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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 1601 by gezelter, Thu Aug 4 20:04:35 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();
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	<
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	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
106	<	//group therefore the total number of cutoff groups in the system is
107	<	//equal to the total number of atoms minus number of atoms belong to
108	<	//cutoff group defined in meta-data file plus the number of cutoff
109	<	//groups defined in meta-data file
110	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
111	<
112	<	//every free atom (atom does not belong to rigid bodies) is an
113	<	//integrable object therefore the total number of integrable objects
114	<	//in the system is equal to the total number of atoms minus number of
115	<	//atoms belong to rigid body defined in meta-data file plus the number
116	<	//of rigid bodies defined in meta-data file
117	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
118	<	+ nGlobalRigidBodies_;
119	<
120	<	nGlobalMols_ = molStampIds_.size();
161	<	molToProcMap_.resize(nGlobalMols_);
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
129	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
130	+
131	+	//every free atom (atom does not belong to rigid bodies) is an
132	+	//integrable object therefore the total number of integrable objects
133	+	//in the system is equal to the total number of atoms minus number of
134	+	//atoms belong to rigid body defined in meta-data file plus the number
135	+	//of rigid bodies defined in meta-data file
136	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
137	+	+ nGlobalRigidBodies_;
138	+
139	+	nGlobalMols_ = molStampIds_.size();
140	+	molToProcMap_.resize(nGlobalMols_);
141	+	}
142	+
143		SimInfo::~SimInfo() {
144	<	std::map<int, Molecule*>::iterator i;
144	>	map<int, Molecule*>::iterator i;
145		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
146		delete i->second;
147		}
#	Line 173 | Line 152 | namespace oopse {
152		delete forceField_;
153		}
154
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	–	}
155
156		bool SimInfo::addMolecule(Molecule* mol) {
157		MoleculeIterator i;
158	<
158	>
159		i = molecules_.find(mol->getGlobalIndex());
160		if (i == molecules_.end() ) {
161	<
162	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
163	<
161	>
162	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
163	>
164		nAtoms_ += mol->getNAtoms();
165		nBonds_ += mol->getNBonds();
166		nBends_ += mol->getNBends();
#	Line 201 | Line 170 | namespace oopse {
170		nIntegrableObjects_ += mol->getNIntegrableObjects();
171		nCutoffGroups_ += mol->getNCutoffGroups();
172		nConstraints_ += mol->getNConstraintPairs();
173	<
173	>
174		addInteractionPairs(mol);
175	<
175	>
176		return true;
177		} else {
178		return false;
179		}
180		}
181	<
181	>
182		bool SimInfo::removeMolecule(Molecule* mol) {
183		MoleculeIterator i;
184		i = molecules_.find(mol->getGlobalIndex());
#	Line 237 | Line 206 | namespace oopse {
206		} else {
207		return false;
208		}
240	–
241	–
209		}
210
211
#	Line 256 | Line 223 | namespace oopse {
223		void SimInfo::calcNdf() {
224		int ndf_local;
225		MoleculeIterator i;
226	<	std::vector<StuntDouble*>::iterator j;
226	>	vector<StuntDouble*>::iterator j;
227		Molecule* mol;
228		StuntDouble* integrableObject;
229
#	Line 301 | Line 268 | namespace oopse {
268		fdf_ = fdf_local;
269		#endif
270		return fdf_;
271	+	}
272	+
273	+	unsigned int SimInfo::getNLocalCutoffGroups(){
274	+	int nLocalCutoffAtoms = 0;
275	+	Molecule* mol;
276	+	MoleculeIterator mi;
277	+	CutoffGroup* cg;
278	+	Molecule::CutoffGroupIterator ci;
279	+
280	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
281	+
282	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
283	+	cg = mol->nextCutoffGroup(ci)) {
284	+	nLocalCutoffAtoms += cg->getNumAtom();
285	+
286	+	}
287	+	}
288	+
289	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
290		}
291
292		void SimInfo::calcNdfRaw() {
293		int ndfRaw_local;
294
295		MoleculeIterator i;
296	<	std::vector<StuntDouble*>::iterator j;
296	>	vector<StuntDouble*>::iterator j;
297		Molecule* mol;
298		StuntDouble* integrableObject;
299
#	Line 356 | Line 342 | namespace oopse {
342
343		void SimInfo::addInteractionPairs(Molecule* mol) {
344		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
345	<	std::vector<Bond*>::iterator bondIter;
346	<	std::vector<Bend*>::iterator bendIter;
347	<	std::vector<Torsion*>::iterator torsionIter;
348	<	std::vector<Inversion*>::iterator inversionIter;
345	>	vector<Bond*>::iterator bondIter;
346	>	vector<Bend*>::iterator bendIter;
347	>	vector<Torsion*>::iterator torsionIter;
348	>	vector<Inversion*>::iterator inversionIter;
349		Bond* bond;
350		Bend* bend;
351		Torsion* torsion;
#	Line 377 | Line 363 | namespace oopse {
363		// always be excluded.  These are done at the bottom of this
364		// function.
365
366	<	std::map<int, std::set<int> > atomGroups;
366	>	map<int, set<int> > atomGroups;
367		Molecule::RigidBodyIterator rbIter;
368		RigidBody* rb;
369		Molecule::IntegrableObjectIterator ii;
#	Line 389 | Line 375 | namespace oopse {
375
376		if (integrableObject->isRigidBody()) {
377		rb = static_cast<RigidBody*>(integrableObject);
378	<	std::vector<Atom*> atoms = rb->getAtoms();
379	<	std::set<int> rigidAtoms;
378	>	vector<Atom*> atoms = rb->getAtoms();
379	>	set<int> rigidAtoms;
380		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
381		rigidAtoms.insert(atoms[i]->getGlobalIndex());
382		}
383		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
384	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
384	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
385		}
386		} else {
387	<	std::set<int> oneAtomSet;
387	>	set<int> oneAtomSet;
388		oneAtomSet.insert(integrableObject->getGlobalIndex());
389	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
389	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
390		}
391		}
392
#	Line 503 | Line 489 | namespace oopse {
489
490		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
491		rb = mol->nextRigidBody(rbIter)) {
492	<	std::vector<Atom*> atoms = rb->getAtoms();
492	>	vector<Atom*> atoms = rb->getAtoms();
493		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
494		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
495		a = atoms[i]->getGlobalIndex();
#	Line 517 | Line 503 | namespace oopse {
503
504		void SimInfo::removeInteractionPairs(Molecule* mol) {
505		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
506	<	std::vector<Bond*>::iterator bondIter;
507	<	std::vector<Bend*>::iterator bendIter;
508	<	std::vector<Torsion*>::iterator torsionIter;
509	<	std::vector<Inversion*>::iterator inversionIter;
506	>	vector<Bond*>::iterator bondIter;
507	>	vector<Bend*>::iterator bendIter;
508	>	vector<Torsion*>::iterator torsionIter;
509	>	vector<Inversion*>::iterator inversionIter;
510		Bond* bond;
511		Bend* bend;
512		Torsion* torsion;
#	Line 530 | Line 516 | namespace oopse {
516		int c;
517		int d;
518
519	<	std::map<int, std::set<int> > atomGroups;
519	>	map<int, set<int> > atomGroups;
520		Molecule::RigidBodyIterator rbIter;
521		RigidBody* rb;
522		Molecule::IntegrableObjectIterator ii;
#	Line 542 | Line 528 | namespace oopse {
528
529		if (integrableObject->isRigidBody()) {
530		rb = static_cast<RigidBody*>(integrableObject);
531	<	std::vector<Atom*> atoms = rb->getAtoms();
532	<	std::set<int> rigidAtoms;
531	>	vector<Atom*> atoms = rb->getAtoms();
532	>	set<int> rigidAtoms;
533		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
534		rigidAtoms.insert(atoms[i]->getGlobalIndex());
535		}
536		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
537	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
537	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
538		}
539		} else {
540	<	std::set<int> oneAtomSet;
540	>	set<int> oneAtomSet;
541		oneAtomSet.insert(integrableObject->getGlobalIndex());
542	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
542	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
543		}
544		}
545
#	Line 656 | Line 642 | namespace oopse {
642
643		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
644		rb = mol->nextRigidBody(rbIter)) {
645	<	std::vector<Atom*> atoms = rb->getAtoms();
645	>	vector<Atom*> atoms = rb->getAtoms();
646		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
647		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
648		a = atoms[i]->getGlobalIndex();
#	Line 679 | Line 665 | namespace oopse {
665		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
666		}
667
682	–	void SimInfo::update() {
668
669	<	setupSimType();
670	<
671	<	#ifdef IS_MPI
672	<	setupFortranParallel();
673	<	#endif
674	<
675	<	setupFortranSim();
676	<
677	<	//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	<
669	>	/**
670	>	* update
671	>	*
672	>	*  Performs the global checks and variable settings after the
673	>	*  objects have been created.
674	>	*
675	>	*/
676	>	void SimInfo::update() {
677	>	setupSimVariables();
678		calcNdf();
679		calcNdfRaw();
680		calcNdfTrans();
712	–
713	–	fortranInitialized_ = true;
681		}
682	<
683	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
682	>
683	>	/**
684	>	* getSimulatedAtomTypes
685	>	*
686	>	* Returns an STL set of AtomType* that are actually present in this
687	>	* simulation.  Must query all processors to assemble this information.
688	>	*
689	>	*/
690	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
691		SimInfo::MoleculeIterator mi;
692		Molecule* mol;
693		Molecule::AtomIterator ai;
694		Atom* atom;
695	<	std::set<AtomType*> atomTypes;
696	<
695	>	set<AtomType*> atomTypes;
696	>
697		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
698	<
699	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
698	>	for(atom = mol->beginAtom(ai); atom != NULL;
699	>	atom = mol->nextAtom(ai)) {
700		atomTypes.insert(atom->getAtomType());
701	<	}
702	<
703	<	}
701	>	}
702	>	}
703	>
704	>	#ifdef IS_MPI
705
706	<	return atomTypes;
707	<	}
733	<
734	<	void SimInfo::setupSimType() {
735	<	std::set<AtomType*>::iterator i;
736	<	std::set<AtomType*> atomTypes;
737	<	atomTypes = getUniqueAtomTypes();
706	>	// loop over the found atom types on this processor, and add their
707	>	// numerical idents to a vector:
708
709	<	int useLennardJones = 0;
710	<	int useElectrostatic = 0;
711	<	int useEAM = 0;
712	<	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;
709	>	vector<int> foundTypes;
710	>	set<AtomType*>::iterator i;
711	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
712	>	foundTypes.push_back( (*i)->getIdent() );
713
714	<	std::string myMethod;
714	>	// count_local holds the number of found types on this processor
715	>	int count_local = foundTypes.size();
716
717	<	// set the useRF logical
763	<	useRF = 0;
764	<	useSF = 0;
765	<	useSP = 0;
766	<	useBoxDipole = 0;
717	>	int nproc = MPI::COMM_WORLD.Get_size();
718
719	+	// we need arrays to hold the counts and displacement vectors for
720	+	// all processors
721	+	vector<int> counts(nproc, 0);
722	+	vector<int> disps(nproc, 0);
723
724	<	if (simParams_->haveElectrostaticSummationMethod()) {
725	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
726	<	toUpper(myMethod);
727	<	if (myMethod == "REACTION_FIELD"){
728	<	useRF = 1;
729	<	} else if (myMethod == "SHIFTED_FORCE"){
730	<	useSF = 1;
731	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
732	<	useSP = 1;
733	<	}
724	>	// fill the counts array
725	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
726	>	1, MPI::INT);
727	>
728	>	// use the processor counts to compute the displacement array
729	>	disps[0] = 0;
730	>	int totalCount = counts[0];
731	>	for (int iproc = 1; iproc < nproc; iproc++) {
732	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
733	>	totalCount += counts[iproc];
734		}
735	+
736	+	// we need a (possibly redundant) set of all found types:
737	+	vector<int> ftGlobal(totalCount);
738
739	<	if (simParams_->haveAccumulateBoxDipole())
740	<	if (simParams_->getAccumulateBoxDipole())
741	<	useBoxDipole = 1;
739	>	// now spray out the foundTypes to all the other processors:
740	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
741	>	&ftGlobal[0], &counts[0], &disps[0],
742	>	MPI::INT);
743
744	<	useAtomicVirial_ = simParams_->getUseAtomicVirial();
744	>	vector<int>::iterator j;
745
746	<	//loop over all of the atom types
747	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
748	<	useLennardJones |= (*i)->isLennardJones();
790	<	useElectrostatic |= (*i)->isElectrostatic();
791	<	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();
800	<	}
746	>	// foundIdents is a stl set, so inserting an already found ident
747	>	// will have no effect.
748	>	set<int> foundIdents;
749
750	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
751	<	useDirectionalAtom = 1;
752	<	}
750	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
751	>	foundIdents.insert((*j));
752	>
753	>	// now iterate over the foundIdents and get the actual atom types
754	>	// that correspond to these:
755	>	set<int>::iterator it;
756	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
757	>	atomTypes.insert( forceField_->getAtomType((*it)) );
758	>
759	>	#endif
760
761	<	if (useCharge || useDipole) {
762	<	useElectrostatics = 1;
808	<	}
761	>	return atomTypes;
762	>	}
763
764	+	void SimInfo::setupSimVariables() {
765	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
766	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
767	+	calcBoxDipole_ = false;
768	+	if ( simParams_->haveAccumulateBoxDipole() )
769	+	if ( simParams_->getAccumulateBoxDipole() ) {
770	+	calcBoxDipole_ = true;
771	+	}
772	+
773	+	set<AtomType*>::iterator i;
774	+	set<AtomType*> atomTypes;
775	+	atomTypes = getSimulatedAtomTypes();
776	+	int usesElectrostatic = 0;
777	+	int usesMetallic = 0;
778	+	int usesDirectional = 0;
779	+	//loop over all of the atom types
780	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
781	+	usesElectrostatic |= (*i)->isElectrostatic();
782	+	usesMetallic |= (*i)->isMetal();
783	+	usesDirectional |= (*i)->isDirectional();
784	+	}
785	+
786		#ifdef IS_MPI
787		int temp;
788	+	temp = usesDirectional;
789	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
790	+
791	+	temp = usesMetallic;
792	+	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
793	+
794	+	temp = usesElectrostatic;
795	+	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
796	+	#else
797
798	<	temp = usePBC;
799	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
798	>	usesDirectionalAtoms_ = usesDirectional;
799	>	usesMetallicAtoms_ = usesMetallic;
800	>	usesElectrostaticAtoms_ = usesElectrostatic;
801
802	<	temp = useDirectionalAtom;
803	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
802	>	#endif
803	>
804	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
805	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
806	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
807	>	}
808
819	–	temp = useLennardJones;
820	–	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
809
810	<	temp = useElectrostatics;
811	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810	>	vector<int> SimInfo::getGlobalAtomIndices() {
811	>	SimInfo::MoleculeIterator mi;
812	>	Molecule* mol;
813	>	Molecule::AtomIterator ai;
814	>	Atom* atom;
815
816	<	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);
816	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
817
818	<	temp = useGayBerne;
819	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
818	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
819	>
820	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
821	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
822	>	}
823	>	}
824	>	return GlobalAtomIndices;
825	>	}
826
840	–	temp = useEAM;
841	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
827
828	<	temp = useSC;
829	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
830	<
831	<	temp = useShape;
832	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
828	>	vector<int> SimInfo::getGlobalGroupIndices() {
829	>	SimInfo::MoleculeIterator mi;
830	>	Molecule* mol;
831	>	Molecule::CutoffGroupIterator ci;
832	>	CutoffGroup* cg;
833
834	<	temp = useFLARB;
835	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
836	<
837	<	temp = useRF;
838	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
839	<
840	<	temp = useSF;
841	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
842	<
843	<	temp = useSP;
844	<	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
845	<
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_;
834	>	vector<int> GlobalGroupIndices;
835	>
836	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
837	>
838	>	//local index of cutoff group is trivial, it only depends on the
839	>	//order of travesing
840	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
841	>	cg = mol->nextCutoffGroup(ci)) {
842	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
843	>	}
844	>	}
845	>	return GlobalGroupIndices;
846		}
847
848	<	void SimInfo::setupFortranSim() {
849	<	int isError;
848	>
849	>	void SimInfo::prepareTopology() {
850		int nExclude, nOneTwo, nOneThree, nOneFour;
892	–	std::vector<int> fortranGlobalGroupMembership;
893	–
894	–	isError = 0;
851
896	–	//globalGroupMembership_ is filled by SimCreator
897	–	for (int i = 0; i < nGlobalAtoms_; i++) {
898	–	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
899	–	}
900	–
852		//calculate mass ratio of cutoff group
902	–	std::vector<RealType> mfact;
853		SimInfo::MoleculeIterator mi;
854		Molecule* mol;
855		Molecule::CutoffGroupIterator ci;
#	Line 908 | Line 858 | namespace oopse {
858		Atom* atom;
859		RealType totalMass;
860
861	<	//to avoid memory reallocation, reserve enough space for mfact
862	<	mfact.reserve(getNCutoffGroups());
861	>	/**
862	>	* The mass factor is the relative mass of an atom to the total
863	>	* mass of the cutoff group it belongs to.  By default, all atoms
864	>	* are their own cutoff groups, and therefore have mass factors of
865	>	* 1.  We need some special handling for massless atoms, which
866	>	* will be treated as carrying the entire mass of the cutoff
867	>	* group.
868	>	*/
869	>	massFactors_.clear();
870	>	massFactors_.resize(getNAtoms(), 1.0);
871
872		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
873	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
873	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
874	>	cg = mol->nextCutoffGroup(ci)) {
875
876		totalMass = cg->getMass();
877		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
878		// Check for massless groups - set mfact to 1 if true
879	<	if (totalMass != 0)
880	<	mfact.push_back(atom->getMass()/totalMass);
879	>	if (totalMass != 0)
880	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
881		else
882	<	mfact.push_back( 1.0 );
882	>	massFactors_[atom->getLocalIndex()] = 1.0;
883		}
884		}
885		}
886
887	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
929	<	std::vector<int> identArray;
887	>	// Build the identArray_
888
889	<	//to avoid memory reallocation, reserve enough space identArray
890	<	identArray.reserve(getNAtoms());
933	<
889	>	identArray_.clear();
890	>	identArray_.reserve(getNAtoms());
891		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
892		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
893	<	identArray.push_back(atom->getIdent());
893	>	identArray_.push_back(atom->getIdent());
894		}
895		}
939	–
940	–	//fill molMembershipArray
941	–	//molMembershipArray is filled by SimCreator
942	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
943	–	for (int i = 0; i < nGlobalAtoms_; i++) {
944	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
945	–	}
896
897	<	//setup fortran simulation
897	>	//scan topology
898
899		nExclude = excludedInteractions_.getSize();
900		nOneTwo = oneTwoInteractions_.getSize();
#	Line 956 | Line 906 | namespace oopse {
906		int* oneThreeList = oneThreeInteractions_.getPairList();
907		int* oneFourList = oneFourInteractions_.getPairList();
908
909	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
960	<	&nExclude, excludeList,
961	<	&nOneTwo, oneTwoList,
962	<	&nOneThree, oneThreeList,
963	<	&nOneFour, oneFourList,
964	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
965	<	&fortranGlobalGroupMembership[0], &isError);
966	<
967	<	if( isError ){
968	<
969	<	sprintf( painCave.errMsg,
970	<	"There was an error setting the simulation information in fortran.\n" );
971	<	painCave.isFatal = 1;
972	<	painCave.severity = OOPSE_ERROR;
973	<	simError();
974	<	}
975	<
976	<
977	<	sprintf( checkPointMsg,
978	<	"succesfully sent the simulation information to fortran.\n");
979	<
980	<	errorCheckPoint();
981	<
982	<	// Setup number of neighbors in neighbor list if present
983	<	if (simParams_->haveNeighborListNeighbors()) {
984	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
985	<	setNeighbors(&nlistNeighbors);
986	<	}
987	<
988	<
989	<	}
990	<
991	<
992	<	void SimInfo::setupFortranParallel() {
993	<	#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;
1003	<	mpiSimData parallelData;
1004	<	int isError;
1005	<
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	<
1020	<	//fill up mpiSimData struct
1021	<	parallelData.nMolGlobal = getNGlobalMolecules();
1022	<	parallelData.nMolLocal = getNMolecules();
1023	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
1024	<	parallelData.nAtomsLocal = getNAtoms();
1025	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1026	<	parallelData.nGroupsLocal = getNCutoffGroups();
1027	<	parallelData.myNode = worldRank;
1028	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1029	<
1030	<	//pass mpiSimData struct and index arrays to fortran
1031	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1032	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1033	<	&localToGlobalCutoffGroupIndex[0], &isError);
1034	<
1035	<	if (isError) {
1036	<	sprintf(painCave.errMsg,
1037	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1038	<	painCave.isFatal = 1;
1039	<	simError();
1040	<	}
1041	<
1042	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
1043	<	errorCheckPoint();
1044	<
1045	<	#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	<	}
1192	<	}
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;
1261	<
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	<	}
1293	<
1294	<	void SimInfo::setupSwitchingFunction() {
1295	<	int ft = CUBIC;
1296	<
1297	<	if (simParams_->haveSwitchingFunctionType()) {
1298	<	std::string funcType = simParams_->getSwitchingFunctionType();
1299	<	toUpper(funcType);
1300	<	if (funcType == "CUBIC") {
1301	<	ft = CUBIC;
1302	<	} else {
1303	<	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1304	<	ft = FIFTH_ORDER_POLY;
1305	<	} else {
1306	<	// throw error
1307	<	sprintf( painCave.errMsg,
1308	<	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1309	<	painCave.isFatal = 1;
1310	<	simError();
1311	<	}
1312	<	}
1313	<	}
1314	<
1315	<	// send switching function notification to switcheroo
1316	<	setFunctionType(&ft);
1317	<
909	>	topologyDone_ = true;
910		}
911
1320	–	void SimInfo::setupAccumulateBoxDipole() {
1321	–
1322	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1323	–	if ( simParams_->haveAccumulateBoxDipole() )
1324	–	if ( simParams_->getAccumulateBoxDipole() ) {
1325	–	setAccumulateBoxDipole();
1326	–	calcBoxDipole_ = true;
1327	–	}
1328	–
1329	–	}
1330	–
912		void SimInfo::addProperty(GenericData* genData) {
913		properties_.addProperty(genData);
914		}
915
916	<	void SimInfo::removeProperty(const std::string& propName) {
916	>	void SimInfo::removeProperty(const string& propName) {
917		properties_.removeProperty(propName);
918		}
919
#	Line 1340 | Line 921 | namespace oopse {
921		properties_.clearProperties();
922		}
923
924	<	std::vector<std::string> SimInfo::getPropertyNames() {
924	>	vector<string> SimInfo::getPropertyNames() {
925		return properties_.getPropertyNames();
926		}
927
928	<	std::vector<GenericData*> SimInfo::getProperties() {
928	>	vector<GenericData*> SimInfo::getProperties() {
929		return properties_.getProperties();
930		}
931
932	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
932	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
933		return properties_.getPropertyByName(propName);
934		}
935
#	Line 1362 | Line 943 | namespace oopse {
943		Molecule* mol;
944		RigidBody* rb;
945		Atom* atom;
946	+	CutoffGroup* cg;
947		SimInfo::MoleculeIterator mi;
948		Molecule::RigidBodyIterator rbIter;
949	<	Molecule::AtomIterator atomIter;;
949	>	Molecule::AtomIterator atomIter;
950	>	Molecule::CutoffGroupIterator cgIter;
951
952		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
953
#	Line 1375 | Line 958 | namespace oopse {
958		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
959		rb->setSnapshotManager(sman_);
960		}
961	+
962	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
963	+	cg->setSnapshotManager(sman_);
964	+	}
965		}
966
967		}
#	Line 1431 | Line 1018 | namespace oopse {
1018
1019		}
1020
1021	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1021	>	ostream& operator <<(ostream& o, SimInfo& info) {
1022
1023		return o;
1024		}
#	Line 1474 | Line 1061 | namespace oopse {
1061
1062
1063		[  Ixx -Ixy  -Ixz ]
1064	<	J =| -Iyx  Iyy  -Iyz |
1064	>	J =| -Iyx  Iyy  -Iyz |
1065		[ -Izx -Iyz   Izz ]
1066		*/
1067
#	Line 1581 | Line 1168 | namespace oopse {
1168		return IOIndexToIntegrableObject.at(index);
1169		}
1170
1171	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1171	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1172		IOIndexToIntegrableObject= v;
1173		}
1174
#	Line 1623 | Line 1210 | namespace oopse {
1210		return;
1211		}
1212		/*
1213	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1213	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1214		assert( v.size() == nAtoms_ + nRigidBodies_);
1215		sdByGlobalIndex_ = v;
1216		}
#	Line 1633 | Line 1220 | namespace oopse {
1220		return sdByGlobalIndex_.at(index);
1221		}
1222		*/
1223	<	}//end namespace oopse
1223	>	int SimInfo::getNGlobalConstraints() {
1224	>	int nGlobalConstraints;
1225	>	#ifdef IS_MPI
1226	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1227	>	MPI_COMM_WORLD);
1228	>	#else
1229	>	nGlobalConstraints =  nConstraints_;
1230	>	#endif
1231	>	return nGlobalConstraints;
1232	>	}
1233
1234	+	}//end namespace OpenMD
1235	+

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 1601 by gezelter, Thu Aug 4 20:04:35 2011 UTC

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