ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing:
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 1627 by gezelter, Tue Sep 13 22:05:04 2011 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"
61	–	#include "UseTheForce/doForces_interface.h"
62	–	#include "UseTheForce/DarkSide/neighborLists_interface.h"
63	–	#include "UseTheForce/DarkSide/electrostatic_interface.h"
64	–	#include "UseTheForce/DarkSide/switcheroo_interface.h"
57		#include "utils/MemoryUtils.hpp"
58		#include "utils/simError.h"
59		#include "selection/SelectionManager.hpp"
60		#include "io/ForceFieldOptions.hpp"
61		#include "UseTheForce/ForceField.hpp"
62	<
71	<
62	>	#include "nonbonded/SwitchingFunction.hpp"
63		#ifdef IS_MPI
64	<	#include "UseTheForce/mpiComponentPlan.h"
65	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
75	<	#endif
64	>	#include <mpi.h>
65	>	#endif
66
67	<	namespace oopse {
68	<	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	<	}
67	>	using namespace std;
68	>	namespace OpenMD {
69
70		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
71		forceField_(ff), simParams_(simParams),
#	Line 92 | Line 74 | namespace oopse {
74		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
75		nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
76		nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
77	<	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
78	<	calcBoxDipole_(false), useAtomicVirial_(true) {
79	<
80	<
81	<	MoleculeStamp* molStamp;
82	<	int nMolWithSameStamp;
83	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
85	<	CutoffGroupStamp* cgStamp;
86	<	RigidBodyStamp* rbStamp;
87	<	int nRigidAtoms = 0;
88	<
89	<	std::vector<Component*> components = simParams->getComponents();
77	>	nConstraints_(0), sman_(NULL), topologyDone_(false),
78	>	calcBoxDipole_(false), useAtomicVirial_(true) {
79	>
80	>	MoleculeStamp* molStamp;
81	>	int nMolWithSameStamp;
82	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
83	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
84	>	CutoffGroupStamp* cgStamp;
85	>	RigidBodyStamp* rbStamp;
86	>	int nRigidAtoms = 0;
87	>
88	>	vector<Component*> components = simParams->getComponents();
89	>
90	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
91	>	molStamp = (*i)->getMoleculeStamp();
92	>	nMolWithSameStamp = (*i)->getNMol();
93
94	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
95	<	molStamp = (*i)->getMoleculeStamp();
96	<	nMolWithSameStamp = (*i)->getNMol();
97	<
98	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
99	<
100	<	//calculate atoms in molecules
101	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
102	<
103	<	//calculate atoms in cutoff groups
104	<	int nAtomsInGroups = 0;
105	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
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	<
94	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
95	>
96	>	//calculate atoms in molecules
97	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
98	>
99	>	//calculate atoms in cutoff groups
100	>	int nAtomsInGroups = 0;
101	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
102	>
103	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
104	>	cgStamp = molStamp->getCutoffGroupStamp(j);
105	>	nAtomsInGroups += cgStamp->getNMembers();
106		}
107	<
108	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
109	<	//group therefore the total number of cutoff groups in the system is
110	<	//equal to the total number of atoms minus number of atoms belong to
111	<	//cutoff group defined in meta-data file plus the number of cutoff
112	<	//groups defined in meta-data file
113	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
114	<
115	<	//every free atom (atom does not belong to rigid bodies) is an
116	<	//integrable object therefore the total number of integrable objects
117	<	//in the system is equal to the total number of atoms minus number of
118	<	//atoms belong to rigid body defined in meta-data file plus the number
119	<	//of rigid bodies defined in meta-data file
120	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
121	<	+ nGlobalRigidBodies_;
122	<
123	<	nGlobalMols_ = molStampIds_.size();
161	<	molToProcMap_.resize(nGlobalMols_);
107	>
108	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
109	>
110	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
111	>
112	>	//calculate atoms in rigid bodies
113	>	int nAtomsInRigidBodies = 0;
114	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
115	>
116	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
117	>	rbStamp = molStamp->getRigidBodyStamp(j);
118	>	nAtomsInRigidBodies += rbStamp->getNMembers();
119	>	}
120	>
121	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
122	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
123	>
124		}
125	+
126	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
127	+	//group therefore the total number of cutoff groups in the system is
128	+	//equal to the total number of atoms minus number of atoms belong to
129	+	//cutoff group defined in meta-data file plus the number of cutoff
130	+	//groups defined in meta-data file
131
132	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
133	+
134	+	//every free atom (atom does not belong to rigid bodies) is an
135	+	//integrable object therefore the total number of integrable objects
136	+	//in the system is equal to the total number of atoms minus number of
137	+	//atoms belong to rigid body defined in meta-data file plus the number
138	+	//of rigid bodies defined in meta-data file
139	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
140	+	+ nGlobalRigidBodies_;
141	+
142	+	nGlobalMols_ = molStampIds_.size();
143	+	molToProcMap_.resize(nGlobalMols_);
144	+	}
145	+
146		SimInfo::~SimInfo() {
147	<	std::map<int, Molecule*>::iterator i;
147	>	map<int, Molecule*>::iterator i;
148		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
149		delete i->second;
150		}
#	Line 173 | Line 155 | namespace oopse {
155		delete forceField_;
156		}
157
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	–	}
158
159		bool SimInfo::addMolecule(Molecule* mol) {
160		MoleculeIterator i;
161	<
161	>
162		i = molecules_.find(mol->getGlobalIndex());
163		if (i == molecules_.end() ) {
164	<
165	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
166	<
164	>
165	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
166	>
167		nAtoms_ += mol->getNAtoms();
168		nBonds_ += mol->getNBonds();
169		nBends_ += mol->getNBends();
#	Line 201 | Line 173 | namespace oopse {
173		nIntegrableObjects_ += mol->getNIntegrableObjects();
174		nCutoffGroups_ += mol->getNCutoffGroups();
175		nConstraints_ += mol->getNConstraintPairs();
176	<
177	<	addExcludePairs(mol);
178	<
176	>
177	>	addInteractionPairs(mol);
178	>
179		return true;
180		} else {
181		return false;
182		}
183		}
184	<
184	>
185		bool SimInfo::removeMolecule(Molecule* mol) {
186		MoleculeIterator i;
187		i = molecules_.find(mol->getGlobalIndex());
#	Line 228 | Line 200 | namespace oopse {
200		nCutoffGroups_ -= mol->getNCutoffGroups();
201		nConstraints_ -= mol->getNConstraintPairs();
202
203	<	removeExcludePairs(mol);
203	>	removeInteractionPairs(mol);
204		molecules_.erase(mol->getGlobalIndex());
205
206		delete mol;
#	Line 237 | Line 209 | namespace oopse {
209		} else {
210		return false;
211		}
240	–
241	–
212		}
213
214
#	Line 256 | Line 226 | namespace oopse {
226		void SimInfo::calcNdf() {
227		int ndf_local;
228		MoleculeIterator i;
229	<	std::vector<StuntDouble*>::iterator j;
229	>	vector<StuntDouble*>::iterator j;
230		Molecule* mol;
231		StuntDouble* integrableObject;
232
#	Line 302 | Line 272 | namespace oopse {
272		#endif
273		return fdf_;
274		}
275	+
276	+	unsigned int SimInfo::getNLocalCutoffGroups(){
277	+	int nLocalCutoffAtoms = 0;
278	+	Molecule* mol;
279	+	MoleculeIterator mi;
280	+	CutoffGroup* cg;
281	+	Molecule::CutoffGroupIterator ci;
282
283	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
284	+
285	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
286	+	cg = mol->nextCutoffGroup(ci)) {
287	+	nLocalCutoffAtoms += cg->getNumAtom();
288	+
289	+	}
290	+	}
291	+
292	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
293	+	}
294	+
295		void SimInfo::calcNdfRaw() {
296		int ndfRaw_local;
297
298		MoleculeIterator i;
299	<	std::vector<StuntDouble*>::iterator j;
299	>	vector<StuntDouble*>::iterator j;
300		Molecule* mol;
301		StuntDouble* integrableObject;
302
#	Line 354 | Line 343 | namespace oopse {
343
344		}
345
346	<	void SimInfo::addExcludePairs(Molecule* mol) {
347	<	std::vector<Bond*>::iterator bondIter;
348	<	std::vector<Bend*>::iterator bendIter;
349	<	std::vector<Torsion*>::iterator torsionIter;
350	<	std::vector<Inversion*>::iterator inversionIter;
346	>	void SimInfo::addInteractionPairs(Molecule* mol) {
347	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
348	>	vector<Bond*>::iterator bondIter;
349	>	vector<Bend*>::iterator bendIter;
350	>	vector<Torsion*>::iterator torsionIter;
351	>	vector<Inversion*>::iterator inversionIter;
352		Bond* bond;
353		Bend* bend;
354		Torsion* torsion;
#	Line 368 | Line 358 | namespace oopse {
358		int c;
359		int d;
360
361	<	std::map<int, std::set<int> > atomGroups;
361	>	// atomGroups can be used to add special interaction maps between
362	>	// groups of atoms that are in two separate rigid bodies.
363	>	// However, most site-site interactions between two rigid bodies
364	>	// are probably not special, just the ones between the physically
365	>	// bonded atoms.  Interactions *within* a single rigid body should
366	>	// always be excluded.  These are done at the bottom of this
367	>	// function.
368
369	+	map<int, set<int> > atomGroups;
370		Molecule::RigidBodyIterator rbIter;
371		RigidBody* rb;
372		Molecule::IntegrableObjectIterator ii;
373		StuntDouble* integrableObject;
374
375	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
376	<	integrableObject = mol->nextIntegrableObject(ii)) {
377	<
375	>	for (integrableObject = mol->beginIntegrableObject(ii);
376	>	integrableObject != NULL;
377	>	integrableObject = mol->nextIntegrableObject(ii)) {
378	>
379		if (integrableObject->isRigidBody()) {
380	<	rb = static_cast<RigidBody*>(integrableObject);
381	<	std::vector<Atom*> atoms = rb->getAtoms();
382	<	std::set<int> rigidAtoms;
383	<	for (int i = 0; i < atoms.size(); ++i) {
384	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
385	<	}
386	<	for (int i = 0; i < atoms.size(); ++i) {
387	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
388	<	}
380	>	rb = static_cast<RigidBody*>(integrableObject);
381	>	vector<Atom*> atoms = rb->getAtoms();
382	>	set<int> rigidAtoms;
383	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
384	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
385	>	}
386	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
387	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
388	>	}
389		} else {
390	<	std::set<int> oneAtomSet;
390	>	set<int> oneAtomSet;
391		oneAtomSet.insert(integrableObject->getGlobalIndex());
392	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
392	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
393		}
394		}
395	+
396	+	for (bond= mol->beginBond(bondIter); bond != NULL;
397	+	bond = mol->nextBond(bondIter)) {
398
398	–
399	–
400	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
399		a = bond->getAtomA()->getGlobalIndex();
400	<	b = bond->getAtomB()->getGlobalIndex();
401	<	exclude_.addPair(a, b);
400	>	b = bond->getAtomB()->getGlobalIndex();
401	>
402	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
403	>	oneTwoInteractions_.addPair(a, b);
404	>	} else {
405	>	excludedInteractions_.addPair(a, b);
406	>	}
407		}
408
409	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
409	>	for (bend= mol->beginBend(bendIter); bend != NULL;
410	>	bend = mol->nextBend(bendIter)) {
411	>
412		a = bend->getAtomA()->getGlobalIndex();
413		b = bend->getAtomB()->getGlobalIndex();
414		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);
415
416	<	//exclude_.addPair(a, b);
417	<	//exclude_.addPair(a, c);
418	<	//exclude_.addPair(b, c);
416	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
417	>	oneTwoInteractions_.addPair(a, b);
418	>	oneTwoInteractions_.addPair(b, c);
419	>	} else {
420	>	excludedInteractions_.addPair(a, b);
421	>	excludedInteractions_.addPair(b, c);
422	>	}
423	>
424	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
425	>	oneThreeInteractions_.addPair(a, c);
426	>	} else {
427	>	excludedInteractions_.addPair(a, c);
428	>	}
429		}
430
431	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
431	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
432	>	torsion = mol->nextTorsion(torsionIter)) {
433	>
434		a = torsion->getAtomA()->getGlobalIndex();
435		b = torsion->getAtomB()->getGlobalIndex();
436		c = torsion->getAtomC()->getGlobalIndex();
437	<	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);
437	>	d = torsion->getAtomD()->getGlobalIndex();
438
439	<	exclude_.addPairs(rigidSetA, rigidSetB);
440	<	exclude_.addPairs(rigidSetA, rigidSetC);
441	<	exclude_.addPairs(rigidSetA, rigidSetD);
442	<	exclude_.addPairs(rigidSetB, rigidSetC);
443	<	exclude_.addPairs(rigidSetB, rigidSetD);
444	<	exclude_.addPairs(rigidSetC, rigidSetD);
439	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
440	>	oneTwoInteractions_.addPair(a, b);
441	>	oneTwoInteractions_.addPair(b, c);
442	>	oneTwoInteractions_.addPair(c, d);
443	>	} else {
444	>	excludedInteractions_.addPair(a, b);
445	>	excludedInteractions_.addPair(b, c);
446	>	excludedInteractions_.addPair(c, d);
447	>	}
448
449	<	/*
450	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
451	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
452	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
453	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
454	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
455	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
456	<
457	<
458	<	exclude_.addPair(a, b);
459	<	exclude_.addPair(a, c);
460	<	exclude_.addPair(a, d);
461	<	exclude_.addPair(b, c);
453	<	exclude_.addPair(b, d);
454	<	exclude_.addPair(c, d);
455	<	*/
449	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
450	>	oneThreeInteractions_.addPair(a, c);
451	>	oneThreeInteractions_.addPair(b, d);
452	>	} else {
453	>	excludedInteractions_.addPair(a, c);
454	>	excludedInteractions_.addPair(b, d);
455	>	}
456	>
457	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
458	>	oneFourInteractions_.addPair(a, d);
459	>	} else {
460	>	excludedInteractions_.addPair(a, d);
461	>	}
462		}
463
464		for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
465		inversion = mol->nextInversion(inversionIter)) {
466	+
467		a = inversion->getAtomA()->getGlobalIndex();
468		b = inversion->getAtomB()->getGlobalIndex();
469		c = inversion->getAtomC()->getGlobalIndex();
470		d = inversion->getAtomD()->getGlobalIndex();
471	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
472	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
473	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
474	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
471	>
472	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
473	>	oneTwoInteractions_.addPair(a, b);
474	>	oneTwoInteractions_.addPair(a, c);
475	>	oneTwoInteractions_.addPair(a, d);
476	>	} else {
477	>	excludedInteractions_.addPair(a, b);
478	>	excludedInteractions_.addPair(a, c);
479	>	excludedInteractions_.addPair(a, d);
480	>	}
481
482	<	exclude_.addPairs(rigidSetA, rigidSetB);
483	<	exclude_.addPairs(rigidSetA, rigidSetC);
484	<	exclude_.addPairs(rigidSetA, rigidSetD);
485	<	exclude_.addPairs(rigidSetB, rigidSetC);
486	<	exclude_.addPairs(rigidSetB, rigidSetD);
487	<	exclude_.addPairs(rigidSetC, rigidSetD);
488	<
489	<	/*
490	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
478	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
479	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
480	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
481	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
482	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
483	<
484	<
485	<	exclude_.addPair(a, b);
486	<	exclude_.addPair(a, c);
487	<	exclude_.addPair(a, d);
488	<	exclude_.addPair(b, c);
489	<	exclude_.addPair(b, d);
490	<	exclude_.addPair(c, d);
491	<	*/
482	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
483	>	oneThreeInteractions_.addPair(b, c);
484	>	oneThreeInteractions_.addPair(b, d);
485	>	oneThreeInteractions_.addPair(c, d);
486	>	} else {
487	>	excludedInteractions_.addPair(b, c);
488	>	excludedInteractions_.addPair(b, d);
489	>	excludedInteractions_.addPair(c, d);
490	>	}
491		}
492
493	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
494	<	std::vector<Atom*> atoms = rb->getAtoms();
495	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
496	<	for (int j = i + 1; j < atoms.size(); ++j) {
493	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
494	>	rb = mol->nextRigidBody(rbIter)) {
495	>	vector<Atom*> atoms = rb->getAtoms();
496	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
497	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
498		a = atoms[i]->getGlobalIndex();
499		b = atoms[j]->getGlobalIndex();
500	<	exclude_.addPair(a, b);
500	>	excludedInteractions_.addPair(a, b);
501		}
502		}
503		}
504
505		}
506
507	<	void SimInfo::removeExcludePairs(Molecule* mol) {
508	<	std::vector<Bond*>::iterator bondIter;
509	<	std::vector<Bend*>::iterator bendIter;
510	<	std::vector<Torsion*>::iterator torsionIter;
511	<	std::vector<Inversion*>::iterator inversionIter;
507	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
508	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
509	>	vector<Bond*>::iterator bondIter;
510	>	vector<Bend*>::iterator bendIter;
511	>	vector<Torsion*>::iterator torsionIter;
512	>	vector<Inversion*>::iterator inversionIter;
513		Bond* bond;
514		Bend* bend;
515		Torsion* torsion;
#	Line 518 | Line 519 | namespace oopse {
519		int c;
520		int d;
521
522	<	std::map<int, std::set<int> > atomGroups;
522	<
522	>	map<int, set<int> > atomGroups;
523		Molecule::RigidBodyIterator rbIter;
524		RigidBody* rb;
525		Molecule::IntegrableObjectIterator ii;
526		StuntDouble* integrableObject;
527
528	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
529	<	integrableObject = mol->nextIntegrableObject(ii)) {
530	<
528	>	for (integrableObject = mol->beginIntegrableObject(ii);
529	>	integrableObject != NULL;
530	>	integrableObject = mol->nextIntegrableObject(ii)) {
531	>
532		if (integrableObject->isRigidBody()) {
533	<	rb = static_cast<RigidBody*>(integrableObject);
534	<	std::vector<Atom*> atoms = rb->getAtoms();
535	<	std::set<int> rigidAtoms;
536	<	for (int i = 0; i < atoms.size(); ++i) {
537	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
538	<	}
539	<	for (int i = 0; i < atoms.size(); ++i) {
540	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
541	<	}
533	>	rb = static_cast<RigidBody*>(integrableObject);
534	>	vector<Atom*> atoms = rb->getAtoms();
535	>	set<int> rigidAtoms;
536	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
537	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
538	>	}
539	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
540	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
541	>	}
542		} else {
543	<	std::set<int> oneAtomSet;
543	>	set<int> oneAtomSet;
544		oneAtomSet.insert(integrableObject->getGlobalIndex());
545	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
545	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
546		}
547		}
548
549	<
550	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
549	>	for (bond= mol->beginBond(bondIter); bond != NULL;
550	>	bond = mol->nextBond(bondIter)) {
551	>
552		a = bond->getAtomA()->getGlobalIndex();
553	<	b = bond->getAtomB()->getGlobalIndex();
554	<	exclude_.removePair(a, b);
553	>	b = bond->getAtomB()->getGlobalIndex();
554	>
555	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
556	>	oneTwoInteractions_.removePair(a, b);
557	>	} else {
558	>	excludedInteractions_.removePair(a, b);
559	>	}
560		}
561
562	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
562	>	for (bend= mol->beginBend(bendIter); bend != NULL;
563	>	bend = mol->nextBend(bendIter)) {
564	>
565		a = bend->getAtomA()->getGlobalIndex();
566		b = bend->getAtomB()->getGlobalIndex();
567		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);
568
569	<	//exclude_.removePair(a, b);
570	<	//exclude_.removePair(a, c);
571	<	//exclude_.removePair(b, c);
569	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
570	>	oneTwoInteractions_.removePair(a, b);
571	>	oneTwoInteractions_.removePair(b, c);
572	>	} else {
573	>	excludedInteractions_.removePair(a, b);
574	>	excludedInteractions_.removePair(b, c);
575	>	}
576	>
577	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
578	>	oneThreeInteractions_.removePair(a, c);
579	>	} else {
580	>	excludedInteractions_.removePair(a, c);
581	>	}
582		}
583
584	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
584	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
585	>	torsion = mol->nextTorsion(torsionIter)) {
586	>
587		a = torsion->getAtomA()->getGlobalIndex();
588		b = torsion->getAtomB()->getGlobalIndex();
589		c = torsion->getAtomC()->getGlobalIndex();
590	<	d = torsion->getAtomD()->getGlobalIndex();
590	>	d = torsion->getAtomD()->getGlobalIndex();
591	>
592	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
593	>	oneTwoInteractions_.removePair(a, b);
594	>	oneTwoInteractions_.removePair(b, c);
595	>	oneTwoInteractions_.removePair(c, d);
596	>	} else {
597	>	excludedInteractions_.removePair(a, b);
598	>	excludedInteractions_.removePair(b, c);
599	>	excludedInteractions_.removePair(c, d);
600	>	}
601
602	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
603	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
604	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
605	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
602	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
603	>	oneThreeInteractions_.removePair(a, c);
604	>	oneThreeInteractions_.removePair(b, d);
605	>	} else {
606	>	excludedInteractions_.removePair(a, c);
607	>	excludedInteractions_.removePair(b, d);
608	>	}
609
610	<	exclude_.removePairs(rigidSetA, rigidSetB);
611	<	exclude_.removePairs(rigidSetA, rigidSetC);
612	<	exclude_.removePairs(rigidSetA, rigidSetD);
613	<	exclude_.removePairs(rigidSetB, rigidSetC);
614	<	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	<	*/
610	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
611	>	oneFourInteractions_.removePair(a, d);
612	>	} else {
613	>	excludedInteractions_.removePair(a, d);
614	>	}
615		}
616
617	<	for (inversion= mol->beginInversion(inversionIter); inversion != NULL; inversion = mol->nextInversion(inversionIter)) {
617	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
618	>	inversion = mol->nextInversion(inversionIter)) {
619	>
620		a = inversion->getAtomA()->getGlobalIndex();
621		b = inversion->getAtomB()->getGlobalIndex();
622		c = inversion->getAtomC()->getGlobalIndex();
623		d = inversion->getAtomD()->getGlobalIndex();
624
625	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
626	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
627	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
628	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
625	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
626	>	oneTwoInteractions_.removePair(a, b);
627	>	oneTwoInteractions_.removePair(a, c);
628	>	oneTwoInteractions_.removePair(a, d);
629	>	} else {
630	>	excludedInteractions_.removePair(a, b);
631	>	excludedInteractions_.removePair(a, c);
632	>	excludedInteractions_.removePair(a, d);
633	>	}
634
635	<	exclude_.removePairs(rigidSetA, rigidSetB);
636	<	exclude_.removePairs(rigidSetA, rigidSetC);
637	<	exclude_.removePairs(rigidSetA, rigidSetD);
638	<	exclude_.removePairs(rigidSetB, rigidSetC);
639	<	exclude_.removePairs(rigidSetB, rigidSetD);
640	<	exclude_.removePairs(rigidSetC, rigidSetD);
641	<
642	<	/*
643	<	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	<	*/
635	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
636	>	oneThreeInteractions_.removePair(b, c);
637	>	oneThreeInteractions_.removePair(b, d);
638	>	oneThreeInteractions_.removePair(c, d);
639	>	} else {
640	>	excludedInteractions_.removePair(b, c);
641	>	excludedInteractions_.removePair(b, d);
642	>	excludedInteractions_.removePair(c, d);
643	>	}
644		}
645
646	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
647	<	std::vector<Atom*> atoms = rb->getAtoms();
648	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
649	<	for (int j = i + 1; j < atoms.size(); ++j) {
646	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
647	>	rb = mol->nextRigidBody(rbIter)) {
648	>	vector<Atom*> atoms = rb->getAtoms();
649	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
650	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
651		a = atoms[i]->getGlobalIndex();
652		b = atoms[j]->getGlobalIndex();
653	<	exclude_.removePair(a, b);
653	>	excludedInteractions_.removePair(a, b);
654		}
655		}
656		}
657	<
657	>
658		}
659	<
660	<
659	>
660	>
661		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
662		int curStampId;
663	<
663	>
664		//index from 0
665		curStampId = moleculeStamps_.size();
666
#	Line 666 | Line 668 | namespace oopse {
668		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
669		}
670
669	–	void SimInfo::update() {
671
672	<	setupSimType();
673	<
674	<	#ifdef IS_MPI
675	<	setupFortranParallel();
676	<	#endif
677	<
678	<	setupFortranSim();
679	<
680	<	//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	<
672	>	/**
673	>	* update
674	>	*
675	>	*  Performs the global checks and variable settings after the
676	>	*  objects have been created.
677	>	*
678	>	*/
679	>	void SimInfo::update() {
680	>	setupSimVariables();
681		calcNdf();
682		calcNdfRaw();
683		calcNdfTrans();
699	–
700	–	fortranInitialized_ = true;
684		}
685	<
686	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
685	>
686	>	/**
687	>	* getSimulatedAtomTypes
688	>	*
689	>	* Returns an STL set of AtomType* that are actually present in this
690	>	* simulation.  Must query all processors to assemble this information.
691	>	*
692	>	*/
693	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
694		SimInfo::MoleculeIterator mi;
695		Molecule* mol;
696		Molecule::AtomIterator ai;
697		Atom* atom;
698	<	std::set<AtomType*> atomTypes;
699	<
698	>	set<AtomType*> atomTypes;
699	>
700		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
701	<
702	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
701	>	for(atom = mol->beginAtom(ai); atom != NULL;
702	>	atom = mol->nextAtom(ai)) {
703		atomTypes.insert(atom->getAtomType());
704	<	}
705	<
706	<	}
704	>	}
705	>	}
706	>
707	>	#ifdef IS_MPI
708
709	<	return atomTypes;
710	<	}
720	<
721	<	void SimInfo::setupSimType() {
722	<	std::set<AtomType*>::iterator i;
723	<	std::set<AtomType*> atomTypes;
724	<	atomTypes = getUniqueAtomTypes();
709	>	// loop over the found atom types on this processor, and add their
710	>	// numerical idents to a vector:
711
712	<	int useLennardJones = 0;
713	<	int useElectrostatic = 0;
714	<	int useEAM = 0;
715	<	int useSC = 0;
730	<	int useCharge = 0;
731	<	int useDirectional = 0;
732	<	int useDipole = 0;
733	<	int useGayBerne = 0;
734	<	int useSticky = 0;
735	<	int useStickyPower = 0;
736	<	int useShape = 0;
737	<	int useFLARB = 0; //it is not in AtomType yet
738	<	int useDirectionalAtom = 0;
739	<	int useElectrostatics = 0;
740	<	//usePBC and useRF are from simParams
741	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
742	<	int useRF;
743	<	int useSF;
744	<	int useSP;
745	<	int useBoxDipole;
712	>	vector<int> foundTypes;
713	>	set<AtomType*>::iterator i;
714	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
715	>	foundTypes.push_back( (*i)->getIdent() );
716
717	<	std::string myMethod;
717	>	// count_local holds the number of found types on this processor
718	>	int count_local = foundTypes.size();
719
720	<	// set the useRF logical
750	<	useRF = 0;
751	<	useSF = 0;
752	<	useSP = 0;
720	>	int nproc = MPI::COMM_WORLD.Get_size();
721
722	+	// we need arrays to hold the counts and displacement vectors for
723	+	// all processors
724	+	vector<int> counts(nproc, 0);
725	+	vector<int> disps(nproc, 0);
726
727	<	if (simParams_->haveElectrostaticSummationMethod()) {
728	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
729	<	toUpper(myMethod);
730	<	if (myMethod == "REACTION_FIELD"){
731	<	useRF = 1;
732	<	} else if (myMethod == "SHIFTED_FORCE"){
733	<	useSF = 1;
734	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
735	<	useSP = 1;
736	<	}
727	>	// fill the counts array
728	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
729	>	1, MPI::INT);
730	>
731	>	// use the processor counts to compute the displacement array
732	>	disps[0] = 0;
733	>	int totalCount = counts[0];
734	>	for (int iproc = 1; iproc < nproc; iproc++) {
735	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
736	>	totalCount += counts[iproc];
737		}
738	+
739	+	// we need a (possibly redundant) set of all found types:
740	+	vector<int> ftGlobal(totalCount);
741
742	<	if (simParams_->haveAccumulateBoxDipole())
743	<	if (simParams_->getAccumulateBoxDipole())
744	<	useBoxDipole = 1;
742	>	// now spray out the foundTypes to all the other processors:
743	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
744	>	&ftGlobal[0], &counts[0], &disps[0],
745	>	MPI::INT);
746
747	<	useAtomicVirial_ = simParams_->getUseAtomicVirial();
747	>	vector<int>::iterator j;
748
749	<	//loop over all of the atom types
750	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
751	<	useLennardJones |= (*i)->isLennardJones();
776	<	useElectrostatic |= (*i)->isElectrostatic();
777	<	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();
786	<	}
749	>	// foundIdents is a stl set, so inserting an already found ident
750	>	// will have no effect.
751	>	set<int> foundIdents;
752
753	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
754	<	useDirectionalAtom = 1;
755	<	}
753	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
754	>	foundIdents.insert((*j));
755	>
756	>	// now iterate over the foundIdents and get the actual atom types
757	>	// that correspond to these:
758	>	set<int>::iterator it;
759	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
760	>	atomTypes.insert( forceField_->getAtomType((*it)) );
761	>
762	>	#endif
763
764	<	if (useCharge || useDipole) {
765	<	useElectrostatics = 1;
794	<	}
764	>	return atomTypes;
765	>	}
766
767	+	void SimInfo::setupSimVariables() {
768	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
769	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
770	+	calcBoxDipole_ = false;
771	+	if ( simParams_->haveAccumulateBoxDipole() )
772	+	if ( simParams_->getAccumulateBoxDipole() ) {
773	+	calcBoxDipole_ = true;
774	+	}
775	+
776	+	set<AtomType*>::iterator i;
777	+	set<AtomType*> atomTypes;
778	+	atomTypes = getSimulatedAtomTypes();
779	+	int usesElectrostatic = 0;
780	+	int usesMetallic = 0;
781	+	int usesDirectional = 0;
782	+	//loop over all of the atom types
783	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
784	+	usesElectrostatic |= (*i)->isElectrostatic();
785	+	usesMetallic |= (*i)->isMetal();
786	+	usesDirectional |= (*i)->isDirectional();
787	+	}
788	+
789		#ifdef IS_MPI
790		int temp;
791	<
792	<	temp = usePBC;
800	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
801	<
802	<	temp = useDirectionalAtom;
803	<	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);
791	>	temp = usesDirectional;
792	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
793
794	<	temp = useGayBerne;
795	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
794	>	temp = usesMetallic;
795	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
796	>
797	>	temp = usesElectrostatic;
798	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
799	>	#else
800
801	<	temp = useEAM;
802	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
801	>	usesDirectionalAtoms_ = usesDirectional;
802	>	usesMetallicAtoms_ = usesMetallic;
803	>	usesElectrostaticAtoms_ = usesElectrostatic;
804
805	<	temp = useSC;
830	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
805	>	#endif
806
807	<	temp = useShape;
808	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
807	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
808	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
809	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
810	>	}
811
835	–	temp = useFLARB;
836	–	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
812
813	<	temp = useRF;
814	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813	>	vector<int> SimInfo::getGlobalAtomIndices() {
814	>	SimInfo::MoleculeIterator mi;
815	>	Molecule* mol;
816	>	Molecule::AtomIterator ai;
817	>	Atom* atom;
818
819	<	temp = useSF;
820	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
820	>
821	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
822	>
823	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
824	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
825	>	}
826	>	}
827	>	return GlobalAtomIndices;
828	>	}
829
844	–	temp = useSP;
845	–	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
830
831	<	temp = useBoxDipole;
832	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
831	>	vector<int> SimInfo::getGlobalGroupIndices() {
832	>	SimInfo::MoleculeIterator mi;
833	>	Molecule* mol;
834	>	Molecule::CutoffGroupIterator ci;
835	>	CutoffGroup* cg;
836
837	<	temp = useAtomicVirial_;
838	<	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
839	<
840	<	#endif
841	<
842	<	fInfo_.SIM_uses_PBC = usePBC;
843	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
844	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
845	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
846	<	fInfo_.SIM_uses_Charges = useCharge;
847	<	fInfo_.SIM_uses_Dipoles = useDipole;
848	<	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_;
837	>	vector<int> GlobalGroupIndices;
838	>
839	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
840	>
841	>	//local index of cutoff group is trivial, it only depends on the
842	>	//order of travesing
843	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
844	>	cg = mol->nextCutoffGroup(ci)) {
845	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
846	>	}
847	>	}
848	>	return GlobalGroupIndices;
849		}
850
875	–	void SimInfo::setupFortranSim() {
876	–	int isError;
877	–	int nExclude;
878	–	std::vector<int> fortranGlobalGroupMembership;
879	–
880	–	nExclude = exclude_.getSize();
881	–	isError = 0;
851
852	<	//globalGroupMembership_ is filled by SimCreator
853	<	for (int i = 0; i < nGlobalAtoms_; i++) {
885	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
886	<	}
852	>	void SimInfo::prepareTopology() {
853	>	int nExclude, nOneTwo, nOneThree, nOneFour;
854
855		//calculate mass ratio of cutoff group
889	–	std::vector<RealType> mfact;
856		SimInfo::MoleculeIterator mi;
857		Molecule* mol;
858		Molecule::CutoffGroupIterator ci;
#	Line 895 | Line 861 | namespace oopse {
861		Atom* atom;
862		RealType totalMass;
863
864	<	//to avoid memory reallocation, reserve enough space for mfact
865	<	mfact.reserve(getNCutoffGroups());
864	>	/**
865	>	* The mass factor is the relative mass of an atom to the total
866	>	* mass of the cutoff group it belongs to.  By default, all atoms
867	>	* are their own cutoff groups, and therefore have mass factors of
868	>	* 1.  We need some special handling for massless atoms, which
869	>	* will be treated as carrying the entire mass of the cutoff
870	>	* group.
871	>	*/
872	>	massFactors_.clear();
873	>	massFactors_.resize(getNAtoms(), 1.0);
874
875		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
876	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
876	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
877	>	cg = mol->nextCutoffGroup(ci)) {
878
879		totalMass = cg->getMass();
880		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
881		// Check for massless groups - set mfact to 1 if true
882	<	if (totalMass != 0)
883	<	mfact.push_back(atom->getMass()/totalMass);
882	>	if (totalMass != 0)
883	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
884		else
885	<	mfact.push_back( 1.0 );
885	>	massFactors_[atom->getLocalIndex()] = 1.0;
886		}
912	–
887		}
888		}
889
890	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
917	<	std::vector<int> identArray;
890	>	// Build the identArray_
891
892	<	//to avoid memory reallocation, reserve enough space identArray
893	<	identArray.reserve(getNAtoms());
921	<
892	>	identArray_.clear();
893	>	identArray_.reserve(getNAtoms());
894		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
895		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
896	<	identArray.push_back(atom->getIdent());
896	>	identArray_.push_back(atom->getIdent());
897		}
898		}
927	–
928	–	//fill molMembershipArray
929	–	//molMembershipArray is filled by SimCreator
930	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
931	–	for (int i = 0; i < nGlobalAtoms_; i++) {
932	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
933	–	}
899
900	<	//setup fortran simulation
936	<	int nGlobalExcludes = 0;
937	<	int* globalExcludes = NULL;
938	<	int* excludeList = exclude_.getExcludeList();
939	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
940	<	&nExclude, excludeList , &nGlobalExcludes, globalExcludes,
941	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
942	<	&fortranGlobalGroupMembership[0], &isError);
943	<
944	<	if( isError ){
945	<
946	<	sprintf( painCave.errMsg,
947	<	"There was an error setting the simulation information in fortran.\n" );
948	<	painCave.isFatal = 1;
949	<	painCave.severity = OOPSE_ERROR;
950	<	simError();
951	<	}
952	<
953	<
954	<	sprintf( checkPointMsg,
955	<	"succesfully sent the simulation information to fortran.\n");
956	<
957	<	errorCheckPoint();
958	<
959	<	// Setup number of neighbors in neighbor list if present
960	<	if (simParams_->haveNeighborListNeighbors()) {
961	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
962	<	setNeighbors(&nlistNeighbors);
963	<	}
964	<
900	>	//scan topology
901
902	<	}
902	>	nExclude = excludedInteractions_.getSize();
903	>	nOneTwo = oneTwoInteractions_.getSize();
904	>	nOneThree = oneThreeInteractions_.getSize();
905	>	nOneFour = oneFourInteractions_.getSize();
906
907	+	int* excludeList = excludedInteractions_.getPairList();
908	+	int* oneTwoList = oneTwoInteractions_.getPairList();
909	+	int* oneThreeList = oneThreeInteractions_.getPairList();
910	+	int* oneFourList = oneFourInteractions_.getPairList();
911
912	<	void SimInfo::setupFortranParallel() {
970	<	#ifdef IS_MPI
971	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
972	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
973	<	std::vector<int> localToGlobalCutoffGroupIndex;
974	<	SimInfo::MoleculeIterator mi;
975	<	Molecule::AtomIterator ai;
976	<	Molecule::CutoffGroupIterator ci;
977	<	Molecule* mol;
978	<	Atom* atom;
979	<	CutoffGroup* cg;
980	<	mpiSimData parallelData;
981	<	int isError;
982	<
983	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
984	<
985	<	//local index(index in DataStorge) of atom is important
986	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
987	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
988	<	}
989	<
990	<	//local index of cutoff group is trivial, it only depends on the order of travesing
991	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
992	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
993	<	}
994	<
995	<	}
996	<
997	<	//fill up mpiSimData struct
998	<	parallelData.nMolGlobal = getNGlobalMolecules();
999	<	parallelData.nMolLocal = getNMolecules();
1000	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
1001	<	parallelData.nAtomsLocal = getNAtoms();
1002	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1003	<	parallelData.nGroupsLocal = getNCutoffGroups();
1004	<	parallelData.myNode = worldRank;
1005	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1006	<
1007	<	//pass mpiSimData struct and index arrays to fortran
1008	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1009	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1010	<	&localToGlobalCutoffGroupIndex[0], &isError);
1011	<
1012	<	if (isError) {
1013	<	sprintf(painCave.errMsg,
1014	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1015	<	painCave.isFatal = 1;
1016	<	simError();
1017	<	}
1018	<
1019	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
1020	<	errorCheckPoint();
1021	<
1022	<	#endif
1023	<	}
1024	<
1025	<	void SimInfo::setupCutoff() {
1026	<
1027	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1028	<
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 );
912	>	topologyDone_ = true;
913		}
914
1271	–	void SimInfo::setupSwitchingFunction() {
1272	–	int ft = CUBIC;
1273	–
1274	–	if (simParams_->haveSwitchingFunctionType()) {
1275	–	std::string funcType = simParams_->getSwitchingFunctionType();
1276	–	toUpper(funcType);
1277	–	if (funcType == "CUBIC") {
1278	–	ft = CUBIC;
1279	–	} else {
1280	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1281	–	ft = FIFTH_ORDER_POLY;
1282	–	} else {
1283	–	// throw error
1284	–	sprintf( painCave.errMsg,
1285	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1286	–	painCave.isFatal = 1;
1287	–	simError();
1288	–	}
1289	–	}
1290	–	}
1291	–
1292	–	// send switching function notification to switcheroo
1293	–	setFunctionType(&ft);
1294	–
1295	–	}
1296	–
1297	–	void SimInfo::setupAccumulateBoxDipole() {
1298	–
1299	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1300	–	if ( simParams_->haveAccumulateBoxDipole() )
1301	–	if ( simParams_->getAccumulateBoxDipole() ) {
1302	–	setAccumulateBoxDipole();
1303	–	calcBoxDipole_ = true;
1304	–	}
1305	–
1306	–	}
1307	–
915		void SimInfo::addProperty(GenericData* genData) {
916		properties_.addProperty(genData);
917		}
918
919	<	void SimInfo::removeProperty(const std::string& propName) {
919	>	void SimInfo::removeProperty(const string& propName) {
920		properties_.removeProperty(propName);
921		}
922
#	Line 1317 | Line 924 | namespace oopse {
924		properties_.clearProperties();
925		}
926
927	<	std::vector<std::string> SimInfo::getPropertyNames() {
927	>	vector<string> SimInfo::getPropertyNames() {
928		return properties_.getPropertyNames();
929		}
930
931	<	std::vector<GenericData*> SimInfo::getProperties() {
931	>	vector<GenericData*> SimInfo::getProperties() {
932		return properties_.getProperties();
933		}
934
935	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
935	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
936		return properties_.getPropertyByName(propName);
937		}
938
#	Line 1339 | Line 946 | namespace oopse {
946		Molecule* mol;
947		RigidBody* rb;
948		Atom* atom;
949	+	CutoffGroup* cg;
950		SimInfo::MoleculeIterator mi;
951		Molecule::RigidBodyIterator rbIter;
952	<	Molecule::AtomIterator atomIter;;
952	>	Molecule::AtomIterator atomIter;
953	>	Molecule::CutoffGroupIterator cgIter;
954
955		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
956
#	Line 1351 | Line 960 | namespace oopse {
960
961		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
962		rb->setSnapshotManager(sman_);
963	+	}
964	+
965	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
966	+	cg->setSnapshotManager(sman_);
967		}
968		}
969
#	Line 1408 | Line 1021 | namespace oopse {
1021
1022		}
1023
1024	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1024	>	ostream& operator <<(ostream& o, SimInfo& info) {
1025
1026		return o;
1027		}
#	Line 1451 | Line 1064 | namespace oopse {
1064
1065
1066		[  Ixx -Ixy  -Ixz ]
1067	<	J =| -Iyx  Iyy  -Iyz |
1067	>	J =| -Iyx  Iyy  -Iyz |
1068		[ -Izx -Iyz   Izz ]
1069		*/
1070
#	Line 1558 | Line 1171 | namespace oopse {
1171		return IOIndexToIntegrableObject.at(index);
1172		}
1173
1174	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1174	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1175		IOIndexToIntegrableObject= v;
1176		}
1177
#	Line 1600 | Line 1213 | namespace oopse {
1213		return;
1214		}
1215		/*
1216	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1216	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1217		assert( v.size() == nAtoms_ + nRigidBodies_);
1218		sdByGlobalIndex_ = v;
1219		}
#	Line 1610 | Line 1223 | namespace oopse {
1223		return sdByGlobalIndex_.at(index);
1224		}
1225		*/
1226	<	}//end namespace oopse
1226	>	int SimInfo::getNGlobalConstraints() {
1227	>	int nGlobalConstraints;
1228	>	#ifdef IS_MPI
1229	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1230	>	MPI_COMM_WORLD);
1231	>	#else
1232	>	nGlobalConstraints =  nConstraints_;
1233	>	#endif
1234	>	return nGlobalConstraints;
1235	>	}
1236
1237	+	}//end namespace OpenMD
1238	+

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 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines