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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 1126 by gezelter, Fri Apr 6 21:53:43 2007 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1535 by gezelter, Fri Dec 31 18:31:56 2010 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 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"
57		#include "UseTheForce/DarkSide/neighborLists_interface.h"
63	–	#include "UseTheForce/DarkSide/electrostatic_interface.h"
64	–	#include "UseTheForce/DarkSide/switcheroo_interface.h"
58		#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60		#include "selection/SelectionManager.hpp"
61		#include "io/ForceFieldOptions.hpp"
62		#include "UseTheForce/ForceField.hpp"
63	+	#include "nonbonded/SwitchingFunction.hpp"
64
71	–
65		#ifdef IS_MPI
66		#include "UseTheForce/mpiComponentPlan.h"
67		#include "UseTheForce/DarkSide/simParallel_interface.h"
68		#endif
69
70	<	namespace oopse {
71	<	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	<	}
70	>	using namespace std;
71	>	namespace OpenMD {
72
73		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
74		forceField_(ff), simParams_(simParams),
75		ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
76		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
77		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
78	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
79	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
80	<	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false),
81	<	useAtomicVirial_(true) {
82	<
83	<	MoleculeStamp* molStamp;
84	<	int nMolWithSameStamp;
85	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
86	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
87	<	CutoffGroupStamp* cgStamp;
88	<	RigidBodyStamp* rbStamp;
89	<	int nRigidAtoms = 0;
90	<	std::vector<Component*> components = simParams->getComponents();
78	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
79	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
80	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
81	>	calcBoxDipole_(false), useAtomicVirial_(true) {
82	>
83	>	MoleculeStamp* molStamp;
84	>	int nMolWithSameStamp;
85	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
86	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
87	>	CutoffGroupStamp* cgStamp;
88	>	RigidBodyStamp* rbStamp;
89	>	int nRigidAtoms = 0;
90	>
91	>	vector<Component*> components = simParams->getComponents();
92	>
93	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
94	>	molStamp = (*i)->getMoleculeStamp();
95	>	nMolWithSameStamp = (*i)->getNMol();
96
97	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
98	<	molStamp = (*i)->getMoleculeStamp();
99	<	nMolWithSameStamp = (*i)->getNMol();
100	<
101	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
102	<
103	<	//calculate atoms in molecules
104	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
105	<
106	<	//calculate atoms in cutoff groups
107	<	int nAtomsInGroups = 0;
108	<	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	<
97	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
98	>
99	>	//calculate atoms in molecules
100	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
101	>
102	>	//calculate atoms in cutoff groups
103	>	int nAtomsInGroups = 0;
104	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
105	>
106	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
107	>	cgStamp = molStamp->getCutoffGroupStamp(j);
108	>	nAtomsInGroups += cgStamp->getNMembers();
109		}
110	<
111	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
112	<	//group therefore the total number of cutoff groups in the system is
113	<	//equal to the total number of atoms minus number of atoms belong to
114	<	//cutoff group defined in meta-data file plus the number of cutoff
115	<	//groups defined in meta-data file
116	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
117	<
118	<	//every free atom (atom does not belong to rigid bodies) is an
119	<	//integrable object therefore the total number of integrable objects
120	<	//in the system is equal to the total number of atoms minus number of
121	<	//atoms belong to rigid body defined in meta-data file plus the number
122	<	//of rigid bodies defined in meta-data file
123	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
124	<	+ nGlobalRigidBodies_;
125	<
126	<	nGlobalMols_ = molStampIds_.size();
159	<
160	<	#ifdef IS_MPI
161	<	molToProcMap_.resize(nGlobalMols_);
162	<	#endif
163	<
110	>
111	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
112	>
113	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
114	>
115	>	//calculate atoms in rigid bodies
116	>	int nAtomsInRigidBodies = 0;
117	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
118	>
119	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
120	>	rbStamp = molStamp->getRigidBodyStamp(j);
121	>	nAtomsInRigidBodies += rbStamp->getNMembers();
122	>	}
123	>
124	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
125	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
126	>
127		}
128	<
128	>
129	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
130	>	//group therefore the total number of cutoff groups in the system is
131	>	//equal to the total number of atoms minus number of atoms belong to
132	>	//cutoff group defined in meta-data file plus the number of cutoff
133	>	//groups defined in meta-data file
134	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
135	>
136	>	//every free atom (atom does not belong to rigid bodies) is an
137	>	//integrable object therefore the total number of integrable objects
138	>	//in the system is equal to the total number of atoms minus number of
139	>	//atoms belong to rigid body defined in meta-data file plus the number
140	>	//of rigid bodies defined in meta-data file
141	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
142	>	+ nGlobalRigidBodies_;
143	>
144	>	nGlobalMols_ = molStampIds_.size();
145	>	molToProcMap_.resize(nGlobalMols_);
146	>	}
147	>
148		SimInfo::~SimInfo() {
149	<	std::map<int, Molecule*>::iterator i;
149	>	map<int, Molecule*>::iterator i;
150		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
151		delete i->second;
152		}
#	Line 175 | Line 157 | namespace oopse {
157		delete forceField_;
158		}
159
178	–	int SimInfo::getNGlobalConstraints() {
179	–	int nGlobalConstraints;
180	–	#ifdef IS_MPI
181	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
182	–	MPI_COMM_WORLD);
183	–	#else
184	–	nGlobalConstraints =  nConstraints_;
185	–	#endif
186	–	return nGlobalConstraints;
187	–	}
160
161		bool SimInfo::addMolecule(Molecule* mol) {
162		MoleculeIterator i;
163	<
163	>
164		i = molecules_.find(mol->getGlobalIndex());
165		if (i == molecules_.end() ) {
166	<
167	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
168	<
166	>
167	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
168	>
169		nAtoms_ += mol->getNAtoms();
170		nBonds_ += mol->getNBonds();
171		nBends_ += mol->getNBends();
172		nTorsions_ += mol->getNTorsions();
173	+	nInversions_ += mol->getNInversions();
174		nRigidBodies_ += mol->getNRigidBodies();
175		nIntegrableObjects_ += mol->getNIntegrableObjects();
176		nCutoffGroups_ += mol->getNCutoffGroups();
177		nConstraints_ += mol->getNConstraintPairs();
178	<
179	<	addExcludePairs(mol);
180	<
178	>
179	>	addInteractionPairs(mol);
180	>
181		return true;
182		} else {
183		return false;
184		}
185		}
186	<
186	>
187		bool SimInfo::removeMolecule(Molecule* mol) {
188		MoleculeIterator i;
189		i = molecules_.find(mol->getGlobalIndex());
#	Line 223 | Line 196 | namespace oopse {
196		nBonds_ -= mol->getNBonds();
197		nBends_ -= mol->getNBends();
198		nTorsions_ -= mol->getNTorsions();
199	+	nInversions_ -= mol->getNInversions();
200		nRigidBodies_ -= mol->getNRigidBodies();
201		nIntegrableObjects_ -= mol->getNIntegrableObjects();
202		nCutoffGroups_ -= mol->getNCutoffGroups();
203		nConstraints_ -= mol->getNConstraintPairs();
204
205	<	removeExcludePairs(mol);
205	>	removeInteractionPairs(mol);
206		molecules_.erase(mol->getGlobalIndex());
207
208		delete mol;
#	Line 237 | Line 211 | namespace oopse {
211		} else {
212		return false;
213		}
240	–
241	–
214		}
215
216
#	Line 256 | Line 228 | namespace oopse {
228		void SimInfo::calcNdf() {
229		int ndf_local;
230		MoleculeIterator i;
231	<	std::vector<StuntDouble*>::iterator j;
231	>	vector<StuntDouble*>::iterator j;
232		Molecule* mol;
233		StuntDouble* integrableObject;
234
#	Line 307 | Line 279 | namespace oopse {
279		int ndfRaw_local;
280
281		MoleculeIterator i;
282	<	std::vector<StuntDouble*>::iterator j;
282	>	vector<StuntDouble*>::iterator j;
283		Molecule* mol;
284		StuntDouble* integrableObject;
285
#	Line 354 | Line 326 | namespace oopse {
326
327		}
328
329	<	void SimInfo::addExcludePairs(Molecule* mol) {
330	<	std::vector<Bond*>::iterator bondIter;
331	<	std::vector<Bend*>::iterator bendIter;
332	<	std::vector<Torsion*>::iterator torsionIter;
329	>	void SimInfo::addInteractionPairs(Molecule* mol) {
330	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
331	>	vector<Bond*>::iterator bondIter;
332	>	vector<Bend*>::iterator bendIter;
333	>	vector<Torsion*>::iterator torsionIter;
334	>	vector<Inversion*>::iterator inversionIter;
335		Bond* bond;
336		Bend* bend;
337		Torsion* torsion;
338	+	Inversion* inversion;
339		int a;
340		int b;
341		int c;
342		int d;
343
344	<	std::map<int, std::set<int> > atomGroups;
344	>	// atomGroups can be used to add special interaction maps between
345	>	// groups of atoms that are in two separate rigid bodies.
346	>	// However, most site-site interactions between two rigid bodies
347	>	// are probably not special, just the ones between the physically
348	>	// bonded atoms.  Interactions *within* a single rigid body should
349	>	// always be excluded.  These are done at the bottom of this
350	>	// function.
351
352	+	map<int, set<int> > atomGroups;
353		Molecule::RigidBodyIterator rbIter;
354		RigidBody* rb;
355		Molecule::IntegrableObjectIterator ii;
356		StuntDouble* integrableObject;
357
358	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
359	<	integrableObject = mol->nextIntegrableObject(ii)) {
360	<
358	>	for (integrableObject = mol->beginIntegrableObject(ii);
359	>	integrableObject != NULL;
360	>	integrableObject = mol->nextIntegrableObject(ii)) {
361	>
362		if (integrableObject->isRigidBody()) {
363	<	rb = static_cast<RigidBody*>(integrableObject);
364	<	std::vector<Atom*> atoms = rb->getAtoms();
365	<	std::set<int> rigidAtoms;
366	<	for (int i = 0; i < atoms.size(); ++i) {
367	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
368	<	}
369	<	for (int i = 0; i < atoms.size(); ++i) {
370	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
371	<	}
363	>	rb = static_cast<RigidBody*>(integrableObject);
364	>	vector<Atom*> atoms = rb->getAtoms();
365	>	set<int> rigidAtoms;
366	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
367	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
368	>	}
369	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
370	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
371	>	}
372		} else {
373	<	std::set<int> oneAtomSet;
373	>	set<int> oneAtomSet;
374		oneAtomSet.insert(integrableObject->getGlobalIndex());
375	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
375	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
376		}
377		}
378	+
379	+	for (bond= mol->beginBond(bondIter); bond != NULL;
380	+	bond = mol->nextBond(bondIter)) {
381
396	–
397	–
398	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
382		a = bond->getAtomA()->getGlobalIndex();
383	<	b = bond->getAtomB()->getGlobalIndex();
384	<	exclude_.addPair(a, b);
383	>	b = bond->getAtomB()->getGlobalIndex();
384	>
385	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
386	>	oneTwoInteractions_.addPair(a, b);
387	>	} else {
388	>	excludedInteractions_.addPair(a, b);
389	>	}
390		}
391
392	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
392	>	for (bend= mol->beginBend(bendIter); bend != NULL;
393	>	bend = mol->nextBend(bendIter)) {
394	>
395		a = bend->getAtomA()->getGlobalIndex();
396		b = bend->getAtomB()->getGlobalIndex();
397		c = bend->getAtomC()->getGlobalIndex();
408	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
409	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
410	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
411	–
412	–	exclude_.addPairs(rigidSetA, rigidSetB);
413	–	exclude_.addPairs(rigidSetA, rigidSetC);
414	–	exclude_.addPairs(rigidSetB, rigidSetC);
398
399	<	//exclude_.addPair(a, b);
400	<	//exclude_.addPair(a, c);
401	<	//exclude_.addPair(b, c);
399	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
400	>	oneTwoInteractions_.addPair(a, b);
401	>	oneTwoInteractions_.addPair(b, c);
402	>	} else {
403	>	excludedInteractions_.addPair(a, b);
404	>	excludedInteractions_.addPair(b, c);
405	>	}
406	>
407	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
408	>	oneThreeInteractions_.addPair(a, c);
409	>	} else {
410	>	excludedInteractions_.addPair(a, c);
411	>	}
412		}
413
414	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
414	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
415	>	torsion = mol->nextTorsion(torsionIter)) {
416	>
417		a = torsion->getAtomA()->getGlobalIndex();
418		b = torsion->getAtomB()->getGlobalIndex();
419		c = torsion->getAtomC()->getGlobalIndex();
420	<	d = torsion->getAtomD()->getGlobalIndex();
426	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
427	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
428	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
429	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
420	>	d = torsion->getAtomD()->getGlobalIndex();
421
422	<	exclude_.addPairs(rigidSetA, rigidSetB);
423	<	exclude_.addPairs(rigidSetA, rigidSetC);
424	<	exclude_.addPairs(rigidSetA, rigidSetD);
425	<	exclude_.addPairs(rigidSetB, rigidSetC);
426	<	exclude_.addPairs(rigidSetB, rigidSetD);
427	<	exclude_.addPairs(rigidSetC, rigidSetD);
422	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
423	>	oneTwoInteractions_.addPair(a, b);
424	>	oneTwoInteractions_.addPair(b, c);
425	>	oneTwoInteractions_.addPair(c, d);
426	>	} else {
427	>	excludedInteractions_.addPair(a, b);
428	>	excludedInteractions_.addPair(b, c);
429	>	excludedInteractions_.addPair(c, d);
430	>	}
431
432	<	/*
433	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
434	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
435	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
436	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
437	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
438	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
439	<
440	<
441	<	exclude_.addPair(a, b);
442	<	exclude_.addPair(a, c);
443	<	exclude_.addPair(a, d);
444	<	exclude_.addPair(b, c);
451	<	exclude_.addPair(b, d);
452	<	exclude_.addPair(c, d);
453	<	*/
432	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
433	>	oneThreeInteractions_.addPair(a, c);
434	>	oneThreeInteractions_.addPair(b, d);
435	>	} else {
436	>	excludedInteractions_.addPair(a, c);
437	>	excludedInteractions_.addPair(b, d);
438	>	}
439	>
440	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
441	>	oneFourInteractions_.addPair(a, d);
442	>	} else {
443	>	excludedInteractions_.addPair(a, d);
444	>	}
445		}
446
447	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
448	<	std::vector<Atom*> atoms = rb->getAtoms();
449	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
450	<	for (int j = i + 1; j < atoms.size(); ++j) {
447	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
448	>	inversion = mol->nextInversion(inversionIter)) {
449	>
450	>	a = inversion->getAtomA()->getGlobalIndex();
451	>	b = inversion->getAtomB()->getGlobalIndex();
452	>	c = inversion->getAtomC()->getGlobalIndex();
453	>	d = inversion->getAtomD()->getGlobalIndex();
454	>
455	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
456	>	oneTwoInteractions_.addPair(a, b);
457	>	oneTwoInteractions_.addPair(a, c);
458	>	oneTwoInteractions_.addPair(a, d);
459	>	} else {
460	>	excludedInteractions_.addPair(a, b);
461	>	excludedInteractions_.addPair(a, c);
462	>	excludedInteractions_.addPair(a, d);
463	>	}
464	>
465	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
466	>	oneThreeInteractions_.addPair(b, c);
467	>	oneThreeInteractions_.addPair(b, d);
468	>	oneThreeInteractions_.addPair(c, d);
469	>	} else {
470	>	excludedInteractions_.addPair(b, c);
471	>	excludedInteractions_.addPair(b, d);
472	>	excludedInteractions_.addPair(c, d);
473	>	}
474	>	}
475	>
476	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
477	>	rb = mol->nextRigidBody(rbIter)) {
478	>	vector<Atom*> atoms = rb->getAtoms();
479	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
480	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
481		a = atoms[i]->getGlobalIndex();
482		b = atoms[j]->getGlobalIndex();
483	<	exclude_.addPair(a, b);
483	>	excludedInteractions_.addPair(a, b);
484		}
485		}
486		}
487
488		}
489
490	<	void SimInfo::removeExcludePairs(Molecule* mol) {
491	<	std::vector<Bond*>::iterator bondIter;
492	<	std::vector<Bend*>::iterator bendIter;
493	<	std::vector<Torsion*>::iterator torsionIter;
490	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
491	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
492	>	vector<Bond*>::iterator bondIter;
493	>	vector<Bend*>::iterator bendIter;
494	>	vector<Torsion*>::iterator torsionIter;
495	>	vector<Inversion*>::iterator inversionIter;
496		Bond* bond;
497		Bend* bend;
498		Torsion* torsion;
499	+	Inversion* inversion;
500		int a;
501		int b;
502		int c;
503		int d;
504
505	<	std::map<int, std::set<int> > atomGroups;
482	<
505	>	map<int, set<int> > atomGroups;
506		Molecule::RigidBodyIterator rbIter;
507		RigidBody* rb;
508		Molecule::IntegrableObjectIterator ii;
509		StuntDouble* integrableObject;
510
511	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
512	<	integrableObject = mol->nextIntegrableObject(ii)) {
513	<
511	>	for (integrableObject = mol->beginIntegrableObject(ii);
512	>	integrableObject != NULL;
513	>	integrableObject = mol->nextIntegrableObject(ii)) {
514	>
515		if (integrableObject->isRigidBody()) {
516	<	rb = static_cast<RigidBody*>(integrableObject);
517	<	std::vector<Atom*> atoms = rb->getAtoms();
518	<	std::set<int> rigidAtoms;
519	<	for (int i = 0; i < atoms.size(); ++i) {
520	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
521	<	}
522	<	for (int i = 0; i < atoms.size(); ++i) {
523	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
524	<	}
516	>	rb = static_cast<RigidBody*>(integrableObject);
517	>	vector<Atom*> atoms = rb->getAtoms();
518	>	set<int> rigidAtoms;
519	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
520	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
521	>	}
522	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
523	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
524	>	}
525		} else {
526	<	std::set<int> oneAtomSet;
526	>	set<int> oneAtomSet;
527		oneAtomSet.insert(integrableObject->getGlobalIndex());
528	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
528	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
529		}
530		}
531
532	<
533	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
532	>	for (bond= mol->beginBond(bondIter); bond != NULL;
533	>	bond = mol->nextBond(bondIter)) {
534	>
535		a = bond->getAtomA()->getGlobalIndex();
536	<	b = bond->getAtomB()->getGlobalIndex();
537	<	exclude_.removePair(a, b);
536	>	b = bond->getAtomB()->getGlobalIndex();
537	>
538	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
539	>	oneTwoInteractions_.removePair(a, b);
540	>	} else {
541	>	excludedInteractions_.removePair(a, b);
542	>	}
543		}
544
545	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
545	>	for (bend= mol->beginBend(bendIter); bend != NULL;
546	>	bend = mol->nextBend(bendIter)) {
547	>
548		a = bend->getAtomA()->getGlobalIndex();
549		b = bend->getAtomB()->getGlobalIndex();
550		c = bend->getAtomC()->getGlobalIndex();
519	–
520	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
521	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
522	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
523	–
524	–	exclude_.removePairs(rigidSetA, rigidSetB);
525	–	exclude_.removePairs(rigidSetA, rigidSetC);
526	–	exclude_.removePairs(rigidSetB, rigidSetC);
551
552	<	//exclude_.removePair(a, b);
553	<	//exclude_.removePair(a, c);
554	<	//exclude_.removePair(b, c);
552	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
553	>	oneTwoInteractions_.removePair(a, b);
554	>	oneTwoInteractions_.removePair(b, c);
555	>	} else {
556	>	excludedInteractions_.removePair(a, b);
557	>	excludedInteractions_.removePair(b, c);
558	>	}
559	>
560	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
561	>	oneThreeInteractions_.removePair(a, c);
562	>	} else {
563	>	excludedInteractions_.removePair(a, c);
564	>	}
565		}
566
567	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
567	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
568	>	torsion = mol->nextTorsion(torsionIter)) {
569	>
570		a = torsion->getAtomA()->getGlobalIndex();
571		b = torsion->getAtomB()->getGlobalIndex();
572		c = torsion->getAtomC()->getGlobalIndex();
573	<	d = torsion->getAtomD()->getGlobalIndex();
573	>	d = torsion->getAtomD()->getGlobalIndex();
574	>
575	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
576	>	oneTwoInteractions_.removePair(a, b);
577	>	oneTwoInteractions_.removePair(b, c);
578	>	oneTwoInteractions_.removePair(c, d);
579	>	} else {
580	>	excludedInteractions_.removePair(a, b);
581	>	excludedInteractions_.removePair(b, c);
582	>	excludedInteractions_.removePair(c, d);
583	>	}
584
585	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
586	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
587	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
588	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
585	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
586	>	oneThreeInteractions_.removePair(a, c);
587	>	oneThreeInteractions_.removePair(b, d);
588	>	} else {
589	>	excludedInteractions_.removePair(a, c);
590	>	excludedInteractions_.removePair(b, d);
591	>	}
592
593	<	exclude_.removePairs(rigidSetA, rigidSetB);
594	<	exclude_.removePairs(rigidSetA, rigidSetC);
595	<	exclude_.removePairs(rigidSetA, rigidSetD);
596	<	exclude_.removePairs(rigidSetB, rigidSetC);
597	<	exclude_.removePairs(rigidSetB, rigidSetD);
598	<	exclude_.removePairs(rigidSetC, rigidSetD);
593	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
594	>	oneFourInteractions_.removePair(a, d);
595	>	} else {
596	>	excludedInteractions_.removePair(a, d);
597	>	}
598	>	}
599
600	<	/*
601	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
553	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
554	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
555	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
556	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
557	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
600	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
601	>	inversion = mol->nextInversion(inversionIter)) {
602
603	<
604	<	exclude_.removePair(a, b);
605	<	exclude_.removePair(a, c);
606	<	exclude_.removePair(a, d);
607	<	exclude_.removePair(b, c);
608	<	exclude_.removePair(b, d);
609	<	exclude_.removePair(c, d);
610	<	*/
603	>	a = inversion->getAtomA()->getGlobalIndex();
604	>	b = inversion->getAtomB()->getGlobalIndex();
605	>	c = inversion->getAtomC()->getGlobalIndex();
606	>	d = inversion->getAtomD()->getGlobalIndex();
607	>
608	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
609	>	oneTwoInteractions_.removePair(a, b);
610	>	oneTwoInteractions_.removePair(a, c);
611	>	oneTwoInteractions_.removePair(a, d);
612	>	} else {
613	>	excludedInteractions_.removePair(a, b);
614	>	excludedInteractions_.removePair(a, c);
615	>	excludedInteractions_.removePair(a, d);
616	>	}
617	>
618	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
619	>	oneThreeInteractions_.removePair(b, c);
620	>	oneThreeInteractions_.removePair(b, d);
621	>	oneThreeInteractions_.removePair(c, d);
622	>	} else {
623	>	excludedInteractions_.removePair(b, c);
624	>	excludedInteractions_.removePair(b, d);
625	>	excludedInteractions_.removePair(c, d);
626	>	}
627		}
628
629	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
630	<	std::vector<Atom*> atoms = rb->getAtoms();
631	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
632	<	for (int j = i + 1; j < atoms.size(); ++j) {
629	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
630	>	rb = mol->nextRigidBody(rbIter)) {
631	>	vector<Atom*> atoms = rb->getAtoms();
632	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
633	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
634		a = atoms[i]->getGlobalIndex();
635		b = atoms[j]->getGlobalIndex();
636	<	exclude_.removePair(a, b);
636	>	excludedInteractions_.removePair(a, b);
637		}
638		}
639		}
640	<
640	>
641		}
642	<
643	<
642	>
643	>
644		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
645		int curStampId;
646	<
646	>
647		//index from 0
648		curStampId = moleculeStamps_.size();
649
#	Line 590 | Line 651 | namespace oopse {
651		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
652		}
653
593	–	void SimInfo::update() {
654
655	<	setupSimType();
656	<
657	<	#ifdef IS_MPI
658	<	setupFortranParallel();
659	<	#endif
660	<
661	<	setupFortranSim();
662	<
663	<	//setup fortran force field
604	<	/** @deprecate */
605	<	int isError = 0;
606	<
607	<	setupCutoff();
608	<
609	<	setupElectrostaticSummationMethod( isError );
610	<	setupSwitchingFunction();
611	<	setupAccumulateBoxDipole();
612	<
613	<	if(isError){
614	<	sprintf( painCave.errMsg,
615	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
616	<	painCave.isFatal = 1;
617	<	simError();
618	<	}
619	<
655	>	/**
656	>	* update
657	>	*
658	>	*  Performs the global checks and variable settings after the
659	>	*  objects have been created.
660	>	*
661	>	*/
662	>	void SimInfo::update() {
663	>	setupSimVariables();
664		calcNdf();
665		calcNdfRaw();
666		calcNdfTrans();
623	–
624	–	fortranInitialized_ = true;
667		}
668	<
669	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
668	>
669	>	/**
670	>	* getSimulatedAtomTypes
671	>	*
672	>	* Returns an STL set of AtomType* that are actually present in this
673	>	* simulation.  Must query all processors to assemble this information.
674	>	*
675	>	*/
676	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
677		SimInfo::MoleculeIterator mi;
678		Molecule* mol;
679		Molecule::AtomIterator ai;
680		Atom* atom;
681	<	std::set<AtomType*> atomTypes;
682	<
683	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
635	<
681	>	set<AtomType*> atomTypes;
682	>
683	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
684		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
685		atomTypes.insert(atom->getAtomType());
686	<	}
687	<
640	<	}
686	>	}
687	>	}
688
689	<	return atomTypes;
643	<	}
689	>	#ifdef IS_MPI
690
691	<	void SimInfo::setupSimType() {
692	<	std::set<AtomType*>::iterator i;
647	<	std::set<AtomType*> atomTypes;
648	<	atomTypes = getUniqueAtomTypes();
649	<
650	<	int useLennardJones = 0;
651	<	int useElectrostatic = 0;
652	<	int useEAM = 0;
653	<	int useSC = 0;
654	<	int useCharge = 0;
655	<	int useDirectional = 0;
656	<	int useDipole = 0;
657	<	int useGayBerne = 0;
658	<	int useSticky = 0;
659	<	int useStickyPower = 0;
660	<	int useShape = 0;
661	<	int useFLARB = 0; //it is not in AtomType yet
662	<	int useDirectionalAtom = 0;
663	<	int useElectrostatics = 0;
664	<	//usePBC and useRF are from simParams
665	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
666	<	int useRF;
667	<	int useSF;
668	<	int useSP;
669	<	int useBoxDipole;
691	>	// loop over the found atom types on this processor, and add their
692	>	// numerical idents to a vector:
693
694	<	std::string myMethod;
694	>	vector<int> foundTypes;
695	>	set<AtomType*>::iterator i;
696	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
697	>	foundTypes.push_back( (*i)->getIdent() );
698
699	<	// set the useRF logical
700	<	useRF = 0;
675	<	useSF = 0;
676	<	useSP = 0;
699	>	// count_local holds the number of found types on this processor
700	>	int count_local = foundTypes.size();
701
702	+	// count holds the total number of found types on all processors
703	+	// (some will be redundant with the ones found locally):
704	+	int count;
705	+	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
706
707	<	if (simParams_->haveElectrostaticSummationMethod()) {
708	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
709	<	toUpper(myMethod);
710	<	if (myMethod == "REACTION_FIELD"){
711	<	useRF = 1;
712	<	} else if (myMethod == "SHIFTED_FORCE"){
713	<	useSF = 1;
714	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
715	<	useSP = 1;
716	<	}
717	<	}
707	>	// create a vector to hold the globally found types, and resize it:
708	>	vector<int> ftGlobal;
709	>	ftGlobal.resize(count);
710	>	vector<int> counts;
711	>
712	>	int nproc = MPI::COMM_WORLD.Get_size();
713	>	counts.resize(nproc);
714	>	vector<int> disps;
715	>	disps.resize(nproc);
716	>
717	>	// now spray out the foundTypes to all the other processors:
718
719	<	if (simParams_->haveAccumulateBoxDipole())
720	<	if (simParams_->getAccumulateBoxDipole())
693	<	useBoxDipole = 1;
719	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
720	>	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
721
722	+	// foundIdents is a stl set, so inserting an already found ident
723	+	// will have no effect.
724	+	set<int> foundIdents;
725	+	vector<int>::iterator j;
726	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
727	+	foundIdents.insert((*j));
728	+
729	+	// now iterate over the foundIdents and get the actual atom types
730	+	// that correspond to these:
731	+	set<int>::iterator it;
732	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
733	+	atomTypes.insert( forceField_->getAtomType((*it)) );
734	+
735	+	#endif
736	+
737	+	return atomTypes;
738	+	}
739	+
740	+	void SimInfo::setupSimVariables() {
741		useAtomicVirial_ = simParams_->getUseAtomicVirial();
742	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
743	+	calcBoxDipole_ = false;
744	+	if ( simParams_->haveAccumulateBoxDipole() )
745	+	if ( simParams_->getAccumulateBoxDipole() ) {
746	+	calcBoxDipole_ = true;
747	+	}
748
749	+	set<AtomType*>::iterator i;
750	+	set<AtomType*> atomTypes;
751	+	atomTypes = getSimulatedAtomTypes();
752	+	int usesElectrostatic = 0;
753	+	int usesMetallic = 0;
754	+	int usesDirectional = 0;
755		//loop over all of the atom types
756		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
757	<	useLennardJones |= (*i)->isLennardJones();
758	<	useElectrostatic |= (*i)->isElectrostatic();
759	<	useEAM |= (*i)->isEAM();
702	<	useSC |= (*i)->isSC();
703	<	useCharge |= (*i)->isCharge();
704	<	useDirectional |= (*i)->isDirectional();
705	<	useDipole |= (*i)->isDipole();
706	<	useGayBerne |= (*i)->isGayBerne();
707	<	useSticky |= (*i)->isSticky();
708	<	useStickyPower |= (*i)->isStickyPower();
709	<	useShape |= (*i)->isShape();
757	>	usesElectrostatic |= (*i)->isElectrostatic();
758	>	usesMetallic |= (*i)->isMetal();
759	>	usesDirectional |= (*i)->isDirectional();
760		}
761
712	–	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
713	–	useDirectionalAtom = 1;
714	–	}
715	–
716	–	if (useCharge || useDipole) {
717	–	useElectrostatics = 1;
718	–	}
719	–
762		#ifdef IS_MPI
763		int temp;
764	+	temp = usesDirectional;
765	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766
767	<	temp = usePBC;
768	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767	>	temp = usesMetallic;
768	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769
770	<	temp = useDirectionalAtom;
771	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
728	<
729	<	temp = useLennardJones;
730	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
731	<
732	<	temp = useElectrostatics;
733	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
734	<
735	<	temp = useCharge;
736	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
737	<
738	<	temp = useDipole;
739	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
740	<
741	<	temp = useSticky;
742	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
743	<
744	<	temp = useStickyPower;
745	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
746	<
747	<	temp = useGayBerne;
748	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
749	<
750	<	temp = useEAM;
751	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
752	<
753	<	temp = useSC;
754	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
755	<
756	<	temp = useShape;
757	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
758	<
759	<	temp = useFLARB;
760	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
761	<
762	<	temp = useRF;
763	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
764	<
765	<	temp = useSF;
766	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767	<
768	<	temp = useSP;
769	<	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770	<
771	<	temp = useBoxDipole;
772	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
773	<
774	<	temp = useAtomicVirial_;
775	<	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776	<
770	>	temp = usesElectrostatic;
771	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
772		#endif
773	<
774	<	fInfo_.SIM_uses_PBC = usePBC;
775	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
776	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
777	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
778	<	fInfo_.SIM_uses_Charges = useCharge;
784	<	fInfo_.SIM_uses_Dipoles = useDipole;
785	<	fInfo_.SIM_uses_Sticky = useSticky;
786	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
787	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
788	<	fInfo_.SIM_uses_EAM = useEAM;
789	<	fInfo_.SIM_uses_SC = useSC;
790	<	fInfo_.SIM_uses_Shapes = useShape;
791	<	fInfo_.SIM_uses_FLARB = useFLARB;
792	<	fInfo_.SIM_uses_RF = useRF;
793	<	fInfo_.SIM_uses_SF = useSF;
794	<	fInfo_.SIM_uses_SP = useSP;
795	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
796	<	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
773	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
774	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
775	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
776	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
777	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
778	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
779		}
780
781	<	void SimInfo::setupFortranSim() {
781	>	void SimInfo::setupFortran() {
782		int isError;
783	<	int nExclude;
784	<	std::vector<int> fortranGlobalGroupMembership;
783	>	int nExclude, nOneTwo, nOneThree, nOneFour;
784	>	vector<int> fortranGlobalGroupMembership;
785
804	–	nExclude = exclude_.getSize();
786		isError = 0;
787
788		//globalGroupMembership_ is filled by SimCreator
#	Line 810 | Line 791 | namespace oopse {
791		}
792
793		//calculate mass ratio of cutoff group
794	<	std::vector<RealType> mfact;
794	>	vector<RealType> mfact;
795		SimInfo::MoleculeIterator mi;
796		Molecule* mol;
797		Molecule::CutoffGroupIterator ci;
#	Line 833 | Line 814 | namespace oopse {
814		else
815		mfact.push_back( 1.0 );
816		}
836	–
817		}
818		}
819
820	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
821	<	std::vector<int> identArray;
820	>	//fill ident array of local atoms (it is actually ident of
821	>	//AtomType, it is so confusing !!!)
822	>	vector<int> identArray;
823
824		//to avoid memory reallocation, reserve enough space identArray
825		identArray.reserve(getNAtoms());
#	Line 851 | Line 832 | namespace oopse {
832
833		//fill molMembershipArray
834		//molMembershipArray is filled by SimCreator
835	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
835	>	vector<int> molMembershipArray(nGlobalAtoms_);
836		for (int i = 0; i < nGlobalAtoms_; i++) {
837		molMembershipArray[i] = globalMolMembership_[i] + 1;
838		}
839
840		//setup fortran simulation
860	–	int nGlobalExcludes = 0;
861	–	int* globalExcludes = NULL;
862	–	int* excludeList = exclude_.getExcludeList();
863	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
864	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
865	–	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
841
842	<	if( isError ){
842	>	nExclude = excludedInteractions_.getSize();
843	>	nOneTwo = oneTwoInteractions_.getSize();
844	>	nOneThree = oneThreeInteractions_.getSize();
845	>	nOneFour = oneFourInteractions_.getSize();
846
847	+	int* excludeList = excludedInteractions_.getPairList();
848	+	int* oneTwoList = oneTwoInteractions_.getPairList();
849	+	int* oneThreeList = oneThreeInteractions_.getPairList();
850	+	int* oneFourList = oneFourInteractions_.getPairList();
851	+
852	+	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
853	+	&nExclude, excludeList,
854	+	&nOneTwo, oneTwoList,
855	+	&nOneThree, oneThreeList,
856	+	&nOneFour, oneFourList,
857	+	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
858	+	&fortranGlobalGroupMembership[0], &isError);
859	+
860	+	if( isError ){
861	+
862		sprintf( painCave.errMsg,
863		"There was an error setting the simulation information in fortran.\n" );
864		painCave.isFatal = 1;
865	<	painCave.severity = OOPSE_ERROR;
865	>	painCave.severity = OPENMD_ERROR;
866		simError();
867		}
868	<
869	<	#ifdef IS_MPI
868	>
869	>
870		sprintf( checkPointMsg,
871		"succesfully sent the simulation information to fortran.\n");
872	<	MPIcheckPoint();
873	<	#endif // is_mpi
874	<
872	>
873	>	errorCheckPoint();
874	>
875		// Setup number of neighbors in neighbor list if present
876		if (simParams_->haveNeighborListNeighbors()) {
877		int nlistNeighbors = simParams_->getNeighborListNeighbors();
878		setNeighbors(&nlistNeighbors);
879		}
880
881	<
882	<	}
883	<
884	<
885	<	#ifdef IS_MPI
893	<	void SimInfo::setupFortranParallel() {
894	<
895	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
896	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
897	<	std::vector<int> localToGlobalCutoffGroupIndex;
898	<	SimInfo::MoleculeIterator mi;
899	<	Molecule::AtomIterator ai;
900	<	Molecule::CutoffGroupIterator ci;
901	<	Molecule* mol;
902	<	Atom* atom;
903	<	CutoffGroup* cg;
881	>	#ifdef IS_MPI
882	>	//SimInfo is responsible for creating localToGlobalAtomIndex and
883	>	//localToGlobalGroupIndex
884	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
885	>	vector<int> localToGlobalCutoffGroupIndex;
886		mpiSimData parallelData;
905	–	int isError;
887
888		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
889
#	Line 941 | Line 922 | namespace oopse {
922		}
923
924		sprintf(checkPointMsg, " mpiRefresh successful.\n");
925	<	MPIcheckPoint();
945	<
946	<
947	<	}
948	<
925	>	errorCheckPoint();
926		#endif
927	<
951	<	void SimInfo::setupCutoff() {
952	<
953	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
954	<
955	<	// Check the cutoff policy
956	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
957	<
958	<	std::string myPolicy;
959	<	if (forceFieldOptions_.haveCutoffPolicy()){
960	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
961	<	}else if (simParams_->haveCutoffPolicy()) {
962	<	myPolicy = simParams_->getCutoffPolicy();
963	<	}
964	<
965	<	if (!myPolicy.empty()){
966	<	toUpper(myPolicy);
967	<	if (myPolicy == "MIX") {
968	<	cp = MIX_CUTOFF_POLICY;
969	<	} else {
970	<	if (myPolicy == "MAX") {
971	<	cp = MAX_CUTOFF_POLICY;
972	<	} else {
973	<	if (myPolicy == "TRADITIONAL") {
974	<	cp = TRADITIONAL_CUTOFF_POLICY;
975	<	} else {
976	<	// throw error
977	<	sprintf( painCave.errMsg,
978	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
979	<	painCave.isFatal = 1;
980	<	simError();
981	<	}
982	<	}
983	<	}
984	<	}
985	<	notifyFortranCutoffPolicy(&cp);
986	<
987	<	// Check the Skin Thickness for neighborlists
988	<	RealType skin;
989	<	if (simParams_->haveSkinThickness()) {
990	<	skin = simParams_->getSkinThickness();
991	<	notifyFortranSkinThickness(&skin);
992	<	}
993	<
994	<	// Check if the cutoff was set explicitly:
995	<	if (simParams_->haveCutoffRadius()) {
996	<	rcut_ = simParams_->getCutoffRadius();
997	<	if (simParams_->haveSwitchingRadius()) {
998	<	rsw_  = simParams_->getSwitchingRadius();
999	<	} else {
1000	<	if (fInfo_.SIM_uses_Charges |
1001	<	fInfo_.SIM_uses_Dipoles |
1002	<	fInfo_.SIM_uses_RF) {
1003	<
1004	<	rsw_ = 0.85 * rcut_;
1005	<	sprintf(painCave.errMsg,
1006	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1007	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1008	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1009	<	painCave.isFatal = 0;
1010	<	simError();
1011	<	} else {
1012	<	rsw_ = rcut_;
1013	<	sprintf(painCave.errMsg,
1014	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1015	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
1016	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1017	<	painCave.isFatal = 0;
1018	<	simError();
1019	<	}
1020	<	}
1021	<
1022	<	notifyFortranCutoffs(&rcut_, &rsw_);
1023	<
1024	<	} else {
1025	<
1026	<	// For electrostatic atoms, we'll assume a large safe value:
1027	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1028	<	sprintf(painCave.errMsg,
1029	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1030	<	"\tOOPSE will use a default value of 15.0 angstroms"
1031	<	"\tfor the cutoffRadius.\n");
1032	<	painCave.isFatal = 0;
1033	<	simError();
1034	<	rcut_ = 15.0;
1035	<
1036	<	if (simParams_->haveElectrostaticSummationMethod()) {
1037	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1038	<	toUpper(myMethod);
1039	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1040	<	if (simParams_->haveSwitchingRadius()){
1041	<	sprintf(painCave.errMsg,
1042	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1043	<	"\teven though the electrostaticSummationMethod was\n"
1044	<	"\tset to %s\n", myMethod.c_str());
1045	<	painCave.isFatal = 1;
1046	<	simError();
1047	<	}
1048	<	}
1049	<	}
1050	<
1051	<	if (simParams_->haveSwitchingRadius()){
1052	<	rsw_ = simParams_->getSwitchingRadius();
1053	<	} else {
1054	<	sprintf(painCave.errMsg,
1055	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1056	<	"\tOOPSE will use a default value of\n"
1057	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1058	<	painCave.isFatal = 0;
1059	<	simError();
1060	<	rsw_ = 0.85 * rcut_;
1061	<	}
1062	<	notifyFortranCutoffs(&rcut_, &rsw_);
1063	<	} else {
1064	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1065	<	// We'll punt and let fortran figure out the cutoffs later.
1066	<
1067	<	notifyFortranYouAreOnYourOwn();
1068	<
1069	<	}
1070	<	}
1071	<	}
1072	<
1073	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1074	<
1075	<	int errorOut;
1076	<	int esm =  NONE;
1077	<	int sm = UNDAMPED;
1078	<	RealType alphaVal;
1079	<	RealType dielectric;
1080	<
1081	<	errorOut = isError;
1082	<
1083	<	if (simParams_->haveElectrostaticSummationMethod()) {
1084	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1085	<	toUpper(myMethod);
1086	<	if (myMethod == "NONE") {
1087	<	esm = NONE;
1088	<	} else {
1089	<	if (myMethod == "SWITCHING_FUNCTION") {
1090	<	esm = SWITCHING_FUNCTION;
1091	<	} else {
1092	<	if (myMethod == "SHIFTED_POTENTIAL") {
1093	<	esm = SHIFTED_POTENTIAL;
1094	<	} else {
1095	<	if (myMethod == "SHIFTED_FORCE") {
1096	<	esm = SHIFTED_FORCE;
1097	<	} else {
1098	<	if (myMethod == "REACTION_FIELD") {
1099	<	esm = REACTION_FIELD;
1100	<	dielectric = simParams_->getDielectric();
1101	<	if (!simParams_->haveDielectric()) {
1102	<	// throw warning
1103	<	sprintf( painCave.errMsg,
1104	<	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1105	<	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1106	<	painCave.isFatal = 0;
1107	<	simError();
1108	<	}
1109	<	} else {
1110	<	// throw error
1111	<	sprintf( painCave.errMsg,
1112	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1113	<	"\t(Input file specified %s .)\n"
1114	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1115	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1116	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1117	<	painCave.isFatal = 1;
1118	<	simError();
1119	<	}
1120	<	}
1121	<	}
1122	<	}
1123	<	}
1124	<	}
1125	<
1126	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1127	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1128	<	toUpper(myScreen);
1129	<	if (myScreen == "UNDAMPED") {
1130	<	sm = UNDAMPED;
1131	<	} else {
1132	<	if (myScreen == "DAMPED") {
1133	<	sm = DAMPED;
1134	<	if (!simParams_->haveDampingAlpha()) {
1135	<	// first set a cutoff dependent alpha value
1136	<	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1137	<	alphaVal = 0.5125 - rcut_* 0.025;
1138	<	// for values rcut > 20.5, alpha is zero
1139	<	if (alphaVal < 0) alphaVal = 0;
1140	<
1141	<	// throw warning
1142	<	sprintf( painCave.errMsg,
1143	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1144	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1145	<	painCave.isFatal = 0;
1146	<	simError();
1147	<	} else {
1148	<	alphaVal = simParams_->getDampingAlpha();
1149	<	}
1150	<
1151	<	} else {
1152	<	// throw error
1153	<	sprintf( painCave.errMsg,
1154	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1155	<	"\t(Input file specified %s .)\n"
1156	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1157	<	"or \"damped\".\n", myScreen.c_str() );
1158	<	painCave.isFatal = 1;
1159	<	simError();
1160	<	}
1161	<	}
1162	<	}
1163	<
1164	<	// let's pass some summation method variables to fortran
1165	<	setElectrostaticSummationMethod( &esm );
1166	<	setFortranElectrostaticMethod( &esm );
1167	<	setScreeningMethod( &sm );
1168	<	setDampingAlpha( &alphaVal );
1169	<	setReactionFieldDielectric( &dielectric );
1170	<	initFortranFF( &errorOut );
1171	<	}
1172	<
1173	<	void SimInfo::setupSwitchingFunction() {
1174	<	int ft = CUBIC;
1175	<
1176	<	if (simParams_->haveSwitchingFunctionType()) {
1177	<	std::string funcType = simParams_->getSwitchingFunctionType();
1178	<	toUpper(funcType);
1179	<	if (funcType == "CUBIC") {
1180	<	ft = CUBIC;
1181	<	} else {
1182	<	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1183	<	ft = FIFTH_ORDER_POLY;
1184	<	} else {
1185	<	// throw error
1186	<	sprintf( painCave.errMsg,
1187	<	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1188	<	painCave.isFatal = 1;
1189	<	simError();
1190	<	}
1191	<	}
1192	<	}
1193	<
1194	<	// send switching function notification to switcheroo
1195	<	setFunctionType(&ft);
1196	<
1197	<	}
1198	<
1199	<	void SimInfo::setupAccumulateBoxDipole() {
1200	<
1201	<	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1202	<	if ( simParams_->haveAccumulateBoxDipole() )
1203	<	if ( simParams_->getAccumulateBoxDipole() ) {
1204	<	setAccumulateBoxDipole();
1205	<	calcBoxDipole_ = true;
1206	<	}
1207	<
927	>	fortranInitialized_ = true;
928		}
929
930		void SimInfo::addProperty(GenericData* genData) {
931		properties_.addProperty(genData);
932		}
933
934	<	void SimInfo::removeProperty(const std::string& propName) {
934	>	void SimInfo::removeProperty(const string& propName) {
935		properties_.removeProperty(propName);
936		}
937
#	Line 1219 | Line 939 | namespace oopse {
939		properties_.clearProperties();
940		}
941
942	<	std::vector<std::string> SimInfo::getPropertyNames() {
942	>	vector<string> SimInfo::getPropertyNames() {
943		return properties_.getPropertyNames();
944		}
945
946	<	std::vector<GenericData*> SimInfo::getProperties() {
946	>	vector<GenericData*> SimInfo::getProperties() {
947		return properties_.getProperties();
948		}
949
950	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
950	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
951		return properties_.getPropertyByName(propName);
952		}
953
#	Line 1310 | Line 1030 | namespace oopse {
1030
1031		}
1032
1033	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1033	>	ostream& operator <<(ostream& o, SimInfo& info) {
1034
1035		return o;
1036		}
#	Line 1353 | Line 1073 | namespace oopse {
1073
1074
1075		[  Ixx -Ixy  -Ixz ]
1076	<	J =| -Iyx  Iyy  -Iyz |
1076	>	J =| -Iyx  Iyy  -Iyz |
1077		[ -Izx -Iyz   Izz ]
1078		*/
1079
#	Line 1460 | Line 1180 | namespace oopse {
1180		return IOIndexToIntegrableObject.at(index);
1181		}
1182
1183	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1183	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1184		IOIndexToIntegrableObject= v;
1185		}
1186
#	Line 1502 | Line 1222 | namespace oopse {
1222		return;
1223		}
1224		/*
1225	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1225	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1226		assert( v.size() == nAtoms_ + nRigidBodies_);
1227		sdByGlobalIndex_ = v;
1228		}
#	Line 1512 | Line 1232 | namespace oopse {
1232		return sdByGlobalIndex_.at(index);
1233		}
1234		*/
1235	<	}//end namespace oopse
1235	>	int SimInfo::getNGlobalConstraints() {
1236	>	int nGlobalConstraints;
1237	>	#ifdef IS_MPI
1238	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1239	>	MPI_COMM_WORLD);
1240	>	#else
1241	>	nGlobalConstraints =  nConstraints_;
1242	>	#endif
1243	>	return nGlobalConstraints;
1244	>	}
1245
1246	+	}//end namespace OpenMD
1247	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 1126 by gezelter, Fri Apr 6 21:53:43 2007 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1535 by gezelter, Fri Dec 31 18:31:56 2010 UTC

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