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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 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 54 | Line 54
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56		#include "primitives/StuntDouble.hpp"
57	–	#include "UseTheForce/fCutoffPolicy.h"
58	–	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	–	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60	–	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
57		#include "UseTheForce/doForces_interface.h"
58		#include "UseTheForce/DarkSide/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
66
67		#ifdef IS_MPI
#	Line 74 | Line 69
69		#include "UseTheForce/DarkSide/simParallel_interface.h"
70		#endif
71
72	<	namespace oopse {
73	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
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	<	}
72	>	using namespace std;
73	>	namespace OpenMD {
74
75		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
76		forceField_(ff), simParams_(simParams),
#	Line 93 | Line 80 | namespace oopse {
80		nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
81		nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
82		nConstraints_(0), sman_(NULL), fortranInitialized_(false),
83	<	calcBoxDipole_(false), useAtomicVirial_(true) {
84	<
85	<
86	<	MoleculeStamp* molStamp;
87	<	int nMolWithSameStamp;
88	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
89	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
90	<	CutoffGroupStamp* cgStamp;
91	<	RigidBodyStamp* rbStamp;
92	<	int nRigidAtoms = 0;
93	<
94	<	std::vector<Component*> components = simParams->getComponents();
83	>	calcBoxDipole_(false), useAtomicVirial_(true) {
84	>
85	>	MoleculeStamp* molStamp;
86	>	int nMolWithSameStamp;
87	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
88	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
89	>	CutoffGroupStamp* cgStamp;
90	>	RigidBodyStamp* rbStamp;
91	>	int nRigidAtoms = 0;
92	>
93	>	vector<Component*> components = simParams->getComponents();
94	>
95	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
96	>	molStamp = (*i)->getMoleculeStamp();
97	>	nMolWithSameStamp = (*i)->getNMol();
98
99	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
100	<	molStamp = (*i)->getMoleculeStamp();
101	<	nMolWithSameStamp = (*i)->getNMol();
102	<
103	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
104	<
105	<	//calculate atoms in molecules
106	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
107	<
108	<	//calculate atoms in cutoff groups
109	<	int nAtomsInGroups = 0;
110	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
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	<
99	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
100	>
101	>	//calculate atoms in molecules
102	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
103	>
104	>	//calculate atoms in cutoff groups
105	>	int nAtomsInGroups = 0;
106	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
107	>
108	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
109	>	cgStamp = molStamp->getCutoffGroupStamp(j);
110	>	nAtomsInGroups += cgStamp->getNMembers();
111		}
112	<
113	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
114	<	//group therefore the total number of cutoff groups in the system is
115	<	//equal to the total number of atoms minus number of atoms belong to
116	<	//cutoff group defined in meta-data file plus the number of cutoff
117	<	//groups defined in meta-data file
118	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
119	<
120	<	//every free atom (atom does not belong to rigid bodies) is an
121	<	//integrable object therefore the total number of integrable objects
122	<	//in the system is equal to the total number of atoms minus number of
123	<	//atoms belong to rigid body defined in meta-data file plus the number
124	<	//of rigid bodies defined in meta-data file
125	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
126	<	+ nGlobalRigidBodies_;
127	<
128	<	nGlobalMols_ = molStampIds_.size();
161	<	molToProcMap_.resize(nGlobalMols_);
112	>
113	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
114	>
115	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
116	>
117	>	//calculate atoms in rigid bodies
118	>	int nAtomsInRigidBodies = 0;
119	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
120	>
121	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
122	>	rbStamp = molStamp->getRigidBodyStamp(j);
123	>	nAtomsInRigidBodies += rbStamp->getNMembers();
124	>	}
125	>
126	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
127	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
128	>
129		}
130	<
130	>
131	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
132	>	//group therefore the total number of cutoff groups in the system is
133	>	//equal to the total number of atoms minus number of atoms belong to
134	>	//cutoff group defined in meta-data file plus the number of cutoff
135	>	//groups defined in meta-data file
136	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
137	>
138	>	//every free atom (atom does not belong to rigid bodies) is an
139	>	//integrable object therefore the total number of integrable objects
140	>	//in the system is equal to the total number of atoms minus number of
141	>	//atoms belong to rigid body defined in meta-data file plus the number
142	>	//of rigid bodies defined in meta-data file
143	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
144	>	+ nGlobalRigidBodies_;
145	>
146	>	nGlobalMols_ = molStampIds_.size();
147	>	molToProcMap_.resize(nGlobalMols_);
148	>	}
149	>
150		SimInfo::~SimInfo() {
151	<	std::map<int, Molecule*>::iterator i;
151	>	map<int, Molecule*>::iterator i;
152		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
153		delete i->second;
154		}
#	Line 173 | Line 159 | namespace oopse {
159		delete forceField_;
160		}
161
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	–	}
162
163		bool SimInfo::addMolecule(Molecule* mol) {
164		MoleculeIterator i;
165	<
165	>
166		i = molecules_.find(mol->getGlobalIndex());
167		if (i == molecules_.end() ) {
168	<
169	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
170	<
168	>
169	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
170	>
171		nAtoms_ += mol->getNAtoms();
172		nBonds_ += mol->getNBonds();
173		nBends_ += mol->getNBends();
#	Line 201 | Line 177 | namespace oopse {
177		nIntegrableObjects_ += mol->getNIntegrableObjects();
178		nCutoffGroups_ += mol->getNCutoffGroups();
179		nConstraints_ += mol->getNConstraintPairs();
180	<
181	<	addExcludePairs(mol);
182	<
180	>
181	>	addInteractionPairs(mol);
182	>
183		return true;
184		} else {
185		return false;
186		}
187		}
188	<
188	>
189		bool SimInfo::removeMolecule(Molecule* mol) {
190		MoleculeIterator i;
191		i = molecules_.find(mol->getGlobalIndex());
#	Line 228 | Line 204 | namespace oopse {
204		nCutoffGroups_ -= mol->getNCutoffGroups();
205		nConstraints_ -= mol->getNConstraintPairs();
206
207	<	removeExcludePairs(mol);
207	>	removeInteractionPairs(mol);
208		molecules_.erase(mol->getGlobalIndex());
209
210		delete mol;
#	Line 237 | Line 213 | namespace oopse {
213		} else {
214		return false;
215		}
240	–
241	–
216		}
217
218
#	Line 256 | Line 230 | namespace oopse {
230		void SimInfo::calcNdf() {
231		int ndf_local;
232		MoleculeIterator i;
233	<	std::vector<StuntDouble*>::iterator j;
233	>	vector<StuntDouble*>::iterator j;
234		Molecule* mol;
235		StuntDouble* integrableObject;
236
#	Line 307 | Line 281 | namespace oopse {
281		int ndfRaw_local;
282
283		MoleculeIterator i;
284	<	std::vector<StuntDouble*>::iterator j;
284	>	vector<StuntDouble*>::iterator j;
285		Molecule* mol;
286		StuntDouble* integrableObject;
287
#	Line 354 | Line 328 | namespace oopse {
328
329		}
330
331	<	void SimInfo::addExcludePairs(Molecule* mol) {
332	<	std::vector<Bond*>::iterator bondIter;
333	<	std::vector<Bend*>::iterator bendIter;
334	<	std::vector<Torsion*>::iterator torsionIter;
335	<	std::vector<Inversion*>::iterator inversionIter;
331	>	void SimInfo::addInteractionPairs(Molecule* mol) {
332	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
333	>	vector<Bond*>::iterator bondIter;
334	>	vector<Bend*>::iterator bendIter;
335	>	vector<Torsion*>::iterator torsionIter;
336	>	vector<Inversion*>::iterator inversionIter;
337		Bond* bond;
338		Bend* bend;
339		Torsion* torsion;
#	Line 368 | Line 343 | namespace oopse {
343		int c;
344		int d;
345
346	<	std::map<int, std::set<int> > atomGroups;
346	>	// atomGroups can be used to add special interaction maps between
347	>	// groups of atoms that are in two separate rigid bodies.
348	>	// However, most site-site interactions between two rigid bodies
349	>	// are probably not special, just the ones between the physically
350	>	// bonded atoms.  Interactions *within* a single rigid body should
351	>	// always be excluded.  These are done at the bottom of this
352	>	// function.
353
354	+	map<int, set<int> > atomGroups;
355		Molecule::RigidBodyIterator rbIter;
356		RigidBody* rb;
357		Molecule::IntegrableObjectIterator ii;
358		StuntDouble* integrableObject;
359
360	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
361	<	integrableObject = mol->nextIntegrableObject(ii)) {
362	<
360	>	for (integrableObject = mol->beginIntegrableObject(ii);
361	>	integrableObject != NULL;
362	>	integrableObject = mol->nextIntegrableObject(ii)) {
363	>
364		if (integrableObject->isRigidBody()) {
365	<	rb = static_cast<RigidBody*>(integrableObject);
366	<	std::vector<Atom*> atoms = rb->getAtoms();
367	<	std::set<int> rigidAtoms;
368	<	for (int i = 0; i < atoms.size(); ++i) {
369	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
370	<	}
371	<	for (int i = 0; i < atoms.size(); ++i) {
372	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
373	<	}
365	>	rb = static_cast<RigidBody*>(integrableObject);
366	>	vector<Atom*> atoms = rb->getAtoms();
367	>	set<int> rigidAtoms;
368	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
369	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
370	>	}
371	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
372	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
373	>	}
374		} else {
375	<	std::set<int> oneAtomSet;
375	>	set<int> oneAtomSet;
376		oneAtomSet.insert(integrableObject->getGlobalIndex());
377	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
377	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
378		}
379		}
380	+
381	+	for (bond= mol->beginBond(bondIter); bond != NULL;
382	+	bond = mol->nextBond(bondIter)) {
383
398	–
399	–
400	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
384		a = bond->getAtomA()->getGlobalIndex();
385	<	b = bond->getAtomB()->getGlobalIndex();
386	<	exclude_.addPair(a, b);
385	>	b = bond->getAtomB()->getGlobalIndex();
386	>
387	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
388	>	oneTwoInteractions_.addPair(a, b);
389	>	} else {
390	>	excludedInteractions_.addPair(a, b);
391	>	}
392		}
393
394	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
394	>	for (bend= mol->beginBend(bendIter); bend != NULL;
395	>	bend = mol->nextBend(bendIter)) {
396	>
397		a = bend->getAtomA()->getGlobalIndex();
398		b = bend->getAtomB()->getGlobalIndex();
399		c = bend->getAtomC()->getGlobalIndex();
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);
400
401	<	//exclude_.addPair(a, b);
402	<	//exclude_.addPair(a, c);
403	<	//exclude_.addPair(b, c);
401	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
402	>	oneTwoInteractions_.addPair(a, b);
403	>	oneTwoInteractions_.addPair(b, c);
404	>	} else {
405	>	excludedInteractions_.addPair(a, b);
406	>	excludedInteractions_.addPair(b, c);
407	>	}
408	>
409	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
410	>	oneThreeInteractions_.addPair(a, c);
411	>	} else {
412	>	excludedInteractions_.addPair(a, c);
413	>	}
414		}
415
416	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
416	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
417	>	torsion = mol->nextTorsion(torsionIter)) {
418	>
419		a = torsion->getAtomA()->getGlobalIndex();
420		b = torsion->getAtomB()->getGlobalIndex();
421		c = torsion->getAtomC()->getGlobalIndex();
422	<	d = torsion->getAtomD()->getGlobalIndex();
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);
422	>	d = torsion->getAtomD()->getGlobalIndex();
423
424	<	exclude_.addPairs(rigidSetA, rigidSetB);
425	<	exclude_.addPairs(rigidSetA, rigidSetC);
426	<	exclude_.addPairs(rigidSetA, rigidSetD);
427	<	exclude_.addPairs(rigidSetB, rigidSetC);
428	<	exclude_.addPairs(rigidSetB, rigidSetD);
429	<	exclude_.addPairs(rigidSetC, rigidSetD);
424	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
425	>	oneTwoInteractions_.addPair(a, b);
426	>	oneTwoInteractions_.addPair(b, c);
427	>	oneTwoInteractions_.addPair(c, d);
428	>	} else {
429	>	excludedInteractions_.addPair(a, b);
430	>	excludedInteractions_.addPair(b, c);
431	>	excludedInteractions_.addPair(c, d);
432	>	}
433
434	<	/*
435	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
436	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
437	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
438	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
439	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
440	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
441	<
442	<
443	<	exclude_.addPair(a, b);
444	<	exclude_.addPair(a, c);
445	<	exclude_.addPair(a, d);
446	<	exclude_.addPair(b, c);
453	<	exclude_.addPair(b, d);
454	<	exclude_.addPair(c, d);
455	<	*/
434	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
435	>	oneThreeInteractions_.addPair(a, c);
436	>	oneThreeInteractions_.addPair(b, d);
437	>	} else {
438	>	excludedInteractions_.addPair(a, c);
439	>	excludedInteractions_.addPair(b, d);
440	>	}
441	>
442	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
443	>	oneFourInteractions_.addPair(a, d);
444	>	} else {
445	>	excludedInteractions_.addPair(a, d);
446	>	}
447		}
448
449		for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
450		inversion = mol->nextInversion(inversionIter)) {
451	+
452		a = inversion->getAtomA()->getGlobalIndex();
453		b = inversion->getAtomB()->getGlobalIndex();
454		c = inversion->getAtomC()->getGlobalIndex();
455		d = inversion->getAtomD()->getGlobalIndex();
464	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
465	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
466	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
467	–	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
456
457	<	exclude_.addPairs(rigidSetA, rigidSetB);
458	<	exclude_.addPairs(rigidSetA, rigidSetC);
459	<	exclude_.addPairs(rigidSetA, rigidSetD);
460	<	exclude_.addPairs(rigidSetB, rigidSetC);
461	<	exclude_.addPairs(rigidSetB, rigidSetD);
462	<	exclude_.addPairs(rigidSetC, rigidSetD);
457	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
458	>	oneTwoInteractions_.addPair(a, b);
459	>	oneTwoInteractions_.addPair(a, c);
460	>	oneTwoInteractions_.addPair(a, d);
461	>	} else {
462	>	excludedInteractions_.addPair(a, b);
463	>	excludedInteractions_.addPair(a, c);
464	>	excludedInteractions_.addPair(a, d);
465	>	}
466
467	<	/*
468	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
469	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
470	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
471	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
472	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
473	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
474	<
475	<
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	<	*/
467	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
468	>	oneThreeInteractions_.addPair(b, c);
469	>	oneThreeInteractions_.addPair(b, d);
470	>	oneThreeInteractions_.addPair(c, d);
471	>	} else {
472	>	excludedInteractions_.addPair(b, c);
473	>	excludedInteractions_.addPair(b, d);
474	>	excludedInteractions_.addPair(c, d);
475	>	}
476		}
477
478	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
479	<	std::vector<Atom*> atoms = rb->getAtoms();
480	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
481	<	for (int j = i + 1; j < atoms.size(); ++j) {
478	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
479	>	rb = mol->nextRigidBody(rbIter)) {
480	>	vector<Atom*> atoms = rb->getAtoms();
481	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
482	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
483		a = atoms[i]->getGlobalIndex();
484		b = atoms[j]->getGlobalIndex();
485	<	exclude_.addPair(a, b);
485	>	excludedInteractions_.addPair(a, b);
486		}
487		}
488		}
489
490		}
491
492	<	void SimInfo::removeExcludePairs(Molecule* mol) {
493	<	std::vector<Bond*>::iterator bondIter;
494	<	std::vector<Bend*>::iterator bendIter;
495	<	std::vector<Torsion*>::iterator torsionIter;
496	<	std::vector<Inversion*>::iterator inversionIter;
492	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
493	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
494	>	vector<Bond*>::iterator bondIter;
495	>	vector<Bend*>::iterator bendIter;
496	>	vector<Torsion*>::iterator torsionIter;
497	>	vector<Inversion*>::iterator inversionIter;
498		Bond* bond;
499		Bend* bend;
500		Torsion* torsion;
#	Line 518 | Line 504 | namespace oopse {
504		int c;
505		int d;
506
507	<	std::map<int, std::set<int> > atomGroups;
522	<
507	>	map<int, set<int> > atomGroups;
508		Molecule::RigidBodyIterator rbIter;
509		RigidBody* rb;
510		Molecule::IntegrableObjectIterator ii;
511		StuntDouble* integrableObject;
512
513	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
514	<	integrableObject = mol->nextIntegrableObject(ii)) {
515	<
513	>	for (integrableObject = mol->beginIntegrableObject(ii);
514	>	integrableObject != NULL;
515	>	integrableObject = mol->nextIntegrableObject(ii)) {
516	>
517		if (integrableObject->isRigidBody()) {
518	<	rb = static_cast<RigidBody*>(integrableObject);
519	<	std::vector<Atom*> atoms = rb->getAtoms();
520	<	std::set<int> rigidAtoms;
521	<	for (int i = 0; i < atoms.size(); ++i) {
522	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
523	<	}
524	<	for (int i = 0; i < atoms.size(); ++i) {
525	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
526	<	}
518	>	rb = static_cast<RigidBody*>(integrableObject);
519	>	vector<Atom*> atoms = rb->getAtoms();
520	>	set<int> rigidAtoms;
521	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
522	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
523	>	}
524	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
525	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
526	>	}
527		} else {
528	<	std::set<int> oneAtomSet;
528	>	set<int> oneAtomSet;
529		oneAtomSet.insert(integrableObject->getGlobalIndex());
530	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
530	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
531		}
532		}
533
534	<
535	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
534	>	for (bond= mol->beginBond(bondIter); bond != NULL;
535	>	bond = mol->nextBond(bondIter)) {
536	>
537		a = bond->getAtomA()->getGlobalIndex();
538	<	b = bond->getAtomB()->getGlobalIndex();
539	<	exclude_.removePair(a, b);
538	>	b = bond->getAtomB()->getGlobalIndex();
539	>
540	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
541	>	oneTwoInteractions_.removePair(a, b);
542	>	} else {
543	>	excludedInteractions_.removePair(a, b);
544	>	}
545		}
546
547	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
547	>	for (bend= mol->beginBend(bendIter); bend != NULL;
548	>	bend = mol->nextBend(bendIter)) {
549	>
550		a = bend->getAtomA()->getGlobalIndex();
551		b = bend->getAtomB()->getGlobalIndex();
552		c = bend->getAtomC()->getGlobalIndex();
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);
553
554	<	//exclude_.removePair(a, b);
555	<	//exclude_.removePair(a, c);
556	<	//exclude_.removePair(b, c);
554	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
555	>	oneTwoInteractions_.removePair(a, b);
556	>	oneTwoInteractions_.removePair(b, c);
557	>	} else {
558	>	excludedInteractions_.removePair(a, b);
559	>	excludedInteractions_.removePair(b, c);
560	>	}
561	>
562	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
563	>	oneThreeInteractions_.removePair(a, c);
564	>	} else {
565	>	excludedInteractions_.removePair(a, c);
566	>	}
567		}
568
569	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
569	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
570	>	torsion = mol->nextTorsion(torsionIter)) {
571	>
572		a = torsion->getAtomA()->getGlobalIndex();
573		b = torsion->getAtomB()->getGlobalIndex();
574		c = torsion->getAtomC()->getGlobalIndex();
575	<	d = torsion->getAtomD()->getGlobalIndex();
575	>	d = torsion->getAtomD()->getGlobalIndex();
576	>
577	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
578	>	oneTwoInteractions_.removePair(a, b);
579	>	oneTwoInteractions_.removePair(b, c);
580	>	oneTwoInteractions_.removePair(c, d);
581	>	} else {
582	>	excludedInteractions_.removePair(a, b);
583	>	excludedInteractions_.removePair(b, c);
584	>	excludedInteractions_.removePair(c, d);
585	>	}
586
587	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
588	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
589	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
590	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
587	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
588	>	oneThreeInteractions_.removePair(a, c);
589	>	oneThreeInteractions_.removePair(b, d);
590	>	} else {
591	>	excludedInteractions_.removePair(a, c);
592	>	excludedInteractions_.removePair(b, d);
593	>	}
594
595	<	exclude_.removePairs(rigidSetA, rigidSetB);
596	<	exclude_.removePairs(rigidSetA, rigidSetC);
597	<	exclude_.removePairs(rigidSetA, rigidSetD);
598	<	exclude_.removePairs(rigidSetB, rigidSetC);
599	<	exclude_.removePairs(rigidSetB, rigidSetD);
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	<	*/
595	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
596	>	oneFourInteractions_.removePair(a, d);
597	>	} else {
598	>	excludedInteractions_.removePair(a, d);
599	>	}
600		}
601
602	<	for (inversion= mol->beginInversion(inversionIter); inversion != NULL; inversion = mol->nextInversion(inversionIter)) {
602	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
603	>	inversion = mol->nextInversion(inversionIter)) {
604	>
605		a = inversion->getAtomA()->getGlobalIndex();
606		b = inversion->getAtomB()->getGlobalIndex();
607		c = inversion->getAtomC()->getGlobalIndex();
608		d = inversion->getAtomD()->getGlobalIndex();
609
610	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
611	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
612	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
613	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
610	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
611	>	oneTwoInteractions_.removePair(a, b);
612	>	oneTwoInteractions_.removePair(a, c);
613	>	oneTwoInteractions_.removePair(a, d);
614	>	} else {
615	>	excludedInteractions_.removePair(a, b);
616	>	excludedInteractions_.removePair(a, c);
617	>	excludedInteractions_.removePair(a, d);
618	>	}
619
620	<	exclude_.removePairs(rigidSetA, rigidSetB);
621	<	exclude_.removePairs(rigidSetA, rigidSetC);
622	<	exclude_.removePairs(rigidSetA, rigidSetD);
623	<	exclude_.removePairs(rigidSetB, rigidSetC);
624	<	exclude_.removePairs(rigidSetB, rigidSetD);
625	<	exclude_.removePairs(rigidSetC, rigidSetD);
626	<
627	<	/*
628	<	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	<	*/
620	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
621	>	oneThreeInteractions_.removePair(b, c);
622	>	oneThreeInteractions_.removePair(b, d);
623	>	oneThreeInteractions_.removePair(c, d);
624	>	} else {
625	>	excludedInteractions_.removePair(b, c);
626	>	excludedInteractions_.removePair(b, d);
627	>	excludedInteractions_.removePair(c, d);
628	>	}
629		}
630
631	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
632	<	std::vector<Atom*> atoms = rb->getAtoms();
633	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
634	<	for (int j = i + 1; j < atoms.size(); ++j) {
631	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
632	>	rb = mol->nextRigidBody(rbIter)) {
633	>	vector<Atom*> atoms = rb->getAtoms();
634	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
635	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
636		a = atoms[i]->getGlobalIndex();
637		b = atoms[j]->getGlobalIndex();
638	<	exclude_.removePair(a, b);
638	>	excludedInteractions_.removePair(a, b);
639		}
640		}
641		}
642	<
642	>
643		}
644	<
645	<
644	>
645	>
646		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
647		int curStampId;
648	<
648	>
649		//index from 0
650		curStampId = moleculeStamps_.size();
651
#	Line 666 | Line 653 | namespace oopse {
653		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
654		}
655
656	+
657	+	/**
658	+	* update
659	+	*
660	+	*  Performs the global checks and variable settings after the objects have been
661	+	*  created.
662	+	*
663	+	*/
664		void SimInfo::update() {
665	+
666	+	setupSimVariables();
667	+	setupCutoffs();
668	+	setupSwitching();
669	+	setupElectrostatics();
670	+	setupNeighborlists();
671
671	–	setupSimType();
672	–
672		#ifdef IS_MPI
673		setupFortranParallel();
674		#endif
676	–
675		setupFortranSim();
676	+	fortranInitialized_ = true;
677
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	–
678		calcNdf();
679		calcNdfRaw();
680		calcNdfTrans();
699	–
700	–	fortranInitialized_ = true;
681		}
682	<
683	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
682	>
683	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
684		SimInfo::MoleculeIterator mi;
685		Molecule* mol;
686		Molecule::AtomIterator ai;
687		Atom* atom;
688	<	std::set<AtomType*> atomTypes;
689	<
690	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
711	<
688	>	set<AtomType*> atomTypes;
689	>
690	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
691		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
692		atomTypes.insert(atom->getAtomType());
693	+	}
694	+	}
695	+	return atomTypes;
696	+	}
697	+
698	+	/**
699	+	* setupCutoffs
700	+	*
701	+	* Sets the values of cutoffRadius and cutoffMethod
702	+	*
703	+	* cutoffRadius : realType
704	+	*  If the cutoffRadius was explicitly set, use that value.
705	+	*  If the cutoffRadius was not explicitly set:
706	+	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
707	+	*      No electrostatic atoms?  Poll the atom types present in the
708	+	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
709	+	*      Use the maximum suggested value that was found.
710	+	*
711	+	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
712	+	*      If cutoffMethod was explicitly set, use that choice.
713	+	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
714	+	*/
715	+	void SimInfo::setupCutoffs() {
716	+
717	+	if (simParams_->haveCutoffRadius()) {
718	+	cutoffRadius_ = simParams_->getCutoffRadius();
719	+	} else {
720	+	if (usesElectrostaticAtoms_) {
721	+	sprintf(painCave.errMsg,
722	+	"SimInfo: No value was set for the cutoffRadius.\n"
723	+	"\tOpenMD will use a default value of 12.0 angstroms"
724	+	"\tfor the cutoffRadius.\n");
725	+	painCave.isFatal = 0;
726	+	painCave.severity = OPENMD_INFO;
727	+	simError();
728	+	cutoffRadius_ = 12.0;
729	+	} else {
730	+	RealType thisCut;
731	+	set<AtomType*>::iterator i;
732	+	set<AtomType*> atomTypes;
733	+	atomTypes = getSimulatedAtomTypes();
734	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
735	+	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
736	+	cutoffRadius_ = max(thisCut, cutoffRadius_);
737	+	}
738	+	sprintf(painCave.errMsg,
739	+	"SimInfo: No value was set for the cutoffRadius.\n"
740	+	"\tOpenMD will use %lf angstroms.\n",
741	+	cutoffRadius_);
742	+	painCave.isFatal = 0;
743	+	painCave.severity = OPENMD_INFO;
744	+	simError();
745	+	}
746	+	}
747	+
748	+	InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
749	+
750	+	map<string, CutoffMethod> stringToCutoffMethod;
751	+	stringToCutoffMethod["HARD"] = HARD;
752	+	stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
753	+	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
754	+	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
755	+
756	+	if (simParams_->haveCutoffMethod()) {
757	+	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
758	+	map<string, CutoffMethod>::iterator i;
759	+	i = stringToCutoffMethod.find(cutMeth);
760	+	if (i == stringToCutoffMethod.end()) {
761	+	sprintf(painCave.errMsg,
762	+	"SimInfo: Could not find chosen cutoffMethod %s\n"
763	+	"\tShould be one of: "
764	+	"HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
765	+	cutMeth.c_str());
766	+	painCave.isFatal = 1;
767	+	painCave.severity = OPENMD_ERROR;
768	+	simError();
769	+	} else {
770	+	cutoffMethod_ = i->second;
771		}
772	<
772	>	} else {
773	>	sprintf(painCave.errMsg,
774	>	"SimInfo: No value was set for the cutoffMethod.\n"
775	>	"\tOpenMD will use SHIFTED_FORCE.\n");
776	>	painCave.isFatal = 0;
777	>	painCave.severity = OPENMD_INFO;
778	>	simError();
779	>	cutoffMethod_ = SHIFTED_FORCE;
780		}
781
782	<	return atomTypes;
782	>	InteractionManager::Instance()->setCutoffMethod(cutoffMethod_);
783		}
784	+
785	+	/**
786	+	* setupSwitching
787	+	*
788	+	* Sets the values of switchingRadius and
789	+	*  If the switchingRadius was explicitly set, use that value (but check it)
790	+	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
791	+	*/
792	+	void SimInfo::setupSwitching() {
793	+
794	+	if (simParams_->haveSwitchingRadius()) {
795	+	switchingRadius_ = simParams_->getSwitchingRadius();
796	+	if (switchingRadius_ > cutoffRadius_) {
797	+	sprintf(painCave.errMsg,
798	+	"SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
799	+	switchingRadius_, cutoffRadius_);
800	+	painCave.isFatal = 1;
801	+	painCave.severity = OPENMD_ERROR;
802	+	simError();
803	+	}
804	+	} else {
805	+	switchingRadius_ = 0.85 * cutoffRadius_;
806	+	sprintf(painCave.errMsg,
807	+	"SimInfo: No value was set for the switchingRadius.\n"
808	+	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
809	+	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
810	+	painCave.isFatal = 0;
811	+	painCave.severity = OPENMD_WARNING;
812	+	simError();
813	+	}
814	+
815	+	InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
816
817	<	void SimInfo::setupSimType() {
722	<	std::set<AtomType*>::iterator i;
723	<	std::set<AtomType*> atomTypes;
724	<	atomTypes = getUniqueAtomTypes();
817	>	SwitchingFunctionType ft;
818
819	<	int useLennardJones = 0;
820	<	int useElectrostatic = 0;
821	<	int useEAM = 0;
822	<	int useSC = 0;
823	<	int useCharge = 0;
824	<	int useDirectional = 0;
825	<	int useDipole = 0;
826	<	int useGayBerne = 0;
827	<	int useSticky = 0;
828	<	int useStickyPower = 0;
829	<	int useShape = 0;
830	<	int useFLARB = 0; //it is not in AtomType yet
831	<	int useDirectionalAtom = 0;
832	<	int useElectrostatics = 0;
833	<	//usePBC and useRF are from simParams
834	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
835	<	int useRF;
836	<	int useSF;
837	<	int useSP;
838	<	int useBoxDipole;
819	>	if (simParams_->haveSwitchingFunctionType()) {
820	>	string funcType = simParams_->getSwitchingFunctionType();
821	>	toUpper(funcType);
822	>	if (funcType == "CUBIC") {
823	>	ft = cubic;
824	>	} else {
825	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
826	>	ft = fifth_order_poly;
827	>	} else {
828	>	// throw error
829	>	sprintf( painCave.errMsg,
830	>	"SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
831	>	"\tswitchingFunctionType must be one of: "
832	>	"\"cubic\" or \"fifth_order_polynomial\".",
833	>	funcType.c_str() );
834	>	painCave.isFatal = 1;
835	>	painCave.severity = OPENMD_ERROR;
836	>	simError();
837	>	}
838	>	}
839	>	}
840
841	<	std::string myMethod;
841	>	InteractionManager::Instance()->setSwitchingFunctionType(ft);
842	>	}
843
844	<	// set the useRF logical
845	<	useRF = 0;
846	<	useSF = 0;
847	<	useSP = 0;
844	>	/**
845	>	* setupSkinThickness
846	>	*
847	>	*  If the skinThickness was explicitly set, use that value (but check it)
848	>	*  If the skinThickness was not explicitly set: use 1.0 angstroms
849	>	*/
850	>	void SimInfo::setupSkinThickness() {
851	>	if (simParams_->haveSkinThickness()) {
852	>	skinThickness_ = simParams_->getSkinThickness();
853	>	} else {
854	>	skinThickness_ = 1.0;
855	>	sprintf(painCave.errMsg,
856	>	"SimInfo Warning: No value was set for the skinThickness.\n"
857	>	"\tOpenMD will use a default value of %f Angstroms\n"
858	>	"\tfor this simulation\n", skinThickness_);
859	>	painCave.isFatal = 0;
860	>	simError();
861	>	}
862	>	}
863
864	+	void SimInfo::setupSimType() {
865	+	set<AtomType*>::iterator i;
866	+	set<AtomType*> atomTypes;
867	+	atomTypes = getSimulatedAtomTypes();
868
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;
764	–	}
765	–	}
766	–
767	–	if (simParams_->haveAccumulateBoxDipole())
768	–	if (simParams_->getAccumulateBoxDipole())
769	–	useBoxDipole = 1;
770	–
869		useAtomicVirial_ = simParams_->getUseAtomicVirial();
870
871	+	int usesElectrostatic = 0;
872	+	int usesMetallic = 0;
873	+	int usesDirectional = 0;
874		//loop over all of the atom types
875		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
876	<	useLennardJones |= (*i)->isLennardJones();
877	<	useElectrostatic |= (*i)->isElectrostatic();
878	<	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();
876	>	usesElectrostatic |= (*i)->isElectrostatic();
877	>	usesMetallic |= (*i)->isMetal();
878	>	usesDirectional |= (*i)->isDirectional();
879		}
880
788	–	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
789	–	useDirectionalAtom = 1;
790	–	}
791	–
792	–	if (useCharge || useDipole) {
793	–	useElectrostatics = 1;
794	–	}
795	–
881		#ifdef IS_MPI
882		int temp;
883	+	temp = usesDirectional;
884	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
885
886	<	temp = usePBC;
887	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
886	>	temp = usesMetallic;
887	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
888
889	<	temp = useDirectionalAtom;
890	<	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	<
889	>	temp = usesElectrostatic;
890	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
891		#endif
892	<
893	<	fInfo_.SIM_uses_PBC = usePBC;
894	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
895	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
896	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
897	<	fInfo_.SIM_uses_Charges = useCharge;
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_;
892	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
893	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
894	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
895	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
896	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
897	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
898		}
899
900		void SimInfo::setupFortranSim() {
901		int isError;
902	<	int nExclude;
903	<	std::vector<int> fortranGlobalGroupMembership;
902	>	int nExclude, nOneTwo, nOneThree, nOneFour;
903	>	vector<int> fortranGlobalGroupMembership;
904
905	<	nExclude = exclude_.getSize();
905	>	notifyFortranSkinThickness(&skinThickness_);
906	>
907	>	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
908	>	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
909	>	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
910	>
911		isError = 0;
912
913		//globalGroupMembership_ is filled by SimCreator
#	Line 886 | Line 916 | namespace oopse {
916		}
917
918		//calculate mass ratio of cutoff group
919	<	std::vector<RealType> mfact;
919	>	vector<RealType> mfact;
920		SimInfo::MoleculeIterator mi;
921		Molecule* mol;
922		Molecule::CutoffGroupIterator ci;
#	Line 909 | Line 939 | namespace oopse {
939		else
940		mfact.push_back( 1.0 );
941		}
912	–
942		}
943		}
944
945		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
946	<	std::vector<int> identArray;
946	>	vector<int> identArray;
947
948		//to avoid memory reallocation, reserve enough space identArray
949		identArray.reserve(getNAtoms());
#	Line 927 | Line 956 | namespace oopse {
956
957		//fill molMembershipArray
958		//molMembershipArray is filled by SimCreator
959	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
959	>	vector<int> molMembershipArray(nGlobalAtoms_);
960		for (int i = 0; i < nGlobalAtoms_; i++) {
961		molMembershipArray[i] = globalMolMembership_[i] + 1;
962		}
963
964		//setup fortran simulation
965	<	int nGlobalExcludes = 0;
966	<	int* globalExcludes = NULL;
967	<	int* excludeList = exclude_.getExcludeList();
965	>
966	>	nExclude = excludedInteractions_.getSize();
967	>	nOneTwo = oneTwoInteractions_.getSize();
968	>	nOneThree = oneThreeInteractions_.getSize();
969	>	nOneFour = oneFourInteractions_.getSize();
970	>
971	>	int* excludeList = excludedInteractions_.getPairList();
972	>	int* oneTwoList = oneTwoInteractions_.getPairList();
973	>	int* oneThreeList = oneThreeInteractions_.getPairList();
974	>	int* oneFourList = oneFourInteractions_.getPairList();
975	>
976		setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
977	<	&nExclude, excludeList , &nGlobalExcludes, globalExcludes,
977	>	&nExclude, excludeList,
978	>	&nOneTwo, oneTwoList,
979	>	&nOneThree, oneThreeList,
980	>	&nOneFour, oneFourList,
981		&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
982		&fortranGlobalGroupMembership[0], &isError);
983
#	Line 946 | Line 986 | namespace oopse {
986		sprintf( painCave.errMsg,
987		"There was an error setting the simulation information in fortran.\n" );
988		painCave.isFatal = 1;
989	<	painCave.severity = OOPSE_ERROR;
989	>	painCave.severity = OPENMD_ERROR;
990		simError();
991		}
992
#	Line 969 | Line 1009 | namespace oopse {
1009		void SimInfo::setupFortranParallel() {
1010		#ifdef IS_MPI
1011		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1012	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1013	<	std::vector<int> localToGlobalCutoffGroupIndex;
1012	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1013	>	vector<int> localToGlobalCutoffGroupIndex;
1014		SimInfo::MoleculeIterator mi;
1015		Molecule::AtomIterator ai;
1016		Molecule::CutoffGroupIterator ci;
#	Line 1022 | Line 1062 | namespace oopse {
1062		#endif
1063		}
1064
1025	–	void SimInfo::setupCutoff() {
1026	–
1027	–	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1065
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	–
1066		void SimInfo::setupSwitchingFunction() {
1272	–	int ft = CUBIC;
1067
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	–
1068		}
1069
1070		void SimInfo::setupAccumulateBoxDipole() {
#	Line 1299 | Line 1072 | namespace oopse {
1072		// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1073		if ( simParams_->haveAccumulateBoxDipole() )
1074		if ( simParams_->getAccumulateBoxDipole() ) {
1302	–	setAccumulateBoxDipole();
1075		calcBoxDipole_ = true;
1076		}
1077
#	Line 1309 | Line 1081 | namespace oopse {
1081		properties_.addProperty(genData);
1082		}
1083
1084	<	void SimInfo::removeProperty(const std::string& propName) {
1084	>	void SimInfo::removeProperty(const string& propName) {
1085		properties_.removeProperty(propName);
1086		}
1087
#	Line 1317 | Line 1089 | namespace oopse {
1089		properties_.clearProperties();
1090		}
1091
1092	<	std::vector<std::string> SimInfo::getPropertyNames() {
1092	>	vector<string> SimInfo::getPropertyNames() {
1093		return properties_.getPropertyNames();
1094		}
1095
1096	<	std::vector<GenericData*> SimInfo::getProperties() {
1096	>	vector<GenericData*> SimInfo::getProperties() {
1097		return properties_.getProperties();
1098		}
1099
1100	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1100	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1101		return properties_.getPropertyByName(propName);
1102		}
1103
#	Line 1408 | Line 1180 | namespace oopse {
1180
1181		}
1182
1183	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1183	>	ostream& operator <<(ostream& o, SimInfo& info) {
1184
1185		return o;
1186		}
#	Line 1451 | Line 1223 | namespace oopse {
1223
1224
1225		[  Ixx -Ixy  -Ixz ]
1226	<	J =| -Iyx  Iyy  -Iyz |
1226	>	J =| -Iyx  Iyy  -Iyz |
1227		[ -Izx -Iyz   Izz ]
1228		*/
1229
#	Line 1558 | Line 1330 | namespace oopse {
1330		return IOIndexToIntegrableObject.at(index);
1331		}
1332
1333	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1333	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1334		IOIndexToIntegrableObject= v;
1335		}
1336
#	Line 1600 | Line 1372 | namespace oopse {
1372		return;
1373		}
1374		/*
1375	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1375	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1376		assert( v.size() == nAtoms_ + nRigidBodies_);
1377		sdByGlobalIndex_ = v;
1378		}
#	Line 1610 | Line 1382 | namespace oopse {
1382		return sdByGlobalIndex_.at(index);
1383		}
1384		*/
1385	<	}//end namespace oopse
1385	>	int SimInfo::getNGlobalConstraints() {
1386	>	int nGlobalConstraints;
1387	>	#ifdef IS_MPI
1388	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1389	>	MPI_COMM_WORLD);
1390	>	#else
1391	>	nGlobalConstraints =  nConstraints_;
1392	>	#endif
1393	>	return nGlobalConstraints;
1394	>	}
1395
1396	+	}//end namespace OpenMD
1397	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 1277 by gezelter, Mon Jul 14 12:35:58 2008 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC

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