	for (int i = 0; i < nGlobalAtoms_; i++) {
897	–	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
898	–	}
899	–
818		//calculate mass ratio of cutoff group
901	–	std::vector<RealType> mfact;
819		SimInfo::MoleculeIterator mi;
820		Molecule* mol;
821		Molecule::CutoffGroupIterator ci;
#	Line 907 | Line 824 | namespace oopse {
824		Atom* atom;
825		RealType totalMass;
826
827	<	//to avoid memory reallocation, reserve enough space for mfact
828	<	mfact.reserve(getNCutoffGroups());
827	>	//to avoid memory reallocation, reserve enough space for massFactors_
828	>	massFactors_.clear();
829	>	massFactors_.reserve(getNCutoffGroups());
830
831		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
832	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
832	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
833	>	cg = mol->nextCutoffGroup(ci)) {
834
835		totalMass = cg->getMass();
836		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
837		// Check for massless groups - set mfact to 1 if true
838		if (totalMass != 0)
839	<	mfact.push_back(atom->getMass()/totalMass);
839	>	massFactors_.push_back(atom->getMass()/totalMass);
840		else
841	<	mfact.push_back( 1.0 );
841	>	massFactors_.push_back( 1.0 );
842		}
843		}
844		}
845
846	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
928	<	std::vector<int> identArray;
846	>	// Build the identArray_
847
848	<	//to avoid memory reallocation, reserve enough space identArray
849	<	identArray.reserve(getNAtoms());
932	<
848	>	identArray_.clear();
849	>	identArray_.reserve(getNAtoms());
850		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
851		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
852	<	identArray.push_back(atom->getIdent());
852	>	identArray_.push_back(atom->getIdent());
853		}
854		}
938	–
939	–	//fill molMembershipArray
940	–	//molMembershipArray is filled by SimCreator
941	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
942	–	for (int i = 0; i < nGlobalAtoms_; i++) {
943	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
944	–	}
855
856	<	//setup fortran simulation
856	>	//scan topology
857
858		nExclude = excludedInteractions_.getSize();
859		nOneTwo = oneTwoInteractions_.getSize();
860		nOneThree = oneThreeInteractions_.getSize();
861		nOneFour = oneFourInteractions_.getSize();
862
953	–	std::cerr << "exculdes:\n";
954	–	std::cerr << excludedInteractions_;
955	–	std::cerr << "\noneTwo:\n";
956	–	std::cerr << oneTwoInteractions_;
957	–	std::cerr << "\noneThree:\n";
958	–	std::cerr << oneThreeInteractions_;
959	–	std::cerr << "\noneFour:\n";
960	–	std::cerr << oneFourInteractions_;
961	–
863		int* excludeList = excludedInteractions_.getPairList();
864		int* oneTwoList = oneTwoInteractions_.getPairList();
865		int* oneThreeList = oneThreeInteractions_.getPairList();
866		int* oneFourList = oneFourInteractions_.getPairList();
867
868	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
869	<	&nExclude, excludeList,
870	<	&nOneTwo, oneTwoList,
871	<	&nOneThree, oneThreeList,
872	<	&nOneFour, oneFourList,
873	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
874	<	&fortranGlobalGroupMembership[0], &isError);
868	>	//setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0],
869	>	//               &nExclude, excludeList,
870	>	//               &nOneTwo, oneTwoList,
871	>	//               &nOneThree, oneThreeList,
872	>	//               &nOneFour, oneFourList,
873	>	//               &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
874	>	//               &fortranGlobalGroupMembership[0], &isError);
875
876	<	if( isError ){
976	<
977	<	sprintf( painCave.errMsg,
978	<	"There was an error setting the simulation information in fortran.\n" );
979	<	painCave.isFatal = 1;
980	<	painCave.severity = OOPSE_ERROR;
981	<	simError();
982	<	}
983	<
984	<
985	<	sprintf( checkPointMsg,
986	<	"succesfully sent the simulation information to fortran.\n");
987	<
988	<	errorCheckPoint();
989	<
990	<	// Setup number of neighbors in neighbor list if present
991	<	if (simParams_->haveNeighborListNeighbors()) {
992	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
993	<	setNeighbors(&nlistNeighbors);
994	<	}
995	<
996	<
997	<	}
998	<
999	<
1000	<	void SimInfo::setupFortranParallel() {
1001	<	#ifdef IS_MPI
1002	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1003	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1004	<	std::vector<int> localToGlobalCutoffGroupIndex;
1005	<	SimInfo::MoleculeIterator mi;
1006	<	Molecule::AtomIterator ai;
1007	<	Molecule::CutoffGroupIterator ci;
1008	<	Molecule* mol;
1009	<	Atom* atom;
1010	<	CutoffGroup* cg;
1011	<	mpiSimData parallelData;
1012	<	int isError;
1013	<
1014	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1015	<
1016	<	//local index(index in DataStorge) of atom is important
1017	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1018	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1019	<	}
1020	<
1021	<	//local index of cutoff group is trivial, it only depends on the order of travesing
1022	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1023	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1024	<	}
1025	<
1026	<	}
1027	<
1028	<	//fill up mpiSimData struct
1029	<	parallelData.nMolGlobal = getNGlobalMolecules();
1030	<	parallelData.nMolLocal = getNMolecules();
1031	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
1032	<	parallelData.nAtomsLocal = getNAtoms();
1033	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1034	<	parallelData.nGroupsLocal = getNCutoffGroups();
1035	<	parallelData.myNode = worldRank;
1036	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1037	<
1038	<	//pass mpiSimData struct and index arrays to fortran
1039	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1040	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1041	<	&localToGlobalCutoffGroupIndex[0], &isError);
1042	<
1043	<	if (isError) {
1044	<	sprintf(painCave.errMsg,
1045	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1046	<	painCave.isFatal = 1;
1047	<	simError();
1048	<	}
1049	<
1050	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
1051	<	errorCheckPoint();
1052	<
1053	<	#endif
1054	<	}
1055	<
1056	<	void SimInfo::setupCutoff() {
1057	<
1058	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1059	<
1060	<	// Check the cutoff policy
1061	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1062	<
1063	<	// Set LJ shifting bools to false
1064	<	ljsp_ = false;
1065	<	ljsf_ = false;
1066	<
1067	<	std::string myPolicy;
1068	<	if (forceFieldOptions_.haveCutoffPolicy()){
1069	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
1070	<	}else if (simParams_->haveCutoffPolicy()) {
1071	<	myPolicy = simParams_->getCutoffPolicy();
1072	<	}
1073	<
1074	<	if (!myPolicy.empty()){
1075	<	toUpper(myPolicy);
1076	<	if (myPolicy == "MIX") {
1077	<	cp = MIX_CUTOFF_POLICY;
1078	<	} else {
1079	<	if (myPolicy == "MAX") {
1080	<	cp = MAX_CUTOFF_POLICY;
1081	<	} else {
1082	<	if (myPolicy == "TRADITIONAL") {
1083	<	cp = TRADITIONAL_CUTOFF_POLICY;
1084	<	} else {
1085	<	// throw error
1086	<	sprintf( painCave.errMsg,
1087	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1088	<	painCave.isFatal = 1;
1089	<	simError();
1090	<	}
1091	<	}
1092	<	}
1093	<	}
1094	<	notifyFortranCutoffPolicy(&cp);
1095	<
1096	<	// Check the Skin Thickness for neighborlists
1097	<	RealType skin;
1098	<	if (simParams_->haveSkinThickness()) {
1099	<	skin = simParams_->getSkinThickness();
1100	<	notifyFortranSkinThickness(&skin);
1101	<	}
1102	<
1103	<	// Check if the cutoff was set explicitly:
1104	<	if (simParams_->haveCutoffRadius()) {
1105	<	rcut_ = simParams_->getCutoffRadius();
1106	<	if (simParams_->haveSwitchingRadius()) {
1107	<	rsw_  = simParams_->getSwitchingRadius();
1108	<	} else {
1109	<	if (fInfo_.SIM_uses_Charges |
1110	<	fInfo_.SIM_uses_Dipoles |
1111	<	fInfo_.SIM_uses_RF) {
1112	<
1113	<	rsw_ = 0.85 * rcut_;
1114	<	sprintf(painCave.errMsg,
1115	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1116	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1117	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1118	<	painCave.isFatal = 0;
1119	<	simError();
1120	<	} else {
1121	<	rsw_ = rcut_;
1122	<	sprintf(painCave.errMsg,
1123	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1124	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
1125	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1126	<	painCave.isFatal = 0;
1127	<	simError();
1128	<	}
1129	<	}
1130	<
1131	<	if (simParams_->haveElectrostaticSummationMethod()) {
1132	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1133	<	toUpper(myMethod);
1134	<
1135	<	if (myMethod == "SHIFTED_POTENTIAL") {
1136	<	ljsp_ = true;
1137	<	} else if (myMethod == "SHIFTED_FORCE") {
1138	<	ljsf_ = true;
1139	<	}
1140	<	}
1141	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1142	<
1143	<	} else {
1144	<
1145	<	// For electrostatic atoms, we'll assume a large safe value:
1146	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1147	<	sprintf(painCave.errMsg,
1148	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1149	<	"\tOOPSE will use a default value of 15.0 angstroms"
1150	<	"\tfor the cutoffRadius.\n");
1151	<	painCave.isFatal = 0;
1152	<	simError();
1153	<	rcut_ = 15.0;
1154	<
1155	<	if (simParams_->haveElectrostaticSummationMethod()) {
1156	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1157	<	toUpper(myMethod);
1158	<
1159	<	// For the time being, we're tethering the LJ shifted behavior to the
1160	<	// electrostaticSummationMethod keyword options
1161	<	if (myMethod == "SHIFTED_POTENTIAL") {
1162	<	ljsp_ = true;
1163	<	} else if (myMethod == "SHIFTED_FORCE") {
1164	<	ljsf_ = true;
1165	<	}
1166	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1167	<	if (simParams_->haveSwitchingRadius()){
1168	<	sprintf(painCave.errMsg,
1169	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1170	<	"\teven though the electrostaticSummationMethod was\n"
1171	<	"\tset to %s\n", myMethod.c_str());
1172	<	painCave.isFatal = 1;
1173	<	simError();
1174	<	}
1175	<	}
1176	<	}
1177	<
1178	<	if (simParams_->haveSwitchingRadius()){
1179	<	rsw_ = simParams_->getSwitchingRadius();
1180	<	} else {
1181	<	sprintf(painCave.errMsg,
1182	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1183	<	"\tOOPSE will use a default value of\n"
1184	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1185	<	painCave.isFatal = 0;
1186	<	simError();
1187	<	rsw_ = 0.85 * rcut_;
1188	<	}
1189	<
1190	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1191	<
1192	<	} else {
1193	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1194	<	// We'll punt and let fortran figure out the cutoffs later.
1195	<
1196	<	notifyFortranYouAreOnYourOwn();
1197	<
1198	<	}
1199	<	}
876	>	topologyDone_ = true;
877		}
878
1202	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1203	–
1204	–	int errorOut;
1205	–	int esm =  NONE;
1206	–	int sm = UNDAMPED;
1207	–	RealType alphaVal;
1208	–	RealType dielectric;
1209	–
1210	–	errorOut = isError;
1211	–
1212	–	if (simParams_->haveElectrostaticSummationMethod()) {
1213	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1214	–	toUpper(myMethod);
1215	–	if (myMethod == "NONE") {
1216	–	esm = NONE;
1217	–	} else {
1218	–	if (myMethod == "SWITCHING_FUNCTION") {
1219	–	esm = SWITCHING_FUNCTION;
1220	–	} else {
1221	–	if (myMethod == "SHIFTED_POTENTIAL") {
1222	–	esm = SHIFTED_POTENTIAL;
1223	–	} else {
1224	–	if (myMethod == "SHIFTED_FORCE") {
1225	–	esm = SHIFTED_FORCE;
1226	–	} else {
1227	–	if (myMethod == "REACTION_FIELD") {
1228	–	esm = REACTION_FIELD;
1229	–	dielectric = simParams_->getDielectric();
1230	–	if (!simParams_->haveDielectric()) {
1231	–	// throw warning
1232	–	sprintf( painCave.errMsg,
1233	–	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1234	–	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1235	–	painCave.isFatal = 0;
1236	–	simError();
1237	–	}
1238	–	} else {
1239	–	// throw error
1240	–	sprintf( painCave.errMsg,
1241	–	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1242	–	"\t(Input file specified %s .)\n"
1243	–	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1244	–	"\t\"shifted_potential\", \"shifted_force\", or \n"
1245	–	"\t\"reaction_field\".\n", myMethod.c_str() );
1246	–	painCave.isFatal = 1;
1247	–	simError();
1248	–	}
1249	–	}
1250	–	}
1251	–	}
1252	–	}
1253	–	}
1254	–
1255	–	if (simParams_->haveElectrostaticScreeningMethod()) {
1256	–	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1257	–	toUpper(myScreen);
1258	–	if (myScreen == "UNDAMPED") {
1259	–	sm = UNDAMPED;
1260	–	} else {
1261	–	if (myScreen == "DAMPED") {
1262	–	sm = DAMPED;
1263	–	if (!simParams_->haveDampingAlpha()) {
1264	–	// first set a cutoff dependent alpha value
1265	–	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1266	–	alphaVal = 0.5125 - rcut_* 0.025;
1267	–	// for values rcut > 20.5, alpha is zero
1268	–	if (alphaVal < 0) alphaVal = 0;
1269	–
1270	–	// throw warning
1271	–	sprintf( painCave.errMsg,
1272	–	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1273	–	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1274	–	painCave.isFatal = 0;
1275	–	simError();
1276	–	} else {
1277	–	alphaVal = simParams_->getDampingAlpha();
1278	–	}
1279	–
1280	–	} else {
1281	–	// throw error
1282	–	sprintf( painCave.errMsg,
1283	–	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1284	–	"\t(Input file specified %s .)\n"
1285	–	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1286	–	"or \"damped\".\n", myScreen.c_str() );
1287	–	painCave.isFatal = 1;
1288	–	simError();
1289	–	}
1290	–	}
1291	–	}
1292	–
1293	–	// let's pass some summation method variables to fortran
1294	–	setElectrostaticSummationMethod( &esm );
1295	–	setFortranElectrostaticMethod( &esm );
1296	–	setScreeningMethod( &sm );
1297	–	setDampingAlpha( &alphaVal );
1298	–	setReactionFieldDielectric( &dielectric );
1299	–	initFortranFF( &errorOut );
1300	–	}
1301	–
1302	–	void SimInfo::setupSwitchingFunction() {
1303	–	int ft = CUBIC;
1304	–
1305	–	if (simParams_->haveSwitchingFunctionType()) {
1306	–	std::string funcType = simParams_->getSwitchingFunctionType();
1307	–	toUpper(funcType);
1308	–	if (funcType == "CUBIC") {
1309	–	ft = CUBIC;
1310	–	} else {
1311	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1312	–	ft = FIFTH_ORDER_POLY;
1313	–	} else {
1314	–	// throw error
1315	–	sprintf( painCave.errMsg,
1316	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1317	–	painCave.isFatal = 1;
1318	–	simError();
1319	–	}
1320	–	}
1321	–	}
1322	–
1323	–	// send switching function notification to switcheroo
1324	–	setFunctionType(&ft);
1325	–
1326	–	}
1327	–
1328	–	void SimInfo::setupAccumulateBoxDipole() {
1329	–
1330	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1331	–	if ( simParams_->haveAccumulateBoxDipole() )
1332	–	if ( simParams_->getAccumulateBoxDipole() ) {
1333	–	setAccumulateBoxDipole();
1334	–	calcBoxDipole_ = true;
1335	–	}
1336	–
1337	–	}
1338	–
879		void SimInfo::addProperty(GenericData* genData) {
880		properties_.addProperty(genData);
881		}
882
883	<	void SimInfo::removeProperty(const std::string& propName) {
883	>	void SimInfo::removeProperty(const string& propName) {
884		properties_.removeProperty(propName);
885		}
886
#	Line 1348 | Line 888 | namespace oopse {
888		properties_.clearProperties();
889		}
890
891	<	std::vector<std::string> SimInfo::getPropertyNames() {
891	>	vector<string> SimInfo::getPropertyNames() {
892		return properties_.getPropertyNames();
893		}
894
895	<	std::vector<GenericData*> SimInfo::getProperties() {
895	>	vector<GenericData*> SimInfo::getProperties() {
896		return properties_.getProperties();
897		}
898
899	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
899	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
900		return properties_.getPropertyByName(propName);
901		}
902
#	Line 1370 | Line 910 | namespace oopse {
910		Molecule* mol;
911		RigidBody* rb;
912		Atom* atom;
913	+	CutoffGroup* cg;
914		SimInfo::MoleculeIterator mi;
915		Molecule::RigidBodyIterator rbIter;
916	<	Molecule::AtomIterator atomIter;;
916	>	Molecule::AtomIterator atomIter;
917	>	Molecule::CutoffGroupIterator cgIter;
918
919		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
920
#	Line 1383 | Line 925 | namespace oopse {
925		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
926		rb->setSnapshotManager(sman_);
927		}
928	+
929	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
930	+	cg->setSnapshotManager(sman_);
931	+	}
932		}
933
934		}
#	Line 1439 | Line 985 | namespace oopse {
985
986		}
987
988	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
988	>	ostream& operator <<(ostream& o, SimInfo& info) {
989
990		return o;
991		}
#	Line 1482 | Line 1028 | namespace oopse {
1028
1029
1030		[  Ixx -Ixy  -Ixz ]
1031	<	J =| -Iyx  Iyy  -Iyz |
1031	>	J =| -Iyx  Iyy  -Iyz |
1032		[ -Izx -Iyz   Izz ]
1033		*/
1034
#	Line 1589 | Line 1135 | namespace oopse {
1135		return IOIndexToIntegrableObject.at(index);
1136		}
1137
1138	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1138	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1139		IOIndexToIntegrableObject= v;
1140		}
1141
#	Line 1631 | Line 1177 | namespace oopse {
1177		return;
1178		}
1179		/*
1180	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1180	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1181		assert( v.size() == nAtoms_ + nRigidBodies_);
1182		sdByGlobalIndex_ = v;
1183		}
#	Line 1641 | Line 1187 | namespace oopse {
1187		return sdByGlobalIndex_.at(index);
1188		}
1189		*/
1190	<	}//end namespace oopse
1190	>	int SimInfo::getNGlobalConstraints() {
1191	>	int nGlobalConstraints;
1192	>	#ifdef IS_MPI
1193	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1194	>	MPI_COMM_WORLD);
1195	>	#else
1196	>	nGlobalConstraints =  nConstraints_;
1197	>	#endif
1198	>	return nGlobalConstraints;
1199	>	}
1200
1201	+	}//end namespace OpenMD
1202	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 1287 by gezelter, Wed Sep 10 18:11:32 2008 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC

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