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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 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 54 | Line 54
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56		#include "primitives/StuntDouble.hpp"
57	–	#include "UseTheForce/fCutoffPolicy.h"
58	–	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	–	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60	–	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
57		#include "UseTheForce/doForces_interface.h"
58		#include "UseTheForce/DarkSide/neighborLists_interface.h"
63	–	#include "UseTheForce/DarkSide/electrostatic_interface.h"
64	–	#include "UseTheForce/DarkSide/switcheroo_interface.h"
59		#include "utils/MemoryUtils.hpp"
60		#include "utils/simError.h"
61		#include "selection/SelectionManager.hpp"
62		#include "io/ForceFieldOptions.hpp"
63		#include "UseTheForce/ForceField.hpp"
64	+	#include "nonbonded/SwitchingFunction.hpp"
65
71	–
66		#ifdef IS_MPI
67		#include "UseTheForce/mpiComponentPlan.h"
68		#include "UseTheForce/DarkSide/simParallel_interface.h"
69		#endif
70
71	<	namespace oopse {
72	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79	<	std::map<int, std::set<int> >::iterator i = container.find(index);
80	<	std::set<int> result;
81	<	if (i != container.end()) {
82	<	result = i->second;
83	<	}
84	<
85	<	return result;
86	<	}
71	>	using namespace std;
72	>	namespace OpenMD {
73
74		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
75		forceField_(ff), simParams_(simParams),
#	Line 93 | Line 79 | namespace oopse {
79		nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
80		nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
81		nConstraints_(0), sman_(NULL), fortranInitialized_(false),
82	<	calcBoxDipole_(false), useAtomicVirial_(true) {
83	<
84	<
85	<	MoleculeStamp* molStamp;
86	<	int nMolWithSameStamp;
87	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
88	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
89	<	CutoffGroupStamp* cgStamp;
90	<	RigidBodyStamp* rbStamp;
91	<	int nRigidAtoms = 0;
92	<
93	<	std::vector<Component*> components = simParams->getComponents();
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();
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	<
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();
161	<	molToProcMap_.resize(nGlobalMols_);
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 173 | Line 158 | namespace oopse {
158		delete forceField_;
159		}
160
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	–	}
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();
#	Line 201 | Line 176 | namespace oopse {
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 228 | Line 203 | namespace oopse {
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 237 | Line 212 | namespace oopse {
212		} else {
213		return false;
214		}
240	–
241	–
215		}
216
217
#	Line 256 | 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 307 | 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 354 | 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;
334	<	std::vector<Inversion*>::iterator inversionIter;
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;
#	Line 368 | Line 342 | namespace oopse {
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
398	–
399	–
400	–	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();
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);
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();
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);
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);
453	<	exclude_.addPair(b, d);
454	<	exclude_.addPair(c, d);
455	<	*/
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 (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	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
456	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
457	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
458	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
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	<	exclude_.addPairs(rigidSetA, rigidSetB);
467	<	exclude_.addPairs(rigidSetA, rigidSetC);
468	<	exclude_.addPairs(rigidSetA, rigidSetD);
469	<	exclude_.addPairs(rigidSetB, rigidSetC);
470	<	exclude_.addPairs(rigidSetB, rigidSetD);
471	<	exclude_.addPairs(rigidSetC, rigidSetD);
472	<
473	<	/*
474	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
478	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
479	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
480	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
481	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
482	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
483	<
484	<
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	<	*/
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; rb = mol->nextRigidBody(rbIter)) {
478	<	std::vector<Atom*> atoms = rb->getAtoms();
479	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
480	<	for (int j = i + 1; j < atoms.size(); ++j) {
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;
495	<	std::vector<Inversion*>::iterator inversionIter;
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;
#	Line 518 | Line 503 | namespace oopse {
503		int c;
504		int d;
505
506	<	std::map<int, std::set<int> > atomGroups;
522	<
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();
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);
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);
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	<	*/
594	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
595	>	oneFourInteractions_.removePair(a, d);
596	>	} else {
597	>	excludedInteractions_.removePair(a, d);
598	>	}
599		}
600
601	<	for (inversion= mol->beginInversion(inversionIter); inversion != NULL; inversion = mol->nextInversion(inversionIter)) {
601	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
602	>	inversion = mol->nextInversion(inversionIter)) {
603	>
604		a = inversion->getAtomA()->getGlobalIndex();
605		b = inversion->getAtomB()->getGlobalIndex();
606		c = inversion->getAtomC()->getGlobalIndex();
607		d = inversion->getAtomD()->getGlobalIndex();
608
609	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
610	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
611	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
612	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
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	<	exclude_.removePairs(rigidSetA, rigidSetB);
620	<	exclude_.removePairs(rigidSetA, rigidSetC);
621	<	exclude_.removePairs(rigidSetA, rigidSetD);
622	<	exclude_.removePairs(rigidSetB, rigidSetC);
623	<	exclude_.removePairs(rigidSetB, rigidSetD);
624	<	exclude_.removePairs(rigidSetC, rigidSetD);
625	<
626	<	/*
627	<	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	<	*/
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 666 | 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
671	–	setupSimType();
672	–
671		#ifdef IS_MPI
672		setupFortranParallel();
673		#endif
676	–
674		setupFortranSim();
675	+	fortranInitialized_ = true;
676
679	–	//setup fortran force field
680	–	/** @deprecate */
681	–	int isError = 0;
682	–
683	–	setupCutoff();
684	–
685	–	setupElectrostaticSummationMethod( isError );
686	–	setupSwitchingFunction();
687	–	setupAccumulateBoxDipole();
688	–
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	–
677		calcNdf();
678		calcNdfRaw();
679		calcNdfTrans();
699	–
700	–	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)) {
711	<
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	<
692	>	}
693	>	}
694	>	return atomTypes;
695	>	}
696	>
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	<	return atomTypes;
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	<	void SimInfo::setupSimType() {
781	<	std::set<AtomType*>::iterator i;
782	<	std::set<AtomType*> atomTypes;
783	<	atomTypes = getUniqueAtomTypes();
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	<	int useLennardJones = 0;
790	<	int useElectrostatic = 0;
791	<	int useEAM = 0;
792	<	int useSC = 0;
793	<	int useCharge = 0;
794	<	int useDirectional = 0;
795	<	int useDipole = 0;
796	<	int useGayBerne = 0;
797	<	int useSticky = 0;
735	<	int useStickyPower = 0;
736	<	int useShape = 0;
737	<	int useFLARB = 0; //it is not in AtomType yet
738	<	int useDirectionalAtom = 0;
739	<	int useElectrostatics = 0;
740	<	//usePBC and useRF are from simParams
741	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
742	<	int useRF;
743	<	int useSF;
744	<	int useSP;
745	<	int useBoxDipole;
746	<
747	<	std::string myMethod;
748	<
749	<	// set the useRF logical
750	<	useRF = 0;
751	<	useSF = 0;
752	<	useSP = 0;
753	<
754	<
755	<	if (simParams_->haveElectrostaticSummationMethod()) {
756	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
757	<	toUpper(myMethod);
758	<	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;
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	<	}
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_->haveAccumulateBoxDipole())
811	<	if (simParams_->getAccumulateBoxDipole())
812	<	useBoxDipole = 1;
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();
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();
871	>	usesElectrostatic |= (*i)->isElectrostatic();
872	>	usesMetallic |= (*i)->isMetal();
873	>	usesDirectional |= (*i)->isDirectional();
874		}
875
788	–	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
789	–	useDirectionalAtom = 1;
790	–	}
791	–
792	–	if (useCharge || useDipole) {
793	–	useElectrostatics = 1;
794	–	}
795	–
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);
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	<
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;
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_;
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 886 | 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 909 | Line 934 | namespace oopse {
934		else
935		mfact.push_back( 1.0 );
936		}
912	–
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 927 | 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
960	<	int nGlobalExcludes = 0;
961	<	int* globalExcludes = NULL;
962	<	int* excludeList = exclude_.getExcludeList();
960	>
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 , &nGlobalExcludes, globalExcludes,
972	>	&nExclude, excludeList,
973	>	&nOneTwo, oneTwoList,
974	>	&nOneThree, oneThreeList,
975	>	&nOneFour, oneFourList,
976		&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
977		&fortranGlobalGroupMembership[0], &isError);
978
#	Line 946 | Line 981 | namespace oopse {
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
#	Line 969 | Line 1004 | namespace oopse {
1004		void SimInfo::setupFortranParallel() {
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 1022 | Line 1057 | namespace oopse {
1057		#endif
1058		}
1059
1025	–	void SimInfo::setupCutoff() {
1026	–
1027	–	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1060
1029	–	// Check the cutoff policy
1030	–	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;
1178	–
1179	–	errorOut = isError;
1180	–
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();
1276	–	toUpper(funcType);
1277	–	if (funcType == "CUBIC") {
1278	–	ft = CUBIC;
1279	–	} else {
1280	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1281	–	ft = FIFTH_ORDER_POLY;
1282	–	} else {
1283	–	// throw error
1284	–	sprintf( painCave.errMsg,
1285	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1286	–	painCave.isFatal = 1;
1287	–	simError();
1288	–	}
1289	–	}
1290	–	}
1291	–
1292	–	// send switching function notification to switcheroo
1293	–	setFunctionType(&ft);
1294	–
1295	–	}
1296	–
1061		void SimInfo::setupAccumulateBoxDipole() {
1062
1299	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1300	–	if ( simParams_->haveAccumulateBoxDipole() )
1301	–	if ( simParams_->getAccumulateBoxDipole() ) {
1302	–	setAccumulateBoxDipole();
1303	–	calcBoxDipole_ = true;
1304	–	}
1063
1064		}
1065
#	Line 1309 | 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 1317 | 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 1408 | 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 1451 | 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 1558 | Line 1316 | namespace oopse {
1316		return IOIndexToIntegrableObject.at(index);
1317		}
1318
1319	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1319	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1320		IOIndexToIntegrableObject= v;
1321		}
1322
#	Line 1600 | Line 1358 | namespace oopse {
1358		return;
1359		}
1360		/*
1361	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1361	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1362		assert( v.size() == nAtoms_ + nRigidBodies_);
1363		sdByGlobalIndex_ = v;
1364		}
#	Line 1610 | Line 1368 | namespace oopse {
1368		return sdByGlobalIndex_.at(index);
1369		}
1370		*/
1371	<	}//end namespace oopse
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 1277 by gezelter, Mon Jul 14 12:35:58 2008 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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