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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 48 | Line 48
48
49		#include <algorithm>
50		#include <set>
51	+	#include <map>
52
53		#include "brains/SimInfo.hpp"
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56	+	#include "primitives/StuntDouble.hpp"
57		#include "UseTheForce/doForces_interface.h"
58	<	#include "UseTheForce/notifyCutoffs_interface.h"
58	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
59		#include "utils/MemoryUtils.hpp"
60		#include "utils/simError.h"
61		#include "selection/SelectionManager.hpp"
62	+	#include "io/ForceFieldOptions.hpp"
63	+	#include "UseTheForce/ForceField.hpp"
64	+	#include "nonbonded/SwitchingFunction.hpp"
65
66	+
67		#ifdef IS_MPI
68		#include "UseTheForce/mpiComponentPlan.h"
69		#include "UseTheForce/DarkSide/simParallel_interface.h"
70		#endif
71
72	<	namespace oopse {
73	<
74	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
75	<	ForceField* ff, Globals* simParams) :
76	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
77	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
72	>	using namespace std;
73	>	namespace OpenMD {
74	>
75	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
76	>	forceField_(ff), simParams_(simParams),
77	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
78		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
79		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
80	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
81	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
82	<	sman_(NULL), fortranInitialized_(false) {
83	<
78	<
79	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
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;
80	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
81	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
82	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
83	>	calcBoxDipole_(false), useAtomicVirial_(true) {
84
85	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
86	<	molStamp = i->first;
87	<	nMolWithSameStamp = i->second;
88	<
89	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
90	<
91	<	//calculate atoms in molecules
92	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
93	<
94	<
95	<	//calculate atoms in cutoff groups
96	<	int nAtomsInGroups = 0;
97	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
98	<
99	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
100	<	cgStamp = molStamp->getCutoffGroup(j);
101	<	nAtomsInGroups += cgStamp->getNMembers();
102	<	}
103	<
104	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
105	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
106	<
107	<	//calculate atoms in rigid bodies
108	<	int nAtomsInRigidBodies = 0;
109	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
110	<
114	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
115	<	rbStamp = molStamp->getRigidBody(j);
116	<	nAtomsInRigidBodies += rbStamp->getNMembers();
117	<	}
118	<
119	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
120	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
121	<
85	>	MoleculeStamp* molStamp;
86	>	int nMolWithSameStamp;
87	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
88	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
89	>	CutoffGroupStamp* cgStamp;
90	>	RigidBodyStamp* rbStamp;
91	>	int nRigidAtoms = 0;
92	>
93	>	vector<Component*> components = simParams->getComponents();
94	>
95	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
96	>	molStamp = (*i)->getMoleculeStamp();
97	>	nMolWithSameStamp = (*i)->getNMol();
98	>
99	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
100	>
101	>	//calculate atoms in molecules
102	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
103	>
104	>	//calculate atoms in cutoff groups
105	>	int nAtomsInGroups = 0;
106	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
107	>
108	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
109	>	cgStamp = molStamp->getCutoffGroupStamp(j);
110	>	nAtomsInGroups += cgStamp->getNMembers();
111		}
112	<
113	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
114	<	//therefore the total number of cutoff groups in the system is equal to
115	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
116	<	//file plus the number of cutoff groups defined in meta-data file
117	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
118	<
119	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
120	<	//therefore the total number of  integrable objects in the system is equal to
121	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
122	<	//file plus the number of  rigid bodies defined in meta-data file
123	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
124	<
125	<	nGlobalMols_ = molStampIds_.size();
126	<
127	<	#ifdef IS_MPI
128	<	molToProcMap_.resize(nGlobalMols_);
140	<	#endif
141	<
112	>
113	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
114	>
115	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
116	>
117	>	//calculate atoms in rigid bodies
118	>	int nAtomsInRigidBodies = 0;
119	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
120	>
121	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
122	>	rbStamp = molStamp->getRigidBodyStamp(j);
123	>	nAtomsInRigidBodies += rbStamp->getNMembers();
124	>	}
125	>
126	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
127	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
128	>
129		}
130	<
130	>
131	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
132	>	//group therefore the total number of cutoff groups in the system is
133	>	//equal to the total number of atoms minus number of atoms belong to
134	>	//cutoff group defined in meta-data file plus the number of cutoff
135	>	//groups defined in meta-data file
136	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
137	>
138	>	//every free atom (atom does not belong to rigid bodies) is an
139	>	//integrable object therefore the total number of integrable objects
140	>	//in the system is equal to the total number of atoms minus number of
141	>	//atoms belong to rigid body defined in meta-data file plus the number
142	>	//of rigid bodies defined in meta-data file
143	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
144	>	+ nGlobalRigidBodies_;
145	>
146	>	nGlobalMols_ = molStampIds_.size();
147	>	molToProcMap_.resize(nGlobalMols_);
148	>	}
149	>
150		SimInfo::~SimInfo() {
151	<	std::map<int, Molecule*>::iterator i;
151	>	map<int, Molecule*>::iterator i;
152		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
153		delete i->second;
154		}
155		molecules_.clear();
156
151	–	delete stamps_;
157		delete sman_;
158		delete simParams_;
159		delete forceField_;
160		}
161
157	–	int SimInfo::getNGlobalConstraints() {
158	–	int nGlobalConstraints;
159	–	#ifdef IS_MPI
160	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
161	–	MPI_COMM_WORLD);
162	–	#else
163	–	nGlobalConstraints =  nConstraints_;
164	–	#endif
165	–	return nGlobalConstraints;
166	–	}
162
163		bool SimInfo::addMolecule(Molecule* mol) {
164		MoleculeIterator i;
165	<
165	>
166		i = molecules_.find(mol->getGlobalIndex());
167		if (i == molecules_.end() ) {
168	<
169	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
170	<
168	>
169	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
170	>
171		nAtoms_ += mol->getNAtoms();
172		nBonds_ += mol->getNBonds();
173		nBends_ += mol->getNBends();
174		nTorsions_ += mol->getNTorsions();
175	+	nInversions_ += mol->getNInversions();
176		nRigidBodies_ += mol->getNRigidBodies();
177		nIntegrableObjects_ += mol->getNIntegrableObjects();
178		nCutoffGroups_ += mol->getNCutoffGroups();
179		nConstraints_ += mol->getNConstraintPairs();
180	<
181	<	addExcludePairs(mol);
182	<
180	>
181	>	addInteractionPairs(mol);
182	>
183		return true;
184		} else {
185		return false;
186		}
187		}
188	<
188	>
189		bool SimInfo::removeMolecule(Molecule* mol) {
190		MoleculeIterator i;
191		i = molecules_.find(mol->getGlobalIndex());
#	Line 202 | Line 198 | namespace oopse {
198		nBonds_ -= mol->getNBonds();
199		nBends_ -= mol->getNBends();
200		nTorsions_ -= mol->getNTorsions();
201	+	nInversions_ -= mol->getNInversions();
202		nRigidBodies_ -= mol->getNRigidBodies();
203		nIntegrableObjects_ -= mol->getNIntegrableObjects();
204		nCutoffGroups_ -= mol->getNCutoffGroups();
205		nConstraints_ -= mol->getNConstraintPairs();
206
207	<	removeExcludePairs(mol);
207	>	removeInteractionPairs(mol);
208		molecules_.erase(mol->getGlobalIndex());
209
210		delete mol;
#	Line 216 | Line 213 | namespace oopse {
213		} else {
214		return false;
215		}
219	–
220	–
216		}
217
218
#	Line 235 | Line 230 | namespace oopse {
230		void SimInfo::calcNdf() {
231		int ndf_local;
232		MoleculeIterator i;
233	<	std::vector<StuntDouble*>::iterator j;
233	>	vector<StuntDouble*>::iterator j;
234		Molecule* mol;
235		StuntDouble* integrableObject;
236
#	Line 255 | Line 250 | namespace oopse {
250		}
251		}
252
253	<	}//end for (integrableObject)
254	<	}// end for (mol)
253	>	}
254	>	}
255
256		// n_constraints is local, so subtract them on each processor
257		ndf_local -= nConstraints_;
#	Line 273 | Line 268 | namespace oopse {
268
269		}
270
271	+	int SimInfo::getFdf() {
272	+	#ifdef IS_MPI
273	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
274	+	#else
275	+	fdf_ = fdf_local;
276	+	#endif
277	+	return fdf_;
278	+	}
279	+
280		void SimInfo::calcNdfRaw() {
281		int ndfRaw_local;
282
283		MoleculeIterator i;
284	<	std::vector<StuntDouble*>::iterator j;
284	>	vector<StuntDouble*>::iterator j;
285		Molecule* mol;
286		StuntDouble* integrableObject;
287
#	Line 324 | Line 328 | namespace oopse {
328
329		}
330
331	<	void SimInfo::addExcludePairs(Molecule* mol) {
332	<	std::vector<Bond*>::iterator bondIter;
333	<	std::vector<Bend*>::iterator bendIter;
334	<	std::vector<Torsion*>::iterator torsionIter;
331	>	void SimInfo::addInteractionPairs(Molecule* mol) {
332	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
333	>	vector<Bond*>::iterator bondIter;
334	>	vector<Bend*>::iterator bendIter;
335	>	vector<Torsion*>::iterator torsionIter;
336	>	vector<Inversion*>::iterator inversionIter;
337		Bond* bond;
338		Bend* bend;
339		Torsion* torsion;
340	+	Inversion* inversion;
341		int a;
342		int b;
343		int c;
344		int d;
345	+
346	+	// atomGroups can be used to add special interaction maps between
347	+	// groups of atoms that are in two separate rigid bodies.
348	+	// However, most site-site interactions between two rigid bodies
349	+	// are probably not special, just the ones between the physically
350	+	// bonded atoms.  Interactions *within* a single rigid body should
351	+	// always be excluded.  These are done at the bottom of this
352	+	// function.
353	+
354	+	map<int, set<int> > atomGroups;
355	+	Molecule::RigidBodyIterator rbIter;
356	+	RigidBody* rb;
357	+	Molecule::IntegrableObjectIterator ii;
358	+	StuntDouble* integrableObject;
359
360	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
360	>	for (integrableObject = mol->beginIntegrableObject(ii);
361	>	integrableObject != NULL;
362	>	integrableObject = mol->nextIntegrableObject(ii)) {
363	>
364	>	if (integrableObject->isRigidBody()) {
365	>	rb = static_cast<RigidBody*>(integrableObject);
366	>	vector<Atom*> atoms = rb->getAtoms();
367	>	set<int> rigidAtoms;
368	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
369	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
370	>	}
371	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
372	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
373	>	}
374	>	} else {
375	>	set<int> oneAtomSet;
376	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
377	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
378	>	}
379	>	}
380	>
381	>	for (bond= mol->beginBond(bondIter); bond != NULL;
382	>	bond = mol->nextBond(bondIter)) {
383	>
384		a = bond->getAtomA()->getGlobalIndex();
385	<	b = bond->getAtomB()->getGlobalIndex();
386	<	exclude_.addPair(a, b);
385	>	b = bond->getAtomB()->getGlobalIndex();
386	>
387	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
388	>	oneTwoInteractions_.addPair(a, b);
389	>	} else {
390	>	excludedInteractions_.addPair(a, b);
391	>	}
392		}
393
394	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
394	>	for (bend= mol->beginBend(bendIter); bend != NULL;
395	>	bend = mol->nextBend(bendIter)) {
396	>
397		a = bend->getAtomA()->getGlobalIndex();
398		b = bend->getAtomB()->getGlobalIndex();
399		c = bend->getAtomC()->getGlobalIndex();
400	+
401	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
402	+	oneTwoInteractions_.addPair(a, b);
403	+	oneTwoInteractions_.addPair(b, c);
404	+	} else {
405	+	excludedInteractions_.addPair(a, b);
406	+	excludedInteractions_.addPair(b, c);
407	+	}
408
409	<	exclude_.addPair(a, b);
410	<	exclude_.addPair(a, c);
411	<	exclude_.addPair(b, c);
409	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
410	>	oneThreeInteractions_.addPair(a, c);
411	>	} else {
412	>	excludedInteractions_.addPair(a, c);
413	>	}
414		}
415
416	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
416	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
417	>	torsion = mol->nextTorsion(torsionIter)) {
418	>
419		a = torsion->getAtomA()->getGlobalIndex();
420		b = torsion->getAtomB()->getGlobalIndex();
421		c = torsion->getAtomC()->getGlobalIndex();
422	<	d = torsion->getAtomD()->getGlobalIndex();
422	>	d = torsion->getAtomD()->getGlobalIndex();
423
424	<	exclude_.addPair(a, b);
425	<	exclude_.addPair(a, c);
426	<	exclude_.addPair(a, d);
427	<	exclude_.addPair(b, c);
428	<	exclude_.addPair(b, d);
429	<	exclude_.addPair(c, d);
424	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
425	>	oneTwoInteractions_.addPair(a, b);
426	>	oneTwoInteractions_.addPair(b, c);
427	>	oneTwoInteractions_.addPair(c, d);
428	>	} else {
429	>	excludedInteractions_.addPair(a, b);
430	>	excludedInteractions_.addPair(b, c);
431	>	excludedInteractions_.addPair(c, d);
432	>	}
433	>
434	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
435	>	oneThreeInteractions_.addPair(a, c);
436	>	oneThreeInteractions_.addPair(b, d);
437	>	} else {
438	>	excludedInteractions_.addPair(a, c);
439	>	excludedInteractions_.addPair(b, d);
440	>	}
441	>
442	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
443	>	oneFourInteractions_.addPair(a, d);
444	>	} else {
445	>	excludedInteractions_.addPair(a, d);
446	>	}
447		}
448
449	<	Molecule::RigidBodyIterator rbIter;
450	<	RigidBody* rb;
451	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
452	<	std::vector<Atom*> atoms = rb->getAtoms();
453	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
454	<	for (int j = i + 1; j < atoms.size(); ++j) {
449	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
450	>	inversion = mol->nextInversion(inversionIter)) {
451	>
452	>	a = inversion->getAtomA()->getGlobalIndex();
453	>	b = inversion->getAtomB()->getGlobalIndex();
454	>	c = inversion->getAtomC()->getGlobalIndex();
455	>	d = inversion->getAtomD()->getGlobalIndex();
456	>
457	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
458	>	oneTwoInteractions_.addPair(a, b);
459	>	oneTwoInteractions_.addPair(a, c);
460	>	oneTwoInteractions_.addPair(a, d);
461	>	} else {
462	>	excludedInteractions_.addPair(a, b);
463	>	excludedInteractions_.addPair(a, c);
464	>	excludedInteractions_.addPair(a, d);
465	>	}
466	>
467	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
468	>	oneThreeInteractions_.addPair(b, c);
469	>	oneThreeInteractions_.addPair(b, d);
470	>	oneThreeInteractions_.addPair(c, d);
471	>	} else {
472	>	excludedInteractions_.addPair(b, c);
473	>	excludedInteractions_.addPair(b, d);
474	>	excludedInteractions_.addPair(c, d);
475	>	}
476	>	}
477	>
478	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
479	>	rb = mol->nextRigidBody(rbIter)) {
480	>	vector<Atom*> atoms = rb->getAtoms();
481	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
482	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
483		a = atoms[i]->getGlobalIndex();
484		b = atoms[j]->getGlobalIndex();
485	<	exclude_.addPair(a, b);
485	>	excludedInteractions_.addPair(a, b);
486		}
487		}
488		}
489
490		}
491
492	<	void SimInfo::removeExcludePairs(Molecule* mol) {
493	<	std::vector<Bond*>::iterator bondIter;
494	<	std::vector<Bend*>::iterator bendIter;
495	<	std::vector<Torsion*>::iterator torsionIter;
492	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
493	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
494	>	vector<Bond*>::iterator bondIter;
495	>	vector<Bend*>::iterator bendIter;
496	>	vector<Torsion*>::iterator torsionIter;
497	>	vector<Inversion*>::iterator inversionIter;
498		Bond* bond;
499		Bend* bend;
500		Torsion* torsion;
501	+	Inversion* inversion;
502		int a;
503		int b;
504		int c;
505		int d;
506	+
507	+	map<int, set<int> > atomGroups;
508	+	Molecule::RigidBodyIterator rbIter;
509	+	RigidBody* rb;
510	+	Molecule::IntegrableObjectIterator ii;
511	+	StuntDouble* integrableObject;
512
513	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
513	>	for (integrableObject = mol->beginIntegrableObject(ii);
514	>	integrableObject != NULL;
515	>	integrableObject = mol->nextIntegrableObject(ii)) {
516	>
517	>	if (integrableObject->isRigidBody()) {
518	>	rb = static_cast<RigidBody*>(integrableObject);
519	>	vector<Atom*> atoms = rb->getAtoms();
520	>	set<int> rigidAtoms;
521	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
522	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
523	>	}
524	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
525	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
526	>	}
527	>	} else {
528	>	set<int> oneAtomSet;
529	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
530	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
531	>	}
532	>	}
533	>
534	>	for (bond= mol->beginBond(bondIter); bond != NULL;
535	>	bond = mol->nextBond(bondIter)) {
536	>
537		a = bond->getAtomA()->getGlobalIndex();
538	<	b = bond->getAtomB()->getGlobalIndex();
539	<	exclude_.removePair(a, b);
538	>	b = bond->getAtomB()->getGlobalIndex();
539	>
540	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
541	>	oneTwoInteractions_.removePair(a, b);
542	>	} else {
543	>	excludedInteractions_.removePair(a, b);
544	>	}
545		}
546
547	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
547	>	for (bend= mol->beginBend(bendIter); bend != NULL;
548	>	bend = mol->nextBend(bendIter)) {
549	>
550		a = bend->getAtomA()->getGlobalIndex();
551		b = bend->getAtomB()->getGlobalIndex();
552		c = bend->getAtomC()->getGlobalIndex();
553	+
554	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
555	+	oneTwoInteractions_.removePair(a, b);
556	+	oneTwoInteractions_.removePair(b, c);
557	+	} else {
558	+	excludedInteractions_.removePair(a, b);
559	+	excludedInteractions_.removePair(b, c);
560	+	}
561
562	<	exclude_.removePair(a, b);
563	<	exclude_.removePair(a, c);
564	<	exclude_.removePair(b, c);
562	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
563	>	oneThreeInteractions_.removePair(a, c);
564	>	} else {
565	>	excludedInteractions_.removePair(a, c);
566	>	}
567		}
568
569	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
569	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
570	>	torsion = mol->nextTorsion(torsionIter)) {
571	>
572		a = torsion->getAtomA()->getGlobalIndex();
573		b = torsion->getAtomB()->getGlobalIndex();
574		c = torsion->getAtomC()->getGlobalIndex();
575	<	d = torsion->getAtomD()->getGlobalIndex();
575	>	d = torsion->getAtomD()->getGlobalIndex();
576	>
577	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
578	>	oneTwoInteractions_.removePair(a, b);
579	>	oneTwoInteractions_.removePair(b, c);
580	>	oneTwoInteractions_.removePair(c, d);
581	>	} else {
582	>	excludedInteractions_.removePair(a, b);
583	>	excludedInteractions_.removePair(b, c);
584	>	excludedInteractions_.removePair(c, d);
585	>	}
586
587	<	exclude_.removePair(a, b);
588	<	exclude_.removePair(a, c);
589	<	exclude_.removePair(a, d);
590	<	exclude_.removePair(b, c);
591	<	exclude_.removePair(b, d);
592	<	exclude_.removePair(c, d);
587	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
588	>	oneThreeInteractions_.removePair(a, c);
589	>	oneThreeInteractions_.removePair(b, d);
590	>	} else {
591	>	excludedInteractions_.removePair(a, c);
592	>	excludedInteractions_.removePair(b, d);
593	>	}
594	>
595	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
596	>	oneFourInteractions_.removePair(a, d);
597	>	} else {
598	>	excludedInteractions_.removePair(a, d);
599	>	}
600		}
601
602	<	Molecule::RigidBodyIterator rbIter;
603	<	RigidBody* rb;
604	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
605	<	std::vector<Atom*> atoms = rb->getAtoms();
606	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
607	<	for (int j = i + 1; j < atoms.size(); ++j) {
602	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
603	>	inversion = mol->nextInversion(inversionIter)) {
604	>
605	>	a = inversion->getAtomA()->getGlobalIndex();
606	>	b = inversion->getAtomB()->getGlobalIndex();
607	>	c = inversion->getAtomC()->getGlobalIndex();
608	>	d = inversion->getAtomD()->getGlobalIndex();
609	>
610	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
611	>	oneTwoInteractions_.removePair(a, b);
612	>	oneTwoInteractions_.removePair(a, c);
613	>	oneTwoInteractions_.removePair(a, d);
614	>	} else {
615	>	excludedInteractions_.removePair(a, b);
616	>	excludedInteractions_.removePair(a, c);
617	>	excludedInteractions_.removePair(a, d);
618	>	}
619	>
620	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
621	>	oneThreeInteractions_.removePair(b, c);
622	>	oneThreeInteractions_.removePair(b, d);
623	>	oneThreeInteractions_.removePair(c, d);
624	>	} else {
625	>	excludedInteractions_.removePair(b, c);
626	>	excludedInteractions_.removePair(b, d);
627	>	excludedInteractions_.removePair(c, d);
628	>	}
629	>	}
630	>
631	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
632	>	rb = mol->nextRigidBody(rbIter)) {
633	>	vector<Atom*> atoms = rb->getAtoms();
634	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
635	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
636		a = atoms[i]->getGlobalIndex();
637		b = atoms[j]->getGlobalIndex();
638	<	exclude_.removePair(a, b);
638	>	excludedInteractions_.removePair(a, b);
639		}
640		}
641		}
642	<
642	>
643		}
644	<
645	<
644	>
645	>
646		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
647		int curStampId;
648	<
648	>
649		//index from 0
650		curStampId = moleculeStamps_.size();
651
#	Line 449 | Line 653 | namespace oopse {
653		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
654		}
655
656	+
657	+	/**
658	+	* update
659	+	*
660	+	*  Performs the global checks and variable settings after the objects have been
661	+	*  created.
662	+	*
663	+	*/
664		void SimInfo::update() {
665	+
666	+	setupSimVariables();
667	+	setupCutoffs();
668	+	setupSwitching();
669	+	setupElectrostatics();
670	+	setupNeighborlists();
671
454	–	setupSimType();
455	–
672		#ifdef IS_MPI
673		setupFortranParallel();
674		#endif
459	–
675		setupFortranSim();
676	+	fortranInitialized_ = true;
677
462	–	//setup fortran force field
463	–	/** @deprecate */
464	–	int isError = 0;
465	–	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
466	–	if(isError){
467	–	sprintf( painCave.errMsg,
468	–	"ForceField error: There was an error initializing the forceField in fortran.\n" );
469	–	painCave.isFatal = 1;
470	–	simError();
471	–	}
472	–
473	–
474	–	setupCutoff();
475	–
678		calcNdf();
679		calcNdfRaw();
680		calcNdfTrans();
479	–
480	–	fortranInitialized_ = true;
681		}
682	<
683	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
682	>
683	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
684		SimInfo::MoleculeIterator mi;
685		Molecule* mol;
686		Molecule::AtomIterator ai;
687		Atom* atom;
688	<	std::set<AtomType*> atomTypes;
689	<
690	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
491	<
688	>	set<AtomType*> atomTypes;
689	>
690	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
691		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
692		atomTypes.insert(atom->getAtomType());
693	<	}
694	<
496	<	}
497	<
693	>	}
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	>	* setupCutoffs
700	>	*
701	>	* Sets the values of cutoffRadius and cutoffMethod
702	>	*
703	>	* cutoffRadius : realType
704	>	*  If the cutoffRadius was explicitly set, use that value.
705	>	*  If the cutoffRadius was not explicitly set:
706	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
707	>	*      No electrostatic atoms?  Poll the atom types present in the
708	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
709	>	*      Use the maximum suggested value that was found.
710	>	*
711	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
712	>	*      If cutoffMethod was explicitly set, use that choice.
713	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
714	>	*/
715	>	void SimInfo::setupCutoffs() {
716
717	<	int useLennardJones = 0;
718	<	int useElectrostatic = 0;
719	<	int useEAM = 0;
720	<	int useCharge = 0;
721	<	int useDirectional = 0;
722	<	int useDipole = 0;
723	<	int useGayBerne = 0;
724	<	int useSticky = 0;
725	<	int useShape = 0;
726	<	int useFLARB = 0; //it is not in AtomType yet
727	<	int useDirectionalAtom = 0;
728	<	int useElectrostatics = 0;
729	<	//usePBC and useRF are from simParams
730	<	int usePBC = simParams_->getPBC();
731	<	int useRF = simParams_->getUseRF();
732	<
733	<	//loop over all of the atom types
734	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
735	<	useLennardJones |= (*i)->isLennardJones();
736	<	useElectrostatic |= (*i)->isElectrostatic();
737	<	useEAM |= (*i)->isEAM();
738	<	useCharge |= (*i)->isCharge();
739	<	useDirectional |= (*i)->isDirectional();
740	<	useDipole |= (*i)->isDipole();
741	<	useGayBerne |= (*i)->isGayBerne();
742	<	useSticky |= (*i)->isSticky();
743	<	useShape |= (*i)->isShape();
717	>	if (simParams_->haveCutoffRadius()) {
718	>	cutoffRadius_ = simParams_->getCutoffRadius();
719	>	} else {
720	>	if (usesElectrostaticAtoms_) {
721	>	sprintf(painCave.errMsg,
722	>	"SimInfo: No value was set for the cutoffRadius.\n"
723	>	"\tOpenMD will use a default value of 12.0 angstroms"
724	>	"\tfor the cutoffRadius.\n");
725	>	painCave.isFatal = 0;
726	>	painCave.severity = OPENMD_INFO;
727	>	simError();
728	>	cutoffRadius_ = 12.0;
729	>	} else {
730	>	RealType thisCut;
731	>	set<AtomType*>::iterator i;
732	>	set<AtomType*> atomTypes;
733	>	atomTypes = getSimulatedAtomTypes();
734	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
735	>	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
736	>	cutoffRadius_ = max(thisCut, cutoffRadius_);
737	>	}
738	>	sprintf(painCave.errMsg,
739	>	"SimInfo: No value was set for the cutoffRadius.\n"
740	>	"\tOpenMD will use %lf angstroms.\n",
741	>	cutoffRadius_);
742	>	painCave.isFatal = 0;
743	>	painCave.severity = OPENMD_INFO;
744	>	simError();
745	>	}
746		}
747
748	<	if (useSticky || useDipole || useGayBerne || useShape) {
536	<	useDirectionalAtom = 1;
537	<	}
748	>	InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
749
750	<	if (useCharge || useDipole) {
751	<	useElectrostatics = 1;
750	>	map<string, CutoffMethod> stringToCutoffMethod;
751	>	stringToCutoffMethod["HARD"] = HARD;
752	>	stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
753	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
754	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
755	>
756	>	if (simParams_->haveCutoffMethod()) {
757	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
758	>	map<string, CutoffMethod>::iterator i;
759	>	i = stringToCutoffMethod.find(cutMeth);
760	>	if (i == stringToCutoffMethod.end()) {
761	>	sprintf(painCave.errMsg,
762	>	"SimInfo: Could not find chosen cutoffMethod %s\n"
763	>	"\tShould be one of: "
764	>	"HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
765	>	cutMeth.c_str());
766	>	painCave.isFatal = 1;
767	>	painCave.severity = OPENMD_ERROR;
768	>	simError();
769	>	} else {
770	>	cutoffMethod_ = i->second;
771	>	}
772	>	} else {
773	>	sprintf(painCave.errMsg,
774	>	"SimInfo: No value was set for the cutoffMethod.\n"
775	>	"\tOpenMD will use SHIFTED_FORCE.\n");
776	>	painCave.isFatal = 0;
777	>	painCave.severity = OPENMD_INFO;
778	>	simError();
779	>	cutoffMethod_ = SHIFTED_FORCE;
780		}
781
782	<	#ifdef IS_MPI
783	<	int temp;
782	>	InteractionManager::Instance()->setCutoffMethod(cutoffMethod_);
783	>	}
784	>
785	>	/**
786	>	* setupSwitching
787	>	*
788	>	* Sets the values of switchingRadius and
789	>	*  If the switchingRadius was explicitly set, use that value (but check it)
790	>	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
791	>	*/
792	>	void SimInfo::setupSwitching() {
793	>
794	>	if (simParams_->haveSwitchingRadius()) {
795	>	switchingRadius_ = simParams_->getSwitchingRadius();
796	>	if (switchingRadius_ > cutoffRadius_) {
797	>	sprintf(painCave.errMsg,
798	>	"SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
799	>	switchingRadius_, cutoffRadius_);
800	>	painCave.isFatal = 1;
801	>	painCave.severity = OPENMD_ERROR;
802	>	simError();
803	>	}
804	>	} else {
805	>	switchingRadius_ = 0.85 * cutoffRadius_;
806	>	sprintf(painCave.errMsg,
807	>	"SimInfo: No value was set for the switchingRadius.\n"
808	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
809	>	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
810	>	painCave.isFatal = 0;
811	>	painCave.severity = OPENMD_WARNING;
812	>	simError();
813	>	}
814	>
815	>	InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
816
817	<	temp = usePBC;
818	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
817	>	SwitchingFunctionType ft;
818	>
819	>	if (simParams_->haveSwitchingFunctionType()) {
820	>	string funcType = simParams_->getSwitchingFunctionType();
821	>	toUpper(funcType);
822	>	if (funcType == "CUBIC") {
823	>	ft = cubic;
824	>	} else {
825	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
826	>	ft = fifth_order_poly;
827	>	} else {
828	>	// throw error
829	>	sprintf( painCave.errMsg,
830	>	"SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
831	>	"\tswitchingFunctionType must be one of: "
832	>	"\"cubic\" or \"fifth_order_polynomial\".",
833	>	funcType.c_str() );
834	>	painCave.isFatal = 1;
835	>	painCave.severity = OPENMD_ERROR;
836	>	simError();
837	>	}
838	>	}
839	>	}
840
841	<	temp = useDirectionalAtom;
842	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
841	>	InteractionManager::Instance()->setSwitchingFunctionType(ft);
842	>	}
843
844	<	temp = useLennardJones;
845	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
844	>	/**
845	>	* setupSkinThickness
846	>	*
847	>	*  If the skinThickness was explicitly set, use that value (but check it)
848	>	*  If the skinThickness was not explicitly set: use 1.0 angstroms
849	>	*/
850	>	void SimInfo::setupSkinThickness() {
851	>	if (simParams_->haveSkinThickness()) {
852	>	skinThickness_ = simParams_->getSkinThickness();
853	>	} else {
854	>	skinThickness_ = 1.0;
855	>	sprintf(painCave.errMsg,
856	>	"SimInfo Warning: No value was set for the skinThickness.\n"
857	>	"\tOpenMD will use a default value of %f Angstroms\n"
858	>	"\tfor this simulation\n", skinThickness_);
859	>	painCave.isFatal = 0;
860	>	simError();
861	>	}
862	>	}
863
864	<	temp = useElectrostatics;
865	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
864	>	void SimInfo::setupSimType() {
865	>	set<AtomType*>::iterator i;
866	>	set<AtomType*> atomTypes;
867	>	atomTypes = getSimulatedAtomTypes();
868
869	<	temp = useCharge;
559	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
869	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
870
871	<	temp = useDipole;
872	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
871	>	int usesElectrostatic = 0;
872	>	int usesMetallic = 0;
873	>	int usesDirectional = 0;
874	>	//loop over all of the atom types
875	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
876	>	usesElectrostatic |= (*i)->isElectrostatic();
877	>	usesMetallic |= (*i)->isMetal();
878	>	usesDirectional |= (*i)->isDirectional();
879	>	}
880
881	<	temp = useSticky;
882	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
881	>	#ifdef IS_MPI
882	>	int temp;
883	>	temp = usesDirectional;
884	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
885
886	<	temp = useGayBerne;
887	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
886	>	temp = usesMetallic;
887	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
888
889	<	temp = useEAM;
890	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
572	<
573	<	temp = useShape;
574	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
575	<
576	<	temp = useFLARB;
577	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
578	<
579	<	temp = useRF;
580	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
581	<
889	>	temp = usesElectrostatic;
890	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
891		#endif
892	<
893	<	fInfo_.SIM_uses_PBC = usePBC;
894	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
895	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
896	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
897	<	fInfo_.SIM_uses_Charges = useCharge;
589	<	fInfo_.SIM_uses_Dipoles = useDipole;
590	<	fInfo_.SIM_uses_Sticky = useSticky;
591	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
592	<	fInfo_.SIM_uses_EAM = useEAM;
593	<	fInfo_.SIM_uses_Shapes = useShape;
594	<	fInfo_.SIM_uses_FLARB = useFLARB;
595	<	fInfo_.SIM_uses_RF = useRF;
596	<
597	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
598	<
599	<	if (simParams_->haveDielectric()) {
600	<	fInfo_.dielect = simParams_->getDielectric();
601	<	} else {
602	<	sprintf(painCave.errMsg,
603	<	"SimSetup Error: No Dielectric constant was set.\n"
604	<	"\tYou are trying to use Reaction Field without"
605	<	"\tsetting a dielectric constant!\n");
606	<	painCave.isFatal = 1;
607	<	simError();
608	<	}
609	<
610	<	} else {
611	<	fInfo_.dielect = 0.0;
612	<	}
613	<
892	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
893	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
894	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
895	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
896	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
897	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
898		}
899
900		void SimInfo::setupFortranSim() {
901		int isError;
902	<	int nExclude;
903	<	std::vector<int> fortranGlobalGroupMembership;
902	>	int nExclude, nOneTwo, nOneThree, nOneFour;
903	>	vector<int> fortranGlobalGroupMembership;
904
905	<	nExclude = exclude_.getSize();
905	>	notifyFortranSkinThickness(&skinThickness_);
906	>
907	>	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
908	>	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
909	>	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
910	>
911		isError = 0;
912
913		//globalGroupMembership_ is filled by SimCreator
#	Line 627 | Line 916 | namespace oopse {
916		}
917
918		//calculate mass ratio of cutoff group
919	<	std::vector<double> mfact;
919	>	vector<RealType> mfact;
920		SimInfo::MoleculeIterator mi;
921		Molecule* mol;
922		Molecule::CutoffGroupIterator ci;
923		CutoffGroup* cg;
924		Molecule::AtomIterator ai;
925		Atom* atom;
926	<	double totalMass;
926	>	RealType totalMass;
927
928		//to avoid memory reallocation, reserve enough space for mfact
929		mfact.reserve(getNCutoffGroups());
#	Line 644 | Line 933 | namespace oopse {
933
934		totalMass = cg->getMass();
935		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
936	<	mfact.push_back(atom->getMass()/totalMass);
936	>	// Check for massless groups - set mfact to 1 if true
937	>	if (totalMass != 0)
938	>	mfact.push_back(atom->getMass()/totalMass);
939	>	else
940	>	mfact.push_back( 1.0 );
941		}
649	–
942		}
943		}
944
945		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
946	<	std::vector<int> identArray;
946	>	vector<int> identArray;
947
948		//to avoid memory reallocation, reserve enough space identArray
949		identArray.reserve(getNAtoms());
#	Line 664 | Line 956 | namespace oopse {
956
957		//fill molMembershipArray
958		//molMembershipArray is filled by SimCreator
959	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
959	>	vector<int> molMembershipArray(nGlobalAtoms_);
960		for (int i = 0; i < nGlobalAtoms_; i++) {
961		molMembershipArray[i] = globalMolMembership_[i] + 1;
962		}
963
964		//setup fortran simulation
673	–	int nGlobalExcludes = 0;
674	–	int* globalExcludes = NULL;
675	–	int* excludeList = exclude_.getExcludeList();
676	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
677	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
678	–	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
965
966	<	if( isError ){
966	>	nExclude = excludedInteractions_.getSize();
967	>	nOneTwo = oneTwoInteractions_.getSize();
968	>	nOneThree = oneThreeInteractions_.getSize();
969	>	nOneFour = oneFourInteractions_.getSize();
970
971	+	int* excludeList = excludedInteractions_.getPairList();
972	+	int* oneTwoList = oneTwoInteractions_.getPairList();
973	+	int* oneThreeList = oneThreeInteractions_.getPairList();
974	+	int* oneFourList = oneFourInteractions_.getPairList();
975	+
976	+	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
977	+	&nExclude, excludeList,
978	+	&nOneTwo, oneTwoList,
979	+	&nOneThree, oneThreeList,
980	+	&nOneFour, oneFourList,
981	+	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
982	+	&fortranGlobalGroupMembership[0], &isError);
983	+
984	+	if( isError ){
985	+
986		sprintf( painCave.errMsg,
987		"There was an error setting the simulation information in fortran.\n" );
988		painCave.isFatal = 1;
989	<	painCave.severity = OOPSE_ERROR;
989	>	painCave.severity = OPENMD_ERROR;
990		simError();
991		}
992	<
993	<	#ifdef IS_MPI
992	>
993	>
994		sprintf( checkPointMsg,
995		"succesfully sent the simulation information to fortran.\n");
996	<	MPIcheckPoint();
997	<	#endif // is_mpi
996	>
997	>	errorCheckPoint();
998	>
999	>	// Setup number of neighbors in neighbor list if present
1000	>	if (simParams_->haveNeighborListNeighbors()) {
1001	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
1002	>	setNeighbors(&nlistNeighbors);
1003	>	}
1004	>
1005	>
1006		}
1007
1008
697	–	#ifdef IS_MPI
1009		void SimInfo::setupFortranParallel() {
1010	<
1010	>	#ifdef IS_MPI
1011		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1012	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1013	<	std::vector<int> localToGlobalCutoffGroupIndex;
1012	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1013	>	vector<int> localToGlobalCutoffGroupIndex;
1014		SimInfo::MoleculeIterator mi;
1015		Molecule::AtomIterator ai;
1016		Molecule::CutoffGroupIterator ci;
#	Line 746 | Line 1057 | namespace oopse {
1057		}
1058
1059		sprintf(checkPointMsg, " mpiRefresh successful.\n");
1060	<	MPIcheckPoint();
1060	>	errorCheckPoint();
1061
1062	<
1062	>	#endif
1063		}
1064
754	–	#endif
1065
1066	<	double SimInfo::calcMaxCutoffRadius() {
757	<
758	<
759	<	std::set<AtomType*> atomTypes;
760	<	std::set<AtomType*>::iterator i;
761	<	std::vector<double> cutoffRadius;
762	<
763	<	//get the unique atom types
764	<	atomTypes = getUniqueAtomTypes();
765	<
766	<	//query the max cutoff radius among these atom types
767	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
768	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
769	<	}
1066	>	void SimInfo::setupSwitchingFunction() {
1067
771	–	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
772	–	#ifdef IS_MPI
773	–	//pick the max cutoff radius among the processors
774	–	#endif
775	–
776	–	return maxCutoffRadius;
1068		}
1069
1070	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
780	<
781	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
782	<
783	<	if (!simParams_->haveRcut()){
784	<	sprintf(painCave.errMsg,
785	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
786	<	"\tOOPSE will use a default value of 15.0 angstroms"
787	<	"\tfor the cutoffRadius.\n");
788	<	painCave.isFatal = 0;
789	<	simError();
790	<	rcut = 15.0;
791	<	} else{
792	<	rcut = simParams_->getRcut();
793	<	}
1070	>	void SimInfo::setupAccumulateBoxDipole() {
1071
1072	<	if (!simParams_->haveRsw()){
1073	<	sprintf(painCave.errMsg,
1074	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1075	<	"\tOOPSE will use a default value of\n"
799	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
800	<	painCave.isFatal = 0;
801	<	simError();
802	<	rsw = 0.95 * rcut;
803	<	} else{
804	<	rsw = simParams_->getRsw();
1072	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1073	>	if ( simParams_->haveAccumulateBoxDipole() )
1074	>	if ( simParams_->getAccumulateBoxDipole() ) {
1075	>	calcBoxDipole_ = true;
1076		}
1077
807	–	} else {
808	–	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
809	–	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
810	–
811	–	if (simParams_->haveRcut()) {
812	–	rcut = simParams_->getRcut();
813	–	} else {
814	–	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
815	–	rcut = calcMaxCutoffRadius();
816	–	}
817	–
818	–	if (simParams_->haveRsw()) {
819	–	rsw  = simParams_->getRsw();
820	–	} else {
821	–	rsw = rcut;
822	–	}
823	–
824	–	}
1078		}
1079
827	–	void SimInfo::setupCutoff() {
828	–	getCutoff(rcut_, rsw_);
829	–	double rnblist = rcut_ + 1; // skin of neighbor list
830	–
831	–	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
832	–	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
833	–	}
834	–
1080		void SimInfo::addProperty(GenericData* genData) {
1081		properties_.addProperty(genData);
1082		}
1083
1084	<	void SimInfo::removeProperty(const std::string& propName) {
1084	>	void SimInfo::removeProperty(const string& propName) {
1085		properties_.removeProperty(propName);
1086		}
1087
#	Line 844 | Line 1089 | namespace oopse {
1089		properties_.clearProperties();
1090		}
1091
1092	<	std::vector<std::string> SimInfo::getPropertyNames() {
1092	>	vector<string> SimInfo::getPropertyNames() {
1093		return properties_.getPropertyNames();
1094		}
1095
1096	<	std::vector<GenericData*> SimInfo::getProperties() {
1096	>	vector<GenericData*> SimInfo::getProperties() {
1097		return properties_.getProperties();
1098		}
1099
1100	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1100	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1101		return properties_.getPropertyByName(propName);
1102		}
1103
#	Line 888 | Line 1133 | namespace oopse {
1133		Molecule* mol;
1134
1135		Vector3d comVel(0.0);
1136	<	double totalMass = 0.0;
1136	>	RealType totalMass = 0.0;
1137
1138
1139		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1140	<	double mass = mol->getMass();
1140	>	RealType mass = mol->getMass();
1141		totalMass += mass;
1142		comVel += mass * mol->getComVel();
1143		}
1144
1145		#ifdef IS_MPI
1146	<	double tmpMass = totalMass;
1146	>	RealType tmpMass = totalMass;
1147		Vector3d tmpComVel(comVel);
1148	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1149	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1148	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1149	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1150		#endif
1151
1152		comVel /= totalMass;
#	Line 914 | Line 1159 | namespace oopse {
1159		Molecule* mol;
1160
1161		Vector3d com(0.0);
1162	<	double totalMass = 0.0;
1162	>	RealType totalMass = 0.0;
1163
1164		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1165	<	double mass = mol->getMass();
1165	>	RealType mass = mol->getMass();
1166		totalMass += mass;
1167		com += mass * mol->getCom();
1168		}
1169
1170		#ifdef IS_MPI
1171	<	double tmpMass = totalMass;
1171	>	RealType tmpMass = totalMass;
1172		Vector3d tmpCom(com);
1173	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1174	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1173	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1174	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1175		#endif
1176
1177		com /= totalMass;
#	Line 935 | Line 1180 | namespace oopse {
1180
1181		}
1182
1183	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1183	>	ostream& operator <<(ostream& o, SimInfo& info) {
1184
1185		return o;
1186		}
1187	+
1188	+
1189	+	/*
1190	+	Returns center of mass and center of mass velocity in one function call.
1191	+	*/
1192	+
1193	+	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1194	+	SimInfo::MoleculeIterator i;
1195	+	Molecule* mol;
1196	+
1197	+
1198	+	RealType totalMass = 0.0;
1199	+
1200
1201	<	}//end namespace oopse
1201	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1202	>	RealType mass = mol->getMass();
1203	>	totalMass += mass;
1204	>	com += mass * mol->getCom();
1205	>	comVel += mass * mol->getComVel();
1206	>	}
1207	>
1208	>	#ifdef IS_MPI
1209	>	RealType tmpMass = totalMass;
1210	>	Vector3d tmpCom(com);
1211	>	Vector3d tmpComVel(comVel);
1212	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1213	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1214	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1215	>	#endif
1216	>
1217	>	com /= totalMass;
1218	>	comVel /= totalMass;
1219	>	}
1220	>
1221	>	/*
1222	>	Return intertia tensor for entire system and angular momentum Vector.
1223
1224	+
1225	+	[  Ixx -Ixy  -Ixz ]
1226	+	J =| -Iyx  Iyy  -Iyz |
1227	+	[ -Izx -Iyz   Izz ]
1228	+	*/
1229	+
1230	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1231	+
1232	+
1233	+	RealType xx = 0.0;
1234	+	RealType yy = 0.0;
1235	+	RealType zz = 0.0;
1236	+	RealType xy = 0.0;
1237	+	RealType xz = 0.0;
1238	+	RealType yz = 0.0;
1239	+	Vector3d com(0.0);
1240	+	Vector3d comVel(0.0);
1241	+
1242	+	getComAll(com, comVel);
1243	+
1244	+	SimInfo::MoleculeIterator i;
1245	+	Molecule* mol;
1246	+
1247	+	Vector3d thisq(0.0);
1248	+	Vector3d thisv(0.0);
1249	+
1250	+	RealType thisMass = 0.0;
1251	+
1252	+
1253	+
1254	+
1255	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1256	+
1257	+	thisq = mol->getCom()-com;
1258	+	thisv = mol->getComVel()-comVel;
1259	+	thisMass = mol->getMass();
1260	+	// Compute moment of intertia coefficients.
1261	+	xx += thisq[0]*thisq[0]*thisMass;
1262	+	yy += thisq[1]*thisq[1]*thisMass;
1263	+	zz += thisq[2]*thisq[2]*thisMass;
1264	+
1265	+	// compute products of intertia
1266	+	xy += thisq[0]*thisq[1]*thisMass;
1267	+	xz += thisq[0]*thisq[2]*thisMass;
1268	+	yz += thisq[1]*thisq[2]*thisMass;
1269	+
1270	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1271	+
1272	+	}
1273	+
1274	+
1275	+	inertiaTensor(0,0) = yy + zz;
1276	+	inertiaTensor(0,1) = -xy;
1277	+	inertiaTensor(0,2) = -xz;
1278	+	inertiaTensor(1,0) = -xy;
1279	+	inertiaTensor(1,1) = xx + zz;
1280	+	inertiaTensor(1,2) = -yz;
1281	+	inertiaTensor(2,0) = -xz;
1282	+	inertiaTensor(2,1) = -yz;
1283	+	inertiaTensor(2,2) = xx + yy;
1284	+
1285	+	#ifdef IS_MPI
1286	+	Mat3x3d tmpI(inertiaTensor);
1287	+	Vector3d tmpAngMom;
1288	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1289	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1290	+	#endif
1291	+
1292	+	return;
1293	+	}
1294	+
1295	+	//Returns the angular momentum of the system
1296	+	Vector3d SimInfo::getAngularMomentum(){
1297	+
1298	+	Vector3d com(0.0);
1299	+	Vector3d comVel(0.0);
1300	+	Vector3d angularMomentum(0.0);
1301	+
1302	+	getComAll(com,comVel);
1303	+
1304	+	SimInfo::MoleculeIterator i;
1305	+	Molecule* mol;
1306	+
1307	+	Vector3d thisr(0.0);
1308	+	Vector3d thisp(0.0);
1309	+
1310	+	RealType thisMass;
1311	+
1312	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1313	+	thisMass = mol->getMass();
1314	+	thisr = mol->getCom()-com;
1315	+	thisp = (mol->getComVel()-comVel)*thisMass;
1316	+
1317	+	angularMomentum += cross( thisr, thisp );
1318	+
1319	+	}
1320	+
1321	+	#ifdef IS_MPI
1322	+	Vector3d tmpAngMom;
1323	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1324	+	#endif
1325	+
1326	+	return angularMomentum;
1327	+	}
1328	+
1329	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1330	+	return IOIndexToIntegrableObject.at(index);
1331	+	}
1332	+
1333	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1334	+	IOIndexToIntegrableObject= v;
1335	+	}
1336	+
1337	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1338	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1339	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1340	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1341	+	*/
1342	+	void SimInfo::getGyrationalVolume(RealType &volume){
1343	+	Mat3x3d intTensor;
1344	+	RealType det;
1345	+	Vector3d dummyAngMom;
1346	+	RealType sysconstants;
1347	+	RealType geomCnst;
1348	+
1349	+	geomCnst = 3.0/2.0;
1350	+	/* Get the inertial tensor and angular momentum for free*/
1351	+	getInertiaTensor(intTensor,dummyAngMom);
1352	+
1353	+	det = intTensor.determinant();
1354	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1355	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1356	+	return;
1357	+	}
1358	+
1359	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1360	+	Mat3x3d intTensor;
1361	+	Vector3d dummyAngMom;
1362	+	RealType sysconstants;
1363	+	RealType geomCnst;
1364	+
1365	+	geomCnst = 3.0/2.0;
1366	+	/* Get the inertial tensor and angular momentum for free*/
1367	+	getInertiaTensor(intTensor,dummyAngMom);
1368	+
1369	+	detI = intTensor.determinant();
1370	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1371	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1372	+	return;
1373	+	}
1374	+	/*
1375	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1376	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1377	+	sdByGlobalIndex_ = v;
1378	+	}
1379	+
1380	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1381	+	//assert(index < nAtoms_ + nRigidBodies_);
1382	+	return sdByGlobalIndex_.at(index);
1383	+	}
1384	+	*/
1385	+	int SimInfo::getNGlobalConstraints() {
1386	+	int nGlobalConstraints;
1387	+	#ifdef IS_MPI
1388	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1389	+	MPI_COMM_WORLD);
1390	+	#else
1391	+	nGlobalConstraints =  nConstraints_;
1392	+	#endif
1393	+	return nGlobalConstraints;
1394	+	}
1395	+
1396	+	}//end namespace OpenMD
1397	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC

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