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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1534 by gezelter, Wed Dec 29 21:53:28 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 53 | Line 53
53		#include "brains/SimInfo.hpp"
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56	<	#include "UseTheForce/fCutoffPolicy.h"
57	<	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
58	<	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
59	<	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
56	>	#include "primitives/StuntDouble.hpp"
57		#include "UseTheForce/doForces_interface.h"
58	<	#include "UseTheForce/DarkSide/electrostatic_interface.h"
62	<	#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		#ifdef IS_MPI
67		#include "UseTheForce/mpiComponentPlan.h"
68		#include "UseTheForce/DarkSide/simParallel_interface.h"
69		#endif
70
71	<	namespace oopse {
72	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
76	<	std::map<int, std::set<int> >::iterator i = container.find(index);
77	<	std::set<int> result;
78	<	if (i != container.end()) {
79	<	result = i->second;
80	<	}
81	<
82	<	return result;
83	<	}
71	>	using namespace std;
72	>	namespace OpenMD {
73
74		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
75		forceField_(ff), simParams_(simParams),
76		ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
77		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
78		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
79	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
80	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
81	<	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) {
82	<
83	<	MoleculeStamp* molStamp;
84	<	int nMolWithSameStamp;
85	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
86	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
87	<	CutoffGroupStamp* cgStamp;
88	<	RigidBodyStamp* rbStamp;
89	<	int nRigidAtoms = 0;
90	<	std::vector<Component*> components = simParams->getComponents();
79	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
80	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
81	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
82	>	calcBoxDipole_(false), useAtomicVirial_(true) {
83	>
84	>	MoleculeStamp* molStamp;
85	>	int nMolWithSameStamp;
86	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
88	>	CutoffGroupStamp* cgStamp;
89	>	RigidBodyStamp* rbStamp;
90	>	int nRigidAtoms = 0;
91	>
92	>	vector<Component*> components = simParams->getComponents();
93	>
94	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
95	>	molStamp = (*i)->getMoleculeStamp();
96	>	nMolWithSameStamp = (*i)->getNMol();
97
98	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
99	<	molStamp = (*i)->getMoleculeStamp();
100	<	nMolWithSameStamp = (*i)->getNMol();
101	<
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();
115	<
116	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
117	<	cgStamp = molStamp->getCutoffGroupStamp(j);
118	<	nAtomsInGroups += cgStamp->getNMembers();
119	<	}
120	<
121	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
122	<
123	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
124	<
125	<	//calculate atoms in rigid bodies
126	<	int nAtomsInRigidBodies = 0;
127	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
128	<
129	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
130	<	rbStamp = molStamp->getRigidBodyStamp(j);
131	<	nAtomsInRigidBodies += rbStamp->getNMembers();
132	<	}
133	<
134	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
135	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
136	<
98	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
99	>
100	>	//calculate atoms in molecules
101	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
102	>
103	>	//calculate atoms in cutoff groups
104	>	int nAtomsInGroups = 0;
105	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
106	>
107	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
108	>	cgStamp = molStamp->getCutoffGroupStamp(j);
109	>	nAtomsInGroups += cgStamp->getNMembers();
110		}
111	<
112	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
113	<	//group therefore the total number of cutoff groups in the system is
114	<	//equal to the total number of atoms minus number of atoms belong to
115	<	//cutoff group defined in meta-data file plus the number of cutoff
116	<	//groups defined in meta-data file
117	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
118	<
119	<	//every free atom (atom does not belong to rigid bodies) is an
120	<	//integrable object therefore the total number of integrable objects
121	<	//in the system is equal to the total number of atoms minus number of
122	<	//atoms belong to rigid body defined in meta-data file plus the number
123	<	//of rigid bodies defined in meta-data file
124	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
125	<	+ nGlobalRigidBodies_;
126	<
127	<	nGlobalMols_ = molStampIds_.size();
155	<
156	<	#ifdef IS_MPI
157	<	molToProcMap_.resize(nGlobalMols_);
158	<	#endif
159	<
111	>
112	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
113	>
114	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
115	>
116	>	//calculate atoms in rigid bodies
117	>	int nAtomsInRigidBodies = 0;
118	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
119	>
120	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
121	>	rbStamp = molStamp->getRigidBodyStamp(j);
122	>	nAtomsInRigidBodies += rbStamp->getNMembers();
123	>	}
124	>
125	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
126	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
127	>
128		}
129	<
129	>
130	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
131	>	//group therefore the total number of cutoff groups in the system is
132	>	//equal to the total number of atoms minus number of atoms belong to
133	>	//cutoff group defined in meta-data file plus the number of cutoff
134	>	//groups defined in meta-data file
135	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
136	>
137	>	//every free atom (atom does not belong to rigid bodies) is an
138	>	//integrable object therefore the total number of integrable objects
139	>	//in the system is equal to the total number of atoms minus number of
140	>	//atoms belong to rigid body defined in meta-data file plus the number
141	>	//of rigid bodies defined in meta-data file
142	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
143	>	+ nGlobalRigidBodies_;
144	>
145	>	nGlobalMols_ = molStampIds_.size();
146	>	molToProcMap_.resize(nGlobalMols_);
147	>	}
148	>
149		SimInfo::~SimInfo() {
150	<	std::map<int, Molecule*>::iterator i;
150	>	map<int, Molecule*>::iterator i;
151		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
152		delete i->second;
153		}
#	Line 171 | Line 158 | namespace oopse {
158		delete forceField_;
159		}
160
174	–	int SimInfo::getNGlobalConstraints() {
175	–	int nGlobalConstraints;
176	–	#ifdef IS_MPI
177	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
178	–	MPI_COMM_WORLD);
179	–	#else
180	–	nGlobalConstraints =  nConstraints_;
181	–	#endif
182	–	return nGlobalConstraints;
183	–	}
161
162		bool SimInfo::addMolecule(Molecule* mol) {
163		MoleculeIterator i;
164	<
164	>
165		i = molecules_.find(mol->getGlobalIndex());
166		if (i == molecules_.end() ) {
167	<
168	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
169	<
167	>
168	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
169	>
170		nAtoms_ += mol->getNAtoms();
171		nBonds_ += mol->getNBonds();
172		nBends_ += mol->getNBends();
173		nTorsions_ += mol->getNTorsions();
174	+	nInversions_ += mol->getNInversions();
175		nRigidBodies_ += mol->getNRigidBodies();
176		nIntegrableObjects_ += mol->getNIntegrableObjects();
177		nCutoffGroups_ += mol->getNCutoffGroups();
178		nConstraints_ += mol->getNConstraintPairs();
179	<
180	<	addExcludePairs(mol);
181	<
179	>
180	>	addInteractionPairs(mol);
181	>
182		return true;
183		} else {
184		return false;
185		}
186		}
187	<
187	>
188		bool SimInfo::removeMolecule(Molecule* mol) {
189		MoleculeIterator i;
190		i = molecules_.find(mol->getGlobalIndex());
#	Line 219 | Line 197 | namespace oopse {
197		nBonds_ -= mol->getNBonds();
198		nBends_ -= mol->getNBends();
199		nTorsions_ -= mol->getNTorsions();
200	+	nInversions_ -= mol->getNInversions();
201		nRigidBodies_ -= mol->getNRigidBodies();
202		nIntegrableObjects_ -= mol->getNIntegrableObjects();
203		nCutoffGroups_ -= mol->getNCutoffGroups();
204		nConstraints_ -= mol->getNConstraintPairs();
205
206	<	removeExcludePairs(mol);
206	>	removeInteractionPairs(mol);
207		molecules_.erase(mol->getGlobalIndex());
208
209		delete mol;
#	Line 233 | Line 212 | namespace oopse {
212		} else {
213		return false;
214		}
236	–
237	–
215		}
216
217
#	Line 252 | Line 229 | namespace oopse {
229		void SimInfo::calcNdf() {
230		int ndf_local;
231		MoleculeIterator i;
232	<	std::vector<StuntDouble*>::iterator j;
232	>	vector<StuntDouble*>::iterator j;
233		Molecule* mol;
234		StuntDouble* integrableObject;
235
#	Line 303 | Line 280 | namespace oopse {
280		int ndfRaw_local;
281
282		MoleculeIterator i;
283	<	std::vector<StuntDouble*>::iterator j;
283	>	vector<StuntDouble*>::iterator j;
284		Molecule* mol;
285		StuntDouble* integrableObject;
286
#	Line 350 | Line 327 | namespace oopse {
327
328		}
329
330	<	void SimInfo::addExcludePairs(Molecule* mol) {
331	<	std::vector<Bond*>::iterator bondIter;
332	<	std::vector<Bend*>::iterator bendIter;
333	<	std::vector<Torsion*>::iterator torsionIter;
330	>	void SimInfo::addInteractionPairs(Molecule* mol) {
331	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
332	>	vector<Bond*>::iterator bondIter;
333	>	vector<Bend*>::iterator bendIter;
334	>	vector<Torsion*>::iterator torsionIter;
335	>	vector<Inversion*>::iterator inversionIter;
336		Bond* bond;
337		Bend* bend;
338		Torsion* torsion;
339	+	Inversion* inversion;
340		int a;
341		int b;
342		int c;
343		int d;
344
345	<	std::map<int, std::set<int> > atomGroups;
345	>	// atomGroups can be used to add special interaction maps between
346	>	// groups of atoms that are in two separate rigid bodies.
347	>	// However, most site-site interactions between two rigid bodies
348	>	// are probably not special, just the ones between the physically
349	>	// bonded atoms.  Interactions *within* a single rigid body should
350	>	// always be excluded.  These are done at the bottom of this
351	>	// function.
352
353	+	map<int, set<int> > atomGroups;
354		Molecule::RigidBodyIterator rbIter;
355		RigidBody* rb;
356		Molecule::IntegrableObjectIterator ii;
357		StuntDouble* integrableObject;
358
359	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
360	<	integrableObject = mol->nextIntegrableObject(ii)) {
361	<
359	>	for (integrableObject = mol->beginIntegrableObject(ii);
360	>	integrableObject != NULL;
361	>	integrableObject = mol->nextIntegrableObject(ii)) {
362	>
363		if (integrableObject->isRigidBody()) {
364	<	rb = static_cast<RigidBody*>(integrableObject);
365	<	std::vector<Atom*> atoms = rb->getAtoms();
366	<	std::set<int> rigidAtoms;
367	<	for (int i = 0; i < atoms.size(); ++i) {
368	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
369	<	}
370	<	for (int i = 0; i < atoms.size(); ++i) {
371	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
372	<	}
364	>	rb = static_cast<RigidBody*>(integrableObject);
365	>	vector<Atom*> atoms = rb->getAtoms();
366	>	set<int> rigidAtoms;
367	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
368	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
369	>	}
370	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
371	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
372	>	}
373		} else {
374	<	std::set<int> oneAtomSet;
374	>	set<int> oneAtomSet;
375		oneAtomSet.insert(integrableObject->getGlobalIndex());
376	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
376	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
377		}
378		}
379	+
380	+	for (bond= mol->beginBond(bondIter); bond != NULL;
381	+	bond = mol->nextBond(bondIter)) {
382
392	–
393	–
394	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
383		a = bond->getAtomA()->getGlobalIndex();
384	<	b = bond->getAtomB()->getGlobalIndex();
385	<	exclude_.addPair(a, b);
384	>	b = bond->getAtomB()->getGlobalIndex();
385	>
386	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
387	>	oneTwoInteractions_.addPair(a, b);
388	>	} else {
389	>	excludedInteractions_.addPair(a, b);
390	>	}
391		}
392
393	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
393	>	for (bend= mol->beginBend(bendIter); bend != NULL;
394	>	bend = mol->nextBend(bendIter)) {
395	>
396		a = bend->getAtomA()->getGlobalIndex();
397		b = bend->getAtomB()->getGlobalIndex();
398		c = bend->getAtomC()->getGlobalIndex();
404	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
405	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
406	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
407	–
408	–	exclude_.addPairs(rigidSetA, rigidSetB);
409	–	exclude_.addPairs(rigidSetA, rigidSetC);
410	–	exclude_.addPairs(rigidSetB, rigidSetC);
399
400	<	//exclude_.addPair(a, b);
401	<	//exclude_.addPair(a, c);
402	<	//exclude_.addPair(b, c);
400	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
401	>	oneTwoInteractions_.addPair(a, b);
402	>	oneTwoInteractions_.addPair(b, c);
403	>	} else {
404	>	excludedInteractions_.addPair(a, b);
405	>	excludedInteractions_.addPair(b, c);
406	>	}
407	>
408	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
409	>	oneThreeInteractions_.addPair(a, c);
410	>	} else {
411	>	excludedInteractions_.addPair(a, c);
412	>	}
413		}
414
415	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
415	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
416	>	torsion = mol->nextTorsion(torsionIter)) {
417	>
418		a = torsion->getAtomA()->getGlobalIndex();
419		b = torsion->getAtomB()->getGlobalIndex();
420		c = torsion->getAtomC()->getGlobalIndex();
421	<	d = torsion->getAtomD()->getGlobalIndex();
422	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
423	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
424	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
425	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
421	>	d = torsion->getAtomD()->getGlobalIndex();
422
423	<	exclude_.addPairs(rigidSetA, rigidSetB);
424	<	exclude_.addPairs(rigidSetA, rigidSetC);
425	<	exclude_.addPairs(rigidSetA, rigidSetD);
426	<	exclude_.addPairs(rigidSetB, rigidSetC);
427	<	exclude_.addPairs(rigidSetB, rigidSetD);
428	<	exclude_.addPairs(rigidSetC, rigidSetD);
423	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
424	>	oneTwoInteractions_.addPair(a, b);
425	>	oneTwoInteractions_.addPair(b, c);
426	>	oneTwoInteractions_.addPair(c, d);
427	>	} else {
428	>	excludedInteractions_.addPair(a, b);
429	>	excludedInteractions_.addPair(b, c);
430	>	excludedInteractions_.addPair(c, d);
431	>	}
432
433	<	/*
434	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
435	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
436	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
437	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
438	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
439	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
440	<
441	<
442	<	exclude_.addPair(a, b);
443	<	exclude_.addPair(a, c);
444	<	exclude_.addPair(a, d);
445	<	exclude_.addPair(b, c);
447	<	exclude_.addPair(b, d);
448	<	exclude_.addPair(c, d);
449	<	*/
433	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
434	>	oneThreeInteractions_.addPair(a, c);
435	>	oneThreeInteractions_.addPair(b, d);
436	>	} else {
437	>	excludedInteractions_.addPair(a, c);
438	>	excludedInteractions_.addPair(b, d);
439	>	}
440	>
441	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
442	>	oneFourInteractions_.addPair(a, d);
443	>	} else {
444	>	excludedInteractions_.addPair(a, d);
445	>	}
446		}
447
448	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
449	<	std::vector<Atom*> atoms = rb->getAtoms();
450	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
451	<	for (int j = i + 1; j < atoms.size(); ++j) {
448	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
449	>	inversion = mol->nextInversion(inversionIter)) {
450	>
451	>	a = inversion->getAtomA()->getGlobalIndex();
452	>	b = inversion->getAtomB()->getGlobalIndex();
453	>	c = inversion->getAtomC()->getGlobalIndex();
454	>	d = inversion->getAtomD()->getGlobalIndex();
455	>
456	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
457	>	oneTwoInteractions_.addPair(a, b);
458	>	oneTwoInteractions_.addPair(a, c);
459	>	oneTwoInteractions_.addPair(a, d);
460	>	} else {
461	>	excludedInteractions_.addPair(a, b);
462	>	excludedInteractions_.addPair(a, c);
463	>	excludedInteractions_.addPair(a, d);
464	>	}
465	>
466	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
467	>	oneThreeInteractions_.addPair(b, c);
468	>	oneThreeInteractions_.addPair(b, d);
469	>	oneThreeInteractions_.addPair(c, d);
470	>	} else {
471	>	excludedInteractions_.addPair(b, c);
472	>	excludedInteractions_.addPair(b, d);
473	>	excludedInteractions_.addPair(c, d);
474	>	}
475	>	}
476	>
477	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
478	>	rb = mol->nextRigidBody(rbIter)) {
479	>	vector<Atom*> atoms = rb->getAtoms();
480	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
481	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
482		a = atoms[i]->getGlobalIndex();
483		b = atoms[j]->getGlobalIndex();
484	<	exclude_.addPair(a, b);
484	>	excludedInteractions_.addPair(a, b);
485		}
486		}
487		}
488
489		}
490
491	<	void SimInfo::removeExcludePairs(Molecule* mol) {
492	<	std::vector<Bond*>::iterator bondIter;
493	<	std::vector<Bend*>::iterator bendIter;
494	<	std::vector<Torsion*>::iterator torsionIter;
491	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
492	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
493	>	vector<Bond*>::iterator bondIter;
494	>	vector<Bend*>::iterator bendIter;
495	>	vector<Torsion*>::iterator torsionIter;
496	>	vector<Inversion*>::iterator inversionIter;
497		Bond* bond;
498		Bend* bend;
499		Torsion* torsion;
500	+	Inversion* inversion;
501		int a;
502		int b;
503		int c;
504		int d;
505
506	<	std::map<int, std::set<int> > atomGroups;
478	<
506	>	map<int, set<int> > atomGroups;
507		Molecule::RigidBodyIterator rbIter;
508		RigidBody* rb;
509		Molecule::IntegrableObjectIterator ii;
510		StuntDouble* integrableObject;
511
512	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
513	<	integrableObject = mol->nextIntegrableObject(ii)) {
514	<
512	>	for (integrableObject = mol->beginIntegrableObject(ii);
513	>	integrableObject != NULL;
514	>	integrableObject = mol->nextIntegrableObject(ii)) {
515	>
516		if (integrableObject->isRigidBody()) {
517	<	rb = static_cast<RigidBody*>(integrableObject);
518	<	std::vector<Atom*> atoms = rb->getAtoms();
519	<	std::set<int> rigidAtoms;
520	<	for (int i = 0; i < atoms.size(); ++i) {
521	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
522	<	}
523	<	for (int i = 0; i < atoms.size(); ++i) {
524	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
525	<	}
517	>	rb = static_cast<RigidBody*>(integrableObject);
518	>	vector<Atom*> atoms = rb->getAtoms();
519	>	set<int> rigidAtoms;
520	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
521	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
522	>	}
523	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
524	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
525	>	}
526		} else {
527	<	std::set<int> oneAtomSet;
527	>	set<int> oneAtomSet;
528		oneAtomSet.insert(integrableObject->getGlobalIndex());
529	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
529	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
530		}
531		}
532
533	<
534	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
533	>	for (bond= mol->beginBond(bondIter); bond != NULL;
534	>	bond = mol->nextBond(bondIter)) {
535	>
536		a = bond->getAtomA()->getGlobalIndex();
537	<	b = bond->getAtomB()->getGlobalIndex();
538	<	exclude_.removePair(a, b);
537	>	b = bond->getAtomB()->getGlobalIndex();
538	>
539	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
540	>	oneTwoInteractions_.removePair(a, b);
541	>	} else {
542	>	excludedInteractions_.removePair(a, b);
543	>	}
544		}
545
546	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
546	>	for (bend= mol->beginBend(bendIter); bend != NULL;
547	>	bend = mol->nextBend(bendIter)) {
548	>
549		a = bend->getAtomA()->getGlobalIndex();
550		b = bend->getAtomB()->getGlobalIndex();
551		c = bend->getAtomC()->getGlobalIndex();
515	–
516	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
517	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
518	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
519	–
520	–	exclude_.removePairs(rigidSetA, rigidSetB);
521	–	exclude_.removePairs(rigidSetA, rigidSetC);
522	–	exclude_.removePairs(rigidSetB, rigidSetC);
552
553	<	//exclude_.removePair(a, b);
554	<	//exclude_.removePair(a, c);
555	<	//exclude_.removePair(b, c);
553	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
554	>	oneTwoInteractions_.removePair(a, b);
555	>	oneTwoInteractions_.removePair(b, c);
556	>	} else {
557	>	excludedInteractions_.removePair(a, b);
558	>	excludedInteractions_.removePair(b, c);
559	>	}
560	>
561	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
562	>	oneThreeInteractions_.removePair(a, c);
563	>	} else {
564	>	excludedInteractions_.removePair(a, c);
565	>	}
566		}
567
568	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
568	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
569	>	torsion = mol->nextTorsion(torsionIter)) {
570	>
571		a = torsion->getAtomA()->getGlobalIndex();
572		b = torsion->getAtomB()->getGlobalIndex();
573		c = torsion->getAtomC()->getGlobalIndex();
574	<	d = torsion->getAtomD()->getGlobalIndex();
574	>	d = torsion->getAtomD()->getGlobalIndex();
575	>
576	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
577	>	oneTwoInteractions_.removePair(a, b);
578	>	oneTwoInteractions_.removePair(b, c);
579	>	oneTwoInteractions_.removePair(c, d);
580	>	} else {
581	>	excludedInteractions_.removePair(a, b);
582	>	excludedInteractions_.removePair(b, c);
583	>	excludedInteractions_.removePair(c, d);
584	>	}
585
586	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
587	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
588	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
589	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
586	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
587	>	oneThreeInteractions_.removePair(a, c);
588	>	oneThreeInteractions_.removePair(b, d);
589	>	} else {
590	>	excludedInteractions_.removePair(a, c);
591	>	excludedInteractions_.removePair(b, d);
592	>	}
593
594	<	exclude_.removePairs(rigidSetA, rigidSetB);
595	<	exclude_.removePairs(rigidSetA, rigidSetC);
596	<	exclude_.removePairs(rigidSetA, rigidSetD);
597	<	exclude_.removePairs(rigidSetB, rigidSetC);
598	<	exclude_.removePairs(rigidSetB, rigidSetD);
599	<	exclude_.removePairs(rigidSetC, rigidSetD);
594	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
595	>	oneFourInteractions_.removePair(a, d);
596	>	} else {
597	>	excludedInteractions_.removePair(a, d);
598	>	}
599	>	}
600
601	<	/*
602	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
549	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
550	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
551	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
552	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
553	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
601	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
602	>	inversion = mol->nextInversion(inversionIter)) {
603
604	<
605	<	exclude_.removePair(a, b);
606	<	exclude_.removePair(a, c);
607	<	exclude_.removePair(a, d);
608	<	exclude_.removePair(b, c);
609	<	exclude_.removePair(b, d);
610	<	exclude_.removePair(c, d);
611	<	*/
604	>	a = inversion->getAtomA()->getGlobalIndex();
605	>	b = inversion->getAtomB()->getGlobalIndex();
606	>	c = inversion->getAtomC()->getGlobalIndex();
607	>	d = inversion->getAtomD()->getGlobalIndex();
608	>
609	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
610	>	oneTwoInteractions_.removePair(a, b);
611	>	oneTwoInteractions_.removePair(a, c);
612	>	oneTwoInteractions_.removePair(a, d);
613	>	} else {
614	>	excludedInteractions_.removePair(a, b);
615	>	excludedInteractions_.removePair(a, c);
616	>	excludedInteractions_.removePair(a, d);
617	>	}
618	>
619	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
620	>	oneThreeInteractions_.removePair(b, c);
621	>	oneThreeInteractions_.removePair(b, d);
622	>	oneThreeInteractions_.removePair(c, d);
623	>	} else {
624	>	excludedInteractions_.removePair(b, c);
625	>	excludedInteractions_.removePair(b, d);
626	>	excludedInteractions_.removePair(c, d);
627	>	}
628		}
629
630	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
631	<	std::vector<Atom*> atoms = rb->getAtoms();
632	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
633	<	for (int j = i + 1; j < atoms.size(); ++j) {
630	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
631	>	rb = mol->nextRigidBody(rbIter)) {
632	>	vector<Atom*> atoms = rb->getAtoms();
633	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
634	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
635		a = atoms[i]->getGlobalIndex();
636		b = atoms[j]->getGlobalIndex();
637	<	exclude_.removePair(a, b);
637	>	excludedInteractions_.removePair(a, b);
638		}
639		}
640		}
641	<
641	>
642		}
643	<
644	<
643	>
644	>
645		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
646		int curStampId;
647	<
647	>
648		//index from 0
649		curStampId = moleculeStamps_.size();
650
#	Line 586 | Line 652 | namespace oopse {
652		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
653		}
654
655	+
656	+	/**
657	+	* update
658	+	*
659	+	*  Performs the global checks and variable settings after the objects have been
660	+	*  created.
661	+	*
662	+	*/
663		void SimInfo::update() {
664	+
665	+	setupSimVariables();
666	+	setupCutoffs();
667	+	setupSwitching();
668	+	setupElectrostatics();
669	+	setupNeighborlists();
670
591	–	setupSimType();
592	–
671		#ifdef IS_MPI
672		setupFortranParallel();
673		#endif
596	–
674		setupFortranSim();
675	+	fortranInitialized_ = true;
676
599	–	//setup fortran force field
600	–	/** @deprecate */
601	–	int isError = 0;
602	–
603	–	setupElectrostaticSummationMethod( isError );
604	–	setupSwitchingFunction();
605	–	setupAccumulateBoxDipole();
606	–
607	–	if(isError){
608	–	sprintf( painCave.errMsg,
609	–	"ForceField error: There was an error initializing the forceField in fortran.\n" );
610	–	painCave.isFatal = 1;
611	–	simError();
612	–	}
613	–
614	–
615	–	setupCutoff();
616	–
677		calcNdf();
678		calcNdfRaw();
679		calcNdfTrans();
620	–
621	–	fortranInitialized_ = true;
680		}
681	<
682	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
681	>
682	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
683		SimInfo::MoleculeIterator mi;
684		Molecule* mol;
685		Molecule::AtomIterator ai;
686		Atom* atom;
687	<	std::set<AtomType*> atomTypes;
688	<
689	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
632	<
687	>	set<AtomType*> atomTypes;
688	>
689	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
690		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
691		atomTypes.insert(atom->getAtomType());
692	<	}
693	<
637	<	}
638	<
692	>	}
693	>	}
694		return atomTypes;
695		}
696
697	<	void SimInfo::setupSimType() {
698	<	std::set<AtomType*>::iterator i;
699	<	std::set<AtomType*> atomTypes;
700	<	atomTypes = getUniqueAtomTypes();
701	<
702	<	int useLennardJones = 0;
703	<	int useElectrostatic = 0;
704	<	int useEAM = 0;
705	<	int useSC = 0;
706	<	int useCharge = 0;
707	<	int useDirectional = 0;
708	<	int useDipole = 0;
709	<	int useGayBerne = 0;
710	<	int useSticky = 0;
711	<	int useStickyPower = 0;
712	<	int useShape = 0;
713	<	int useFLARB = 0; //it is not in AtomType yet
714	<	int useDirectionalAtom = 0;
715	<	int useElectrostatics = 0;
716	<	//usePBC and useRF are from simParams
717	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
718	<	int useRF;
719	<	int useSF;
720	<	int useSP;
721	<	int useBoxDipole;
722	<	std::string myMethod;
723	<
724	<	// set the useRF logical
725	<	useRF = 0;
726	<	useSF = 0;
727	<
728	<
729	<	if (simParams_->haveElectrostaticSummationMethod()) {
730	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
731	<	toUpper(myMethod);
732	<	if (myMethod == "REACTION_FIELD"){
733	<	useRF=1;
734	<	} else if (myMethod == "SHIFTED_FORCE"){
735	<	useSF = 1;
736	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
737	<	useSP = 1;
697	>	/**
698	>	* setupCutoffs
699	>	*
700	>	* Sets the values of cutoffRadius and cutoffMethod
701	>	*
702	>	* cutoffRadius : realType
703	>	*  If the cutoffRadius was explicitly set, use that value.
704	>	*  If the cutoffRadius was not explicitly set:
705	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
706	>	*      No electrostatic atoms?  Poll the atom types present in the
707	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
708	>	*      Use the maximum suggested value that was found.
709	>	*
710	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
711	>	*      If cutoffMethod was explicitly set, use that choice.
712	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
713	>	*/
714	>	void SimInfo::setupCutoffs() {
715	>
716	>	if (simParams_->haveCutoffRadius()) {
717	>	cutoffRadius_ = simParams_->getCutoffRadius();
718	>	} else {
719	>	if (usesElectrostaticAtoms_) {
720	>	sprintf(painCave.errMsg,
721	>	"SimInfo: No value was set for the cutoffRadius.\n"
722	>	"\tOpenMD will use a default value of 12.0 angstroms"
723	>	"\tfor the cutoffRadius.\n");
724	>	painCave.isFatal = 0;
725	>	painCave.severity = OPENMD_INFO;
726	>	simError();
727	>	cutoffRadius_ = 12.0;
728	>	} else {
729	>	RealType thisCut;
730	>	set<AtomType*>::iterator i;
731	>	set<AtomType*> atomTypes;
732	>	atomTypes = getSimulatedAtomTypes();
733	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
734	>	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
735	>	cutoffRadius_ = max(thisCut, cutoffRadius_);
736	>	}
737	>	sprintf(painCave.errMsg,
738	>	"SimInfo: No value was set for the cutoffRadius.\n"
739	>	"\tOpenMD will use %lf angstroms.\n",
740	>	cutoffRadius_);
741	>	painCave.isFatal = 0;
742	>	painCave.severity = OPENMD_INFO;
743	>	simError();
744	>	}
745	>	}
746	>
747	>	map<string, CutoffMethod> stringToCutoffMethod;
748	>	stringToCutoffMethod["HARD"] = HARD;
749	>	stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
750	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
751	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
752	>
753	>	if (simParams_->haveCutoffMethod()) {
754	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
755	>	map<string, CutoffMethod>::iterator i;
756	>	i = stringToCutoffMethod.find(cutMeth);
757	>	if (i == stringToCutoffMethod.end()) {
758	>	sprintf(painCave.errMsg,
759	>	"SimInfo: Could not find chosen cutoffMethod %s\n"
760	>	"\tShould be one of: "
761	>	"HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
762	>	cutMeth.c_str());
763	>	painCave.isFatal = 1;
764	>	painCave.severity = OPENMD_ERROR;
765	>	simError();
766	>	} else {
767	>	cutoffMethod_ = i->second;
768		}
769	+	} else {
770	+	sprintf(painCave.errMsg,
771	+	"SimInfo: No value was set for the cutoffMethod.\n"
772	+	"\tOpenMD will use SHIFTED_FORCE.\n");
773	+	painCave.isFatal = 0;
774	+	painCave.severity = OPENMD_INFO;
775	+	simError();
776	+	cutoffMethod_ = SHIFTED_FORCE;
777		}
778	+	}
779	+
780	+	/**
781	+	* setupSwitching
782	+	*
783	+	* Sets the values of switchingRadius and
784	+	*  If the switchingRadius was explicitly set, use that value (but check it)
785	+	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
786	+	*/
787	+	void SimInfo::setupSwitching() {
788
789	<	if (simParams_->haveAccumulateBoxDipole())
790	<	if (simParams_->getAccumulateBoxDipole())
791	<	useBoxDipole = 1;
789	>	if (simParams_->haveSwitchingRadius()) {
790	>	switchingRadius_ = simParams_->getSwitchingRadius();
791	>	if (switchingRadius_ > cutoffRadius_) {
792	>	sprintf(painCave.errMsg,
793	>	"SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
794	>	switchingRadius_, cutoffRadius_);
795	>	painCave.isFatal = 1;
796	>	painCave.severity = OPENMD_ERROR;
797	>	simError();
798	>	}
799	>	} else {
800	>	switchingRadius_ = 0.85 * cutoffRadius_;
801	>	sprintf(painCave.errMsg,
802	>	"SimInfo: No value was set for the switchingRadius.\n"
803	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
804	>	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
805	>	painCave.isFatal = 0;
806	>	painCave.severity = OPENMD_WARNING;
807	>	simError();
808	>	}
809	>
810	>	if (simParams_->haveSwitchingFunctionType()) {
811	>	string funcType = simParams_->getSwitchingFunctionType();
812	>	toUpper(funcType);
813	>	if (funcType == "CUBIC") {
814	>	sft_ = cubic;
815	>	} else {
816	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
817	>	sft_ = fifth_order_poly;
818	>	} else {
819	>	// throw error
820	>	sprintf( painCave.errMsg,
821	>	"SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
822	>	"\tswitchingFunctionType must be one of: "
823	>	"\"cubic\" or \"fifth_order_polynomial\".",
824	>	funcType.c_str() );
825	>	painCave.isFatal = 1;
826	>	painCave.severity = OPENMD_ERROR;
827	>	simError();
828	>	}
829	>	}
830	>	}
831	>	}
832
833	+	/**
834	+	* setupNeighborlists
835	+	*
836	+	*  If the skinThickness was explicitly set, use that value (but check it)
837	+	*  If the skinThickness was not explicitly set: use 1.0 angstroms
838	+	*/
839	+	void SimInfo::setupNeighborlists() {
840	+	if (simParams_->haveSkinThickness()) {
841	+	skinThickness_ = simParams_->getSkinThickness();
842	+	} else {
843	+	skinThickness_ = 1.0;
844	+	sprintf(painCave.errMsg,
845	+	"SimInfo: No value was set for the skinThickness.\n"
846	+	"\tOpenMD will use a default value of %f Angstroms\n"
847	+	"\tfor this simulation\n", skinThickness_);
848	+	painCave.severity = OPENMD_INFO;
849	+	painCave.isFatal = 0;
850	+	simError();
851	+	}
852	+	}
853	+
854	+	void SimInfo::setupSimVariables() {
855	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
856	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
857	+	calcBoxDipole_ = false;
858	+	if ( simParams_->haveAccumulateBoxDipole() )
859	+	if ( simParams_->getAccumulateBoxDipole() ) {
860	+	calcBoxDipole_ = true;
861	+	}
862	+
863	+	set<AtomType*>::iterator i;
864	+	set<AtomType*> atomTypes;
865	+	atomTypes = getSimulatedAtomTypes();
866	+	int usesElectrostatic = 0;
867	+	int usesMetallic = 0;
868	+	int usesDirectional = 0;
869		//loop over all of the atom types
870		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
871	<	useLennardJones |= (*i)->isLennardJones();
872	<	useElectrostatic |= (*i)->isElectrostatic();
873	<	useEAM |= (*i)->isEAM();
695	<	useSC |= (*i)->isSC();
696	<	useCharge |= (*i)->isCharge();
697	<	useDirectional |= (*i)->isDirectional();
698	<	useDipole |= (*i)->isDipole();
699	<	useGayBerne |= (*i)->isGayBerne();
700	<	useSticky |= (*i)->isSticky();
701	<	useStickyPower |= (*i)->isStickyPower();
702	<	useShape |= (*i)->isShape();
871	>	usesElectrostatic |= (*i)->isElectrostatic();
872	>	usesMetallic |= (*i)->isMetal();
873	>	usesDirectional |= (*i)->isDirectional();
874		}
875
705	–	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
706	–	useDirectionalAtom = 1;
707	–	}
708	–
709	–	if (useCharge || useDipole) {
710	–	useElectrostatics = 1;
711	–	}
712	–
876		#ifdef IS_MPI
877		int temp;
878	+	temp = usesDirectional;
879	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
880
881	<	temp = usePBC;
882	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
881	>	temp = usesMetallic;
882	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
883
884	<	temp = useDirectionalAtom;
885	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
721	<
722	<	temp = useLennardJones;
723	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
724	<
725	<	temp = useElectrostatics;
726	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
727	<
728	<	temp = useCharge;
729	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
730	<
731	<	temp = useDipole;
732	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
733	<
734	<	temp = useSticky;
735	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
736	<
737	<	temp = useStickyPower;
738	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
739	<
740	<	temp = useGayBerne;
741	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
742	<
743	<	temp = useEAM;
744	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
745	<
746	<	temp = useSC;
747	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
748	<
749	<	temp = useShape;
750	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
751	<
752	<	temp = useFLARB;
753	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
754	<
755	<	temp = useRF;
756	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
757	<
758	<	temp = useSF;
759	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
760	<
761	<	temp = useSP;
762	<	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
763	<
764	<	temp = useBoxDipole;
765	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766	<
884	>	temp = usesElectrostatic;
885	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
886		#endif
887	<
888	<	fInfo_.SIM_uses_PBC = usePBC;
889	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
890	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
891	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
892	<	fInfo_.SIM_uses_Charges = useCharge;
774	<	fInfo_.SIM_uses_Dipoles = useDipole;
775	<	fInfo_.SIM_uses_Sticky = useSticky;
776	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
777	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
778	<	fInfo_.SIM_uses_EAM = useEAM;
779	<	fInfo_.SIM_uses_SC = useSC;
780	<	fInfo_.SIM_uses_Shapes = useShape;
781	<	fInfo_.SIM_uses_FLARB = useFLARB;
782	<	fInfo_.SIM_uses_RF = useRF;
783	<	fInfo_.SIM_uses_SF = useSF;
784	<	fInfo_.SIM_uses_SP = useSP;
785	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
786	<
787	<	if( myMethod == "REACTION_FIELD") {
788	<
789	<	if (simParams_->haveDielectric()) {
790	<	fInfo_.dielect = simParams_->getDielectric();
791	<	} else {
792	<	sprintf(painCave.errMsg,
793	<	"SimSetup Error: No Dielectric constant was set.\n"
794	<	"\tYou are trying to use Reaction Field without"
795	<	"\tsetting a dielectric constant!\n");
796	<	painCave.isFatal = 1;
797	<	simError();
798	<	}
799	<	}
800	<
887	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
888	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
889	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
890	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
891	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
892	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
893		}
894
895		void SimInfo::setupFortranSim() {
896		int isError;
897	<	int nExclude;
898	<	std::vector<int> fortranGlobalGroupMembership;
897	>	int nExclude, nOneTwo, nOneThree, nOneFour;
898	>	vector<int> fortranGlobalGroupMembership;
899
900	<	nExclude = exclude_.getSize();
900	>	notifyFortranSkinThickness(&skinThickness_);
901	>
902	>	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
903	>	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
904	>	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
905	>
906		isError = 0;
907
908		//globalGroupMembership_ is filled by SimCreator
#	Line 814 | Line 911 | namespace oopse {
911		}
912
913		//calculate mass ratio of cutoff group
914	<	std::vector<RealType> mfact;
914	>	vector<RealType> mfact;
915		SimInfo::MoleculeIterator mi;
916		Molecule* mol;
917		Molecule::CutoffGroupIterator ci;
#	Line 837 | Line 934 | namespace oopse {
934		else
935		mfact.push_back( 1.0 );
936		}
840	–
937		}
938		}
939
940		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
941	<	std::vector<int> identArray;
941	>	vector<int> identArray;
942
943		//to avoid memory reallocation, reserve enough space identArray
944		identArray.reserve(getNAtoms());
#	Line 855 | Line 951 | namespace oopse {
951
952		//fill molMembershipArray
953		//molMembershipArray is filled by SimCreator
954	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
954	>	vector<int> molMembershipArray(nGlobalAtoms_);
955		for (int i = 0; i < nGlobalAtoms_; i++) {
956		molMembershipArray[i] = globalMolMembership_[i] + 1;
957		}
958
959		//setup fortran simulation
864	–	int nGlobalExcludes = 0;
865	–	int* globalExcludes = NULL;
866	–	int* excludeList = exclude_.getExcludeList();
867	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
868	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
869	–	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
960
961	<	if( isError ){
961	>	nExclude = excludedInteractions_.getSize();
962	>	nOneTwo = oneTwoInteractions_.getSize();
963	>	nOneThree = oneThreeInteractions_.getSize();
964	>	nOneFour = oneFourInteractions_.getSize();
965
966	+	int* excludeList = excludedInteractions_.getPairList();
967	+	int* oneTwoList = oneTwoInteractions_.getPairList();
968	+	int* oneThreeList = oneThreeInteractions_.getPairList();
969	+	int* oneFourList = oneFourInteractions_.getPairList();
970	+
971	+	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
972	+	&nExclude, excludeList,
973	+	&nOneTwo, oneTwoList,
974	+	&nOneThree, oneThreeList,
975	+	&nOneFour, oneFourList,
976	+	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
977	+	&fortranGlobalGroupMembership[0], &isError);
978	+
979	+	if( isError ){
980	+
981		sprintf( painCave.errMsg,
982		"There was an error setting the simulation information in fortran.\n" );
983		painCave.isFatal = 1;
984	<	painCave.severity = OOPSE_ERROR;
984	>	painCave.severity = OPENMD_ERROR;
985		simError();
986		}
987	<
988	<	#ifdef IS_MPI
987	>
988	>
989		sprintf( checkPointMsg,
990		"succesfully sent the simulation information to fortran.\n");
991	<	MPIcheckPoint();
992	<	#endif // is_mpi
991	>
992	>	errorCheckPoint();
993	>
994	>	// Setup number of neighbors in neighbor list if present
995	>	if (simParams_->haveNeighborListNeighbors()) {
996	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
997	>	setNeighbors(&nlistNeighbors);
998	>	}
999	>
1000	>
1001		}
1002
1003
888	–	#ifdef IS_MPI
1004		void SimInfo::setupFortranParallel() {
1005	<
1005	>	#ifdef IS_MPI
1006		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1007	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1008	<	std::vector<int> localToGlobalCutoffGroupIndex;
1007	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1008	>	vector<int> localToGlobalCutoffGroupIndex;
1009		SimInfo::MoleculeIterator mi;
1010		Molecule::AtomIterator ai;
1011		Molecule::CutoffGroupIterator ci;
#	Line 937 | Line 1052 | namespace oopse {
1052		}
1053
1054		sprintf(checkPointMsg, " mpiRefresh successful.\n");
1055	<	MPIcheckPoint();
1055	>	errorCheckPoint();
1056
942	–
943	–	}
944	–
1057		#endif
946	–
947	–	void SimInfo::setupCutoff() {
948	–
949	–	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
950	–
951	–	// Check the cutoff policy
952	–	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
953	–
954	–	std::string myPolicy;
955	–	if (forceFieldOptions_.haveCutoffPolicy()){
956	–	myPolicy = forceFieldOptions_.getCutoffPolicy();
957	–	}else if (simParams_->haveCutoffPolicy()) {
958	–	myPolicy = simParams_->getCutoffPolicy();
959	–	}
960	–
961	–	if (!myPolicy.empty()){
962	–	toUpper(myPolicy);
963	–	if (myPolicy == "MIX") {
964	–	cp = MIX_CUTOFF_POLICY;
965	–	} else {
966	–	if (myPolicy == "MAX") {
967	–	cp = MAX_CUTOFF_POLICY;
968	–	} else {
969	–	if (myPolicy == "TRADITIONAL") {
970	–	cp = TRADITIONAL_CUTOFF_POLICY;
971	–	} else {
972	–	// throw error
973	–	sprintf( painCave.errMsg,
974	–	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
975	–	painCave.isFatal = 1;
976	–	simError();
977	–	}
978	–	}
979	–	}
980	–	}
981	–	notifyFortranCutoffPolicy(&cp);
982	–
983	–	// Check the Skin Thickness for neighborlists
984	–	RealType skin;
985	–	if (simParams_->haveSkinThickness()) {
986	–	skin = simParams_->getSkinThickness();
987	–	notifyFortranSkinThickness(&skin);
988	–	}
989	–
990	–	// Check if the cutoff was set explicitly:
991	–	if (simParams_->haveCutoffRadius()) {
992	–	rcut_ = simParams_->getCutoffRadius();
993	–	if (simParams_->haveSwitchingRadius()) {
994	–	rsw_  = simParams_->getSwitchingRadius();
995	–	} else {
996	–	if (fInfo_.SIM_uses_Charges |
997	–	fInfo_.SIM_uses_Dipoles |
998	–	fInfo_.SIM_uses_RF) {
999	–
1000	–	rsw_ = 0.85 * rcut_;
1001	–	sprintf(painCave.errMsg,
1002	–	"SimCreator Warning: No value was set for the switchingRadius.\n"
1003	–	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1004	–	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1005	–	painCave.isFatal = 0;
1006	–	simError();
1007	–	} else {
1008	–	rsw_ = rcut_;
1009	–	sprintf(painCave.errMsg,
1010	–	"SimCreator Warning: No value was set for the switchingRadius.\n"
1011	–	"\tOOPSE will use the same value as the cutoffRadius.\n"
1012	–	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1013	–	painCave.isFatal = 0;
1014	–	simError();
1015	–	}
1016	–	}
1017	–
1018	–	notifyFortranCutoffs(&rcut_, &rsw_);
1019	–
1020	–	} else {
1021	–
1022	–	// For electrostatic atoms, we'll assume a large safe value:
1023	–	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1024	–	sprintf(painCave.errMsg,
1025	–	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1026	–	"\tOOPSE will use a default value of 15.0 angstroms"
1027	–	"\tfor the cutoffRadius.\n");
1028	–	painCave.isFatal = 0;
1029	–	simError();
1030	–	rcut_ = 15.0;
1031	–
1032	–	if (simParams_->haveElectrostaticSummationMethod()) {
1033	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1034	–	toUpper(myMethod);
1035	–	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1036	–	if (simParams_->haveSwitchingRadius()){
1037	–	sprintf(painCave.errMsg,
1038	–	"SimInfo Warning: A value was set for the switchingRadius\n"
1039	–	"\teven though the electrostaticSummationMethod was\n"
1040	–	"\tset to %s\n", myMethod.c_str());
1041	–	painCave.isFatal = 1;
1042	–	simError();
1043	–	}
1044	–	}
1045	–	}
1046	–
1047	–	if (simParams_->haveSwitchingRadius()){
1048	–	rsw_ = simParams_->getSwitchingRadius();
1049	–	} else {
1050	–	sprintf(painCave.errMsg,
1051	–	"SimCreator Warning: No value was set for switchingRadius.\n"
1052	–	"\tOOPSE will use a default value of\n"
1053	–	"\t0.85 * cutoffRadius for the switchingRadius\n");
1054	–	painCave.isFatal = 0;
1055	–	simError();
1056	–	rsw_ = 0.85 * rcut_;
1057	–	}
1058	–	notifyFortranCutoffs(&rcut_, &rsw_);
1059	–	} else {
1060	–	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1061	–	// We'll punt and let fortran figure out the cutoffs later.
1062	–
1063	–	notifyFortranYouAreOnYourOwn();
1064	–
1065	–	}
1066	–	}
1058		}
1059
1069	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1070	–
1071	–	int errorOut;
1072	–	int esm =  NONE;
1073	–	int sm = UNDAMPED;
1074	–	RealType alphaVal;
1075	–	RealType dielectric;
1060
1077	–	errorOut = isError;
1078	–	alphaVal = simParams_->getDampingAlpha();
1079	–	dielectric = simParams_->getDielectric();
1080	–
1081	–	if (simParams_->haveElectrostaticSummationMethod()) {
1082	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1083	–	toUpper(myMethod);
1084	–	if (myMethod == "NONE") {
1085	–	esm = NONE;
1086	–	} else {
1087	–	if (myMethod == "SWITCHING_FUNCTION") {
1088	–	esm = SWITCHING_FUNCTION;
1089	–	} else {
1090	–	if (myMethod == "SHIFTED_POTENTIAL") {
1091	–	esm = SHIFTED_POTENTIAL;
1092	–	} else {
1093	–	if (myMethod == "SHIFTED_FORCE") {
1094	–	esm = SHIFTED_FORCE;
1095	–	} else {
1096	–	if (myMethod == "REACTION_FIELD") {
1097	–	esm = REACTION_FIELD;
1098	–	} else {
1099	–	// throw error
1100	–	sprintf( painCave.errMsg,
1101	–	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1102	–	"\t(Input file specified %s .)\n"
1103	–	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1104	–	"\t\"shifted_potential\", \"shifted_force\", or \n"
1105	–	"\t\"reaction_field\".\n", myMethod.c_str() );
1106	–	painCave.isFatal = 1;
1107	–	simError();
1108	–	}
1109	–	}
1110	–	}
1111	–	}
1112	–	}
1113	–	}
1114	–
1115	–	if (simParams_->haveElectrostaticScreeningMethod()) {
1116	–	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1117	–	toUpper(myScreen);
1118	–	if (myScreen == "UNDAMPED") {
1119	–	sm = UNDAMPED;
1120	–	} else {
1121	–	if (myScreen == "DAMPED") {
1122	–	sm = DAMPED;
1123	–	if (!simParams_->haveDampingAlpha()) {
1124	–	//throw error
1125	–	sprintf( painCave.errMsg,
1126	–	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1127	–	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1128	–	painCave.isFatal = 0;
1129	–	simError();
1130	–	}
1131	–	} else {
1132	–	// throw error
1133	–	sprintf( painCave.errMsg,
1134	–	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1135	–	"\t(Input file specified %s .)\n"
1136	–	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1137	–	"or \"damped\".\n", myScreen.c_str() );
1138	–	painCave.isFatal = 1;
1139	–	simError();
1140	–	}
1141	–	}
1142	–	}
1143	–
1144	–	// let's pass some summation method variables to fortran
1145	–	setElectrostaticSummationMethod( &esm );
1146	–	setFortranElectrostaticMethod( &esm );
1147	–	setScreeningMethod( &sm );
1148	–	setDampingAlpha( &alphaVal );
1149	–	setReactionFieldDielectric( &dielectric );
1150	–	initFortranFF( &errorOut );
1151	–	}
1152	–
1153	–	void SimInfo::setupSwitchingFunction() {
1154	–	int ft = CUBIC;
1155	–
1156	–	if (simParams_->haveSwitchingFunctionType()) {
1157	–	std::string funcType = simParams_->getSwitchingFunctionType();
1158	–	toUpper(funcType);
1159	–	if (funcType == "CUBIC") {
1160	–	ft = CUBIC;
1161	–	} else {
1162	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1163	–	ft = FIFTH_ORDER_POLY;
1164	–	} else {
1165	–	// throw error
1166	–	sprintf( painCave.errMsg,
1167	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1168	–	painCave.isFatal = 1;
1169	–	simError();
1170	–	}
1171	–	}
1172	–	}
1173	–
1174	–	// send switching function notification to switcheroo
1175	–	setFunctionType(&ft);
1176	–
1177	–	}
1178	–
1061		void SimInfo::setupAccumulateBoxDipole() {
1062
1181	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1182	–	if ( simParams_->haveAccumulateBoxDipole() )
1183	–	if ( simParams_->getAccumulateBoxDipole() ) {
1184	–	setAccumulateBoxDipole();
1185	–	calcBoxDipole_ = true;
1186	–	}
1063
1064		}
1065
#	Line 1191 | Line 1067 | namespace oopse {
1067		properties_.addProperty(genData);
1068		}
1069
1070	<	void SimInfo::removeProperty(const std::string& propName) {
1070	>	void SimInfo::removeProperty(const string& propName) {
1071		properties_.removeProperty(propName);
1072		}
1073
#	Line 1199 | Line 1075 | namespace oopse {
1075		properties_.clearProperties();
1076		}
1077
1078	<	std::vector<std::string> SimInfo::getPropertyNames() {
1078	>	vector<string> SimInfo::getPropertyNames() {
1079		return properties_.getPropertyNames();
1080		}
1081
1082	<	std::vector<GenericData*> SimInfo::getProperties() {
1082	>	vector<GenericData*> SimInfo::getProperties() {
1083		return properties_.getProperties();
1084		}
1085
1086	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1086	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1087		return properties_.getPropertyByName(propName);
1088		}
1089
#	Line 1290 | Line 1166 | namespace oopse {
1166
1167		}
1168
1169	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1169	>	ostream& operator <<(ostream& o, SimInfo& info) {
1170
1171		return o;
1172		}
#	Line 1333 | Line 1209 | namespace oopse {
1209
1210
1211		[  Ixx -Ixy  -Ixz ]
1212	<	J =| -Iyx  Iyy  -Iyz |
1212	>	J =| -Iyx  Iyy  -Iyz |
1213		[ -Izx -Iyz   Izz ]
1214		*/
1215
#	Line 1436 | Line 1312 | namespace oopse {
1312		return angularMomentum;
1313		}
1314
1315	<
1316	<	}//end namespace oopse
1315	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1316	>	return IOIndexToIntegrableObject.at(index);
1317	>	}
1318	>
1319	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1320	>	IOIndexToIntegrableObject= v;
1321	>	}
1322
1323	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1324	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1325	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1326	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1327	+	*/
1328	+	void SimInfo::getGyrationalVolume(RealType &volume){
1329	+	Mat3x3d intTensor;
1330	+	RealType det;
1331	+	Vector3d dummyAngMom;
1332	+	RealType sysconstants;
1333	+	RealType geomCnst;
1334	+
1335	+	geomCnst = 3.0/2.0;
1336	+	/* Get the inertial tensor and angular momentum for free*/
1337	+	getInertiaTensor(intTensor,dummyAngMom);
1338	+
1339	+	det = intTensor.determinant();
1340	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1341	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1342	+	return;
1343	+	}
1344	+
1345	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1346	+	Mat3x3d intTensor;
1347	+	Vector3d dummyAngMom;
1348	+	RealType sysconstants;
1349	+	RealType geomCnst;
1350	+
1351	+	geomCnst = 3.0/2.0;
1352	+	/* Get the inertial tensor and angular momentum for free*/
1353	+	getInertiaTensor(intTensor,dummyAngMom);
1354	+
1355	+	detI = intTensor.determinant();
1356	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1357	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1358	+	return;
1359	+	}
1360	+	/*
1361	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1362	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1363	+	sdByGlobalIndex_ = v;
1364	+	}
1365	+
1366	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1367	+	//assert(index < nAtoms_ + nRigidBodies_);
1368	+	return sdByGlobalIndex_.at(index);
1369	+	}
1370	+	*/
1371	+	int SimInfo::getNGlobalConstraints() {
1372	+	int nGlobalConstraints;
1373	+	#ifdef IS_MPI
1374	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1375	+	MPI_COMM_WORLD);
1376	+	#else
1377	+	nGlobalConstraints =  nConstraints_;
1378	+	#endif
1379	+	return nGlobalConstraints;
1380	+	}
1381	+
1382	+	}//end namespace OpenMD
1383	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1534 by gezelter, Wed Dec 29 21:53:28 2010 UTC

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