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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 1277 by gezelter, Mon Jul 14 12:35:58 2008 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1529 by gezelter, Mon Dec 27 18:35:59 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 55 | Line 55
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"
58		#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
59		#include "UseTheForce/doForces_interface.h"
60		#include "UseTheForce/DarkSide/neighborLists_interface.h"
63	–	#include "UseTheForce/DarkSide/electrostatic_interface.h"
61		#include "UseTheForce/DarkSide/switcheroo_interface.h"
62		#include "utils/MemoryUtils.hpp"
63		#include "utils/simError.h"
64		#include "selection/SelectionManager.hpp"
65		#include "io/ForceFieldOptions.hpp"
66		#include "UseTheForce/ForceField.hpp"
67	+	#include "nonbonded/InteractionManager.hpp"
68
69
70		#ifdef IS_MPI
#	Line 74 | Line 72
72		#include "UseTheForce/DarkSide/simParallel_interface.h"
73		#endif
74
75	<	namespace oopse {
76	<	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	<	}
75	>	using namespace std;
76	>	namespace OpenMD {
77
78		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
79		forceField_(ff), simParams_(simParams),
#	Line 93 | Line 83 | namespace oopse {
83		nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
84		nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
85		nConstraints_(0), sman_(NULL), fortranInitialized_(false),
86	<	calcBoxDipole_(false), useAtomicVirial_(true) {
87	<
88	<
89	<	MoleculeStamp* molStamp;
90	<	int nMolWithSameStamp;
91	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
92	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
93	<	CutoffGroupStamp* cgStamp;
94	<	RigidBodyStamp* rbStamp;
95	<	int nRigidAtoms = 0;
96	<
97	<	std::vector<Component*> components = simParams->getComponents();
86	>	calcBoxDipole_(false), useAtomicVirial_(true) {
87	>
88	>	MoleculeStamp* molStamp;
89	>	int nMolWithSameStamp;
90	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
91	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
92	>	CutoffGroupStamp* cgStamp;
93	>	RigidBodyStamp* rbStamp;
94	>	int nRigidAtoms = 0;
95	>
96	>	vector<Component*> components = simParams->getComponents();
97	>
98	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
99	>	molStamp = (*i)->getMoleculeStamp();
100	>	nMolWithSameStamp = (*i)->getNMol();
101
102	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
103	<	molStamp = (*i)->getMoleculeStamp();
104	<	nMolWithSameStamp = (*i)->getNMol();
105	<
106	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
107	<
108	<	//calculate atoms in molecules
109	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
110	<
111	<	//calculate atoms in cutoff groups
112	<	int nAtomsInGroups = 0;
113	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
121	<
122	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
123	<	cgStamp = molStamp->getCutoffGroupStamp(j);
124	<	nAtomsInGroups += cgStamp->getNMembers();
125	<	}
126	<
127	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
128	<
129	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
130	<
131	<	//calculate atoms in rigid bodies
132	<	int nAtomsInRigidBodies = 0;
133	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
134	<
135	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
136	<	rbStamp = molStamp->getRigidBodyStamp(j);
137	<	nAtomsInRigidBodies += rbStamp->getNMembers();
138	<	}
139	<
140	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
141	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
142	<
102	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
103	>
104	>	//calculate atoms in molecules
105	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
106	>
107	>	//calculate atoms in cutoff groups
108	>	int nAtomsInGroups = 0;
109	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
110	>
111	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
112	>	cgStamp = molStamp->getCutoffGroupStamp(j);
113	>	nAtomsInGroups += cgStamp->getNMembers();
114		}
115	<
116	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
117	<	//group therefore the total number of cutoff groups in the system is
118	<	//equal to the total number of atoms minus number of atoms belong to
119	<	//cutoff group defined in meta-data file plus the number of cutoff
120	<	//groups defined in meta-data file
121	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
122	<
123	<	//every free atom (atom does not belong to rigid bodies) is an
124	<	//integrable object therefore the total number of integrable objects
125	<	//in the system is equal to the total number of atoms minus number of
126	<	//atoms belong to rigid body defined in meta-data file plus the number
127	<	//of rigid bodies defined in meta-data file
128	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
129	<	+ nGlobalRigidBodies_;
130	<
131	<	nGlobalMols_ = molStampIds_.size();
161	<	molToProcMap_.resize(nGlobalMols_);
115	>
116	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
117	>
118	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
119	>
120	>	//calculate atoms in rigid bodies
121	>	int nAtomsInRigidBodies = 0;
122	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
123	>
124	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
125	>	rbStamp = molStamp->getRigidBodyStamp(j);
126	>	nAtomsInRigidBodies += rbStamp->getNMembers();
127	>	}
128	>
129	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
130	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
131	>
132		}
133	<
133	>
134	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
135	>	//group therefore the total number of cutoff groups in the system is
136	>	//equal to the total number of atoms minus number of atoms belong to
137	>	//cutoff group defined in meta-data file plus the number of cutoff
138	>	//groups defined in meta-data file
139	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
140	>
141	>	//every free atom (atom does not belong to rigid bodies) is an
142	>	//integrable object therefore the total number of integrable objects
143	>	//in the system is equal to the total number of atoms minus number of
144	>	//atoms belong to rigid body defined in meta-data file plus the number
145	>	//of rigid bodies defined in meta-data file
146	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
147	>	+ nGlobalRigidBodies_;
148	>
149	>	nGlobalMols_ = molStampIds_.size();
150	>	molToProcMap_.resize(nGlobalMols_);
151	>	}
152	>
153		SimInfo::~SimInfo() {
154	<	std::map<int, Molecule*>::iterator i;
154	>	map<int, Molecule*>::iterator i;
155		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
156		delete i->second;
157		}
#	Line 173 | Line 162 | namespace oopse {
162		delete forceField_;
163		}
164
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	–	}
165
166		bool SimInfo::addMolecule(Molecule* mol) {
167		MoleculeIterator i;
168	<
168	>
169		i = molecules_.find(mol->getGlobalIndex());
170		if (i == molecules_.end() ) {
171	<
172	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
173	<
171	>
172	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
173	>
174		nAtoms_ += mol->getNAtoms();
175		nBonds_ += mol->getNBonds();
176		nBends_ += mol->getNBends();
#	Line 201 | Line 180 | namespace oopse {
180		nIntegrableObjects_ += mol->getNIntegrableObjects();
181		nCutoffGroups_ += mol->getNCutoffGroups();
182		nConstraints_ += mol->getNConstraintPairs();
183	<
184	<	addExcludePairs(mol);
185	<
183	>
184	>	addInteractionPairs(mol);
185	>
186		return true;
187		} else {
188		return false;
189		}
190		}
191	<
191	>
192		bool SimInfo::removeMolecule(Molecule* mol) {
193		MoleculeIterator i;
194		i = molecules_.find(mol->getGlobalIndex());
#	Line 228 | Line 207 | namespace oopse {
207		nCutoffGroups_ -= mol->getNCutoffGroups();
208		nConstraints_ -= mol->getNConstraintPairs();
209
210	<	removeExcludePairs(mol);
210	>	removeInteractionPairs(mol);
211		molecules_.erase(mol->getGlobalIndex());
212
213		delete mol;
#	Line 237 | Line 216 | namespace oopse {
216		} else {
217		return false;
218		}
240	–
241	–
219		}
220
221
#	Line 256 | Line 233 | namespace oopse {
233		void SimInfo::calcNdf() {
234		int ndf_local;
235		MoleculeIterator i;
236	<	std::vector<StuntDouble*>::iterator j;
236	>	vector<StuntDouble*>::iterator j;
237		Molecule* mol;
238		StuntDouble* integrableObject;
239
#	Line 307 | Line 284 | namespace oopse {
284		int ndfRaw_local;
285
286		MoleculeIterator i;
287	<	std::vector<StuntDouble*>::iterator j;
287	>	vector<StuntDouble*>::iterator j;
288		Molecule* mol;
289		StuntDouble* integrableObject;
290
#	Line 354 | Line 331 | namespace oopse {
331
332		}
333
334	<	void SimInfo::addExcludePairs(Molecule* mol) {
335	<	std::vector<Bond*>::iterator bondIter;
336	<	std::vector<Bend*>::iterator bendIter;
337	<	std::vector<Torsion*>::iterator torsionIter;
338	<	std::vector<Inversion*>::iterator inversionIter;
334	>	void SimInfo::addInteractionPairs(Molecule* mol) {
335	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
336	>	vector<Bond*>::iterator bondIter;
337	>	vector<Bend*>::iterator bendIter;
338	>	vector<Torsion*>::iterator torsionIter;
339	>	vector<Inversion*>::iterator inversionIter;
340		Bond* bond;
341		Bend* bend;
342		Torsion* torsion;
#	Line 368 | Line 346 | namespace oopse {
346		int c;
347		int d;
348
349	<	std::map<int, std::set<int> > atomGroups;
349	>	// atomGroups can be used to add special interaction maps between
350	>	// groups of atoms that are in two separate rigid bodies.
351	>	// However, most site-site interactions between two rigid bodies
352	>	// are probably not special, just the ones between the physically
353	>	// bonded atoms.  Interactions *within* a single rigid body should
354	>	// always be excluded.  These are done at the bottom of this
355	>	// function.
356
357	+	map<int, set<int> > atomGroups;
358		Molecule::RigidBodyIterator rbIter;
359		RigidBody* rb;
360		Molecule::IntegrableObjectIterator ii;
361		StuntDouble* integrableObject;
362
363	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
364	<	integrableObject = mol->nextIntegrableObject(ii)) {
365	<
363	>	for (integrableObject = mol->beginIntegrableObject(ii);
364	>	integrableObject != NULL;
365	>	integrableObject = mol->nextIntegrableObject(ii)) {
366	>
367		if (integrableObject->isRigidBody()) {
368	<	rb = static_cast<RigidBody*>(integrableObject);
369	<	std::vector<Atom*> atoms = rb->getAtoms();
370	<	std::set<int> rigidAtoms;
371	<	for (int i = 0; i < atoms.size(); ++i) {
372	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
373	<	}
374	<	for (int i = 0; i < atoms.size(); ++i) {
375	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
376	<	}
368	>	rb = static_cast<RigidBody*>(integrableObject);
369	>	vector<Atom*> atoms = rb->getAtoms();
370	>	set<int> rigidAtoms;
371	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
372	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
373	>	}
374	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
375	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
376	>	}
377		} else {
378	<	std::set<int> oneAtomSet;
378	>	set<int> oneAtomSet;
379		oneAtomSet.insert(integrableObject->getGlobalIndex());
380	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
380	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
381		}
382		}
383	+
384	+	for (bond= mol->beginBond(bondIter); bond != NULL;
385	+	bond = mol->nextBond(bondIter)) {
386
398	–
399	–
400	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
387		a = bond->getAtomA()->getGlobalIndex();
388	<	b = bond->getAtomB()->getGlobalIndex();
389	<	exclude_.addPair(a, b);
388	>	b = bond->getAtomB()->getGlobalIndex();
389	>
390	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
391	>	oneTwoInteractions_.addPair(a, b);
392	>	} else {
393	>	excludedInteractions_.addPair(a, b);
394	>	}
395		}
396
397	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
397	>	for (bend= mol->beginBend(bendIter); bend != NULL;
398	>	bend = mol->nextBend(bendIter)) {
399	>
400		a = bend->getAtomA()->getGlobalIndex();
401		b = bend->getAtomB()->getGlobalIndex();
402		c = bend->getAtomC()->getGlobalIndex();
410	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
411	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
412	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
413	–
414	–	exclude_.addPairs(rigidSetA, rigidSetB);
415	–	exclude_.addPairs(rigidSetA, rigidSetC);
416	–	exclude_.addPairs(rigidSetB, rigidSetC);
403
404	<	//exclude_.addPair(a, b);
405	<	//exclude_.addPair(a, c);
406	<	//exclude_.addPair(b, c);
404	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
405	>	oneTwoInteractions_.addPair(a, b);
406	>	oneTwoInteractions_.addPair(b, c);
407	>	} else {
408	>	excludedInteractions_.addPair(a, b);
409	>	excludedInteractions_.addPair(b, c);
410	>	}
411	>
412	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
413	>	oneThreeInteractions_.addPair(a, c);
414	>	} else {
415	>	excludedInteractions_.addPair(a, c);
416	>	}
417		}
418
419	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
419	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
420	>	torsion = mol->nextTorsion(torsionIter)) {
421	>
422		a = torsion->getAtomA()->getGlobalIndex();
423		b = torsion->getAtomB()->getGlobalIndex();
424		c = torsion->getAtomC()->getGlobalIndex();
425	<	d = torsion->getAtomD()->getGlobalIndex();
428	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
429	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
430	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
431	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
425	>	d = torsion->getAtomD()->getGlobalIndex();
426
427	<	exclude_.addPairs(rigidSetA, rigidSetB);
428	<	exclude_.addPairs(rigidSetA, rigidSetC);
429	<	exclude_.addPairs(rigidSetA, rigidSetD);
430	<	exclude_.addPairs(rigidSetB, rigidSetC);
431	<	exclude_.addPairs(rigidSetB, rigidSetD);
432	<	exclude_.addPairs(rigidSetC, rigidSetD);
427	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
428	>	oneTwoInteractions_.addPair(a, b);
429	>	oneTwoInteractions_.addPair(b, c);
430	>	oneTwoInteractions_.addPair(c, d);
431	>	} else {
432	>	excludedInteractions_.addPair(a, b);
433	>	excludedInteractions_.addPair(b, c);
434	>	excludedInteractions_.addPair(c, d);
435	>	}
436
437	<	/*
438	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
439	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
440	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
441	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
442	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
443	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
444	<
445	<
446	<	exclude_.addPair(a, b);
447	<	exclude_.addPair(a, c);
448	<	exclude_.addPair(a, d);
449	<	exclude_.addPair(b, c);
453	<	exclude_.addPair(b, d);
454	<	exclude_.addPair(c, d);
455	<	*/
437	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
438	>	oneThreeInteractions_.addPair(a, c);
439	>	oneThreeInteractions_.addPair(b, d);
440	>	} else {
441	>	excludedInteractions_.addPair(a, c);
442	>	excludedInteractions_.addPair(b, d);
443	>	}
444	>
445	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
446	>	oneFourInteractions_.addPair(a, d);
447	>	} else {
448	>	excludedInteractions_.addPair(a, d);
449	>	}
450		}
451
452		for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
453		inversion = mol->nextInversion(inversionIter)) {
454	+
455		a = inversion->getAtomA()->getGlobalIndex();
456		b = inversion->getAtomB()->getGlobalIndex();
457		c = inversion->getAtomC()->getGlobalIndex();
458		d = inversion->getAtomD()->getGlobalIndex();
464	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
465	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
466	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
467	–	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
459
460	<	exclude_.addPairs(rigidSetA, rigidSetB);
461	<	exclude_.addPairs(rigidSetA, rigidSetC);
462	<	exclude_.addPairs(rigidSetA, rigidSetD);
463	<	exclude_.addPairs(rigidSetB, rigidSetC);
464	<	exclude_.addPairs(rigidSetB, rigidSetD);
465	<	exclude_.addPairs(rigidSetC, rigidSetD);
460	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
461	>	oneTwoInteractions_.addPair(a, b);
462	>	oneTwoInteractions_.addPair(a, c);
463	>	oneTwoInteractions_.addPair(a, d);
464	>	} else {
465	>	excludedInteractions_.addPair(a, b);
466	>	excludedInteractions_.addPair(a, c);
467	>	excludedInteractions_.addPair(a, d);
468	>	}
469
470	<	/*
471	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
472	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
473	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
474	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
475	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
476	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
477	<
478	<
485	<	exclude_.addPair(a, b);
486	<	exclude_.addPair(a, c);
487	<	exclude_.addPair(a, d);
488	<	exclude_.addPair(b, c);
489	<	exclude_.addPair(b, d);
490	<	exclude_.addPair(c, d);
491	<	*/
470	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
471	>	oneThreeInteractions_.addPair(b, c);
472	>	oneThreeInteractions_.addPair(b, d);
473	>	oneThreeInteractions_.addPair(c, d);
474	>	} else {
475	>	excludedInteractions_.addPair(b, c);
476	>	excludedInteractions_.addPair(b, d);
477	>	excludedInteractions_.addPair(c, d);
478	>	}
479		}
480
481	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
482	<	std::vector<Atom*> atoms = rb->getAtoms();
483	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
484	<	for (int j = i + 1; j < atoms.size(); ++j) {
481	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
482	>	rb = mol->nextRigidBody(rbIter)) {
483	>	vector<Atom*> atoms = rb->getAtoms();
484	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
485	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
486		a = atoms[i]->getGlobalIndex();
487		b = atoms[j]->getGlobalIndex();
488	<	exclude_.addPair(a, b);
488	>	excludedInteractions_.addPair(a, b);
489		}
490		}
491		}
492
493		}
494
495	<	void SimInfo::removeExcludePairs(Molecule* mol) {
496	<	std::vector<Bond*>::iterator bondIter;
497	<	std::vector<Bend*>::iterator bendIter;
498	<	std::vector<Torsion*>::iterator torsionIter;
499	<	std::vector<Inversion*>::iterator inversionIter;
495	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
496	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
497	>	vector<Bond*>::iterator bondIter;
498	>	vector<Bend*>::iterator bendIter;
499	>	vector<Torsion*>::iterator torsionIter;
500	>	vector<Inversion*>::iterator inversionIter;
501		Bond* bond;
502		Bend* bend;
503		Torsion* torsion;
#	Line 518 | Line 507 | namespace oopse {
507		int c;
508		int d;
509
510	<	std::map<int, std::set<int> > atomGroups;
522	<
510	>	map<int, set<int> > atomGroups;
511		Molecule::RigidBodyIterator rbIter;
512		RigidBody* rb;
513		Molecule::IntegrableObjectIterator ii;
514		StuntDouble* integrableObject;
515
516	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
517	<	integrableObject = mol->nextIntegrableObject(ii)) {
518	<
516	>	for (integrableObject = mol->beginIntegrableObject(ii);
517	>	integrableObject != NULL;
518	>	integrableObject = mol->nextIntegrableObject(ii)) {
519	>
520		if (integrableObject->isRigidBody()) {
521	<	rb = static_cast<RigidBody*>(integrableObject);
522	<	std::vector<Atom*> atoms = rb->getAtoms();
523	<	std::set<int> rigidAtoms;
524	<	for (int i = 0; i < atoms.size(); ++i) {
525	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
526	<	}
527	<	for (int i = 0; i < atoms.size(); ++i) {
528	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
529	<	}
521	>	rb = static_cast<RigidBody*>(integrableObject);
522	>	vector<Atom*> atoms = rb->getAtoms();
523	>	set<int> rigidAtoms;
524	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
525	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
526	>	}
527	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
528	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
529	>	}
530		} else {
531	<	std::set<int> oneAtomSet;
531	>	set<int> oneAtomSet;
532		oneAtomSet.insert(integrableObject->getGlobalIndex());
533	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
533	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
534		}
535		}
536
537	<
538	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
537	>	for (bond= mol->beginBond(bondIter); bond != NULL;
538	>	bond = mol->nextBond(bondIter)) {
539	>
540		a = bond->getAtomA()->getGlobalIndex();
541	<	b = bond->getAtomB()->getGlobalIndex();
542	<	exclude_.removePair(a, b);
541	>	b = bond->getAtomB()->getGlobalIndex();
542	>
543	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
544	>	oneTwoInteractions_.removePair(a, b);
545	>	} else {
546	>	excludedInteractions_.removePair(a, b);
547	>	}
548		}
549
550	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
550	>	for (bend= mol->beginBend(bendIter); bend != NULL;
551	>	bend = mol->nextBend(bendIter)) {
552	>
553		a = bend->getAtomA()->getGlobalIndex();
554		b = bend->getAtomB()->getGlobalIndex();
555		c = bend->getAtomC()->getGlobalIndex();
559	–
560	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
561	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
562	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
563	–
564	–	exclude_.removePairs(rigidSetA, rigidSetB);
565	–	exclude_.removePairs(rigidSetA, rigidSetC);
566	–	exclude_.removePairs(rigidSetB, rigidSetC);
556
557	<	//exclude_.removePair(a, b);
558	<	//exclude_.removePair(a, c);
559	<	//exclude_.removePair(b, c);
557	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
558	>	oneTwoInteractions_.removePair(a, b);
559	>	oneTwoInteractions_.removePair(b, c);
560	>	} else {
561	>	excludedInteractions_.removePair(a, b);
562	>	excludedInteractions_.removePair(b, c);
563	>	}
564	>
565	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
566	>	oneThreeInteractions_.removePair(a, c);
567	>	} else {
568	>	excludedInteractions_.removePair(a, c);
569	>	}
570		}
571
572	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
572	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
573	>	torsion = mol->nextTorsion(torsionIter)) {
574	>
575		a = torsion->getAtomA()->getGlobalIndex();
576		b = torsion->getAtomB()->getGlobalIndex();
577		c = torsion->getAtomC()->getGlobalIndex();
578	<	d = torsion->getAtomD()->getGlobalIndex();
578	>	d = torsion->getAtomD()->getGlobalIndex();
579	>
580	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
581	>	oneTwoInteractions_.removePair(a, b);
582	>	oneTwoInteractions_.removePair(b, c);
583	>	oneTwoInteractions_.removePair(c, d);
584	>	} else {
585	>	excludedInteractions_.removePair(a, b);
586	>	excludedInteractions_.removePair(b, c);
587	>	excludedInteractions_.removePair(c, d);
588	>	}
589
590	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
591	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
592	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
593	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
590	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
591	>	oneThreeInteractions_.removePair(a, c);
592	>	oneThreeInteractions_.removePair(b, d);
593	>	} else {
594	>	excludedInteractions_.removePair(a, c);
595	>	excludedInteractions_.removePair(b, d);
596	>	}
597
598	<	exclude_.removePairs(rigidSetA, rigidSetB);
599	<	exclude_.removePairs(rigidSetA, rigidSetC);
600	<	exclude_.removePairs(rigidSetA, rigidSetD);
601	<	exclude_.removePairs(rigidSetB, rigidSetC);
602	<	exclude_.removePairs(rigidSetB, rigidSetD);
589	<	exclude_.removePairs(rigidSetC, rigidSetD);
590	<
591	<	/*
592	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
593	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
594	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
595	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
596	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
597	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
598	<
599	<
600	<	exclude_.removePair(a, b);
601	<	exclude_.removePair(a, c);
602	<	exclude_.removePair(a, d);
603	<	exclude_.removePair(b, c);
604	<	exclude_.removePair(b, d);
605	<	exclude_.removePair(c, d);
606	<	*/
598	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
599	>	oneFourInteractions_.removePair(a, d);
600	>	} else {
601	>	excludedInteractions_.removePair(a, d);
602	>	}
603		}
604
605	<	for (inversion= mol->beginInversion(inversionIter); inversion != NULL; inversion = mol->nextInversion(inversionIter)) {
605	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
606	>	inversion = mol->nextInversion(inversionIter)) {
607	>
608		a = inversion->getAtomA()->getGlobalIndex();
609		b = inversion->getAtomB()->getGlobalIndex();
610		c = inversion->getAtomC()->getGlobalIndex();
611		d = inversion->getAtomD()->getGlobalIndex();
612
613	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
614	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
615	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
616	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
613	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
614	>	oneTwoInteractions_.removePair(a, b);
615	>	oneTwoInteractions_.removePair(a, c);
616	>	oneTwoInteractions_.removePair(a, d);
617	>	} else {
618	>	excludedInteractions_.removePair(a, b);
619	>	excludedInteractions_.removePair(a, c);
620	>	excludedInteractions_.removePair(a, d);
621	>	}
622
623	<	exclude_.removePairs(rigidSetA, rigidSetB);
624	<	exclude_.removePairs(rigidSetA, rigidSetC);
625	<	exclude_.removePairs(rigidSetA, rigidSetD);
626	<	exclude_.removePairs(rigidSetB, rigidSetC);
627	<	exclude_.removePairs(rigidSetB, rigidSetD);
628	<	exclude_.removePairs(rigidSetC, rigidSetD);
629	<
630	<	/*
631	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
629	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
630	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
631	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
632	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
633	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
634	<
635	<
636	<	exclude_.removePair(a, b);
637	<	exclude_.removePair(a, c);
638	<	exclude_.removePair(a, d);
639	<	exclude_.removePair(b, c);
640	<	exclude_.removePair(b, d);
641	<	exclude_.removePair(c, d);
642	<	*/
623	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
624	>	oneThreeInteractions_.removePair(b, c);
625	>	oneThreeInteractions_.removePair(b, d);
626	>	oneThreeInteractions_.removePair(c, d);
627	>	} else {
628	>	excludedInteractions_.removePair(b, c);
629	>	excludedInteractions_.removePair(b, d);
630	>	excludedInteractions_.removePair(c, d);
631	>	}
632		}
633
634	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
635	<	std::vector<Atom*> atoms = rb->getAtoms();
636	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
637	<	for (int j = i + 1; j < atoms.size(); ++j) {
634	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
635	>	rb = mol->nextRigidBody(rbIter)) {
636	>	vector<Atom*> atoms = rb->getAtoms();
637	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
638	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
639		a = atoms[i]->getGlobalIndex();
640		b = atoms[j]->getGlobalIndex();
641	<	exclude_.removePair(a, b);
641	>	excludedInteractions_.removePair(a, b);
642		}
643		}
644		}
645	<
645	>
646		}
647	<
648	<
647	>
648	>
649		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
650		int curStampId;
651	<
651	>
652		//index from 0
653		curStampId = moleculeStamps_.size();
654
#	Line 669 | Line 659 | namespace oopse {
659		void SimInfo::update() {
660
661		setupSimType();
662	+	setupCutoffRadius();
663	+	setupSwitchingRadius();
664	+	setupCutoffMethod();
665	+	setupSkinThickness();
666	+	setupSwitchingFunction();
667	+	setupAccumulateBoxDipole();
668
669		#ifdef IS_MPI
670		setupFortranParallel();
671		#endif
676	–
672		setupFortranSim();
673	<
679	<	//setup fortran force field
680	<	/** @deprecate */
681	<	int isError = 0;
682	<
683	<	setupCutoff();
684	<
685	<	setupElectrostaticSummationMethod( isError );
686	<	setupSwitchingFunction();
687	<	setupAccumulateBoxDipole();
673	>	fortranInitialized_ = true;
674
689	–	if(isError){
690	–	sprintf( painCave.errMsg,
691	–	"ForceField error: There was an error initializing the forceField in fortran.\n" );
692	–	painCave.isFatal = 1;
693	–	simError();
694	–	}
695	–
675		calcNdf();
676		calcNdfRaw();
677		calcNdfTrans();
699	–
700	–	fortranInitialized_ = true;
678		}
679	<
680	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
679	>
680	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
681		SimInfo::MoleculeIterator mi;
682		Molecule* mol;
683		Molecule::AtomIterator ai;
684		Atom* atom;
685	<	std::set<AtomType*> atomTypes;
686	<
687	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
711	<
685	>	set<AtomType*> atomTypes;
686	>
687	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
688		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
689		atomTypes.insert(atom->getAtomType());
690	<	}
691	<
716	<	}
717	<
690	>	}
691	>	}
692		return atomTypes;
693		}
694
695	<	void SimInfo::setupSimType() {
696	<	std::set<AtomType*>::iterator i;
697	<	std::set<AtomType*> atomTypes;
698	<	atomTypes = getUniqueAtomTypes();
695	>	/**
696	>	* setupCutoffRadius
697	>	*
698	>	*  If the cutoffRadius was explicitly set, use that value.
699	>	*  If the cutoffRadius was not explicitly set:
700	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
701	>	*      No electrostatic atoms?  Poll the atom types present in the
702	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
703	>	*      Use the maximum suggested value that was found.
704	>	*/
705	>	void SimInfo::setupCutoffRadius() {
706
707	<	int useLennardJones = 0;
708	<	int useElectrostatic = 0;
709	<	int useEAM = 0;
710	<	int useSC = 0;
711	<	int useCharge = 0;
712	<	int useDirectional = 0;
713	<	int useDipole = 0;
714	<	int useGayBerne = 0;
715	<	int useSticky = 0;
716	<	int useStickyPower = 0;
717	<	int useShape = 0;
718	<	int useFLARB = 0; //it is not in AtomType yet
719	<	int useDirectionalAtom = 0;
720	<	int useElectrostatics = 0;
721	<	//usePBC and useRF are from simParams
722	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
723	<	int useRF;
724	<	int useSF;
725	<	int useSP;
726	<	int useBoxDipole;
707	>	if (simParams_->haveCutoffRadius()) {
708	>	cutoffRadius_ = simParams_->getCutoffRadius();
709	>	} else {
710	>	if (usesElectrostaticAtoms_) {
711	>	sprintf(painCave.errMsg,
712	>	"SimInfo Warning: No value was set for the cutoffRadius.\n"
713	>	"\tOpenMD will use a default value of 12.0 angstroms"
714	>	"\tfor the cutoffRadius.\n");
715	>	painCave.isFatal = 0;
716	>	simError();
717	>	cutoffRadius_ = 12.0;
718	>	} else {
719	>	RealType thisCut;
720	>	set<AtomType*>::iterator i;
721	>	set<AtomType*> atomTypes;
722	>	atomTypes = getSimulatedAtomTypes();
723	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
724	>	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
725	>	cutoffRadius_ = max(thisCut, cutoffRadius_);
726	>	}
727	>	sprintf(painCave.errMsg,
728	>	"SimInfo Warning: No value was set for the cutoffRadius.\n"
729	>	"\tOpenMD will use %lf angstroms.\n",
730	>	cutoffRadius_);
731	>	painCave.isFatal = 0;
732	>	simError();
733	>	}
734	>	}
735
736	<	std::string myMethod;
736	>	InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
737	>	}
738	>
739	>	/**
740	>	* setupSwitchingRadius
741	>	*
742	>	*  If the switchingRadius was explicitly set, use that value (but check it)
743	>	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
744	>	*/
745	>	void SimInfo::setupSwitchingRadius() {
746	>
747	>	if (simParams_->haveSwitchingRadius()) {
748	>	switchingRadius_ = simParams_->getSwitchingRadius();
749	>	if (switchingRadius_ > cutoffRadius_) {
750	>	sprintf(painCave.errMsg,
751	>	"SimInfo Error: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
752	>	switchingRadius_, cutoffRadius_);
753	>	painCave.isFatal = 1;
754	>	simError();
755
756	<	// set the useRF logical
757	<	useRF = 0;
758	<	useSF = 0;
759	<	useSP = 0;
756	>	}
757	>	} else {
758	>	switchingRadius_ = 0.85 * cutoffRadius_;
759	>	sprintf(painCave.errMsg,
760	>	"SimInfo Warning: No value was set for the switchingRadius.\n"
761	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
762	>	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
763	>	painCave.isFatal = 0;
764	>	simError();
765	>	}
766	>	InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
767	>	}
768
769	+	/**
770	+	* setupSkinThickness
771	+	*
772	+	*  If the skinThickness was explicitly set, use that value (but check it)
773	+	*  If the skinThickness was not explicitly set: use 1.0 angstroms
774	+	*/
775	+	void SimInfo::setupSkinThickness() {
776	+	if (simParams_->haveSkinThickness()) {
777	+	skinThickness_ = simParams_->getSkinThickness();
778	+	} else {
779	+	skinThickness_ = 1.0;
780	+	sprintf(painCave.errMsg,
781	+	"SimInfo Warning: No value was set for the skinThickness.\n"
782	+	"\tOpenMD will use a default value of %f Angstroms\n"
783	+	"\tfor this simulation\n", skinThickness_);
784	+	painCave.isFatal = 0;
785	+	simError();
786	+	}
787	+	}
788
789	<	if (simParams_->haveElectrostaticSummationMethod()) {
790	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
791	<	toUpper(myMethod);
792	<	if (myMethod == "REACTION_FIELD"){
759	<	useRF = 1;
760	<	} else if (myMethod == "SHIFTED_FORCE"){
761	<	useSF = 1;
762	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
763	<	useSP = 1;
764	<	}
765	<	}
766	<
767	<	if (simParams_->haveAccumulateBoxDipole())
768	<	if (simParams_->getAccumulateBoxDipole())
769	<	useBoxDipole = 1;
789	>	void SimInfo::setupSimType() {
790	>	set<AtomType*>::iterator i;
791	>	set<AtomType*> atomTypes;
792	>	atomTypes = getSimulatedAtomTypes();
793
794		useAtomicVirial_ = simParams_->getUseAtomicVirial();
795
796	+	int usesElectrostatic = 0;
797	+	int usesMetallic = 0;
798	+	int usesDirectional = 0;
799		//loop over all of the atom types
800		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
801	<	useLennardJones |= (*i)->isLennardJones();
802	<	useElectrostatic |= (*i)->isElectrostatic();
803	<	useEAM |= (*i)->isEAM();
778	<	useSC |= (*i)->isSC();
779	<	useCharge |= (*i)->isCharge();
780	<	useDirectional |= (*i)->isDirectional();
781	<	useDipole |= (*i)->isDipole();
782	<	useGayBerne |= (*i)->isGayBerne();
783	<	useSticky |= (*i)->isSticky();
784	<	useStickyPower |= (*i)->isStickyPower();
785	<	useShape |= (*i)->isShape();
801	>	usesElectrostatic |= (*i)->isElectrostatic();
802	>	usesMetallic |= (*i)->isMetal();
803	>	usesDirectional |= (*i)->isDirectional();
804		}
805
788	–	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
789	–	useDirectionalAtom = 1;
790	–	}
791	–
792	–	if (useCharge || useDipole) {
793	–	useElectrostatics = 1;
794	–	}
795	–
806		#ifdef IS_MPI
807		int temp;
808	+	temp = usesDirectional;
809	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810
811	<	temp = usePBC;
812	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
811	>	temp = usesMetallic;
812	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813
814	<	temp = useDirectionalAtom;
815	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
804	<
805	<	temp = useLennardJones;
806	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
807	<
808	<	temp = useElectrostatics;
809	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810	<
811	<	temp = useCharge;
812	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813	<
814	<	temp = useDipole;
815	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816	<
817	<	temp = useSticky;
818	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819	<
820	<	temp = useStickyPower;
821	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
822	<
823	<	temp = useGayBerne;
824	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
825	<
826	<	temp = useEAM;
827	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
828	<
829	<	temp = useSC;
830	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
831	<
832	<	temp = useShape;
833	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
834	<
835	<	temp = useFLARB;
836	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
837	<
838	<	temp = useRF;
839	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
840	<
841	<	temp = useSF;
842	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
843	<
844	<	temp = useSP;
845	<	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
846	<
847	<	temp = useBoxDipole;
848	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
849	<
850	<	temp = useAtomicVirial_;
851	<	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
852	<
814	>	temp = usesElectrostatic;
815	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816		#endif
817	<
818	<	fInfo_.SIM_uses_PBC = usePBC;
819	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
820	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
821	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
822	<	fInfo_.SIM_uses_Charges = useCharge;
860	<	fInfo_.SIM_uses_Dipoles = useDipole;
861	<	fInfo_.SIM_uses_Sticky = useSticky;
862	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
863	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
864	<	fInfo_.SIM_uses_EAM = useEAM;
865	<	fInfo_.SIM_uses_SC = useSC;
866	<	fInfo_.SIM_uses_Shapes = useShape;
867	<	fInfo_.SIM_uses_FLARB = useFLARB;
868	<	fInfo_.SIM_uses_RF = useRF;
869	<	fInfo_.SIM_uses_SF = useSF;
870	<	fInfo_.SIM_uses_SP = useSP;
871	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
872	<	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
817	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
818	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
819	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
820	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
821	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
822	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
823		}
824
825		void SimInfo::setupFortranSim() {
826		int isError;
827	<	int nExclude;
828	<	std::vector<int> fortranGlobalGroupMembership;
827	>	int nExclude, nOneTwo, nOneThree, nOneFour;
828	>	vector<int> fortranGlobalGroupMembership;
829
830	<	nExclude = exclude_.getSize();
830	>	notifyFortranSkinThickness(&skinThickness_);
831	>
832	>	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
833	>	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
834	>	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
835	>
836		isError = 0;
837
838		//globalGroupMembership_ is filled by SimCreator
#	Line 886 | Line 841 | namespace oopse {
841		}
842
843		//calculate mass ratio of cutoff group
844	<	std::vector<RealType> mfact;
844	>	vector<RealType> mfact;
845		SimInfo::MoleculeIterator mi;
846		Molecule* mol;
847		Molecule::CutoffGroupIterator ci;
#	Line 909 | Line 864 | namespace oopse {
864		else
865		mfact.push_back( 1.0 );
866		}
912	–
867		}
868		}
869
870		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
871	<	std::vector<int> identArray;
871	>	vector<int> identArray;
872
873		//to avoid memory reallocation, reserve enough space identArray
874		identArray.reserve(getNAtoms());
#	Line 927 | Line 881 | namespace oopse {
881
882		//fill molMembershipArray
883		//molMembershipArray is filled by SimCreator
884	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
884	>	vector<int> molMembershipArray(nGlobalAtoms_);
885		for (int i = 0; i < nGlobalAtoms_; i++) {
886		molMembershipArray[i] = globalMolMembership_[i] + 1;
887		}
888
889		//setup fortran simulation
890	<	int nGlobalExcludes = 0;
891	<	int* globalExcludes = NULL;
892	<	int* excludeList = exclude_.getExcludeList();
890	>
891	>	nExclude = excludedInteractions_.getSize();
892	>	nOneTwo = oneTwoInteractions_.getSize();
893	>	nOneThree = oneThreeInteractions_.getSize();
894	>	nOneFour = oneFourInteractions_.getSize();
895	>
896	>	int* excludeList = excludedInteractions_.getPairList();
897	>	int* oneTwoList = oneTwoInteractions_.getPairList();
898	>	int* oneThreeList = oneThreeInteractions_.getPairList();
899	>	int* oneFourList = oneFourInteractions_.getPairList();
900	>
901		setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
902	<	&nExclude, excludeList , &nGlobalExcludes, globalExcludes,
902	>	&nExclude, excludeList,
903	>	&nOneTwo, oneTwoList,
904	>	&nOneThree, oneThreeList,
905	>	&nOneFour, oneFourList,
906		&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
907		&fortranGlobalGroupMembership[0], &isError);
908
#	Line 946 | Line 911 | namespace oopse {
911		sprintf( painCave.errMsg,
912		"There was an error setting the simulation information in fortran.\n" );
913		painCave.isFatal = 1;
914	<	painCave.severity = OOPSE_ERROR;
914	>	painCave.severity = OPENMD_ERROR;
915		simError();
916		}
917
#	Line 969 | Line 934 | namespace oopse {
934		void SimInfo::setupFortranParallel() {
935		#ifdef IS_MPI
936		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
937	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
938	<	std::vector<int> localToGlobalCutoffGroupIndex;
937	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
938	>	vector<int> localToGlobalCutoffGroupIndex;
939		SimInfo::MoleculeIterator mi;
940		Molecule::AtomIterator ai;
941		Molecule::CutoffGroupIterator ci;
#	Line 1022 | Line 987 | namespace oopse {
987		#endif
988		}
989
1025	–	void SimInfo::setupCutoff() {
1026	–
1027	–	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
990
991	<	// Check the cutoff policy
992	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1031	<
1032	<	// Set LJ shifting bools to false
1033	<	ljsp_ = false;
1034	<	ljsf_ = false;
1035	<
1036	<	std::string myPolicy;
1037	<	if (forceFieldOptions_.haveCutoffPolicy()){
1038	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
1039	<	}else if (simParams_->haveCutoffPolicy()) {
1040	<	myPolicy = simParams_->getCutoffPolicy();
1041	<	}
1042	<
1043	<	if (!myPolicy.empty()){
1044	<	toUpper(myPolicy);
1045	<	if (myPolicy == "MIX") {
1046	<	cp = MIX_CUTOFF_POLICY;
1047	<	} else {
1048	<	if (myPolicy == "MAX") {
1049	<	cp = MAX_CUTOFF_POLICY;
1050	<	} else {
1051	<	if (myPolicy == "TRADITIONAL") {
1052	<	cp = TRADITIONAL_CUTOFF_POLICY;
1053	<	} else {
1054	<	// throw error
1055	<	sprintf( painCave.errMsg,
1056	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1057	<	painCave.isFatal = 1;
1058	<	simError();
1059	<	}
1060	<	}
1061	<	}
1062	<	}
1063	<	notifyFortranCutoffPolicy(&cp);
1064	<
1065	<	// Check the Skin Thickness for neighborlists
1066	<	RealType skin;
1067	<	if (simParams_->haveSkinThickness()) {
1068	<	skin = simParams_->getSkinThickness();
1069	<	notifyFortranSkinThickness(&skin);
1070	<	}
1071	<
1072	<	// Check if the cutoff was set explicitly:
1073	<	if (simParams_->haveCutoffRadius()) {
1074	<	rcut_ = simParams_->getCutoffRadius();
1075	<	if (simParams_->haveSwitchingRadius()) {
1076	<	rsw_  = simParams_->getSwitchingRadius();
1077	<	} else {
1078	<	if (fInfo_.SIM_uses_Charges |
1079	<	fInfo_.SIM_uses_Dipoles |
1080	<	fInfo_.SIM_uses_RF) {
1081	<
1082	<	rsw_ = 0.85 * rcut_;
1083	<	sprintf(painCave.errMsg,
1084	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1085	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1086	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1087	<	painCave.isFatal = 0;
1088	<	simError();
1089	<	} else {
1090	<	rsw_ = rcut_;
1091	<	sprintf(painCave.errMsg,
1092	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1093	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
1094	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1095	<	painCave.isFatal = 0;
1096	<	simError();
1097	<	}
1098	<	}
1099	<
1100	<	if (simParams_->haveElectrostaticSummationMethod()) {
1101	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1102	<	toUpper(myMethod);
1103	<
1104	<	if (myMethod == "SHIFTED_POTENTIAL") {
1105	<	ljsp_ = true;
1106	<	} else if (myMethod == "SHIFTED_FORCE") {
1107	<	ljsf_ = true;
1108	<	}
1109	<	}
1110	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1111	<
1112	<	} else {
1113	<
1114	<	// For electrostatic atoms, we'll assume a large safe value:
1115	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1116	<	sprintf(painCave.errMsg,
1117	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1118	<	"\tOOPSE will use a default value of 15.0 angstroms"
1119	<	"\tfor the cutoffRadius.\n");
1120	<	painCave.isFatal = 0;
1121	<	simError();
1122	<	rcut_ = 15.0;
1123	<
1124	<	if (simParams_->haveElectrostaticSummationMethod()) {
1125	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1126	<	toUpper(myMethod);
1127	<
1128	<	// For the time being, we're tethering the LJ shifted behavior to the
1129	<	// electrostaticSummationMethod keyword options
1130	<	if (myMethod == "SHIFTED_POTENTIAL") {
1131	<	ljsp_ = true;
1132	<	} else if (myMethod == "SHIFTED_FORCE") {
1133	<	ljsf_ = true;
1134	<	}
1135	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1136	<	if (simParams_->haveSwitchingRadius()){
1137	<	sprintf(painCave.errMsg,
1138	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1139	<	"\teven though the electrostaticSummationMethod was\n"
1140	<	"\tset to %s\n", myMethod.c_str());
1141	<	painCave.isFatal = 1;
1142	<	simError();
1143	<	}
1144	<	}
1145	<	}
1146	<
1147	<	if (simParams_->haveSwitchingRadius()){
1148	<	rsw_ = simParams_->getSwitchingRadius();
1149	<	} else {
1150	<	sprintf(painCave.errMsg,
1151	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1152	<	"\tOOPSE will use a default value of\n"
1153	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1154	<	painCave.isFatal = 0;
1155	<	simError();
1156	<	rsw_ = 0.85 * rcut_;
1157	<	}
1158	<
1159	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1160	<
1161	<	} else {
1162	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1163	<	// We'll punt and let fortran figure out the cutoffs later.
1164	<
1165	<	notifyFortranYouAreOnYourOwn();
1166	<
1167	<	}
1168	<	}
1169	<	}
1170	<
1171	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1172	<
1173	<	int errorOut;
1174	<	int esm =  NONE;
1175	<	int sm = UNDAMPED;
1176	<	RealType alphaVal;
1177	<	RealType dielectric;
991	>	void SimInfo::setupSwitchingFunction() {
992	>	int ft = CUBIC;
993
994	<	errorOut = isError;
995	<
1181	<	if (simParams_->haveElectrostaticSummationMethod()) {
1182	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1183	<	toUpper(myMethod);
1184	<	if (myMethod == "NONE") {
1185	<	esm = NONE;
1186	<	} else {
1187	<	if (myMethod == "SWITCHING_FUNCTION") {
1188	<	esm = SWITCHING_FUNCTION;
1189	<	} else {
1190	<	if (myMethod == "SHIFTED_POTENTIAL") {
1191	<	esm = SHIFTED_POTENTIAL;
1192	<	} else {
1193	<	if (myMethod == "SHIFTED_FORCE") {
1194	<	esm = SHIFTED_FORCE;
1195	<	} else {
1196	<	if (myMethod == "REACTION_FIELD") {
1197	<	esm = REACTION_FIELD;
1198	<	dielectric = simParams_->getDielectric();
1199	<	if (!simParams_->haveDielectric()) {
1200	<	// throw warning
1201	<	sprintf( painCave.errMsg,
1202	<	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1203	<	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1204	<	painCave.isFatal = 0;
1205	<	simError();
1206	<	}
1207	<	} else {
1208	<	// throw error
1209	<	sprintf( painCave.errMsg,
1210	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1211	<	"\t(Input file specified %s .)\n"
1212	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1213	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1214	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1215	<	painCave.isFatal = 1;
1216	<	simError();
1217	<	}
1218	<	}
1219	<	}
1220	<	}
1221	<	}
1222	<	}
1223	<
1224	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1225	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1226	<	toUpper(myScreen);
1227	<	if (myScreen == "UNDAMPED") {
1228	<	sm = UNDAMPED;
1229	<	} else {
1230	<	if (myScreen == "DAMPED") {
1231	<	sm = DAMPED;
1232	<	if (!simParams_->haveDampingAlpha()) {
1233	<	// first set a cutoff dependent alpha value
1234	<	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1235	<	alphaVal = 0.5125 - rcut_* 0.025;
1236	<	// for values rcut > 20.5, alpha is zero
1237	<	if (alphaVal < 0) alphaVal = 0;
1238	<
1239	<	// throw warning
1240	<	sprintf( painCave.errMsg,
1241	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1242	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1243	<	painCave.isFatal = 0;
1244	<	simError();
1245	<	} else {
1246	<	alphaVal = simParams_->getDampingAlpha();
1247	<	}
1248	<
1249	<	} else {
1250	<	// throw error
1251	<	sprintf( painCave.errMsg,
1252	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1253	<	"\t(Input file specified %s .)\n"
1254	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1255	<	"or \"damped\".\n", myScreen.c_str() );
1256	<	painCave.isFatal = 1;
1257	<	simError();
1258	<	}
1259	<	}
1260	<	}
1261	<
1262	<	// let's pass some summation method variables to fortran
1263	<	setElectrostaticSummationMethod( &esm );
1264	<	setFortranElectrostaticMethod( &esm );
1265	<	setScreeningMethod( &sm );
1266	<	setDampingAlpha( &alphaVal );
1267	<	setReactionFieldDielectric( &dielectric );
1268	<	initFortranFF( &errorOut );
1269	<	}
1270	<
1271	<	void SimInfo::setupSwitchingFunction() {
1272	<	int ft = CUBIC;
1273	<
1274	<	if (simParams_->haveSwitchingFunctionType()) {
1275	<	std::string funcType = simParams_->getSwitchingFunctionType();
994	>	if (simParams_->haveSwitchingFunctionType()) {
995	>	string funcType = simParams_->getSwitchingFunctionType();
996		toUpper(funcType);
997		if (funcType == "CUBIC") {
998		ft = CUBIC;
#	Line 1282 | Line 1002 | namespace oopse {
1002		} else {
1003		// throw error
1004		sprintf( painCave.errMsg,
1005	<	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1005	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n"
1006	>	"\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".",
1007	>	funcType.c_str() );
1008		painCave.isFatal = 1;
1009		simError();
1010		}
#	Line 1299 | Line 1021 | namespace oopse {
1021		// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1022		if ( simParams_->haveAccumulateBoxDipole() )
1023		if ( simParams_->getAccumulateBoxDipole() ) {
1302	–	setAccumulateBoxDipole();
1024		calcBoxDipole_ = true;
1025		}
1026
#	Line 1309 | Line 1030 | namespace oopse {
1030		properties_.addProperty(genData);
1031		}
1032
1033	<	void SimInfo::removeProperty(const std::string& propName) {
1033	>	void SimInfo::removeProperty(const string& propName) {
1034		properties_.removeProperty(propName);
1035		}
1036
#	Line 1317 | Line 1038 | namespace oopse {
1038		properties_.clearProperties();
1039		}
1040
1041	<	std::vector<std::string> SimInfo::getPropertyNames() {
1041	>	vector<string> SimInfo::getPropertyNames() {
1042		return properties_.getPropertyNames();
1043		}
1044
1045	<	std::vector<GenericData*> SimInfo::getProperties() {
1045	>	vector<GenericData*> SimInfo::getProperties() {
1046		return properties_.getProperties();
1047		}
1048
1049	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1049	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1050		return properties_.getPropertyByName(propName);
1051		}
1052
#	Line 1408 | Line 1129 | namespace oopse {
1129
1130		}
1131
1132	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1132	>	ostream& operator <<(ostream& o, SimInfo& info) {
1133
1134		return o;
1135		}
#	Line 1451 | Line 1172 | namespace oopse {
1172
1173
1174		[  Ixx -Ixy  -Ixz ]
1175	<	J =| -Iyx  Iyy  -Iyz |
1175	>	J =| -Iyx  Iyy  -Iyz |
1176		[ -Izx -Iyz   Izz ]
1177		*/
1178
#	Line 1558 | Line 1279 | namespace oopse {
1279		return IOIndexToIntegrableObject.at(index);
1280		}
1281
1282	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1282	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1283		IOIndexToIntegrableObject= v;
1284		}
1285
#	Line 1600 | Line 1321 | namespace oopse {
1321		return;
1322		}
1323		/*
1324	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1324	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1325		assert( v.size() == nAtoms_ + nRigidBodies_);
1326		sdByGlobalIndex_ = v;
1327		}
#	Line 1610 | Line 1331 | namespace oopse {
1331		return sdByGlobalIndex_.at(index);
1332		}
1333		*/
1334	<	}//end namespace oopse
1334	>	int SimInfo::getNGlobalConstraints() {
1335	>	int nGlobalConstraints;
1336	>	#ifdef IS_MPI
1337	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1338	>	MPI_COMM_WORLD);
1339	>	#else
1340	>	nGlobalConstraints =  nConstraints_;
1341	>	#endif
1342	>	return nGlobalConstraints;
1343	>	}
1344
1345	+	}//end namespace OpenMD
1346	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 1277 by gezelter, Mon Jul 14 12:35:58 2008 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1529 by gezelter, Mon Dec 27 18:35:59 2010 UTC

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