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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1597 by gezelter, Tue Jul 26 15:49:24 2011 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 54 | Line 54
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56		#include "primitives/StuntDouble.hpp"
57	–	#include "UseTheForce/fCutoffPolicy.h"
58	–	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	–	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60	–	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61	–	#include "UseTheForce/doForces_interface.h"
62	–	#include "UseTheForce/DarkSide/neighborLists_interface.h"
63	–	#include "UseTheForce/DarkSide/electrostatic_interface.h"
64	–	#include "UseTheForce/DarkSide/switcheroo_interface.h"
57		#include "utils/MemoryUtils.hpp"
58		#include "utils/simError.h"
59		#include "selection/SelectionManager.hpp"
60		#include "io/ForceFieldOptions.hpp"
61		#include "UseTheForce/ForceField.hpp"
62	+	#include "nonbonded/SwitchingFunction.hpp"
63
64	<
65	<	#ifdef IS_MPI
73	<	#include "UseTheForce/mpiComponentPlan.h"
74	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
75	<	#endif
76	<
77	<	namespace oopse {
78	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79	<	std::map<int, std::set<int> >::iterator i = container.find(index);
80	<	std::set<int> result;
81	<	if (i != container.end()) {
82	<	result = i->second;
83	<	}
84	<
85	<	return result;
86	<	}
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	<	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	<	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();
119	<
120	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
121	<	cgStamp = molStamp->getCutoffGroupStamp(j);
122	<	nAtomsInGroups += cgStamp->getNMembers();
123	<	}
124	<
125	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
126	<
127	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
128	<
129	<	//calculate atoms in rigid bodies
130	<	int nAtomsInRigidBodies = 0;
131	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
132	<
133	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
134	<	rbStamp = molStamp->getRigidBodyStamp(j);
135	<	nAtomsInRigidBodies += rbStamp->getNMembers();
136	<	}
137	<
138	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
139	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
140	<
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();
159	<	molToProcMap_.resize(nGlobalMols_);
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 171 | Line 152 | namespace oopse {
152		delete forceField_;
153		}
154
174	–	int SimInfo::getNGlobalConstraints() {
175	–	int nGlobalConstraints;
176	–	#ifdef IS_MPI
177	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
178	–	MPI_COMM_WORLD);
179	–	#else
180	–	nGlobalConstraints =  nConstraints_;
181	–	#endif
182	–	return nGlobalConstraints;
183	–	}
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 219 | 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 233 | Line 206 | namespace oopse {
206		} else {
207		return false;
208		}
236	–
237	–
209		}
210
211
#	Line 252 | 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 298 | 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 350 | 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
392	–
393	–
394	–	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();
404	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
405	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
406	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
407	–
408	–	exclude_.addPairs(rigidSetA, rigidSetB);
409	–	exclude_.addPairs(rigidSetA, rigidSetC);
410	–	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();
422	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
423	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
424	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
425	<	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);
447	<	exclude_.addPair(b, d);
448	<	exclude_.addPair(c, d);
449	<	*/
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;
478	<
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();
515	–
516	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
517	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
518	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
519	–
520	–	exclude_.removePairs(rigidSetA, rigidSetB);
521	–	exclude_.removePairs(rigidSetA, rigidSetC);
522	–	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());
549	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
550	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
551	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
552	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
553	<	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 586 | Line 665 | namespace oopse {
665		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
666		}
667
589	–	void SimInfo::update() {
668
669	<	setupSimType();
670	<
671	<	#ifdef IS_MPI
672	<	setupFortranParallel();
673	<	#endif
674	<
675	<	setupFortranSim();
676	<
677	<	//setup fortran force field
600	<	/** @deprecate */
601	<	int isError = 0;
602	<
603	<	setupCutoff();
604	<
605	<	setupElectrostaticSummationMethod( isError );
606	<	setupSwitchingFunction();
607	<	setupAccumulateBoxDipole();
608	<
609	<	if(isError){
610	<	sprintf( painCave.errMsg,
611	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
612	<	painCave.isFatal = 1;
613	<	simError();
614	<	}
615	<
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();
619	–
620	–	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	<
636	<	}
637	<
638	<	return atomTypes;
639	<	}
640	<
641	<	void SimInfo::setupSimType() {
642	<	std::set<AtomType*>::iterator i;
643	<	std::set<AtomType*> atomTypes;
644	<	atomTypes = getUniqueAtomTypes();
701	>	}
702	>	}
703
704	<	int useLennardJones = 0;
647	<	int useElectrostatic = 0;
648	<	int useEAM = 0;
649	<	int useSC = 0;
650	<	int useCharge = 0;
651	<	int useDirectional = 0;
652	<	int useDipole = 0;
653	<	int useGayBerne = 0;
654	<	int useSticky = 0;
655	<	int useStickyPower = 0;
656	<	int useShape = 0;
657	<	int useFLARB = 0; //it is not in AtomType yet
658	<	int useDirectionalAtom = 0;
659	<	int useElectrostatics = 0;
660	<	//usePBC and useRF are from simParams
661	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
662	<	int useRF;
663	<	int useSF;
664	<	int useSP;
665	<	int useBoxDipole;
704	>	#ifdef IS_MPI
705
706	<	std::string myMethod;
707	<
708	<	// set the useRF logical
709	<	useRF = 0;
710	<	useSF = 0;
711	<	useSP = 0;
706	>	// loop over the found atom types on this processor, and add their
707	>	// numerical idents to a vector:
708	>
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	+	// count_local holds the number of found types on this processor
715	+	int count_local = foundTypes.size();
716
717	<	if (simParams_->haveElectrostaticSummationMethod()) {
676	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
677	<	toUpper(myMethod);
678	<	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;
717	>	int nproc = MPI::COMM_WORLD.Get_size();
718
719	<	useAtomicVirial_ = simParams_->getUseAtomicVirial();
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();
703	<	useSticky |= (*i)->isSticky();
704	<	useStickyPower |= (*i)->isStickyPower();
705	<	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) {
713	<	useElectrostatics = 1;
714	<	}
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);
733	<
734	<	temp = useDipole;
735	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
736	<
737	<	temp = useSticky;
738	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
739	<
740	<	temp = useStickyPower;
741	<	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;
750	<	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
755	–	temp = useFLARB;
756	–	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	>	cerr << "LI = " << atom->getLocalIndex() << "GAI = " << GlobalAtomIndices[atom->getLocalIndex()] << "\n";
823	>	}
824	>	}
825	>	return GlobalAtomIndices;
826	>	}
827
764	–	temp = useSP;
765	–	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
828
829	<	temp = useBoxDipole;
830	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
829	>	vector<int> SimInfo::getGlobalGroupIndices() {
830	>	SimInfo::MoleculeIterator mi;
831	>	Molecule* mol;
832	>	Molecule::CutoffGroupIterator ci;
833	>	CutoffGroup* cg;
834
835	<	temp = useAtomicVirial_;
836	<	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
837	<
838	<	#endif
839	<
840	<	fInfo_.SIM_uses_PBC = usePBC;
841	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
842	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
843	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
844	<	fInfo_.SIM_uses_Charges = useCharge;
845	<	fInfo_.SIM_uses_Dipoles = useDipole;
846	<	fInfo_.SIM_uses_Sticky = useSticky;
847	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
783	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
784	<	fInfo_.SIM_uses_EAM = useEAM;
785	<	fInfo_.SIM_uses_SC = useSC;
786	<	fInfo_.SIM_uses_Shapes = useShape;
787	<	fInfo_.SIM_uses_FLARB = useFLARB;
788	<	fInfo_.SIM_uses_RF = useRF;
789	<	fInfo_.SIM_uses_SF = useSF;
790	<	fInfo_.SIM_uses_SP = useSP;
791	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
792	<	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
835	>	vector<int> GlobalGroupIndices;
836	>
837	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
838	>
839	>	//local index of cutoff group is trivial, it only depends on the
840	>	//order of travesing
841	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
842	>	cg = mol->nextCutoffGroup(ci)) {
843	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
844	>	cerr << "LI, GGI = " << GlobalGroupIndices.size() << " " << cg->getGlobalIndex() << "\n";
845	>	}
846	>	}
847	>	return GlobalGroupIndices;
848		}
849
795	–	void SimInfo::setupFortranSim() {
796	–	int isError;
797	–	int nExclude;
798	–	std::vector<int> fortranGlobalGroupMembership;
799	–
800	–	nExclude = exclude_.getSize();
801	–	isError = 0;
850
851	<	//globalGroupMembership_ is filled by SimCreator
852	<	for (int i = 0; i < nGlobalAtoms_; i++) {
805	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
806	<	}
851	>	void SimInfo::prepareTopology() {
852	>	int nExclude, nOneTwo, nOneThree, nOneFour;
853
854		//calculate mass ratio of cutoff group
809	–	std::vector<RealType> mfact;
855		SimInfo::MoleculeIterator mi;
856		Molecule* mol;
857		Molecule::CutoffGroupIterator ci;
#	Line 815 | Line 860 | namespace oopse {
860		Atom* atom;
861		RealType totalMass;
862
863	<	//to avoid memory reallocation, reserve enough space for mfact
864	<	mfact.reserve(getNCutoffGroups());
863	>	/**
864	>	* The mass factor is the relative mass of an atom to the total
865	>	* mass of the cutoff group it belongs to.  By default, all atoms
866	>	* are their own cutoff groups, and therefore have mass factors of
867	>	* 1.  We need some special handling for massless atoms, which
868	>	* will be treated as carrying the entire mass of the cutoff
869	>	* group.
870	>	*/
871	>	massFactors_.clear();
872	>	massFactors_.resize(getNAtoms(), 1.0);
873
874		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
875	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
875	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
876	>	cg = mol->nextCutoffGroup(ci)) {
877
878		totalMass = cg->getMass();
879		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
880		// Check for massless groups - set mfact to 1 if true
881	<	if (totalMass != 0)
882	<	mfact.push_back(atom->getMass()/totalMass);
881	>	if (totalMass != 0)
882	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
883		else
884	<	mfact.push_back( 1.0 );
884	>	massFactors_[atom->getLocalIndex()] = 1.0;
885		}
832	–
886		}
887		}
888
889	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
837	<	std::vector<int> identArray;
889	>	// Build the identArray_
890
891	<	//to avoid memory reallocation, reserve enough space identArray
892	<	identArray.reserve(getNAtoms());
841	<
891	>	identArray_.clear();
892	>	identArray_.reserve(getNAtoms());
893		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
894		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
895	<	identArray.push_back(atom->getIdent());
895	>	identArray_.push_back(atom->getIdent());
896		}
897		}
847	–
848	–	//fill molMembershipArray
849	–	//molMembershipArray is filled by SimCreator
850	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
851	–	for (int i = 0; i < nGlobalAtoms_; i++) {
852	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
853	–	}
898
899	<	//setup fortran simulation
856	<	int nGlobalExcludes = 0;
857	<	int* globalExcludes = NULL;
858	<	int* excludeList = exclude_.getExcludeList();
859	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
860	<	&nExclude, excludeList , &nGlobalExcludes, globalExcludes,
861	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
862	<	&fortranGlobalGroupMembership[0], &isError);
863	<
864	<	if( isError ){
865	<
866	<	sprintf( painCave.errMsg,
867	<	"There was an error setting the simulation information in fortran.\n" );
868	<	painCave.isFatal = 1;
869	<	painCave.severity = OOPSE_ERROR;
870	<	simError();
871	<	}
872	<
873	<
874	<	sprintf( checkPointMsg,
875	<	"succesfully sent the simulation information to fortran.\n");
876	<
877	<	errorCheckPoint();
878	<
879	<	// Setup number of neighbors in neighbor list if present
880	<	if (simParams_->haveNeighborListNeighbors()) {
881	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
882	<	setNeighbors(&nlistNeighbors);
883	<	}
884	<
899	>	//scan topology
900
901	<	}
901	>	nExclude = excludedInteractions_.getSize();
902	>	nOneTwo = oneTwoInteractions_.getSize();
903	>	nOneThree = oneThreeInteractions_.getSize();
904	>	nOneFour = oneFourInteractions_.getSize();
905
906	<
907	<	void SimInfo::setupFortranParallel() {
908	<	#ifdef IS_MPI
909	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
892	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
893	<	std::vector<int> localToGlobalCutoffGroupIndex;
894	<	SimInfo::MoleculeIterator mi;
895	<	Molecule::AtomIterator ai;
896	<	Molecule::CutoffGroupIterator ci;
897	<	Molecule* mol;
898	<	Atom* atom;
899	<	CutoffGroup* cg;
900	<	mpiSimData parallelData;
901	<	int isError;
902	<
903	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
904	<
905	<	//local index(index in DataStorge) of atom is important
906	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
907	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
908	<	}
909	<
910	<	//local index of cutoff group is trivial, it only depends on the order of travesing
911	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
912	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
913	<	}
914	<
915	<	}
916	<
917	<	//fill up mpiSimData struct
918	<	parallelData.nMolGlobal = getNGlobalMolecules();
919	<	parallelData.nMolLocal = getNMolecules();
920	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
921	<	parallelData.nAtomsLocal = getNAtoms();
922	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
923	<	parallelData.nGroupsLocal = getNCutoffGroups();
924	<	parallelData.myNode = worldRank;
925	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
906	>	int* excludeList = excludedInteractions_.getPairList();
907	>	int* oneTwoList = oneTwoInteractions_.getPairList();
908	>	int* oneThreeList = oneThreeInteractions_.getPairList();
909	>	int* oneFourList = oneFourInteractions_.getPairList();
910
911	<	//pass mpiSimData struct and index arrays to fortran
928	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
929	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
930	<	&localToGlobalCutoffGroupIndex[0], &isError);
931	<
932	<	if (isError) {
933	<	sprintf(painCave.errMsg,
934	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
935	<	painCave.isFatal = 1;
936	<	simError();
937	<	}
938	<
939	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
940	<	errorCheckPoint();
941	<
942	<	#endif
943	<	}
944	<
945	<	void SimInfo::setupCutoff() {
946	<
947	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
948	<
949	<	// Check the cutoff policy
950	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
951	<
952	<	// Set LJ shifting bools to false
953	<	ljsp_ = false;
954	<	ljsf_ = false;
955	<
956	<	std::string myPolicy;
957	<	if (forceFieldOptions_.haveCutoffPolicy()){
958	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
959	<	}else if (simParams_->haveCutoffPolicy()) {
960	<	myPolicy = simParams_->getCutoffPolicy();
961	<	}
962	<
963	<	if (!myPolicy.empty()){
964	<	toUpper(myPolicy);
965	<	if (myPolicy == "MIX") {
966	<	cp = MIX_CUTOFF_POLICY;
967	<	} else {
968	<	if (myPolicy == "MAX") {
969	<	cp = MAX_CUTOFF_POLICY;
970	<	} else {
971	<	if (myPolicy == "TRADITIONAL") {
972	<	cp = TRADITIONAL_CUTOFF_POLICY;
973	<	} else {
974	<	// throw error
975	<	sprintf( painCave.errMsg,
976	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
977	<	painCave.isFatal = 1;
978	<	simError();
979	<	}
980	<	}
981	<	}
982	<	}
983	<	notifyFortranCutoffPolicy(&cp);
984	<
985	<	// Check the Skin Thickness for neighborlists
986	<	RealType skin;
987	<	if (simParams_->haveSkinThickness()) {
988	<	skin = simParams_->getSkinThickness();
989	<	notifyFortranSkinThickness(&skin);
990	<	}
991	<
992	<	// Check if the cutoff was set explicitly:
993	<	if (simParams_->haveCutoffRadius()) {
994	<	rcut_ = simParams_->getCutoffRadius();
995	<	if (simParams_->haveSwitchingRadius()) {
996	<	rsw_  = simParams_->getSwitchingRadius();
997	<	} else {
998	<	if (fInfo_.SIM_uses_Charges |
999	<	fInfo_.SIM_uses_Dipoles |
1000	<	fInfo_.SIM_uses_RF) {
1001	<
1002	<	rsw_ = 0.85 * rcut_;
1003	<	sprintf(painCave.errMsg,
1004	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1005	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1006	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1007	<	painCave.isFatal = 0;
1008	<	simError();
1009	<	} else {
1010	<	rsw_ = rcut_;
1011	<	sprintf(painCave.errMsg,
1012	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1013	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
1014	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1015	<	painCave.isFatal = 0;
1016	<	simError();
1017	<	}
1018	<	}
1019	<
1020	<	if (simParams_->haveElectrostaticSummationMethod()) {
1021	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1022	<	toUpper(myMethod);
1023	<
1024	<	if (myMethod == "SHIFTED_POTENTIAL") {
1025	<	ljsp_ = true;
1026	<	} else if (myMethod == "SHIFTED_FORCE") {
1027	<	ljsf_ = true;
1028	<	}
1029	<	}
1030	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1031	<
1032	<	} else {
1033	<
1034	<	// For electrostatic atoms, we'll assume a large safe value:
1035	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1036	<	sprintf(painCave.errMsg,
1037	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1038	<	"\tOOPSE will use a default value of 15.0 angstroms"
1039	<	"\tfor the cutoffRadius.\n");
1040	<	painCave.isFatal = 0;
1041	<	simError();
1042	<	rcut_ = 15.0;
1043	<
1044	<	if (simParams_->haveElectrostaticSummationMethod()) {
1045	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1046	<	toUpper(myMethod);
1047	<
1048	<	// For the time being, we're tethering the LJ shifted behavior to the
1049	<	// electrostaticSummationMethod keyword options
1050	<	if (myMethod == "SHIFTED_POTENTIAL") {
1051	<	ljsp_ = true;
1052	<	} else if (myMethod == "SHIFTED_FORCE") {
1053	<	ljsf_ = true;
1054	<	}
1055	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1056	<	if (simParams_->haveSwitchingRadius()){
1057	<	sprintf(painCave.errMsg,
1058	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1059	<	"\teven though the electrostaticSummationMethod was\n"
1060	<	"\tset to %s\n", myMethod.c_str());
1061	<	painCave.isFatal = 1;
1062	<	simError();
1063	<	}
1064	<	}
1065	<	}
1066	<
1067	<	if (simParams_->haveSwitchingRadius()){
1068	<	rsw_ = simParams_->getSwitchingRadius();
1069	<	} else {
1070	<	sprintf(painCave.errMsg,
1071	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1072	<	"\tOOPSE will use a default value of\n"
1073	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1074	<	painCave.isFatal = 0;
1075	<	simError();
1076	<	rsw_ = 0.85 * rcut_;
1077	<	}
1078	<
1079	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1080	<
1081	<	} else {
1082	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1083	<	// We'll punt and let fortran figure out the cutoffs later.
1084	<
1085	<	notifyFortranYouAreOnYourOwn();
1086	<
1087	<	}
1088	<	}
1089	<	}
1090	<
1091	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1092	<
1093	<	int errorOut;
1094	<	int esm =  NONE;
1095	<	int sm = UNDAMPED;
1096	<	RealType alphaVal;
1097	<	RealType dielectric;
1098	<
1099	<	errorOut = isError;
1100	<
1101	<	if (simParams_->haveElectrostaticSummationMethod()) {
1102	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1103	<	toUpper(myMethod);
1104	<	if (myMethod == "NONE") {
1105	<	esm = NONE;
1106	<	} else {
1107	<	if (myMethod == "SWITCHING_FUNCTION") {
1108	<	esm = SWITCHING_FUNCTION;
1109	<	} else {
1110	<	if (myMethod == "SHIFTED_POTENTIAL") {
1111	<	esm = SHIFTED_POTENTIAL;
1112	<	} else {
1113	<	if (myMethod == "SHIFTED_FORCE") {
1114	<	esm = SHIFTED_FORCE;
1115	<	} else {
1116	<	if (myMethod == "REACTION_FIELD") {
1117	<	esm = REACTION_FIELD;
1118	<	dielectric = simParams_->getDielectric();
1119	<	if (!simParams_->haveDielectric()) {
1120	<	// throw warning
1121	<	sprintf( painCave.errMsg,
1122	<	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1123	<	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1124	<	painCave.isFatal = 0;
1125	<	simError();
1126	<	}
1127	<	} else {
1128	<	// throw error
1129	<	sprintf( painCave.errMsg,
1130	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1131	<	"\t(Input file specified %s .)\n"
1132	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1133	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1134	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1135	<	painCave.isFatal = 1;
1136	<	simError();
1137	<	}
1138	<	}
1139	<	}
1140	<	}
1141	<	}
1142	<	}
1143	<
1144	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1145	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1146	<	toUpper(myScreen);
1147	<	if (myScreen == "UNDAMPED") {
1148	<	sm = UNDAMPED;
1149	<	} else {
1150	<	if (myScreen == "DAMPED") {
1151	<	sm = DAMPED;
1152	<	if (!simParams_->haveDampingAlpha()) {
1153	<	// first set a cutoff dependent alpha value
1154	<	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1155	<	alphaVal = 0.5125 - rcut_* 0.025;
1156	<	// for values rcut > 20.5, alpha is zero
1157	<	if (alphaVal < 0) alphaVal = 0;
1158	<
1159	<	// throw warning
1160	<	sprintf( painCave.errMsg,
1161	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1162	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1163	<	painCave.isFatal = 0;
1164	<	simError();
1165	<	} else {
1166	<	alphaVal = simParams_->getDampingAlpha();
1167	<	}
1168	<
1169	<	} else {
1170	<	// throw error
1171	<	sprintf( painCave.errMsg,
1172	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1173	<	"\t(Input file specified %s .)\n"
1174	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1175	<	"or \"damped\".\n", myScreen.c_str() );
1176	<	painCave.isFatal = 1;
1177	<	simError();
1178	<	}
1179	<	}
1180	<	}
1181	<
1182	<	// let's pass some summation method variables to fortran
1183	<	setElectrostaticSummationMethod( &esm );
1184	<	setFortranElectrostaticMethod( &esm );
1185	<	setScreeningMethod( &sm );
1186	<	setDampingAlpha( &alphaVal );
1187	<	setReactionFieldDielectric( &dielectric );
1188	<	initFortranFF( &errorOut );
1189	<	}
1190	<
1191	<	void SimInfo::setupSwitchingFunction() {
1192	<	int ft = CUBIC;
1193	<
1194	<	if (simParams_->haveSwitchingFunctionType()) {
1195	<	std::string funcType = simParams_->getSwitchingFunctionType();
1196	<	toUpper(funcType);
1197	<	if (funcType == "CUBIC") {
1198	<	ft = CUBIC;
1199	<	} else {
1200	<	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1201	<	ft = FIFTH_ORDER_POLY;
1202	<	} else {
1203	<	// throw error
1204	<	sprintf( painCave.errMsg,
1205	<	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1206	<	painCave.isFatal = 1;
1207	<	simError();
1208	<	}
1209	<	}
1210	<	}
1211	<
1212	<	// send switching function notification to switcheroo
1213	<	setFunctionType(&ft);
1214	<
1215	<	}
1216	<
1217	<	void SimInfo::setupAccumulateBoxDipole() {
1218	<
1219	<	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1220	<	if ( simParams_->haveAccumulateBoxDipole() )
1221	<	if ( simParams_->getAccumulateBoxDipole() ) {
1222	<	setAccumulateBoxDipole();
1223	<	calcBoxDipole_ = true;
1224	<	}
1225	<
911	>	topologyDone_ = true;
912		}
913
914		void SimInfo::addProperty(GenericData* genData) {
915		properties_.addProperty(genData);
916		}
917
918	<	void SimInfo::removeProperty(const std::string& propName) {
918	>	void SimInfo::removeProperty(const string& propName) {
919		properties_.removeProperty(propName);
920		}
921
#	Line 1237 | Line 923 | namespace oopse {
923		properties_.clearProperties();
924		}
925
926	<	std::vector<std::string> SimInfo::getPropertyNames() {
926	>	vector<string> SimInfo::getPropertyNames() {
927		return properties_.getPropertyNames();
928		}
929
930	<	std::vector<GenericData*> SimInfo::getProperties() {
930	>	vector<GenericData*> SimInfo::getProperties() {
931		return properties_.getProperties();
932		}
933
934	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
934	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
935		return properties_.getPropertyByName(propName);
936		}
937
#	Line 1259 | Line 945 | namespace oopse {
945		Molecule* mol;
946		RigidBody* rb;
947		Atom* atom;
948	+	CutoffGroup* cg;
949		SimInfo::MoleculeIterator mi;
950		Molecule::RigidBodyIterator rbIter;
951	<	Molecule::AtomIterator atomIter;;
951	>	Molecule::AtomIterator atomIter;
952	>	Molecule::CutoffGroupIterator cgIter;
953
954		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
955
#	Line 1272 | Line 960 | namespace oopse {
960		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
961		rb->setSnapshotManager(sman_);
962		}
963	+
964	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
965	+	cg->setSnapshotManager(sman_);
966	+	}
967		}
968
969		}
#	Line 1328 | Line 1020 | namespace oopse {
1020
1021		}
1022
1023	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1023	>	ostream& operator <<(ostream& o, SimInfo& info) {
1024
1025		return o;
1026		}
#	Line 1371 | Line 1063 | namespace oopse {
1063
1064
1065		[  Ixx -Ixy  -Ixz ]
1066	<	J =| -Iyx  Iyy  -Iyz |
1066	>	J =| -Iyx  Iyy  -Iyz |
1067		[ -Izx -Iyz   Izz ]
1068		*/
1069
#	Line 1478 | Line 1170 | namespace oopse {
1170		return IOIndexToIntegrableObject.at(index);
1171		}
1172
1173	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1173	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1174		IOIndexToIntegrableObject= v;
1175		}
1176
#	Line 1520 | Line 1212 | namespace oopse {
1212		return;
1213		}
1214		/*
1215	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1215	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1216		assert( v.size() == nAtoms_ + nRigidBodies_);
1217		sdByGlobalIndex_ = v;
1218		}
#	Line 1530 | Line 1222 | namespace oopse {
1222		return sdByGlobalIndex_.at(index);
1223		}
1224		*/
1225	<	}//end namespace oopse
1225	>	int SimInfo::getNGlobalConstraints() {
1226	>	int nGlobalConstraints;
1227	>	#ifdef IS_MPI
1228	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1229	>	MPI_COMM_WORLD);
1230	>	#else
1231	>	nGlobalConstraints =  nConstraints_;
1232	>	#endif
1233	>	return nGlobalConstraints;
1234	>	}
1235
1236	+	}//end namespace OpenMD
1237	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1597 by gezelter, Tue Jul 26 15:49:24 2011 UTC

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