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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 1544 by gezelter, Fri Mar 18 19:31:52 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"
57		#include "UseTheForce/DarkSide/neighborLists_interface.h"
58	<	#include "UseTheForce/DarkSide/electrostatic_interface.h"
64	<	#include "UseTheForce/DarkSide/switcheroo_interface.h"
58	>	#include "UseTheForce/doForces_interface.h"
59		#include "utils/MemoryUtils.hpp"
60		#include "utils/simError.h"
61		#include "selection/SelectionManager.hpp"
62		#include "io/ForceFieldOptions.hpp"
63		#include "UseTheForce/ForceField.hpp"
64	+	#include "nonbonded/SwitchingFunction.hpp"
65
71	–
66		#ifdef IS_MPI
67		#include "UseTheForce/mpiComponentPlan.h"
68		#include "UseTheForce/DarkSide/simParallel_interface.h"
69		#endif
70
71	<	namespace oopse {
72	<	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	<	}
71	>	using namespace std;
72	>	namespace OpenMD {
73
74		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
75		forceField_(ff), simParams_(simParams),
#	Line 93 | Line 79 | namespace oopse {
79		nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
80		nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
81		nConstraints_(0), sman_(NULL), fortranInitialized_(false),
82	<	calcBoxDipole_(false), useAtomicVirial_(true) {
83	<
84	<
85	<	MoleculeStamp* molStamp;
86	<	int nMolWithSameStamp;
87	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
88	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
89	<	CutoffGroupStamp* cgStamp;
90	<	RigidBodyStamp* rbStamp;
91	<	int nRigidAtoms = 0;
92	<
93	<	std::vector<Component*> components = simParams->getComponents();
94	<
95	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
96	<	molStamp = (*i)->getMoleculeStamp();
97	<	nMolWithSameStamp = (*i)->getNMol();
98	<
99	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
100	<
101	<	//calculate atoms in molecules
102	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
103	<
104	<	//calculate atoms in cutoff groups
105	<	int nAtomsInGroups = 0;
106	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
107	<
108	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
109	<	cgStamp = molStamp->getCutoffGroupStamp(j);
110	<	nAtomsInGroups += cgStamp->getNMembers();
111	<	}
112	<
113	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
114	<
115	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
116	<
117	<	//calculate atoms in rigid bodies
118	<	int nAtomsInRigidBodies = 0;
119	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
120	<
121	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
122	<	rbStamp = molStamp->getRigidBodyStamp(j);
123	<	nAtomsInRigidBodies += rbStamp->getNMembers();
124	<	}
125	<
126	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
127	<	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_);
82	>	calcBoxDipole_(false), useAtomicVirial_(true) {
83	>
84	>	MoleculeStamp* molStamp;
85	>	int nMolWithSameStamp;
86	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
88	>	CutoffGroupStamp* cgStamp;
89	>	RigidBodyStamp* rbStamp;
90	>	int nRigidAtoms = 0;
91	>
92	>	vector<Component*> components = simParams->getComponents();
93	>
94	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
95	>	molStamp = (*i)->getMoleculeStamp();
96	>	nMolWithSameStamp = (*i)->getNMol();
97	>
98	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
99	>
100	>	//calculate atoms in molecules
101	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
102	>
103	>	//calculate atoms in cutoff groups
104	>	int nAtomsInGroups = 0;
105	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
106	>
107	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
108	>	cgStamp = molStamp->getCutoffGroupStamp(j);
109	>	nAtomsInGroups += cgStamp->getNMembers();
110	>	}
111	>
112	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
113	>
114	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
115	>
116	>	//calculate atoms in rigid bodies
117	>	int nAtomsInRigidBodies = 0;
118	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
119	>
120	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
121	>	rbStamp = molStamp->getRigidBodyStamp(j);
122	>	nAtomsInRigidBodies += rbStamp->getNMembers();
123	>	}
124	>
125	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
126	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
127	>
128		}
129	+
130	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
131	+	//group therefore the total number of cutoff groups in the system is
132	+	//equal to the total number of atoms minus number of atoms belong to
133	+	//cutoff group defined in meta-data file plus the number of cutoff
134	+	//groups defined in meta-data file
135	+	std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
136	+	std::cerr << "nCA = " << nCutoffAtoms << "\n";
137	+	std::cerr << "nG = " << nGroups << "\n";
138
139	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
140	+
141	+	std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
142	+
143	+	//every free atom (atom does not belong to rigid bodies) is an
144	+	//integrable object therefore the total number of integrable objects
145	+	//in the system is equal to the total number of atoms minus number of
146	+	//atoms belong to rigid body defined in meta-data file plus the number
147	+	//of rigid bodies defined in meta-data file
148	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
149	+	+ nGlobalRigidBodies_;
150	+
151	+	nGlobalMols_ = molStampIds_.size();
152	+	molToProcMap_.resize(nGlobalMols_);
153	+	}
154	+
155		SimInfo::~SimInfo() {
156	<	std::map<int, Molecule*>::iterator i;
156	>	map<int, Molecule*>::iterator i;
157		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
158		delete i->second;
159		}
#	Line 173 | Line 164 | namespace oopse {
164		delete forceField_;
165		}
166
176	–	int SimInfo::getNGlobalConstraints() {
177	–	int nGlobalConstraints;
178	–	#ifdef IS_MPI
179	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
180	–	MPI_COMM_WORLD);
181	–	#else
182	–	nGlobalConstraints =  nConstraints_;
183	–	#endif
184	–	return nGlobalConstraints;
185	–	}
167
168		bool SimInfo::addMolecule(Molecule* mol) {
169		MoleculeIterator i;
170	<
170	>
171		i = molecules_.find(mol->getGlobalIndex());
172		if (i == molecules_.end() ) {
173	<
174	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
175	<
173	>
174	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
175	>
176		nAtoms_ += mol->getNAtoms();
177		nBonds_ += mol->getNBonds();
178		nBends_ += mol->getNBends();
#	Line 201 | Line 182 | namespace oopse {
182		nIntegrableObjects_ += mol->getNIntegrableObjects();
183		nCutoffGroups_ += mol->getNCutoffGroups();
184		nConstraints_ += mol->getNConstraintPairs();
185	<
185	>
186		addInteractionPairs(mol);
187	<
187	>
188		return true;
189		} else {
190		return false;
191		}
192		}
193	<
193	>
194		bool SimInfo::removeMolecule(Molecule* mol) {
195		MoleculeIterator i;
196		i = molecules_.find(mol->getGlobalIndex());
#	Line 237 | Line 218 | namespace oopse {
218		} else {
219		return false;
220		}
240	–
241	–
221		}
222
223
#	Line 256 | Line 235 | namespace oopse {
235		void SimInfo::calcNdf() {
236		int ndf_local;
237		MoleculeIterator i;
238	<	std::vector<StuntDouble*>::iterator j;
238	>	vector<StuntDouble*>::iterator j;
239		Molecule* mol;
240		StuntDouble* integrableObject;
241
#	Line 307 | Line 286 | namespace oopse {
286		int ndfRaw_local;
287
288		MoleculeIterator i;
289	<	std::vector<StuntDouble*>::iterator j;
289	>	vector<StuntDouble*>::iterator j;
290		Molecule* mol;
291		StuntDouble* integrableObject;
292
#	Line 356 | Line 335 | namespace oopse {
335
336		void SimInfo::addInteractionPairs(Molecule* mol) {
337		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
338	<	std::vector<Bond*>::iterator bondIter;
339	<	std::vector<Bend*>::iterator bendIter;
340	<	std::vector<Torsion*>::iterator torsionIter;
341	<	std::vector<Inversion*>::iterator inversionIter;
338	>	vector<Bond*>::iterator bondIter;
339	>	vector<Bend*>::iterator bendIter;
340	>	vector<Torsion*>::iterator torsionIter;
341	>	vector<Inversion*>::iterator inversionIter;
342		Bond* bond;
343		Bend* bend;
344		Torsion* torsion;
#	Line 377 | Line 356 | namespace oopse {
356		// always be excluded.  These are done at the bottom of this
357		// function.
358
359	<	std::map<int, std::set<int> > atomGroups;
359	>	map<int, set<int> > atomGroups;
360		Molecule::RigidBodyIterator rbIter;
361		RigidBody* rb;
362		Molecule::IntegrableObjectIterator ii;
#	Line 389 | Line 368 | namespace oopse {
368
369		if (integrableObject->isRigidBody()) {
370		rb = static_cast<RigidBody*>(integrableObject);
371	<	std::vector<Atom*> atoms = rb->getAtoms();
372	<	std::set<int> rigidAtoms;
371	>	vector<Atom*> atoms = rb->getAtoms();
372	>	set<int> rigidAtoms;
373		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
374		rigidAtoms.insert(atoms[i]->getGlobalIndex());
375		}
376		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
377	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
377	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
378		}
379		} else {
380	<	std::set<int> oneAtomSet;
380	>	set<int> oneAtomSet;
381		oneAtomSet.insert(integrableObject->getGlobalIndex());
382	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
382	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
383		}
384		}
385
#	Line 503 | Line 482 | namespace oopse {
482
483		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
484		rb = mol->nextRigidBody(rbIter)) {
485	<	std::vector<Atom*> atoms = rb->getAtoms();
485	>	vector<Atom*> atoms = rb->getAtoms();
486		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
487		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
488		a = atoms[i]->getGlobalIndex();
#	Line 517 | Line 496 | namespace oopse {
496
497		void SimInfo::removeInteractionPairs(Molecule* mol) {
498		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
499	<	std::vector<Bond*>::iterator bondIter;
500	<	std::vector<Bend*>::iterator bendIter;
501	<	std::vector<Torsion*>::iterator torsionIter;
502	<	std::vector<Inversion*>::iterator inversionIter;
499	>	vector<Bond*>::iterator bondIter;
500	>	vector<Bend*>::iterator bendIter;
501	>	vector<Torsion*>::iterator torsionIter;
502	>	vector<Inversion*>::iterator inversionIter;
503		Bond* bond;
504		Bend* bend;
505		Torsion* torsion;
#	Line 530 | Line 509 | namespace oopse {
509		int c;
510		int d;
511
512	<	std::map<int, std::set<int> > atomGroups;
512	>	map<int, set<int> > atomGroups;
513		Molecule::RigidBodyIterator rbIter;
514		RigidBody* rb;
515		Molecule::IntegrableObjectIterator ii;
#	Line 542 | Line 521 | namespace oopse {
521
522		if (integrableObject->isRigidBody()) {
523		rb = static_cast<RigidBody*>(integrableObject);
524	<	std::vector<Atom*> atoms = rb->getAtoms();
525	<	std::set<int> rigidAtoms;
524	>	vector<Atom*> atoms = rb->getAtoms();
525	>	set<int> rigidAtoms;
526		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
527		rigidAtoms.insert(atoms[i]->getGlobalIndex());
528		}
529		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
530	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
530	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
531		}
532		} else {
533	<	std::set<int> oneAtomSet;
533	>	set<int> oneAtomSet;
534		oneAtomSet.insert(integrableObject->getGlobalIndex());
535	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
535	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
536		}
537		}
538
#	Line 656 | Line 635 | namespace oopse {
635
636		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
637		rb = mol->nextRigidBody(rbIter)) {
638	<	std::vector<Atom*> atoms = rb->getAtoms();
638	>	vector<Atom*> atoms = rb->getAtoms();
639		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
640		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
641		a = atoms[i]->getGlobalIndex();
#	Line 679 | Line 658 | namespace oopse {
658		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
659		}
660
682	–	void SimInfo::update() {
661
662	<	setupSimType();
663	<
664	<	#ifdef IS_MPI
665	<	setupFortranParallel();
666	<	#endif
667	<
668	<	setupFortranSim();
669	<
670	<	//setup fortran force field
693	<	/** @deprecate */
694	<	int isError = 0;
695	<
696	<	setupCutoff();
697	<
698	<	setupElectrostaticSummationMethod( isError );
699	<	setupSwitchingFunction();
700	<	setupAccumulateBoxDipole();
701	<
702	<	if(isError){
703	<	sprintf( painCave.errMsg,
704	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
705	<	painCave.isFatal = 1;
706	<	simError();
707	<	}
708	<
662	>	/**
663	>	* update
664	>	*
665	>	*  Performs the global checks and variable settings after the
666	>	*  objects have been created.
667	>	*
668	>	*/
669	>	void SimInfo::update() {
670	>	setupSimVariables();
671		calcNdf();
672		calcNdfRaw();
673		calcNdfTrans();
712	–
713	–	fortranInitialized_ = true;
674		}
675	<
676	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
675	>
676	>	/**
677	>	* getSimulatedAtomTypes
678	>	*
679	>	* Returns an STL set of AtomType* that are actually present in this
680	>	* simulation.  Must query all processors to assemble this information.
681	>	*
682	>	*/
683	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
684		SimInfo::MoleculeIterator mi;
685		Molecule* mol;
686		Molecule::AtomIterator ai;
687		Atom* atom;
688	<	std::set<AtomType*> atomTypes;
689	<
690	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
724	<
688	>	set<AtomType*> atomTypes;
689	>
690	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
691		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
692		atomTypes.insert(atom->getAtomType());
693	<	}
694	<
729	<	}
693	>	}
694	>	}
695
696	<	return atomTypes;
732	<	}
696	>	#ifdef IS_MPI
697
698	<	void SimInfo::setupSimType() {
699	<	std::set<AtomType*>::iterator i;
736	<	std::set<AtomType*> atomTypes;
737	<	atomTypes = getUniqueAtomTypes();
738	<
739	<	int useLennardJones = 0;
740	<	int useElectrostatic = 0;
741	<	int useEAM = 0;
742	<	int useSC = 0;
743	<	int useCharge = 0;
744	<	int useDirectional = 0;
745	<	int useDipole = 0;
746	<	int useGayBerne = 0;
747	<	int useSticky = 0;
748	<	int useStickyPower = 0;
749	<	int useShape = 0;
750	<	int useFLARB = 0; //it is not in AtomType yet
751	<	int useDirectionalAtom = 0;
752	<	int useElectrostatics = 0;
753	<	//usePBC and useRF are from simParams
754	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
755	<	int useRF;
756	<	int useSF;
757	<	int useSP;
758	<	int useBoxDipole;
759	<
760	<	std::string myMethod;
761	<
762	<	// set the useRF logical
763	<	useRF = 0;
764	<	useSF = 0;
765	<	useSP = 0;
766	<	useBoxDipole = 0;
698	>	// loop over the found atom types on this processor, and add their
699	>	// numerical idents to a vector:
700
701	+	vector<int> foundTypes;
702	+	set<AtomType*>::iterator i;
703	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
704	+	foundTypes.push_back( (*i)->getIdent() );
705
706	<	if (simParams_->haveElectrostaticSummationMethod()) {
707	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
708	<	toUpper(myMethod);
709	<	if (myMethod == "REACTION_FIELD"){
710	<	useRF = 1;
711	<	} else if (myMethod == "SHIFTED_FORCE"){
712	<	useSF = 1;
713	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
714	<	useSP = 1;
715	<	}
716	<	}
706	>	// count_local holds the number of found types on this processor
707	>	int count_local = foundTypes.size();
708	>
709	>	// count holds the total number of found types on all processors
710	>	// (some will be redundant with the ones found locally):
711	>	int count;
712	>	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
713	>
714	>	// create a vector to hold the globally found types, and resize it:
715	>	vector<int> ftGlobal;
716	>	ftGlobal.resize(count);
717	>	vector<int> counts;
718	>
719	>	int nproc = MPI::COMM_WORLD.Get_size();
720	>	counts.resize(nproc);
721	>	vector<int> disps;
722	>	disps.resize(nproc);
723	>
724	>	// now spray out the foundTypes to all the other processors:
725
726	<	if (simParams_->haveAccumulateBoxDipole())
727	<	if (simParams_->getAccumulateBoxDipole())
783	<	useBoxDipole = 1;
726	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
727	>	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
728
729	+	// foundIdents is a stl set, so inserting an already found ident
730	+	// will have no effect.
731	+	set<int> foundIdents;
732	+	vector<int>::iterator j;
733	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
734	+	foundIdents.insert((*j));
735	+
736	+	// now iterate over the foundIdents and get the actual atom types
737	+	// that correspond to these:
738	+	set<int>::iterator it;
739	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
740	+	atomTypes.insert( forceField_->getAtomType((*it)) );
741	+
742	+	#endif
743	+
744	+	return atomTypes;
745	+	}
746	+
747	+	void SimInfo::setupSimVariables() {
748		useAtomicVirial_ = simParams_->getUseAtomicVirial();
749	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
750	+	calcBoxDipole_ = false;
751	+	if ( simParams_->haveAccumulateBoxDipole() )
752	+	if ( simParams_->getAccumulateBoxDipole() ) {
753	+	calcBoxDipole_ = true;
754	+	}
755
756	+	set<AtomType*>::iterator i;
757	+	set<AtomType*> atomTypes;
758	+	atomTypes = getSimulatedAtomTypes();
759	+	int usesElectrostatic = 0;
760	+	int usesMetallic = 0;
761	+	int usesDirectional = 0;
762		//loop over all of the atom types
763		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
764	<	useLennardJones |= (*i)->isLennardJones();
765	<	useElectrostatic |= (*i)->isElectrostatic();
766	<	useEAM |= (*i)->isEAM();
792	<	useSC |= (*i)->isSC();
793	<	useCharge |= (*i)->isCharge();
794	<	useDirectional |= (*i)->isDirectional();
795	<	useDipole |= (*i)->isDipole();
796	<	useGayBerne |= (*i)->isGayBerne();
797	<	useSticky |= (*i)->isSticky();
798	<	useStickyPower |= (*i)->isStickyPower();
799	<	useShape |= (*i)->isShape();
764	>	usesElectrostatic |= (*i)->isElectrostatic();
765	>	usesMetallic |= (*i)->isMetal();
766	>	usesDirectional |= (*i)->isDirectional();
767		}
768
802	–	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
803	–	useDirectionalAtom = 1;
804	–	}
805	–
806	–	if (useCharge || useDipole) {
807	–	useElectrostatics = 1;
808	–	}
809	–
769		#ifdef IS_MPI
770		int temp;
771	<
772	<	temp = usePBC;
814	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
815	<
816	<	temp = useDirectionalAtom;
817	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
818	<
819	<	temp = useLennardJones;
820	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
771	>	temp = usesDirectional;
772	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
773
774	<	temp = useElectrostatics;
775	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
774	>	temp = usesMetallic;
775	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776
777	<	temp = useCharge;
778	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
827	<
828	<	temp = useDipole;
829	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
830	<
831	<	temp = useSticky;
832	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
833	<
834	<	temp = useStickyPower;
835	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
836	<
837	<	temp = useGayBerne;
838	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
839	<
840	<	temp = useEAM;
841	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
842	<
843	<	temp = useSC;
844	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
845	<
846	<	temp = useShape;
847	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
848	<
849	<	temp = useFLARB;
850	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
851	<
852	<	temp = useRF;
853	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
854	<
855	<	temp = useSF;
856	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
857	<
858	<	temp = useSP;
859	<	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860	<
861	<	temp = useBoxDipole;
862	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
863	<
864	<	temp = useAtomicVirial_;
865	<	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
866	<
777	>	temp = usesElectrostatic;
778	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
779		#endif
780	<
781	<	fInfo_.SIM_uses_PBC = usePBC;
782	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
783	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
784	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
785	<	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_;
780	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
781	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
782	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
783	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
784	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
785	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
786		}
787
788	<	void SimInfo::setupFortranSim() {
788	>	void SimInfo::setupFortran() {
789		int isError;
790		int nExclude, nOneTwo, nOneThree, nOneFour;
791	<	std::vector<int> fortranGlobalGroupMembership;
791	>	vector<int> fortranGlobalGroupMembership;
792
793		isError = 0;
794
#	Line 899 | Line 798 | namespace oopse {
798		}
799
800		//calculate mass ratio of cutoff group
801	<	std::vector<RealType> mfact;
801	>	vector<RealType> mfact;
802		SimInfo::MoleculeIterator mi;
803		Molecule* mol;
804		Molecule::CutoffGroupIterator ci;
#	Line 925 | Line 824 | namespace oopse {
824		}
825		}
826
827	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
929	<	std::vector<int> identArray;
827	>	// Build the identArray_
828
829	<	//to avoid memory reallocation, reserve enough space identArray
830	<	identArray.reserve(getNAtoms());
933	<
829	>	identArray_.clear();
830	>	identArray_.reserve(getNAtoms());
831		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
832		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
833	<	identArray.push_back(atom->getIdent());
833	>	identArray_.push_back(atom->getIdent());
834		}
835		}
836
837		//fill molMembershipArray
838		//molMembershipArray is filled by SimCreator
839	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
839	>	vector<int> molMembershipArray(nGlobalAtoms_);
840		for (int i = 0; i < nGlobalAtoms_; i++) {
841		molMembershipArray[i] = globalMolMembership_[i] + 1;
842		}
#	Line 969 | Line 866 | namespace oopse {
866		sprintf( painCave.errMsg,
867		"There was an error setting the simulation information in fortran.\n" );
868		painCave.isFatal = 1;
869	<	painCave.severity = OOPSE_ERROR;
869	>	painCave.severity = OPENMD_ERROR;
870		simError();
871		}
872
#	Line 985 | Line 882 | namespace oopse {
882		setNeighbors(&nlistNeighbors);
883		}
884
988	–
989	–	}
990	–
991	–
992	–	void SimInfo::setupFortranParallel() {
885		#ifdef IS_MPI
886	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
887	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
888	<	std::vector<int> localToGlobalCutoffGroupIndex;
889	<	SimInfo::MoleculeIterator mi;
998	<	Molecule::AtomIterator ai;
999	<	Molecule::CutoffGroupIterator ci;
1000	<	Molecule* mol;
1001	<	Atom* atom;
1002	<	CutoffGroup* cg;
886	>	//SimInfo is responsible for creating localToGlobalAtomIndex and
887	>	//localToGlobalGroupIndex
888	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
889	>	vector<int> localToGlobalCutoffGroupIndex;
890		mpiSimData parallelData;
1004	–	int isError;
891
892		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
893
#	Line 1041 | Line 927 | namespace oopse {
927
928		sprintf(checkPointMsg, " mpiRefresh successful.\n");
929		errorCheckPoint();
1044	–
930		#endif
1046	–	}
931
932	<	void SimInfo::setupCutoff() {
933	<
934	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
935	<
936	<	// Check the cutoff policy
937	<	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();
932	>	initFortranFF(&isError);
933	>	if (isError) {
934	>	sprintf(painCave.errMsg,
935	>	"initFortranFF errror: fortran didn't like something we gave it.\n");
936	>	painCave.isFatal = 1;
937	>	simError();
938		}
939	<
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	<
939	>	fortranInitialized_ = true;
940		}
941
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	–
942		void SimInfo::addProperty(GenericData* genData) {
943		properties_.addProperty(genData);
944		}
945
946	<	void SimInfo::removeProperty(const std::string& propName) {
946	>	void SimInfo::removeProperty(const string& propName) {
947		properties_.removeProperty(propName);
948		}
949
#	Line 1340 | Line 951 | namespace oopse {
951		properties_.clearProperties();
952		}
953
954	<	std::vector<std::string> SimInfo::getPropertyNames() {
954	>	vector<string> SimInfo::getPropertyNames() {
955		return properties_.getPropertyNames();
956		}
957
958	<	std::vector<GenericData*> SimInfo::getProperties() {
958	>	vector<GenericData*> SimInfo::getProperties() {
959		return properties_.getProperties();
960		}
961
962	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
962	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
963		return properties_.getPropertyByName(propName);
964		}
965
#	Line 1362 | Line 973 | namespace oopse {
973		Molecule* mol;
974		RigidBody* rb;
975		Atom* atom;
976	+	CutoffGroup* cg;
977		SimInfo::MoleculeIterator mi;
978		Molecule::RigidBodyIterator rbIter;
979	<	Molecule::AtomIterator atomIter;;
979	>	Molecule::AtomIterator atomIter;
980	>	Molecule::CutoffGroupIterator cgIter;
981
982		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
983
#	Line 1375 | Line 988 | namespace oopse {
988		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
989		rb->setSnapshotManager(sman_);
990		}
991	+
992	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
993	+	cg->setSnapshotManager(sman_);
994	+	}
995		}
996
997		}
#	Line 1431 | Line 1048 | namespace oopse {
1048
1049		}
1050
1051	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1051	>	ostream& operator <<(ostream& o, SimInfo& info) {
1052
1053		return o;
1054		}
#	Line 1474 | Line 1091 | namespace oopse {
1091
1092
1093		[  Ixx -Ixy  -Ixz ]
1094	<	J =| -Iyx  Iyy  -Iyz |
1094	>	J =| -Iyx  Iyy  -Iyz |
1095		[ -Izx -Iyz   Izz ]
1096		*/
1097
#	Line 1581 | Line 1198 | namespace oopse {
1198		return IOIndexToIntegrableObject.at(index);
1199		}
1200
1201	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1201	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1202		IOIndexToIntegrableObject= v;
1203		}
1204
#	Line 1623 | Line 1240 | namespace oopse {
1240		return;
1241		}
1242		/*
1243	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1243	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1244		assert( v.size() == nAtoms_ + nRigidBodies_);
1245		sdByGlobalIndex_ = v;
1246		}
#	Line 1633 | Line 1250 | namespace oopse {
1250		return sdByGlobalIndex_.at(index);
1251		}
1252		*/
1253	<	}//end namespace oopse
1253	>	int SimInfo::getNGlobalConstraints() {
1254	>	int nGlobalConstraints;
1255	>	#ifdef IS_MPI
1256	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1257	>	MPI_COMM_WORLD);
1258	>	#else
1259	>	nGlobalConstraints =  nConstraints_;
1260	>	#endif
1261	>	return nGlobalConstraints;
1262	>	}
1263
1264	+	}//end namespace OpenMD
1265	+

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 1544 by gezelter, Fri Mar 18 19:31:52 2011 UTC

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