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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 1024 by tim, Wed Aug 30 18:42:29 2006 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1668 by gezelter, Fri Jan 6 19:03:05 2012 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 54 | Line 55
55		#include "math/Vector3.hpp"
56		#include "primitives/Molecule.hpp"
57		#include "primitives/StuntDouble.hpp"
57	–	#include "UseTheForce/fCutoffPolicy.h"
58	–	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	–	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60	–	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61	–	#include "UseTheForce/doForces_interface.h"
62	–	#include "UseTheForce/DarkSide/electrostatic_interface.h"
63	–	#include "UseTheForce/DarkSide/switcheroo_interface.h"
58		#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60		#include "selection/SelectionManager.hpp"
61		#include "io/ForceFieldOptions.hpp"
62		#include "UseTheForce/ForceField.hpp"
63	<
63	>	#include "nonbonded/SwitchingFunction.hpp"
64		#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
73	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68	<	namespace oopse {
69	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
77	<	std::map<int, std::set<int> >::iterator i = container.find(index);
78	<	std::set<int> result;
79	<	if (i != container.end()) {
80	<	result = i->second;
81	<	}
82	<
83	<	return result;
84	<	}
68	>	using namespace std;
69	>	namespace OpenMD {
70
71		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72		forceField_(ff), simParams_(simParams),
73		ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
77	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
78	<	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) {
79	<
80	<	MoleculeStamp* molStamp;
81	<	int nMolWithSameStamp;
82	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
83	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
84	<	CutoffGroupStamp* cgStamp;
85	<	RigidBodyStamp* rbStamp;
86	<	int nRigidAtoms = 0;
87	<	std::vector<Component*> components = simParams->getComponents();
76	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78	>	nConstraints_(0), sman_(NULL), topologyDone_(false),
79	>	calcBoxDipole_(false), useAtomicVirial_(true) {
80	>
81	>	MoleculeStamp* molStamp;
82	>	int nMolWithSameStamp;
83	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
85	>	CutoffGroupStamp* cgStamp;
86	>	RigidBodyStamp* rbStamp;
87	>	int nRigidAtoms = 0;
88	>
89	>	vector<Component*> components = simParams->getComponents();
90	>
91	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
92	>	molStamp = (*i)->getMoleculeStamp();
93	>	nMolWithSameStamp = (*i)->getNMol();
94
95	<	for (std::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();
116	<
117	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
118	<	cgStamp = molStamp->getCutoffGroupStamp(j);
119	<	nAtomsInGroups += cgStamp->getNMembers();
120	<	}
121	<
122	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
123	<
124	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
125	<
126	<	//calculate atoms in rigid bodies
127	<	int nAtomsInRigidBodies = 0;
128	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
129	<
130	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
131	<	rbStamp = molStamp->getRigidBodyStamp(j);
132	<	nAtomsInRigidBodies += rbStamp->getNMembers();
133	<	}
134	<
135	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
136	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
137	<
95	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
96	>
97	>	//calculate atoms in molecules
98	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
99	>
100	>	//calculate atoms in cutoff groups
101	>	int nAtomsInGroups = 0;
102	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
103	>
104	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
105	>	cgStamp = molStamp->getCutoffGroupStamp(j);
106	>	nAtomsInGroups += cgStamp->getNMembers();
107		}
108	<
109	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
110	<	//group therefore the total number of cutoff groups in the system is
111	<	//equal to the total number of atoms minus number of atoms belong to
112	<	//cutoff group defined in meta-data file plus the number of cutoff
113	<	//groups defined in meta-data file
114	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
115	<
116	<	//every free atom (atom does not belong to rigid bodies) is an
117	<	//integrable object therefore the total number of integrable objects
118	<	//in the system is equal to the total number of atoms minus number of
119	<	//atoms belong to rigid body defined in meta-data file plus the number
120	<	//of rigid bodies defined in meta-data file
121	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
122	<	+ nGlobalRigidBodies_;
123	<
124	<	nGlobalMols_ = molStampIds_.size();
156	<
157	<	#ifdef IS_MPI
158	<	molToProcMap_.resize(nGlobalMols_);
159	<	#endif
160	<
108	>
109	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
110	>
111	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
112	>
113	>	//calculate atoms in rigid bodies
114	>	int nAtomsInRigidBodies = 0;
115	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
116	>
117	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
118	>	rbStamp = molStamp->getRigidBodyStamp(j);
119	>	nAtomsInRigidBodies += rbStamp->getNMembers();
120	>	}
121	>
122	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
123	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
124	>
125		}
126	+
127	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
128	+	//group therefore the total number of cutoff groups in the system is
129	+	//equal to the total number of atoms minus number of atoms belong to
130	+	//cutoff group defined in meta-data file plus the number of cutoff
131	+	//groups defined in meta-data file
132
133	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134	+
135	+	//every free atom (atom does not belong to rigid bodies) is an
136	+	//integrable object therefore the total number of integrable objects
137	+	//in the system is equal to the total number of atoms minus number of
138	+	//atoms belong to rigid body defined in meta-data file plus the number
139	+	//of rigid bodies defined in meta-data file
140	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
141	+	+ nGlobalRigidBodies_;
142	+
143	+	nGlobalMols_ = molStampIds_.size();
144	+	molToProcMap_.resize(nGlobalMols_);
145	+	}
146	+
147		SimInfo::~SimInfo() {
148	<	std::map<int, Molecule*>::iterator i;
148	>	map<int, Molecule*>::iterator i;
149		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
150		delete i->second;
151		}
#	Line 172 | Line 156 | namespace oopse {
156		delete forceField_;
157		}
158
175	–	int SimInfo::getNGlobalConstraints() {
176	–	int nGlobalConstraints;
177	–	#ifdef IS_MPI
178	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
179	–	MPI_COMM_WORLD);
180	–	#else
181	–	nGlobalConstraints =  nConstraints_;
182	–	#endif
183	–	return nGlobalConstraints;
184	–	}
159
160		bool SimInfo::addMolecule(Molecule* mol) {
161		MoleculeIterator i;
162	<
162	>
163		i = molecules_.find(mol->getGlobalIndex());
164		if (i == molecules_.end() ) {
165	<
166	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
167	<
165	>
166	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
167	>
168		nAtoms_ += mol->getNAtoms();
169		nBonds_ += mol->getNBonds();
170		nBends_ += mol->getNBends();
171		nTorsions_ += mol->getNTorsions();
172	+	nInversions_ += mol->getNInversions();
173		nRigidBodies_ += mol->getNRigidBodies();
174		nIntegrableObjects_ += mol->getNIntegrableObjects();
175		nCutoffGroups_ += mol->getNCutoffGroups();
176		nConstraints_ += mol->getNConstraintPairs();
177	<
178	<	addExcludePairs(mol);
179	<
177	>
178	>	addInteractionPairs(mol);
179	>
180		return true;
181		} else {
182		return false;
183		}
184		}
185	<
185	>
186		bool SimInfo::removeMolecule(Molecule* mol) {
187		MoleculeIterator i;
188		i = molecules_.find(mol->getGlobalIndex());
#	Line 220 | Line 195 | namespace oopse {
195		nBonds_ -= mol->getNBonds();
196		nBends_ -= mol->getNBends();
197		nTorsions_ -= mol->getNTorsions();
198	+	nInversions_ -= mol->getNInversions();
199		nRigidBodies_ -= mol->getNRigidBodies();
200		nIntegrableObjects_ -= mol->getNIntegrableObjects();
201		nCutoffGroups_ -= mol->getNCutoffGroups();
202		nConstraints_ -= mol->getNConstraintPairs();
203
204	<	removeExcludePairs(mol);
204	>	removeInteractionPairs(mol);
205		molecules_.erase(mol->getGlobalIndex());
206
207		delete mol;
#	Line 234 | Line 210 | namespace oopse {
210		} else {
211		return false;
212		}
237	–
238	–
213		}
214
215
#	Line 253 | Line 227 | namespace oopse {
227		void SimInfo::calcNdf() {
228		int ndf_local;
229		MoleculeIterator i;
230	<	std::vector<StuntDouble*>::iterator j;
230	>	vector<StuntDouble*>::iterator j;
231		Molecule* mol;
232		StuntDouble* integrableObject;
233
#	Line 299 | Line 273 | namespace oopse {
273		#endif
274		return fdf_;
275		}
276	+
277	+	unsigned int SimInfo::getNLocalCutoffGroups(){
278	+	int nLocalCutoffAtoms = 0;
279	+	Molecule* mol;
280	+	MoleculeIterator mi;
281	+	CutoffGroup* cg;
282	+	Molecule::CutoffGroupIterator ci;
283
284	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
285	+
286	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
287	+	cg = mol->nextCutoffGroup(ci)) {
288	+	nLocalCutoffAtoms += cg->getNumAtom();
289	+
290	+	}
291	+	}
292	+
293	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
294	+	}
295	+
296		void SimInfo::calcNdfRaw() {
297		int ndfRaw_local;
298
299		MoleculeIterator i;
300	<	std::vector<StuntDouble*>::iterator j;
300	>	vector<StuntDouble*>::iterator j;
301		Molecule* mol;
302		StuntDouble* integrableObject;
303
#	Line 351 | Line 344 | namespace oopse {
344
345		}
346
347	<	void SimInfo::addExcludePairs(Molecule* mol) {
348	<	std::vector<Bond*>::iterator bondIter;
349	<	std::vector<Bend*>::iterator bendIter;
350	<	std::vector<Torsion*>::iterator torsionIter;
347	>	void SimInfo::addInteractionPairs(Molecule* mol) {
348	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
349	>	vector<Bond*>::iterator bondIter;
350	>	vector<Bend*>::iterator bendIter;
351	>	vector<Torsion*>::iterator torsionIter;
352	>	vector<Inversion*>::iterator inversionIter;
353		Bond* bond;
354		Bend* bend;
355		Torsion* torsion;
356	+	Inversion* inversion;
357		int a;
358		int b;
359		int c;
360		int d;
361
362	<	std::map<int, std::set<int> > atomGroups;
362	>	// atomGroups can be used to add special interaction maps between
363	>	// groups of atoms that are in two separate rigid bodies.
364	>	// However, most site-site interactions between two rigid bodies
365	>	// are probably not special, just the ones between the physically
366	>	// bonded atoms.  Interactions *within* a single rigid body should
367	>	// always be excluded.  These are done at the bottom of this
368	>	// function.
369
370	+	map<int, set<int> > atomGroups;
371		Molecule::RigidBodyIterator rbIter;
372		RigidBody* rb;
373		Molecule::IntegrableObjectIterator ii;
374		StuntDouble* integrableObject;
375
376	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
377	<	integrableObject = mol->nextIntegrableObject(ii)) {
378	<
376	>	for (integrableObject = mol->beginIntegrableObject(ii);
377	>	integrableObject != NULL;
378	>	integrableObject = mol->nextIntegrableObject(ii)) {
379	>
380		if (integrableObject->isRigidBody()) {
381	<	rb = static_cast<RigidBody*>(integrableObject);
382	<	std::vector<Atom*> atoms = rb->getAtoms();
383	<	std::set<int> rigidAtoms;
384	<	for (int i = 0; i < atoms.size(); ++i) {
385	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
386	<	}
387	<	for (int i = 0; i < atoms.size(); ++i) {
388	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
389	<	}
381	>	rb = static_cast<RigidBody*>(integrableObject);
382	>	vector<Atom*> atoms = rb->getAtoms();
383	>	set<int> rigidAtoms;
384	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
385	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
386	>	}
387	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
388	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
389	>	}
390		} else {
391	<	std::set<int> oneAtomSet;
391	>	set<int> oneAtomSet;
392		oneAtomSet.insert(integrableObject->getGlobalIndex());
393	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
393	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
394		}
395		}
396	+
397	+	for (bond= mol->beginBond(bondIter); bond != NULL;
398	+	bond = mol->nextBond(bondIter)) {
399
393	–
394	–
395	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
400		a = bond->getAtomA()->getGlobalIndex();
401	<	b = bond->getAtomB()->getGlobalIndex();
402	<	exclude_.addPair(a, b);
401	>	b = bond->getAtomB()->getGlobalIndex();
402	>
403	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
404	>	oneTwoInteractions_.addPair(a, b);
405	>	} else {
406	>	excludedInteractions_.addPair(a, b);
407	>	}
408		}
409
410	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
410	>	for (bend= mol->beginBend(bendIter); bend != NULL;
411	>	bend = mol->nextBend(bendIter)) {
412	>
413		a = bend->getAtomA()->getGlobalIndex();
414		b = bend->getAtomB()->getGlobalIndex();
415		c = bend->getAtomC()->getGlobalIndex();
405	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
406	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
407	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
408	–
409	–	exclude_.addPairs(rigidSetA, rigidSetB);
410	–	exclude_.addPairs(rigidSetA, rigidSetC);
411	–	exclude_.addPairs(rigidSetB, rigidSetC);
416
417	<	//exclude_.addPair(a, b);
418	<	//exclude_.addPair(a, c);
419	<	//exclude_.addPair(b, c);
417	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
418	>	oneTwoInteractions_.addPair(a, b);
419	>	oneTwoInteractions_.addPair(b, c);
420	>	} else {
421	>	excludedInteractions_.addPair(a, b);
422	>	excludedInteractions_.addPair(b, c);
423	>	}
424	>
425	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
426	>	oneThreeInteractions_.addPair(a, c);
427	>	} else {
428	>	excludedInteractions_.addPair(a, c);
429	>	}
430		}
431
432	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
432	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
433	>	torsion = mol->nextTorsion(torsionIter)) {
434	>
435		a = torsion->getAtomA()->getGlobalIndex();
436		b = torsion->getAtomB()->getGlobalIndex();
437		c = torsion->getAtomC()->getGlobalIndex();
438	<	d = torsion->getAtomD()->getGlobalIndex();
423	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
424	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
425	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
426	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
438	>	d = torsion->getAtomD()->getGlobalIndex();
439
440	<	exclude_.addPairs(rigidSetA, rigidSetB);
441	<	exclude_.addPairs(rigidSetA, rigidSetC);
442	<	exclude_.addPairs(rigidSetA, rigidSetD);
443	<	exclude_.addPairs(rigidSetB, rigidSetC);
444	<	exclude_.addPairs(rigidSetB, rigidSetD);
445	<	exclude_.addPairs(rigidSetC, rigidSetD);
440	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
441	>	oneTwoInteractions_.addPair(a, b);
442	>	oneTwoInteractions_.addPair(b, c);
443	>	oneTwoInteractions_.addPair(c, d);
444	>	} else {
445	>	excludedInteractions_.addPair(a, b);
446	>	excludedInteractions_.addPair(b, c);
447	>	excludedInteractions_.addPair(c, d);
448	>	}
449
450	<	/*
451	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
452	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
453	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
454	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
455	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
456	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
457	<
458	<
459	<	exclude_.addPair(a, b);
460	<	exclude_.addPair(a, c);
461	<	exclude_.addPair(a, d);
462	<	exclude_.addPair(b, c);
448	<	exclude_.addPair(b, d);
449	<	exclude_.addPair(c, d);
450	<	*/
450	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
451	>	oneThreeInteractions_.addPair(a, c);
452	>	oneThreeInteractions_.addPair(b, d);
453	>	} else {
454	>	excludedInteractions_.addPair(a, c);
455	>	excludedInteractions_.addPair(b, d);
456	>	}
457	>
458	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
459	>	oneFourInteractions_.addPair(a, d);
460	>	} else {
461	>	excludedInteractions_.addPair(a, d);
462	>	}
463		}
464
465	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
466	<	std::vector<Atom*> atoms = rb->getAtoms();
467	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
468	<	for (int j = i + 1; j < atoms.size(); ++j) {
465	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
466	>	inversion = mol->nextInversion(inversionIter)) {
467	>
468	>	a = inversion->getAtomA()->getGlobalIndex();
469	>	b = inversion->getAtomB()->getGlobalIndex();
470	>	c = inversion->getAtomC()->getGlobalIndex();
471	>	d = inversion->getAtomD()->getGlobalIndex();
472	>
473	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
474	>	oneTwoInteractions_.addPair(a, b);
475	>	oneTwoInteractions_.addPair(a, c);
476	>	oneTwoInteractions_.addPair(a, d);
477	>	} else {
478	>	excludedInteractions_.addPair(a, b);
479	>	excludedInteractions_.addPair(a, c);
480	>	excludedInteractions_.addPair(a, d);
481	>	}
482	>
483	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
484	>	oneThreeInteractions_.addPair(b, c);
485	>	oneThreeInteractions_.addPair(b, d);
486	>	oneThreeInteractions_.addPair(c, d);
487	>	} else {
488	>	excludedInteractions_.addPair(b, c);
489	>	excludedInteractions_.addPair(b, d);
490	>	excludedInteractions_.addPair(c, d);
491	>	}
492	>	}
493	>
494	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
495	>	rb = mol->nextRigidBody(rbIter)) {
496	>	vector<Atom*> atoms = rb->getAtoms();
497	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
498	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
499		a = atoms[i]->getGlobalIndex();
500		b = atoms[j]->getGlobalIndex();
501	<	exclude_.addPair(a, b);
501	>	excludedInteractions_.addPair(a, b);
502		}
503		}
504		}
505
506		}
507
508	<	void SimInfo::removeExcludePairs(Molecule* mol) {
509	<	std::vector<Bond*>::iterator bondIter;
510	<	std::vector<Bend*>::iterator bendIter;
511	<	std::vector<Torsion*>::iterator torsionIter;
508	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
509	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
510	>	vector<Bond*>::iterator bondIter;
511	>	vector<Bend*>::iterator bendIter;
512	>	vector<Torsion*>::iterator torsionIter;
513	>	vector<Inversion*>::iterator inversionIter;
514		Bond* bond;
515		Bend* bend;
516		Torsion* torsion;
517	+	Inversion* inversion;
518		int a;
519		int b;
520		int c;
521		int d;
522
523	<	std::map<int, std::set<int> > atomGroups;
479	<
523	>	map<int, set<int> > atomGroups;
524		Molecule::RigidBodyIterator rbIter;
525		RigidBody* rb;
526		Molecule::IntegrableObjectIterator ii;
527		StuntDouble* integrableObject;
528
529	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
530	<	integrableObject = mol->nextIntegrableObject(ii)) {
531	<
529	>	for (integrableObject = mol->beginIntegrableObject(ii);
530	>	integrableObject != NULL;
531	>	integrableObject = mol->nextIntegrableObject(ii)) {
532	>
533		if (integrableObject->isRigidBody()) {
534	<	rb = static_cast<RigidBody*>(integrableObject);
535	<	std::vector<Atom*> atoms = rb->getAtoms();
536	<	std::set<int> rigidAtoms;
537	<	for (int i = 0; i < atoms.size(); ++i) {
538	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
539	<	}
540	<	for (int i = 0; i < atoms.size(); ++i) {
541	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
542	<	}
534	>	rb = static_cast<RigidBody*>(integrableObject);
535	>	vector<Atom*> atoms = rb->getAtoms();
536	>	set<int> rigidAtoms;
537	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
538	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
539	>	}
540	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
541	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
542	>	}
543		} else {
544	<	std::set<int> oneAtomSet;
544	>	set<int> oneAtomSet;
545		oneAtomSet.insert(integrableObject->getGlobalIndex());
546	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
546	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
547		}
548		}
549
550	<
551	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
550	>	for (bond= mol->beginBond(bondIter); bond != NULL;
551	>	bond = mol->nextBond(bondIter)) {
552	>
553		a = bond->getAtomA()->getGlobalIndex();
554	<	b = bond->getAtomB()->getGlobalIndex();
555	<	exclude_.removePair(a, b);
554	>	b = bond->getAtomB()->getGlobalIndex();
555	>
556	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
557	>	oneTwoInteractions_.removePair(a, b);
558	>	} else {
559	>	excludedInteractions_.removePair(a, b);
560	>	}
561		}
562
563	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
563	>	for (bend= mol->beginBend(bendIter); bend != NULL;
564	>	bend = mol->nextBend(bendIter)) {
565	>
566		a = bend->getAtomA()->getGlobalIndex();
567		b = bend->getAtomB()->getGlobalIndex();
568		c = bend->getAtomC()->getGlobalIndex();
516	–
517	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
518	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
519	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
520	–
521	–	exclude_.removePairs(rigidSetA, rigidSetB);
522	–	exclude_.removePairs(rigidSetA, rigidSetC);
523	–	exclude_.removePairs(rigidSetB, rigidSetC);
569
570	<	//exclude_.removePair(a, b);
571	<	//exclude_.removePair(a, c);
572	<	//exclude_.removePair(b, c);
570	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
571	>	oneTwoInteractions_.removePair(a, b);
572	>	oneTwoInteractions_.removePair(b, c);
573	>	} else {
574	>	excludedInteractions_.removePair(a, b);
575	>	excludedInteractions_.removePair(b, c);
576	>	}
577	>
578	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
579	>	oneThreeInteractions_.removePair(a, c);
580	>	} else {
581	>	excludedInteractions_.removePair(a, c);
582	>	}
583		}
584
585	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
585	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
586	>	torsion = mol->nextTorsion(torsionIter)) {
587	>
588		a = torsion->getAtomA()->getGlobalIndex();
589		b = torsion->getAtomB()->getGlobalIndex();
590		c = torsion->getAtomC()->getGlobalIndex();
591	<	d = torsion->getAtomD()->getGlobalIndex();
591	>	d = torsion->getAtomD()->getGlobalIndex();
592	>
593	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
594	>	oneTwoInteractions_.removePair(a, b);
595	>	oneTwoInteractions_.removePair(b, c);
596	>	oneTwoInteractions_.removePair(c, d);
597	>	} else {
598	>	excludedInteractions_.removePair(a, b);
599	>	excludedInteractions_.removePair(b, c);
600	>	excludedInteractions_.removePair(c, d);
601	>	}
602
603	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
604	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
605	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
606	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
603	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
604	>	oneThreeInteractions_.removePair(a, c);
605	>	oneThreeInteractions_.removePair(b, d);
606	>	} else {
607	>	excludedInteractions_.removePair(a, c);
608	>	excludedInteractions_.removePair(b, d);
609	>	}
610
611	<	exclude_.removePairs(rigidSetA, rigidSetB);
612	<	exclude_.removePairs(rigidSetA, rigidSetC);
613	<	exclude_.removePairs(rigidSetA, rigidSetD);
614	<	exclude_.removePairs(rigidSetB, rigidSetC);
615	<	exclude_.removePairs(rigidSetB, rigidSetD);
616	<	exclude_.removePairs(rigidSetC, rigidSetD);
611	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
612	>	oneFourInteractions_.removePair(a, d);
613	>	} else {
614	>	excludedInteractions_.removePair(a, d);
615	>	}
616	>	}
617
618	<	/*
619	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
550	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
551	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
552	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
553	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
554	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
618	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
619	>	inversion = mol->nextInversion(inversionIter)) {
620
621	<
622	<	exclude_.removePair(a, b);
623	<	exclude_.removePair(a, c);
624	<	exclude_.removePair(a, d);
625	<	exclude_.removePair(b, c);
626	<	exclude_.removePair(b, d);
627	<	exclude_.removePair(c, d);
628	<	*/
621	>	a = inversion->getAtomA()->getGlobalIndex();
622	>	b = inversion->getAtomB()->getGlobalIndex();
623	>	c = inversion->getAtomC()->getGlobalIndex();
624	>	d = inversion->getAtomD()->getGlobalIndex();
625	>
626	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
627	>	oneTwoInteractions_.removePair(a, b);
628	>	oneTwoInteractions_.removePair(a, c);
629	>	oneTwoInteractions_.removePair(a, d);
630	>	} else {
631	>	excludedInteractions_.removePair(a, b);
632	>	excludedInteractions_.removePair(a, c);
633	>	excludedInteractions_.removePair(a, d);
634	>	}
635	>
636	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
637	>	oneThreeInteractions_.removePair(b, c);
638	>	oneThreeInteractions_.removePair(b, d);
639	>	oneThreeInteractions_.removePair(c, d);
640	>	} else {
641	>	excludedInteractions_.removePair(b, c);
642	>	excludedInteractions_.removePair(b, d);
643	>	excludedInteractions_.removePair(c, d);
644	>	}
645		}
646
647	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
648	<	std::vector<Atom*> atoms = rb->getAtoms();
649	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
650	<	for (int j = i + 1; j < atoms.size(); ++j) {
647	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
648	>	rb = mol->nextRigidBody(rbIter)) {
649	>	vector<Atom*> atoms = rb->getAtoms();
650	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
651	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
652		a = atoms[i]->getGlobalIndex();
653		b = atoms[j]->getGlobalIndex();
654	<	exclude_.removePair(a, b);
654	>	excludedInteractions_.removePair(a, b);
655		}
656		}
657		}
658	<
658	>
659		}
660	<
661	<
660	>
661	>
662		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
663		int curStampId;
664	<
664	>
665		//index from 0
666		curStampId = moleculeStamps_.size();
667
#	Line 587 | Line 669 | namespace oopse {
669		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
670		}
671
590	–	void SimInfo::update() {
672
673	<	setupSimType();
674	<
675	<	#ifdef IS_MPI
676	<	setupFortranParallel();
677	<	#endif
678	<
679	<	setupFortranSim();
680	<
681	<	//setup fortran force field
601	<	/** @deprecate */
602	<	int isError = 0;
603	<
604	<	setupElectrostaticSummationMethod( isError );
605	<	setupSwitchingFunction();
606	<	setupAccumulateBoxDipole();
607	<
608	<	if(isError){
609	<	sprintf( painCave.errMsg,
610	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
611	<	painCave.isFatal = 1;
612	<	simError();
613	<	}
614	<
615	<
616	<	setupCutoff();
617	<
673	>	/**
674	>	* update
675	>	*
676	>	*  Performs the global checks and variable settings after the
677	>	*  objects have been created.
678	>	*
679	>	*/
680	>	void SimInfo::update() {
681	>	setupSimVariables();
682		calcNdf();
683		calcNdfRaw();
684		calcNdfTrans();
621	–
622	–	fortranInitialized_ = true;
685		}
686	<
687	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
686	>
687	>	/**
688	>	* getSimulatedAtomTypes
689	>	*
690	>	* Returns an STL set of AtomType* that are actually present in this
691	>	* simulation.  Must query all processors to assemble this information.
692	>	*
693	>	*/
694	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
695		SimInfo::MoleculeIterator mi;
696		Molecule* mol;
697		Molecule::AtomIterator ai;
698		Atom* atom;
699	<	std::set<AtomType*> atomTypes;
700	<
699	>	set<AtomType*> atomTypes;
700	>
701		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
702	<
703	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
702	>	for(atom = mol->beginAtom(ai); atom != NULL;
703	>	atom = mol->nextAtom(ai)) {
704		atomTypes.insert(atom->getAtomType());
705	<	}
706	<
707	<	}
705	>	}
706	>	}
707	>
708	>	#ifdef IS_MPI
709
710	<	return atomTypes;
711	<	}
642	<
643	<	void SimInfo::setupSimType() {
644	<	std::set<AtomType*>::iterator i;
645	<	std::set<AtomType*> atomTypes;
646	<	atomTypes = getUniqueAtomTypes();
710	>	// loop over the found atom types on this processor, and add their
711	>	// numerical idents to a vector:
712
713	<	int useLennardJones = 0;
714	<	int useElectrostatic = 0;
715	<	int useEAM = 0;
716	<	int useSC = 0;
652	<	int useCharge = 0;
653	<	int useDirectional = 0;
654	<	int useDipole = 0;
655	<	int useGayBerne = 0;
656	<	int useSticky = 0;
657	<	int useStickyPower = 0;
658	<	int useShape = 0;
659	<	int useFLARB = 0; //it is not in AtomType yet
660	<	int useDirectionalAtom = 0;
661	<	int useElectrostatics = 0;
662	<	//usePBC and useRF are from simParams
663	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
664	<	int useRF;
665	<	int useSF;
666	<	int useSP;
667	<	int useBoxDipole;
668	<	std::string myMethod;
713	>	vector<int> foundTypes;
714	>	set<AtomType*>::iterator i;
715	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
716	>	foundTypes.push_back( (*i)->getIdent() );
717
718	<	// set the useRF logical
719	<	useRF = 0;
672	<	useSF = 0;
718	>	// count_local holds the number of found types on this processor
719	>	int count_local = foundTypes.size();
720
721	+	int nproc = MPI::COMM_WORLD.Get_size();
722
723	<	if (simParams_->haveElectrostaticSummationMethod()) {
724	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
725	<	toUpper(myMethod);
726	<	if (myMethod == "REACTION_FIELD"){
679	<	useRF=1;
680	<	} else if (myMethod == "SHIFTED_FORCE"){
681	<	useSF = 1;
682	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
683	<	useSP = 1;
684	<	}
685	<	}
686	<
687	<	if (simParams_->haveAccumulateBoxDipole())
688	<	if (simParams_->getAccumulateBoxDipole())
689	<	useBoxDipole = 1;
723	>	// we need arrays to hold the counts and displacement vectors for
724	>	// all processors
725	>	vector<int> counts(nproc, 0);
726	>	vector<int> disps(nproc, 0);
727
728	<	//loop over all of the atom types
729	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
730	<	useLennardJones |= (*i)->isLennardJones();
731	<	useElectrostatic |= (*i)->isElectrostatic();
732	<	useEAM |= (*i)->isEAM();
733	<	useSC |= (*i)->isSC();
734	<	useCharge |= (*i)->isCharge();
735	<	useDirectional |= (*i)->isDirectional();
736	<	useDipole |= (*i)->isDipole();
737	<	useGayBerne |= (*i)->isGayBerne();
701	<	useSticky |= (*i)->isSticky();
702	<	useStickyPower |= (*i)->isStickyPower();
703	<	useShape |= (*i)->isShape();
728	>	// fill the counts array
729	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
730	>	1, MPI::INT);
731	>
732	>	// use the processor counts to compute the displacement array
733	>	disps[0] = 0;
734	>	int totalCount = counts[0];
735	>	for (int iproc = 1; iproc < nproc; iproc++) {
736	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
737	>	totalCount += counts[iproc];
738		}
739
740	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
741	<	useDirectionalAtom = 1;
742	<	}
740	>	// we need a (possibly redundant) set of all found types:
741	>	vector<int> ftGlobal(totalCount);
742	>
743	>	// now spray out the foundTypes to all the other processors:
744	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
745	>	&ftGlobal[0], &counts[0], &disps[0],
746	>	MPI::INT);
747
748	<	if (useCharge || useDipole) {
711	<	useElectrostatics = 1;
712	<	}
748	>	vector<int>::iterator j;
749
750	<	#ifdef IS_MPI
751	<	int temp;
750	>	// foundIdents is a stl set, so inserting an already found ident
751	>	// will have no effect.
752	>	set<int> foundIdents;
753
754	<	temp = usePBC;
755	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
754	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
755	>	foundIdents.insert((*j));
756	>
757	>	// now iterate over the foundIdents and get the actual atom types
758	>	// that correspond to these:
759	>	set<int>::iterator it;
760	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
761	>	atomTypes.insert( forceField_->getAtomType((*it)) );
762	>
763	>	#endif
764
765	<	temp = useDirectionalAtom;
766	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
765	>	return atomTypes;
766	>	}
767
768	<	temp = useLennardJones;
769	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770	<
771	<	temp = useElectrostatics;
772	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
773	<
774	<	temp = useCharge;
775	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
731	<
732	<	temp = useDipole;
733	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
734	<
735	<	temp = useSticky;
736	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
737	<
738	<	temp = useStickyPower;
739	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
768	>	void SimInfo::setupSimVariables() {
769	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
770	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
771	>	calcBoxDipole_ = false;
772	>	if ( simParams_->haveAccumulateBoxDipole() )
773	>	if ( simParams_->getAccumulateBoxDipole() ) {
774	>	calcBoxDipole_ = true;
775	>	}
776
777	<	temp = useGayBerne;
778	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
777	>	set<AtomType*>::iterator i;
778	>	set<AtomType*> atomTypes;
779	>	atomTypes = getSimulatedAtomTypes();
780	>	int usesElectrostatic = 0;
781	>	int usesMetallic = 0;
782	>	int usesDirectional = 0;
783	>	//loop over all of the atom types
784	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
785	>	usesElectrostatic |= (*i)->isElectrostatic();
786	>	usesMetallic |= (*i)->isMetal();
787	>	usesDirectional |= (*i)->isDirectional();
788	>	}
789	>
790	>	#ifdef IS_MPI
791	>	int temp;
792	>	temp = usesDirectional;
793	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
794	>
795	>	temp = usesMetallic;
796	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
797	>
798	>	temp = usesElectrostatic;
799	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
800	>	#else
801
802	<	temp = useEAM;
803	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
802	>	usesDirectionalAtoms_ = usesDirectional;
803	>	usesMetallicAtoms_ = usesMetallic;
804	>	usesElectrostaticAtoms_ = usesElectrostatic;
805
806	<	temp = useSC;
748	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
806	>	#endif
807
808	<	temp = useShape;
809	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
808	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
809	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
810	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
811	>	}
812
753	–	temp = useFLARB;
754	–	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813
814	<	temp = useRF;
815	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814	>	vector<int> SimInfo::getGlobalAtomIndices() {
815	>	SimInfo::MoleculeIterator mi;
816	>	Molecule* mol;
817	>	Molecule::AtomIterator ai;
818	>	Atom* atom;
819
820	<	temp = useSF;
821	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
820	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
821	>
822	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
823	>
824	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
825	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
826	>	}
827	>	}
828	>	return GlobalAtomIndices;
829	>	}
830
762	–	temp = useSP;
763	–	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
831
832	<	temp = useBoxDipole;
833	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
832	>	vector<int> SimInfo::getGlobalGroupIndices() {
833	>	SimInfo::MoleculeIterator mi;
834	>	Molecule* mol;
835	>	Molecule::CutoffGroupIterator ci;
836	>	CutoffGroup* cg;
837
838	<	#endif
839	<
840	<	fInfo_.SIM_uses_PBC = usePBC;
771	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
772	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
773	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
774	<	fInfo_.SIM_uses_Charges = useCharge;
775	<	fInfo_.SIM_uses_Dipoles = useDipole;
776	<	fInfo_.SIM_uses_Sticky = useSticky;
777	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
778	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
779	<	fInfo_.SIM_uses_EAM = useEAM;
780	<	fInfo_.SIM_uses_SC = useSC;
781	<	fInfo_.SIM_uses_Shapes = useShape;
782	<	fInfo_.SIM_uses_FLARB = useFLARB;
783	<	fInfo_.SIM_uses_RF = useRF;
784	<	fInfo_.SIM_uses_SF = useSF;
785	<	fInfo_.SIM_uses_SP = useSP;
786	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
787	<
788	<	if( myMethod == "REACTION_FIELD") {
838	>	vector<int> GlobalGroupIndices;
839	>
840	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
841
842	<	if (simParams_->haveDielectric()) {
843	<	fInfo_.dielect = simParams_->getDielectric();
844	<	} else {
845	<	sprintf(painCave.errMsg,
846	<	"SimSetup Error: No Dielectric constant was set.\n"
847	<	"\tYou are trying to use Reaction Field without"
796	<	"\tsetting a dielectric constant!\n");
797	<	painCave.isFatal = 1;
798	<	simError();
799	<	}
842	>	//local index of cutoff group is trivial, it only depends on the
843	>	//order of travesing
844	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
845	>	cg = mol->nextCutoffGroup(ci)) {
846	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
847	>	}
848		}
849	<
849	>	return GlobalGroupIndices;
850		}
851
804	–	void SimInfo::setupFortranSim() {
805	–	int isError;
806	–	int nExclude;
807	–	std::vector<int> fortranGlobalGroupMembership;
808	–
809	–	nExclude = exclude_.getSize();
810	–	isError = 0;
852
853	<	//globalGroupMembership_ is filled by SimCreator
854	<	for (int i = 0; i < nGlobalAtoms_; i++) {
814	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
815	<	}
853	>	void SimInfo::prepareTopology() {
854	>	int nExclude, nOneTwo, nOneThree, nOneFour;
855
856		//calculate mass ratio of cutoff group
818	–	std::vector<RealType> mfact;
857		SimInfo::MoleculeIterator mi;
858		Molecule* mol;
859		Molecule::CutoffGroupIterator ci;
#	Line 824 | Line 862 | namespace oopse {
862		Atom* atom;
863		RealType totalMass;
864
865	<	//to avoid memory reallocation, reserve enough space for mfact
866	<	mfact.reserve(getNCutoffGroups());
865	>	/**
866	>	* The mass factor is the relative mass of an atom to the total
867	>	* mass of the cutoff group it belongs to.  By default, all atoms
868	>	* are their own cutoff groups, and therefore have mass factors of
869	>	* 1.  We need some special handling for massless atoms, which
870	>	* will be treated as carrying the entire mass of the cutoff
871	>	* group.
872	>	*/
873	>	massFactors_.clear();
874	>	massFactors_.resize(getNAtoms(), 1.0);
875
876		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
877	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
877	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
878	>	cg = mol->nextCutoffGroup(ci)) {
879
880		totalMass = cg->getMass();
881		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
882		// Check for massless groups - set mfact to 1 if true
883	<	if (totalMass != 0)
884	<	mfact.push_back(atom->getMass()/totalMass);
883	>	if (totalMass != 0)
884	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
885		else
886	<	mfact.push_back( 1.0 );
886	>	massFactors_[atom->getLocalIndex()] = 1.0;
887		}
841	–
888		}
889		}
890
891	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
846	<	std::vector<int> identArray;
891	>	// Build the identArray_
892
893	<	//to avoid memory reallocation, reserve enough space identArray
894	<	identArray.reserve(getNAtoms());
850	<
893	>	identArray_.clear();
894	>	identArray_.reserve(getNAtoms());
895		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
896		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
897	<	identArray.push_back(atom->getIdent());
897	>	identArray_.push_back(atom->getIdent());
898		}
899		}
856	–
857	–	//fill molMembershipArray
858	–	//molMembershipArray is filled by SimCreator
859	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
860	–	for (int i = 0; i < nGlobalAtoms_; i++) {
861	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
862	–	}
900
901	<	//setup fortran simulation
865	<	int nGlobalExcludes = 0;
866	<	int* globalExcludes = NULL;
867	<	int* excludeList = exclude_.getExcludeList();
868	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
869	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
870	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
901	>	//scan topology
902
903	<	if( isError ){
903	>	nExclude = excludedInteractions_.getSize();
904	>	nOneTwo = oneTwoInteractions_.getSize();
905	>	nOneThree = oneThreeInteractions_.getSize();
906	>	nOneFour = oneFourInteractions_.getSize();
907
908	<	sprintf( painCave.errMsg,
909	<	"There was an error setting the simulation information in fortran.\n" );
910	<	painCave.isFatal = 1;
911	<	painCave.severity = OOPSE_ERROR;
878	<	simError();
879	<	}
880	<
881	<	#ifdef IS_MPI
882	<	sprintf( checkPointMsg,
883	<	"succesfully sent the simulation information to fortran.\n");
884	<	MPIcheckPoint();
885	<	#endif // is_mpi
886	<	}
887	<
888	<
889	<	#ifdef IS_MPI
890	<	void SimInfo::setupFortranParallel() {
891	<
892	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
893	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
894	<	std::vector<int> localToGlobalCutoffGroupIndex;
895	<	SimInfo::MoleculeIterator mi;
896	<	Molecule::AtomIterator ai;
897	<	Molecule::CutoffGroupIterator ci;
898	<	Molecule* mol;
899	<	Atom* atom;
900	<	CutoffGroup* cg;
901	<	mpiSimData parallelData;
902	<	int isError;
903	<
904	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
905	<
906	<	//local index(index in DataStorge) of atom is important
907	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
908	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
909	<	}
910	<
911	<	//local index of cutoff group is trivial, it only depends on the order of travesing
912	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
913	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
914	<	}
915	<
916	<	}
917	<
918	<	//fill up mpiSimData struct
919	<	parallelData.nMolGlobal = getNGlobalMolecules();
920	<	parallelData.nMolLocal = getNMolecules();
921	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
922	<	parallelData.nAtomsLocal = getNAtoms();
923	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
924	<	parallelData.nGroupsLocal = getNCutoffGroups();
925	<	parallelData.myNode = worldRank;
926	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
908	>	int* excludeList = excludedInteractions_.getPairList();
909	>	int* oneTwoList = oneTwoInteractions_.getPairList();
910	>	int* oneThreeList = oneThreeInteractions_.getPairList();
911	>	int* oneFourList = oneFourInteractions_.getPairList();
912
913	<	//pass mpiSimData struct and index arrays to fortran
929	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
930	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
931	<	&localToGlobalCutoffGroupIndex[0], &isError);
932	<
933	<	if (isError) {
934	<	sprintf(painCave.errMsg,
935	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
936	<	painCave.isFatal = 1;
937	<	simError();
938	<	}
939	<
940	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
941	<	MPIcheckPoint();
942	<
943	<
944	<	}
945	<
946	<	#endif
947	<
948	<	void SimInfo::setupCutoff() {
949	<
950	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
951	<
952	<	// Check the cutoff policy
953	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
954	<
955	<	std::string myPolicy;
956	<	if (forceFieldOptions_.haveCutoffPolicy()){
957	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
958	<	}else if (simParams_->haveCutoffPolicy()) {
959	<	myPolicy = simParams_->getCutoffPolicy();
960	<	}
961	<
962	<	if (!myPolicy.empty()){
963	<	toUpper(myPolicy);
964	<	if (myPolicy == "MIX") {
965	<	cp = MIX_CUTOFF_POLICY;
966	<	} else {
967	<	if (myPolicy == "MAX") {
968	<	cp = MAX_CUTOFF_POLICY;
969	<	} else {
970	<	if (myPolicy == "TRADITIONAL") {
971	<	cp = TRADITIONAL_CUTOFF_POLICY;
972	<	} else {
973	<	// throw error
974	<	sprintf( painCave.errMsg,
975	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
976	<	painCave.isFatal = 1;
977	<	simError();
978	<	}
979	<	}
980	<	}
981	<	}
982	<	notifyFortranCutoffPolicy(&cp);
983	<
984	<	// Check the Skin Thickness for neighborlists
985	<	RealType skin;
986	<	if (simParams_->haveSkinThickness()) {
987	<	skin = simParams_->getSkinThickness();
988	<	notifyFortranSkinThickness(&skin);
989	<	}
990	<
991	<	// Check if the cutoff was set explicitly:
992	<	if (simParams_->haveCutoffRadius()) {
993	<	rcut_ = simParams_->getCutoffRadius();
994	<	if (simParams_->haveSwitchingRadius()) {
995	<	rsw_  = simParams_->getSwitchingRadius();
996	<	} else {
997	<	if (fInfo_.SIM_uses_Charges |
998	<	fInfo_.SIM_uses_Dipoles |
999	<	fInfo_.SIM_uses_RF) {
1000	<
1001	<	rsw_ = 0.85 * rcut_;
1002	<	sprintf(painCave.errMsg,
1003	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1004	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1005	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1006	<	painCave.isFatal = 0;
1007	<	simError();
1008	<	} else {
1009	<	rsw_ = rcut_;
1010	<	sprintf(painCave.errMsg,
1011	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1012	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
1013	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1014	<	painCave.isFatal = 0;
1015	<	simError();
1016	<	}
1017	<	}
1018	<
1019	<	notifyFortranCutoffs(&rcut_, &rsw_);
1020	<
1021	<	} else {
1022	<
1023	<	// For electrostatic atoms, we'll assume a large safe value:
1024	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1025	<	sprintf(painCave.errMsg,
1026	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1027	<	"\tOOPSE will use a default value of 15.0 angstroms"
1028	<	"\tfor the cutoffRadius.\n");
1029	<	painCave.isFatal = 0;
1030	<	simError();
1031	<	rcut_ = 15.0;
1032	<
1033	<	if (simParams_->haveElectrostaticSummationMethod()) {
1034	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1035	<	toUpper(myMethod);
1036	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1037	<	if (simParams_->haveSwitchingRadius()){
1038	<	sprintf(painCave.errMsg,
1039	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1040	<	"\teven though the electrostaticSummationMethod was\n"
1041	<	"\tset to %s\n", myMethod.c_str());
1042	<	painCave.isFatal = 1;
1043	<	simError();
1044	<	}
1045	<	}
1046	<	}
1047	<
1048	<	if (simParams_->haveSwitchingRadius()){
1049	<	rsw_ = simParams_->getSwitchingRadius();
1050	<	} else {
1051	<	sprintf(painCave.errMsg,
1052	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1053	<	"\tOOPSE will use a default value of\n"
1054	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1055	<	painCave.isFatal = 0;
1056	<	simError();
1057	<	rsw_ = 0.85 * rcut_;
1058	<	}
1059	<	notifyFortranCutoffs(&rcut_, &rsw_);
1060	<	} else {
1061	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1062	<	// We'll punt and let fortran figure out the cutoffs later.
1063	<
1064	<	notifyFortranYouAreOnYourOwn();
1065	<
1066	<	}
1067	<	}
1068	<	}
1069	<
1070	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1071	<
1072	<	int errorOut;
1073	<	int esm =  NONE;
1074	<	int sm = UNDAMPED;
1075	<	RealType alphaVal;
1076	<	RealType dielectric;
1077	<
1078	<	errorOut = isError;
1079	<	alphaVal = simParams_->getDampingAlpha();
1080	<	dielectric = simParams_->getDielectric();
1081	<
1082	<	if (simParams_->haveElectrostaticSummationMethod()) {
1083	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1084	<	toUpper(myMethod);
1085	<	if (myMethod == "NONE") {
1086	<	esm = NONE;
1087	<	} else {
1088	<	if (myMethod == "SWITCHING_FUNCTION") {
1089	<	esm = SWITCHING_FUNCTION;
1090	<	} else {
1091	<	if (myMethod == "SHIFTED_POTENTIAL") {
1092	<	esm = SHIFTED_POTENTIAL;
1093	<	} else {
1094	<	if (myMethod == "SHIFTED_FORCE") {
1095	<	esm = SHIFTED_FORCE;
1096	<	} else {
1097	<	if (myMethod == "REACTION_FIELD") {
1098	<	esm = REACTION_FIELD;
1099	<	} else {
1100	<	// throw error
1101	<	sprintf( painCave.errMsg,
1102	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1103	<	"\t(Input file specified %s .)\n"
1104	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1105	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1106	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1107	<	painCave.isFatal = 1;
1108	<	simError();
1109	<	}
1110	<	}
1111	<	}
1112	<	}
1113	<	}
1114	<	}
1115	<
1116	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1117	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1118	<	toUpper(myScreen);
1119	<	if (myScreen == "UNDAMPED") {
1120	<	sm = UNDAMPED;
1121	<	} else {
1122	<	if (myScreen == "DAMPED") {
1123	<	sm = DAMPED;
1124	<	if (!simParams_->haveDampingAlpha()) {
1125	<	//throw error
1126	<	sprintf( painCave.errMsg,
1127	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1128	<	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1129	<	painCave.isFatal = 0;
1130	<	simError();
1131	<	}
1132	<	} else {
1133	<	// throw error
1134	<	sprintf( painCave.errMsg,
1135	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1136	<	"\t(Input file specified %s .)\n"
1137	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1138	<	"or \"damped\".\n", myScreen.c_str() );
1139	<	painCave.isFatal = 1;
1140	<	simError();
1141	<	}
1142	<	}
1143	<	}
1144	<
1145	<	// let's pass some summation method variables to fortran
1146	<	setElectrostaticSummationMethod( &esm );
1147	<	setFortranElectrostaticMethod( &esm );
1148	<	setScreeningMethod( &sm );
1149	<	setDampingAlpha( &alphaVal );
1150	<	setReactionFieldDielectric( &dielectric );
1151	<	initFortranFF( &errorOut );
1152	<	}
1153	<
1154	<	void SimInfo::setupSwitchingFunction() {
1155	<	int ft = CUBIC;
1156	<
1157	<	if (simParams_->haveSwitchingFunctionType()) {
1158	<	std::string funcType = simParams_->getSwitchingFunctionType();
1159	<	toUpper(funcType);
1160	<	if (funcType == "CUBIC") {
1161	<	ft = CUBIC;
1162	<	} else {
1163	<	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1164	<	ft = FIFTH_ORDER_POLY;
1165	<	} else {
1166	<	// throw error
1167	<	sprintf( painCave.errMsg,
1168	<	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1169	<	painCave.isFatal = 1;
1170	<	simError();
1171	<	}
1172	<	}
1173	<	}
1174	<
1175	<	// send switching function notification to switcheroo
1176	<	setFunctionType(&ft);
1177	<
1178	<	}
1179	<
1180	<	void SimInfo::setupAccumulateBoxDipole() {
1181	<
1182	<	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1183	<	if ( simParams_->haveAccumulateBoxDipole() )
1184	<	if ( simParams_->getAccumulateBoxDipole() ) {
1185	<	setAccumulateBoxDipole();
1186	<	calcBoxDipole_ = true;
1187	<	}
1188	<
913	>	topologyDone_ = true;
914		}
915
916		void SimInfo::addProperty(GenericData* genData) {
917		properties_.addProperty(genData);
918		}
919
920	<	void SimInfo::removeProperty(const std::string& propName) {
920	>	void SimInfo::removeProperty(const string& propName) {
921		properties_.removeProperty(propName);
922		}
923
#	Line 1200 | Line 925 | namespace oopse {
925		properties_.clearProperties();
926		}
927
928	<	std::vector<std::string> SimInfo::getPropertyNames() {
928	>	vector<string> SimInfo::getPropertyNames() {
929		return properties_.getPropertyNames();
930		}
931
932	<	std::vector<GenericData*> SimInfo::getProperties() {
932	>	vector<GenericData*> SimInfo::getProperties() {
933		return properties_.getProperties();
934		}
935
936	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
936	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
937		return properties_.getPropertyByName(propName);
938		}
939
#	Line 1222 | Line 947 | namespace oopse {
947		Molecule* mol;
948		RigidBody* rb;
949		Atom* atom;
950	+	CutoffGroup* cg;
951		SimInfo::MoleculeIterator mi;
952		Molecule::RigidBodyIterator rbIter;
953	<	Molecule::AtomIterator atomIter;;
953	>	Molecule::AtomIterator atomIter;
954	>	Molecule::CutoffGroupIterator cgIter;
955
956		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
957
#	Line 1235 | Line 962 | namespace oopse {
962		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
963		rb->setSnapshotManager(sman_);
964		}
965	+
966	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
967	+	cg->setSnapshotManager(sman_);
968	+	}
969		}
970
971		}
#	Line 1291 | Line 1022 | namespace oopse {
1022
1023		}
1024
1025	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1025	>	ostream& operator <<(ostream& o, SimInfo& info) {
1026
1027		return o;
1028		}
#	Line 1334 | Line 1065 | namespace oopse {
1065
1066
1067		[  Ixx -Ixy  -Ixz ]
1068	<	J =| -Iyx  Iyy  -Iyz |
1068	>	J =| -Iyx  Iyy  -Iyz |
1069		[ -Izx -Iyz   Izz ]
1070		*/
1071
#	Line 1441 | Line 1172 | namespace oopse {
1172		return IOIndexToIntegrableObject.at(index);
1173		}
1174
1175	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1175	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1176		IOIndexToIntegrableObject= v;
1177		}
1178
1179	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1180	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1181	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1182	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1183	+	*/
1184	+	void SimInfo::getGyrationalVolume(RealType &volume){
1185	+	Mat3x3d intTensor;
1186	+	RealType det;
1187	+	Vector3d dummyAngMom;
1188	+	RealType sysconstants;
1189	+	RealType geomCnst;
1190	+
1191	+	geomCnst = 3.0/2.0;
1192	+	/* Get the inertial tensor and angular momentum for free*/
1193	+	getInertiaTensor(intTensor,dummyAngMom);
1194	+
1195	+	det = intTensor.determinant();
1196	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1197	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1198	+	return;
1199	+	}
1200	+
1201	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1202	+	Mat3x3d intTensor;
1203	+	Vector3d dummyAngMom;
1204	+	RealType sysconstants;
1205	+	RealType geomCnst;
1206	+
1207	+	geomCnst = 3.0/2.0;
1208	+	/* Get the inertial tensor and angular momentum for free*/
1209	+	getInertiaTensor(intTensor,dummyAngMom);
1210	+
1211	+	detI = intTensor.determinant();
1212	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1213	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1214	+	return;
1215	+	}
1216		/*
1217	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1217	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1218		assert( v.size() == nAtoms_ + nRigidBodies_);
1219		sdByGlobalIndex_ = v;
1220		}
#	Line 1456 | Line 1224 | namespace oopse {
1224		return sdByGlobalIndex_.at(index);
1225		}
1226		*/
1227	<	}//end namespace oopse
1227	>	int SimInfo::getNGlobalConstraints() {
1228	>	int nGlobalConstraints;
1229	>	#ifdef IS_MPI
1230	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1231	>	MPI_COMM_WORLD);
1232	>	#else
1233	>	nGlobalConstraints =  nConstraints_;
1234	>	#endif
1235	>	return nGlobalConstraints;
1236	>	}
1237
1238	+	}//end namespace OpenMD
1239	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 1024 by tim, Wed Aug 30 18:42:29 2006 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1668 by gezelter, Fri Jan 6 19:03:05 2012 UTC

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