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 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1534 by gezelter, Wed Dec 29 21:53:28 2010 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 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		#ifdef IS_MPI
67		#include "UseTheForce/mpiComponentPlan.h"
68		#include "UseTheForce/DarkSide/simParallel_interface.h"
69		#endif
70
71	<	namespace oopse {
72	<
73	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
74	<	ForceField* ff, Globals* simParams) :
75	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
76	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
71	>	using namespace std;
72	>	namespace OpenMD {
73	>
74	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
75	>	forceField_(ff), simParams_(simParams),
76	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
77		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
78		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
79	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
80	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
81	<	sman_(NULL), fortranInitialized_(false) {
82	<
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;
79	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
80	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
81	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
82	>	calcBoxDipole_(false), useAtomicVirial_(true) {
83
84	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
85	<	molStamp = i->first;
86	<	nMolWithSameStamp = i->second;
87	<
88	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
89	<
90	<	//calculate atoms in molecules
91	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
92	<
93	<
94	<	//calculate atoms in cutoff groups
95	<	int nAtomsInGroups = 0;
96	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
97	<
98	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
99	<	cgStamp = molStamp->getCutoffGroup(j);
100	<	nAtomsInGroups += cgStamp->getNMembers();
101	<	}
102	<
103	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
104	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
105	<
106	<	//calculate atoms in rigid bodies
107	<	int nAtomsInRigidBodies = 0;
108	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
109	<
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	<
84	>	MoleculeStamp* molStamp;
85	>	int nMolWithSameStamp;
86	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
88	>	CutoffGroupStamp* cgStamp;
89	>	RigidBodyStamp* rbStamp;
90	>	int nRigidAtoms = 0;
91	>
92	>	vector<Component*> components = simParams->getComponents();
93	>
94	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
95	>	molStamp = (*i)->getMoleculeStamp();
96	>	nMolWithSameStamp = (*i)->getNMol();
97	>
98	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
99	>
100	>	//calculate atoms in molecules
101	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
102	>
103	>	//calculate atoms in cutoff groups
104	>	int nAtomsInGroups = 0;
105	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
106	>
107	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
108	>	cgStamp = molStamp->getCutoffGroupStamp(j);
109	>	nAtomsInGroups += cgStamp->getNMembers();
110		}
111	<
112	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
113	<	//therefore the total number of cutoff groups in the system is equal to
114	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
115	<	//file plus the number of cutoff groups defined in meta-data file
116	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
117	<
118	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
119	<	//therefore the total number of  integrable objects in the system is equal to
120	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
121	<	//file plus the number of  rigid bodies defined in meta-data file
122	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
123	<
124	<	nGlobalMols_ = molStampIds_.size();
125	<
126	<	#ifdef IS_MPI
127	<	molToProcMap_.resize(nGlobalMols_);
140	<	#endif
141	<
111	>
112	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
113	>
114	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
115	>
116	>	//calculate atoms in rigid bodies
117	>	int nAtomsInRigidBodies = 0;
118	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
119	>
120	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
121	>	rbStamp = molStamp->getRigidBodyStamp(j);
122	>	nAtomsInRigidBodies += rbStamp->getNMembers();
123	>	}
124	>
125	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
126	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
127	>
128		}
129	<
129	>
130	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
131	>	//group therefore the total number of cutoff groups in the system is
132	>	//equal to the total number of atoms minus number of atoms belong to
133	>	//cutoff group defined in meta-data file plus the number of cutoff
134	>	//groups defined in meta-data file
135	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
136	>
137	>	//every free atom (atom does not belong to rigid bodies) is an
138	>	//integrable object therefore the total number of integrable objects
139	>	//in the system is equal to the total number of atoms minus number of
140	>	//atoms belong to rigid body defined in meta-data file plus the number
141	>	//of rigid bodies defined in meta-data file
142	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
143	>	+ nGlobalRigidBodies_;
144	>
145	>	nGlobalMols_ = molStampIds_.size();
146	>	molToProcMap_.resize(nGlobalMols_);
147	>	}
148	>
149		SimInfo::~SimInfo() {
150	<	std::map<int, Molecule*>::iterator i;
150	>	map<int, Molecule*>::iterator i;
151		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
152		delete i->second;
153		}
154		molecules_.clear();
155
151	–	delete stamps_;
156		delete sman_;
157		delete simParams_;
158		delete forceField_;
159		}
160
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	–	}
161
162		bool SimInfo::addMolecule(Molecule* mol) {
163		MoleculeIterator i;
164	<
164	>
165		i = molecules_.find(mol->getGlobalIndex());
166		if (i == molecules_.end() ) {
167	<
168	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
169	<
167	>
168	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
169	>
170		nAtoms_ += mol->getNAtoms();
171		nBonds_ += mol->getNBonds();
172		nBends_ += mol->getNBends();
173		nTorsions_ += mol->getNTorsions();
174	+	nInversions_ += mol->getNInversions();
175		nRigidBodies_ += mol->getNRigidBodies();
176		nIntegrableObjects_ += mol->getNIntegrableObjects();
177		nCutoffGroups_ += mol->getNCutoffGroups();
178		nConstraints_ += mol->getNConstraintPairs();
179	<
180	<	addExcludePairs(mol);
181	<
179	>
180	>	addInteractionPairs(mol);
181	>
182		return true;
183		} else {
184		return false;
185		}
186		}
187	<
187	>
188		bool SimInfo::removeMolecule(Molecule* mol) {
189		MoleculeIterator i;
190		i = molecules_.find(mol->getGlobalIndex());
#	Line 202 | Line 197 | namespace oopse {
197		nBonds_ -= mol->getNBonds();
198		nBends_ -= mol->getNBends();
199		nTorsions_ -= mol->getNTorsions();
200	+	nInversions_ -= mol->getNInversions();
201		nRigidBodies_ -= mol->getNRigidBodies();
202		nIntegrableObjects_ -= mol->getNIntegrableObjects();
203		nCutoffGroups_ -= mol->getNCutoffGroups();
204		nConstraints_ -= mol->getNConstraintPairs();
205
206	<	removeExcludePairs(mol);
206	>	removeInteractionPairs(mol);
207		molecules_.erase(mol->getGlobalIndex());
208
209		delete mol;
#	Line 216 | Line 212 | namespace oopse {
212		} else {
213		return false;
214		}
219	–
220	–
215		}
216
217
#	Line 235 | Line 229 | namespace oopse {
229		void SimInfo::calcNdf() {
230		int ndf_local;
231		MoleculeIterator i;
232	<	std::vector<StuntDouble*>::iterator j;
232	>	vector<StuntDouble*>::iterator j;
233		Molecule* mol;
234		StuntDouble* integrableObject;
235
#	Line 255 | Line 249 | namespace oopse {
249		}
250		}
251
252	<	}//end for (integrableObject)
253	<	}// end for (mol)
252	>	}
253	>	}
254
255		// n_constraints is local, so subtract them on each processor
256		ndf_local -= nConstraints_;
#	Line 273 | Line 267 | namespace oopse {
267
268		}
269
270	+	int SimInfo::getFdf() {
271	+	#ifdef IS_MPI
272	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
273	+	#else
274	+	fdf_ = fdf_local;
275	+	#endif
276	+	return fdf_;
277	+	}
278	+
279		void SimInfo::calcNdfRaw() {
280		int ndfRaw_local;
281
282		MoleculeIterator i;
283	<	std::vector<StuntDouble*>::iterator j;
283	>	vector<StuntDouble*>::iterator j;
284		Molecule* mol;
285		StuntDouble* integrableObject;
286
#	Line 324 | Line 327 | namespace oopse {
327
328		}
329
330	<	void SimInfo::addExcludePairs(Molecule* mol) {
331	<	std::vector<Bond*>::iterator bondIter;
332	<	std::vector<Bend*>::iterator bendIter;
333	<	std::vector<Torsion*>::iterator torsionIter;
330	>	void SimInfo::addInteractionPairs(Molecule* mol) {
331	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
332	>	vector<Bond*>::iterator bondIter;
333	>	vector<Bend*>::iterator bendIter;
334	>	vector<Torsion*>::iterator torsionIter;
335	>	vector<Inversion*>::iterator inversionIter;
336		Bond* bond;
337		Bend* bend;
338		Torsion* torsion;
339	+	Inversion* inversion;
340		int a;
341		int b;
342		int c;
343		int d;
344	+
345	+	// atomGroups can be used to add special interaction maps between
346	+	// groups of atoms that are in two separate rigid bodies.
347	+	// However, most site-site interactions between two rigid bodies
348	+	// are probably not special, just the ones between the physically
349	+	// bonded atoms.  Interactions *within* a single rigid body should
350	+	// always be excluded.  These are done at the bottom of this
351	+	// function.
352	+
353	+	map<int, set<int> > atomGroups;
354	+	Molecule::RigidBodyIterator rbIter;
355	+	RigidBody* rb;
356	+	Molecule::IntegrableObjectIterator ii;
357	+	StuntDouble* integrableObject;
358
359	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
359	>	for (integrableObject = mol->beginIntegrableObject(ii);
360	>	integrableObject != NULL;
361	>	integrableObject = mol->nextIntegrableObject(ii)) {
362	>
363	>	if (integrableObject->isRigidBody()) {
364	>	rb = static_cast<RigidBody*>(integrableObject);
365	>	vector<Atom*> atoms = rb->getAtoms();
366	>	set<int> rigidAtoms;
367	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
368	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
369	>	}
370	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
371	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
372	>	}
373	>	} else {
374	>	set<int> oneAtomSet;
375	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
376	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
377	>	}
378	>	}
379	>
380	>	for (bond= mol->beginBond(bondIter); bond != NULL;
381	>	bond = mol->nextBond(bondIter)) {
382	>
383		a = bond->getAtomA()->getGlobalIndex();
384	<	b = bond->getAtomB()->getGlobalIndex();
385	<	exclude_.addPair(a, b);
384	>	b = bond->getAtomB()->getGlobalIndex();
385	>
386	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
387	>	oneTwoInteractions_.addPair(a, b);
388	>	} else {
389	>	excludedInteractions_.addPair(a, b);
390	>	}
391		}
392
393	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
393	>	for (bend= mol->beginBend(bendIter); bend != NULL;
394	>	bend = mol->nextBend(bendIter)) {
395	>
396		a = bend->getAtomA()->getGlobalIndex();
397		b = bend->getAtomB()->getGlobalIndex();
398		c = bend->getAtomC()->getGlobalIndex();
399	+
400	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
401	+	oneTwoInteractions_.addPair(a, b);
402	+	oneTwoInteractions_.addPair(b, c);
403	+	} else {
404	+	excludedInteractions_.addPair(a, b);
405	+	excludedInteractions_.addPair(b, c);
406	+	}
407
408	<	exclude_.addPair(a, b);
409	<	exclude_.addPair(a, c);
410	<	exclude_.addPair(b, c);
408	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
409	>	oneThreeInteractions_.addPair(a, c);
410	>	} else {
411	>	excludedInteractions_.addPair(a, c);
412	>	}
413		}
414
415	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
415	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
416	>	torsion = mol->nextTorsion(torsionIter)) {
417	>
418		a = torsion->getAtomA()->getGlobalIndex();
419		b = torsion->getAtomB()->getGlobalIndex();
420		c = torsion->getAtomC()->getGlobalIndex();
421	<	d = torsion->getAtomD()->getGlobalIndex();
421	>	d = torsion->getAtomD()->getGlobalIndex();
422
423	<	exclude_.addPair(a, b);
424	<	exclude_.addPair(a, c);
425	<	exclude_.addPair(a, d);
426	<	exclude_.addPair(b, c);
427	<	exclude_.addPair(b, d);
428	<	exclude_.addPair(c, d);
423	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
424	>	oneTwoInteractions_.addPair(a, b);
425	>	oneTwoInteractions_.addPair(b, c);
426	>	oneTwoInteractions_.addPair(c, d);
427	>	} else {
428	>	excludedInteractions_.addPair(a, b);
429	>	excludedInteractions_.addPair(b, c);
430	>	excludedInteractions_.addPair(c, d);
431	>	}
432	>
433	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
434	>	oneThreeInteractions_.addPair(a, c);
435	>	oneThreeInteractions_.addPair(b, d);
436	>	} else {
437	>	excludedInteractions_.addPair(a, c);
438	>	excludedInteractions_.addPair(b, d);
439	>	}
440	>
441	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
442	>	oneFourInteractions_.addPair(a, d);
443	>	} else {
444	>	excludedInteractions_.addPair(a, d);
445	>	}
446		}
447
448	<	Molecule::RigidBodyIterator rbIter;
449	<	RigidBody* rb;
450	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
451	<	std::vector<Atom*> atoms = rb->getAtoms();
452	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
453	<	for (int j = i + 1; j < atoms.size(); ++j) {
448	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
449	>	inversion = mol->nextInversion(inversionIter)) {
450	>
451	>	a = inversion->getAtomA()->getGlobalIndex();
452	>	b = inversion->getAtomB()->getGlobalIndex();
453	>	c = inversion->getAtomC()->getGlobalIndex();
454	>	d = inversion->getAtomD()->getGlobalIndex();
455	>
456	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
457	>	oneTwoInteractions_.addPair(a, b);
458	>	oneTwoInteractions_.addPair(a, c);
459	>	oneTwoInteractions_.addPair(a, d);
460	>	} else {
461	>	excludedInteractions_.addPair(a, b);
462	>	excludedInteractions_.addPair(a, c);
463	>	excludedInteractions_.addPair(a, d);
464	>	}
465	>
466	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
467	>	oneThreeInteractions_.addPair(b, c);
468	>	oneThreeInteractions_.addPair(b, d);
469	>	oneThreeInteractions_.addPair(c, d);
470	>	} else {
471	>	excludedInteractions_.addPair(b, c);
472	>	excludedInteractions_.addPair(b, d);
473	>	excludedInteractions_.addPair(c, d);
474	>	}
475	>	}
476	>
477	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
478	>	rb = mol->nextRigidBody(rbIter)) {
479	>	vector<Atom*> atoms = rb->getAtoms();
480	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
481	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
482		a = atoms[i]->getGlobalIndex();
483		b = atoms[j]->getGlobalIndex();
484	<	exclude_.addPair(a, b);
484	>	excludedInteractions_.addPair(a, b);
485		}
486		}
487		}
488
489		}
490
491	<	void SimInfo::removeExcludePairs(Molecule* mol) {
492	<	std::vector<Bond*>::iterator bondIter;
493	<	std::vector<Bend*>::iterator bendIter;
494	<	std::vector<Torsion*>::iterator torsionIter;
491	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
492	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
493	>	vector<Bond*>::iterator bondIter;
494	>	vector<Bend*>::iterator bendIter;
495	>	vector<Torsion*>::iterator torsionIter;
496	>	vector<Inversion*>::iterator inversionIter;
497		Bond* bond;
498		Bend* bend;
499		Torsion* torsion;
500	+	Inversion* inversion;
501		int a;
502		int b;
503		int c;
504		int d;
505	+
506	+	map<int, set<int> > atomGroups;
507	+	Molecule::RigidBodyIterator rbIter;
508	+	RigidBody* rb;
509	+	Molecule::IntegrableObjectIterator ii;
510	+	StuntDouble* integrableObject;
511
512	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
512	>	for (integrableObject = mol->beginIntegrableObject(ii);
513	>	integrableObject != NULL;
514	>	integrableObject = mol->nextIntegrableObject(ii)) {
515	>
516	>	if (integrableObject->isRigidBody()) {
517	>	rb = static_cast<RigidBody*>(integrableObject);
518	>	vector<Atom*> atoms = rb->getAtoms();
519	>	set<int> rigidAtoms;
520	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
521	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
522	>	}
523	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
524	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
525	>	}
526	>	} else {
527	>	set<int> oneAtomSet;
528	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
529	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
530	>	}
531	>	}
532	>
533	>	for (bond= mol->beginBond(bondIter); bond != NULL;
534	>	bond = mol->nextBond(bondIter)) {
535	>
536		a = bond->getAtomA()->getGlobalIndex();
537	<	b = bond->getAtomB()->getGlobalIndex();
538	<	exclude_.removePair(a, b);
537	>	b = bond->getAtomB()->getGlobalIndex();
538	>
539	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
540	>	oneTwoInteractions_.removePair(a, b);
541	>	} else {
542	>	excludedInteractions_.removePair(a, b);
543	>	}
544		}
545
546	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
546	>	for (bend= mol->beginBend(bendIter); bend != NULL;
547	>	bend = mol->nextBend(bendIter)) {
548	>
549		a = bend->getAtomA()->getGlobalIndex();
550		b = bend->getAtomB()->getGlobalIndex();
551		c = bend->getAtomC()->getGlobalIndex();
552	+
553	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
554	+	oneTwoInteractions_.removePair(a, b);
555	+	oneTwoInteractions_.removePair(b, c);
556	+	} else {
557	+	excludedInteractions_.removePair(a, b);
558	+	excludedInteractions_.removePair(b, c);
559	+	}
560
561	<	exclude_.removePair(a, b);
562	<	exclude_.removePair(a, c);
563	<	exclude_.removePair(b, c);
561	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
562	>	oneThreeInteractions_.removePair(a, c);
563	>	} else {
564	>	excludedInteractions_.removePair(a, c);
565	>	}
566		}
567
568	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
568	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
569	>	torsion = mol->nextTorsion(torsionIter)) {
570	>
571		a = torsion->getAtomA()->getGlobalIndex();
572		b = torsion->getAtomB()->getGlobalIndex();
573		c = torsion->getAtomC()->getGlobalIndex();
574	<	d = torsion->getAtomD()->getGlobalIndex();
574	>	d = torsion->getAtomD()->getGlobalIndex();
575	>
576	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
577	>	oneTwoInteractions_.removePair(a, b);
578	>	oneTwoInteractions_.removePair(b, c);
579	>	oneTwoInteractions_.removePair(c, d);
580	>	} else {
581	>	excludedInteractions_.removePair(a, b);
582	>	excludedInteractions_.removePair(b, c);
583	>	excludedInteractions_.removePair(c, d);
584	>	}
585
586	<	exclude_.removePair(a, b);
587	<	exclude_.removePair(a, c);
588	<	exclude_.removePair(a, d);
589	<	exclude_.removePair(b, c);
590	<	exclude_.removePair(b, d);
591	<	exclude_.removePair(c, d);
586	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
587	>	oneThreeInteractions_.removePair(a, c);
588	>	oneThreeInteractions_.removePair(b, d);
589	>	} else {
590	>	excludedInteractions_.removePair(a, c);
591	>	excludedInteractions_.removePair(b, d);
592	>	}
593	>
594	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
595	>	oneFourInteractions_.removePair(a, d);
596	>	} else {
597	>	excludedInteractions_.removePair(a, d);
598	>	}
599		}
600
601	<	Molecule::RigidBodyIterator rbIter;
602	<	RigidBody* rb;
603	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
604	<	std::vector<Atom*> atoms = rb->getAtoms();
605	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
606	<	for (int j = i + 1; j < atoms.size(); ++j) {
601	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
602	>	inversion = mol->nextInversion(inversionIter)) {
603	>
604	>	a = inversion->getAtomA()->getGlobalIndex();
605	>	b = inversion->getAtomB()->getGlobalIndex();
606	>	c = inversion->getAtomC()->getGlobalIndex();
607	>	d = inversion->getAtomD()->getGlobalIndex();
608	>
609	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
610	>	oneTwoInteractions_.removePair(a, b);
611	>	oneTwoInteractions_.removePair(a, c);
612	>	oneTwoInteractions_.removePair(a, d);
613	>	} else {
614	>	excludedInteractions_.removePair(a, b);
615	>	excludedInteractions_.removePair(a, c);
616	>	excludedInteractions_.removePair(a, d);
617	>	}
618	>
619	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
620	>	oneThreeInteractions_.removePair(b, c);
621	>	oneThreeInteractions_.removePair(b, d);
622	>	oneThreeInteractions_.removePair(c, d);
623	>	} else {
624	>	excludedInteractions_.removePair(b, c);
625	>	excludedInteractions_.removePair(b, d);
626	>	excludedInteractions_.removePair(c, d);
627	>	}
628	>	}
629	>
630	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
631	>	rb = mol->nextRigidBody(rbIter)) {
632	>	vector<Atom*> atoms = rb->getAtoms();
633	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
634	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
635		a = atoms[i]->getGlobalIndex();
636		b = atoms[j]->getGlobalIndex();
637	<	exclude_.removePair(a, b);
637	>	excludedInteractions_.removePair(a, b);
638		}
639		}
640		}
641	<
641	>
642		}
643	<
644	<
643	>
644	>
645		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
646		int curStampId;
647	<
647	>
648		//index from 0
649		curStampId = moleculeStamps_.size();
650
#	Line 449 | Line 652 | namespace oopse {
652		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
653		}
654
655	+
656	+	/**
657	+	* update
658	+	*
659	+	*  Performs the global checks and variable settings after the objects have been
660	+	*  created.
661	+	*
662	+	*/
663		void SimInfo::update() {
664	+
665	+	setupSimVariables();
666	+	setupCutoffs();
667	+	setupSwitching();
668	+	setupElectrostatics();
669	+	setupNeighborlists();
670
454	–	setupSimType();
455	–
671		#ifdef IS_MPI
672		setupFortranParallel();
673		#endif
459	–
674		setupFortranSim();
675	+	fortranInitialized_ = true;
676
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	–
677		calcNdf();
678		calcNdfRaw();
679		calcNdfTrans();
479	–
480	–	fortranInitialized_ = true;
680		}
681	<
682	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
681	>
682	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
683		SimInfo::MoleculeIterator mi;
684		Molecule* mol;
685		Molecule::AtomIterator ai;
686		Atom* atom;
687	<	std::set<AtomType*> atomTypes;
688	<
689	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
491	<
687	>	set<AtomType*> atomTypes;
688	>
689	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
690		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
691		atomTypes.insert(atom->getAtomType());
692	<	}
693	<
496	<	}
497	<
692	>	}
693	>	}
694		return atomTypes;
695		}
696
697	<	void SimInfo::setupSimType() {
698	<	std::set<AtomType*>::iterator i;
699	<	std::set<AtomType*> atomTypes;
700	<	atomTypes = getUniqueAtomTypes();
697	>	/**
698	>	* setupCutoffs
699	>	*
700	>	* Sets the values of cutoffRadius and cutoffMethod
701	>	*
702	>	* cutoffRadius : realType
703	>	*  If the cutoffRadius was explicitly set, use that value.
704	>	*  If the cutoffRadius was not explicitly set:
705	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
706	>	*      No electrostatic atoms?  Poll the atom types present in the
707	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
708	>	*      Use the maximum suggested value that was found.
709	>	*
710	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
711	>	*      If cutoffMethod was explicitly set, use that choice.
712	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
713	>	*/
714	>	void SimInfo::setupCutoffs() {
715
716	<	int useLennardJones = 0;
717	<	int useElectrostatic = 0;
718	<	int useEAM = 0;
719	<	int useCharge = 0;
720	<	int useDirectional = 0;
721	<	int useDipole = 0;
722	<	int useGayBerne = 0;
723	<	int useSticky = 0;
724	<	int useShape = 0;
725	<	int useFLARB = 0; //it is not in AtomType yet
726	<	int useDirectionalAtom = 0;
727	<	int useElectrostatics = 0;
728	<	//usePBC and useRF are from simParams
729	<	int usePBC = simParams_->getPBC();
730	<	int useRF = simParams_->getUseRF();
731	<
732	<	//loop over all of the atom types
733	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
734	<	useLennardJones |= (*i)->isLennardJones();
735	<	useElectrostatic |= (*i)->isElectrostatic();
736	<	useEAM |= (*i)->isEAM();
737	<	useCharge |= (*i)->isCharge();
738	<	useDirectional |= (*i)->isDirectional();
739	<	useDipole |= (*i)->isDipole();
740	<	useGayBerne |= (*i)->isGayBerne();
741	<	useSticky |= (*i)->isSticky();
742	<	useShape |= (*i)->isShape();
716	>	if (simParams_->haveCutoffRadius()) {
717	>	cutoffRadius_ = simParams_->getCutoffRadius();
718	>	} else {
719	>	if (usesElectrostaticAtoms_) {
720	>	sprintf(painCave.errMsg,
721	>	"SimInfo: No value was set for the cutoffRadius.\n"
722	>	"\tOpenMD will use a default value of 12.0 angstroms"
723	>	"\tfor the cutoffRadius.\n");
724	>	painCave.isFatal = 0;
725	>	painCave.severity = OPENMD_INFO;
726	>	simError();
727	>	cutoffRadius_ = 12.0;
728	>	} else {
729	>	RealType thisCut;
730	>	set<AtomType*>::iterator i;
731	>	set<AtomType*> atomTypes;
732	>	atomTypes = getSimulatedAtomTypes();
733	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
734	>	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
735	>	cutoffRadius_ = max(thisCut, cutoffRadius_);
736	>	}
737	>	sprintf(painCave.errMsg,
738	>	"SimInfo: No value was set for the cutoffRadius.\n"
739	>	"\tOpenMD will use %lf angstroms.\n",
740	>	cutoffRadius_);
741	>	painCave.isFatal = 0;
742	>	painCave.severity = OPENMD_INFO;
743	>	simError();
744	>	}
745		}
746
747	<	if (useSticky || useDipole || useGayBerne || useShape) {
748	<	useDirectionalAtom = 1;
747	>	map<string, CutoffMethod> stringToCutoffMethod;
748	>	stringToCutoffMethod["HARD"] = HARD;
749	>	stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
750	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
751	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
752	>
753	>	if (simParams_->haveCutoffMethod()) {
754	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
755	>	map<string, CutoffMethod>::iterator i;
756	>	i = stringToCutoffMethod.find(cutMeth);
757	>	if (i == stringToCutoffMethod.end()) {
758	>	sprintf(painCave.errMsg,
759	>	"SimInfo: Could not find chosen cutoffMethod %s\n"
760	>	"\tShould be one of: "
761	>	"HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
762	>	cutMeth.c_str());
763	>	painCave.isFatal = 1;
764	>	painCave.severity = OPENMD_ERROR;
765	>	simError();
766	>	} else {
767	>	cutoffMethod_ = i->second;
768	>	}
769	>	} else {
770	>	sprintf(painCave.errMsg,
771	>	"SimInfo: No value was set for the cutoffMethod.\n"
772	>	"\tOpenMD will use SHIFTED_FORCE.\n");
773	>	painCave.isFatal = 0;
774	>	painCave.severity = OPENMD_INFO;
775	>	simError();
776	>	cutoffMethod_ = SHIFTED_FORCE;
777		}
778	+	}
779	+
780	+	/**
781	+	* setupSwitching
782	+	*
783	+	* Sets the values of switchingRadius and
784	+	*  If the switchingRadius was explicitly set, use that value (but check it)
785	+	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
786	+	*/
787	+	void SimInfo::setupSwitching() {
788	+
789	+	if (simParams_->haveSwitchingRadius()) {
790	+	switchingRadius_ = simParams_->getSwitchingRadius();
791	+	if (switchingRadius_ > cutoffRadius_) {
792	+	sprintf(painCave.errMsg,
793	+	"SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
794	+	switchingRadius_, cutoffRadius_);
795	+	painCave.isFatal = 1;
796	+	painCave.severity = OPENMD_ERROR;
797	+	simError();
798	+	}
799	+	} else {
800	+	switchingRadius_ = 0.85 * cutoffRadius_;
801	+	sprintf(painCave.errMsg,
802	+	"SimInfo: No value was set for the switchingRadius.\n"
803	+	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
804	+	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
805	+	painCave.isFatal = 0;
806	+	painCave.severity = OPENMD_WARNING;
807	+	simError();
808	+	}
809	+
810	+	if (simParams_->haveSwitchingFunctionType()) {
811	+	string funcType = simParams_->getSwitchingFunctionType();
812	+	toUpper(funcType);
813	+	if (funcType == "CUBIC") {
814	+	sft_ = cubic;
815	+	} else {
816	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
817	+	sft_ = fifth_order_poly;
818	+	} else {
819	+	// throw error
820	+	sprintf( painCave.errMsg,
821	+	"SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
822	+	"\tswitchingFunctionType must be one of: "
823	+	"\"cubic\" or \"fifth_order_polynomial\".",
824	+	funcType.c_str() );
825	+	painCave.isFatal = 1;
826	+	painCave.severity = OPENMD_ERROR;
827	+	simError();
828	+	}
829	+	}
830	+	}
831	+	}
832
833	<	if (useCharge || useDipole) {
834	<	useElectrostatics = 1;
833	>	/**
834	>	* setupNeighborlists
835	>	*
836	>	*  If the skinThickness was explicitly set, use that value (but check it)
837	>	*  If the skinThickness was not explicitly set: use 1.0 angstroms
838	>	*/
839	>	void SimInfo::setupNeighborlists() {
840	>	if (simParams_->haveSkinThickness()) {
841	>	skinThickness_ = simParams_->getSkinThickness();
842	>	} else {
843	>	skinThickness_ = 1.0;
844	>	sprintf(painCave.errMsg,
845	>	"SimInfo: No value was set for the skinThickness.\n"
846	>	"\tOpenMD will use a default value of %f Angstroms\n"
847	>	"\tfor this simulation\n", skinThickness_);
848	>	painCave.severity = OPENMD_INFO;
849	>	painCave.isFatal = 0;
850	>	simError();
851	>	}
852	>	}
853	>
854	>	void SimInfo::setupSimVariables() {
855	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
856	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
857	>	calcBoxDipole_ = false;
858	>	if ( simParams_->haveAccumulateBoxDipole() )
859	>	if ( simParams_->getAccumulateBoxDipole() ) {
860	>	calcBoxDipole_ = true;
861	>	}
862	>
863	>	set<AtomType*>::iterator i;
864	>	set<AtomType*> atomTypes;
865	>	atomTypes = getSimulatedAtomTypes();
866	>	int usesElectrostatic = 0;
867	>	int usesMetallic = 0;
868	>	int usesDirectional = 0;
869	>	//loop over all of the atom types
870	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
871	>	usesElectrostatic |= (*i)->isElectrostatic();
872	>	usesMetallic |= (*i)->isMetal();
873	>	usesDirectional |= (*i)->isDirectional();
874		}
875
876		#ifdef IS_MPI
877		int temp;
878	+	temp = usesDirectional;
879	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
880
881	<	temp = usePBC;
882	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
548	<
549	<	temp = useDirectionalAtom;
550	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
551	<
552	<	temp = useLennardJones;
553	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
554	<
555	<	temp = useElectrostatics;
556	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
881	>	temp = usesMetallic;
882	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
883
884	<	temp = useCharge;
885	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
560	<
561	<	temp = useDipole;
562	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
563	<
564	<	temp = useSticky;
565	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
566	<
567	<	temp = useGayBerne;
568	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
569	<
570	<	temp = useEAM;
571	<	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	<
884	>	temp = usesElectrostatic;
885	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
886		#endif
887	<
888	<	fInfo_.SIM_uses_PBC = usePBC;
889	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
890	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
891	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
892	<	fInfo_.SIM_uses_Charges = useCharge;
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	<
887	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
888	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
889	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
890	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
891	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
892	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
893		}
894
895		void SimInfo::setupFortranSim() {
896		int isError;
897	<	int nExclude;
898	<	std::vector<int> fortranGlobalGroupMembership;
897	>	int nExclude, nOneTwo, nOneThree, nOneFour;
898	>	vector<int> fortranGlobalGroupMembership;
899
900	<	nExclude = exclude_.getSize();
900	>	notifyFortranSkinThickness(&skinThickness_);
901	>
902	>	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
903	>	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
904	>	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
905	>
906		isError = 0;
907
908		//globalGroupMembership_ is filled by SimCreator
#	Line 627 | Line 911 | namespace oopse {
911		}
912
913		//calculate mass ratio of cutoff group
914	<	std::vector<double> mfact;
914	>	vector<RealType> mfact;
915		SimInfo::MoleculeIterator mi;
916		Molecule* mol;
917		Molecule::CutoffGroupIterator ci;
918		CutoffGroup* cg;
919		Molecule::AtomIterator ai;
920		Atom* atom;
921	<	double totalMass;
921	>	RealType totalMass;
922
923		//to avoid memory reallocation, reserve enough space for mfact
924		mfact.reserve(getNCutoffGroups());
#	Line 644 | Line 928 | namespace oopse {
928
929		totalMass = cg->getMass();
930		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
931	<	mfact.push_back(atom->getMass()/totalMass);
931	>	// Check for massless groups - set mfact to 1 if true
932	>	if (totalMass != 0)
933	>	mfact.push_back(atom->getMass()/totalMass);
934	>	else
935	>	mfact.push_back( 1.0 );
936		}
649	–
937		}
938		}
939
940		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
941	<	std::vector<int> identArray;
941	>	vector<int> identArray;
942
943		//to avoid memory reallocation, reserve enough space identArray
944		identArray.reserve(getNAtoms());
#	Line 664 | Line 951 | namespace oopse {
951
952		//fill molMembershipArray
953		//molMembershipArray is filled by SimCreator
954	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
954	>	vector<int> molMembershipArray(nGlobalAtoms_);
955		for (int i = 0; i < nGlobalAtoms_; i++) {
956		molMembershipArray[i] = globalMolMembership_[i] + 1;
957		}
958
959		//setup fortran simulation
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);
960
961	<	if( isError ){
961	>	nExclude = excludedInteractions_.getSize();
962	>	nOneTwo = oneTwoInteractions_.getSize();
963	>	nOneThree = oneThreeInteractions_.getSize();
964	>	nOneFour = oneFourInteractions_.getSize();
965
966	+	int* excludeList = excludedInteractions_.getPairList();
967	+	int* oneTwoList = oneTwoInteractions_.getPairList();
968	+	int* oneThreeList = oneThreeInteractions_.getPairList();
969	+	int* oneFourList = oneFourInteractions_.getPairList();
970	+
971	+	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
972	+	&nExclude, excludeList,
973	+	&nOneTwo, oneTwoList,
974	+	&nOneThree, oneThreeList,
975	+	&nOneFour, oneFourList,
976	+	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
977	+	&fortranGlobalGroupMembership[0], &isError);
978	+
979	+	if( isError ){
980	+
981		sprintf( painCave.errMsg,
982		"There was an error setting the simulation information in fortran.\n" );
983		painCave.isFatal = 1;
984	<	painCave.severity = OOPSE_ERROR;
984	>	painCave.severity = OPENMD_ERROR;
985		simError();
986		}
987	<
988	<	#ifdef IS_MPI
987	>
988	>
989		sprintf( checkPointMsg,
990		"succesfully sent the simulation information to fortran.\n");
991	<	MPIcheckPoint();
992	<	#endif // is_mpi
991	>
992	>	errorCheckPoint();
993	>
994	>	// Setup number of neighbors in neighbor list if present
995	>	if (simParams_->haveNeighborListNeighbors()) {
996	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
997	>	setNeighbors(&nlistNeighbors);
998	>	}
999	>
1000	>
1001		}
1002
1003
697	–	#ifdef IS_MPI
1004		void SimInfo::setupFortranParallel() {
1005	<
1005	>	#ifdef IS_MPI
1006		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1007	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1008	<	std::vector<int> localToGlobalCutoffGroupIndex;
1007	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1008	>	vector<int> localToGlobalCutoffGroupIndex;
1009		SimInfo::MoleculeIterator mi;
1010		Molecule::AtomIterator ai;
1011		Molecule::CutoffGroupIterator ci;
#	Line 746 | Line 1052 | namespace oopse {
1052		}
1053
1054		sprintf(checkPointMsg, " mpiRefresh successful.\n");
1055	<	MPIcheckPoint();
750	<
751	<
752	<	}
753	<
754	<	#endif
755	<
756	<	double SimInfo::calcMaxCutoffRadius() {
757	<
758	<
759	<	std::set<AtomType*> atomTypes;
760	<	std::set<AtomType*>::iterator i;
761	<	std::vector<double> cutoffRadius;
1055	>	errorCheckPoint();
1056
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	–	}
770	–
771	–	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
772	–	#ifdef IS_MPI
773	–	//pick the max cutoff radius among the processors
1057		#endif
775	–
776	–	return maxCutoffRadius;
1058		}
1059
779	–	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	–	}
1060
1061	<	if (!simParams_->haveRsw()){
796	<	sprintf(painCave.errMsg,
797	<	"SimCreator Warning: No value was set for switchingRadius.\n"
798	<	"\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();
805	<	}
1061	>	void SimInfo::setupAccumulateBoxDipole() {
1062
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	–	}
1063
818	–	if (simParams_->haveRsw()) {
819	–	rsw  = simParams_->getRsw();
820	–	} else {
821	–	rsw = rcut;
822	–	}
823	–
824	–	}
1064		}
1065
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	–
1066		void SimInfo::addProperty(GenericData* genData) {
1067		properties_.addProperty(genData);
1068		}
1069
1070	<	void SimInfo::removeProperty(const std::string& propName) {
1070	>	void SimInfo::removeProperty(const string& propName) {
1071		properties_.removeProperty(propName);
1072		}
1073
#	Line 844 | Line 1075 | namespace oopse {
1075		properties_.clearProperties();
1076		}
1077
1078	<	std::vector<std::string> SimInfo::getPropertyNames() {
1078	>	vector<string> SimInfo::getPropertyNames() {
1079		return properties_.getPropertyNames();
1080		}
1081
1082	<	std::vector<GenericData*> SimInfo::getProperties() {
1082	>	vector<GenericData*> SimInfo::getProperties() {
1083		return properties_.getProperties();
1084		}
1085
1086	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1086	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1087		return properties_.getPropertyByName(propName);
1088		}
1089
#	Line 888 | Line 1119 | namespace oopse {
1119		Molecule* mol;
1120
1121		Vector3d comVel(0.0);
1122	<	double totalMass = 0.0;
1122	>	RealType totalMass = 0.0;
1123
1124
1125		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1126	<	double mass = mol->getMass();
1126	>	RealType mass = mol->getMass();
1127		totalMass += mass;
1128		comVel += mass * mol->getComVel();
1129		}
1130
1131		#ifdef IS_MPI
1132	<	double tmpMass = totalMass;
1132	>	RealType tmpMass = totalMass;
1133		Vector3d tmpComVel(comVel);
1134	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1135	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1134	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1135	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1136		#endif
1137
1138		comVel /= totalMass;
#	Line 914 | Line 1145 | namespace oopse {
1145		Molecule* mol;
1146
1147		Vector3d com(0.0);
1148	<	double totalMass = 0.0;
1148	>	RealType totalMass = 0.0;
1149
1150		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1151	<	double mass = mol->getMass();
1151	>	RealType mass = mol->getMass();
1152		totalMass += mass;
1153		com += mass * mol->getCom();
1154		}
1155
1156		#ifdef IS_MPI
1157	<	double tmpMass = totalMass;
1157	>	RealType tmpMass = totalMass;
1158		Vector3d tmpCom(com);
1159	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1160	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1159	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1160	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1161		#endif
1162
1163		com /= totalMass;
#	Line 935 | Line 1166 | namespace oopse {
1166
1167		}
1168
1169	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1169	>	ostream& operator <<(ostream& o, SimInfo& info) {
1170
1171		return o;
1172		}
1173	+
1174	+
1175	+	/*
1176	+	Returns center of mass and center of mass velocity in one function call.
1177	+	*/
1178	+
1179	+	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1180	+	SimInfo::MoleculeIterator i;
1181	+	Molecule* mol;
1182	+
1183	+
1184	+	RealType totalMass = 0.0;
1185	+
1186
1187	<	}//end namespace oopse
1187	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1188	>	RealType mass = mol->getMass();
1189	>	totalMass += mass;
1190	>	com += mass * mol->getCom();
1191	>	comVel += mass * mol->getComVel();
1192	>	}
1193	>
1194	>	#ifdef IS_MPI
1195	>	RealType tmpMass = totalMass;
1196	>	Vector3d tmpCom(com);
1197	>	Vector3d tmpComVel(comVel);
1198	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1199	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1200	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1201	>	#endif
1202	>
1203	>	com /= totalMass;
1204	>	comVel /= totalMass;
1205	>	}
1206	>
1207	>	/*
1208	>	Return intertia tensor for entire system and angular momentum Vector.
1209	>
1210	>
1211	>	[  Ixx -Ixy  -Ixz ]
1212	>	J =| -Iyx  Iyy  -Iyz |
1213	>	[ -Izx -Iyz   Izz ]
1214	>	*/
1215	>
1216	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1217	>
1218	>
1219	>	RealType xx = 0.0;
1220	>	RealType yy = 0.0;
1221	>	RealType zz = 0.0;
1222	>	RealType xy = 0.0;
1223	>	RealType xz = 0.0;
1224	>	RealType yz = 0.0;
1225	>	Vector3d com(0.0);
1226	>	Vector3d comVel(0.0);
1227	>
1228	>	getComAll(com, comVel);
1229	>
1230	>	SimInfo::MoleculeIterator i;
1231	>	Molecule* mol;
1232	>
1233	>	Vector3d thisq(0.0);
1234	>	Vector3d thisv(0.0);
1235
1236	+	RealType thisMass = 0.0;
1237	+
1238	+
1239	+
1240	+
1241	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1242	+
1243	+	thisq = mol->getCom()-com;
1244	+	thisv = mol->getComVel()-comVel;
1245	+	thisMass = mol->getMass();
1246	+	// Compute moment of intertia coefficients.
1247	+	xx += thisq[0]*thisq[0]*thisMass;
1248	+	yy += thisq[1]*thisq[1]*thisMass;
1249	+	zz += thisq[2]*thisq[2]*thisMass;
1250	+
1251	+	// compute products of intertia
1252	+	xy += thisq[0]*thisq[1]*thisMass;
1253	+	xz += thisq[0]*thisq[2]*thisMass;
1254	+	yz += thisq[1]*thisq[2]*thisMass;
1255	+
1256	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1257	+
1258	+	}
1259	+
1260	+
1261	+	inertiaTensor(0,0) = yy + zz;
1262	+	inertiaTensor(0,1) = -xy;
1263	+	inertiaTensor(0,2) = -xz;
1264	+	inertiaTensor(1,0) = -xy;
1265	+	inertiaTensor(1,1) = xx + zz;
1266	+	inertiaTensor(1,2) = -yz;
1267	+	inertiaTensor(2,0) = -xz;
1268	+	inertiaTensor(2,1) = -yz;
1269	+	inertiaTensor(2,2) = xx + yy;
1270	+
1271	+	#ifdef IS_MPI
1272	+	Mat3x3d tmpI(inertiaTensor);
1273	+	Vector3d tmpAngMom;
1274	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1275	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1276	+	#endif
1277	+
1278	+	return;
1279	+	}
1280	+
1281	+	//Returns the angular momentum of the system
1282	+	Vector3d SimInfo::getAngularMomentum(){
1283	+
1284	+	Vector3d com(0.0);
1285	+	Vector3d comVel(0.0);
1286	+	Vector3d angularMomentum(0.0);
1287	+
1288	+	getComAll(com,comVel);
1289	+
1290	+	SimInfo::MoleculeIterator i;
1291	+	Molecule* mol;
1292	+
1293	+	Vector3d thisr(0.0);
1294	+	Vector3d thisp(0.0);
1295	+
1296	+	RealType thisMass;
1297	+
1298	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1299	+	thisMass = mol->getMass();
1300	+	thisr = mol->getCom()-com;
1301	+	thisp = (mol->getComVel()-comVel)*thisMass;
1302	+
1303	+	angularMomentum += cross( thisr, thisp );
1304	+
1305	+	}
1306	+
1307	+	#ifdef IS_MPI
1308	+	Vector3d tmpAngMom;
1309	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1310	+	#endif
1311	+
1312	+	return angularMomentum;
1313	+	}
1314	+
1315	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1316	+	return IOIndexToIntegrableObject.at(index);
1317	+	}
1318	+
1319	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1320	+	IOIndexToIntegrableObject= v;
1321	+	}
1322	+
1323	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1324	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1325	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1326	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1327	+	*/
1328	+	void SimInfo::getGyrationalVolume(RealType &volume){
1329	+	Mat3x3d intTensor;
1330	+	RealType det;
1331	+	Vector3d dummyAngMom;
1332	+	RealType sysconstants;
1333	+	RealType geomCnst;
1334	+
1335	+	geomCnst = 3.0/2.0;
1336	+	/* Get the inertial tensor and angular momentum for free*/
1337	+	getInertiaTensor(intTensor,dummyAngMom);
1338	+
1339	+	det = intTensor.determinant();
1340	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1341	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1342	+	return;
1343	+	}
1344	+
1345	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1346	+	Mat3x3d intTensor;
1347	+	Vector3d dummyAngMom;
1348	+	RealType sysconstants;
1349	+	RealType geomCnst;
1350	+
1351	+	geomCnst = 3.0/2.0;
1352	+	/* Get the inertial tensor and angular momentum for free*/
1353	+	getInertiaTensor(intTensor,dummyAngMom);
1354	+
1355	+	detI = intTensor.determinant();
1356	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1357	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1358	+	return;
1359	+	}
1360	+	/*
1361	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1362	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1363	+	sdByGlobalIndex_ = v;
1364	+	}
1365	+
1366	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1367	+	//assert(index < nAtoms_ + nRigidBodies_);
1368	+	return sdByGlobalIndex_.at(index);
1369	+	}
1370	+	*/
1371	+	int SimInfo::getNGlobalConstraints() {
1372	+	int nGlobalConstraints;
1373	+	#ifdef IS_MPI
1374	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1375	+	MPI_COMM_WORLD);
1376	+	#else
1377	+	nGlobalConstraints =  nConstraints_;
1378	+	#endif
1379	+	return nGlobalConstraints;
1380	+	}
1381	+
1382	+	}//end namespace OpenMD
1383	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1534 by gezelter, Wed Dec 29 21:53:28 2010 UTC

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

Diff Legend

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