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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 878 by chrisfen, Wed Feb 1 20:54:46 2006 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1553 by gezelter, Fri Apr 29 17:25:12 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 53 | Line 53
53		#include "brains/SimInfo.hpp"
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56	<	#include "UseTheForce/fCutoffPolicy.h"
57	<	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
58	<	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
59	<	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
60	<	#include "UseTheForce/doForces_interface.h"
61	<	#include "UseTheForce/DarkSide/electrostatic_interface.h"
62	<	#include "UseTheForce/DarkSide/switcheroo_interface.h"
56	>	#include "primitives/StuntDouble.hpp"
57		#include "utils/MemoryUtils.hpp"
58		#include "utils/simError.h"
59		#include "selection/SelectionManager.hpp"
60		#include "io/ForceFieldOptions.hpp"
61		#include "UseTheForce/ForceField.hpp"
62	+	#include "nonbonded/SwitchingFunction.hpp"
63
64	<	#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
71	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
72	<	#endif
73	<
74	<	namespace oopse {
75	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
76	<	std::map<int, std::set<int> >::iterator i = container.find(index);
77	<	std::set<int> result;
78	<	if (i != container.end()) {
79	<	result = i->second;
80	<	}
81	<
82	<	return result;
83	<	}
64	>	using namespace std;
65	>	namespace OpenMD {
66
67		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
68		forceField_(ff), simParams_(simParams),
69	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
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) {
75	<
76	<	MoleculeStamp* molStamp;
77	<	int nMolWithSameStamp;
78	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
79	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
80	<	CutoffGroupStamp* cgStamp;
81	<	RigidBodyStamp* rbStamp;
82	<	int nRigidAtoms = 0;
83	<	std::vector<Component*> components = simParams->getComponents();
72	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
73	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
74	>	nConstraints_(0), sman_(NULL), fortranInitialized_(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();
115	<
116	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
117	<	cgStamp = molStamp->getCutoffGroupStamp(j);
118	<	nAtomsInGroups += cgStamp->getNMembers();
119	<	}
120	<
121	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
122	<
123	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
124	<
125	<	//calculate atoms in rigid bodies
126	<	int nAtomsInRigidBodies = 0;
127	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
128	<
129	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
130	<	rbStamp = molStamp->getRigidBodyStamp(j);
131	<	nAtomsInRigidBodies += rbStamp->getNMembers();
132	<	}
133	<
134	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
135	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
136	<
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	+	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	+	std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
129	+	std::cerr << "nCA = " << nCutoffAtoms << "\n";
130	+	std::cerr << "nG = " << nGroups << "\n";
131
132	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
140	<	//group therefore the total number of cutoff groups in the system is
141	<	//equal to the total number of atoms minus number of atoms belong to
142	<	//cutoff group defined in meta-data file plus the number of cutoff
143	<	//groups defined in meta-data file
144	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
132	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
133
134	<	//every free atom (atom does not belong to rigid bodies) is an
135	<	//integrable object therefore the total number of integrable objects
136	<	//in the system is equal to the total number of atoms minus number of
137	<	//atoms belong to rigid body defined in meta-data file plus the number
138	<	//of rigid bodies defined in meta-data file
139	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
140	<	+ nGlobalRigidBodies_;
134	>	std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
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
154	–	nGlobalMols_ = molStampIds_.size();
155	–
156	–	#ifdef IS_MPI
157	–	molToProcMap_.resize(nGlobalMols_);
158	–	#endif
159	–
160	–	}
161	–
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 171 | Line 157 | namespace oopse {
157		delete forceField_;
158		}
159
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	–	}
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 219 | 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 233 | Line 211 | namespace oopse {
211		} else {
212		return false;
213		}
236	–
237	–
214		}
215
216
#	Line 252 | 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 290 | Line 266 | namespace oopse {
266
267		}
268
269	+	int SimInfo::getFdf() {
270	+	#ifdef IS_MPI
271	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
272	+	#else
273	+	fdf_ = fdf_local;
274	+	#endif
275	+	return fdf_;
276	+	}
277	+
278		void SimInfo::calcNdfRaw() {
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 341 | 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
383	–
384	–
385	–	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();
398	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
399	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
400	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
398	>
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	<	exclude_.addPairs(rigidSetA, rigidSetB);
408	<	exclude_.addPairs(rigidSetA, rigidSetC);
409	<	exclude_.addPairs(rigidSetB, rigidSetC);
410	<
411	<	//exclude_.addPair(a, b);
404	<	//exclude_.addPair(a, c);
405	<	//exclude_.addPair(b, c);
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();
413	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
414	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
415	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
416	<	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);
438	<	exclude_.addPair(b, d);
439	<	exclude_.addPair(c, d);
440	<	*/
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;
469	<
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();
506	–
507	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
508	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
509	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
510	–
511	–	exclude_.removePairs(rigidSetA, rigidSetB);
512	–	exclude_.removePairs(rigidSetA, rigidSetC);
513	–	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());
540	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
541	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
542	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
543	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
544	<	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 577 | Line 651 | namespace oopse {
651		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
652		}
653
580	–	void SimInfo::update() {
654
655	<	setupSimType();
656	<
657	<	#ifdef IS_MPI
658	<	setupFortranParallel();
659	<	#endif
660	<
661	<	setupFortranSim();
662	<
663	<	//setup fortran force field
591	<	/** @deprecate */
592	<	int isError = 0;
593	<
594	<	setupElectrostaticSummationMethod( isError );
595	<	setupSwitchingFunction();
596	<
597	<	if(isError){
598	<	sprintf( painCave.errMsg,
599	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
600	<	painCave.isFatal = 1;
601	<	simError();
602	<	}
603	<
604	<
605	<	setupCutoff();
606	<
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();
610	–
611	–	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)) {
622	<
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	<
627	<	}
686	>	}
687	>	}
688
689	<	return atomTypes;
630	<	}
689	>	#ifdef IS_MPI
690
691	<	void SimInfo::setupSimType() {
692	<	std::set<AtomType*>::iterator i;
634	<	std::set<AtomType*> atomTypes;
635	<	atomTypes = getUniqueAtomTypes();
636	<
637	<	int useLennardJones = 0;
638	<	int useElectrostatic = 0;
639	<	int useEAM = 0;
640	<	int useSC = 0;
641	<	int useCharge = 0;
642	<	int useDirectional = 0;
643	<	int useDipole = 0;
644	<	int useGayBerne = 0;
645	<	int useSticky = 0;
646	<	int useStickyPower = 0;
647	<	int useShape = 0;
648	<	int useFLARB = 0; //it is not in AtomType yet
649	<	int useDirectionalAtom = 0;
650	<	int useElectrostatics = 0;
651	<	//usePBC and useRF are from simParams
652	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
653	<	int useRF;
654	<	int useSF;
655	<	std::string myMethod;
691	>	// loop over the found atom types on this processor, and add their
692	>	// numerical idents to a vector:
693
694	<	// set the useRF logical
695	<	useRF = 0;
696	<	useSF = 0;
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	+	// count_local holds the number of found types on this processor
700	+	int count_local = foundTypes.size();
701
702	<	if (simParams_->haveElectrostaticSummationMethod()) {
703	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
704	<	toUpper(myMethod);
705	<	if (myMethod == "REACTION_FIELD") {
666	<	useRF=1;
667	<	} else {
668	<	if (myMethod == "SHIFTED_FORCE") {
669	<	useSF = 1;
670	<	}
671	<	}
672	<	}
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	+	// 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	+	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();
679	<	useSC |= (*i)->isSC();
680	<	useCharge |= (*i)->isCharge();
681	<	useDirectional |= (*i)->isDirectional();
682	<	useDipole |= (*i)->isDipole();
683	<	useGayBerne |= (*i)->isGayBerne();
684	<	useSticky |= (*i)->isSticky();
685	<	useStickyPower |= (*i)->isStickyPower();
686	<	useShape |= (*i)->isShape();
757	>	usesElectrostatic |= (*i)->isElectrostatic();
758	>	usesMetallic |= (*i)->isMetal();
759	>	usesDirectional |= (*i)->isDirectional();
760		}
761
689	–	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
690	–	useDirectionalAtom = 1;
691	–	}
692	–
693	–	if (useCharge || useDipole) {
694	–	useElectrostatics = 1;
695	–	}
696	–
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);
770	>	temp = usesElectrostatic;
771	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
772	>	#endif
773	>	}
774
706	–	temp = useLennardJones;
707	–	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
775
776	<	temp = useElectrostatics;
777	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776	>	vector<int> SimInfo::getGlobalAtomIndices() {
777	>	SimInfo::MoleculeIterator mi;
778	>	Molecule* mol;
779	>	Molecule::AtomIterator ai;
780	>	Atom* atom;
781
782	<	temp = useCharge;
713	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
714	<
715	<	temp = useDipole;
716	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
717	<
718	<	temp = useSticky;
719	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
720	<
721	<	temp = useStickyPower;
722	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
782	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
783
784	<	temp = useGayBerne;
785	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
784	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
785	>
786	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
787	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
788	>	}
789	>	}
790	>	return GlobalAtomIndices;
791	>	}
792
727	–	temp = useEAM;
728	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
793
794	<	temp = useSC;
795	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
796	<
797	<	temp = useShape;
798	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
794	>	vector<int> SimInfo::getGlobalGroupIndices() {
795	>	SimInfo::MoleculeIterator mi;
796	>	Molecule* mol;
797	>	Molecule::CutoffGroupIterator ci;
798	>	CutoffGroup* cg;
799
800	<	temp = useFLARB;
801	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
802	<
739	<	temp = useRF;
740	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
741	<
742	<	temp = useSF;
743	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
744	<
745	<	#endif
746	<
747	<	fInfo_.SIM_uses_PBC = usePBC;
748	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
749	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
750	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
751	<	fInfo_.SIM_uses_Charges = useCharge;
752	<	fInfo_.SIM_uses_Dipoles = useDipole;
753	<	fInfo_.SIM_uses_Sticky = useSticky;
754	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
755	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
756	<	fInfo_.SIM_uses_EAM = useEAM;
757	<	fInfo_.SIM_uses_SC = useSC;
758	<	fInfo_.SIM_uses_Shapes = useShape;
759	<	fInfo_.SIM_uses_FLARB = useFLARB;
760	<	fInfo_.SIM_uses_RF = useRF;
761	<	fInfo_.SIM_uses_SF = useSF;
762	<
763	<	if( myMethod == "REACTION_FIELD") {
800	>	vector<int> GlobalGroupIndices;
801	>
802	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
803
804	<	if (simParams_->haveDielectric()) {
805	<	fInfo_.dielect = simParams_->getDielectric();
806	<	} else {
807	<	sprintf(painCave.errMsg,
808	<	"SimSetup Error: No Dielectric constant was set.\n"
809	<	"\tYou are trying to use Reaction Field without"
771	<	"\tsetting a dielectric constant!\n");
772	<	painCave.isFatal = 1;
773	<	simError();
774	<	}
804	>	//local index of cutoff group is trivial, it only depends on the
805	>	//order of travesing
806	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
807	>	cg = mol->nextCutoffGroup(ci)) {
808	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
809	>	}
810		}
811	<
811	>	return GlobalGroupIndices;
812		}
813
814	<	void SimInfo::setupFortranSim() {
814	>
815	>	void SimInfo::setupFortran() {
816		int isError;
817	<	int nExclude;
818	<	std::vector<int> fortranGlobalGroupMembership;
817	>	int nExclude, nOneTwo, nOneThree, nOneFour;
818	>	vector<int> fortranGlobalGroupMembership;
819
784	–	nExclude = exclude_.getSize();
820		isError = 0;
821
822		//globalGroupMembership_ is filled by SimCreator
#	Line 790 | Line 825 | namespace oopse {
825		}
826
827		//calculate mass ratio of cutoff group
828	<	std::vector<double> mfact;
828	>	vector<RealType> mfact;
829		SimInfo::MoleculeIterator mi;
830		Molecule* mol;
831		Molecule::CutoffGroupIterator ci;
832		CutoffGroup* cg;
833		Molecule::AtomIterator ai;
834		Atom* atom;
835	<	double totalMass;
835	>	RealType totalMass;
836
837		//to avoid memory reallocation, reserve enough space for mfact
838		mfact.reserve(getNCutoffGroups());
#	Line 813 | Line 848 | namespace oopse {
848		else
849		mfact.push_back( 1.0 );
850		}
816	–
851		}
852		}
853
854	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
821	<	std::vector<int> identArray;
854	>	// Build the identArray_
855
856	<	//to avoid memory reallocation, reserve enough space identArray
857	<	identArray.reserve(getNAtoms());
825	<
856	>	identArray_.clear();
857	>	identArray_.reserve(getNAtoms());
858		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
859		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
860	<	identArray.push_back(atom->getIdent());
860	>	identArray_.push_back(atom->getIdent());
861		}
862		}
863
864		//fill molMembershipArray
865		//molMembershipArray is filled by SimCreator
866	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
866	>	vector<int> molMembershipArray(nGlobalAtoms_);
867		for (int i = 0; i < nGlobalAtoms_; i++) {
868		molMembershipArray[i] = globalMolMembership_[i] + 1;
869		}
870
871		//setup fortran simulation
840	–	int nGlobalExcludes = 0;
841	–	int* globalExcludes = NULL;
842	–	int* excludeList = exclude_.getExcludeList();
843	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
844	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
845	–	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
872
873	<	if( isError ){
873	>	nExclude = excludedInteractions_.getSize();
874	>	nOneTwo = oneTwoInteractions_.getSize();
875	>	nOneThree = oneThreeInteractions_.getSize();
876	>	nOneFour = oneFourInteractions_.getSize();
877
878	<	sprintf( painCave.errMsg,
879	<	"There was an error setting the simulation information in fortran.\n" );
880	<	painCave.isFatal = 1;
881	<	painCave.severity = OOPSE_ERROR;
853	<	simError();
854	<	}
878	>	int* excludeList = excludedInteractions_.getPairList();
879	>	int* oneTwoList = oneTwoInteractions_.getPairList();
880	>	int* oneThreeList = oneThreeInteractions_.getPairList();
881	>	int* oneFourList = oneFourInteractions_.getPairList();
882
883	<	#ifdef IS_MPI
884	<	sprintf( checkPointMsg,
885	<	"succesfully sent the simulation information to fortran.\n");
886	<	MPIcheckPoint();
887	<	#endif // is_mpi
888	<	}
889	<
863	<
864	<	#ifdef IS_MPI
865	<	void SimInfo::setupFortranParallel() {
883	>	//setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0],
884	>	//               &nExclude, excludeList,
885	>	//               &nOneTwo, oneTwoList,
886	>	//               &nOneThree, oneThreeList,
887	>	//               &nOneFour, oneFourList,
888	>	//               &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
889	>	//               &fortranGlobalGroupMembership[0], &isError);
890
891	<	//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;
891	>	// if( isError ){
892	>	//
893	>	//  sprintf( painCave.errMsg,
894	>	//         "There was an error setting the simulation information in fortran.\n" );
895	>	//  painCave.isFatal = 1;
896	>	//  painCave.severity = OPENMD_ERROR;
897	>	//  simError();
898	>	//}
899	>
900	>
901	>	// sprintf( checkPointMsg,
902	>	//          "succesfully sent the simulation information to fortran.\n");
903	>
904	>	// errorCheckPoint();
905	>
906	>	// Setup number of neighbors in neighbor list if present
907	>	//if (simParams_->haveNeighborListNeighbors()) {
908	>	//  int nlistNeighbors = simParams_->getNeighborListNeighbors();
909	>	//  setNeighbors(&nlistNeighbors);
910	>	//}
911	>
912	>	#ifdef IS_MPI
913	>	// mpiSimData parallelData;
914
879	–	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
880	–
881	–	//local index(index in DataStorge) of atom is important
882	–	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
883	–	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
884	–	}
885	–
886	–	//local index of cutoff group is trivial, it only depends on the order of travesing
887	–	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
888	–	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
889	–	}
890	–
891	–	}
892	–
915		//fill up mpiSimData struct
916	<	parallelData.nMolGlobal = getNGlobalMolecules();
917	<	parallelData.nMolLocal = getNMolecules();
918	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
919	<	parallelData.nAtomsLocal = getNAtoms();
920	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
921	<	parallelData.nGroupsLocal = getNCutoffGroups();
922	<	parallelData.myNode = worldRank;
923	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
916	>	// parallelData.nMolGlobal = getNGlobalMolecules();
917	>	// parallelData.nMolLocal = getNMolecules();
918	>	// parallelData.nAtomsGlobal = getNGlobalAtoms();
919	>	// parallelData.nAtomsLocal = getNAtoms();
920	>	// parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
921	>	// parallelData.nGroupsLocal = getNCutoffGroups();
922	>	// parallelData.myNode = worldRank;
923	>	// MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
924
925		//pass mpiSimData struct and index arrays to fortran
926	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
927	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
928	<	&localToGlobalCutoffGroupIndex[0], &isError);
926	>	//setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
927	>	//                &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
928	>	//                &localToGlobalCutoffGroupIndex[0], &isError);
929
930	<	if (isError) {
931	<	sprintf(painCave.errMsg,
932	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
933	<	painCave.isFatal = 1;
934	<	simError();
935	<	}
930	>	// if (isError) {
931	>	//   sprintf(painCave.errMsg,
932	>	//           "mpiRefresh errror: fortran didn't like something we gave it.\n");
933	>	//   painCave.isFatal = 1;
934	>	//   simError();
935	>	// }
936
937	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
938	<	MPIcheckPoint();
917	<
918	<
919	<	}
920	<
937	>	// sprintf(checkPointMsg, " mpiRefresh successful.\n");
938	>	// errorCheckPoint();
939		#endif
940
941	<	void SimInfo::setupCutoff() {
942	<
943	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
944	<
945	<	// Check the cutoff policy
946	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
947	<
948	<	std::string myPolicy;
931	<	if (forceFieldOptions_.haveCutoffPolicy()){
932	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
933	<	}else if (simParams_->haveCutoffPolicy()) {
934	<	myPolicy = simParams_->getCutoffPolicy();
935	<	}
936	<
937	<	if (!myPolicy.empty()){
938	<	toUpper(myPolicy);
939	<	if (myPolicy == "MIX") {
940	<	cp = MIX_CUTOFF_POLICY;
941	<	} else {
942	<	if (myPolicy == "MAX") {
943	<	cp = MAX_CUTOFF_POLICY;
944	<	} else {
945	<	if (myPolicy == "TRADITIONAL") {
946	<	cp = TRADITIONAL_CUTOFF_POLICY;
947	<	} else {
948	<	// throw error
949	<	sprintf( painCave.errMsg,
950	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
951	<	painCave.isFatal = 1;
952	<	simError();
953	<	}
954	<	}
955	<	}
956	<	}
957	<	notifyFortranCutoffPolicy(&cp);
958	<
959	<	// Check the Skin Thickness for neighborlists
960	<	double skin;
961	<	if (simParams_->haveSkinThickness()) {
962	<	skin = simParams_->getSkinThickness();
963	<	notifyFortranSkinThickness(&skin);
964	<	}
965	<
966	<	// Check if the cutoff was set explicitly:
967	<	if (simParams_->haveCutoffRadius()) {
968	<	rcut_ = simParams_->getCutoffRadius();
969	<	if (simParams_->haveSwitchingRadius()) {
970	<	rsw_  = simParams_->getSwitchingRadius();
971	<	} else {
972	<	if (fInfo_.SIM_uses_Charges |
973	<	fInfo_.SIM_uses_Dipoles |
974	<	fInfo_.SIM_uses_RF) {
975	<
976	<	rsw_ = 0.85 * rcut_;
977	<	sprintf(painCave.errMsg,
978	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
979	<	"\tOOPSE will use a default value of 85\% of the cutoffRadius"
980	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
981	<	painCave.isFatal = 0;
982	<	simError();
983	<	} else {
984	<	rsw_ = rcut_;
985	<	sprintf(painCave.errMsg,
986	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
987	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
988	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
989	<	painCave.isFatal = 0;
990	<	simError();
991	<	}
992	<
993	<	notifyFortranCutoffs(&rcut_, &rsw_);
994	<
995	<	} else {
996	<
997	<	// For electrostatic atoms, we'll assume a large safe value:
998	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
999	<	sprintf(painCave.errMsg,
1000	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1001	<	"\tOOPSE will use a default value of 15.0 angstroms"
1002	<	"\tfor the cutoffRadius.\n");
1003	<	painCave.isFatal = 0;
1004	<	simError();
1005	<	rcut_ = 15.0;
1006	<
1007	<	if (simParams_->haveElectrostaticSummationMethod()) {
1008	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1009	<	toUpper(myMethod);
1010	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1011	<	if (simParams_->haveSwitchingRadius()){
1012	<	sprintf(painCave.errMsg,
1013	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1014	<	"\teven though the electrostaticSummationMethod was\n"
1015	<	"\tset to %s\n", myMethod.c_str());
1016	<	painCave.isFatal = 1;
1017	<	simError();
1018	<	}
1019	<	}
1020	<	}
1021	<
1022	<	if (simParams_->haveSwitchingRadius()){
1023	<	rsw_ = simParams_->getSwitchingRadius();
1024	<	} else {
1025	<	sprintf(painCave.errMsg,
1026	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1027	<	"\tOOPSE will use a default value of\n"
1028	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1029	<	painCave.isFatal = 0;
1030	<	simError();
1031	<	rsw_ = 0.85 * rcut_;
1032	<	}
1033	<	notifyFortranCutoffs(&rcut_, &rsw_);
1034	<	} else {
1035	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1036	<	// We'll punt and let fortran figure out the cutoffs later.
1037	<
1038	<	notifyFortranYouAreOnYourOwn();
1039	<
1040	<	}
1041	<	}
1042	<	}
1043	<
1044	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1045	<
1046	<	int errorOut;
1047	<	int esm =  NONE;
1048	<	int sm = UNDAMPED;
1049	<	double alphaVal;
1050	<	double dielectric;
1051	<
1052	<	errorOut = isError;
1053	<	alphaVal = simParams_->getDampingAlpha();
1054	<	dielectric = simParams_->getDielectric();
1055	<
1056	<	if (simParams_->haveElectrostaticSummationMethod()) {
1057	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1058	<	toUpper(myMethod);
1059	<	if (myMethod == "NONE") {
1060	<	esm = NONE;
1061	<	} else {
1062	<	if (myMethod == "SWITCHING_FUNCTION") {
1063	<	esm = SWITCHING_FUNCTION;
1064	<	} else {
1065	<	if (myMethod == "SHIFTED_POTENTIAL") {
1066	<	esm = SHIFTED_POTENTIAL;
1067	<	} else {
1068	<	if (myMethod == "SHIFTED_FORCE") {
1069	<	esm = SHIFTED_FORCE;
1070	<	} else {
1071	<	if (myMethod == "REACTION_FIELD") {
1072	<	esm = REACTION_FIELD;
1073	<	} else {
1074	<	// throw error
1075	<	sprintf( painCave.errMsg,
1076	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1077	<	"\t(Input file specified %s .)\n"
1078	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1079	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1080	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1081	<	painCave.isFatal = 1;
1082	<	simError();
1083	<	}
1084	<	}
1085	<	}
1086	<	}
1087	<	}
1088	<	}
1089	<
1090	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1091	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1092	<	toUpper(myScreen);
1093	<	if (myScreen == "UNDAMPED") {
1094	<	sm = UNDAMPED;
1095	<	} else {
1096	<	if (myScreen == "DAMPED") {
1097	<	sm = DAMPED;
1098	<	if (!simParams_->haveDampingAlpha()) {
1099	<	//throw error
1100	<	sprintf( painCave.errMsg,
1101	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1102	<	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1103	<	painCave.isFatal = 0;
1104	<	simError();
1105	<	}
1106	<	} else {
1107	<	// throw error
1108	<	sprintf( painCave.errMsg,
1109	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1110	<	"\t(Input file specified %s .)\n"
1111	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1112	<	"or \"damped\".\n", myScreen.c_str() );
1113	<	painCave.isFatal = 1;
1114	<	simError();
1115	<	}
1116	<	}
1117	<	}
1118	<
1119	<	// let's pass some summation method variables to fortran
1120	<	setElectrostaticSummationMethod( &esm );
1121	<	setFortranElectrostaticMethod( &esm );
1122	<	setScreeningMethod( &sm );
1123	<	setDampingAlpha( &alphaVal );
1124	<	setReactionFieldDielectric( &dielectric );
1125	<	initFortranFF( &errorOut );
1126	<	}
1127	<
1128	<	void SimInfo::setupSwitchingFunction() {
1129	<	int ft = CUBIC;
1130	<
1131	<	if (simParams_->haveSwitchingFunctionType()) {
1132	<	std::string funcType = simParams_->getSwitchingFunctionType();
1133	<	toUpper(funcType);
1134	<	if (funcType == "CUBIC") {
1135	<	ft = CUBIC;
1136	<	} else {
1137	<	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1138	<	ft = FIFTH_ORDER_POLY;
1139	<	} else {
1140	<	// throw error
1141	<	sprintf( painCave.errMsg,
1142	<	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1143	<	painCave.isFatal = 1;
1144	<	simError();
1145	<	}
1146	<	}
1147	<	}
1148	<
1149	<	// send switching function notification to switcheroo
1150	<	setFunctionType(&ft);
1151	<
941	>	// initFortranFF(&isError);
942	>	// if (isError) {
943	>	//   sprintf(painCave.errMsg,
944	>	//           "initFortranFF errror: fortran didn't like something we gave it.\n");
945	>	//   painCave.isFatal = 1;
946	>	//   simError();
947	>	// }
948	>	// fortranInitialized_ = true;
949		}
950
951		void SimInfo::addProperty(GenericData* genData) {
952		properties_.addProperty(genData);
953		}
954
955	<	void SimInfo::removeProperty(const std::string& propName) {
955	>	void SimInfo::removeProperty(const string& propName) {
956		properties_.removeProperty(propName);
957		}
958
#	Line 1163 | Line 960 | namespace oopse {
960		properties_.clearProperties();
961		}
962
963	<	std::vector<std::string> SimInfo::getPropertyNames() {
963	>	vector<string> SimInfo::getPropertyNames() {
964		return properties_.getPropertyNames();
965		}
966
967	<	std::vector<GenericData*> SimInfo::getProperties() {
967	>	vector<GenericData*> SimInfo::getProperties() {
968		return properties_.getProperties();
969		}
970
971	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
971	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
972		return properties_.getPropertyByName(propName);
973		}
974
#	Line 1185 | Line 982 | namespace oopse {
982		Molecule* mol;
983		RigidBody* rb;
984		Atom* atom;
985	+	CutoffGroup* cg;
986		SimInfo::MoleculeIterator mi;
987		Molecule::RigidBodyIterator rbIter;
988	<	Molecule::AtomIterator atomIter;;
988	>	Molecule::AtomIterator atomIter;
989	>	Molecule::CutoffGroupIterator cgIter;
990
991		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
992
#	Line 1198 | Line 997 | namespace oopse {
997		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
998		rb->setSnapshotManager(sman_);
999		}
1000	+
1001	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
1002	+	cg->setSnapshotManager(sman_);
1003	+	}
1004		}
1005
1006		}
#	Line 1207 | Line 1010 | namespace oopse {
1010		Molecule* mol;
1011
1012		Vector3d comVel(0.0);
1013	<	double totalMass = 0.0;
1013	>	RealType totalMass = 0.0;
1014
1015
1016		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1017	<	double mass = mol->getMass();
1017	>	RealType mass = mol->getMass();
1018		totalMass += mass;
1019		comVel += mass * mol->getComVel();
1020		}
1021
1022		#ifdef IS_MPI
1023	<	double tmpMass = totalMass;
1023	>	RealType tmpMass = totalMass;
1024		Vector3d tmpComVel(comVel);
1025	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1026	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1025	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1026	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1027		#endif
1028
1029		comVel /= totalMass;
#	Line 1233 | Line 1036 | namespace oopse {
1036		Molecule* mol;
1037
1038		Vector3d com(0.0);
1039	<	double totalMass = 0.0;
1039	>	RealType totalMass = 0.0;
1040
1041		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1042	<	double mass = mol->getMass();
1042	>	RealType mass = mol->getMass();
1043		totalMass += mass;
1044		com += mass * mol->getCom();
1045		}
1046
1047		#ifdef IS_MPI
1048	<	double tmpMass = totalMass;
1048	>	RealType tmpMass = totalMass;
1049		Vector3d tmpCom(com);
1050	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1051	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1050	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1051	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1052		#endif
1053
1054		com /= totalMass;
#	Line 1254 | Line 1057 | namespace oopse {
1057
1058		}
1059
1060	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1060	>	ostream& operator <<(ostream& o, SimInfo& info) {
1061
1062		return o;
1063		}
#	Line 1269 | Line 1072 | namespace oopse {
1072		Molecule* mol;
1073
1074
1075	<	double totalMass = 0.0;
1075	>	RealType totalMass = 0.0;
1076
1077
1078		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1079	<	double mass = mol->getMass();
1079	>	RealType mass = mol->getMass();
1080		totalMass += mass;
1081		com += mass * mol->getCom();
1082		comVel += mass * mol->getComVel();
1083		}
1084
1085		#ifdef IS_MPI
1086	<	double tmpMass = totalMass;
1086	>	RealType tmpMass = totalMass;
1087		Vector3d tmpCom(com);
1088		Vector3d tmpComVel(comVel);
1089	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1090	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1091	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1089	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1090	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1091	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1092		#endif
1093
1094		com /= totalMass;
#	Line 1297 | Line 1100 | namespace oopse {
1100
1101
1102		[  Ixx -Ixy  -Ixz ]
1103	<	J =| -Iyx  Iyy  -Iyz |
1103	>	J =| -Iyx  Iyy  -Iyz |
1104		[ -Izx -Iyz   Izz ]
1105		*/
1106
1107		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1108
1109
1110	<	double xx = 0.0;
1111	<	double yy = 0.0;
1112	<	double zz = 0.0;
1113	<	double xy = 0.0;
1114	<	double xz = 0.0;
1115	<	double yz = 0.0;
1110	>	RealType xx = 0.0;
1111	>	RealType yy = 0.0;
1112	>	RealType zz = 0.0;
1113	>	RealType xy = 0.0;
1114	>	RealType xz = 0.0;
1115	>	RealType yz = 0.0;
1116		Vector3d com(0.0);
1117		Vector3d comVel(0.0);
1118
#	Line 1321 | Line 1124 | namespace oopse {
1124		Vector3d thisq(0.0);
1125		Vector3d thisv(0.0);
1126
1127	<	double thisMass = 0.0;
1127	>	RealType thisMass = 0.0;
1128
1129
1130
#	Line 1359 | Line 1162 | namespace oopse {
1162		#ifdef IS_MPI
1163		Mat3x3d tmpI(inertiaTensor);
1164		Vector3d tmpAngMom;
1165	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1166	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1165	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1166	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1167		#endif
1168
1169		return;
#	Line 1381 | Line 1184 | namespace oopse {
1184		Vector3d thisr(0.0);
1185		Vector3d thisp(0.0);
1186
1187	<	double thisMass;
1187	>	RealType thisMass;
1188
1189		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1190		thisMass = mol->getMass();
#	Line 1394 | Line 1197 | namespace oopse {
1197
1198		#ifdef IS_MPI
1199		Vector3d tmpAngMom;
1200	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1200	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1201		#endif
1202
1203		return angularMomentum;
1204		}
1205
1206	<
1207	<	}//end namespace oopse
1206	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1207	>	return IOIndexToIntegrableObject.at(index);
1208	>	}
1209	>
1210	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1211	>	IOIndexToIntegrableObject= v;
1212	>	}
1213
1214	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1215	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1216	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1217	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1218	+	*/
1219	+	void SimInfo::getGyrationalVolume(RealType &volume){
1220	+	Mat3x3d intTensor;
1221	+	RealType det;
1222	+	Vector3d dummyAngMom;
1223	+	RealType sysconstants;
1224	+	RealType geomCnst;
1225	+
1226	+	geomCnst = 3.0/2.0;
1227	+	/* Get the inertial tensor and angular momentum for free*/
1228	+	getInertiaTensor(intTensor,dummyAngMom);
1229	+
1230	+	det = intTensor.determinant();
1231	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1232	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1233	+	return;
1234	+	}
1235	+
1236	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1237	+	Mat3x3d intTensor;
1238	+	Vector3d dummyAngMom;
1239	+	RealType sysconstants;
1240	+	RealType geomCnst;
1241	+
1242	+	geomCnst = 3.0/2.0;
1243	+	/* Get the inertial tensor and angular momentum for free*/
1244	+	getInertiaTensor(intTensor,dummyAngMom);
1245	+
1246	+	detI = intTensor.determinant();
1247	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1248	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1249	+	return;
1250	+	}
1251	+	/*
1252	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1253	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1254	+	sdByGlobalIndex_ = v;
1255	+	}
1256	+
1257	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1258	+	//assert(index < nAtoms_ + nRigidBodies_);
1259	+	return sdByGlobalIndex_.at(index);
1260	+	}
1261	+	*/
1262	+	int SimInfo::getNGlobalConstraints() {
1263	+	int nGlobalConstraints;
1264	+	#ifdef IS_MPI
1265	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1266	+	MPI_COMM_WORLD);
1267	+	#else
1268	+	nGlobalConstraints =  nConstraints_;
1269	+	#endif
1270	+	return nGlobalConstraints;
1271	+	}
1272	+
1273	+	}//end namespace OpenMD
1274	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 878 by chrisfen, Wed Feb 1 20:54:46 2006 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1553 by gezelter, Fri Apr 29 17:25:12 2011 UTC

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