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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 1078 by gezelter, Wed Oct 18 21:58:48 2006 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1601 by gezelter, Thu Aug 4 20:04:35 2011 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 54 | Line 54
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56		#include "primitives/StuntDouble.hpp"
57	–	#include "UseTheForce/fCutoffPolicy.h"
58	–	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	–	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60	–	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61	–	#include "UseTheForce/doForces_interface.h"
62	–	#include "UseTheForce/DarkSide/electrostatic_interface.h"
63	–	#include "UseTheForce/DarkSide/switcheroo_interface.h"
57		#include "utils/MemoryUtils.hpp"
58		#include "utils/simError.h"
59		#include "selection/SelectionManager.hpp"
60		#include "io/ForceFieldOptions.hpp"
61		#include "UseTheForce/ForceField.hpp"
62	+	#include "nonbonded/SwitchingFunction.hpp"
63
64	<	#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
72	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
73	<	#endif
74	<
75	<	namespace oopse {
76	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
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	<	}
64	>	using namespace std;
65	>	namespace OpenMD {
66
67		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
68		forceField_(ff), simParams_(simParams),
69		ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
70		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
71		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
72	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
73	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
74	<	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) {
75	<
76	<	MoleculeStamp* molStamp;
77	<	int nMolWithSameStamp;
78	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
79	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
80	<	CutoffGroupStamp* cgStamp;
81	<	RigidBodyStamp* rbStamp;
82	<	int nRigidAtoms = 0;
83	<	std::vector<Component*> components = simParams->getComponents();
72	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
73	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
74	>	nConstraints_(0), sman_(NULL), topologyDone_(false),
75	>	calcBoxDipole_(false), useAtomicVirial_(true) {
76	>
77	>	MoleculeStamp* molStamp;
78	>	int nMolWithSameStamp;
79	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
80	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
81	>	CutoffGroupStamp* cgStamp;
82	>	RigidBodyStamp* rbStamp;
83	>	int nRigidAtoms = 0;
84	>
85	>	vector<Component*> components = simParams->getComponents();
86	>
87	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
88	>	molStamp = (*i)->getMoleculeStamp();
89	>	nMolWithSameStamp = (*i)->getNMol();
90
91	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
92	<	molStamp = (*i)->getMoleculeStamp();
93	<	nMolWithSameStamp = (*i)->getNMol();
94	<
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();
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	<
91	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
92	>
93	>	//calculate atoms in molecules
94	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
95	>
96	>	//calculate atoms in cutoff groups
97	>	int nAtomsInGroups = 0;
98	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
99	>
100	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
101	>	cgStamp = molStamp->getCutoffGroupStamp(j);
102	>	nAtomsInGroups += cgStamp->getNMembers();
103		}
104	<
105	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
106	<	//group therefore the total number of cutoff groups in the system is
107	<	//equal to the total number of atoms minus number of atoms belong to
108	<	//cutoff group defined in meta-data file plus the number of cutoff
109	<	//groups defined in meta-data file
110	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
111	<
112	<	//every free atom (atom does not belong to rigid bodies) is an
113	<	//integrable object therefore the total number of integrable objects
114	<	//in the system is equal to the total number of atoms minus number of
115	<	//atoms belong to rigid body defined in meta-data file plus the number
116	<	//of rigid bodies defined in meta-data file
117	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
118	<	+ nGlobalRigidBodies_;
119	<
120	<	nGlobalMols_ = molStampIds_.size();
156	<
157	<	#ifdef IS_MPI
158	<	molToProcMap_.resize(nGlobalMols_);
159	<	#endif
160	<
104	>
105	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
106	>
107	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
108	>
109	>	//calculate atoms in rigid bodies
110	>	int nAtomsInRigidBodies = 0;
111	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
112	>
113	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
114	>	rbStamp = molStamp->getRigidBodyStamp(j);
115	>	nAtomsInRigidBodies += rbStamp->getNMembers();
116	>	}
117	>
118	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
119	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
120	>
121		}
122	+
123	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
124	+	//group therefore the total number of cutoff groups in the system is
125	+	//equal to the total number of atoms minus number of atoms belong to
126	+	//cutoff group defined in meta-data file plus the number of cutoff
127	+	//groups defined in meta-data file
128
129	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
130	+
131	+	//every free atom (atom does not belong to rigid bodies) is an
132	+	//integrable object therefore the total number of integrable objects
133	+	//in the system is equal to the total number of atoms minus number of
134	+	//atoms belong to rigid body defined in meta-data file plus the number
135	+	//of rigid bodies defined in meta-data file
136	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
137	+	+ nGlobalRigidBodies_;
138	+
139	+	nGlobalMols_ = molStampIds_.size();
140	+	molToProcMap_.resize(nGlobalMols_);
141	+	}
142	+
143		SimInfo::~SimInfo() {
144	<	std::map<int, Molecule*>::iterator i;
144	>	map<int, Molecule*>::iterator i;
145		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
146		delete i->second;
147		}
#	Line 172 | Line 152 | namespace oopse {
152		delete forceField_;
153		}
154
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	–	}
155
156		bool SimInfo::addMolecule(Molecule* mol) {
157		MoleculeIterator i;
158	<
158	>
159		i = molecules_.find(mol->getGlobalIndex());
160		if (i == molecules_.end() ) {
161	<
162	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
163	<
161	>
162	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
163	>
164		nAtoms_ += mol->getNAtoms();
165		nBonds_ += mol->getNBonds();
166		nBends_ += mol->getNBends();
167		nTorsions_ += mol->getNTorsions();
168	+	nInversions_ += mol->getNInversions();
169		nRigidBodies_ += mol->getNRigidBodies();
170		nIntegrableObjects_ += mol->getNIntegrableObjects();
171		nCutoffGroups_ += mol->getNCutoffGroups();
172		nConstraints_ += mol->getNConstraintPairs();
173	<
174	<	addExcludePairs(mol);
175	<
173	>
174	>	addInteractionPairs(mol);
175	>
176		return true;
177		} else {
178		return false;
179		}
180		}
181	<
181	>
182		bool SimInfo::removeMolecule(Molecule* mol) {
183		MoleculeIterator i;
184		i = molecules_.find(mol->getGlobalIndex());
#	Line 220 | Line 191 | namespace oopse {
191		nBonds_ -= mol->getNBonds();
192		nBends_ -= mol->getNBends();
193		nTorsions_ -= mol->getNTorsions();
194	+	nInversions_ -= mol->getNInversions();
195		nRigidBodies_ -= mol->getNRigidBodies();
196		nIntegrableObjects_ -= mol->getNIntegrableObjects();
197		nCutoffGroups_ -= mol->getNCutoffGroups();
198		nConstraints_ -= mol->getNConstraintPairs();
199
200	<	removeExcludePairs(mol);
200	>	removeInteractionPairs(mol);
201		molecules_.erase(mol->getGlobalIndex());
202
203		delete mol;
#	Line 234 | Line 206 | namespace oopse {
206		} else {
207		return false;
208		}
237	–
238	–
209		}
210
211
#	Line 253 | Line 223 | namespace oopse {
223		void SimInfo::calcNdf() {
224		int ndf_local;
225		MoleculeIterator i;
226	<	std::vector<StuntDouble*>::iterator j;
226	>	vector<StuntDouble*>::iterator j;
227		Molecule* mol;
228		StuntDouble* integrableObject;
229
#	Line 299 | Line 269 | namespace oopse {
269		#endif
270		return fdf_;
271		}
272	+
273	+	unsigned int SimInfo::getNLocalCutoffGroups(){
274	+	int nLocalCutoffAtoms = 0;
275	+	Molecule* mol;
276	+	MoleculeIterator mi;
277	+	CutoffGroup* cg;
278	+	Molecule::CutoffGroupIterator ci;
279
280	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
281	+
282	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
283	+	cg = mol->nextCutoffGroup(ci)) {
284	+	nLocalCutoffAtoms += cg->getNumAtom();
285	+
286	+	}
287	+	}
288	+
289	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
290	+	}
291	+
292		void SimInfo::calcNdfRaw() {
293		int ndfRaw_local;
294
295		MoleculeIterator i;
296	<	std::vector<StuntDouble*>::iterator j;
296	>	vector<StuntDouble*>::iterator j;
297		Molecule* mol;
298		StuntDouble* integrableObject;
299
#	Line 351 | Line 340 | namespace oopse {
340
341		}
342
343	<	void SimInfo::addExcludePairs(Molecule* mol) {
344	<	std::vector<Bond*>::iterator bondIter;
345	<	std::vector<Bend*>::iterator bendIter;
346	<	std::vector<Torsion*>::iterator torsionIter;
343	>	void SimInfo::addInteractionPairs(Molecule* mol) {
344	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
345	>	vector<Bond*>::iterator bondIter;
346	>	vector<Bend*>::iterator bendIter;
347	>	vector<Torsion*>::iterator torsionIter;
348	>	vector<Inversion*>::iterator inversionIter;
349		Bond* bond;
350		Bend* bend;
351		Torsion* torsion;
352	+	Inversion* inversion;
353		int a;
354		int b;
355		int c;
356		int d;
357
358	<	std::map<int, std::set<int> > atomGroups;
358	>	// atomGroups can be used to add special interaction maps between
359	>	// groups of atoms that are in two separate rigid bodies.
360	>	// However, most site-site interactions between two rigid bodies
361	>	// are probably not special, just the ones between the physically
362	>	// bonded atoms.  Interactions *within* a single rigid body should
363	>	// always be excluded.  These are done at the bottom of this
364	>	// function.
365
366	+	map<int, set<int> > atomGroups;
367		Molecule::RigidBodyIterator rbIter;
368		RigidBody* rb;
369		Molecule::IntegrableObjectIterator ii;
370		StuntDouble* integrableObject;
371
372	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
373	<	integrableObject = mol->nextIntegrableObject(ii)) {
374	<
372	>	for (integrableObject = mol->beginIntegrableObject(ii);
373	>	integrableObject != NULL;
374	>	integrableObject = mol->nextIntegrableObject(ii)) {
375	>
376		if (integrableObject->isRigidBody()) {
377	<	rb = static_cast<RigidBody*>(integrableObject);
378	<	std::vector<Atom*> atoms = rb->getAtoms();
379	<	std::set<int> rigidAtoms;
380	<	for (int i = 0; i < atoms.size(); ++i) {
381	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
382	<	}
383	<	for (int i = 0; i < atoms.size(); ++i) {
384	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
385	<	}
377	>	rb = static_cast<RigidBody*>(integrableObject);
378	>	vector<Atom*> atoms = rb->getAtoms();
379	>	set<int> rigidAtoms;
380	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
381	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
382	>	}
383	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
384	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
385	>	}
386		} else {
387	<	std::set<int> oneAtomSet;
387	>	set<int> oneAtomSet;
388		oneAtomSet.insert(integrableObject->getGlobalIndex());
389	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
389	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
390		}
391		}
392	+
393	+	for (bond= mol->beginBond(bondIter); bond != NULL;
394	+	bond = mol->nextBond(bondIter)) {
395
393	–
394	–
395	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
396		a = bond->getAtomA()->getGlobalIndex();
397	<	b = bond->getAtomB()->getGlobalIndex();
398	<	exclude_.addPair(a, b);
397	>	b = bond->getAtomB()->getGlobalIndex();
398	>
399	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
400	>	oneTwoInteractions_.addPair(a, b);
401	>	} else {
402	>	excludedInteractions_.addPair(a, b);
403	>	}
404		}
405
406	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
406	>	for (bend= mol->beginBend(bendIter); bend != NULL;
407	>	bend = mol->nextBend(bendIter)) {
408	>
409		a = bend->getAtomA()->getGlobalIndex();
410		b = bend->getAtomB()->getGlobalIndex();
411		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);
412
413	<	//exclude_.addPair(a, b);
414	<	//exclude_.addPair(a, c);
415	<	//exclude_.addPair(b, c);
413	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
414	>	oneTwoInteractions_.addPair(a, b);
415	>	oneTwoInteractions_.addPair(b, c);
416	>	} else {
417	>	excludedInteractions_.addPair(a, b);
418	>	excludedInteractions_.addPair(b, c);
419	>	}
420	>
421	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
422	>	oneThreeInteractions_.addPair(a, c);
423	>	} else {
424	>	excludedInteractions_.addPair(a, c);
425	>	}
426		}
427
428	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
428	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
429	>	torsion = mol->nextTorsion(torsionIter)) {
430	>
431		a = torsion->getAtomA()->getGlobalIndex();
432		b = torsion->getAtomB()->getGlobalIndex();
433		c = torsion->getAtomC()->getGlobalIndex();
434	<	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);
434	>	d = torsion->getAtomD()->getGlobalIndex();
435
436	<	exclude_.addPairs(rigidSetA, rigidSetB);
437	<	exclude_.addPairs(rigidSetA, rigidSetC);
438	<	exclude_.addPairs(rigidSetA, rigidSetD);
439	<	exclude_.addPairs(rigidSetB, rigidSetC);
440	<	exclude_.addPairs(rigidSetB, rigidSetD);
441	<	exclude_.addPairs(rigidSetC, rigidSetD);
436	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
437	>	oneTwoInteractions_.addPair(a, b);
438	>	oneTwoInteractions_.addPair(b, c);
439	>	oneTwoInteractions_.addPair(c, d);
440	>	} else {
441	>	excludedInteractions_.addPair(a, b);
442	>	excludedInteractions_.addPair(b, c);
443	>	excludedInteractions_.addPair(c, d);
444	>	}
445
446	<	/*
447	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
448	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
449	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
450	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
451	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
452	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
453	<
454	<
455	<	exclude_.addPair(a, b);
456	<	exclude_.addPair(a, c);
457	<	exclude_.addPair(a, d);
458	<	exclude_.addPair(b, c);
448	<	exclude_.addPair(b, d);
449	<	exclude_.addPair(c, d);
450	<	*/
446	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
447	>	oneThreeInteractions_.addPair(a, c);
448	>	oneThreeInteractions_.addPair(b, d);
449	>	} else {
450	>	excludedInteractions_.addPair(a, c);
451	>	excludedInteractions_.addPair(b, d);
452	>	}
453	>
454	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
455	>	oneFourInteractions_.addPair(a, d);
456	>	} else {
457	>	excludedInteractions_.addPair(a, d);
458	>	}
459		}
460
461	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
462	<	std::vector<Atom*> atoms = rb->getAtoms();
463	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
464	<	for (int j = i + 1; j < atoms.size(); ++j) {
461	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
462	>	inversion = mol->nextInversion(inversionIter)) {
463	>
464	>	a = inversion->getAtomA()->getGlobalIndex();
465	>	b = inversion->getAtomB()->getGlobalIndex();
466	>	c = inversion->getAtomC()->getGlobalIndex();
467	>	d = inversion->getAtomD()->getGlobalIndex();
468	>
469	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
470	>	oneTwoInteractions_.addPair(a, b);
471	>	oneTwoInteractions_.addPair(a, c);
472	>	oneTwoInteractions_.addPair(a, d);
473	>	} else {
474	>	excludedInteractions_.addPair(a, b);
475	>	excludedInteractions_.addPair(a, c);
476	>	excludedInteractions_.addPair(a, d);
477	>	}
478	>
479	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
480	>	oneThreeInteractions_.addPair(b, c);
481	>	oneThreeInteractions_.addPair(b, d);
482	>	oneThreeInteractions_.addPair(c, d);
483	>	} else {
484	>	excludedInteractions_.addPair(b, c);
485	>	excludedInteractions_.addPair(b, d);
486	>	excludedInteractions_.addPair(c, d);
487	>	}
488	>	}
489	>
490	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
491	>	rb = mol->nextRigidBody(rbIter)) {
492	>	vector<Atom*> atoms = rb->getAtoms();
493	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
494	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
495		a = atoms[i]->getGlobalIndex();
496		b = atoms[j]->getGlobalIndex();
497	<	exclude_.addPair(a, b);
497	>	excludedInteractions_.addPair(a, b);
498		}
499		}
500		}
501
502		}
503
504	<	void SimInfo::removeExcludePairs(Molecule* mol) {
505	<	std::vector<Bond*>::iterator bondIter;
506	<	std::vector<Bend*>::iterator bendIter;
507	<	std::vector<Torsion*>::iterator torsionIter;
504	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
505	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
506	>	vector<Bond*>::iterator bondIter;
507	>	vector<Bend*>::iterator bendIter;
508	>	vector<Torsion*>::iterator torsionIter;
509	>	vector<Inversion*>::iterator inversionIter;
510		Bond* bond;
511		Bend* bend;
512		Torsion* torsion;
513	+	Inversion* inversion;
514		int a;
515		int b;
516		int c;
517		int d;
518
519	<	std::map<int, std::set<int> > atomGroups;
479	<
519	>	map<int, set<int> > atomGroups;
520		Molecule::RigidBodyIterator rbIter;
521		RigidBody* rb;
522		Molecule::IntegrableObjectIterator ii;
523		StuntDouble* integrableObject;
524
525	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
526	<	integrableObject = mol->nextIntegrableObject(ii)) {
527	<
525	>	for (integrableObject = mol->beginIntegrableObject(ii);
526	>	integrableObject != NULL;
527	>	integrableObject = mol->nextIntegrableObject(ii)) {
528	>
529		if (integrableObject->isRigidBody()) {
530	<	rb = static_cast<RigidBody*>(integrableObject);
531	<	std::vector<Atom*> atoms = rb->getAtoms();
532	<	std::set<int> rigidAtoms;
533	<	for (int i = 0; i < atoms.size(); ++i) {
534	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
535	<	}
536	<	for (int i = 0; i < atoms.size(); ++i) {
537	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
538	<	}
530	>	rb = static_cast<RigidBody*>(integrableObject);
531	>	vector<Atom*> atoms = rb->getAtoms();
532	>	set<int> rigidAtoms;
533	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
534	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
535	>	}
536	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
537	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
538	>	}
539		} else {
540	<	std::set<int> oneAtomSet;
540	>	set<int> oneAtomSet;
541		oneAtomSet.insert(integrableObject->getGlobalIndex());
542	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
542	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
543		}
544		}
545
546	<
547	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
546	>	for (bond= mol->beginBond(bondIter); bond != NULL;
547	>	bond = mol->nextBond(bondIter)) {
548	>
549		a = bond->getAtomA()->getGlobalIndex();
550	<	b = bond->getAtomB()->getGlobalIndex();
551	<	exclude_.removePair(a, b);
550	>	b = bond->getAtomB()->getGlobalIndex();
551	>
552	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
553	>	oneTwoInteractions_.removePair(a, b);
554	>	} else {
555	>	excludedInteractions_.removePair(a, b);
556	>	}
557		}
558
559	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
559	>	for (bend= mol->beginBend(bendIter); bend != NULL;
560	>	bend = mol->nextBend(bendIter)) {
561	>
562		a = bend->getAtomA()->getGlobalIndex();
563		b = bend->getAtomB()->getGlobalIndex();
564		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);
565
566	<	//exclude_.removePair(a, b);
567	<	//exclude_.removePair(a, c);
568	<	//exclude_.removePair(b, c);
566	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
567	>	oneTwoInteractions_.removePair(a, b);
568	>	oneTwoInteractions_.removePair(b, c);
569	>	} else {
570	>	excludedInteractions_.removePair(a, b);
571	>	excludedInteractions_.removePair(b, c);
572	>	}
573	>
574	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
575	>	oneThreeInteractions_.removePair(a, c);
576	>	} else {
577	>	excludedInteractions_.removePair(a, c);
578	>	}
579		}
580
581	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
581	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
582	>	torsion = mol->nextTorsion(torsionIter)) {
583	>
584		a = torsion->getAtomA()->getGlobalIndex();
585		b = torsion->getAtomB()->getGlobalIndex();
586		c = torsion->getAtomC()->getGlobalIndex();
587	<	d = torsion->getAtomD()->getGlobalIndex();
587	>	d = torsion->getAtomD()->getGlobalIndex();
588	>
589	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
590	>	oneTwoInteractions_.removePair(a, b);
591	>	oneTwoInteractions_.removePair(b, c);
592	>	oneTwoInteractions_.removePair(c, d);
593	>	} else {
594	>	excludedInteractions_.removePair(a, b);
595	>	excludedInteractions_.removePair(b, c);
596	>	excludedInteractions_.removePair(c, d);
597	>	}
598
599	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
600	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
601	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
602	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
599	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
600	>	oneThreeInteractions_.removePair(a, c);
601	>	oneThreeInteractions_.removePair(b, d);
602	>	} else {
603	>	excludedInteractions_.removePair(a, c);
604	>	excludedInteractions_.removePair(b, d);
605	>	}
606
607	<	exclude_.removePairs(rigidSetA, rigidSetB);
608	<	exclude_.removePairs(rigidSetA, rigidSetC);
609	<	exclude_.removePairs(rigidSetA, rigidSetD);
610	<	exclude_.removePairs(rigidSetB, rigidSetC);
611	<	exclude_.removePairs(rigidSetB, rigidSetD);
612	<	exclude_.removePairs(rigidSetC, rigidSetD);
607	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
608	>	oneFourInteractions_.removePair(a, d);
609	>	} else {
610	>	excludedInteractions_.removePair(a, d);
611	>	}
612	>	}
613
614	<	/*
615	<	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());
614	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
615	>	inversion = mol->nextInversion(inversionIter)) {
616
617	<
618	<	exclude_.removePair(a, b);
619	<	exclude_.removePair(a, c);
620	<	exclude_.removePair(a, d);
621	<	exclude_.removePair(b, c);
622	<	exclude_.removePair(b, d);
623	<	exclude_.removePair(c, d);
624	<	*/
617	>	a = inversion->getAtomA()->getGlobalIndex();
618	>	b = inversion->getAtomB()->getGlobalIndex();
619	>	c = inversion->getAtomC()->getGlobalIndex();
620	>	d = inversion->getAtomD()->getGlobalIndex();
621	>
622	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
623	>	oneTwoInteractions_.removePair(a, b);
624	>	oneTwoInteractions_.removePair(a, c);
625	>	oneTwoInteractions_.removePair(a, d);
626	>	} else {
627	>	excludedInteractions_.removePair(a, b);
628	>	excludedInteractions_.removePair(a, c);
629	>	excludedInteractions_.removePair(a, d);
630	>	}
631	>
632	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
633	>	oneThreeInteractions_.removePair(b, c);
634	>	oneThreeInteractions_.removePair(b, d);
635	>	oneThreeInteractions_.removePair(c, d);
636	>	} else {
637	>	excludedInteractions_.removePair(b, c);
638	>	excludedInteractions_.removePair(b, d);
639	>	excludedInteractions_.removePair(c, d);
640	>	}
641		}
642
643	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
644	<	std::vector<Atom*> atoms = rb->getAtoms();
645	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
646	<	for (int j = i + 1; j < atoms.size(); ++j) {
643	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
644	>	rb = mol->nextRigidBody(rbIter)) {
645	>	vector<Atom*> atoms = rb->getAtoms();
646	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
647	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
648		a = atoms[i]->getGlobalIndex();
649		b = atoms[j]->getGlobalIndex();
650	<	exclude_.removePair(a, b);
650	>	excludedInteractions_.removePair(a, b);
651		}
652		}
653		}
654	<
654	>
655		}
656	<
657	<
656	>
657	>
658		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
659		int curStampId;
660	<
660	>
661		//index from 0
662		curStampId = moleculeStamps_.size();
663
#	Line 587 | Line 665 | namespace oopse {
665		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
666		}
667
590	–	void SimInfo::update() {
668
669	<	setupSimType();
670	<
671	<	#ifdef IS_MPI
672	<	setupFortranParallel();
673	<	#endif
674	<
675	<	setupFortranSim();
676	<
677	<	//setup fortran force field
601	<	/** @deprecate */
602	<	int isError = 0;
603	<
604	<	setupCutoff();
605	<
606	<	setupElectrostaticSummationMethod( isError );
607	<	setupSwitchingFunction();
608	<	setupAccumulateBoxDipole();
609	<
610	<	if(isError){
611	<	sprintf( painCave.errMsg,
612	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
613	<	painCave.isFatal = 1;
614	<	simError();
615	<	}
616	<
669	>	/**
670	>	* update
671	>	*
672	>	*  Performs the global checks and variable settings after the
673	>	*  objects have been created.
674	>	*
675	>	*/
676	>	void SimInfo::update() {
677	>	setupSimVariables();
678		calcNdf();
679		calcNdfRaw();
680		calcNdfTrans();
620	–
621	–	fortranInitialized_ = true;
681		}
682	<
683	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
682	>
683	>	/**
684	>	* getSimulatedAtomTypes
685	>	*
686	>	* Returns an STL set of AtomType* that are actually present in this
687	>	* simulation.  Must query all processors to assemble this information.
688	>	*
689	>	*/
690	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
691		SimInfo::MoleculeIterator mi;
692		Molecule* mol;
693		Molecule::AtomIterator ai;
694		Atom* atom;
695	<	std::set<AtomType*> atomTypes;
696	<
695	>	set<AtomType*> atomTypes;
696	>
697		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
698	<
699	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
698	>	for(atom = mol->beginAtom(ai); atom != NULL;
699	>	atom = mol->nextAtom(ai)) {
700		atomTypes.insert(atom->getAtomType());
701	<	}
702	<
703	<	}
701	>	}
702	>	}
703	>
704	>	#ifdef IS_MPI
705
706	<	return atomTypes;
707	<	}
641	<
642	<	void SimInfo::setupSimType() {
643	<	std::set<AtomType*>::iterator i;
644	<	std::set<AtomType*> atomTypes;
645	<	atomTypes = getUniqueAtomTypes();
706	>	// loop over the found atom types on this processor, and add their
707	>	// numerical idents to a vector:
708
709	<	int useLennardJones = 0;
710	<	int useElectrostatic = 0;
711	<	int useEAM = 0;
712	<	int useSC = 0;
651	<	int useCharge = 0;
652	<	int useDirectional = 0;
653	<	int useDipole = 0;
654	<	int useGayBerne = 0;
655	<	int useSticky = 0;
656	<	int useStickyPower = 0;
657	<	int useShape = 0;
658	<	int useFLARB = 0; //it is not in AtomType yet
659	<	int useDirectionalAtom = 0;
660	<	int useElectrostatics = 0;
661	<	//usePBC and useRF are from simParams
662	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
663	<	int useRF;
664	<	int useSF;
665	<	int useSP;
666	<	int useBoxDipole;
667	<	std::string myMethod;
709	>	vector<int> foundTypes;
710	>	set<AtomType*>::iterator i;
711	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
712	>	foundTypes.push_back( (*i)->getIdent() );
713
714	<	// set the useRF logical
715	<	useRF = 0;
671	<	useSF = 0;
672	<	useSP = 0;
714	>	// count_local holds the number of found types on this processor
715	>	int count_local = foundTypes.size();
716
717	+	int nproc = MPI::COMM_WORLD.Get_size();
718
719	<	if (simParams_->haveElectrostaticSummationMethod()) {
720	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
721	<	toUpper(myMethod);
722	<	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;
719	>	// we need arrays to hold the counts and displacement vectors for
720	>	// all processors
721	>	vector<int> counts(nproc, 0);
722	>	vector<int> disps(nproc, 0);
723
724	<	//loop over all of the atom types
725	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
726	<	useLennardJones |= (*i)->isLennardJones();
727	<	useElectrostatic |= (*i)->isElectrostatic();
728	<	useEAM |= (*i)->isEAM();
729	<	useSC |= (*i)->isSC();
730	<	useCharge |= (*i)->isCharge();
731	<	useDirectional |= (*i)->isDirectional();
732	<	useDipole |= (*i)->isDipole();
733	<	useGayBerne |= (*i)->isGayBerne();
701	<	useSticky |= (*i)->isSticky();
702	<	useStickyPower |= (*i)->isStickyPower();
703	<	useShape |= (*i)->isShape();
724	>	// fill the counts array
725	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
726	>	1, MPI::INT);
727	>
728	>	// use the processor counts to compute the displacement array
729	>	disps[0] = 0;
730	>	int totalCount = counts[0];
731	>	for (int iproc = 1; iproc < nproc; iproc++) {
732	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
733	>	totalCount += counts[iproc];
734		}
735
736	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
737	<	useDirectionalAtom = 1;
738	<	}
736	>	// we need a (possibly redundant) set of all found types:
737	>	vector<int> ftGlobal(totalCount);
738	>
739	>	// now spray out the foundTypes to all the other processors:
740	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
741	>	&ftGlobal[0], &counts[0], &disps[0],
742	>	MPI::INT);
743
744	<	if (useCharge || useDipole) {
711	<	useElectrostatics = 1;
712	<	}
744	>	vector<int>::iterator j;
745
746	<	#ifdef IS_MPI
747	<	int temp;
746	>	// foundIdents is a stl set, so inserting an already found ident
747	>	// will have no effect.
748	>	set<int> foundIdents;
749
750	<	temp = usePBC;
751	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
750	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
751	>	foundIdents.insert((*j));
752	>
753	>	// now iterate over the foundIdents and get the actual atom types
754	>	// that correspond to these:
755	>	set<int>::iterator it;
756	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
757	>	atomTypes.insert( forceField_->getAtomType((*it)) );
758	>
759	>	#endif
760
761	<	temp = useDirectionalAtom;
762	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
761	>	return atomTypes;
762	>	}
763
764	<	temp = useLennardJones;
765	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766	<
767	<	temp = useElectrostatics;
768	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769	<
770	<	temp = useCharge;
771	<	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);
764	>	void SimInfo::setupSimVariables() {
765	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
766	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
767	>	calcBoxDipole_ = false;
768	>	if ( simParams_->haveAccumulateBoxDipole() )
769	>	if ( simParams_->getAccumulateBoxDipole() ) {
770	>	calcBoxDipole_ = true;
771	>	}
772
773	<	temp = useGayBerne;
774	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
773	>	set<AtomType*>::iterator i;
774	>	set<AtomType*> atomTypes;
775	>	atomTypes = getSimulatedAtomTypes();
776	>	int usesElectrostatic = 0;
777	>	int usesMetallic = 0;
778	>	int usesDirectional = 0;
779	>	//loop over all of the atom types
780	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
781	>	usesElectrostatic |= (*i)->isElectrostatic();
782	>	usesMetallic |= (*i)->isMetal();
783	>	usesDirectional |= (*i)->isDirectional();
784	>	}
785	>
786	>	#ifdef IS_MPI
787	>	int temp;
788	>	temp = usesDirectional;
789	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
790	>
791	>	temp = usesMetallic;
792	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
793	>
794	>	temp = usesElectrostatic;
795	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
796	>	#else
797
798	<	temp = useEAM;
799	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
798	>	usesDirectionalAtoms_ = usesDirectional;
799	>	usesMetallicAtoms_ = usesMetallic;
800	>	usesElectrostaticAtoms_ = usesElectrostatic;
801
802	<	temp = useSC;
748	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
802	>	#endif
803
804	<	temp = useShape;
805	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
804	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
805	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
806	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
807	>	}
808
753	–	temp = useFLARB;
754	–	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
809
810	<	temp = useRF;
811	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810	>	vector<int> SimInfo::getGlobalAtomIndices() {
811	>	SimInfo::MoleculeIterator mi;
812	>	Molecule* mol;
813	>	Molecule::AtomIterator ai;
814	>	Atom* atom;
815
816	<	temp = useSF;
817	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
817	>
818	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
819	>
820	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
821	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
822	>	}
823	>	}
824	>	return GlobalAtomIndices;
825	>	}
826
762	–	temp = useSP;
763	–	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
827
828	<	temp = useBoxDipole;
829	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
828	>	vector<int> SimInfo::getGlobalGroupIndices() {
829	>	SimInfo::MoleculeIterator mi;
830	>	Molecule* mol;
831	>	Molecule::CutoffGroupIterator ci;
832	>	CutoffGroup* cg;
833
834	<	#endif
835	<
836	<	fInfo_.SIM_uses_PBC = usePBC;
837	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
838	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
839	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
840	<	fInfo_.SIM_uses_Charges = useCharge;
841	<	fInfo_.SIM_uses_Dipoles = useDipole;
842	<	fInfo_.SIM_uses_Sticky = useSticky;
843	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
844	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
845	<	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;
834	>	vector<int> GlobalGroupIndices;
835	>
836	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
837	>
838	>	//local index of cutoff group is trivial, it only depends on the
839	>	//order of travesing
840	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
841	>	cg = mol->nextCutoffGroup(ci)) {
842	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
843	>	}
844	>	}
845	>	return GlobalGroupIndices;
846		}
847
789	–	void SimInfo::setupFortranSim() {
790	–	int isError;
791	–	int nExclude;
792	–	std::vector<int> fortranGlobalGroupMembership;
793	–
794	–	nExclude = exclude_.getSize();
795	–	isError = 0;
848
849	<	//globalGroupMembership_ is filled by SimCreator
850	<	for (int i = 0; i < nGlobalAtoms_; i++) {
799	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
800	<	}
849	>	void SimInfo::prepareTopology() {
850	>	int nExclude, nOneTwo, nOneThree, nOneFour;
851
852		//calculate mass ratio of cutoff group
803	–	std::vector<RealType> mfact;
853		SimInfo::MoleculeIterator mi;
854		Molecule* mol;
855		Molecule::CutoffGroupIterator ci;
#	Line 809 | Line 858 | namespace oopse {
858		Atom* atom;
859		RealType totalMass;
860
861	<	//to avoid memory reallocation, reserve enough space for mfact
862	<	mfact.reserve(getNCutoffGroups());
861	>	/**
862	>	* The mass factor is the relative mass of an atom to the total
863	>	* mass of the cutoff group it belongs to.  By default, all atoms
864	>	* are their own cutoff groups, and therefore have mass factors of
865	>	* 1.  We need some special handling for massless atoms, which
866	>	* will be treated as carrying the entire mass of the cutoff
867	>	* group.
868	>	*/
869	>	massFactors_.clear();
870	>	massFactors_.resize(getNAtoms(), 1.0);
871
872		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
873	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
873	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
874	>	cg = mol->nextCutoffGroup(ci)) {
875
876		totalMass = cg->getMass();
877		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
878		// Check for massless groups - set mfact to 1 if true
879	<	if (totalMass != 0)
880	<	mfact.push_back(atom->getMass()/totalMass);
879	>	if (totalMass != 0)
880	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
881		else
882	<	mfact.push_back( 1.0 );
882	>	massFactors_[atom->getLocalIndex()] = 1.0;
883		}
826	–
884		}
885		}
886
887	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
831	<	std::vector<int> identArray;
887	>	// Build the identArray_
888
889	<	//to avoid memory reallocation, reserve enough space identArray
890	<	identArray.reserve(getNAtoms());
835	<
889	>	identArray_.clear();
890	>	identArray_.reserve(getNAtoms());
891		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
892		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
893	<	identArray.push_back(atom->getIdent());
893	>	identArray_.push_back(atom->getIdent());
894		}
895		}
841	–
842	–	//fill molMembershipArray
843	–	//molMembershipArray is filled by SimCreator
844	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
845	–	for (int i = 0; i < nGlobalAtoms_; i++) {
846	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
847	–	}
896
897	<	//setup fortran simulation
850	<	int nGlobalExcludes = 0;
851	<	int* globalExcludes = NULL;
852	<	int* excludeList = exclude_.getExcludeList();
853	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
854	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
855	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
897	>	//scan topology
898
899	<	if( isError ){
900	<
901	<	sprintf( painCave.errMsg,
902	<	"There was an error setting the simulation information in fortran.\n" );
861	<	painCave.isFatal = 1;
862	<	painCave.severity = OOPSE_ERROR;
863	<	simError();
864	<	}
865	<
866	<	#ifdef IS_MPI
867	<	sprintf( checkPointMsg,
868	<	"succesfully sent the simulation information to fortran.\n");
869	<	MPIcheckPoint();
870	<	#endif // is_mpi
871	<	}
872	<
873	<
874	<	#ifdef IS_MPI
875	<	void SimInfo::setupFortranParallel() {
876	<
877	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
878	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
879	<	std::vector<int> localToGlobalCutoffGroupIndex;
880	<	SimInfo::MoleculeIterator mi;
881	<	Molecule::AtomIterator ai;
882	<	Molecule::CutoffGroupIterator ci;
883	<	Molecule* mol;
884	<	Atom* atom;
885	<	CutoffGroup* cg;
886	<	mpiSimData parallelData;
887	<	int isError;
888	<
889	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
890	<
891	<	//local index(index in DataStorge) of atom is important
892	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
893	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
894	<	}
895	<
896	<	//local index of cutoff group is trivial, it only depends on the order of travesing
897	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
898	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
899	<	}
900	<
901	<	}
902	<
903	<	//fill up mpiSimData struct
904	<	parallelData.nMolGlobal = getNGlobalMolecules();
905	<	parallelData.nMolLocal = getNMolecules();
906	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
907	<	parallelData.nAtomsLocal = getNAtoms();
908	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
909	<	parallelData.nGroupsLocal = getNCutoffGroups();
910	<	parallelData.myNode = worldRank;
911	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
912	<
913	<	//pass mpiSimData struct and index arrays to fortran
914	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
915	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
916	<	&localToGlobalCutoffGroupIndex[0], &isError);
917	<
918	<	if (isError) {
919	<	sprintf(painCave.errMsg,
920	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
921	<	painCave.isFatal = 1;
922	<	simError();
923	<	}
924	<
925	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
926	<	MPIcheckPoint();
899	>	nExclude = excludedInteractions_.getSize();
900	>	nOneTwo = oneTwoInteractions_.getSize();
901	>	nOneThree = oneThreeInteractions_.getSize();
902	>	nOneFour = oneFourInteractions_.getSize();
903
904	+	int* excludeList = excludedInteractions_.getPairList();
905	+	int* oneTwoList = oneTwoInteractions_.getPairList();
906	+	int* oneThreeList = oneThreeInteractions_.getPairList();
907	+	int* oneFourList = oneFourInteractions_.getPairList();
908
909	<	}
930	<
931	<	#endif
932	<
933	<	void SimInfo::setupCutoff() {
934	<
935	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
936	<
937	<	// Check the cutoff policy
938	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
939	<
940	<	std::string myPolicy;
941	<	if (forceFieldOptions_.haveCutoffPolicy()){
942	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
943	<	}else if (simParams_->haveCutoffPolicy()) {
944	<	myPolicy = simParams_->getCutoffPolicy();
945	<	}
946	<
947	<	if (!myPolicy.empty()){
948	<	toUpper(myPolicy);
949	<	if (myPolicy == "MIX") {
950	<	cp = MIX_CUTOFF_POLICY;
951	<	} else {
952	<	if (myPolicy == "MAX") {
953	<	cp = MAX_CUTOFF_POLICY;
954	<	} else {
955	<	if (myPolicy == "TRADITIONAL") {
956	<	cp = TRADITIONAL_CUTOFF_POLICY;
957	<	} else {
958	<	// throw error
959	<	sprintf( painCave.errMsg,
960	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
961	<	painCave.isFatal = 1;
962	<	simError();
963	<	}
964	<	}
965	<	}
966	<	}
967	<	notifyFortranCutoffPolicy(&cp);
968	<
969	<	// Check the Skin Thickness for neighborlists
970	<	RealType skin;
971	<	if (simParams_->haveSkinThickness()) {
972	<	skin = simParams_->getSkinThickness();
973	<	notifyFortranSkinThickness(&skin);
974	<	}
975	<
976	<	// Check if the cutoff was set explicitly:
977	<	if (simParams_->haveCutoffRadius()) {
978	<	rcut_ = simParams_->getCutoffRadius();
979	<	if (simParams_->haveSwitchingRadius()) {
980	<	rsw_  = simParams_->getSwitchingRadius();
981	<	} else {
982	<	if (fInfo_.SIM_uses_Charges |
983	<	fInfo_.SIM_uses_Dipoles |
984	<	fInfo_.SIM_uses_RF) {
985	<
986	<	rsw_ = 0.85 * rcut_;
987	<	sprintf(painCave.errMsg,
988	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
989	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
990	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
991	<	painCave.isFatal = 0;
992	<	simError();
993	<	} else {
994	<	rsw_ = rcut_;
995	<	sprintf(painCave.errMsg,
996	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
997	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
998	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
999	<	painCave.isFatal = 0;
1000	<	simError();
1001	<	}
1002	<	}
1003	<
1004	<	notifyFortranCutoffs(&rcut_, &rsw_);
1005	<
1006	<	} else {
1007	<
1008	<	// For electrostatic atoms, we'll assume a large safe value:
1009	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1010	<	sprintf(painCave.errMsg,
1011	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1012	<	"\tOOPSE will use a default value of 15.0 angstroms"
1013	<	"\tfor the cutoffRadius.\n");
1014	<	painCave.isFatal = 0;
1015	<	simError();
1016	<	rcut_ = 15.0;
1017	<
1018	<	if (simParams_->haveElectrostaticSummationMethod()) {
1019	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1020	<	toUpper(myMethod);
1021	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1022	<	if (simParams_->haveSwitchingRadius()){
1023	<	sprintf(painCave.errMsg,
1024	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1025	<	"\teven though the electrostaticSummationMethod was\n"
1026	<	"\tset to %s\n", myMethod.c_str());
1027	<	painCave.isFatal = 1;
1028	<	simError();
1029	<	}
1030	<	}
1031	<	}
1032	<
1033	<	if (simParams_->haveSwitchingRadius()){
1034	<	rsw_ = simParams_->getSwitchingRadius();
1035	<	} else {
1036	<	sprintf(painCave.errMsg,
1037	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1038	<	"\tOOPSE will use a default value of\n"
1039	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1040	<	painCave.isFatal = 0;
1041	<	simError();
1042	<	rsw_ = 0.85 * rcut_;
1043	<	}
1044	<	notifyFortranCutoffs(&rcut_, &rsw_);
1045	<	} else {
1046	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1047	<	// We'll punt and let fortran figure out the cutoffs later.
1048	<
1049	<	notifyFortranYouAreOnYourOwn();
1050	<
1051	<	}
1052	<	}
1053	<	}
1054	<
1055	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1056	<
1057	<	int errorOut;
1058	<	int esm =  NONE;
1059	<	int sm = UNDAMPED;
1060	<	RealType alphaVal;
1061	<	RealType dielectric;
1062	<
1063	<	errorOut = isError;
1064	<
1065	<	if (simParams_->haveElectrostaticSummationMethod()) {
1066	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1067	<	toUpper(myMethod);
1068	<	if (myMethod == "NONE") {
1069	<	esm = NONE;
1070	<	} else {
1071	<	if (myMethod == "SWITCHING_FUNCTION") {
1072	<	esm = SWITCHING_FUNCTION;
1073	<	} else {
1074	<	if (myMethod == "SHIFTED_POTENTIAL") {
1075	<	esm = SHIFTED_POTENTIAL;
1076	<	} else {
1077	<	if (myMethod == "SHIFTED_FORCE") {
1078	<	esm = SHIFTED_FORCE;
1079	<	} else {
1080	<	if (myMethod == "REACTION_FIELD") {
1081	<	esm = REACTION_FIELD;
1082	<	dielectric = simParams_->getDielectric();
1083	<	if (!simParams_->haveDielectric()) {
1084	<	// throw warning
1085	<	sprintf( painCave.errMsg,
1086	<	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1087	<	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1088	<	painCave.isFatal = 0;
1089	<	simError();
1090	<	}
1091	<	} else {
1092	<	// throw error
1093	<	sprintf( painCave.errMsg,
1094	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1095	<	"\t(Input file specified %s .)\n"
1096	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1097	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1098	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1099	<	painCave.isFatal = 1;
1100	<	simError();
1101	<	}
1102	<	}
1103	<	}
1104	<	}
1105	<	}
1106	<	}
1107	<
1108	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1109	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1110	<	toUpper(myScreen);
1111	<	if (myScreen == "UNDAMPED") {
1112	<	sm = UNDAMPED;
1113	<	} else {
1114	<	if (myScreen == "DAMPED") {
1115	<	sm = DAMPED;
1116	<	if (!simParams_->haveDampingAlpha()) {
1117	<	// first set a cutoff dependent alpha value
1118	<	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1119	<	alphaVal = 0.5125 - rcut_* 0.025;
1120	<	// for values rcut > 20.5, alpha is zero
1121	<	if (alphaVal < 0) alphaVal = 0;
1122	<
1123	<	// throw warning
1124	<	sprintf( painCave.errMsg,
1125	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1126	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1127	<	painCave.isFatal = 0;
1128	<	simError();
1129	<	}
1130	<	} else {
1131	<	// throw error
1132	<	sprintf( painCave.errMsg,
1133	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1134	<	"\t(Input file specified %s .)\n"
1135	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1136	<	"or \"damped\".\n", myScreen.c_str() );
1137	<	painCave.isFatal = 1;
1138	<	simError();
1139	<	}
1140	<	}
1141	<	}
1142	<
1143	<	// let's pass some summation method variables to fortran
1144	<	setElectrostaticSummationMethod( &esm );
1145	<	setFortranElectrostaticMethod( &esm );
1146	<	setScreeningMethod( &sm );
1147	<	setDampingAlpha( &alphaVal );
1148	<	setReactionFieldDielectric( &dielectric );
1149	<	initFortranFF( &errorOut );
1150	<	}
1151	<
1152	<	void SimInfo::setupSwitchingFunction() {
1153	<	int ft = CUBIC;
1154	<
1155	<	if (simParams_->haveSwitchingFunctionType()) {
1156	<	std::string funcType = simParams_->getSwitchingFunctionType();
1157	<	toUpper(funcType);
1158	<	if (funcType == "CUBIC") {
1159	<	ft = CUBIC;
1160	<	} else {
1161	<	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1162	<	ft = FIFTH_ORDER_POLY;
1163	<	} else {
1164	<	// throw error
1165	<	sprintf( painCave.errMsg,
1166	<	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1167	<	painCave.isFatal = 1;
1168	<	simError();
1169	<	}
1170	<	}
1171	<	}
1172	<
1173	<	// send switching function notification to switcheroo
1174	<	setFunctionType(&ft);
1175	<
1176	<	}
1177	<
1178	<	void SimInfo::setupAccumulateBoxDipole() {
1179	<
1180	<	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1181	<	if ( simParams_->haveAccumulateBoxDipole() )
1182	<	if ( simParams_->getAccumulateBoxDipole() ) {
1183	<	setAccumulateBoxDipole();
1184	<	calcBoxDipole_ = true;
1185	<	}
1186	<
909	>	topologyDone_ = true;
910		}
911
912		void SimInfo::addProperty(GenericData* genData) {
913		properties_.addProperty(genData);
914		}
915
916	<	void SimInfo::removeProperty(const std::string& propName) {
916	>	void SimInfo::removeProperty(const string& propName) {
917		properties_.removeProperty(propName);
918		}
919
#	Line 1198 | Line 921 | namespace oopse {
921		properties_.clearProperties();
922		}
923
924	<	std::vector<std::string> SimInfo::getPropertyNames() {
924	>	vector<string> SimInfo::getPropertyNames() {
925		return properties_.getPropertyNames();
926		}
927
928	<	std::vector<GenericData*> SimInfo::getProperties() {
928	>	vector<GenericData*> SimInfo::getProperties() {
929		return properties_.getProperties();
930		}
931
932	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
932	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
933		return properties_.getPropertyByName(propName);
934		}
935
#	Line 1220 | Line 943 | namespace oopse {
943		Molecule* mol;
944		RigidBody* rb;
945		Atom* atom;
946	+	CutoffGroup* cg;
947		SimInfo::MoleculeIterator mi;
948		Molecule::RigidBodyIterator rbIter;
949	<	Molecule::AtomIterator atomIter;;
949	>	Molecule::AtomIterator atomIter;
950	>	Molecule::CutoffGroupIterator cgIter;
951
952		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
953
#	Line 1233 | Line 958 | namespace oopse {
958		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
959		rb->setSnapshotManager(sman_);
960		}
961	+
962	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
963	+	cg->setSnapshotManager(sman_);
964	+	}
965		}
966
967		}
#	Line 1289 | Line 1018 | namespace oopse {
1018
1019		}
1020
1021	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1021	>	ostream& operator <<(ostream& o, SimInfo& info) {
1022
1023		return o;
1024		}
#	Line 1332 | Line 1061 | namespace oopse {
1061
1062
1063		[  Ixx -Ixy  -Ixz ]
1064	<	J =| -Iyx  Iyy  -Iyz |
1064	>	J =| -Iyx  Iyy  -Iyz |
1065		[ -Izx -Iyz   Izz ]
1066		*/
1067
#	Line 1439 | Line 1168 | namespace oopse {
1168		return IOIndexToIntegrableObject.at(index);
1169		}
1170
1171	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1171	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1172		IOIndexToIntegrableObject= v;
1173		}
1174
1175	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1176	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1177	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1178	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1179	+	*/
1180	+	void SimInfo::getGyrationalVolume(RealType &volume){
1181	+	Mat3x3d intTensor;
1182	+	RealType det;
1183	+	Vector3d dummyAngMom;
1184	+	RealType sysconstants;
1185	+	RealType geomCnst;
1186	+
1187	+	geomCnst = 3.0/2.0;
1188	+	/* Get the inertial tensor and angular momentum for free*/
1189	+	getInertiaTensor(intTensor,dummyAngMom);
1190	+
1191	+	det = intTensor.determinant();
1192	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1193	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1194	+	return;
1195	+	}
1196	+
1197	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1198	+	Mat3x3d intTensor;
1199	+	Vector3d dummyAngMom;
1200	+	RealType sysconstants;
1201	+	RealType geomCnst;
1202	+
1203	+	geomCnst = 3.0/2.0;
1204	+	/* Get the inertial tensor and angular momentum for free*/
1205	+	getInertiaTensor(intTensor,dummyAngMom);
1206	+
1207	+	detI = intTensor.determinant();
1208	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1209	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1210	+	return;
1211	+	}
1212		/*
1213	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1213	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1214		assert( v.size() == nAtoms_ + nRigidBodies_);
1215		sdByGlobalIndex_ = v;
1216		}
#	Line 1454 | Line 1220 | namespace oopse {
1220		return sdByGlobalIndex_.at(index);
1221		}
1222		*/
1223	<	}//end namespace oopse
1223	>	int SimInfo::getNGlobalConstraints() {
1224	>	int nGlobalConstraints;
1225	>	#ifdef IS_MPI
1226	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1227	>	MPI_COMM_WORLD);
1228	>	#else
1229	>	nGlobalConstraints =  nConstraints_;
1230	>	#endif
1231	>	return nGlobalConstraints;
1232	>	}
1233
1234	+	}//end namespace OpenMD
1235	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 1078 by gezelter, Wed Oct 18 21:58:48 2006 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1601 by gezelter, Thu Aug 4 20:04:35 2011 UTC

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