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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 749 by tim, Wed Nov 16 23:10:02 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1627 by gezelter, Tue Sep 13 22:05:04 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/notifyCutoffs_interface.h"
63	<	#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	<
60	>	#include "io/ForceFieldOptions.hpp"
61	>	#include "UseTheForce/ForceField.hpp"
62	>	#include "nonbonded/SwitchingFunction.hpp"
63		#ifdef IS_MPI
64	<	#include "UseTheForce/mpiComponentPlan.h"
65	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
71	<	#endif
64	>	#include <mpi.h>
65	>	#endif
66
67	<	namespace oopse {
68	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
75	<	std::map<int, std::set<int> >::iterator i = container.find(index);
76	<	std::set<int> result;
77	<	if (i != container.end()) {
78	<	result = i->second;
79	<	}
80	<
81	<	return result;
82	<	}
67	>	using namespace std;
68	>	namespace OpenMD {
69
70	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
71	<	ForceField* ff, Globals* simParams) :
72	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
87	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
70	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
71	>	forceField_(ff), simParams_(simParams),
72	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
73		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
74		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
75	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
76	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
77	<	sman_(NULL), fortranInitialized_(false) {
78	<
94	<
95	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
96	<	MoleculeStamp* molStamp;
97	<	int nMolWithSameStamp;
98	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
99	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
100	<	CutoffGroupStamp* cgStamp;
101	<	RigidBodyStamp* rbStamp;
102	<	int nRigidAtoms = 0;
75	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
76	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
77	>	nConstraints_(0), sman_(NULL), topologyDone_(false),
78	>	calcBoxDipole_(false), useAtomicVirial_(true) {
79
80	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
81	<	molStamp = i->first;
82	<	nMolWithSameStamp = i->second;
83	<
84	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
85	<
86	<	//calculate atoms in molecules
87	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
88	<
89	<
90	<	//calculate atoms in cutoff groups
91	<	int nAtomsInGroups = 0;
92	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
93	<
94	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
95	<	cgStamp = molStamp->getCutoffGroup(j);
96	<	nAtomsInGroups += cgStamp->getNMembers();
97	<	}
98	<
99	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
100	<
101	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
102	<
103	<	//calculate atoms in rigid bodies
104	<	int nAtomsInRigidBodies = 0;
105	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
130	<
131	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
132	<	rbStamp = molStamp->getRigidBody(j);
133	<	nAtomsInRigidBodies += rbStamp->getNMembers();
134	<	}
135	<
136	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
137	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
138	<
80	>	MoleculeStamp* molStamp;
81	>	int nMolWithSameStamp;
82	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
83	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
84	>	CutoffGroupStamp* cgStamp;
85	>	RigidBodyStamp* rbStamp;
86	>	int nRigidAtoms = 0;
87	>
88	>	vector<Component*> components = simParams->getComponents();
89	>
90	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
91	>	molStamp = (*i)->getMoleculeStamp();
92	>	nMolWithSameStamp = (*i)->getNMol();
93	>
94	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
95	>
96	>	//calculate atoms in molecules
97	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
98	>
99	>	//calculate atoms in cutoff groups
100	>	int nAtomsInGroups = 0;
101	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
102	>
103	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
104	>	cgStamp = molStamp->getCutoffGroupStamp(j);
105	>	nAtomsInGroups += cgStamp->getNMembers();
106		}
107	<
108	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
109	<	//group therefore the total number of cutoff groups in the system is
110	<	//equal to the total number of atoms minus number of atoms belong to
111	<	//cutoff group defined in meta-data file plus the number of cutoff
112	<	//groups defined in meta-data file
113	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
114	<
115	<	//every free atom (atom does not belong to rigid bodies) is an
116	<	//integrable object therefore the total number of integrable objects
117	<	//in the system is equal to the total number of atoms minus number of
118	<	//atoms belong to rigid body defined in meta-data file plus the number
119	<	//of rigid bodies defined in meta-data file
120	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
121	<	+ nGlobalRigidBodies_;
122	<
123	<	nGlobalMols_ = molStampIds_.size();
157	<
158	<	#ifdef IS_MPI
159	<	molToProcMap_.resize(nGlobalMols_);
160	<	#endif
161	<
107	>
108	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
109	>
110	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
111	>
112	>	//calculate atoms in rigid bodies
113	>	int nAtomsInRigidBodies = 0;
114	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
115	>
116	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
117	>	rbStamp = molStamp->getRigidBodyStamp(j);
118	>	nAtomsInRigidBodies += rbStamp->getNMembers();
119	>	}
120	>
121	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
122	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
123	>
124		}
125	+
126	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
127	+	//group therefore the total number of cutoff groups in the system is
128	+	//equal to the total number of atoms minus number of atoms belong to
129	+	//cutoff group defined in meta-data file plus the number of cutoff
130	+	//groups defined in meta-data file
131
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_;
141	+
142	+	nGlobalMols_ = molStampIds_.size();
143	+	molToProcMap_.resize(nGlobalMols_);
144	+	}
145	+
146		SimInfo::~SimInfo() {
147	<	std::map<int, Molecule*>::iterator i;
147	>	map<int, Molecule*>::iterator i;
148		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
149		delete i->second;
150		}
151		molecules_.clear();
152
171	–	delete stamps_;
153		delete sman_;
154		delete simParams_;
155		delete forceField_;
156		}
157
177	–	int SimInfo::getNGlobalConstraints() {
178	–	int nGlobalConstraints;
179	–	#ifdef IS_MPI
180	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
181	–	MPI_COMM_WORLD);
182	–	#else
183	–	nGlobalConstraints =  nConstraints_;
184	–	#endif
185	–	return nGlobalConstraints;
186	–	}
158
159		bool SimInfo::addMolecule(Molecule* mol) {
160		MoleculeIterator i;
161	<
161	>
162		i = molecules_.find(mol->getGlobalIndex());
163		if (i == molecules_.end() ) {
164	<
165	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
166	<
164	>
165	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
166	>
167		nAtoms_ += mol->getNAtoms();
168		nBonds_ += mol->getNBonds();
169		nBends_ += mol->getNBends();
170		nTorsions_ += mol->getNTorsions();
171	+	nInversions_ += mol->getNInversions();
172		nRigidBodies_ += mol->getNRigidBodies();
173		nIntegrableObjects_ += mol->getNIntegrableObjects();
174		nCutoffGroups_ += mol->getNCutoffGroups();
175		nConstraints_ += mol->getNConstraintPairs();
176	<
177	<	addExcludePairs(mol);
178	<
176	>
177	>	addInteractionPairs(mol);
178	>
179		return true;
180		} else {
181		return false;
182		}
183		}
184	<
184	>
185		bool SimInfo::removeMolecule(Molecule* mol) {
186		MoleculeIterator i;
187		i = molecules_.find(mol->getGlobalIndex());
#	Line 222 | Line 194 | namespace oopse {
194		nBonds_ -= mol->getNBonds();
195		nBends_ -= mol->getNBends();
196		nTorsions_ -= mol->getNTorsions();
197	+	nInversions_ -= mol->getNInversions();
198		nRigidBodies_ -= mol->getNRigidBodies();
199		nIntegrableObjects_ -= mol->getNIntegrableObjects();
200		nCutoffGroups_ -= mol->getNCutoffGroups();
201		nConstraints_ -= mol->getNConstraintPairs();
202
203	<	removeExcludePairs(mol);
203	>	removeInteractionPairs(mol);
204		molecules_.erase(mol->getGlobalIndex());
205
206		delete mol;
#	Line 236 | Line 209 | namespace oopse {
209		} else {
210		return false;
211		}
239	–
240	–
212		}
213
214
#	Line 255 | Line 226 | namespace oopse {
226		void SimInfo::calcNdf() {
227		int ndf_local;
228		MoleculeIterator i;
229	<	std::vector<StuntDouble*>::iterator j;
229	>	vector<StuntDouble*>::iterator j;
230		Molecule* mol;
231		StuntDouble* integrableObject;
232
#	Line 275 | Line 246 | namespace oopse {
246		}
247		}
248
249	<	}//end for (integrableObject)
250	<	}// end for (mol)
249	>	}
250	>	}
251
252		// n_constraints is local, so subtract them on each processor
253		ndf_local -= nConstraints_;
#	Line 293 | Line 264 | namespace oopse {
264
265		}
266
267	+	int SimInfo::getFdf() {
268	+	#ifdef IS_MPI
269	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
270	+	#else
271	+	fdf_ = fdf_local;
272	+	#endif
273	+	return fdf_;
274	+	}
275	+
276	+	unsigned int SimInfo::getNLocalCutoffGroups(){
277	+	int nLocalCutoffAtoms = 0;
278	+	Molecule* mol;
279	+	MoleculeIterator mi;
280	+	CutoffGroup* cg;
281	+	Molecule::CutoffGroupIterator ci;
282	+
283	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
284	+
285	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
286	+	cg = mol->nextCutoffGroup(ci)) {
287	+	nLocalCutoffAtoms += cg->getNumAtom();
288	+
289	+	}
290	+	}
291	+
292	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
293	+	}
294	+
295		void SimInfo::calcNdfRaw() {
296		int ndfRaw_local;
297
298		MoleculeIterator i;
299	<	std::vector<StuntDouble*>::iterator j;
299	>	vector<StuntDouble*>::iterator j;
300		Molecule* mol;
301		StuntDouble* integrableObject;
302
#	Line 344 | Line 343 | namespace oopse {
343
344		}
345
346	<	void SimInfo::addExcludePairs(Molecule* mol) {
347	<	std::vector<Bond*>::iterator bondIter;
348	<	std::vector<Bend*>::iterator bendIter;
349	<	std::vector<Torsion*>::iterator torsionIter;
346	>	void SimInfo::addInteractionPairs(Molecule* mol) {
347	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
348	>	vector<Bond*>::iterator bondIter;
349	>	vector<Bend*>::iterator bendIter;
350	>	vector<Torsion*>::iterator torsionIter;
351	>	vector<Inversion*>::iterator inversionIter;
352		Bond* bond;
353		Bend* bend;
354		Torsion* torsion;
355	+	Inversion* inversion;
356		int a;
357		int b;
358		int c;
359		int d;
360
361	<	std::map<int, std::set<int> > atomGroups;
361	>	// atomGroups can be used to add special interaction maps between
362	>	// groups of atoms that are in two separate rigid bodies.
363	>	// However, most site-site interactions between two rigid bodies
364	>	// are probably not special, just the ones between the physically
365	>	// bonded atoms.  Interactions *within* a single rigid body should
366	>	// always be excluded.  These are done at the bottom of this
367	>	// function.
368
369	+	map<int, set<int> > atomGroups;
370		Molecule::RigidBodyIterator rbIter;
371		RigidBody* rb;
372		Molecule::IntegrableObjectIterator ii;
373		StuntDouble* integrableObject;
374
375	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
376	<	integrableObject = mol->nextIntegrableObject(ii)) {
377	<
375	>	for (integrableObject = mol->beginIntegrableObject(ii);
376	>	integrableObject != NULL;
377	>	integrableObject = mol->nextIntegrableObject(ii)) {
378	>
379		if (integrableObject->isRigidBody()) {
380	<	rb = static_cast<RigidBody*>(integrableObject);
381	<	std::vector<Atom*> atoms = rb->getAtoms();
382	<	std::set<int> rigidAtoms;
383	<	for (int i = 0; i < atoms.size(); ++i) {
384	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
385	<	}
386	<	for (int i = 0; i < atoms.size(); ++i) {
387	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
388	<	}
380	>	rb = static_cast<RigidBody*>(integrableObject);
381	>	vector<Atom*> atoms = rb->getAtoms();
382	>	set<int> rigidAtoms;
383	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
384	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
385	>	}
386	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
387	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
388	>	}
389		} else {
390	<	std::set<int> oneAtomSet;
390	>	set<int> oneAtomSet;
391		oneAtomSet.insert(integrableObject->getGlobalIndex());
392	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
392	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
393		}
394		}
395	+
396	+	for (bond= mol->beginBond(bondIter); bond != NULL;
397	+	bond = mol->nextBond(bondIter)) {
398
386	–
387	–
388	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
399		a = bond->getAtomA()->getGlobalIndex();
400	<	b = bond->getAtomB()->getGlobalIndex();
401	<	exclude_.addPair(a, b);
400	>	b = bond->getAtomB()->getGlobalIndex();
401	>
402	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
403	>	oneTwoInteractions_.addPair(a, b);
404	>	} else {
405	>	excludedInteractions_.addPair(a, b);
406	>	}
407		}
408
409	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
409	>	for (bend= mol->beginBend(bendIter); bend != NULL;
410	>	bend = mol->nextBend(bendIter)) {
411	>
412		a = bend->getAtomA()->getGlobalIndex();
413		b = bend->getAtomB()->getGlobalIndex();
414		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);
401	–
402	–	exclude_.addPairs(rigidSetA, rigidSetB);
403	–	exclude_.addPairs(rigidSetA, rigidSetC);
404	–	exclude_.addPairs(rigidSetB, rigidSetC);
415
416	<	//exclude_.addPair(a, b);
417	<	//exclude_.addPair(a, c);
418	<	//exclude_.addPair(b, c);
416	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
417	>	oneTwoInteractions_.addPair(a, b);
418	>	oneTwoInteractions_.addPair(b, c);
419	>	} else {
420	>	excludedInteractions_.addPair(a, b);
421	>	excludedInteractions_.addPair(b, c);
422	>	}
423	>
424	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
425	>	oneThreeInteractions_.addPair(a, c);
426	>	} else {
427	>	excludedInteractions_.addPair(a, c);
428	>	}
429		}
430
431	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
431	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
432	>	torsion = mol->nextTorsion(torsionIter)) {
433	>
434		a = torsion->getAtomA()->getGlobalIndex();
435		b = torsion->getAtomB()->getGlobalIndex();
436		c = torsion->getAtomC()->getGlobalIndex();
437	<	d = torsion->getAtomD()->getGlobalIndex();
416	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
417	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
418	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
419	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
437	>	d = torsion->getAtomD()->getGlobalIndex();
438
439	<	exclude_.addPairs(rigidSetA, rigidSetB);
440	<	exclude_.addPairs(rigidSetA, rigidSetC);
441	<	exclude_.addPairs(rigidSetA, rigidSetD);
442	<	exclude_.addPairs(rigidSetB, rigidSetC);
443	<	exclude_.addPairs(rigidSetB, rigidSetD);
444	<	exclude_.addPairs(rigidSetC, rigidSetD);
439	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
440	>	oneTwoInteractions_.addPair(a, b);
441	>	oneTwoInteractions_.addPair(b, c);
442	>	oneTwoInteractions_.addPair(c, d);
443	>	} else {
444	>	excludedInteractions_.addPair(a, b);
445	>	excludedInteractions_.addPair(b, c);
446	>	excludedInteractions_.addPair(c, d);
447	>	}
448
449	<	/*
450	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
451	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
452	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
453	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
454	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
455	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
456	<
457	<
458	<	exclude_.addPair(a, b);
459	<	exclude_.addPair(a, c);
460	<	exclude_.addPair(a, d);
461	<	exclude_.addPair(b, c);
441	<	exclude_.addPair(b, d);
442	<	exclude_.addPair(c, d);
443	<	*/
449	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
450	>	oneThreeInteractions_.addPair(a, c);
451	>	oneThreeInteractions_.addPair(b, d);
452	>	} else {
453	>	excludedInteractions_.addPair(a, c);
454	>	excludedInteractions_.addPair(b, d);
455	>	}
456	>
457	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
458	>	oneFourInteractions_.addPair(a, d);
459	>	} else {
460	>	excludedInteractions_.addPair(a, d);
461	>	}
462		}
463
464	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
465	<	std::vector<Atom*> atoms = rb->getAtoms();
466	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
467	<	for (int j = i + 1; j < atoms.size(); ++j) {
464	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
465	>	inversion = mol->nextInversion(inversionIter)) {
466	>
467	>	a = inversion->getAtomA()->getGlobalIndex();
468	>	b = inversion->getAtomB()->getGlobalIndex();
469	>	c = inversion->getAtomC()->getGlobalIndex();
470	>	d = inversion->getAtomD()->getGlobalIndex();
471	>
472	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
473	>	oneTwoInteractions_.addPair(a, b);
474	>	oneTwoInteractions_.addPair(a, c);
475	>	oneTwoInteractions_.addPair(a, d);
476	>	} else {
477	>	excludedInteractions_.addPair(a, b);
478	>	excludedInteractions_.addPair(a, c);
479	>	excludedInteractions_.addPair(a, d);
480	>	}
481	>
482	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
483	>	oneThreeInteractions_.addPair(b, c);
484	>	oneThreeInteractions_.addPair(b, d);
485	>	oneThreeInteractions_.addPair(c, d);
486	>	} else {
487	>	excludedInteractions_.addPair(b, c);
488	>	excludedInteractions_.addPair(b, d);
489	>	excludedInteractions_.addPair(c, d);
490	>	}
491	>	}
492	>
493	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
494	>	rb = mol->nextRigidBody(rbIter)) {
495	>	vector<Atom*> atoms = rb->getAtoms();
496	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
497	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
498		a = atoms[i]->getGlobalIndex();
499		b = atoms[j]->getGlobalIndex();
500	<	exclude_.addPair(a, b);
500	>	excludedInteractions_.addPair(a, b);
501		}
502		}
503		}
504
505		}
506
507	<	void SimInfo::removeExcludePairs(Molecule* mol) {
508	<	std::vector<Bond*>::iterator bondIter;
509	<	std::vector<Bend*>::iterator bendIter;
510	<	std::vector<Torsion*>::iterator torsionIter;
507	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
508	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
509	>	vector<Bond*>::iterator bondIter;
510	>	vector<Bend*>::iterator bendIter;
511	>	vector<Torsion*>::iterator torsionIter;
512	>	vector<Inversion*>::iterator inversionIter;
513		Bond* bond;
514		Bend* bend;
515		Torsion* torsion;
516	+	Inversion* inversion;
517		int a;
518		int b;
519		int c;
520		int d;
521
522	<	std::map<int, std::set<int> > atomGroups;
472	<
522	>	map<int, set<int> > atomGroups;
523		Molecule::RigidBodyIterator rbIter;
524		RigidBody* rb;
525		Molecule::IntegrableObjectIterator ii;
526		StuntDouble* integrableObject;
527
528	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
529	<	integrableObject = mol->nextIntegrableObject(ii)) {
530	<
528	>	for (integrableObject = mol->beginIntegrableObject(ii);
529	>	integrableObject != NULL;
530	>	integrableObject = mol->nextIntegrableObject(ii)) {
531	>
532		if (integrableObject->isRigidBody()) {
533	<	rb = static_cast<RigidBody*>(integrableObject);
534	<	std::vector<Atom*> atoms = rb->getAtoms();
535	<	std::set<int> rigidAtoms;
536	<	for (int i = 0; i < atoms.size(); ++i) {
537	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
538	<	}
539	<	for (int i = 0; i < atoms.size(); ++i) {
540	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
541	<	}
533	>	rb = static_cast<RigidBody*>(integrableObject);
534	>	vector<Atom*> atoms = rb->getAtoms();
535	>	set<int> rigidAtoms;
536	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
537	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
538	>	}
539	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
540	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
541	>	}
542		} else {
543	<	std::set<int> oneAtomSet;
543	>	set<int> oneAtomSet;
544		oneAtomSet.insert(integrableObject->getGlobalIndex());
545	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
545	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
546		}
547		}
548
549	<
550	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
549	>	for (bond= mol->beginBond(bondIter); bond != NULL;
550	>	bond = mol->nextBond(bondIter)) {
551	>
552		a = bond->getAtomA()->getGlobalIndex();
553	<	b = bond->getAtomB()->getGlobalIndex();
554	<	exclude_.removePair(a, b);
553	>	b = bond->getAtomB()->getGlobalIndex();
554	>
555	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
556	>	oneTwoInteractions_.removePair(a, b);
557	>	} else {
558	>	excludedInteractions_.removePair(a, b);
559	>	}
560		}
561
562	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
562	>	for (bend= mol->beginBend(bendIter); bend != NULL;
563	>	bend = mol->nextBend(bendIter)) {
564	>
565		a = bend->getAtomA()->getGlobalIndex();
566		b = bend->getAtomB()->getGlobalIndex();
567		c = bend->getAtomC()->getGlobalIndex();
509	–
510	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
511	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
512	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
513	–
514	–	exclude_.removePairs(rigidSetA, rigidSetB);
515	–	exclude_.removePairs(rigidSetA, rigidSetC);
516	–	exclude_.removePairs(rigidSetB, rigidSetC);
568
569	<	//exclude_.removePair(a, b);
570	<	//exclude_.removePair(a, c);
571	<	//exclude_.removePair(b, c);
569	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
570	>	oneTwoInteractions_.removePair(a, b);
571	>	oneTwoInteractions_.removePair(b, c);
572	>	} else {
573	>	excludedInteractions_.removePair(a, b);
574	>	excludedInteractions_.removePair(b, c);
575	>	}
576	>
577	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
578	>	oneThreeInteractions_.removePair(a, c);
579	>	} else {
580	>	excludedInteractions_.removePair(a, c);
581	>	}
582		}
583
584	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
584	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
585	>	torsion = mol->nextTorsion(torsionIter)) {
586	>
587		a = torsion->getAtomA()->getGlobalIndex();
588		b = torsion->getAtomB()->getGlobalIndex();
589		c = torsion->getAtomC()->getGlobalIndex();
590	<	d = torsion->getAtomD()->getGlobalIndex();
590	>	d = torsion->getAtomD()->getGlobalIndex();
591	>
592	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
593	>	oneTwoInteractions_.removePair(a, b);
594	>	oneTwoInteractions_.removePair(b, c);
595	>	oneTwoInteractions_.removePair(c, d);
596	>	} else {
597	>	excludedInteractions_.removePair(a, b);
598	>	excludedInteractions_.removePair(b, c);
599	>	excludedInteractions_.removePair(c, d);
600	>	}
601
602	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
603	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
604	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
605	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
602	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
603	>	oneThreeInteractions_.removePair(a, c);
604	>	oneThreeInteractions_.removePair(b, d);
605	>	} else {
606	>	excludedInteractions_.removePair(a, c);
607	>	excludedInteractions_.removePair(b, d);
608	>	}
609
610	<	exclude_.removePairs(rigidSetA, rigidSetB);
611	<	exclude_.removePairs(rigidSetA, rigidSetC);
612	<	exclude_.removePairs(rigidSetA, rigidSetD);
613	<	exclude_.removePairs(rigidSetB, rigidSetC);
614	<	exclude_.removePairs(rigidSetB, rigidSetD);
615	<	exclude_.removePairs(rigidSetC, rigidSetD);
610	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
611	>	oneFourInteractions_.removePair(a, d);
612	>	} else {
613	>	excludedInteractions_.removePair(a, d);
614	>	}
615	>	}
616
617	<	/*
618	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
543	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
544	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
545	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
546	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
547	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
617	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
618	>	inversion = mol->nextInversion(inversionIter)) {
619
620	<
621	<	exclude_.removePair(a, b);
622	<	exclude_.removePair(a, c);
623	<	exclude_.removePair(a, d);
624	<	exclude_.removePair(b, c);
625	<	exclude_.removePair(b, d);
626	<	exclude_.removePair(c, d);
627	<	*/
620	>	a = inversion->getAtomA()->getGlobalIndex();
621	>	b = inversion->getAtomB()->getGlobalIndex();
622	>	c = inversion->getAtomC()->getGlobalIndex();
623	>	d = inversion->getAtomD()->getGlobalIndex();
624	>
625	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
626	>	oneTwoInteractions_.removePair(a, b);
627	>	oneTwoInteractions_.removePair(a, c);
628	>	oneTwoInteractions_.removePair(a, d);
629	>	} else {
630	>	excludedInteractions_.removePair(a, b);
631	>	excludedInteractions_.removePair(a, c);
632	>	excludedInteractions_.removePair(a, d);
633	>	}
634	>
635	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
636	>	oneThreeInteractions_.removePair(b, c);
637	>	oneThreeInteractions_.removePair(b, d);
638	>	oneThreeInteractions_.removePair(c, d);
639	>	} else {
640	>	excludedInteractions_.removePair(b, c);
641	>	excludedInteractions_.removePair(b, d);
642	>	excludedInteractions_.removePair(c, d);
643	>	}
644		}
645
646	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
647	<	std::vector<Atom*> atoms = rb->getAtoms();
648	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
649	<	for (int j = i + 1; j < atoms.size(); ++j) {
646	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
647	>	rb = mol->nextRigidBody(rbIter)) {
648	>	vector<Atom*> atoms = rb->getAtoms();
649	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
650	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
651		a = atoms[i]->getGlobalIndex();
652		b = atoms[j]->getGlobalIndex();
653	<	exclude_.removePair(a, b);
653	>	excludedInteractions_.removePair(a, b);
654		}
655		}
656		}
657	<
657	>
658		}
659	<
660	<
659	>
660	>
661		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
662		int curStampId;
663	<
663	>
664		//index from 0
665		curStampId = moleculeStamps_.size();
666
#	Line 580 | Line 668 | namespace oopse {
668		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
669		}
670
583	–	void SimInfo::update() {
671
672	<	setupSimType();
673	<
674	<	#ifdef IS_MPI
675	<	setupFortranParallel();
676	<	#endif
677	<
678	<	setupFortranSim();
679	<
680	<	//setup fortran force field
594	<	/** @deprecate */
595	<	int isError = 0;
596	<
597	<	setupElectrostaticSummationMethod( isError );
598	<	setupSwitchingFunction();
599	<
600	<	if(isError){
601	<	sprintf( painCave.errMsg,
602	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
603	<	painCave.isFatal = 1;
604	<	simError();
605	<	}
606	<
607	<
608	<	setupCutoff();
609	<
672	>	/**
673	>	* update
674	>	*
675	>	*  Performs the global checks and variable settings after the
676	>	*  objects have been created.
677	>	*
678	>	*/
679	>	void SimInfo::update() {
680	>	setupSimVariables();
681		calcNdf();
682		calcNdfRaw();
683		calcNdfTrans();
613	–
614	–	fortranInitialized_ = true;
684		}
685	<
686	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
685	>
686	>	/**
687	>	* getSimulatedAtomTypes
688	>	*
689	>	* Returns an STL set of AtomType* that are actually present in this
690	>	* simulation.  Must query all processors to assemble this information.
691	>	*
692	>	*/
693	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
694		SimInfo::MoleculeIterator mi;
695		Molecule* mol;
696		Molecule::AtomIterator ai;
697		Atom* atom;
698	<	std::set<AtomType*> atomTypes;
699	<
698	>	set<AtomType*> atomTypes;
699	>
700		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
701	<
702	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
701	>	for(atom = mol->beginAtom(ai); atom != NULL;
702	>	atom = mol->nextAtom(ai)) {
703		atomTypes.insert(atom->getAtomType());
704	<	}
705	<
706	<	}
704	>	}
705	>	}
706	>
707	>	#ifdef IS_MPI
708
709	<	return atomTypes;
710	<	}
634	<
635	<	void SimInfo::setupSimType() {
636	<	std::set<AtomType*>::iterator i;
637	<	std::set<AtomType*> atomTypes;
638	<	atomTypes = getUniqueAtomTypes();
709	>	// loop over the found atom types on this processor, and add their
710	>	// numerical idents to a vector:
711
712	<	int useLennardJones = 0;
713	<	int useElectrostatic = 0;
714	<	int useEAM = 0;
715	<	int useSC = 0;
644	<	int useCharge = 0;
645	<	int useDirectional = 0;
646	<	int useDipole = 0;
647	<	int useGayBerne = 0;
648	<	int useSticky = 0;
649	<	int useStickyPower = 0;
650	<	int useShape = 0;
651	<	int useFLARB = 0; //it is not in AtomType yet
652	<	int useDirectionalAtom = 0;
653	<	int useElectrostatics = 0;
654	<	//usePBC and useRF are from simParams
655	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
656	<	int useRF;
657	<	int useSF;
658	<	std::string myMethod;
712	>	vector<int> foundTypes;
713	>	set<AtomType*>::iterator i;
714	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
715	>	foundTypes.push_back( (*i)->getIdent() );
716
717	<	// set the useRF logical
718	<	useRF = 0;
662	<	useSF = 0;
717	>	// count_local holds the number of found types on this processor
718	>	int count_local = foundTypes.size();
719
720	+	int nproc = MPI::COMM_WORLD.Get_size();
721
722	<	if (simParams_->haveElectrostaticSummationMethod()) {
723	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
724	<	toUpper(myMethod);
725	<	if (myMethod == "REACTION_FIELD") {
669	<	useRF=1;
670	<	} else {
671	<	if (myMethod == "SHIFTED_FORCE") {
672	<	useSF = 1;
673	<	}
674	<	}
675	<	}
722	>	// we need arrays to hold the counts and displacement vectors for
723	>	// all processors
724	>	vector<int> counts(nproc, 0);
725	>	vector<int> disps(nproc, 0);
726
727	<	//loop over all of the atom types
728	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
729	<	useLennardJones |= (*i)->isLennardJones();
730	<	useElectrostatic |= (*i)->isElectrostatic();
731	<	useEAM |= (*i)->isEAM();
732	<	useSC |= (*i)->isSC();
733	<	useCharge |= (*i)->isCharge();
734	<	useDirectional |= (*i)->isDirectional();
735	<	useDipole |= (*i)->isDipole();
736	<	useGayBerne |= (*i)->isGayBerne();
687	<	useSticky |= (*i)->isSticky();
688	<	useStickyPower |= (*i)->isStickyPower();
689	<	useShape |= (*i)->isShape();
727	>	// fill the counts array
728	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
729	>	1, MPI::INT);
730	>
731	>	// use the processor counts to compute the displacement array
732	>	disps[0] = 0;
733	>	int totalCount = counts[0];
734	>	for (int iproc = 1; iproc < nproc; iproc++) {
735	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
736	>	totalCount += counts[iproc];
737		}
738
739	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
740	<	useDirectionalAtom = 1;
741	<	}
739	>	// we need a (possibly redundant) set of all found types:
740	>	vector<int> ftGlobal(totalCount);
741	>
742	>	// now spray out the foundTypes to all the other processors:
743	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
744	>	&ftGlobal[0], &counts[0], &disps[0],
745	>	MPI::INT);
746
747	<	if (useCharge || useDipole) {
697	<	useElectrostatics = 1;
698	<	}
747	>	vector<int>::iterator j;
748
749	<	#ifdef IS_MPI
750	<	int temp;
749	>	// foundIdents is a stl set, so inserting an already found ident
750	>	// will have no effect.
751	>	set<int> foundIdents;
752
753	<	temp = usePBC;
754	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
753	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
754	>	foundIdents.insert((*j));
755	>
756	>	// now iterate over the foundIdents and get the actual atom types
757	>	// that correspond to these:
758	>	set<int>::iterator it;
759	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
760	>	atomTypes.insert( forceField_->getAtomType((*it)) );
761	>
762	>	#endif
763
764	<	temp = useDirectionalAtom;
765	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
764	>	return atomTypes;
765	>	}
766
767	<	temp = useLennardJones;
768	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769	<
770	<	temp = useElectrostatics;
771	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
772	<
773	<	temp = useCharge;
774	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
717	<
718	<	temp = useDipole;
719	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
720	<
721	<	temp = useSticky;
722	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
723	<
724	<	temp = useStickyPower;
725	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767	>	void SimInfo::setupSimVariables() {
768	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
769	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
770	>	calcBoxDipole_ = false;
771	>	if ( simParams_->haveAccumulateBoxDipole() )
772	>	if ( simParams_->getAccumulateBoxDipole() ) {
773	>	calcBoxDipole_ = true;
774	>	}
775
776	<	temp = useGayBerne;
777	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776	>	set<AtomType*>::iterator i;
777	>	set<AtomType*> atomTypes;
778	>	atomTypes = getSimulatedAtomTypes();
779	>	int usesElectrostatic = 0;
780	>	int usesMetallic = 0;
781	>	int usesDirectional = 0;
782	>	//loop over all of the atom types
783	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
784	>	usesElectrostatic |= (*i)->isElectrostatic();
785	>	usesMetallic |= (*i)->isMetal();
786	>	usesDirectional |= (*i)->isDirectional();
787	>	}
788	>
789	>	#ifdef IS_MPI
790	>	int temp;
791	>	temp = usesDirectional;
792	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
793	>
794	>	temp = usesMetallic;
795	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
796	>
797	>	temp = usesElectrostatic;
798	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
799	>	#else
800
801	<	temp = useEAM;
802	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
801	>	usesDirectionalAtoms_ = usesDirectional;
802	>	usesMetallicAtoms_ = usesMetallic;
803	>	usesElectrostaticAtoms_ = usesElectrostatic;
804
805	<	temp = useSC;
734	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
805	>	#endif
806
807	<	temp = useShape;
808	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
807	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
808	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
809	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
810	>	}
811
739	–	temp = useFLARB;
740	–	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
812
813	<	temp = useRF;
814	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813	>	vector<int> SimInfo::getGlobalAtomIndices() {
814	>	SimInfo::MoleculeIterator mi;
815	>	Molecule* mol;
816	>	Molecule::AtomIterator ai;
817	>	Atom* atom;
818
819	<	temp = useSF;
820	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
820	>
821	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
822	>
823	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
824	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
825	>	}
826	>	}
827	>	return GlobalAtomIndices;
828	>	}
829
748	–	#endif
830
831	<	fInfo_.SIM_uses_PBC = usePBC;
832	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
833	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
834	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
835	<	fInfo_.SIM_uses_Charges = useCharge;
755	<	fInfo_.SIM_uses_Dipoles = useDipole;
756	<	fInfo_.SIM_uses_Sticky = useSticky;
757	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
758	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
759	<	fInfo_.SIM_uses_EAM = useEAM;
760	<	fInfo_.SIM_uses_SC = useSC;
761	<	fInfo_.SIM_uses_Shapes = useShape;
762	<	fInfo_.SIM_uses_FLARB = useFLARB;
763	<	fInfo_.SIM_uses_RF = useRF;
764	<	fInfo_.SIM_uses_SF = useSF;
831	>	vector<int> SimInfo::getGlobalGroupIndices() {
832	>	SimInfo::MoleculeIterator mi;
833	>	Molecule* mol;
834	>	Molecule::CutoffGroupIterator ci;
835	>	CutoffGroup* cg;
836
837	<	if( myMethod == "REACTION_FIELD") {
837	>	vector<int> GlobalGroupIndices;
838	>
839	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
840
841	<	if (simParams_->haveDielectric()) {
842	<	fInfo_.dielect = simParams_->getDielectric();
843	<	} else {
844	<	sprintf(painCave.errMsg,
845	<	"SimSetup Error: No Dielectric constant was set.\n"
846	<	"\tYou are trying to use Reaction Field without"
774	<	"\tsetting a dielectric constant!\n");
775	<	painCave.isFatal = 1;
776	<	simError();
777	<	}
841	>	//local index of cutoff group is trivial, it only depends on the
842	>	//order of travesing
843	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
844	>	cg = mol->nextCutoffGroup(ci)) {
845	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
846	>	}
847		}
848	<
848	>	return GlobalGroupIndices;
849		}
850
782	–	void SimInfo::setupFortranSim() {
783	–	int isError;
784	–	int nExclude;
785	–	std::vector<int> fortranGlobalGroupMembership;
786	–
787	–	nExclude = exclude_.getSize();
788	–	isError = 0;
851
852	<	//globalGroupMembership_ is filled by SimCreator
853	<	for (int i = 0; i < nGlobalAtoms_; i++) {
792	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
793	<	}
852	>	void SimInfo::prepareTopology() {
853	>	int nExclude, nOneTwo, nOneThree, nOneFour;
854
855		//calculate mass ratio of cutoff group
796	–	std::vector<double> mfact;
856		SimInfo::MoleculeIterator mi;
857		Molecule* mol;
858		Molecule::CutoffGroupIterator ci;
859		CutoffGroup* cg;
860		Molecule::AtomIterator ai;
861		Atom* atom;
862	<	double totalMass;
862	>	RealType totalMass;
863
864	<	//to avoid memory reallocation, reserve enough space for mfact
865	<	mfact.reserve(getNCutoffGroups());
864	>	/**
865	>	* The mass factor is the relative mass of an atom to the total
866	>	* mass of the cutoff group it belongs to.  By default, all atoms
867	>	* are their own cutoff groups, and therefore have mass factors of
868	>	* 1.  We need some special handling for massless atoms, which
869	>	* will be treated as carrying the entire mass of the cutoff
870	>	* group.
871	>	*/
872	>	massFactors_.clear();
873	>	massFactors_.resize(getNAtoms(), 1.0);
874
875		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
876	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
876	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
877	>	cg = mol->nextCutoffGroup(ci)) {
878
879		totalMass = cg->getMass();
880		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
881		// Check for massless groups - set mfact to 1 if true
882	<	if (totalMass != 0)
883	<	mfact.push_back(atom->getMass()/totalMass);
882	>	if (totalMass != 0)
883	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
884		else
885	<	mfact.push_back( 1.0 );
885	>	massFactors_[atom->getLocalIndex()] = 1.0;
886		}
819	–
887		}
888		}
889
890	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
824	<	std::vector<int> identArray;
890	>	// Build the identArray_
891
892	<	//to avoid memory reallocation, reserve enough space identArray
893	<	identArray.reserve(getNAtoms());
828	<
892	>	identArray_.clear();
893	>	identArray_.reserve(getNAtoms());
894		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
895		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
896	<	identArray.push_back(atom->getIdent());
896	>	identArray_.push_back(atom->getIdent());
897		}
898		}
834	–
835	–	//fill molMembershipArray
836	–	//molMembershipArray is filled by SimCreator
837	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
838	–	for (int i = 0; i < nGlobalAtoms_; i++) {
839	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
840	–	}
899
900	<	//setup fortran simulation
843	<	int nGlobalExcludes = 0;
844	<	int* globalExcludes = NULL;
845	<	int* excludeList = exclude_.getExcludeList();
846	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
847	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
848	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
900	>	//scan topology
901
902	<	if( isError ){
902	>	nExclude = excludedInteractions_.getSize();
903	>	nOneTwo = oneTwoInteractions_.getSize();
904	>	nOneThree = oneThreeInteractions_.getSize();
905	>	nOneFour = oneFourInteractions_.getSize();
906
907	<	sprintf( painCave.errMsg,
908	<	"There was an error setting the simulation information in fortran.\n" );
909	<	painCave.isFatal = 1;
910	<	painCave.severity = OOPSE_ERROR;
856	<	simError();
857	<	}
858	<
859	<	#ifdef IS_MPI
860	<	sprintf( checkPointMsg,
861	<	"succesfully sent the simulation information to fortran.\n");
862	<	MPIcheckPoint();
863	<	#endif // is_mpi
864	<	}
865	<
866	<
867	<	#ifdef IS_MPI
868	<	void SimInfo::setupFortranParallel() {
869	<
870	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
871	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
872	<	std::vector<int> localToGlobalCutoffGroupIndex;
873	<	SimInfo::MoleculeIterator mi;
874	<	Molecule::AtomIterator ai;
875	<	Molecule::CutoffGroupIterator ci;
876	<	Molecule* mol;
877	<	Atom* atom;
878	<	CutoffGroup* cg;
879	<	mpiSimData parallelData;
880	<	int isError;
881	<
882	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
883	<
884	<	//local index(index in DataStorge) of atom is important
885	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
886	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
887	<	}
888	<
889	<	//local index of cutoff group is trivial, it only depends on the order of travesing
890	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
891	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
892	<	}
893	<
894	<	}
895	<
896	<	//fill up mpiSimData struct
897	<	parallelData.nMolGlobal = getNGlobalMolecules();
898	<	parallelData.nMolLocal = getNMolecules();
899	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
900	<	parallelData.nAtomsLocal = getNAtoms();
901	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
902	<	parallelData.nGroupsLocal = getNCutoffGroups();
903	<	parallelData.myNode = worldRank;
904	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
905	<
906	<	//pass mpiSimData struct and index arrays to fortran
907	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
908	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
909	<	&localToGlobalCutoffGroupIndex[0], &isError);
910	<
911	<	if (isError) {
912	<	sprintf(painCave.errMsg,
913	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
914	<	painCave.isFatal = 1;
915	<	simError();
916	<	}
917	<
918	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
919	<	MPIcheckPoint();
920	<
921	<
922	<	}
923	<
924	<	#endif
925	<
926	<	double SimInfo::calcMaxCutoffRadius() {
927	<
928	<
929	<	std::set<AtomType*> atomTypes;
930	<	std::set<AtomType*>::iterator i;
931	<	std::vector<double> cutoffRadius;
932	<
933	<	//get the unique atom types
934	<	atomTypes = getUniqueAtomTypes();
935	<
936	<	//query the max cutoff radius among these atom types
937	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
938	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
939	<	}
940	<
941	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
942	<	#ifdef IS_MPI
943	<	//pick the max cutoff radius among the processors
944	<	#endif
945	<
946	<	return maxCutoffRadius;
947	<	}
948	<
949	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
950	<
951	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
952	<
953	<	if (!simParams_->haveCutoffRadius()){
954	<	sprintf(painCave.errMsg,
955	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
956	<	"\tOOPSE will use a default value of 15.0 angstroms"
957	<	"\tfor the cutoffRadius.\n");
958	<	painCave.isFatal = 0;
959	<	simError();
960	<	rcut = 15.0;
961	<	} else{
962	<	rcut = simParams_->getCutoffRadius();
963	<	}
964	<
965	<	if (!simParams_->haveSwitchingRadius()){
966	<	sprintf(painCave.errMsg,
967	<	"SimCreator Warning: No value was set for switchingRadius.\n"
968	<	"\tOOPSE will use a default value of\n"
969	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
970	<	painCave.isFatal = 0;
971	<	simError();
972	<	rsw = 0.85 * rcut;
973	<	} else{
974	<	rsw = simParams_->getSwitchingRadius();
975	<	}
976	<
977	<	} else {
978	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
979	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
980	<
981	<	if (simParams_->haveCutoffRadius()) {
982	<	rcut = simParams_->getCutoffRadius();
983	<	} else {
984	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
985	<	rcut = calcMaxCutoffRadius();
986	<	}
987	<
988	<	if (simParams_->haveSwitchingRadius()) {
989	<	rsw  = simParams_->getSwitchingRadius();
990	<	} else {
991	<	rsw = rcut;
992	<	}
993	<
994	<	}
995	<	}
996	<
997	<	void SimInfo::setupCutoff() {
998	<	getCutoff(rcut_, rsw_);
999	<	double rnblist = rcut_ + 1; // skin of neighbor list
1000	<
1001	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1002	<
1003	<	int cp =  TRADITIONAL_CUTOFF_POLICY;
1004	<	if (simParams_->haveCutoffPolicy()) {
1005	<	std::string myPolicy = simParams_->getCutoffPolicy();
1006	<	toUpper(myPolicy);
1007	<	if (myPolicy == "MIX") {
1008	<	cp = MIX_CUTOFF_POLICY;
1009	<	} else {
1010	<	if (myPolicy == "MAX") {
1011	<	cp = MAX_CUTOFF_POLICY;
1012	<	} else {
1013	<	if (myPolicy == "TRADITIONAL") {
1014	<	cp = TRADITIONAL_CUTOFF_POLICY;
1015	<	} else {
1016	<	// throw error
1017	<	sprintf( painCave.errMsg,
1018	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1019	<	painCave.isFatal = 1;
1020	<	simError();
1021	<	}
1022	<	}
1023	<	}
1024	<	}
1025	<
1026	<
1027	<	if (simParams_->haveSkinThickness()) {
1028	<	double skinThickness = simParams_->getSkinThickness();
1029	<	}
1030	<
1031	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1032	<	// also send cutoff notification to electrostatics
1033	<	setElectrostaticCutoffRadius(&rcut_, &rsw_);
1034	<	}
1035	<
1036	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1037	<
1038	<	int errorOut;
1039	<	int esm =  NONE;
1040	<	int sm = UNDAMPED;
1041	<	double alphaVal;
1042	<	double dielectric;
1043	<
1044	<	errorOut = isError;
1045	<	alphaVal = simParams_->getDampingAlpha();
1046	<	dielectric = simParams_->getDielectric();
1047	<
1048	<	if (simParams_->haveElectrostaticSummationMethod()) {
1049	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1050	<	toUpper(myMethod);
1051	<	if (myMethod == "NONE") {
1052	<	esm = NONE;
1053	<	} else {
1054	<	if (myMethod == "SWITCHING_FUNCTION") {
1055	<	esm = SWITCHING_FUNCTION;
1056	<	} else {
1057	<	if (myMethod == "SHIFTED_POTENTIAL") {
1058	<	esm = SHIFTED_POTENTIAL;
1059	<	} else {
1060	<	if (myMethod == "SHIFTED_FORCE") {
1061	<	esm = SHIFTED_FORCE;
1062	<	} else {
1063	<	if (myMethod == "REACTION_FIELD") {
1064	<	esm = REACTION_FIELD;
1065	<	} else {
1066	<	// throw error
1067	<	sprintf( painCave.errMsg,
1068	<	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() );
1069	<	painCave.isFatal = 1;
1070	<	simError();
1071	<	}
1072	<	}
1073	<	}
1074	<	}
1075	<	}
1076	<	}
1077	<
1078	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1079	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1080	<	toUpper(myScreen);
1081	<	if (myScreen == "UNDAMPED") {
1082	<	sm = UNDAMPED;
1083	<	} else {
1084	<	if (myScreen == "DAMPED") {
1085	<	sm = DAMPED;
1086	<	if (!simParams_->haveDampingAlpha()) {
1087	<	//throw error
1088	<	sprintf( painCave.errMsg,
1089	<	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
1090	<	painCave.isFatal = 0;
1091	<	simError();
1092	<	}
1093	<	} else {
1094	<	// throw error
1095	<	sprintf( painCave.errMsg,
1096	<	"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
1097	<	painCave.isFatal = 1;
1098	<	simError();
1099	<	}
1100	<	}
1101	<	}
1102	<
1103	<	// let's pass some summation method variables to fortran
1104	<	setElectrostaticSummationMethod( &esm );
1105	<	setScreeningMethod( &sm );
1106	<	setDampingAlpha( &alphaVal );
1107	<	setReactionFieldDielectric( &dielectric );
1108	<	initFortranFF( &esm, &errorOut );
1109	<	}
907	>	int* excludeList = excludedInteractions_.getPairList();
908	>	int* oneTwoList = oneTwoInteractions_.getPairList();
909	>	int* oneThreeList = oneThreeInteractions_.getPairList();
910	>	int* oneFourList = oneFourInteractions_.getPairList();
911
912	<	void SimInfo::setupSwitchingFunction() {
1112	<	int ft = CUBIC;
1113	<
1114	<	if (simParams_->haveSwitchingFunctionType()) {
1115	<	std::string funcType = simParams_->getSwitchingFunctionType();
1116	<	toUpper(funcType);
1117	<	if (funcType == "CUBIC") {
1118	<	ft = CUBIC;
1119	<	} else {
1120	<	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1121	<	ft = FIFTH_ORDER_POLY;
1122	<	} else {
1123	<	// throw error
1124	<	sprintf( painCave.errMsg,
1125	<	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1126	<	painCave.isFatal = 1;
1127	<	simError();
1128	<	}
1129	<	}
1130	<	}
1131	<
1132	<	// send switching function notification to switcheroo
1133	<	setFunctionType(&ft);
1134	<
912	>	topologyDone_ = true;
913		}
914
915		void SimInfo::addProperty(GenericData* genData) {
916		properties_.addProperty(genData);
917		}
918
919	<	void SimInfo::removeProperty(const std::string& propName) {
919	>	void SimInfo::removeProperty(const string& propName) {
920		properties_.removeProperty(propName);
921		}
922
#	Line 1146 | Line 924 | namespace oopse {
924		properties_.clearProperties();
925		}
926
927	<	std::vector<std::string> SimInfo::getPropertyNames() {
927	>	vector<string> SimInfo::getPropertyNames() {
928		return properties_.getPropertyNames();
929		}
930
931	<	std::vector<GenericData*> SimInfo::getProperties() {
931	>	vector<GenericData*> SimInfo::getProperties() {
932		return properties_.getProperties();
933		}
934
935	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
935	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
936		return properties_.getPropertyByName(propName);
937		}
938
#	Line 1168 | Line 946 | namespace oopse {
946		Molecule* mol;
947		RigidBody* rb;
948		Atom* atom;
949	+	CutoffGroup* cg;
950		SimInfo::MoleculeIterator mi;
951		Molecule::RigidBodyIterator rbIter;
952	<	Molecule::AtomIterator atomIter;;
952	>	Molecule::AtomIterator atomIter;
953	>	Molecule::CutoffGroupIterator cgIter;
954
955		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
956
#	Line 1181 | Line 961 | namespace oopse {
961		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
962		rb->setSnapshotManager(sman_);
963		}
964	+
965	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
966	+	cg->setSnapshotManager(sman_);
967	+	}
968		}
969
970		}
#	Line 1190 | Line 974 | namespace oopse {
974		Molecule* mol;
975
976		Vector3d comVel(0.0);
977	<	double totalMass = 0.0;
977	>	RealType totalMass = 0.0;
978
979
980		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
981	<	double mass = mol->getMass();
981	>	RealType mass = mol->getMass();
982		totalMass += mass;
983		comVel += mass * mol->getComVel();
984		}
985
986		#ifdef IS_MPI
987	<	double tmpMass = totalMass;
987	>	RealType tmpMass = totalMass;
988		Vector3d tmpComVel(comVel);
989	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
990	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
989	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
990	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
991		#endif
992
993		comVel /= totalMass;
#	Line 1216 | Line 1000 | namespace oopse {
1000		Molecule* mol;
1001
1002		Vector3d com(0.0);
1003	<	double totalMass = 0.0;
1003	>	RealType totalMass = 0.0;
1004
1005		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1006	<	double mass = mol->getMass();
1006	>	RealType mass = mol->getMass();
1007		totalMass += mass;
1008		com += mass * mol->getCom();
1009		}
1010
1011		#ifdef IS_MPI
1012	<	double tmpMass = totalMass;
1012	>	RealType tmpMass = totalMass;
1013		Vector3d tmpCom(com);
1014	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1015	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1014	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1015	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1016		#endif
1017
1018		com /= totalMass;
#	Line 1237 | Line 1021 | namespace oopse {
1021
1022		}
1023
1024	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1024	>	ostream& operator <<(ostream& o, SimInfo& info) {
1025
1026		return o;
1027		}
#	Line 1252 | Line 1036 | namespace oopse {
1036		Molecule* mol;
1037
1038
1039	<	double totalMass = 0.0;
1039	>	RealType totalMass = 0.0;
1040
1041
1042		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1043	<	double mass = mol->getMass();
1043	>	RealType mass = mol->getMass();
1044		totalMass += mass;
1045		com += mass * mol->getCom();
1046		comVel += mass * mol->getComVel();
1047		}
1048
1049		#ifdef IS_MPI
1050	<	double tmpMass = totalMass;
1050	>	RealType tmpMass = totalMass;
1051		Vector3d tmpCom(com);
1052		Vector3d tmpComVel(comVel);
1053	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1054	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1055	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1053	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1054	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1055	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1056		#endif
1057
1058		com /= totalMass;
#	Line 1280 | Line 1064 | namespace oopse {
1064
1065
1066		[  Ixx -Ixy  -Ixz ]
1067	<	J =| -Iyx  Iyy  -Iyz |
1067	>	J =| -Iyx  Iyy  -Iyz |
1068		[ -Izx -Iyz   Izz ]
1069		*/
1070
1071		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1072
1073
1074	<	double xx = 0.0;
1075	<	double yy = 0.0;
1076	<	double zz = 0.0;
1077	<	double xy = 0.0;
1078	<	double xz = 0.0;
1079	<	double yz = 0.0;
1074	>	RealType xx = 0.0;
1075	>	RealType yy = 0.0;
1076	>	RealType zz = 0.0;
1077	>	RealType xy = 0.0;
1078	>	RealType xz = 0.0;
1079	>	RealType yz = 0.0;
1080		Vector3d com(0.0);
1081		Vector3d comVel(0.0);
1082
#	Line 1304 | Line 1088 | namespace oopse {
1088		Vector3d thisq(0.0);
1089		Vector3d thisv(0.0);
1090
1091	<	double thisMass = 0.0;
1091	>	RealType thisMass = 0.0;
1092
1093
1094
#	Line 1342 | Line 1126 | namespace oopse {
1126		#ifdef IS_MPI
1127		Mat3x3d tmpI(inertiaTensor);
1128		Vector3d tmpAngMom;
1129	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1130	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1129	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1130	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1131		#endif
1132
1133		return;
#	Line 1364 | Line 1148 | namespace oopse {
1148		Vector3d thisr(0.0);
1149		Vector3d thisp(0.0);
1150
1151	<	double thisMass;
1151	>	RealType thisMass;
1152
1153		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1154		thisMass = mol->getMass();
#	Line 1377 | Line 1161 | namespace oopse {
1161
1162		#ifdef IS_MPI
1163		Vector3d tmpAngMom;
1164	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1164	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1165		#endif
1166
1167		return angularMomentum;
1168		}
1169
1170	<
1171	<	}//end namespace oopse
1170	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1171	>	return IOIndexToIntegrableObject.at(index);
1172	>	}
1173	>
1174	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1175	>	IOIndexToIntegrableObject= v;
1176	>	}
1177
1178	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1179	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1180	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1181	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1182	+	*/
1183	+	void SimInfo::getGyrationalVolume(RealType &volume){
1184	+	Mat3x3d intTensor;
1185	+	RealType det;
1186	+	Vector3d dummyAngMom;
1187	+	RealType sysconstants;
1188	+	RealType geomCnst;
1189	+
1190	+	geomCnst = 3.0/2.0;
1191	+	/* Get the inertial tensor and angular momentum for free*/
1192	+	getInertiaTensor(intTensor,dummyAngMom);
1193	+
1194	+	det = intTensor.determinant();
1195	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1196	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1197	+	return;
1198	+	}
1199	+
1200	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1201	+	Mat3x3d intTensor;
1202	+	Vector3d dummyAngMom;
1203	+	RealType sysconstants;
1204	+	RealType geomCnst;
1205	+
1206	+	geomCnst = 3.0/2.0;
1207	+	/* Get the inertial tensor and angular momentum for free*/
1208	+	getInertiaTensor(intTensor,dummyAngMom);
1209	+
1210	+	detI = intTensor.determinant();
1211	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1212	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1213	+	return;
1214	+	}
1215	+	/*
1216	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1217	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1218	+	sdByGlobalIndex_ = v;
1219	+	}
1220	+
1221	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1222	+	//assert(index < nAtoms_ + nRigidBodies_);
1223	+	return sdByGlobalIndex_.at(index);
1224	+	}
1225	+	*/
1226	+	int SimInfo::getNGlobalConstraints() {
1227	+	int nGlobalConstraints;
1228	+	#ifdef IS_MPI
1229	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1230	+	MPI_COMM_WORLD);
1231	+	#else
1232	+	nGlobalConstraints =  nConstraints_;
1233	+	#endif
1234	+	return nGlobalConstraints;
1235	+	}
1236	+
1237	+	}//end namespace OpenMD
1238	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 749 by tim, Wed Nov 16 23:10:02 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC

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