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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 879 by chrisfen, Wed Feb 1 21:06:43 2006 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1577 by gezelter, Wed Jun 8 20:26:56 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), topologyDone_(false),
75	>	calcBoxDipole_(false), useAtomicVirial_(true) {
76	>
77	>	MoleculeStamp* molStamp;
78	>	int nMolWithSameStamp;
79	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
80	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
81	>	CutoffGroupStamp* cgStamp;
82	>	RigidBodyStamp* rbStamp;
83	>	int nRigidAtoms = 0;
84	>
85	>	vector<Component*> components = simParams->getComponents();
86	>
87	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
88	>	molStamp = (*i)->getMoleculeStamp();
89	>	nMolWithSameStamp = (*i)->getNMol();
90
91	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
92	<	molStamp = (*i)->getMoleculeStamp();
93	<	nMolWithSameStamp = (*i)->getNMol();
94	<
95	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
96	<
97	<	//calculate atoms in molecules
98	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
99	<
100	<	//calculate atoms in cutoff groups
101	<	int nAtomsInGroups = 0;
102	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
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	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
106	<	//group therefore the total number of cutoff groups in the system is
107	<	//equal to the total number of atoms minus number of atoms belong to
108	<	//cutoff group defined in meta-data file plus the number of cutoff
109	<	//groups defined in meta-data file
110	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
111	<
112	<	//every free atom (atom does not belong to rigid bodies) is an
113	<	//integrable object therefore the total number of integrable objects
114	<	//in the system is equal to the total number of atoms minus number of
115	<	//atoms belong to rigid body defined in meta-data file plus the number
116	<	//of rigid bodies defined in meta-data file
117	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
118	<	+ nGlobalRigidBodies_;
119	<
120	<	nGlobalMols_ = molStampIds_.size();
155	<
156	<	#ifdef IS_MPI
157	<	molToProcMap_.resize(nGlobalMols_);
158	<	#endif
159	<
104	>
105	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
106	>
107	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
108	>
109	>	//calculate atoms in rigid bodies
110	>	int nAtomsInRigidBodies = 0;
111	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
112	>
113	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
114	>	rbStamp = molStamp->getRigidBodyStamp(j);
115	>	nAtomsInRigidBodies += rbStamp->getNMembers();
116	>	}
117	>
118	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
119	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
120	>
121		}
122	+
123	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
124	+	//group therefore the total number of cutoff groups in the system is
125	+	//equal to the total number of atoms minus number of atoms belong to
126	+	//cutoff group defined in meta-data file plus the number of cutoff
127	+	//groups defined in meta-data file
128
129	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
130	+
131	+	//every free atom (atom does not belong to rigid bodies) is an
132	+	//integrable object therefore the total number of integrable objects
133	+	//in the system is equal to the total number of atoms minus number of
134	+	//atoms belong to rigid body defined in meta-data file plus the number
135	+	//of rigid bodies defined in meta-data file
136	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
137	+	+ nGlobalRigidBodies_;
138	+
139	+	nGlobalMols_ = molStampIds_.size();
140	+	molToProcMap_.resize(nGlobalMols_);
141	+	}
142	+
143		SimInfo::~SimInfo() {
144	<	std::map<int, Molecule*>::iterator i;
144	>	map<int, Molecule*>::iterator i;
145		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
146		delete i->second;
147		}
#	Line 171 | Line 152 | namespace oopse {
152		delete forceField_;
153		}
154
174	–	int SimInfo::getNGlobalConstraints() {
175	–	int nGlobalConstraints;
176	–	#ifdef IS_MPI
177	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
178	–	MPI_COMM_WORLD);
179	–	#else
180	–	nGlobalConstraints =  nConstraints_;
181	–	#endif
182	–	return nGlobalConstraints;
183	–	}
155
156		bool SimInfo::addMolecule(Molecule* mol) {
157		MoleculeIterator i;
158	<
158	>
159		i = molecules_.find(mol->getGlobalIndex());
160		if (i == molecules_.end() ) {
161	<
162	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
163	<
161	>
162	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
163	>
164		nAtoms_ += mol->getNAtoms();
165		nBonds_ += mol->getNBonds();
166		nBends_ += mol->getNBends();
167		nTorsions_ += mol->getNTorsions();
168	+	nInversions_ += mol->getNInversions();
169		nRigidBodies_ += mol->getNRigidBodies();
170		nIntegrableObjects_ += mol->getNIntegrableObjects();
171		nCutoffGroups_ += mol->getNCutoffGroups();
172		nConstraints_ += mol->getNConstraintPairs();
173	<
174	<	addExcludePairs(mol);
175	<
173	>
174	>	addInteractionPairs(mol);
175	>
176		return true;
177		} else {
178		return false;
179		}
180		}
181	<
181	>
182		bool SimInfo::removeMolecule(Molecule* mol) {
183		MoleculeIterator i;
184		i = molecules_.find(mol->getGlobalIndex());
#	Line 219 | Line 191 | namespace oopse {
191		nBonds_ -= mol->getNBonds();
192		nBends_ -= mol->getNBends();
193		nTorsions_ -= mol->getNTorsions();
194	+	nInversions_ -= mol->getNInversions();
195		nRigidBodies_ -= mol->getNRigidBodies();
196		nIntegrableObjects_ -= mol->getNIntegrableObjects();
197		nCutoffGroups_ -= mol->getNCutoffGroups();
198		nConstraints_ -= mol->getNConstraintPairs();
199
200	<	removeExcludePairs(mol);
200	>	removeInteractionPairs(mol);
201		molecules_.erase(mol->getGlobalIndex());
202
203		delete mol;
#	Line 233 | Line 206 | namespace oopse {
206		} else {
207		return false;
208		}
236	–
237	–
209		}
210
211
#	Line 252 | Line 223 | namespace oopse {
223		void SimInfo::calcNdf() {
224		int ndf_local;
225		MoleculeIterator i;
226	<	std::vector<StuntDouble*>::iterator j;
226	>	vector<StuntDouble*>::iterator j;
227		Molecule* mol;
228		StuntDouble* integrableObject;
229
#	Line 290 | Line 261 | namespace oopse {
261
262		}
263
264	+	int SimInfo::getFdf() {
265	+	#ifdef IS_MPI
266	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
267	+	#else
268	+	fdf_ = fdf_local;
269	+	#endif
270	+	return fdf_;
271	+	}
272	+
273	+	unsigned int SimInfo::getNLocalCutoffGroups(){
274	+	int nLocalCutoffAtoms = 0;
275	+	Molecule* mol;
276	+	MoleculeIterator mi;
277	+	CutoffGroup* cg;
278	+	Molecule::CutoffGroupIterator ci;
279	+
280	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
281	+
282	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
283	+	cg = mol->nextCutoffGroup(ci)) {
284	+	nLocalCutoffAtoms += cg->getNumAtom();
285	+
286	+	}
287	+	}
288	+
289	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
290	+	}
291	+
292		void SimInfo::calcNdfRaw() {
293		int ndfRaw_local;
294
295		MoleculeIterator i;
296	<	std::vector<StuntDouble*>::iterator j;
296	>	vector<StuntDouble*>::iterator j;
297		Molecule* mol;
298		StuntDouble* integrableObject;
299
#	Line 341 | Line 340 | namespace oopse {
340
341		}
342
343	<	void SimInfo::addExcludePairs(Molecule* mol) {
344	<	std::vector<Bond*>::iterator bondIter;
345	<	std::vector<Bend*>::iterator bendIter;
346	<	std::vector<Torsion*>::iterator torsionIter;
343	>	void SimInfo::addInteractionPairs(Molecule* mol) {
344	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
345	>	vector<Bond*>::iterator bondIter;
346	>	vector<Bend*>::iterator bendIter;
347	>	vector<Torsion*>::iterator torsionIter;
348	>	vector<Inversion*>::iterator inversionIter;
349		Bond* bond;
350		Bend* bend;
351		Torsion* torsion;
352	+	Inversion* inversion;
353		int a;
354		int b;
355		int c;
356		int d;
357
358	<	std::map<int, std::set<int> > atomGroups;
358	>	// atomGroups can be used to add special interaction maps between
359	>	// groups of atoms that are in two separate rigid bodies.
360	>	// However, most site-site interactions between two rigid bodies
361	>	// are probably not special, just the ones between the physically
362	>	// bonded atoms.  Interactions *within* a single rigid body should
363	>	// always be excluded.  These are done at the bottom of this
364	>	// function.
365
366	+	map<int, set<int> > atomGroups;
367		Molecule::RigidBodyIterator rbIter;
368		RigidBody* rb;
369		Molecule::IntegrableObjectIterator ii;
370		StuntDouble* integrableObject;
371
372	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
373	<	integrableObject = mol->nextIntegrableObject(ii)) {
374	<
372	>	for (integrableObject = mol->beginIntegrableObject(ii);
373	>	integrableObject != NULL;
374	>	integrableObject = mol->nextIntegrableObject(ii)) {
375	>
376		if (integrableObject->isRigidBody()) {
377	<	rb = static_cast<RigidBody*>(integrableObject);
378	<	std::vector<Atom*> atoms = rb->getAtoms();
379	<	std::set<int> rigidAtoms;
380	<	for (int i = 0; i < atoms.size(); ++i) {
381	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
382	<	}
383	<	for (int i = 0; i < atoms.size(); ++i) {
384	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
385	<	}
377	>	rb = static_cast<RigidBody*>(integrableObject);
378	>	vector<Atom*> atoms = rb->getAtoms();
379	>	set<int> rigidAtoms;
380	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
381	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
382	>	}
383	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
384	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
385	>	}
386		} else {
387	<	std::set<int> oneAtomSet;
387	>	set<int> oneAtomSet;
388		oneAtomSet.insert(integrableObject->getGlobalIndex());
389	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
389	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
390		}
391		}
392	+
393	+	for (bond= mol->beginBond(bondIter); bond != NULL;
394	+	bond = mol->nextBond(bondIter)) {
395
383	–
384	–
385	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
396		a = bond->getAtomA()->getGlobalIndex();
397	<	b = bond->getAtomB()->getGlobalIndex();
398	<	exclude_.addPair(a, b);
397	>	b = bond->getAtomB()->getGlobalIndex();
398	>
399	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
400	>	oneTwoInteractions_.addPair(a, b);
401	>	} else {
402	>	excludedInteractions_.addPair(a, b);
403	>	}
404		}
405
406	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
406	>	for (bend= mol->beginBend(bendIter); bend != NULL;
407	>	bend = mol->nextBend(bendIter)) {
408	>
409		a = bend->getAtomA()->getGlobalIndex();
410		b = bend->getAtomB()->getGlobalIndex();
411		c = bend->getAtomC()->getGlobalIndex();
395	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
396	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
397	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
398	–
399	–	exclude_.addPairs(rigidSetA, rigidSetB);
400	–	exclude_.addPairs(rigidSetA, rigidSetC);
401	–	exclude_.addPairs(rigidSetB, rigidSetC);
412
413	<	//exclude_.addPair(a, b);
414	<	//exclude_.addPair(a, c);
415	<	//exclude_.addPair(b, c);
413	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
414	>	oneTwoInteractions_.addPair(a, b);
415	>	oneTwoInteractions_.addPair(b, c);
416	>	} else {
417	>	excludedInteractions_.addPair(a, b);
418	>	excludedInteractions_.addPair(b, c);
419	>	}
420	>
421	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
422	>	oneThreeInteractions_.addPair(a, c);
423	>	} else {
424	>	excludedInteractions_.addPair(a, c);
425	>	}
426		}
427
428	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
428	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
429	>	torsion = mol->nextTorsion(torsionIter)) {
430	>
431		a = torsion->getAtomA()->getGlobalIndex();
432		b = torsion->getAtomB()->getGlobalIndex();
433		c = torsion->getAtomC()->getGlobalIndex();
434	<	d = torsion->getAtomD()->getGlobalIndex();
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);
434	>	d = torsion->getAtomD()->getGlobalIndex();
435
436	<	exclude_.addPairs(rigidSetA, rigidSetB);
437	<	exclude_.addPairs(rigidSetA, rigidSetC);
438	<	exclude_.addPairs(rigidSetA, rigidSetD);
439	<	exclude_.addPairs(rigidSetB, rigidSetC);
440	<	exclude_.addPairs(rigidSetB, rigidSetD);
441	<	exclude_.addPairs(rigidSetC, rigidSetD);
436	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
437	>	oneTwoInteractions_.addPair(a, b);
438	>	oneTwoInteractions_.addPair(b, c);
439	>	oneTwoInteractions_.addPair(c, d);
440	>	} else {
441	>	excludedInteractions_.addPair(a, b);
442	>	excludedInteractions_.addPair(b, c);
443	>	excludedInteractions_.addPair(c, d);
444	>	}
445
446	<	/*
447	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
448	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
449	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
450	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
451	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
452	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
453	<
454	<
455	<	exclude_.addPair(a, b);
456	<	exclude_.addPair(a, c);
457	<	exclude_.addPair(a, d);
458	<	exclude_.addPair(b, c);
438	<	exclude_.addPair(b, d);
439	<	exclude_.addPair(c, d);
440	<	*/
446	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
447	>	oneThreeInteractions_.addPair(a, c);
448	>	oneThreeInteractions_.addPair(b, d);
449	>	} else {
450	>	excludedInteractions_.addPair(a, c);
451	>	excludedInteractions_.addPair(b, d);
452	>	}
453	>
454	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
455	>	oneFourInteractions_.addPair(a, d);
456	>	} else {
457	>	excludedInteractions_.addPair(a, d);
458	>	}
459		}
460
461	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
462	<	std::vector<Atom*> atoms = rb->getAtoms();
463	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
464	<	for (int j = i + 1; j < atoms.size(); ++j) {
461	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
462	>	inversion = mol->nextInversion(inversionIter)) {
463	>
464	>	a = inversion->getAtomA()->getGlobalIndex();
465	>	b = inversion->getAtomB()->getGlobalIndex();
466	>	c = inversion->getAtomC()->getGlobalIndex();
467	>	d = inversion->getAtomD()->getGlobalIndex();
468	>
469	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
470	>	oneTwoInteractions_.addPair(a, b);
471	>	oneTwoInteractions_.addPair(a, c);
472	>	oneTwoInteractions_.addPair(a, d);
473	>	} else {
474	>	excludedInteractions_.addPair(a, b);
475	>	excludedInteractions_.addPair(a, c);
476	>	excludedInteractions_.addPair(a, d);
477	>	}
478	>
479	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
480	>	oneThreeInteractions_.addPair(b, c);
481	>	oneThreeInteractions_.addPair(b, d);
482	>	oneThreeInteractions_.addPair(c, d);
483	>	} else {
484	>	excludedInteractions_.addPair(b, c);
485	>	excludedInteractions_.addPair(b, d);
486	>	excludedInteractions_.addPair(c, d);
487	>	}
488	>	}
489	>
490	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
491	>	rb = mol->nextRigidBody(rbIter)) {
492	>	vector<Atom*> atoms = rb->getAtoms();
493	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
494	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
495		a = atoms[i]->getGlobalIndex();
496		b = atoms[j]->getGlobalIndex();
497	<	exclude_.addPair(a, b);
497	>	excludedInteractions_.addPair(a, b);
498		}
499		}
500		}
501
502		}
503
504	<	void SimInfo::removeExcludePairs(Molecule* mol) {
505	<	std::vector<Bond*>::iterator bondIter;
506	<	std::vector<Bend*>::iterator bendIter;
507	<	std::vector<Torsion*>::iterator torsionIter;
504	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
505	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
506	>	vector<Bond*>::iterator bondIter;
507	>	vector<Bend*>::iterator bendIter;
508	>	vector<Torsion*>::iterator torsionIter;
509	>	vector<Inversion*>::iterator inversionIter;
510		Bond* bond;
511		Bend* bend;
512		Torsion* torsion;
513	+	Inversion* inversion;
514		int a;
515		int b;
516		int c;
517		int d;
518
519	<	std::map<int, std::set<int> > atomGroups;
469	<
519	>	map<int, set<int> > atomGroups;
520		Molecule::RigidBodyIterator rbIter;
521		RigidBody* rb;
522		Molecule::IntegrableObjectIterator ii;
523		StuntDouble* integrableObject;
524
525	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
526	<	integrableObject = mol->nextIntegrableObject(ii)) {
527	<
525	>	for (integrableObject = mol->beginIntegrableObject(ii);
526	>	integrableObject != NULL;
527	>	integrableObject = mol->nextIntegrableObject(ii)) {
528	>
529		if (integrableObject->isRigidBody()) {
530	<	rb = static_cast<RigidBody*>(integrableObject);
531	<	std::vector<Atom*> atoms = rb->getAtoms();
532	<	std::set<int> rigidAtoms;
533	<	for (int i = 0; i < atoms.size(); ++i) {
534	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
535	<	}
536	<	for (int i = 0; i < atoms.size(); ++i) {
537	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
538	<	}
530	>	rb = static_cast<RigidBody*>(integrableObject);
531	>	vector<Atom*> atoms = rb->getAtoms();
532	>	set<int> rigidAtoms;
533	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
534	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
535	>	}
536	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
537	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
538	>	}
539		} else {
540	<	std::set<int> oneAtomSet;
540	>	set<int> oneAtomSet;
541		oneAtomSet.insert(integrableObject->getGlobalIndex());
542	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
542	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
543		}
544		}
545
546	<
547	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
546	>	for (bond= mol->beginBond(bondIter); bond != NULL;
547	>	bond = mol->nextBond(bondIter)) {
548	>
549		a = bond->getAtomA()->getGlobalIndex();
550	<	b = bond->getAtomB()->getGlobalIndex();
551	<	exclude_.removePair(a, b);
550	>	b = bond->getAtomB()->getGlobalIndex();
551	>
552	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
553	>	oneTwoInteractions_.removePair(a, b);
554	>	} else {
555	>	excludedInteractions_.removePair(a, b);
556	>	}
557		}
558
559	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
559	>	for (bend= mol->beginBend(bendIter); bend != NULL;
560	>	bend = mol->nextBend(bendIter)) {
561	>
562		a = bend->getAtomA()->getGlobalIndex();
563		b = bend->getAtomB()->getGlobalIndex();
564		c = bend->getAtomC()->getGlobalIndex();
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);
565
566	<	//exclude_.removePair(a, b);
567	<	//exclude_.removePair(a, c);
568	<	//exclude_.removePair(b, c);
566	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
567	>	oneTwoInteractions_.removePair(a, b);
568	>	oneTwoInteractions_.removePair(b, c);
569	>	} else {
570	>	excludedInteractions_.removePair(a, b);
571	>	excludedInteractions_.removePair(b, c);
572	>	}
573	>
574	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
575	>	oneThreeInteractions_.removePair(a, c);
576	>	} else {
577	>	excludedInteractions_.removePair(a, c);
578	>	}
579		}
580
581	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
581	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
582	>	torsion = mol->nextTorsion(torsionIter)) {
583	>
584		a = torsion->getAtomA()->getGlobalIndex();
585		b = torsion->getAtomB()->getGlobalIndex();
586		c = torsion->getAtomC()->getGlobalIndex();
587	<	d = torsion->getAtomD()->getGlobalIndex();
587	>	d = torsion->getAtomD()->getGlobalIndex();
588	>
589	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
590	>	oneTwoInteractions_.removePair(a, b);
591	>	oneTwoInteractions_.removePair(b, c);
592	>	oneTwoInteractions_.removePair(c, d);
593	>	} else {
594	>	excludedInteractions_.removePair(a, b);
595	>	excludedInteractions_.removePair(b, c);
596	>	excludedInteractions_.removePair(c, d);
597	>	}
598
599	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
600	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
601	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
602	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
599	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
600	>	oneThreeInteractions_.removePair(a, c);
601	>	oneThreeInteractions_.removePair(b, d);
602	>	} else {
603	>	excludedInteractions_.removePair(a, c);
604	>	excludedInteractions_.removePair(b, d);
605	>	}
606
607	<	exclude_.removePairs(rigidSetA, rigidSetB);
608	<	exclude_.removePairs(rigidSetA, rigidSetC);
609	<	exclude_.removePairs(rigidSetA, rigidSetD);
610	<	exclude_.removePairs(rigidSetB, rigidSetC);
611	<	exclude_.removePairs(rigidSetB, rigidSetD);
612	<	exclude_.removePairs(rigidSetC, rigidSetD);
607	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
608	>	oneFourInteractions_.removePair(a, d);
609	>	} else {
610	>	excludedInteractions_.removePair(a, d);
611	>	}
612	>	}
613
614	<	/*
615	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
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());
614	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
615	>	inversion = mol->nextInversion(inversionIter)) {
616
617	<
618	<	exclude_.removePair(a, b);
619	<	exclude_.removePair(a, c);
620	<	exclude_.removePair(a, d);
621	<	exclude_.removePair(b, c);
622	<	exclude_.removePair(b, d);
623	<	exclude_.removePair(c, d);
624	<	*/
617	>	a = inversion->getAtomA()->getGlobalIndex();
618	>	b = inversion->getAtomB()->getGlobalIndex();
619	>	c = inversion->getAtomC()->getGlobalIndex();
620	>	d = inversion->getAtomD()->getGlobalIndex();
621	>
622	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
623	>	oneTwoInteractions_.removePair(a, b);
624	>	oneTwoInteractions_.removePair(a, c);
625	>	oneTwoInteractions_.removePair(a, d);
626	>	} else {
627	>	excludedInteractions_.removePair(a, b);
628	>	excludedInteractions_.removePair(a, c);
629	>	excludedInteractions_.removePair(a, d);
630	>	}
631	>
632	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
633	>	oneThreeInteractions_.removePair(b, c);
634	>	oneThreeInteractions_.removePair(b, d);
635	>	oneThreeInteractions_.removePair(c, d);
636	>	} else {
637	>	excludedInteractions_.removePair(b, c);
638	>	excludedInteractions_.removePair(b, d);
639	>	excludedInteractions_.removePair(c, d);
640	>	}
641		}
642
643	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
644	<	std::vector<Atom*> atoms = rb->getAtoms();
645	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
646	<	for (int j = i + 1; j < atoms.size(); ++j) {
643	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
644	>	rb = mol->nextRigidBody(rbIter)) {
645	>	vector<Atom*> atoms = rb->getAtoms();
646	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
647	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
648		a = atoms[i]->getGlobalIndex();
649		b = atoms[j]->getGlobalIndex();
650	<	exclude_.removePair(a, b);
650	>	excludedInteractions_.removePair(a, b);
651		}
652		}
653		}
654	<
654	>
655		}
656	<
657	<
656	>
657	>
658		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
659		int curStampId;
660	<
660	>
661		//index from 0
662		curStampId = moleculeStamps_.size();
663
#	Line 577 | Line 665 | namespace oopse {
665		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
666		}
667
580	–	void SimInfo::update() {
668
669	<	setupSimType();
670	<
671	<	#ifdef IS_MPI
672	<	setupFortranParallel();
673	<	#endif
674	<
675	<	setupFortranSim();
676	<
677	<	//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	<
669	>	/**
670	>	* update
671	>	*
672	>	*  Performs the global checks and variable settings after the
673	>	*  objects have been created.
674	>	*
675	>	*/
676	>	void SimInfo::update() {
677	>	setupSimVariables();
678		calcNdf();
679		calcNdfRaw();
680		calcNdfTrans();
610	–
611	–	fortranInitialized_ = true;
681		}
682	<
683	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
682	>
683	>	/**
684	>	* getSimulatedAtomTypes
685	>	*
686	>	* Returns an STL set of AtomType* that are actually present in this
687	>	* simulation.  Must query all processors to assemble this information.
688	>	*
689	>	*/
690	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
691		SimInfo::MoleculeIterator mi;
692		Molecule* mol;
693		Molecule::AtomIterator ai;
694		Atom* atom;
695	<	std::set<AtomType*> atomTypes;
696	<
697	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
622	<
695	>	set<AtomType*> atomTypes;
696	>
697	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
698		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
699		atomTypes.insert(atom->getAtomType());
700	<	}
701	<
627	<	}
700	>	}
701	>	}
702
703	<	return atomTypes;
630	<	}
703	>	#ifdef IS_MPI
704
705	<	void SimInfo::setupSimType() {
706	<	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;
705	>	// loop over the found atom types on this processor, and add their
706	>	// numerical idents to a vector:
707
708	<	// set the useRF logical
709	<	useRF = 0;
710	<	useSF = 0;
708	>	vector<int> foundTypes;
709	>	set<AtomType*>::iterator i;
710	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
711	>	foundTypes.push_back( (*i)->getIdent() );
712
713	+	// count_local holds the number of found types on this processor
714	+	int count_local = foundTypes.size();
715
716	<	if (simParams_->haveElectrostaticSummationMethod()) {
717	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
718	<	toUpper(myMethod);
719	<	if (myMethod == "REACTION_FIELD") {
666	<	useRF=1;
667	<	} else {
668	<	if (myMethod == "SHIFTED_FORCE") {
669	<	useSF = 1;
670	<	}
671	<	}
672	<	}
716	>	// count holds the total number of found types on all processors
717	>	// (some will be redundant with the ones found locally):
718	>	int count;
719	>	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
720
721	+	// create a vector to hold the globally found types, and resize it:
722	+	vector<int> ftGlobal;
723	+	ftGlobal.resize(count);
724	+	vector<int> counts;
725	+
726	+	int nproc = MPI::COMM_WORLD.Get_size();
727	+	counts.resize(nproc);
728	+	vector<int> disps;
729	+	disps.resize(nproc);
730	+
731	+	// now spray out the foundTypes to all the other processors:
732	+
733	+	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
734	+	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
735	+
736	+	// foundIdents is a stl set, so inserting an already found ident
737	+	// will have no effect.
738	+	set<int> foundIdents;
739	+	vector<int>::iterator j;
740	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
741	+	foundIdents.insert((*j));
742	+
743	+	// now iterate over the foundIdents and get the actual atom types
744	+	// that correspond to these:
745	+	set<int>::iterator it;
746	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
747	+	atomTypes.insert( forceField_->getAtomType((*it)) );
748	+
749	+	#endif
750	+
751	+	return atomTypes;
752	+	}
753	+
754	+	void SimInfo::setupSimVariables() {
755	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
756	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
757	+	calcBoxDipole_ = false;
758	+	if ( simParams_->haveAccumulateBoxDipole() )
759	+	if ( simParams_->getAccumulateBoxDipole() ) {
760	+	calcBoxDipole_ = true;
761	+	}
762	+
763	+	set<AtomType*>::iterator i;
764	+	set<AtomType*> atomTypes;
765	+	atomTypes = getSimulatedAtomTypes();
766	+	int usesElectrostatic = 0;
767	+	int usesMetallic = 0;
768	+	int usesDirectional = 0;
769		//loop over all of the atom types
770		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
771	<	useLennardJones |= (*i)->isLennardJones();
772	<	useElectrostatic |= (*i)->isElectrostatic();
773	<	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();
771	>	usesElectrostatic |= (*i)->isElectrostatic();
772	>	usesMetallic |= (*i)->isMetal();
773	>	usesDirectional |= (*i)->isDirectional();
774		}
775
689	–	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
690	–	useDirectionalAtom = 1;
691	–	}
692	–
693	–	if (useCharge || useDipole) {
694	–	useElectrostatics = 1;
695	–	}
696	–
776		#ifdef IS_MPI
777		int temp;
778	+	temp = usesDirectional;
779	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
780
781	<	temp = usePBC;
782	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
781	>	temp = usesMetallic;
782	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
783
784	<	temp = useDirectionalAtom;
785	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
784	>	temp = usesElectrostatic;
785	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
786	>	#endif
787	>	}
788
706	–	temp = useLennardJones;
707	–	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
789
790	<	temp = useElectrostatics;
791	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
790	>	vector<int> SimInfo::getGlobalAtomIndices() {
791	>	SimInfo::MoleculeIterator mi;
792	>	Molecule* mol;
793	>	Molecule::AtomIterator ai;
794	>	Atom* atom;
795
796	<	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);
796	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
797
798	<	temp = useGayBerne;
799	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
798	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
799	>
800	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
801	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
802	>	}
803	>	}
804	>	return GlobalAtomIndices;
805	>	}
806
727	–	temp = useEAM;
728	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
807
808	<	temp = useSC;
809	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810	<
811	<	temp = useShape;
812	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
808	>	vector<int> SimInfo::getGlobalGroupIndices() {
809	>	SimInfo::MoleculeIterator mi;
810	>	Molecule* mol;
811	>	Molecule::CutoffGroupIterator ci;
812	>	CutoffGroup* cg;
813
814	<	temp = useFLARB;
815	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816	<
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") {
814	>	vector<int> GlobalGroupIndices;
815	>
816	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
817
818	<	if (simParams_->haveDielectric()) {
819	<	fInfo_.dielect = simParams_->getDielectric();
820	<	} else {
821	<	sprintf(painCave.errMsg,
822	<	"SimSetup Error: No Dielectric constant was set.\n"
823	<	"\tYou are trying to use Reaction Field without"
771	<	"\tsetting a dielectric constant!\n");
772	<	painCave.isFatal = 1;
773	<	simError();
774	<	}
818	>	//local index of cutoff group is trivial, it only depends on the
819	>	//order of travesing
820	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
821	>	cg = mol->nextCutoffGroup(ci)) {
822	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
823	>	}
824		}
825	<
825	>	return GlobalGroupIndices;
826		}
827
779	–	void SimInfo::setupFortranSim() {
780	–	int isError;
781	–	int nExclude;
782	–	std::vector<int> fortranGlobalGroupMembership;
783	–
784	–	nExclude = exclude_.getSize();
785	–	isError = 0;
828
829	<	//globalGroupMembership_ is filled by SimCreator
830	<	for (int i = 0; i < nGlobalAtoms_; i++) {
789	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
790	<	}
829	>	void SimInfo::prepareTopology() {
830	>	int nExclude, nOneTwo, nOneThree, nOneFour;
831
832		//calculate mass ratio of cutoff group
793	–	std::vector<double> mfact;
833		SimInfo::MoleculeIterator mi;
834		Molecule* mol;
835		Molecule::CutoffGroupIterator ci;
836		CutoffGroup* cg;
837		Molecule::AtomIterator ai;
838		Atom* atom;
839	<	double totalMass;
839	>	RealType totalMass;
840
841	<	//to avoid memory reallocation, reserve enough space for mfact
842	<	mfact.reserve(getNCutoffGroups());
841	>	//to avoid memory reallocation, reserve enough space for massFactors_
842	>	massFactors_.clear();
843	>	massFactors_.reserve(getNCutoffGroups());
844
845		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
846	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
846	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
847	>	cg = mol->nextCutoffGroup(ci)) {
848
849		totalMass = cg->getMass();
850		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
851		// Check for massless groups - set mfact to 1 if true
852		if (totalMass != 0)
853	<	mfact.push_back(atom->getMass()/totalMass);
853	>	massFactors_.push_back(atom->getMass()/totalMass);
854		else
855	<	mfact.push_back( 1.0 );
855	>	massFactors_.push_back( 1.0 );
856		}
816	–
857		}
858		}
859
860	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
821	<	std::vector<int> identArray;
860	>	// Build the identArray_
861
862	<	//to avoid memory reallocation, reserve enough space identArray
863	<	identArray.reserve(getNAtoms());
825	<
862	>	identArray_.clear();
863	>	identArray_.reserve(getNAtoms());
864		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
865		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
866	<	identArray.push_back(atom->getIdent());
866	>	identArray_.push_back(atom->getIdent());
867		}
868		}
831	–
832	–	//fill molMembershipArray
833	–	//molMembershipArray is filled by SimCreator
834	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
835	–	for (int i = 0; i < nGlobalAtoms_; i++) {
836	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
837	–	}
869
870	<	//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);
870	>	//scan topology
871
872	<	if( isError ){
872	>	nExclude = excludedInteractions_.getSize();
873	>	nOneTwo = oneTwoInteractions_.getSize();
874	>	nOneThree = oneThreeInteractions_.getSize();
875	>	nOneFour = oneFourInteractions_.getSize();
876
877	<	sprintf( painCave.errMsg,
878	<	"There was an error setting the simulation information in fortran.\n" );
879	<	painCave.isFatal = 1;
880	<	painCave.severity = OOPSE_ERROR;
853	<	simError();
854	<	}
877	>	int* excludeList = excludedInteractions_.getPairList();
878	>	int* oneTwoList = oneTwoInteractions_.getPairList();
879	>	int* oneThreeList = oneThreeInteractions_.getPairList();
880	>	int* oneFourList = oneFourInteractions_.getPairList();
881
882	<	#ifdef IS_MPI
883	<	sprintf( checkPointMsg,
884	<	"succesfully sent the simulation information to fortran.\n");
885	<	MPIcheckPoint();
886	<	#endif // is_mpi
887	<	}
888	<
863	<
864	<	#ifdef IS_MPI
865	<	void SimInfo::setupFortranParallel() {
882	>	//setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0],
883	>	//               &nExclude, excludeList,
884	>	//               &nOneTwo, oneTwoList,
885	>	//               &nOneThree, oneThreeList,
886	>	//               &nOneFour, oneFourList,
887	>	//               &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
888	>	//               &fortranGlobalGroupMembership[0], &isError);
889
890	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
868	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
869	<	std::vector<int> localToGlobalCutoffGroupIndex;
870	<	SimInfo::MoleculeIterator mi;
871	<	Molecule::AtomIterator ai;
872	<	Molecule::CutoffGroupIterator ci;
873	<	Molecule* mol;
874	<	Atom* atom;
875	<	CutoffGroup* cg;
876	<	mpiSimData parallelData;
877	<	int isError;
878	<
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	<
893	<	//fill up mpiSimData struct
894	<	parallelData.nMolGlobal = getNGlobalMolecules();
895	<	parallelData.nMolLocal = getNMolecules();
896	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
897	<	parallelData.nAtomsLocal = getNAtoms();
898	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
899	<	parallelData.nGroupsLocal = getNCutoffGroups();
900	<	parallelData.myNode = worldRank;
901	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
902	<
903	<	//pass mpiSimData struct and index arrays to fortran
904	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
905	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
906	<	&localToGlobalCutoffGroupIndex[0], &isError);
907	<
908	<	if (isError) {
909	<	sprintf(painCave.errMsg,
910	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
911	<	painCave.isFatal = 1;
912	<	simError();
913	<	}
914	<
915	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
916	<	MPIcheckPoint();
917	<
918	<
919	<	}
920	<
921	<	#endif
922	<
923	<	void SimInfo::setupCutoff() {
924	<
925	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
926	<
927	<	// Check the cutoff policy
928	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
929	<
930	<	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 percent of the cutoffRadius.\n"
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	<
994	<	notifyFortranCutoffs(&rcut_, &rsw_);
995	<
996	<	} else {
997	<
998	<	// For electrostatic atoms, we'll assume a large safe value:
999	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1000	<	sprintf(painCave.errMsg,
1001	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1002	<	"\tOOPSE will use a default value of 15.0 angstroms"
1003	<	"\tfor the cutoffRadius.\n");
1004	<	painCave.isFatal = 0;
1005	<	simError();
1006	<	rcut_ = 15.0;
1007	<
1008	<	if (simParams_->haveElectrostaticSummationMethod()) {
1009	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1010	<	toUpper(myMethod);
1011	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1012	<	if (simParams_->haveSwitchingRadius()){
1013	<	sprintf(painCave.errMsg,
1014	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1015	<	"\teven though the electrostaticSummationMethod was\n"
1016	<	"\tset to %s\n", myMethod.c_str());
1017	<	painCave.isFatal = 1;
1018	<	simError();
1019	<	}
1020	<	}
1021	<	}
1022	<
1023	<	if (simParams_->haveSwitchingRadius()){
1024	<	rsw_ = simParams_->getSwitchingRadius();
1025	<	} else {
1026	<	sprintf(painCave.errMsg,
1027	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1028	<	"\tOOPSE will use a default value of\n"
1029	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1030	<	painCave.isFatal = 0;
1031	<	simError();
1032	<	rsw_ = 0.85 * rcut_;
1033	<	}
1034	<	notifyFortranCutoffs(&rcut_, &rsw_);
1035	<	} else {
1036	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1037	<	// We'll punt and let fortran figure out the cutoffs later.
1038	<
1039	<	notifyFortranYouAreOnYourOwn();
1040	<
1041	<	}
1042	<	}
890	>	topologyDone_ = true;
891		}
892
1045	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1046	–
1047	–	int errorOut;
1048	–	int esm =  NONE;
1049	–	int sm = UNDAMPED;
1050	–	double alphaVal;
1051	–	double dielectric;
1052	–
1053	–	errorOut = isError;
1054	–	alphaVal = simParams_->getDampingAlpha();
1055	–	dielectric = simParams_->getDielectric();
1056	–
1057	–	if (simParams_->haveElectrostaticSummationMethod()) {
1058	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1059	–	toUpper(myMethod);
1060	–	if (myMethod == "NONE") {
1061	–	esm = NONE;
1062	–	} else {
1063	–	if (myMethod == "SWITCHING_FUNCTION") {
1064	–	esm = SWITCHING_FUNCTION;
1065	–	} else {
1066	–	if (myMethod == "SHIFTED_POTENTIAL") {
1067	–	esm = SHIFTED_POTENTIAL;
1068	–	} else {
1069	–	if (myMethod == "SHIFTED_FORCE") {
1070	–	esm = SHIFTED_FORCE;
1071	–	} else {
1072	–	if (myMethod == "REACTION_FIELD") {
1073	–	esm = REACTION_FIELD;
1074	–	} else {
1075	–	// throw error
1076	–	sprintf( painCave.errMsg,
1077	–	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1078	–	"\t(Input file specified %s .)\n"
1079	–	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1080	–	"\t\"shifted_potential\", \"shifted_force\", or \n"
1081	–	"\t\"reaction_field\".\n", myMethod.c_str() );
1082	–	painCave.isFatal = 1;
1083	–	simError();
1084	–	}
1085	–	}
1086	–	}
1087	–	}
1088	–	}
1089	–	}
1090	–
1091	–	if (simParams_->haveElectrostaticScreeningMethod()) {
1092	–	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1093	–	toUpper(myScreen);
1094	–	if (myScreen == "UNDAMPED") {
1095	–	sm = UNDAMPED;
1096	–	} else {
1097	–	if (myScreen == "DAMPED") {
1098	–	sm = DAMPED;
1099	–	if (!simParams_->haveDampingAlpha()) {
1100	–	//throw error
1101	–	sprintf( painCave.errMsg,
1102	–	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1103	–	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1104	–	painCave.isFatal = 0;
1105	–	simError();
1106	–	}
1107	–	} else {
1108	–	// throw error
1109	–	sprintf( painCave.errMsg,
1110	–	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1111	–	"\t(Input file specified %s .)\n"
1112	–	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1113	–	"or \"damped\".\n", myScreen.c_str() );
1114	–	painCave.isFatal = 1;
1115	–	simError();
1116	–	}
1117	–	}
1118	–	}
1119	–
1120	–	// let's pass some summation method variables to fortran
1121	–	setElectrostaticSummationMethod( &esm );
1122	–	setFortranElectrostaticMethod( &esm );
1123	–	setScreeningMethod( &sm );
1124	–	setDampingAlpha( &alphaVal );
1125	–	setReactionFieldDielectric( &dielectric );
1126	–	initFortranFF( &errorOut );
1127	–	}
1128	–
1129	–	void SimInfo::setupSwitchingFunction() {
1130	–	int ft = CUBIC;
1131	–
1132	–	if (simParams_->haveSwitchingFunctionType()) {
1133	–	std::string funcType = simParams_->getSwitchingFunctionType();
1134	–	toUpper(funcType);
1135	–	if (funcType == "CUBIC") {
1136	–	ft = CUBIC;
1137	–	} else {
1138	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1139	–	ft = FIFTH_ORDER_POLY;
1140	–	} else {
1141	–	// throw error
1142	–	sprintf( painCave.errMsg,
1143	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1144	–	painCave.isFatal = 1;
1145	–	simError();
1146	–	}
1147	–	}
1148	–	}
1149	–
1150	–	// send switching function notification to switcheroo
1151	–	setFunctionType(&ft);
1152	–
1153	–	}
1154	–
893		void SimInfo::addProperty(GenericData* genData) {
894		properties_.addProperty(genData);
895		}
896
897	<	void SimInfo::removeProperty(const std::string& propName) {
897	>	void SimInfo::removeProperty(const string& propName) {
898		properties_.removeProperty(propName);
899		}
900
#	Line 1164 | Line 902 | namespace oopse {
902		properties_.clearProperties();
903		}
904
905	<	std::vector<std::string> SimInfo::getPropertyNames() {
905	>	vector<string> SimInfo::getPropertyNames() {
906		return properties_.getPropertyNames();
907		}
908
909	<	std::vector<GenericData*> SimInfo::getProperties() {
909	>	vector<GenericData*> SimInfo::getProperties() {
910		return properties_.getProperties();
911		}
912
913	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
913	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
914		return properties_.getPropertyByName(propName);
915		}
916
#	Line 1186 | Line 924 | namespace oopse {
924		Molecule* mol;
925		RigidBody* rb;
926		Atom* atom;
927	+	CutoffGroup* cg;
928		SimInfo::MoleculeIterator mi;
929		Molecule::RigidBodyIterator rbIter;
930	<	Molecule::AtomIterator atomIter;;
930	>	Molecule::AtomIterator atomIter;
931	>	Molecule::CutoffGroupIterator cgIter;
932
933		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
934
#	Line 1199 | Line 939 | namespace oopse {
939		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
940		rb->setSnapshotManager(sman_);
941		}
942	+
943	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
944	+	cg->setSnapshotManager(sman_);
945	+	}
946		}
947
948		}
#	Line 1208 | Line 952 | namespace oopse {
952		Molecule* mol;
953
954		Vector3d comVel(0.0);
955	<	double totalMass = 0.0;
955	>	RealType totalMass = 0.0;
956
957
958		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
959	<	double mass = mol->getMass();
959	>	RealType mass = mol->getMass();
960		totalMass += mass;
961		comVel += mass * mol->getComVel();
962		}
963
964		#ifdef IS_MPI
965	<	double tmpMass = totalMass;
965	>	RealType tmpMass = totalMass;
966		Vector3d tmpComVel(comVel);
967	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
968	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
967	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
968	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
969		#endif
970
971		comVel /= totalMass;
#	Line 1234 | Line 978 | namespace oopse {
978		Molecule* mol;
979
980		Vector3d com(0.0);
981	<	double totalMass = 0.0;
981	>	RealType totalMass = 0.0;
982
983		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
984	<	double mass = mol->getMass();
984	>	RealType mass = mol->getMass();
985		totalMass += mass;
986		com += mass * mol->getCom();
987		}
988
989		#ifdef IS_MPI
990	<	double tmpMass = totalMass;
990	>	RealType tmpMass = totalMass;
991		Vector3d tmpCom(com);
992	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
993	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
992	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
993	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
994		#endif
995
996		com /= totalMass;
#	Line 1255 | Line 999 | namespace oopse {
999
1000		}
1001
1002	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1002	>	ostream& operator <<(ostream& o, SimInfo& info) {
1003
1004		return o;
1005		}
#	Line 1270 | Line 1014 | namespace oopse {
1014		Molecule* mol;
1015
1016
1017	<	double totalMass = 0.0;
1017	>	RealType totalMass = 0.0;
1018
1019
1020		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1021	<	double mass = mol->getMass();
1021	>	RealType mass = mol->getMass();
1022		totalMass += mass;
1023		com += mass * mol->getCom();
1024		comVel += mass * mol->getComVel();
1025		}
1026
1027		#ifdef IS_MPI
1028	<	double tmpMass = totalMass;
1028	>	RealType tmpMass = totalMass;
1029		Vector3d tmpCom(com);
1030		Vector3d tmpComVel(comVel);
1031	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1032	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1033	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1031	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1032	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1033	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1034		#endif
1035
1036		com /= totalMass;
#	Line 1298 | Line 1042 | namespace oopse {
1042
1043
1044		[  Ixx -Ixy  -Ixz ]
1045	<	J =| -Iyx  Iyy  -Iyz |
1045	>	J =| -Iyx  Iyy  -Iyz |
1046		[ -Izx -Iyz   Izz ]
1047		*/
1048
1049		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1050
1051
1052	<	double xx = 0.0;
1053	<	double yy = 0.0;
1054	<	double zz = 0.0;
1055	<	double xy = 0.0;
1056	<	double xz = 0.0;
1057	<	double yz = 0.0;
1052	>	RealType xx = 0.0;
1053	>	RealType yy = 0.0;
1054	>	RealType zz = 0.0;
1055	>	RealType xy = 0.0;
1056	>	RealType xz = 0.0;
1057	>	RealType yz = 0.0;
1058		Vector3d com(0.0);
1059		Vector3d comVel(0.0);
1060
#	Line 1322 | Line 1066 | namespace oopse {
1066		Vector3d thisq(0.0);
1067		Vector3d thisv(0.0);
1068
1069	<	double thisMass = 0.0;
1069	>	RealType thisMass = 0.0;
1070
1071
1072
#	Line 1360 | Line 1104 | namespace oopse {
1104		#ifdef IS_MPI
1105		Mat3x3d tmpI(inertiaTensor);
1106		Vector3d tmpAngMom;
1107	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1108	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1107	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1108	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1109		#endif
1110
1111		return;
#	Line 1382 | Line 1126 | namespace oopse {
1126		Vector3d thisr(0.0);
1127		Vector3d thisp(0.0);
1128
1129	<	double thisMass;
1129	>	RealType thisMass;
1130
1131		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1132		thisMass = mol->getMass();
#	Line 1395 | Line 1139 | namespace oopse {
1139
1140		#ifdef IS_MPI
1141		Vector3d tmpAngMom;
1142	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1142	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1143		#endif
1144
1145		return angularMomentum;
1146		}
1147
1148	<
1149	<	}//end namespace oopse
1148	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1149	>	return IOIndexToIntegrableObject.at(index);
1150	>	}
1151	>
1152	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1153	>	IOIndexToIntegrableObject= v;
1154	>	}
1155
1156	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1157	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1158	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1159	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1160	+	*/
1161	+	void SimInfo::getGyrationalVolume(RealType &volume){
1162	+	Mat3x3d intTensor;
1163	+	RealType det;
1164	+	Vector3d dummyAngMom;
1165	+	RealType sysconstants;
1166	+	RealType geomCnst;
1167	+
1168	+	geomCnst = 3.0/2.0;
1169	+	/* Get the inertial tensor and angular momentum for free*/
1170	+	getInertiaTensor(intTensor,dummyAngMom);
1171	+
1172	+	det = intTensor.determinant();
1173	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1174	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1175	+	return;
1176	+	}
1177	+
1178	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1179	+	Mat3x3d intTensor;
1180	+	Vector3d dummyAngMom;
1181	+	RealType sysconstants;
1182	+	RealType geomCnst;
1183	+
1184	+	geomCnst = 3.0/2.0;
1185	+	/* Get the inertial tensor and angular momentum for free*/
1186	+	getInertiaTensor(intTensor,dummyAngMom);
1187	+
1188	+	detI = intTensor.determinant();
1189	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1190	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1191	+	return;
1192	+	}
1193	+	/*
1194	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1195	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1196	+	sdByGlobalIndex_ = v;
1197	+	}
1198	+
1199	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1200	+	//assert(index < nAtoms_ + nRigidBodies_);
1201	+	return sdByGlobalIndex_.at(index);
1202	+	}
1203	+	*/
1204	+	int SimInfo::getNGlobalConstraints() {
1205	+	int nGlobalConstraints;
1206	+	#ifdef IS_MPI
1207	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1208	+	MPI_COMM_WORLD);
1209	+	#else
1210	+	nGlobalConstraints =  nConstraints_;
1211	+	#endif
1212	+	return nGlobalConstraints;
1213	+	}
1214	+
1215	+	}//end namespace OpenMD
1216	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 879 by chrisfen, Wed Feb 1 21:06:43 2006 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1577 by gezelter, Wed Jun 8 20:26:56 2011 UTC

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