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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 1089 by chrisfen, Wed Nov 1 22:22:44 2006 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 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"
57		#include "UseTheForce/doForces_interface.h"
58	<	#include "UseTheForce/DarkSide/electrostatic_interface.h"
63	<	#include "UseTheForce/DarkSide/switcheroo_interface.h"
58	>	#include "UseTheForce/DarkSide/neighborLists_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
66	+
67		#ifdef IS_MPI
68		#include "UseTheForce/mpiComponentPlan.h"
69		#include "UseTheForce/DarkSide/simParallel_interface.h"
70		#endif
71
72	<	namespace oopse {
73	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
77	<	std::map<int, std::set<int> >::iterator i = container.find(index);
78	<	std::set<int> result;
79	<	if (i != container.end()) {
80	<	result = i->second;
81	<	}
82	<
83	<	return result;
84	<	}
72	>	using namespace std;
73	>	namespace OpenMD {
74
75		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
76		forceField_(ff), simParams_(simParams),
77		ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
78		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
79		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
80	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
81	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
82	<	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) {
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	<	std::vector<Component*> components = simParams->getComponents();
80	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
81	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
82	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
83	>	calcBoxDipole_(false), useAtomicVirial_(true) {
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	>	vector<Component*> components = simParams->getComponents();
94	>
95	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
96	>	molStamp = (*i)->getMoleculeStamp();
97	>	nMolWithSameStamp = (*i)->getNMol();
98
99	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
100	<	molStamp = (*i)->getMoleculeStamp();
101	<	nMolWithSameStamp = (*i)->getNMol();
102	<
103	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
104	<
105	<	//calculate atoms in molecules
106	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
107	<
108	<	//calculate atoms in cutoff groups
109	<	int nAtomsInGroups = 0;
110	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
116	<
117	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
118	<	cgStamp = molStamp->getCutoffGroupStamp(j);
119	<	nAtomsInGroups += cgStamp->getNMembers();
120	<	}
121	<
122	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
123	<
124	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
125	<
126	<	//calculate atoms in rigid bodies
127	<	int nAtomsInRigidBodies = 0;
128	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
129	<
130	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
131	<	rbStamp = molStamp->getRigidBodyStamp(j);
132	<	nAtomsInRigidBodies += rbStamp->getNMembers();
133	<	}
134	<
135	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
136	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
137	<
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	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
114	<	//group therefore the total number of cutoff groups in the system is
115	<	//equal to the total number of atoms minus number of atoms belong to
116	<	//cutoff group defined in meta-data file plus the number of cutoff
117	<	//groups defined in meta-data file
118	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
119	<
120	<	//every free atom (atom does not belong to rigid bodies) is an
121	<	//integrable object therefore the total number of integrable objects
122	<	//in the system is equal to the total number of atoms minus number of
123	<	//atoms belong to rigid body defined in meta-data file plus the number
124	<	//of rigid bodies defined in meta-data file
125	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
126	<	+ nGlobalRigidBodies_;
127	<
128	<	nGlobalMols_ = molStampIds_.size();
156	<
157	<	#ifdef IS_MPI
158	<	molToProcMap_.resize(nGlobalMols_);
159	<	#endif
160	<
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;
128	>
129		}
130	<
130	>
131	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
132	>	//group therefore the total number of cutoff groups in the system is
133	>	//equal to the total number of atoms minus number of atoms belong to
134	>	//cutoff group defined in meta-data file plus the number of cutoff
135	>	//groups defined in meta-data file
136	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
137	>
138	>	//every free atom (atom does not belong to rigid bodies) is an
139	>	//integrable object therefore the total number of integrable objects
140	>	//in the system is equal to the total number of atoms minus number of
141	>	//atoms belong to rigid body defined in meta-data file plus the number
142	>	//of rigid bodies defined in meta-data file
143	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
144	>	+ nGlobalRigidBodies_;
145	>
146	>	nGlobalMols_ = molStampIds_.size();
147	>	molToProcMap_.resize(nGlobalMols_);
148	>	}
149	>
150		SimInfo::~SimInfo() {
151	<	std::map<int, Molecule*>::iterator i;
151	>	map<int, Molecule*>::iterator i;
152		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
153		delete i->second;
154		}
#	Line 172 | Line 159 | namespace oopse {
159		delete forceField_;
160		}
161
175	–	int SimInfo::getNGlobalConstraints() {
176	–	int nGlobalConstraints;
177	–	#ifdef IS_MPI
178	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
179	–	MPI_COMM_WORLD);
180	–	#else
181	–	nGlobalConstraints =  nConstraints_;
182	–	#endif
183	–	return nGlobalConstraints;
184	–	}
162
163		bool SimInfo::addMolecule(Molecule* mol) {
164		MoleculeIterator i;
165	<
165	>
166		i = molecules_.find(mol->getGlobalIndex());
167		if (i == molecules_.end() ) {
168	<
169	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
170	<
168	>
169	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
170	>
171		nAtoms_ += mol->getNAtoms();
172		nBonds_ += mol->getNBonds();
173		nBends_ += mol->getNBends();
174		nTorsions_ += mol->getNTorsions();
175	+	nInversions_ += mol->getNInversions();
176		nRigidBodies_ += mol->getNRigidBodies();
177		nIntegrableObjects_ += mol->getNIntegrableObjects();
178		nCutoffGroups_ += mol->getNCutoffGroups();
179		nConstraints_ += mol->getNConstraintPairs();
180	<
181	<	addExcludePairs(mol);
182	<
180	>
181	>	addInteractionPairs(mol);
182	>
183		return true;
184		} else {
185		return false;
186		}
187		}
188	<
188	>
189		bool SimInfo::removeMolecule(Molecule* mol) {
190		MoleculeIterator i;
191		i = molecules_.find(mol->getGlobalIndex());
#	Line 220 | Line 198 | namespace oopse {
198		nBonds_ -= mol->getNBonds();
199		nBends_ -= mol->getNBends();
200		nTorsions_ -= mol->getNTorsions();
201	+	nInversions_ -= mol->getNInversions();
202		nRigidBodies_ -= mol->getNRigidBodies();
203		nIntegrableObjects_ -= mol->getNIntegrableObjects();
204		nCutoffGroups_ -= mol->getNCutoffGroups();
205		nConstraints_ -= mol->getNConstraintPairs();
206
207	<	removeExcludePairs(mol);
207	>	removeInteractionPairs(mol);
208		molecules_.erase(mol->getGlobalIndex());
209
210		delete mol;
#	Line 234 | Line 213 | namespace oopse {
213		} else {
214		return false;
215		}
237	–
238	–
216		}
217
218
#	Line 253 | Line 230 | namespace oopse {
230		void SimInfo::calcNdf() {
231		int ndf_local;
232		MoleculeIterator i;
233	<	std::vector<StuntDouble*>::iterator j;
233	>	vector<StuntDouble*>::iterator j;
234		Molecule* mol;
235		StuntDouble* integrableObject;
236
#	Line 304 | Line 281 | namespace oopse {
281		int ndfRaw_local;
282
283		MoleculeIterator i;
284	<	std::vector<StuntDouble*>::iterator j;
284	>	vector<StuntDouble*>::iterator j;
285		Molecule* mol;
286		StuntDouble* integrableObject;
287
#	Line 351 | Line 328 | namespace oopse {
328
329		}
330
331	<	void SimInfo::addExcludePairs(Molecule* mol) {
332	<	std::vector<Bond*>::iterator bondIter;
333	<	std::vector<Bend*>::iterator bendIter;
334	<	std::vector<Torsion*>::iterator torsionIter;
331	>	void SimInfo::addInteractionPairs(Molecule* mol) {
332	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
333	>	vector<Bond*>::iterator bondIter;
334	>	vector<Bend*>::iterator bendIter;
335	>	vector<Torsion*>::iterator torsionIter;
336	>	vector<Inversion*>::iterator inversionIter;
337		Bond* bond;
338		Bend* bend;
339		Torsion* torsion;
340	+	Inversion* inversion;
341		int a;
342		int b;
343		int c;
344		int d;
345
346	<	std::map<int, std::set<int> > atomGroups;
346	>	// atomGroups can be used to add special interaction maps between
347	>	// groups of atoms that are in two separate rigid bodies.
348	>	// However, most site-site interactions between two rigid bodies
349	>	// are probably not special, just the ones between the physically
350	>	// bonded atoms.  Interactions *within* a single rigid body should
351	>	// always be excluded.  These are done at the bottom of this
352	>	// function.
353
354	+	map<int, set<int> > atomGroups;
355		Molecule::RigidBodyIterator rbIter;
356		RigidBody* rb;
357		Molecule::IntegrableObjectIterator ii;
358		StuntDouble* integrableObject;
359
360	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
361	<	integrableObject = mol->nextIntegrableObject(ii)) {
362	<
360	>	for (integrableObject = mol->beginIntegrableObject(ii);
361	>	integrableObject != NULL;
362	>	integrableObject = mol->nextIntegrableObject(ii)) {
363	>
364		if (integrableObject->isRigidBody()) {
365	<	rb = static_cast<RigidBody*>(integrableObject);
366	<	std::vector<Atom*> atoms = rb->getAtoms();
367	<	std::set<int> rigidAtoms;
368	<	for (int i = 0; i < atoms.size(); ++i) {
369	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
370	<	}
371	<	for (int i = 0; i < atoms.size(); ++i) {
372	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
373	<	}
365	>	rb = static_cast<RigidBody*>(integrableObject);
366	>	vector<Atom*> atoms = rb->getAtoms();
367	>	set<int> rigidAtoms;
368	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
369	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
370	>	}
371	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
372	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
373	>	}
374		} else {
375	<	std::set<int> oneAtomSet;
375	>	set<int> oneAtomSet;
376		oneAtomSet.insert(integrableObject->getGlobalIndex());
377	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
377	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
378		}
379		}
380	+
381	+	for (bond= mol->beginBond(bondIter); bond != NULL;
382	+	bond = mol->nextBond(bondIter)) {
383
393	–
394	–
395	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
384		a = bond->getAtomA()->getGlobalIndex();
385	<	b = bond->getAtomB()->getGlobalIndex();
386	<	exclude_.addPair(a, b);
385	>	b = bond->getAtomB()->getGlobalIndex();
386	>
387	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
388	>	oneTwoInteractions_.addPair(a, b);
389	>	} else {
390	>	excludedInteractions_.addPair(a, b);
391	>	}
392		}
393
394	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
394	>	for (bend= mol->beginBend(bendIter); bend != NULL;
395	>	bend = mol->nextBend(bendIter)) {
396	>
397		a = bend->getAtomA()->getGlobalIndex();
398		b = bend->getAtomB()->getGlobalIndex();
399		c = bend->getAtomC()->getGlobalIndex();
405	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
406	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
407	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
408	–
409	–	exclude_.addPairs(rigidSetA, rigidSetB);
410	–	exclude_.addPairs(rigidSetA, rigidSetC);
411	–	exclude_.addPairs(rigidSetB, rigidSetC);
400
401	<	//exclude_.addPair(a, b);
402	<	//exclude_.addPair(a, c);
403	<	//exclude_.addPair(b, c);
401	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
402	>	oneTwoInteractions_.addPair(a, b);
403	>	oneTwoInteractions_.addPair(b, c);
404	>	} else {
405	>	excludedInteractions_.addPair(a, b);
406	>	excludedInteractions_.addPair(b, c);
407	>	}
408	>
409	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
410	>	oneThreeInteractions_.addPair(a, c);
411	>	} else {
412	>	excludedInteractions_.addPair(a, c);
413	>	}
414		}
415
416	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
416	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
417	>	torsion = mol->nextTorsion(torsionIter)) {
418	>
419		a = torsion->getAtomA()->getGlobalIndex();
420		b = torsion->getAtomB()->getGlobalIndex();
421		c = torsion->getAtomC()->getGlobalIndex();
422	<	d = torsion->getAtomD()->getGlobalIndex();
423	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
424	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
425	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
426	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
422	>	d = torsion->getAtomD()->getGlobalIndex();
423
424	<	exclude_.addPairs(rigidSetA, rigidSetB);
425	<	exclude_.addPairs(rigidSetA, rigidSetC);
426	<	exclude_.addPairs(rigidSetA, rigidSetD);
427	<	exclude_.addPairs(rigidSetB, rigidSetC);
428	<	exclude_.addPairs(rigidSetB, rigidSetD);
429	<	exclude_.addPairs(rigidSetC, rigidSetD);
424	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
425	>	oneTwoInteractions_.addPair(a, b);
426	>	oneTwoInteractions_.addPair(b, c);
427	>	oneTwoInteractions_.addPair(c, d);
428	>	} else {
429	>	excludedInteractions_.addPair(a, b);
430	>	excludedInteractions_.addPair(b, c);
431	>	excludedInteractions_.addPair(c, d);
432	>	}
433
434	<	/*
435	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
436	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
437	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
438	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
439	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
440	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
441	<
442	<
443	<	exclude_.addPair(a, b);
444	<	exclude_.addPair(a, c);
445	<	exclude_.addPair(a, d);
446	<	exclude_.addPair(b, c);
448	<	exclude_.addPair(b, d);
449	<	exclude_.addPair(c, d);
450	<	*/
434	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
435	>	oneThreeInteractions_.addPair(a, c);
436	>	oneThreeInteractions_.addPair(b, d);
437	>	} else {
438	>	excludedInteractions_.addPair(a, c);
439	>	excludedInteractions_.addPair(b, d);
440	>	}
441	>
442	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
443	>	oneFourInteractions_.addPair(a, d);
444	>	} else {
445	>	excludedInteractions_.addPair(a, d);
446	>	}
447		}
448
449	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
450	<	std::vector<Atom*> atoms = rb->getAtoms();
451	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
452	<	for (int j = i + 1; j < atoms.size(); ++j) {
449	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
450	>	inversion = mol->nextInversion(inversionIter)) {
451	>
452	>	a = inversion->getAtomA()->getGlobalIndex();
453	>	b = inversion->getAtomB()->getGlobalIndex();
454	>	c = inversion->getAtomC()->getGlobalIndex();
455	>	d = inversion->getAtomD()->getGlobalIndex();
456	>
457	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
458	>	oneTwoInteractions_.addPair(a, b);
459	>	oneTwoInteractions_.addPair(a, c);
460	>	oneTwoInteractions_.addPair(a, d);
461	>	} else {
462	>	excludedInteractions_.addPair(a, b);
463	>	excludedInteractions_.addPair(a, c);
464	>	excludedInteractions_.addPair(a, d);
465	>	}
466	>
467	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
468	>	oneThreeInteractions_.addPair(b, c);
469	>	oneThreeInteractions_.addPair(b, d);
470	>	oneThreeInteractions_.addPair(c, d);
471	>	} else {
472	>	excludedInteractions_.addPair(b, c);
473	>	excludedInteractions_.addPair(b, d);
474	>	excludedInteractions_.addPair(c, d);
475	>	}
476	>	}
477	>
478	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
479	>	rb = mol->nextRigidBody(rbIter)) {
480	>	vector<Atom*> atoms = rb->getAtoms();
481	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
482	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
483		a = atoms[i]->getGlobalIndex();
484		b = atoms[j]->getGlobalIndex();
485	<	exclude_.addPair(a, b);
485	>	excludedInteractions_.addPair(a, b);
486		}
487		}
488		}
489
490		}
491
492	<	void SimInfo::removeExcludePairs(Molecule* mol) {
493	<	std::vector<Bond*>::iterator bondIter;
494	<	std::vector<Bend*>::iterator bendIter;
495	<	std::vector<Torsion*>::iterator torsionIter;
492	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
493	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
494	>	vector<Bond*>::iterator bondIter;
495	>	vector<Bend*>::iterator bendIter;
496	>	vector<Torsion*>::iterator torsionIter;
497	>	vector<Inversion*>::iterator inversionIter;
498		Bond* bond;
499		Bend* bend;
500		Torsion* torsion;
501	+	Inversion* inversion;
502		int a;
503		int b;
504		int c;
505		int d;
506
507	<	std::map<int, std::set<int> > atomGroups;
479	<
507	>	map<int, set<int> > atomGroups;
508		Molecule::RigidBodyIterator rbIter;
509		RigidBody* rb;
510		Molecule::IntegrableObjectIterator ii;
511		StuntDouble* integrableObject;
512
513	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
514	<	integrableObject = mol->nextIntegrableObject(ii)) {
515	<
513	>	for (integrableObject = mol->beginIntegrableObject(ii);
514	>	integrableObject != NULL;
515	>	integrableObject = mol->nextIntegrableObject(ii)) {
516	>
517		if (integrableObject->isRigidBody()) {
518	<	rb = static_cast<RigidBody*>(integrableObject);
519	<	std::vector<Atom*> atoms = rb->getAtoms();
520	<	std::set<int> rigidAtoms;
521	<	for (int i = 0; i < atoms.size(); ++i) {
522	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
523	<	}
524	<	for (int i = 0; i < atoms.size(); ++i) {
525	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
526	<	}
518	>	rb = static_cast<RigidBody*>(integrableObject);
519	>	vector<Atom*> atoms = rb->getAtoms();
520	>	set<int> rigidAtoms;
521	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
522	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
523	>	}
524	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
525	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
526	>	}
527		} else {
528	<	std::set<int> oneAtomSet;
528	>	set<int> oneAtomSet;
529		oneAtomSet.insert(integrableObject->getGlobalIndex());
530	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
530	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
531		}
532		}
533
534	<
535	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
534	>	for (bond= mol->beginBond(bondIter); bond != NULL;
535	>	bond = mol->nextBond(bondIter)) {
536	>
537		a = bond->getAtomA()->getGlobalIndex();
538	<	b = bond->getAtomB()->getGlobalIndex();
539	<	exclude_.removePair(a, b);
538	>	b = bond->getAtomB()->getGlobalIndex();
539	>
540	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
541	>	oneTwoInteractions_.removePair(a, b);
542	>	} else {
543	>	excludedInteractions_.removePair(a, b);
544	>	}
545		}
546
547	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
547	>	for (bend= mol->beginBend(bendIter); bend != NULL;
548	>	bend = mol->nextBend(bendIter)) {
549	>
550		a = bend->getAtomA()->getGlobalIndex();
551		b = bend->getAtomB()->getGlobalIndex();
552		c = bend->getAtomC()->getGlobalIndex();
516	–
517	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
518	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
519	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
520	–
521	–	exclude_.removePairs(rigidSetA, rigidSetB);
522	–	exclude_.removePairs(rigidSetA, rigidSetC);
523	–	exclude_.removePairs(rigidSetB, rigidSetC);
553
554	<	//exclude_.removePair(a, b);
555	<	//exclude_.removePair(a, c);
556	<	//exclude_.removePair(b, c);
554	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
555	>	oneTwoInteractions_.removePair(a, b);
556	>	oneTwoInteractions_.removePair(b, c);
557	>	} else {
558	>	excludedInteractions_.removePair(a, b);
559	>	excludedInteractions_.removePair(b, c);
560	>	}
561	>
562	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
563	>	oneThreeInteractions_.removePair(a, c);
564	>	} else {
565	>	excludedInteractions_.removePair(a, c);
566	>	}
567		}
568
569	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
569	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
570	>	torsion = mol->nextTorsion(torsionIter)) {
571	>
572		a = torsion->getAtomA()->getGlobalIndex();
573		b = torsion->getAtomB()->getGlobalIndex();
574		c = torsion->getAtomC()->getGlobalIndex();
575	<	d = torsion->getAtomD()->getGlobalIndex();
575	>	d = torsion->getAtomD()->getGlobalIndex();
576	>
577	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
578	>	oneTwoInteractions_.removePair(a, b);
579	>	oneTwoInteractions_.removePair(b, c);
580	>	oneTwoInteractions_.removePair(c, d);
581	>	} else {
582	>	excludedInteractions_.removePair(a, b);
583	>	excludedInteractions_.removePair(b, c);
584	>	excludedInteractions_.removePair(c, d);
585	>	}
586
587	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
588	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
589	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
590	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
587	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
588	>	oneThreeInteractions_.removePair(a, c);
589	>	oneThreeInteractions_.removePair(b, d);
590	>	} else {
591	>	excludedInteractions_.removePair(a, c);
592	>	excludedInteractions_.removePair(b, d);
593	>	}
594
595	<	exclude_.removePairs(rigidSetA, rigidSetB);
596	<	exclude_.removePairs(rigidSetA, rigidSetC);
597	<	exclude_.removePairs(rigidSetA, rigidSetD);
598	<	exclude_.removePairs(rigidSetB, rigidSetC);
599	<	exclude_.removePairs(rigidSetB, rigidSetD);
600	<	exclude_.removePairs(rigidSetC, rigidSetD);
595	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
596	>	oneFourInteractions_.removePair(a, d);
597	>	} else {
598	>	excludedInteractions_.removePair(a, d);
599	>	}
600	>	}
601
602	<	/*
603	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
550	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
551	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
552	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
553	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
554	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
602	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
603	>	inversion = mol->nextInversion(inversionIter)) {
604
605	<
606	<	exclude_.removePair(a, b);
607	<	exclude_.removePair(a, c);
608	<	exclude_.removePair(a, d);
609	<	exclude_.removePair(b, c);
610	<	exclude_.removePair(b, d);
611	<	exclude_.removePair(c, d);
612	<	*/
605	>	a = inversion->getAtomA()->getGlobalIndex();
606	>	b = inversion->getAtomB()->getGlobalIndex();
607	>	c = inversion->getAtomC()->getGlobalIndex();
608	>	d = inversion->getAtomD()->getGlobalIndex();
609	>
610	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
611	>	oneTwoInteractions_.removePair(a, b);
612	>	oneTwoInteractions_.removePair(a, c);
613	>	oneTwoInteractions_.removePair(a, d);
614	>	} else {
615	>	excludedInteractions_.removePair(a, b);
616	>	excludedInteractions_.removePair(a, c);
617	>	excludedInteractions_.removePair(a, d);
618	>	}
619	>
620	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
621	>	oneThreeInteractions_.removePair(b, c);
622	>	oneThreeInteractions_.removePair(b, d);
623	>	oneThreeInteractions_.removePair(c, d);
624	>	} else {
625	>	excludedInteractions_.removePair(b, c);
626	>	excludedInteractions_.removePair(b, d);
627	>	excludedInteractions_.removePair(c, d);
628	>	}
629		}
630
631	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
632	<	std::vector<Atom*> atoms = rb->getAtoms();
633	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
634	<	for (int j = i + 1; j < atoms.size(); ++j) {
631	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
632	>	rb = mol->nextRigidBody(rbIter)) {
633	>	vector<Atom*> atoms = rb->getAtoms();
634	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
635	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
636		a = atoms[i]->getGlobalIndex();
637		b = atoms[j]->getGlobalIndex();
638	<	exclude_.removePair(a, b);
638	>	excludedInteractions_.removePair(a, b);
639		}
640		}
641		}
642	<
642	>
643		}
644	<
645	<
644	>
645	>
646		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
647		int curStampId;
648	<
648	>
649		//index from 0
650		curStampId = moleculeStamps_.size();
651
#	Line 587 | Line 653 | namespace oopse {
653		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
654		}
655
656	+
657	+	/**
658	+	* update
659	+	*
660	+	*  Performs the global checks and variable settings after the objects have been
661	+	*  created.
662	+	*
663	+	*/
664		void SimInfo::update() {
665	+
666	+	setupSimVariables();
667	+	setupCutoffs();
668	+	setupSwitching();
669	+	setupElectrostatics();
670	+	setupNeighborlists();
671
592	–	setupSimType();
593	–
672		#ifdef IS_MPI
673		setupFortranParallel();
674		#endif
597	–
675		setupFortranSim();
676	+	fortranInitialized_ = true;
677
600	–	//setup fortran force field
601	–	/** @deprecate */
602	–	int isError = 0;
603	–
604	–	setupCutoff();
605	–
606	–	setupElectrostaticSummationMethod( isError );
607	–	setupSwitchingFunction();
608	–	setupAccumulateBoxDipole();
609	–
610	–	if(isError){
611	–	sprintf( painCave.errMsg,
612	–	"ForceField error: There was an error initializing the forceField in fortran.\n" );
613	–	painCave.isFatal = 1;
614	–	simError();
615	–	}
616	–
678		calcNdf();
679		calcNdfRaw();
680		calcNdfTrans();
620	–
621	–	fortranInitialized_ = true;
681		}
682	<
683	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
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)) {
632	<
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	<
637	<	}
638	<
693	>	}
694	>	}
695		return atomTypes;
696		}
697
698	<	void SimInfo::setupSimType() {
699	<	std::set<AtomType*>::iterator i;
700	<	std::set<AtomType*> atomTypes;
701	<	atomTypes = getUniqueAtomTypes();
702	<
703	<	int useLennardJones = 0;
704	<	int useElectrostatic = 0;
705	<	int useEAM = 0;
706	<	int useSC = 0;
707	<	int useCharge = 0;
708	<	int useDirectional = 0;
709	<	int useDipole = 0;
710	<	int useGayBerne = 0;
711	<	int useSticky = 0;
712	<	int useStickyPower = 0;
713	<	int useShape = 0;
714	<	int useFLARB = 0; //it is not in AtomType yet
715	<	int useDirectionalAtom = 0;
660	<	int useElectrostatics = 0;
661	<	//usePBC and useRF are from simParams
662	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
663	<	int useRF;
664	<	int useSF;
665	<	int useSP;
666	<	int useBoxDipole;
667	<	std::string myMethod;
668	<
669	<	// set the useRF logical
670	<	useRF = 0;
671	<	useSF = 0;
672	<	useSP = 0;
673	<
674	<
675	<	if (simParams_->haveElectrostaticSummationMethod()) {
676	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
677	<	toUpper(myMethod);
678	<	if (myMethod == "REACTION_FIELD"){
679	<	useRF = 1;
680	<	} else if (myMethod == "SHIFTED_FORCE"){
681	<	useSF = 1;
682	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
683	<	useSP = 1;
684	<	}
685	<	}
698	>	/**
699	>	* setupCutoffs
700	>	*
701	>	* Sets the values of cutoffRadius and cutoffMethod
702	>	*
703	>	* cutoffRadius : realType
704	>	*  If the cutoffRadius was explicitly set, use that value.
705	>	*  If the cutoffRadius was not explicitly set:
706	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
707	>	*      No electrostatic atoms?  Poll the atom types present in the
708	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
709	>	*      Use the maximum suggested value that was found.
710	>	*
711	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
712	>	*      If cutoffMethod was explicitly set, use that choice.
713	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
714	>	*/
715	>	void SimInfo::setupCutoffs() {
716
717	<	if (simParams_->haveAccumulateBoxDipole())
718	<	if (simParams_->getAccumulateBoxDipole())
719	<	useBoxDipole = 1;
720	<
721	<	//loop over all of the atom types
722	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
723	<	useLennardJones |= (*i)->isLennardJones();
724	<	useElectrostatic |= (*i)->isElectrostatic();
725	<	useEAM |= (*i)->isEAM();
726	<	useSC |= (*i)->isSC();
727	<	useCharge |= (*i)->isCharge();
728	<	useDirectional |= (*i)->isDirectional();
729	<	useDipole |= (*i)->isDipole();
730	<	useGayBerne |= (*i)->isGayBerne();
731	<	useSticky |= (*i)->isSticky();
732	<	useStickyPower |= (*i)->isStickyPower();
733	<	useShape |= (*i)->isShape();
717	>	if (simParams_->haveCutoffRadius()) {
718	>	cutoffRadius_ = simParams_->getCutoffRadius();
719	>	} else {
720	>	if (usesElectrostaticAtoms_) {
721	>	sprintf(painCave.errMsg,
722	>	"SimInfo: No value was set for the cutoffRadius.\n"
723	>	"\tOpenMD will use a default value of 12.0 angstroms"
724	>	"\tfor the cutoffRadius.\n");
725	>	painCave.isFatal = 0;
726	>	painCave.severity = OPENMD_INFO;
727	>	simError();
728	>	cutoffRadius_ = 12.0;
729	>	} else {
730	>	RealType thisCut;
731	>	set<AtomType*>::iterator i;
732	>	set<AtomType*> atomTypes;
733	>	atomTypes = getSimulatedAtomTypes();
734	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
735	>	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
736	>	cutoffRadius_ = max(thisCut, cutoffRadius_);
737	>	}
738	>	sprintf(painCave.errMsg,
739	>	"SimInfo: No value was set for the cutoffRadius.\n"
740	>	"\tOpenMD will use %lf angstroms.\n",
741	>	cutoffRadius_);
742	>	painCave.isFatal = 0;
743	>	painCave.severity = OPENMD_INFO;
744	>	simError();
745	>	}
746		}
747
748	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
707	<	useDirectionalAtom = 1;
708	<	}
748	>	InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
749
750	<	if (useCharge || useDipole) {
751	<	useElectrostatics = 1;
750	>	map<string, CutoffMethod> stringToCutoffMethod;
751	>	stringToCutoffMethod["HARD"] = HARD;
752	>	stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
753	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
754	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
755	>
756	>	if (simParams_->haveCutoffMethod()) {
757	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
758	>	map<string, CutoffMethod>::iterator i;
759	>	i = stringToCutoffMethod.find(cutMeth);
760	>	if (i == stringToCutoffMethod.end()) {
761	>	sprintf(painCave.errMsg,
762	>	"SimInfo: Could not find chosen cutoffMethod %s\n"
763	>	"\tShould be one of: "
764	>	"HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
765	>	cutMeth.c_str());
766	>	painCave.isFatal = 1;
767	>	painCave.severity = OPENMD_ERROR;
768	>	simError();
769	>	} else {
770	>	cutoffMethod_ = i->second;
771	>	}
772	>	} else {
773	>	sprintf(painCave.errMsg,
774	>	"SimInfo: No value was set for the cutoffMethod.\n"
775	>	"\tOpenMD will use SHIFTED_FORCE.\n");
776	>	painCave.isFatal = 0;
777	>	painCave.severity = OPENMD_INFO;
778	>	simError();
779	>	cutoffMethod_ = SHIFTED_FORCE;
780		}
781
782	<	#ifdef IS_MPI
783	<	int temp;
782	>	InteractionManager::Instance()->setCutoffMethod(cutoffMethod_);
783	>	}
784	>
785	>	/**
786	>	* setupSwitching
787	>	*
788	>	* Sets the values of switchingRadius and
789	>	*  If the switchingRadius was explicitly set, use that value (but check it)
790	>	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
791	>	*/
792	>	void SimInfo::setupSwitching() {
793	>
794	>	if (simParams_->haveSwitchingRadius()) {
795	>	switchingRadius_ = simParams_->getSwitchingRadius();
796	>	if (switchingRadius_ > cutoffRadius_) {
797	>	sprintf(painCave.errMsg,
798	>	"SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
799	>	switchingRadius_, cutoffRadius_);
800	>	painCave.isFatal = 1;
801	>	painCave.severity = OPENMD_ERROR;
802	>	simError();
803	>	}
804	>	} else {
805	>	switchingRadius_ = 0.85 * cutoffRadius_;
806	>	sprintf(painCave.errMsg,
807	>	"SimInfo: No value was set for the switchingRadius.\n"
808	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
809	>	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
810	>	painCave.isFatal = 0;
811	>	painCave.severity = OPENMD_WARNING;
812	>	simError();
813	>	}
814	>
815	>	InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
816
817	<	temp = usePBC;
718	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
719	<
720	<	temp = useDirectionalAtom;
721	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
722	<
723	<	temp = useLennardJones;
724	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
725	<
726	<	temp = useElectrostatics;
727	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
728	<
729	<	temp = useCharge;
730	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
731	<
732	<	temp = useDipole;
733	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
734	<
735	<	temp = useSticky;
736	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
737	<
738	<	temp = useStickyPower;
739	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
817	>	SwitchingFunctionType ft;
818
819	<	temp = useGayBerne;
820	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819	>	if (simParams_->haveSwitchingFunctionType()) {
820	>	string funcType = simParams_->getSwitchingFunctionType();
821	>	toUpper(funcType);
822	>	if (funcType == "CUBIC") {
823	>	ft = cubic;
824	>	} else {
825	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
826	>	ft = fifth_order_poly;
827	>	} else {
828	>	// throw error
829	>	sprintf( painCave.errMsg,
830	>	"SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
831	>	"\tswitchingFunctionType must be one of: "
832	>	"\"cubic\" or \"fifth_order_polynomial\".",
833	>	funcType.c_str() );
834	>	painCave.isFatal = 1;
835	>	painCave.severity = OPENMD_ERROR;
836	>	simError();
837	>	}
838	>	}
839	>	}
840
841	<	temp = useEAM;
842	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
841	>	InteractionManager::Instance()->setSwitchingFunctionType(ft);
842	>	}
843
844	<	temp = useSC;
845	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
846	<
847	<	temp = useShape;
848	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
844	>	/**
845	>	* setupSkinThickness
846	>	*
847	>	*  If the skinThickness was explicitly set, use that value (but check it)
848	>	*  If the skinThickness was not explicitly set: use 1.0 angstroms
849	>	*/
850	>	void SimInfo::setupSkinThickness() {
851	>	if (simParams_->haveSkinThickness()) {
852	>	skinThickness_ = simParams_->getSkinThickness();
853	>	} else {
854	>	skinThickness_ = 1.0;
855	>	sprintf(painCave.errMsg,
856	>	"SimInfo Warning: No value was set for the skinThickness.\n"
857	>	"\tOpenMD will use a default value of %f Angstroms\n"
858	>	"\tfor this simulation\n", skinThickness_);
859	>	painCave.isFatal = 0;
860	>	simError();
861	>	}
862	>	}
863
864	<	temp = useFLARB;
865	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
864	>	void SimInfo::setupSimType() {
865	>	set<AtomType*>::iterator i;
866	>	set<AtomType*> atomTypes;
867	>	atomTypes = getSimulatedAtomTypes();
868
869	<	temp = useRF;
757	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
869	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
870
871	<	temp = useSF;
872	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
871	>	int usesElectrostatic = 0;
872	>	int usesMetallic = 0;
873	>	int usesDirectional = 0;
874	>	//loop over all of the atom types
875	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
876	>	usesElectrostatic |= (*i)->isElectrostatic();
877	>	usesMetallic |= (*i)->isMetal();
878	>	usesDirectional |= (*i)->isDirectional();
879	>	}
880
881	<	temp = useSP;
882	<	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
881	>	#ifdef IS_MPI
882	>	int temp;
883	>	temp = usesDirectional;
884	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
885
886	<	temp = useBoxDipole;
887	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
886	>	temp = usesMetallic;
887	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
888
889	+	temp = usesElectrostatic;
890	+	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
891		#endif
892	<
893	<	fInfo_.SIM_uses_PBC = usePBC;
894	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
895	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
896	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
897	<	fInfo_.SIM_uses_Charges = useCharge;
775	<	fInfo_.SIM_uses_Dipoles = useDipole;
776	<	fInfo_.SIM_uses_Sticky = useSticky;
777	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
778	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
779	<	fInfo_.SIM_uses_EAM = useEAM;
780	<	fInfo_.SIM_uses_SC = useSC;
781	<	fInfo_.SIM_uses_Shapes = useShape;
782	<	fInfo_.SIM_uses_FLARB = useFLARB;
783	<	fInfo_.SIM_uses_RF = useRF;
784	<	fInfo_.SIM_uses_SF = useSF;
785	<	fInfo_.SIM_uses_SP = useSP;
786	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
892	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
893	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
894	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
895	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
896	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
897	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
898		}
899
900		void SimInfo::setupFortranSim() {
901		int isError;
902	<	int nExclude;
903	<	std::vector<int> fortranGlobalGroupMembership;
902	>	int nExclude, nOneTwo, nOneThree, nOneFour;
903	>	vector<int> fortranGlobalGroupMembership;
904
905	<	nExclude = exclude_.getSize();
905	>	notifyFortranSkinThickness(&skinThickness_);
906	>
907	>	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
908	>	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
909	>	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
910	>
911		isError = 0;
912
913		//globalGroupMembership_ is filled by SimCreator
#	Line 800 | Line 916 | namespace oopse {
916		}
917
918		//calculate mass ratio of cutoff group
919	<	std::vector<RealType> mfact;
919	>	vector<RealType> mfact;
920		SimInfo::MoleculeIterator mi;
921		Molecule* mol;
922		Molecule::CutoffGroupIterator ci;
#	Line 823 | Line 939 | namespace oopse {
939		else
940		mfact.push_back( 1.0 );
941		}
826	–
942		}
943		}
944
945		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
946	<	std::vector<int> identArray;
946	>	vector<int> identArray;
947
948		//to avoid memory reallocation, reserve enough space identArray
949		identArray.reserve(getNAtoms());
#	Line 841 | Line 956 | namespace oopse {
956
957		//fill molMembershipArray
958		//molMembershipArray is filled by SimCreator
959	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
959	>	vector<int> molMembershipArray(nGlobalAtoms_);
960		for (int i = 0; i < nGlobalAtoms_; i++) {
961		molMembershipArray[i] = globalMolMembership_[i] + 1;
962		}
963
964		//setup fortran simulation
850	–	int nGlobalExcludes = 0;
851	–	int* globalExcludes = NULL;
852	–	int* excludeList = exclude_.getExcludeList();
853	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
854	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
855	–	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
965
966	<	if( isError ){
966	>	nExclude = excludedInteractions_.getSize();
967	>	nOneTwo = oneTwoInteractions_.getSize();
968	>	nOneThree = oneThreeInteractions_.getSize();
969	>	nOneFour = oneFourInteractions_.getSize();
970
971	+	int* excludeList = excludedInteractions_.getPairList();
972	+	int* oneTwoList = oneTwoInteractions_.getPairList();
973	+	int* oneThreeList = oneThreeInteractions_.getPairList();
974	+	int* oneFourList = oneFourInteractions_.getPairList();
975	+
976	+	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
977	+	&nExclude, excludeList,
978	+	&nOneTwo, oneTwoList,
979	+	&nOneThree, oneThreeList,
980	+	&nOneFour, oneFourList,
981	+	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
982	+	&fortranGlobalGroupMembership[0], &isError);
983	+
984	+	if( isError ){
985	+
986		sprintf( painCave.errMsg,
987		"There was an error setting the simulation information in fortran.\n" );
988		painCave.isFatal = 1;
989	<	painCave.severity = OOPSE_ERROR;
989	>	painCave.severity = OPENMD_ERROR;
990		simError();
991		}
992	<
993	<	#ifdef IS_MPI
992	>
993	>
994		sprintf( checkPointMsg,
995		"succesfully sent the simulation information to fortran.\n");
996	<	MPIcheckPoint();
997	<	#endif // is_mpi
996	>
997	>	errorCheckPoint();
998	>
999	>	// Setup number of neighbors in neighbor list if present
1000	>	if (simParams_->haveNeighborListNeighbors()) {
1001	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
1002	>	setNeighbors(&nlistNeighbors);
1003	>	}
1004	>
1005	>
1006		}
1007
1008
874	–	#ifdef IS_MPI
1009		void SimInfo::setupFortranParallel() {
1010	<
1010	>	#ifdef IS_MPI
1011		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1012	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1013	<	std::vector<int> localToGlobalCutoffGroupIndex;
1012	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1013	>	vector<int> localToGlobalCutoffGroupIndex;
1014		SimInfo::MoleculeIterator mi;
1015		Molecule::AtomIterator ai;
1016		Molecule::CutoffGroupIterator ci;
#	Line 923 | Line 1057 | namespace oopse {
1057		}
1058
1059		sprintf(checkPointMsg, " mpiRefresh successful.\n");
1060	<	MPIcheckPoint();
1060	>	errorCheckPoint();
1061
928	–
929	–	}
930	–
1062		#endif
932	–
933	–	void SimInfo::setupCutoff() {
934	–
935	–	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
936	–
937	–	// Check the cutoff policy
938	–	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
939	–
940	–	std::string myPolicy;
941	–	if (forceFieldOptions_.haveCutoffPolicy()){
942	–	myPolicy = forceFieldOptions_.getCutoffPolicy();
943	–	}else if (simParams_->haveCutoffPolicy()) {
944	–	myPolicy = simParams_->getCutoffPolicy();
945	–	}
946	–
947	–	if (!myPolicy.empty()){
948	–	toUpper(myPolicy);
949	–	if (myPolicy == "MIX") {
950	–	cp = MIX_CUTOFF_POLICY;
951	–	} else {
952	–	if (myPolicy == "MAX") {
953	–	cp = MAX_CUTOFF_POLICY;
954	–	} else {
955	–	if (myPolicy == "TRADITIONAL") {
956	–	cp = TRADITIONAL_CUTOFF_POLICY;
957	–	} else {
958	–	// throw error
959	–	sprintf( painCave.errMsg,
960	–	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
961	–	painCave.isFatal = 1;
962	–	simError();
963	–	}
964	–	}
965	–	}
966	–	}
967	–	notifyFortranCutoffPolicy(&cp);
968	–
969	–	// Check the Skin Thickness for neighborlists
970	–	RealType skin;
971	–	if (simParams_->haveSkinThickness()) {
972	–	skin = simParams_->getSkinThickness();
973	–	notifyFortranSkinThickness(&skin);
974	–	}
975	–
976	–	// Check if the cutoff was set explicitly:
977	–	if (simParams_->haveCutoffRadius()) {
978	–	rcut_ = simParams_->getCutoffRadius();
979	–	if (simParams_->haveSwitchingRadius()) {
980	–	rsw_  = simParams_->getSwitchingRadius();
981	–	} else {
982	–	if (fInfo_.SIM_uses_Charges |
983	–	fInfo_.SIM_uses_Dipoles |
984	–	fInfo_.SIM_uses_RF) {
985	–
986	–	rsw_ = 0.85 * rcut_;
987	–	sprintf(painCave.errMsg,
988	–	"SimCreator Warning: No value was set for the switchingRadius.\n"
989	–	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
990	–	"\tswitchingRadius = %f. for this simulation\n", rsw_);
991	–	painCave.isFatal = 0;
992	–	simError();
993	–	} else {
994	–	rsw_ = rcut_;
995	–	sprintf(painCave.errMsg,
996	–	"SimCreator Warning: No value was set for the switchingRadius.\n"
997	–	"\tOOPSE will use the same value as the cutoffRadius.\n"
998	–	"\tswitchingRadius = %f. for this simulation\n", rsw_);
999	–	painCave.isFatal = 0;
1000	–	simError();
1001	–	}
1002	–	}
1003	–
1004	–	notifyFortranCutoffs(&rcut_, &rsw_);
1005	–
1006	–	} else {
1007	–
1008	–	// For electrostatic atoms, we'll assume a large safe value:
1009	–	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1010	–	sprintf(painCave.errMsg,
1011	–	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1012	–	"\tOOPSE will use a default value of 15.0 angstroms"
1013	–	"\tfor the cutoffRadius.\n");
1014	–	painCave.isFatal = 0;
1015	–	simError();
1016	–	rcut_ = 15.0;
1017	–
1018	–	if (simParams_->haveElectrostaticSummationMethod()) {
1019	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1020	–	toUpper(myMethod);
1021	–	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1022	–	if (simParams_->haveSwitchingRadius()){
1023	–	sprintf(painCave.errMsg,
1024	–	"SimInfo Warning: A value was set for the switchingRadius\n"
1025	–	"\teven though the electrostaticSummationMethod was\n"
1026	–	"\tset to %s\n", myMethod.c_str());
1027	–	painCave.isFatal = 1;
1028	–	simError();
1029	–	}
1030	–	}
1031	–	}
1032	–
1033	–	if (simParams_->haveSwitchingRadius()){
1034	–	rsw_ = simParams_->getSwitchingRadius();
1035	–	} else {
1036	–	sprintf(painCave.errMsg,
1037	–	"SimCreator Warning: No value was set for switchingRadius.\n"
1038	–	"\tOOPSE will use a default value of\n"
1039	–	"\t0.85 * cutoffRadius for the switchingRadius\n");
1040	–	painCave.isFatal = 0;
1041	–	simError();
1042	–	rsw_ = 0.85 * rcut_;
1043	–	}
1044	–	notifyFortranCutoffs(&rcut_, &rsw_);
1045	–	} else {
1046	–	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1047	–	// We'll punt and let fortran figure out the cutoffs later.
1048	–
1049	–	notifyFortranYouAreOnYourOwn();
1050	–
1051	–	}
1052	–	}
1063		}
1064
1055	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1056	–
1057	–	int errorOut;
1058	–	int esm =  NONE;
1059	–	int sm = UNDAMPED;
1060	–	RealType alphaVal;
1061	–	RealType dielectric;
1062	–
1063	–	errorOut = isError;
1065
1065	–	if (simParams_->haveElectrostaticSummationMethod()) {
1066	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1067	–	toUpper(myMethod);
1068	–	if (myMethod == "NONE") {
1069	–	esm = NONE;
1070	–	} else {
1071	–	if (myMethod == "SWITCHING_FUNCTION") {
1072	–	esm = SWITCHING_FUNCTION;
1073	–	} else {
1074	–	if (myMethod == "SHIFTED_POTENTIAL") {
1075	–	esm = SHIFTED_POTENTIAL;
1076	–	} else {
1077	–	if (myMethod == "SHIFTED_FORCE") {
1078	–	esm = SHIFTED_FORCE;
1079	–	} else {
1080	–	if (myMethod == "REACTION_FIELD") {
1081	–	esm = REACTION_FIELD;
1082	–	dielectric = simParams_->getDielectric();
1083	–	if (!simParams_->haveDielectric()) {
1084	–	// throw warning
1085	–	sprintf( painCave.errMsg,
1086	–	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1087	–	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1088	–	painCave.isFatal = 0;
1089	–	simError();
1090	–	}
1091	–	} else {
1092	–	// throw error
1093	–	sprintf( painCave.errMsg,
1094	–	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1095	–	"\t(Input file specified %s .)\n"
1096	–	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1097	–	"\t\"shifted_potential\", \"shifted_force\", or \n"
1098	–	"\t\"reaction_field\".\n", myMethod.c_str() );
1099	–	painCave.isFatal = 1;
1100	–	simError();
1101	–	}
1102	–	}
1103	–	}
1104	–	}
1105	–	}
1106	–	}
1107	–
1108	–	if (simParams_->haveElectrostaticScreeningMethod()) {
1109	–	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1110	–	toUpper(myScreen);
1111	–	if (myScreen == "UNDAMPED") {
1112	–	sm = UNDAMPED;
1113	–	} else {
1114	–	if (myScreen == "DAMPED") {
1115	–	sm = DAMPED;
1116	–	if (!simParams_->haveDampingAlpha()) {
1117	–	// first set a cutoff dependent alpha value
1118	–	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1119	–	alphaVal = 0.5125 - rcut_* 0.025;
1120	–	// for values rcut > 20.5, alpha is zero
1121	–	if (alphaVal < 0) alphaVal = 0;
1122	–
1123	–	// throw warning
1124	–	sprintf( painCave.errMsg,
1125	–	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1126	–	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1127	–	painCave.isFatal = 0;
1128	–	simError();
1129	–	} else {
1130	–	alphaVal = simParams_->getDampingAlpha();
1131	–	}
1132	–
1133	–	} else {
1134	–	// throw error
1135	–	sprintf( painCave.errMsg,
1136	–	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1137	–	"\t(Input file specified %s .)\n"
1138	–	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1139	–	"or \"damped\".\n", myScreen.c_str() );
1140	–	painCave.isFatal = 1;
1141	–	simError();
1142	–	}
1143	–	}
1144	–	}
1145	–
1146	–	// let's pass some summation method variables to fortran
1147	–	setElectrostaticSummationMethod( &esm );
1148	–	setFortranElectrostaticMethod( &esm );
1149	–	setScreeningMethod( &sm );
1150	–	setDampingAlpha( &alphaVal );
1151	–	setReactionFieldDielectric( &dielectric );
1152	–	initFortranFF( &errorOut );
1153	–	}
1154	–
1066		void SimInfo::setupSwitchingFunction() {
1156	–	int ft = CUBIC;
1067
1158	–	if (simParams_->haveSwitchingFunctionType()) {
1159	–	std::string funcType = simParams_->getSwitchingFunctionType();
1160	–	toUpper(funcType);
1161	–	if (funcType == "CUBIC") {
1162	–	ft = CUBIC;
1163	–	} else {
1164	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1165	–	ft = FIFTH_ORDER_POLY;
1166	–	} else {
1167	–	// throw error
1168	–	sprintf( painCave.errMsg,
1169	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1170	–	painCave.isFatal = 1;
1171	–	simError();
1172	–	}
1173	–	}
1174	–	}
1175	–
1176	–	// send switching function notification to switcheroo
1177	–	setFunctionType(&ft);
1178	–
1068		}
1069
1070		void SimInfo::setupAccumulateBoxDipole() {
#	Line 1183 | Line 1072 | namespace oopse {
1072		// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1073		if ( simParams_->haveAccumulateBoxDipole() )
1074		if ( simParams_->getAccumulateBoxDipole() ) {
1186	–	setAccumulateBoxDipole();
1075		calcBoxDipole_ = true;
1076		}
1077
#	Line 1193 | Line 1081 | namespace oopse {
1081		properties_.addProperty(genData);
1082		}
1083
1084	<	void SimInfo::removeProperty(const std::string& propName) {
1084	>	void SimInfo::removeProperty(const string& propName) {
1085		properties_.removeProperty(propName);
1086		}
1087
#	Line 1201 | Line 1089 | namespace oopse {
1089		properties_.clearProperties();
1090		}
1091
1092	<	std::vector<std::string> SimInfo::getPropertyNames() {
1092	>	vector<string> SimInfo::getPropertyNames() {
1093		return properties_.getPropertyNames();
1094		}
1095
1096	<	std::vector<GenericData*> SimInfo::getProperties() {
1096	>	vector<GenericData*> SimInfo::getProperties() {
1097		return properties_.getProperties();
1098		}
1099
1100	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1100	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1101		return properties_.getPropertyByName(propName);
1102		}
1103
#	Line 1292 | Line 1180 | namespace oopse {
1180
1181		}
1182
1183	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1183	>	ostream& operator <<(ostream& o, SimInfo& info) {
1184
1185		return o;
1186		}
#	Line 1335 | Line 1223 | namespace oopse {
1223
1224
1225		[  Ixx -Ixy  -Ixz ]
1226	<	J =| -Iyx  Iyy  -Iyz |
1226	>	J =| -Iyx  Iyy  -Iyz |
1227		[ -Izx -Iyz   Izz ]
1228		*/
1229
#	Line 1442 | Line 1330 | namespace oopse {
1330		return IOIndexToIntegrableObject.at(index);
1331		}
1332
1333	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1333	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1334		IOIndexToIntegrableObject= v;
1335		}
1336
1337	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1338	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1339	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1340	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1341	+	*/
1342	+	void SimInfo::getGyrationalVolume(RealType &volume){
1343	+	Mat3x3d intTensor;
1344	+	RealType det;
1345	+	Vector3d dummyAngMom;
1346	+	RealType sysconstants;
1347	+	RealType geomCnst;
1348	+
1349	+	geomCnst = 3.0/2.0;
1350	+	/* Get the inertial tensor and angular momentum for free*/
1351	+	getInertiaTensor(intTensor,dummyAngMom);
1352	+
1353	+	det = intTensor.determinant();
1354	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1355	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1356	+	return;
1357	+	}
1358	+
1359	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1360	+	Mat3x3d intTensor;
1361	+	Vector3d dummyAngMom;
1362	+	RealType sysconstants;
1363	+	RealType geomCnst;
1364	+
1365	+	geomCnst = 3.0/2.0;
1366	+	/* Get the inertial tensor and angular momentum for free*/
1367	+	getInertiaTensor(intTensor,dummyAngMom);
1368	+
1369	+	detI = intTensor.determinant();
1370	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1371	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1372	+	return;
1373	+	}
1374		/*
1375	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1375	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1376		assert( v.size() == nAtoms_ + nRigidBodies_);
1377		sdByGlobalIndex_ = v;
1378		}
#	Line 1457 | Line 1382 | namespace oopse {
1382		return sdByGlobalIndex_.at(index);
1383		}
1384		*/
1385	<	}//end namespace oopse
1385	>	int SimInfo::getNGlobalConstraints() {
1386	>	int nGlobalConstraints;
1387	>	#ifdef IS_MPI
1388	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1389	>	MPI_COMM_WORLD);
1390	>	#else
1391	>	nGlobalConstraints =  nConstraints_;
1392	>	#endif
1393	>	return nGlobalConstraints;
1394	>	}
1395
1396	+	}//end namespace OpenMD
1397	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 1089 by chrisfen, Wed Nov 1 22:22:44 2006 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC

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