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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1528 by gezelter, Fri Dec 17 20:11:05 2010 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 55 | Line 55
55		#include "primitives/Molecule.hpp"
56		#include "primitives/StuntDouble.hpp"
57		#include "UseTheForce/fCutoffPolicy.h"
58	–	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	–	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
58		#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
59		#include "UseTheForce/doForces_interface.h"
60		#include "UseTheForce/DarkSide/neighborLists_interface.h"
63	–	#include "UseTheForce/DarkSide/electrostatic_interface.h"
61		#include "UseTheForce/DarkSide/switcheroo_interface.h"
62		#include "utils/MemoryUtils.hpp"
63		#include "utils/simError.h"
64		#include "selection/SelectionManager.hpp"
65		#include "io/ForceFieldOptions.hpp"
66		#include "UseTheForce/ForceField.hpp"
67	+	#include "nonbonded/InteractionManager.hpp"
68
69
70		#ifdef IS_MPI
#	Line 74 | Line 72
72		#include "UseTheForce/DarkSide/simParallel_interface.h"
73		#endif
74
75	<	namespace oopse {
76	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79	<	std::map<int, std::set<int> >::iterator i = container.find(index);
80	<	std::set<int> result;
81	<	if (i != container.end()) {
82	<	result = i->second;
83	<	}
84	<
85	<	return result;
86	<	}
75	>	using namespace std;
76	>	namespace OpenMD {
77
78		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
79		forceField_(ff), simParams_(simParams),
80		ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
81		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
82		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
83	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
84	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
85	<	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false),
86	<	useAtomicVirial_(true) {
87	<
88	<	MoleculeStamp* molStamp;
89	<	int nMolWithSameStamp;
90	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
91	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
92	<	CutoffGroupStamp* cgStamp;
93	<	RigidBodyStamp* rbStamp;
94	<	int nRigidAtoms = 0;
95	<	std::vector<Component*> components = simParams->getComponents();
83	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
84	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
85	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
86	>	calcBoxDipole_(false), useAtomicVirial_(true) {
87	>
88	>	MoleculeStamp* molStamp;
89	>	int nMolWithSameStamp;
90	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
91	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
92	>	CutoffGroupStamp* cgStamp;
93	>	RigidBodyStamp* rbStamp;
94	>	int nRigidAtoms = 0;
95	>
96	>	vector<Component*> components = simParams->getComponents();
97	>
98	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
99	>	molStamp = (*i)->getMoleculeStamp();
100	>	nMolWithSameStamp = (*i)->getNMol();
101
102	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
103	<	molStamp = (*i)->getMoleculeStamp();
104	<	nMolWithSameStamp = (*i)->getNMol();
105	<
106	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
107	<
108	<	//calculate atoms in molecules
109	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
110	<
111	<	//calculate atoms in cutoff groups
112	<	int nAtomsInGroups = 0;
113	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
119	<
120	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
121	<	cgStamp = molStamp->getCutoffGroupStamp(j);
122	<	nAtomsInGroups += cgStamp->getNMembers();
123	<	}
124	<
125	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
126	<
127	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
128	<
129	<	//calculate atoms in rigid bodies
130	<	int nAtomsInRigidBodies = 0;
131	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
132	<
133	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
134	<	rbStamp = molStamp->getRigidBodyStamp(j);
135	<	nAtomsInRigidBodies += rbStamp->getNMembers();
136	<	}
137	<
138	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
139	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
140	<
102	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
103	>
104	>	//calculate atoms in molecules
105	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
106	>
107	>	//calculate atoms in cutoff groups
108	>	int nAtomsInGroups = 0;
109	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
110	>
111	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
112	>	cgStamp = molStamp->getCutoffGroupStamp(j);
113	>	nAtomsInGroups += cgStamp->getNMembers();
114		}
115	<
116	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
117	<	//group therefore the total number of cutoff groups in the system is
118	<	//equal to the total number of atoms minus number of atoms belong to
119	<	//cutoff group defined in meta-data file plus the number of cutoff
120	<	//groups defined in meta-data file
121	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
122	<
123	<	//every free atom (atom does not belong to rigid bodies) is an
124	<	//integrable object therefore the total number of integrable objects
125	<	//in the system is equal to the total number of atoms minus number of
126	<	//atoms belong to rigid body defined in meta-data file plus the number
127	<	//of rigid bodies defined in meta-data file
128	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
129	<	+ nGlobalRigidBodies_;
130	<
131	<	nGlobalMols_ = molStampIds_.size();
159	<	molToProcMap_.resize(nGlobalMols_);
115	>
116	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
117	>
118	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
119	>
120	>	//calculate atoms in rigid bodies
121	>	int nAtomsInRigidBodies = 0;
122	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
123	>
124	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
125	>	rbStamp = molStamp->getRigidBodyStamp(j);
126	>	nAtomsInRigidBodies += rbStamp->getNMembers();
127	>	}
128	>
129	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
130	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
131	>
132		}
133	<
133	>
134	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
135	>	//group therefore the total number of cutoff groups in the system is
136	>	//equal to the total number of atoms minus number of atoms belong to
137	>	//cutoff group defined in meta-data file plus the number of cutoff
138	>	//groups defined in meta-data file
139	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
140	>
141	>	//every free atom (atom does not belong to rigid bodies) is an
142	>	//integrable object therefore the total number of integrable objects
143	>	//in the system is equal to the total number of atoms minus number of
144	>	//atoms belong to rigid body defined in meta-data file plus the number
145	>	//of rigid bodies defined in meta-data file
146	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
147	>	+ nGlobalRigidBodies_;
148	>
149	>	nGlobalMols_ = molStampIds_.size();
150	>	molToProcMap_.resize(nGlobalMols_);
151	>	}
152	>
153		SimInfo::~SimInfo() {
154	<	std::map<int, Molecule*>::iterator i;
154	>	map<int, Molecule*>::iterator i;
155		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
156		delete i->second;
157		}
#	Line 171 | Line 162 | namespace oopse {
162		delete forceField_;
163		}
164
174	–	int SimInfo::getNGlobalConstraints() {
175	–	int nGlobalConstraints;
176	–	#ifdef IS_MPI
177	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
178	–	MPI_COMM_WORLD);
179	–	#else
180	–	nGlobalConstraints =  nConstraints_;
181	–	#endif
182	–	return nGlobalConstraints;
183	–	}
165
166		bool SimInfo::addMolecule(Molecule* mol) {
167		MoleculeIterator i;
168	<
168	>
169		i = molecules_.find(mol->getGlobalIndex());
170		if (i == molecules_.end() ) {
171	<
172	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
173	<
171	>
172	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
173	>
174		nAtoms_ += mol->getNAtoms();
175		nBonds_ += mol->getNBonds();
176		nBends_ += mol->getNBends();
177		nTorsions_ += mol->getNTorsions();
178	+	nInversions_ += mol->getNInversions();
179		nRigidBodies_ += mol->getNRigidBodies();
180		nIntegrableObjects_ += mol->getNIntegrableObjects();
181		nCutoffGroups_ += mol->getNCutoffGroups();
182		nConstraints_ += mol->getNConstraintPairs();
183	<
184	<	addExcludePairs(mol);
185	<
183	>
184	>	addInteractionPairs(mol);
185	>
186		return true;
187		} else {
188		return false;
189		}
190		}
191	<
191	>
192		bool SimInfo::removeMolecule(Molecule* mol) {
193		MoleculeIterator i;
194		i = molecules_.find(mol->getGlobalIndex());
#	Line 219 | Line 201 | namespace oopse {
201		nBonds_ -= mol->getNBonds();
202		nBends_ -= mol->getNBends();
203		nTorsions_ -= mol->getNTorsions();
204	+	nInversions_ -= mol->getNInversions();
205		nRigidBodies_ -= mol->getNRigidBodies();
206		nIntegrableObjects_ -= mol->getNIntegrableObjects();
207		nCutoffGroups_ -= mol->getNCutoffGroups();
208		nConstraints_ -= mol->getNConstraintPairs();
209
210	<	removeExcludePairs(mol);
210	>	removeInteractionPairs(mol);
211		molecules_.erase(mol->getGlobalIndex());
212
213		delete mol;
#	Line 233 | Line 216 | namespace oopse {
216		} else {
217		return false;
218		}
236	–
237	–
219		}
220
221
#	Line 252 | Line 233 | namespace oopse {
233		void SimInfo::calcNdf() {
234		int ndf_local;
235		MoleculeIterator i;
236	<	std::vector<StuntDouble*>::iterator j;
236	>	vector<StuntDouble*>::iterator j;
237		Molecule* mol;
238		StuntDouble* integrableObject;
239
#	Line 303 | Line 284 | namespace oopse {
284		int ndfRaw_local;
285
286		MoleculeIterator i;
287	<	std::vector<StuntDouble*>::iterator j;
287	>	vector<StuntDouble*>::iterator j;
288		Molecule* mol;
289		StuntDouble* integrableObject;
290
#	Line 350 | Line 331 | namespace oopse {
331
332		}
333
334	<	void SimInfo::addExcludePairs(Molecule* mol) {
335	<	std::vector<Bond*>::iterator bondIter;
336	<	std::vector<Bend*>::iterator bendIter;
337	<	std::vector<Torsion*>::iterator torsionIter;
334	>	void SimInfo::addInteractionPairs(Molecule* mol) {
335	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
336	>	vector<Bond*>::iterator bondIter;
337	>	vector<Bend*>::iterator bendIter;
338	>	vector<Torsion*>::iterator torsionIter;
339	>	vector<Inversion*>::iterator inversionIter;
340		Bond* bond;
341		Bend* bend;
342		Torsion* torsion;
343	+	Inversion* inversion;
344		int a;
345		int b;
346		int c;
347		int d;
348
349	<	std::map<int, std::set<int> > atomGroups;
349	>	// atomGroups can be used to add special interaction maps between
350	>	// groups of atoms that are in two separate rigid bodies.
351	>	// However, most site-site interactions between two rigid bodies
352	>	// are probably not special, just the ones between the physically
353	>	// bonded atoms.  Interactions *within* a single rigid body should
354	>	// always be excluded.  These are done at the bottom of this
355	>	// function.
356
357	+	map<int, set<int> > atomGroups;
358		Molecule::RigidBodyIterator rbIter;
359		RigidBody* rb;
360		Molecule::IntegrableObjectIterator ii;
361		StuntDouble* integrableObject;
362
363	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
364	<	integrableObject = mol->nextIntegrableObject(ii)) {
365	<
363	>	for (integrableObject = mol->beginIntegrableObject(ii);
364	>	integrableObject != NULL;
365	>	integrableObject = mol->nextIntegrableObject(ii)) {
366	>
367		if (integrableObject->isRigidBody()) {
368	<	rb = static_cast<RigidBody*>(integrableObject);
369	<	std::vector<Atom*> atoms = rb->getAtoms();
370	<	std::set<int> rigidAtoms;
371	<	for (int i = 0; i < atoms.size(); ++i) {
372	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
373	<	}
374	<	for (int i = 0; i < atoms.size(); ++i) {
375	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
376	<	}
368	>	rb = static_cast<RigidBody*>(integrableObject);
369	>	vector<Atom*> atoms = rb->getAtoms();
370	>	set<int> rigidAtoms;
371	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
372	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
373	>	}
374	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
375	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
376	>	}
377		} else {
378	<	std::set<int> oneAtomSet;
378	>	set<int> oneAtomSet;
379		oneAtomSet.insert(integrableObject->getGlobalIndex());
380	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
380	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
381		}
382		}
383	+
384	+	for (bond= mol->beginBond(bondIter); bond != NULL;
385	+	bond = mol->nextBond(bondIter)) {
386
392	–
393	–
394	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
387		a = bond->getAtomA()->getGlobalIndex();
388	<	b = bond->getAtomB()->getGlobalIndex();
389	<	exclude_.addPair(a, b);
388	>	b = bond->getAtomB()->getGlobalIndex();
389	>
390	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
391	>	oneTwoInteractions_.addPair(a, b);
392	>	} else {
393	>	excludedInteractions_.addPair(a, b);
394	>	}
395		}
396
397	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
397	>	for (bend= mol->beginBend(bendIter); bend != NULL;
398	>	bend = mol->nextBend(bendIter)) {
399	>
400		a = bend->getAtomA()->getGlobalIndex();
401		b = bend->getAtomB()->getGlobalIndex();
402		c = bend->getAtomC()->getGlobalIndex();
404	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
405	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
406	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
407	–
408	–	exclude_.addPairs(rigidSetA, rigidSetB);
409	–	exclude_.addPairs(rigidSetA, rigidSetC);
410	–	exclude_.addPairs(rigidSetB, rigidSetC);
403
404	<	//exclude_.addPair(a, b);
405	<	//exclude_.addPair(a, c);
406	<	//exclude_.addPair(b, c);
404	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
405	>	oneTwoInteractions_.addPair(a, b);
406	>	oneTwoInteractions_.addPair(b, c);
407	>	} else {
408	>	excludedInteractions_.addPair(a, b);
409	>	excludedInteractions_.addPair(b, c);
410	>	}
411	>
412	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
413	>	oneThreeInteractions_.addPair(a, c);
414	>	} else {
415	>	excludedInteractions_.addPair(a, c);
416	>	}
417		}
418
419	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
419	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
420	>	torsion = mol->nextTorsion(torsionIter)) {
421	>
422		a = torsion->getAtomA()->getGlobalIndex();
423		b = torsion->getAtomB()->getGlobalIndex();
424		c = torsion->getAtomC()->getGlobalIndex();
425	<	d = torsion->getAtomD()->getGlobalIndex();
422	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
423	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
424	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
425	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
425	>	d = torsion->getAtomD()->getGlobalIndex();
426
427	<	exclude_.addPairs(rigidSetA, rigidSetB);
428	<	exclude_.addPairs(rigidSetA, rigidSetC);
429	<	exclude_.addPairs(rigidSetA, rigidSetD);
430	<	exclude_.addPairs(rigidSetB, rigidSetC);
431	<	exclude_.addPairs(rigidSetB, rigidSetD);
432	<	exclude_.addPairs(rigidSetC, rigidSetD);
427	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
428	>	oneTwoInteractions_.addPair(a, b);
429	>	oneTwoInteractions_.addPair(b, c);
430	>	oneTwoInteractions_.addPair(c, d);
431	>	} else {
432	>	excludedInteractions_.addPair(a, b);
433	>	excludedInteractions_.addPair(b, c);
434	>	excludedInteractions_.addPair(c, d);
435	>	}
436
437	<	/*
438	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
439	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
440	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
441	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
442	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
443	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
444	<
445	<
446	<	exclude_.addPair(a, b);
447	<	exclude_.addPair(a, c);
448	<	exclude_.addPair(a, d);
449	<	exclude_.addPair(b, c);
447	<	exclude_.addPair(b, d);
448	<	exclude_.addPair(c, d);
449	<	*/
437	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
438	>	oneThreeInteractions_.addPair(a, c);
439	>	oneThreeInteractions_.addPair(b, d);
440	>	} else {
441	>	excludedInteractions_.addPair(a, c);
442	>	excludedInteractions_.addPair(b, d);
443	>	}
444	>
445	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
446	>	oneFourInteractions_.addPair(a, d);
447	>	} else {
448	>	excludedInteractions_.addPair(a, d);
449	>	}
450		}
451
452	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
453	<	std::vector<Atom*> atoms = rb->getAtoms();
454	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
455	<	for (int j = i + 1; j < atoms.size(); ++j) {
452	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
453	>	inversion = mol->nextInversion(inversionIter)) {
454	>
455	>	a = inversion->getAtomA()->getGlobalIndex();
456	>	b = inversion->getAtomB()->getGlobalIndex();
457	>	c = inversion->getAtomC()->getGlobalIndex();
458	>	d = inversion->getAtomD()->getGlobalIndex();
459	>
460	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
461	>	oneTwoInteractions_.addPair(a, b);
462	>	oneTwoInteractions_.addPair(a, c);
463	>	oneTwoInteractions_.addPair(a, d);
464	>	} else {
465	>	excludedInteractions_.addPair(a, b);
466	>	excludedInteractions_.addPair(a, c);
467	>	excludedInteractions_.addPair(a, d);
468	>	}
469	>
470	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
471	>	oneThreeInteractions_.addPair(b, c);
472	>	oneThreeInteractions_.addPair(b, d);
473	>	oneThreeInteractions_.addPair(c, d);
474	>	} else {
475	>	excludedInteractions_.addPair(b, c);
476	>	excludedInteractions_.addPair(b, d);
477	>	excludedInteractions_.addPair(c, d);
478	>	}
479	>	}
480	>
481	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
482	>	rb = mol->nextRigidBody(rbIter)) {
483	>	vector<Atom*> atoms = rb->getAtoms();
484	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
485	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
486		a = atoms[i]->getGlobalIndex();
487		b = atoms[j]->getGlobalIndex();
488	<	exclude_.addPair(a, b);
488	>	excludedInteractions_.addPair(a, b);
489		}
490		}
491		}
492
493		}
494
495	<	void SimInfo::removeExcludePairs(Molecule* mol) {
496	<	std::vector<Bond*>::iterator bondIter;
497	<	std::vector<Bend*>::iterator bendIter;
498	<	std::vector<Torsion*>::iterator torsionIter;
495	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
496	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
497	>	vector<Bond*>::iterator bondIter;
498	>	vector<Bend*>::iterator bendIter;
499	>	vector<Torsion*>::iterator torsionIter;
500	>	vector<Inversion*>::iterator inversionIter;
501		Bond* bond;
502		Bend* bend;
503		Torsion* torsion;
504	+	Inversion* inversion;
505		int a;
506		int b;
507		int c;
508		int d;
509
510	<	std::map<int, std::set<int> > atomGroups;
478	<
510	>	map<int, set<int> > atomGroups;
511		Molecule::RigidBodyIterator rbIter;
512		RigidBody* rb;
513		Molecule::IntegrableObjectIterator ii;
514		StuntDouble* integrableObject;
515
516	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
517	<	integrableObject = mol->nextIntegrableObject(ii)) {
518	<
516	>	for (integrableObject = mol->beginIntegrableObject(ii);
517	>	integrableObject != NULL;
518	>	integrableObject = mol->nextIntegrableObject(ii)) {
519	>
520		if (integrableObject->isRigidBody()) {
521	<	rb = static_cast<RigidBody*>(integrableObject);
522	<	std::vector<Atom*> atoms = rb->getAtoms();
523	<	std::set<int> rigidAtoms;
524	<	for (int i = 0; i < atoms.size(); ++i) {
525	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
526	<	}
527	<	for (int i = 0; i < atoms.size(); ++i) {
528	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
529	<	}
521	>	rb = static_cast<RigidBody*>(integrableObject);
522	>	vector<Atom*> atoms = rb->getAtoms();
523	>	set<int> rigidAtoms;
524	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
525	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
526	>	}
527	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
528	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
529	>	}
530		} else {
531	<	std::set<int> oneAtomSet;
531	>	set<int> oneAtomSet;
532		oneAtomSet.insert(integrableObject->getGlobalIndex());
533	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
533	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
534		}
535		}
536
537	<
538	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
537	>	for (bond= mol->beginBond(bondIter); bond != NULL;
538	>	bond = mol->nextBond(bondIter)) {
539	>
540		a = bond->getAtomA()->getGlobalIndex();
541	<	b = bond->getAtomB()->getGlobalIndex();
542	<	exclude_.removePair(a, b);
541	>	b = bond->getAtomB()->getGlobalIndex();
542	>
543	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
544	>	oneTwoInteractions_.removePair(a, b);
545	>	} else {
546	>	excludedInteractions_.removePair(a, b);
547	>	}
548		}
549
550	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
550	>	for (bend= mol->beginBend(bendIter); bend != NULL;
551	>	bend = mol->nextBend(bendIter)) {
552	>
553		a = bend->getAtomA()->getGlobalIndex();
554		b = bend->getAtomB()->getGlobalIndex();
555		c = bend->getAtomC()->getGlobalIndex();
515	–
516	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
517	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
518	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
519	–
520	–	exclude_.removePairs(rigidSetA, rigidSetB);
521	–	exclude_.removePairs(rigidSetA, rigidSetC);
522	–	exclude_.removePairs(rigidSetB, rigidSetC);
556
557	<	//exclude_.removePair(a, b);
558	<	//exclude_.removePair(a, c);
559	<	//exclude_.removePair(b, c);
557	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
558	>	oneTwoInteractions_.removePair(a, b);
559	>	oneTwoInteractions_.removePair(b, c);
560	>	} else {
561	>	excludedInteractions_.removePair(a, b);
562	>	excludedInteractions_.removePair(b, c);
563	>	}
564	>
565	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
566	>	oneThreeInteractions_.removePair(a, c);
567	>	} else {
568	>	excludedInteractions_.removePair(a, c);
569	>	}
570		}
571
572	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
572	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
573	>	torsion = mol->nextTorsion(torsionIter)) {
574	>
575		a = torsion->getAtomA()->getGlobalIndex();
576		b = torsion->getAtomB()->getGlobalIndex();
577		c = torsion->getAtomC()->getGlobalIndex();
578	<	d = torsion->getAtomD()->getGlobalIndex();
578	>	d = torsion->getAtomD()->getGlobalIndex();
579	>
580	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
581	>	oneTwoInteractions_.removePair(a, b);
582	>	oneTwoInteractions_.removePair(b, c);
583	>	oneTwoInteractions_.removePair(c, d);
584	>	} else {
585	>	excludedInteractions_.removePair(a, b);
586	>	excludedInteractions_.removePair(b, c);
587	>	excludedInteractions_.removePair(c, d);
588	>	}
589
590	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
591	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
592	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
593	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
590	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
591	>	oneThreeInteractions_.removePair(a, c);
592	>	oneThreeInteractions_.removePair(b, d);
593	>	} else {
594	>	excludedInteractions_.removePair(a, c);
595	>	excludedInteractions_.removePair(b, d);
596	>	}
597
598	<	exclude_.removePairs(rigidSetA, rigidSetB);
599	<	exclude_.removePairs(rigidSetA, rigidSetC);
600	<	exclude_.removePairs(rigidSetA, rigidSetD);
601	<	exclude_.removePairs(rigidSetB, rigidSetC);
602	<	exclude_.removePairs(rigidSetB, rigidSetD);
603	<	exclude_.removePairs(rigidSetC, rigidSetD);
598	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
599	>	oneFourInteractions_.removePair(a, d);
600	>	} else {
601	>	excludedInteractions_.removePair(a, d);
602	>	}
603	>	}
604
605	<	/*
606	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
549	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
550	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
551	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
552	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
553	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
605	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
606	>	inversion = mol->nextInversion(inversionIter)) {
607
608	<
609	<	exclude_.removePair(a, b);
610	<	exclude_.removePair(a, c);
611	<	exclude_.removePair(a, d);
612	<	exclude_.removePair(b, c);
613	<	exclude_.removePair(b, d);
614	<	exclude_.removePair(c, d);
615	<	*/
608	>	a = inversion->getAtomA()->getGlobalIndex();
609	>	b = inversion->getAtomB()->getGlobalIndex();
610	>	c = inversion->getAtomC()->getGlobalIndex();
611	>	d = inversion->getAtomD()->getGlobalIndex();
612	>
613	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
614	>	oneTwoInteractions_.removePair(a, b);
615	>	oneTwoInteractions_.removePair(a, c);
616	>	oneTwoInteractions_.removePair(a, d);
617	>	} else {
618	>	excludedInteractions_.removePair(a, b);
619	>	excludedInteractions_.removePair(a, c);
620	>	excludedInteractions_.removePair(a, d);
621	>	}
622	>
623	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
624	>	oneThreeInteractions_.removePair(b, c);
625	>	oneThreeInteractions_.removePair(b, d);
626	>	oneThreeInteractions_.removePair(c, d);
627	>	} else {
628	>	excludedInteractions_.removePair(b, c);
629	>	excludedInteractions_.removePair(b, d);
630	>	excludedInteractions_.removePair(c, d);
631	>	}
632		}
633
634	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
635	<	std::vector<Atom*> atoms = rb->getAtoms();
636	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
637	<	for (int j = i + 1; j < atoms.size(); ++j) {
634	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
635	>	rb = mol->nextRigidBody(rbIter)) {
636	>	vector<Atom*> atoms = rb->getAtoms();
637	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
638	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
639		a = atoms[i]->getGlobalIndex();
640		b = atoms[j]->getGlobalIndex();
641	<	exclude_.removePair(a, b);
641	>	excludedInteractions_.removePair(a, b);
642		}
643		}
644		}
645	<
645	>
646		}
647	<
648	<
647	>
648	>
649		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
650		int curStampId;
651	<
651	>
652		//index from 0
653		curStampId = moleculeStamps_.size();
654
#	Line 589 | Line 659 | namespace oopse {
659		void SimInfo::update() {
660
661		setupSimType();
662	+	setupCutoffRadius();
663	+	setupSwitchingRadius();
664	+	setupCutoffMethod();
665	+	setupSkinThickness();
666	+	setupSwitchingFunction();
667	+	setupAccumulateBoxDipole();
668
669		#ifdef IS_MPI
670		setupFortranParallel();
671		#endif
596	–
672		setupFortranSim();
673	+	fortranInitialized_ = true;
674
599	–	//setup fortran force field
600	–	/** @deprecate */
601	–	int isError = 0;
602	–
603	–	setupCutoff();
604	–
605	–	setupElectrostaticSummationMethod( isError );
606	–	setupSwitchingFunction();
607	–	setupAccumulateBoxDipole();
608	–
609	–	if(isError){
610	–	sprintf( painCave.errMsg,
611	–	"ForceField error: There was an error initializing the forceField in fortran.\n" );
612	–	painCave.isFatal = 1;
613	–	simError();
614	–	}
615	–
675		calcNdf();
676		calcNdfRaw();
677		calcNdfTrans();
619	–
620	–	fortranInitialized_ = true;
678		}
679	<
680	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
679	>
680	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
681		SimInfo::MoleculeIterator mi;
682		Molecule* mol;
683		Molecule::AtomIterator ai;
684		Atom* atom;
685	<	std::set<AtomType*> atomTypes;
686	<
685	>	set<AtomType*> atomTypes;
686	>
687		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
688	<
688	>
689		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
690		atomTypes.insert(atom->getAtomType());
691		}
692	<
692	>
693		}
694	<
694	>
695		return atomTypes;
696		}
697
698	<	void SimInfo::setupSimType() {
699	<	std::set<AtomType*>::iterator i;
700	<	std::set<AtomType*> atomTypes;
701	<	atomTypes = getUniqueAtomTypes();
698	>	/**
699	>	* setupCutoffRadius
700	>	*
701	>	*  If the cutoffRadius was explicitly set, use that value.
702	>	*  If the cutoffRadius was not explicitly set:
703	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
704	>	*      No electrostatic atoms?  Poll the atom types present in the
705	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
706	>	*      Use the maximum suggested value that was found.
707	>	*/
708	>	void SimInfo::setupCutoffRadius() {
709
710	<	int useLennardJones = 0;
711	<	int useElectrostatic = 0;
712	<	int useEAM = 0;
713	<	int useSC = 0;
714	<	int useCharge = 0;
715	<	int useDirectional = 0;
716	<	int useDipole = 0;
717	<	int useGayBerne = 0;
718	<	int useSticky = 0;
719	<	int useStickyPower = 0;
720	<	int useShape = 0;
721	<	int useFLARB = 0; //it is not in AtomType yet
722	<	int useDirectionalAtom = 0;
723	<	int useElectrostatics = 0;
724	<	//usePBC and useRF are from simParams
725	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
726	<	int useRF;
727	<	int useSF;
728	<	int useSP;
729	<	int useBoxDipole;
710	>	if (simParams_->haveCutoffRadius()) {
711	>	cutoffRadius_ = simParams_->getCutoffRadius();
712	>	} else {
713	>	if (usesElectrostaticAtoms_) {
714	>	sprintf(painCave.errMsg,
715	>	"SimInfo Warning: No value was set for the cutoffRadius.\n"
716	>	"\tOpenMD will use a default value of 12.0 angstroms"
717	>	"\tfor the cutoffRadius.\n");
718	>	painCave.isFatal = 0;
719	>	simError();
720	>	cutoffRadius_ = 12.0;
721	>	} else {
722	>	RealType thisCut;
723	>	set<AtomType*>::iterator i;
724	>	set<AtomType*> atomTypes;
725	>	atomTypes = getSimulatedAtomTypes();
726	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
727	>	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
728	>	cutoffRadius_ = max(thisCut, cutoffRadius_);
729	>	}
730	>	sprintf(painCave.errMsg,
731	>	"SimInfo Warning: No value was set for the cutoffRadius.\n"
732	>	"\tOpenMD will use %lf angstroms.\n",
733	>	cutoffRadius_);
734	>	painCave.isFatal = 0;
735	>	simError();
736	>	}
737	>	}
738
739	<	std::string myMethod;
739	>	InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
740	>	}
741	>
742	>	/**
743	>	* setupSwitchingRadius
744	>	*
745	>	*  If the switchingRadius was explicitly set, use that value (but check it)
746	>	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
747	>	*/
748	>	void SimInfo::setupSwitchingRadius() {
749	>
750	>	if (simParams_->haveSwitchingRadius()) {
751	>	switchingRadius_ = simParams_->getSwitchingRadius();
752	>	if (switchingRadius_ > cutoffRadius_) {
753	>	sprintf(painCave.errMsg,
754	>	"SimInfo Error: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
755	>	switchingRadius_, cutoffRadius_);
756	>	painCave.isFatal = 1;
757	>	simError();
758
759	<	// set the useRF logical
760	<	useRF = 0;
761	<	useSF = 0;
762	<	useSP = 0;
759	>	}
760	>	} else {
761	>	switchingRadius_ = 0.85 * cutoffRadius_;
762	>	sprintf(painCave.errMsg,
763	>	"SimInfo Warning: No value was set for the switchingRadius.\n"
764	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
765	>	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
766	>	painCave.isFatal = 0;
767	>	simError();
768	>	}
769	>	InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
770	>	}
771
772	+	/**
773	+	* setupSkinThickness
774	+	*
775	+	*  If the skinThickness was explicitly set, use that value (but check it)
776	+	*  If the skinThickness was not explicitly set: use 1.0 angstroms
777	+	*/
778	+	void SimInfo::setupSkinThickness() {
779	+	if (simParams_->haveSkinThickness()) {
780	+	skinThickness_ = simParams_->getSkinThickness();
781	+	} else {
782	+	skinThickness_ = 1.0;
783	+	sprintf(painCave.errMsg,
784	+	"SimInfo Warning: No value was set for the skinThickness.\n"
785	+	"\tOpenMD will use a default value of %f Angstroms\n"
786	+	"\tfor this simulation\n", skinThickness_);
787	+	painCave.isFatal = 0;
788	+	simError();
789	+	}
790	+	}
791
792	<	if (simParams_->haveElectrostaticSummationMethod()) {
793	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
794	<	toUpper(myMethod);
795	<	if (myMethod == "REACTION_FIELD"){
679	<	useRF = 1;
680	<	} else if (myMethod == "SHIFTED_FORCE"){
681	<	useSF = 1;
682	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
683	<	useSP = 1;
684	<	}
685	<	}
686	<
687	<	if (simParams_->haveAccumulateBoxDipole())
688	<	if (simParams_->getAccumulateBoxDipole())
689	<	useBoxDipole = 1;
792	>	void SimInfo::setupSimType() {
793	>	set<AtomType*>::iterator i;
794	>	set<AtomType*> atomTypes;
795	>	atomTypes = getSimulatedAtomTypes();
796
797		useAtomicVirial_ = simParams_->getUseAtomicVirial();
798
799	+	int usesElectrostatic = 0;
800	+	int usesMetallic = 0;
801	+	int usesDirectional = 0;
802		//loop over all of the atom types
803		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
804	<	useLennardJones |= (*i)->isLennardJones();
805	<	useElectrostatic |= (*i)->isElectrostatic();
806	<	useEAM |= (*i)->isEAM();
698	<	useSC |= (*i)->isSC();
699	<	useCharge |= (*i)->isCharge();
700	<	useDirectional |= (*i)->isDirectional();
701	<	useDipole |= (*i)->isDipole();
702	<	useGayBerne |= (*i)->isGayBerne();
703	<	useSticky |= (*i)->isSticky();
704	<	useStickyPower |= (*i)->isStickyPower();
705	<	useShape |= (*i)->isShape();
804	>	usesElectrostatic |= (*i)->isElectrostatic();
805	>	usesMetallic |= (*i)->isMetal();
806	>	usesDirectional |= (*i)->isDirectional();
807		}
808
708	–	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
709	–	useDirectionalAtom = 1;
710	–	}
711	–
712	–	if (useCharge || useDipole) {
713	–	useElectrostatics = 1;
714	–	}
715	–
809		#ifdef IS_MPI
810		int temp;
811	+	temp = usesDirectional;
812	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813
814	<	temp = usePBC;
815	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814	>	temp = usesMetallic;
815	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816
817	<	temp = useDirectionalAtom;
818	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
724	<
725	<	temp = useLennardJones;
726	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
727	<
728	<	temp = useElectrostatics;
729	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
730	<
731	<	temp = useCharge;
732	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
733	<
734	<	temp = useDipole;
735	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
736	<
737	<	temp = useSticky;
738	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
739	<
740	<	temp = useStickyPower;
741	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
742	<
743	<	temp = useGayBerne;
744	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
745	<
746	<	temp = useEAM;
747	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
748	<
749	<	temp = useSC;
750	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
751	<
752	<	temp = useShape;
753	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
754	<
755	<	temp = useFLARB;
756	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
757	<
758	<	temp = useRF;
759	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
760	<
761	<	temp = useSF;
762	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
763	<
764	<	temp = useSP;
765	<	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766	<
767	<	temp = useBoxDipole;
768	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769	<
770	<	temp = useAtomicVirial_;
771	<	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
772	<
817	>	temp = usesElectrostatic;
818	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819		#endif
820	<
821	<	fInfo_.SIM_uses_PBC = usePBC;
822	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
823	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
824	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
825	<	fInfo_.SIM_uses_Charges = useCharge;
780	<	fInfo_.SIM_uses_Dipoles = useDipole;
781	<	fInfo_.SIM_uses_Sticky = useSticky;
782	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
783	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
784	<	fInfo_.SIM_uses_EAM = useEAM;
785	<	fInfo_.SIM_uses_SC = useSC;
786	<	fInfo_.SIM_uses_Shapes = useShape;
787	<	fInfo_.SIM_uses_FLARB = useFLARB;
788	<	fInfo_.SIM_uses_RF = useRF;
789	<	fInfo_.SIM_uses_SF = useSF;
790	<	fInfo_.SIM_uses_SP = useSP;
791	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
792	<	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
820	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
821	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
822	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
823	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
824	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
825	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
826		}
827
828		void SimInfo::setupFortranSim() {
829		int isError;
830	<	int nExclude;
831	<	std::vector<int> fortranGlobalGroupMembership;
830	>	int nExclude, nOneTwo, nOneThree, nOneFour;
831	>	vector<int> fortranGlobalGroupMembership;
832
833	<	nExclude = exclude_.getSize();
833	>	notifyFortranSkinThickness(&skinThickness_);
834	>
835	>	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
836	>	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
837	>	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
838	>
839		isError = 0;
840
841		//globalGroupMembership_ is filled by SimCreator
#	Line 806 | Line 844 | namespace oopse {
844		}
845
846		//calculate mass ratio of cutoff group
847	<	std::vector<RealType> mfact;
847	>	vector<RealType> mfact;
848		SimInfo::MoleculeIterator mi;
849		Molecule* mol;
850		Molecule::CutoffGroupIterator ci;
#	Line 829 | Line 867 | namespace oopse {
867		else
868		mfact.push_back( 1.0 );
869		}
832	–
870		}
871		}
872
873		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
874	<	std::vector<int> identArray;
874	>	vector<int> identArray;
875
876		//to avoid memory reallocation, reserve enough space identArray
877		identArray.reserve(getNAtoms());
#	Line 847 | Line 884 | namespace oopse {
884
885		//fill molMembershipArray
886		//molMembershipArray is filled by SimCreator
887	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
887	>	vector<int> molMembershipArray(nGlobalAtoms_);
888		for (int i = 0; i < nGlobalAtoms_; i++) {
889		molMembershipArray[i] = globalMolMembership_[i] + 1;
890		}
891
892		//setup fortran simulation
893	<	int nGlobalExcludes = 0;
894	<	int* globalExcludes = NULL;
895	<	int* excludeList = exclude_.getExcludeList();
893	>
894	>	nExclude = excludedInteractions_.getSize();
895	>	nOneTwo = oneTwoInteractions_.getSize();
896	>	nOneThree = oneThreeInteractions_.getSize();
897	>	nOneFour = oneFourInteractions_.getSize();
898	>
899	>	int* excludeList = excludedInteractions_.getPairList();
900	>	int* oneTwoList = oneTwoInteractions_.getPairList();
901	>	int* oneThreeList = oneThreeInteractions_.getPairList();
902	>	int* oneFourList = oneFourInteractions_.getPairList();
903	>
904		setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
905	<	&nExclude, excludeList , &nGlobalExcludes, globalExcludes,
905	>	&nExclude, excludeList,
906	>	&nOneTwo, oneTwoList,
907	>	&nOneThree, oneThreeList,
908	>	&nOneFour, oneFourList,
909		&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
910		&fortranGlobalGroupMembership[0], &isError);
911
#	Line 866 | Line 914 | namespace oopse {
914		sprintf( painCave.errMsg,
915		"There was an error setting the simulation information in fortran.\n" );
916		painCave.isFatal = 1;
917	<	painCave.severity = OOPSE_ERROR;
917	>	painCave.severity = OPENMD_ERROR;
918		simError();
919		}
920
#	Line 889 | Line 937 | namespace oopse {
937		void SimInfo::setupFortranParallel() {
938		#ifdef IS_MPI
939		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
940	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
941	<	std::vector<int> localToGlobalCutoffGroupIndex;
940	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
941	>	vector<int> localToGlobalCutoffGroupIndex;
942		SimInfo::MoleculeIterator mi;
943		Molecule::AtomIterator ai;
944		Molecule::CutoffGroupIterator ci;
#	Line 940 | Line 988 | namespace oopse {
988		errorCheckPoint();
989
990		#endif
943	–	}
944	–
945	–	void SimInfo::setupCutoff() {
946	–
947	–	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
948	–
949	–	// Check the cutoff policy
950	–	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
951	–
952	–	// Set LJ shifting bools to false
953	–	ljsp_ = false;
954	–	ljsf_ = false;
955	–
956	–	std::string myPolicy;
957	–	if (forceFieldOptions_.haveCutoffPolicy()){
958	–	myPolicy = forceFieldOptions_.getCutoffPolicy();
959	–	}else if (simParams_->haveCutoffPolicy()) {
960	–	myPolicy = simParams_->getCutoffPolicy();
961	–	}
962	–
963	–	if (!myPolicy.empty()){
964	–	toUpper(myPolicy);
965	–	if (myPolicy == "MIX") {
966	–	cp = MIX_CUTOFF_POLICY;
967	–	} else {
968	–	if (myPolicy == "MAX") {
969	–	cp = MAX_CUTOFF_POLICY;
970	–	} else {
971	–	if (myPolicy == "TRADITIONAL") {
972	–	cp = TRADITIONAL_CUTOFF_POLICY;
973	–	} else {
974	–	// throw error
975	–	sprintf( painCave.errMsg,
976	–	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
977	–	painCave.isFatal = 1;
978	–	simError();
979	–	}
980	–	}
981	–	}
982	–	}
983	–	notifyFortranCutoffPolicy(&cp);
984	–
985	–	// Check the Skin Thickness for neighborlists
986	–	RealType skin;
987	–	if (simParams_->haveSkinThickness()) {
988	–	skin = simParams_->getSkinThickness();
989	–	notifyFortranSkinThickness(&skin);
990	–	}
991	–
992	–	// Check if the cutoff was set explicitly:
993	–	if (simParams_->haveCutoffRadius()) {
994	–	rcut_ = simParams_->getCutoffRadius();
995	–	if (simParams_->haveSwitchingRadius()) {
996	–	rsw_  = simParams_->getSwitchingRadius();
997	–	} else {
998	–	if (fInfo_.SIM_uses_Charges |
999	–	fInfo_.SIM_uses_Dipoles |
1000	–	fInfo_.SIM_uses_RF) {
1001	–
1002	–	rsw_ = 0.85 * rcut_;
1003	–	sprintf(painCave.errMsg,
1004	–	"SimCreator Warning: No value was set for the switchingRadius.\n"
1005	–	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1006	–	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1007	–	painCave.isFatal = 0;
1008	–	simError();
1009	–	} else {
1010	–	rsw_ = rcut_;
1011	–	sprintf(painCave.errMsg,
1012	–	"SimCreator Warning: No value was set for the switchingRadius.\n"
1013	–	"\tOOPSE will use the same value as the cutoffRadius.\n"
1014	–	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1015	–	painCave.isFatal = 0;
1016	–	simError();
1017	–	}
1018	–	}
1019	–
1020	–	if (simParams_->haveElectrostaticSummationMethod()) {
1021	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1022	–	toUpper(myMethod);
1023	–
1024	–	if (myMethod == "SHIFTED_POTENTIAL") {
1025	–	ljsp_ = true;
1026	–	} else if (myMethod == "SHIFTED_FORCE") {
1027	–	ljsf_ = true;
1028	–	}
1029	–	}
1030	–	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1031	–
1032	–	} else {
1033	–
1034	–	// For electrostatic atoms, we'll assume a large safe value:
1035	–	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1036	–	sprintf(painCave.errMsg,
1037	–	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1038	–	"\tOOPSE will use a default value of 15.0 angstroms"
1039	–	"\tfor the cutoffRadius.\n");
1040	–	painCave.isFatal = 0;
1041	–	simError();
1042	–	rcut_ = 15.0;
1043	–
1044	–	if (simParams_->haveElectrostaticSummationMethod()) {
1045	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1046	–	toUpper(myMethod);
1047	–
1048	–	// For the time being, we're tethering the LJ shifted behavior to the
1049	–	// electrostaticSummationMethod keyword options
1050	–	if (myMethod == "SHIFTED_POTENTIAL") {
1051	–	ljsp_ = true;
1052	–	} else if (myMethod == "SHIFTED_FORCE") {
1053	–	ljsf_ = true;
1054	–	}
1055	–	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1056	–	if (simParams_->haveSwitchingRadius()){
1057	–	sprintf(painCave.errMsg,
1058	–	"SimInfo Warning: A value was set for the switchingRadius\n"
1059	–	"\teven though the electrostaticSummationMethod was\n"
1060	–	"\tset to %s\n", myMethod.c_str());
1061	–	painCave.isFatal = 1;
1062	–	simError();
1063	–	}
1064	–	}
1065	–	}
1066	–
1067	–	if (simParams_->haveSwitchingRadius()){
1068	–	rsw_ = simParams_->getSwitchingRadius();
1069	–	} else {
1070	–	sprintf(painCave.errMsg,
1071	–	"SimCreator Warning: No value was set for switchingRadius.\n"
1072	–	"\tOOPSE will use a default value of\n"
1073	–	"\t0.85 * cutoffRadius for the switchingRadius\n");
1074	–	painCave.isFatal = 0;
1075	–	simError();
1076	–	rsw_ = 0.85 * rcut_;
1077	–	}
1078	–
1079	–	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1080	–
1081	–	} else {
1082	–	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1083	–	// We'll punt and let fortran figure out the cutoffs later.
1084	–
1085	–	notifyFortranYouAreOnYourOwn();
1086	–
1087	–	}
1088	–	}
991		}
992
1091	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1092	–
1093	–	int errorOut;
1094	–	int esm =  NONE;
1095	–	int sm = UNDAMPED;
1096	–	RealType alphaVal;
1097	–	RealType dielectric;
1098	–
1099	–	errorOut = isError;
993
1101	–	if (simParams_->haveElectrostaticSummationMethod()) {
1102	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1103	–	toUpper(myMethod);
1104	–	if (myMethod == "NONE") {
1105	–	esm = NONE;
1106	–	} else {
1107	–	if (myMethod == "SWITCHING_FUNCTION") {
1108	–	esm = SWITCHING_FUNCTION;
1109	–	} else {
1110	–	if (myMethod == "SHIFTED_POTENTIAL") {
1111	–	esm = SHIFTED_POTENTIAL;
1112	–	} else {
1113	–	if (myMethod == "SHIFTED_FORCE") {
1114	–	esm = SHIFTED_FORCE;
1115	–	} else {
1116	–	if (myMethod == "REACTION_FIELD") {
1117	–	esm = REACTION_FIELD;
1118	–	dielectric = simParams_->getDielectric();
1119	–	if (!simParams_->haveDielectric()) {
1120	–	// throw warning
1121	–	sprintf( painCave.errMsg,
1122	–	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1123	–	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1124	–	painCave.isFatal = 0;
1125	–	simError();
1126	–	}
1127	–	} else {
1128	–	// throw error
1129	–	sprintf( painCave.errMsg,
1130	–	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1131	–	"\t(Input file specified %s .)\n"
1132	–	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1133	–	"\t\"shifted_potential\", \"shifted_force\", or \n"
1134	–	"\t\"reaction_field\".\n", myMethod.c_str() );
1135	–	painCave.isFatal = 1;
1136	–	simError();
1137	–	}
1138	–	}
1139	–	}
1140	–	}
1141	–	}
1142	–	}
1143	–
1144	–	if (simParams_->haveElectrostaticScreeningMethod()) {
1145	–	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1146	–	toUpper(myScreen);
1147	–	if (myScreen == "UNDAMPED") {
1148	–	sm = UNDAMPED;
1149	–	} else {
1150	–	if (myScreen == "DAMPED") {
1151	–	sm = DAMPED;
1152	–	if (!simParams_->haveDampingAlpha()) {
1153	–	// first set a cutoff dependent alpha value
1154	–	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1155	–	alphaVal = 0.5125 - rcut_* 0.025;
1156	–	// for values rcut > 20.5, alpha is zero
1157	–	if (alphaVal < 0) alphaVal = 0;
1158	–
1159	–	// throw warning
1160	–	sprintf( painCave.errMsg,
1161	–	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1162	–	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1163	–	painCave.isFatal = 0;
1164	–	simError();
1165	–	} else {
1166	–	alphaVal = simParams_->getDampingAlpha();
1167	–	}
1168	–
1169	–	} else {
1170	–	// throw error
1171	–	sprintf( painCave.errMsg,
1172	–	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1173	–	"\t(Input file specified %s .)\n"
1174	–	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1175	–	"or \"damped\".\n", myScreen.c_str() );
1176	–	painCave.isFatal = 1;
1177	–	simError();
1178	–	}
1179	–	}
1180	–	}
1181	–
1182	–	// let's pass some summation method variables to fortran
1183	–	setElectrostaticSummationMethod( &esm );
1184	–	setFortranElectrostaticMethod( &esm );
1185	–	setScreeningMethod( &sm );
1186	–	setDampingAlpha( &alphaVal );
1187	–	setReactionFieldDielectric( &dielectric );
1188	–	initFortranFF( &errorOut );
1189	–	}
1190	–
994		void SimInfo::setupSwitchingFunction() {
995		int ft = CUBIC;
996	<
996	>
997		if (simParams_->haveSwitchingFunctionType()) {
998	<	std::string funcType = simParams_->getSwitchingFunctionType();
998	>	string funcType = simParams_->getSwitchingFunctionType();
999		toUpper(funcType);
1000		if (funcType == "CUBIC") {
1001		ft = CUBIC;
#	Line 1219 | Line 1022 | namespace oopse {
1022		// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1023		if ( simParams_->haveAccumulateBoxDipole() )
1024		if ( simParams_->getAccumulateBoxDipole() ) {
1222	–	setAccumulateBoxDipole();
1025		calcBoxDipole_ = true;
1026		}
1027
#	Line 1229 | Line 1031 | namespace oopse {
1031		properties_.addProperty(genData);
1032		}
1033
1034	<	void SimInfo::removeProperty(const std::string& propName) {
1034	>	void SimInfo::removeProperty(const string& propName) {
1035		properties_.removeProperty(propName);
1036		}
1037
#	Line 1237 | Line 1039 | namespace oopse {
1039		properties_.clearProperties();
1040		}
1041
1042	<	std::vector<std::string> SimInfo::getPropertyNames() {
1042	>	vector<string> SimInfo::getPropertyNames() {
1043		return properties_.getPropertyNames();
1044		}
1045
1046	<	std::vector<GenericData*> SimInfo::getProperties() {
1046	>	vector<GenericData*> SimInfo::getProperties() {
1047		return properties_.getProperties();
1048		}
1049
1050	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1050	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1051		return properties_.getPropertyByName(propName);
1052		}
1053
#	Line 1328 | Line 1130 | namespace oopse {
1130
1131		}
1132
1133	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1133	>	ostream& operator <<(ostream& o, SimInfo& info) {
1134
1135		return o;
1136		}
#	Line 1371 | Line 1173 | namespace oopse {
1173
1174
1175		[  Ixx -Ixy  -Ixz ]
1176	<	J =| -Iyx  Iyy  -Iyz |
1176	>	J =| -Iyx  Iyy  -Iyz |
1177		[ -Izx -Iyz   Izz ]
1178		*/
1179
#	Line 1478 | Line 1280 | namespace oopse {
1280		return IOIndexToIntegrableObject.at(index);
1281		}
1282
1283	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1283	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1284		IOIndexToIntegrableObject= v;
1285		}
1286
#	Line 1520 | Line 1322 | namespace oopse {
1322		return;
1323		}
1324		/*
1325	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1325	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1326		assert( v.size() == nAtoms_ + nRigidBodies_);
1327		sdByGlobalIndex_ = v;
1328		}
#	Line 1530 | Line 1332 | namespace oopse {
1332		return sdByGlobalIndex_.at(index);
1333		}
1334		*/
1335	<	}//end namespace oopse
1335	>	int SimInfo::getNGlobalConstraints() {
1336	>	int nGlobalConstraints;
1337	>	#ifdef IS_MPI
1338	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1339	>	MPI_COMM_WORLD);
1340	>	#else
1341	>	nGlobalConstraints =  nConstraints_;
1342	>	#endif
1343	>	return nGlobalConstraints;
1344	>	}
1345
1346	+	}//end namespace OpenMD
1347	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1528 by gezelter, Fri Dec 17 20:11:05 2010 UTC

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