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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 1529 by gezelter, Mon Dec 27 18:35:59 2010 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 53 | Line 53
53		#include "brains/SimInfo.hpp"
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56	+	#include "primitives/StuntDouble.hpp"
57		#include "UseTheForce/fCutoffPolicy.h"
57	–	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
58	–	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
58		#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
59		#include "UseTheForce/doForces_interface.h"
60	<	#include "UseTheForce/DarkSide/electrostatic_interface.h"
62	<	#include "UseTheForce/notifyCutoffs_interface.h"
60	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
61		#include "UseTheForce/DarkSide/switcheroo_interface.h"
62		#include "utils/MemoryUtils.hpp"
63		#include "utils/simError.h"
64		#include "selection/SelectionManager.hpp"
65	+	#include "io/ForceFieldOptions.hpp"
66	+	#include "UseTheForce/ForceField.hpp"
67	+	#include "nonbonded/InteractionManager.hpp"
68
69	+
70		#ifdef IS_MPI
71		#include "UseTheForce/mpiComponentPlan.h"
72		#include "UseTheForce/DarkSide/simParallel_interface.h"
73		#endif
74
75	<	namespace oopse {
76	<	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	<	}
75	>	using namespace std;
76	>	namespace OpenMD {
77
78	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
79	<	ForceField* ff, Globals* simParams) :
80	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
87	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
78	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
79	>	forceField_(ff), simParams_(simParams),
80	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
81		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
82		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
83	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
84	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
85	<	sman_(NULL), fortranInitialized_(false) {
86	<
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;
83	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
84	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
85	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
86	>	calcBoxDipole_(false), useAtomicVirial_(true) {
87
88	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
89	<	molStamp = i->first;
90	<	nMolWithSameStamp = i->second;
91	<
92	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
93	<
94	<	//calculate atoms in molecules
95	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
96	<
97	<
98	<	//calculate atoms in cutoff groups
99	<	int nAtomsInGroups = 0;
100	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
101	<
102	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
103	<	cgStamp = molStamp->getCutoffGroup(j);
104	<	nAtomsInGroups += cgStamp->getNMembers();
105	<	}
106	<
107	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
108	<
109	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
110	<
111	<	//calculate atoms in rigid bodies
112	<	int nAtomsInRigidBodies = 0;
113	<	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	<
88	>	MoleculeStamp* molStamp;
89	>	int nMolWithSameStamp;
90	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
91	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
92	>	CutoffGroupStamp* cgStamp;
93	>	RigidBodyStamp* rbStamp;
94	>	int nRigidAtoms = 0;
95	>
96	>	vector<Component*> components = simParams->getComponents();
97	>
98	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
99	>	molStamp = (*i)->getMoleculeStamp();
100	>	nMolWithSameStamp = (*i)->getNMol();
101	>
102	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
103	>
104	>	//calculate atoms in molecules
105	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
106	>
107	>	//calculate atoms in cutoff groups
108	>	int nAtomsInGroups = 0;
109	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
110	>
111	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
112	>	cgStamp = molStamp->getCutoffGroupStamp(j);
113	>	nAtomsInGroups += cgStamp->getNMembers();
114		}
115	<
116	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
117	<	//group therefore the total number of cutoff groups in the system is
118	<	//equal to the total number of atoms minus number of atoms belong to
119	<	//cutoff group defined in meta-data file plus the number of cutoff
120	<	//groups defined in meta-data file
121	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
122	<
123	<	//every free atom (atom does not belong to rigid bodies) is an
124	<	//integrable object therefore the total number of integrable objects
125	<	//in the system is equal to the total number of atoms minus number of
126	<	//atoms belong to rigid body defined in meta-data file plus the number
127	<	//of rigid bodies defined in meta-data file
128	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
129	<	+ nGlobalRigidBodies_;
130	<
131	<	nGlobalMols_ = molStampIds_.size();
157	<
158	<	#ifdef IS_MPI
159	<	molToProcMap_.resize(nGlobalMols_);
160	<	#endif
161	<
115	>
116	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
117	>
118	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
119	>
120	>	//calculate atoms in rigid bodies
121	>	int nAtomsInRigidBodies = 0;
122	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
123	>
124	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
125	>	rbStamp = molStamp->getRigidBodyStamp(j);
126	>	nAtomsInRigidBodies += rbStamp->getNMembers();
127	>	}
128	>
129	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
130	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
131	>
132		}
133	<
133	>
134	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
135	>	//group therefore the total number of cutoff groups in the system is
136	>	//equal to the total number of atoms minus number of atoms belong to
137	>	//cutoff group defined in meta-data file plus the number of cutoff
138	>	//groups defined in meta-data file
139	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
140	>
141	>	//every free atom (atom does not belong to rigid bodies) is an
142	>	//integrable object therefore the total number of integrable objects
143	>	//in the system is equal to the total number of atoms minus number of
144	>	//atoms belong to rigid body defined in meta-data file plus the number
145	>	//of rigid bodies defined in meta-data file
146	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
147	>	+ nGlobalRigidBodies_;
148	>
149	>	nGlobalMols_ = molStampIds_.size();
150	>	molToProcMap_.resize(nGlobalMols_);
151	>	}
152	>
153		SimInfo::~SimInfo() {
154	<	std::map<int, Molecule*>::iterator i;
154	>	map<int, Molecule*>::iterator i;
155		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
156		delete i->second;
157		}
158		molecules_.clear();
159
171	–	delete stamps_;
160		delete sman_;
161		delete simParams_;
162		delete forceField_;
163		}
164
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	–	}
165
166		bool SimInfo::addMolecule(Molecule* mol) {
167		MoleculeIterator i;
168	<
168	>
169		i = molecules_.find(mol->getGlobalIndex());
170		if (i == molecules_.end() ) {
171	<
172	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
173	<
171	>
172	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
173	>
174		nAtoms_ += mol->getNAtoms();
175		nBonds_ += mol->getNBonds();
176		nBends_ += mol->getNBends();
177		nTorsions_ += mol->getNTorsions();
178	+	nInversions_ += mol->getNInversions();
179		nRigidBodies_ += mol->getNRigidBodies();
180		nIntegrableObjects_ += mol->getNIntegrableObjects();
181		nCutoffGroups_ += mol->getNCutoffGroups();
182		nConstraints_ += mol->getNConstraintPairs();
183	<
184	<	addExcludePairs(mol);
185	<
183	>
184	>	addInteractionPairs(mol);
185	>
186		return true;
187		} else {
188		return false;
189		}
190		}
191	<
191	>
192		bool SimInfo::removeMolecule(Molecule* mol) {
193		MoleculeIterator i;
194		i = molecules_.find(mol->getGlobalIndex());
#	Line 222 | Line 201 | namespace oopse {
201		nBonds_ -= mol->getNBonds();
202		nBends_ -= mol->getNBends();
203		nTorsions_ -= mol->getNTorsions();
204	+	nInversions_ -= mol->getNInversions();
205		nRigidBodies_ -= mol->getNRigidBodies();
206		nIntegrableObjects_ -= mol->getNIntegrableObjects();
207		nCutoffGroups_ -= mol->getNCutoffGroups();
208		nConstraints_ -= mol->getNConstraintPairs();
209
210	<	removeExcludePairs(mol);
210	>	removeInteractionPairs(mol);
211		molecules_.erase(mol->getGlobalIndex());
212
213		delete mol;
#	Line 236 | Line 216 | namespace oopse {
216		} else {
217		return false;
218		}
239	–
240	–
219		}
220
221
#	Line 255 | Line 233 | namespace oopse {
233		void SimInfo::calcNdf() {
234		int ndf_local;
235		MoleculeIterator i;
236	<	std::vector<StuntDouble*>::iterator j;
236	>	vector<StuntDouble*>::iterator j;
237		Molecule* mol;
238		StuntDouble* integrableObject;
239
#	Line 275 | Line 253 | namespace oopse {
253		}
254		}
255
256	<	}//end for (integrableObject)
257	<	}// end for (mol)
256	>	}
257	>	}
258
259		// n_constraints is local, so subtract them on each processor
260		ndf_local -= nConstraints_;
#	Line 293 | Line 271 | namespace oopse {
271
272		}
273
274	+	int SimInfo::getFdf() {
275	+	#ifdef IS_MPI
276	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
277	+	#else
278	+	fdf_ = fdf_local;
279	+	#endif
280	+	return fdf_;
281	+	}
282	+
283		void SimInfo::calcNdfRaw() {
284		int ndfRaw_local;
285
286		MoleculeIterator i;
287	<	std::vector<StuntDouble*>::iterator j;
287	>	vector<StuntDouble*>::iterator j;
288		Molecule* mol;
289		StuntDouble* integrableObject;
290
#	Line 344 | Line 331 | namespace oopse {
331
332		}
333
334	<	void SimInfo::addExcludePairs(Molecule* mol) {
335	<	std::vector<Bond*>::iterator bondIter;
336	<	std::vector<Bend*>::iterator bendIter;
337	<	std::vector<Torsion*>::iterator torsionIter;
334	>	void SimInfo::addInteractionPairs(Molecule* mol) {
335	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
336	>	vector<Bond*>::iterator bondIter;
337	>	vector<Bend*>::iterator bendIter;
338	>	vector<Torsion*>::iterator torsionIter;
339	>	vector<Inversion*>::iterator inversionIter;
340		Bond* bond;
341		Bend* bend;
342		Torsion* torsion;
343	+	Inversion* inversion;
344		int a;
345		int b;
346		int c;
347		int d;
348
349	<	std::map<int, std::set<int> > atomGroups;
349	>	// atomGroups can be used to add special interaction maps between
350	>	// groups of atoms that are in two separate rigid bodies.
351	>	// However, most site-site interactions between two rigid bodies
352	>	// are probably not special, just the ones between the physically
353	>	// bonded atoms.  Interactions *within* a single rigid body should
354	>	// always be excluded.  These are done at the bottom of this
355	>	// function.
356
357	+	map<int, set<int> > atomGroups;
358		Molecule::RigidBodyIterator rbIter;
359		RigidBody* rb;
360		Molecule::IntegrableObjectIterator ii;
361		StuntDouble* integrableObject;
362
363	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
364	<	integrableObject = mol->nextIntegrableObject(ii)) {
365	<
363	>	for (integrableObject = mol->beginIntegrableObject(ii);
364	>	integrableObject != NULL;
365	>	integrableObject = mol->nextIntegrableObject(ii)) {
366	>
367		if (integrableObject->isRigidBody()) {
368	<	rb = static_cast<RigidBody*>(integrableObject);
369	<	std::vector<Atom*> atoms = rb->getAtoms();
370	<	std::set<int> rigidAtoms;
371	<	for (int i = 0; i < atoms.size(); ++i) {
372	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
373	<	}
374	<	for (int i = 0; i < atoms.size(); ++i) {
375	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
376	<	}
368	>	rb = static_cast<RigidBody*>(integrableObject);
369	>	vector<Atom*> atoms = rb->getAtoms();
370	>	set<int> rigidAtoms;
371	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
372	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
373	>	}
374	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
375	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
376	>	}
377		} else {
378	<	std::set<int> oneAtomSet;
378	>	set<int> oneAtomSet;
379		oneAtomSet.insert(integrableObject->getGlobalIndex());
380	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
380	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
381		}
382		}
383	+
384	+	for (bond= mol->beginBond(bondIter); bond != NULL;
385	+	bond = mol->nextBond(bondIter)) {
386
386	–
387	–
388	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
387		a = bond->getAtomA()->getGlobalIndex();
388	<	b = bond->getAtomB()->getGlobalIndex();
389	<	exclude_.addPair(a, b);
388	>	b = bond->getAtomB()->getGlobalIndex();
389	>
390	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
391	>	oneTwoInteractions_.addPair(a, b);
392	>	} else {
393	>	excludedInteractions_.addPair(a, b);
394	>	}
395		}
396
397	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
397	>	for (bend= mol->beginBend(bendIter); bend != NULL;
398	>	bend = mol->nextBend(bendIter)) {
399	>
400		a = bend->getAtomA()->getGlobalIndex();
401		b = bend->getAtomB()->getGlobalIndex();
402		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);
403
404	<	//exclude_.addPair(a, b);
405	<	//exclude_.addPair(a, c);
406	<	//exclude_.addPair(b, c);
404	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
405	>	oneTwoInteractions_.addPair(a, b);
406	>	oneTwoInteractions_.addPair(b, c);
407	>	} else {
408	>	excludedInteractions_.addPair(a, b);
409	>	excludedInteractions_.addPair(b, c);
410	>	}
411	>
412	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
413	>	oneThreeInteractions_.addPair(a, c);
414	>	} else {
415	>	excludedInteractions_.addPair(a, c);
416	>	}
417		}
418
419	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
419	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
420	>	torsion = mol->nextTorsion(torsionIter)) {
421	>
422		a = torsion->getAtomA()->getGlobalIndex();
423		b = torsion->getAtomB()->getGlobalIndex();
424		c = torsion->getAtomC()->getGlobalIndex();
425	<	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);
425	>	d = torsion->getAtomD()->getGlobalIndex();
426
427	<	exclude_.addPairs(rigidSetA, rigidSetB);
428	<	exclude_.addPairs(rigidSetA, rigidSetC);
429	<	exclude_.addPairs(rigidSetA, rigidSetD);
430	<	exclude_.addPairs(rigidSetB, rigidSetC);
431	<	exclude_.addPairs(rigidSetB, rigidSetD);
432	<	exclude_.addPairs(rigidSetC, rigidSetD);
427	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
428	>	oneTwoInteractions_.addPair(a, b);
429	>	oneTwoInteractions_.addPair(b, c);
430	>	oneTwoInteractions_.addPair(c, d);
431	>	} else {
432	>	excludedInteractions_.addPair(a, b);
433	>	excludedInteractions_.addPair(b, c);
434	>	excludedInteractions_.addPair(c, d);
435	>	}
436
437	<	/*
438	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
439	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
440	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
441	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
442	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
443	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
444	<
445	<
446	<	exclude_.addPair(a, b);
447	<	exclude_.addPair(a, c);
448	<	exclude_.addPair(a, d);
449	<	exclude_.addPair(b, c);
441	<	exclude_.addPair(b, d);
442	<	exclude_.addPair(c, d);
443	<	*/
437	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
438	>	oneThreeInteractions_.addPair(a, c);
439	>	oneThreeInteractions_.addPair(b, d);
440	>	} else {
441	>	excludedInteractions_.addPair(a, c);
442	>	excludedInteractions_.addPair(b, d);
443	>	}
444	>
445	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
446	>	oneFourInteractions_.addPair(a, d);
447	>	} else {
448	>	excludedInteractions_.addPair(a, d);
449	>	}
450		}
451
452	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
453	<	std::vector<Atom*> atoms = rb->getAtoms();
454	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
455	<	for (int j = i + 1; j < atoms.size(); ++j) {
452	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
453	>	inversion = mol->nextInversion(inversionIter)) {
454	>
455	>	a = inversion->getAtomA()->getGlobalIndex();
456	>	b = inversion->getAtomB()->getGlobalIndex();
457	>	c = inversion->getAtomC()->getGlobalIndex();
458	>	d = inversion->getAtomD()->getGlobalIndex();
459	>
460	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
461	>	oneTwoInteractions_.addPair(a, b);
462	>	oneTwoInteractions_.addPair(a, c);
463	>	oneTwoInteractions_.addPair(a, d);
464	>	} else {
465	>	excludedInteractions_.addPair(a, b);
466	>	excludedInteractions_.addPair(a, c);
467	>	excludedInteractions_.addPair(a, d);
468	>	}
469	>
470	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
471	>	oneThreeInteractions_.addPair(b, c);
472	>	oneThreeInteractions_.addPair(b, d);
473	>	oneThreeInteractions_.addPair(c, d);
474	>	} else {
475	>	excludedInteractions_.addPair(b, c);
476	>	excludedInteractions_.addPair(b, d);
477	>	excludedInteractions_.addPair(c, d);
478	>	}
479	>	}
480	>
481	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
482	>	rb = mol->nextRigidBody(rbIter)) {
483	>	vector<Atom*> atoms = rb->getAtoms();
484	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
485	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
486		a = atoms[i]->getGlobalIndex();
487		b = atoms[j]->getGlobalIndex();
488	<	exclude_.addPair(a, b);
488	>	excludedInteractions_.addPair(a, b);
489		}
490		}
491		}
492
493		}
494
495	<	void SimInfo::removeExcludePairs(Molecule* mol) {
496	<	std::vector<Bond*>::iterator bondIter;
497	<	std::vector<Bend*>::iterator bendIter;
498	<	std::vector<Torsion*>::iterator torsionIter;
495	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
496	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
497	>	vector<Bond*>::iterator bondIter;
498	>	vector<Bend*>::iterator bendIter;
499	>	vector<Torsion*>::iterator torsionIter;
500	>	vector<Inversion*>::iterator inversionIter;
501		Bond* bond;
502		Bend* bend;
503		Torsion* torsion;
504	+	Inversion* inversion;
505		int a;
506		int b;
507		int c;
508		int d;
509
510	<	std::map<int, std::set<int> > atomGroups;
472	<
510	>	map<int, set<int> > atomGroups;
511		Molecule::RigidBodyIterator rbIter;
512		RigidBody* rb;
513		Molecule::IntegrableObjectIterator ii;
514		StuntDouble* integrableObject;
515
516	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
517	<	integrableObject = mol->nextIntegrableObject(ii)) {
518	<
516	>	for (integrableObject = mol->beginIntegrableObject(ii);
517	>	integrableObject != NULL;
518	>	integrableObject = mol->nextIntegrableObject(ii)) {
519	>
520		if (integrableObject->isRigidBody()) {
521	<	rb = static_cast<RigidBody*>(integrableObject);
522	<	std::vector<Atom*> atoms = rb->getAtoms();
523	<	std::set<int> rigidAtoms;
524	<	for (int i = 0; i < atoms.size(); ++i) {
525	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
526	<	}
527	<	for (int i = 0; i < atoms.size(); ++i) {
528	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
529	<	}
521	>	rb = static_cast<RigidBody*>(integrableObject);
522	>	vector<Atom*> atoms = rb->getAtoms();
523	>	set<int> rigidAtoms;
524	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
525	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
526	>	}
527	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
528	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
529	>	}
530		} else {
531	<	std::set<int> oneAtomSet;
531	>	set<int> oneAtomSet;
532		oneAtomSet.insert(integrableObject->getGlobalIndex());
533	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
533	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
534		}
535		}
536
537	<
538	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
537	>	for (bond= mol->beginBond(bondIter); bond != NULL;
538	>	bond = mol->nextBond(bondIter)) {
539	>
540		a = bond->getAtomA()->getGlobalIndex();
541	<	b = bond->getAtomB()->getGlobalIndex();
542	<	exclude_.removePair(a, b);
541	>	b = bond->getAtomB()->getGlobalIndex();
542	>
543	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
544	>	oneTwoInteractions_.removePair(a, b);
545	>	} else {
546	>	excludedInteractions_.removePair(a, b);
547	>	}
548		}
549
550	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
550	>	for (bend= mol->beginBend(bendIter); bend != NULL;
551	>	bend = mol->nextBend(bendIter)) {
552	>
553		a = bend->getAtomA()->getGlobalIndex();
554		b = bend->getAtomB()->getGlobalIndex();
555		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);
556
557	<	//exclude_.removePair(a, b);
558	<	//exclude_.removePair(a, c);
559	<	//exclude_.removePair(b, c);
557	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
558	>	oneTwoInteractions_.removePair(a, b);
559	>	oneTwoInteractions_.removePair(b, c);
560	>	} else {
561	>	excludedInteractions_.removePair(a, b);
562	>	excludedInteractions_.removePair(b, c);
563	>	}
564	>
565	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
566	>	oneThreeInteractions_.removePair(a, c);
567	>	} else {
568	>	excludedInteractions_.removePair(a, c);
569	>	}
570		}
571
572	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
572	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
573	>	torsion = mol->nextTorsion(torsionIter)) {
574	>
575		a = torsion->getAtomA()->getGlobalIndex();
576		b = torsion->getAtomB()->getGlobalIndex();
577		c = torsion->getAtomC()->getGlobalIndex();
578	<	d = torsion->getAtomD()->getGlobalIndex();
578	>	d = torsion->getAtomD()->getGlobalIndex();
579	>
580	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
581	>	oneTwoInteractions_.removePair(a, b);
582	>	oneTwoInteractions_.removePair(b, c);
583	>	oneTwoInteractions_.removePair(c, d);
584	>	} else {
585	>	excludedInteractions_.removePair(a, b);
586	>	excludedInteractions_.removePair(b, c);
587	>	excludedInteractions_.removePair(c, d);
588	>	}
589
590	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
591	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
592	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
593	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
590	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
591	>	oneThreeInteractions_.removePair(a, c);
592	>	oneThreeInteractions_.removePair(b, d);
593	>	} else {
594	>	excludedInteractions_.removePair(a, c);
595	>	excludedInteractions_.removePair(b, d);
596	>	}
597
598	<	exclude_.removePairs(rigidSetA, rigidSetB);
599	<	exclude_.removePairs(rigidSetA, rigidSetC);
600	<	exclude_.removePairs(rigidSetA, rigidSetD);
601	<	exclude_.removePairs(rigidSetB, rigidSetC);
602	<	exclude_.removePairs(rigidSetB, rigidSetD);
603	<	exclude_.removePairs(rigidSetC, rigidSetD);
598	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
599	>	oneFourInteractions_.removePair(a, d);
600	>	} else {
601	>	excludedInteractions_.removePair(a, d);
602	>	}
603	>	}
604
605	<	/*
606	<	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());
605	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
606	>	inversion = mol->nextInversion(inversionIter)) {
607
608	<
609	<	exclude_.removePair(a, b);
610	<	exclude_.removePair(a, c);
611	<	exclude_.removePair(a, d);
612	<	exclude_.removePair(b, c);
613	<	exclude_.removePair(b, d);
614	<	exclude_.removePair(c, d);
615	<	*/
608	>	a = inversion->getAtomA()->getGlobalIndex();
609	>	b = inversion->getAtomB()->getGlobalIndex();
610	>	c = inversion->getAtomC()->getGlobalIndex();
611	>	d = inversion->getAtomD()->getGlobalIndex();
612	>
613	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
614	>	oneTwoInteractions_.removePair(a, b);
615	>	oneTwoInteractions_.removePair(a, c);
616	>	oneTwoInteractions_.removePair(a, d);
617	>	} else {
618	>	excludedInteractions_.removePair(a, b);
619	>	excludedInteractions_.removePair(a, c);
620	>	excludedInteractions_.removePair(a, d);
621	>	}
622	>
623	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
624	>	oneThreeInteractions_.removePair(b, c);
625	>	oneThreeInteractions_.removePair(b, d);
626	>	oneThreeInteractions_.removePair(c, d);
627	>	} else {
628	>	excludedInteractions_.removePair(b, c);
629	>	excludedInteractions_.removePair(b, d);
630	>	excludedInteractions_.removePair(c, d);
631	>	}
632		}
633
634	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
635	<	std::vector<Atom*> atoms = rb->getAtoms();
636	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
637	<	for (int j = i + 1; j < atoms.size(); ++j) {
634	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
635	>	rb = mol->nextRigidBody(rbIter)) {
636	>	vector<Atom*> atoms = rb->getAtoms();
637	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
638	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
639		a = atoms[i]->getGlobalIndex();
640		b = atoms[j]->getGlobalIndex();
641	<	exclude_.removePair(a, b);
641	>	excludedInteractions_.removePair(a, b);
642		}
643		}
644		}
645	<
645	>
646		}
647	<
648	<
647	>
648	>
649		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
650		int curStampId;
651	<
651	>
652		//index from 0
653		curStampId = moleculeStamps_.size();
654
#	Line 583 | Line 659 | namespace oopse {
659		void SimInfo::update() {
660
661		setupSimType();
662	+	setupCutoffRadius();
663	+	setupSwitchingRadius();
664	+	setupCutoffMethod();
665	+	setupSkinThickness();
666	+	setupSwitchingFunction();
667	+	setupAccumulateBoxDipole();
668
669		#ifdef IS_MPI
670		setupFortranParallel();
671		#endif
590	–
672		setupFortranSim();
673	+	fortranInitialized_ = true;
674
593	–	//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	–
675		calcNdf();
676		calcNdfRaw();
677		calcNdfTrans();
613	–
614	–	fortranInitialized_ = true;
678		}
679	<
680	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
679	>
680	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
681		SimInfo::MoleculeIterator mi;
682		Molecule* mol;
683		Molecule::AtomIterator ai;
684		Atom* atom;
685	<	std::set<AtomType*> atomTypes;
686	<
687	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
625	<
685	>	set<AtomType*> atomTypes;
686	>
687	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
688		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
689		atomTypes.insert(atom->getAtomType());
690	<	}
691	<
690	>	}
691	>	}
692	>	return atomTypes;
693	>	}
694	>
695	>	/**
696	>	* setupCutoffRadius
697	>	*
698	>	*  If the cutoffRadius was explicitly set, use that value.
699	>	*  If the cutoffRadius was not explicitly set:
700	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
701	>	*      No electrostatic atoms?  Poll the atom types present in the
702	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
703	>	*      Use the maximum suggested value that was found.
704	>	*/
705	>	void SimInfo::setupCutoffRadius() {
706	>
707	>	if (simParams_->haveCutoffRadius()) {
708	>	cutoffRadius_ = simParams_->getCutoffRadius();
709	>	} else {
710	>	if (usesElectrostaticAtoms_) {
711	>	sprintf(painCave.errMsg,
712	>	"SimInfo Warning: No value was set for the cutoffRadius.\n"
713	>	"\tOpenMD will use a default value of 12.0 angstroms"
714	>	"\tfor the cutoffRadius.\n");
715	>	painCave.isFatal = 0;
716	>	simError();
717	>	cutoffRadius_ = 12.0;
718	>	} else {
719	>	RealType thisCut;
720	>	set<AtomType*>::iterator i;
721	>	set<AtomType*> atomTypes;
722	>	atomTypes = getSimulatedAtomTypes();
723	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
724	>	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
725	>	cutoffRadius_ = max(thisCut, cutoffRadius_);
726	>	}
727	>	sprintf(painCave.errMsg,
728	>	"SimInfo Warning: No value was set for the cutoffRadius.\n"
729	>	"\tOpenMD will use %lf angstroms.\n",
730	>	cutoffRadius_);
731	>	painCave.isFatal = 0;
732	>	simError();
733	>	}
734		}
735
736	<	return atomTypes;
736	>	InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
737		}
738	<
739	<	void SimInfo::setupSimType() {
740	<	std::set<AtomType*>::iterator i;
741	<	std::set<AtomType*> atomTypes;
742	<	atomTypes = getUniqueAtomTypes();
738	>
739	>	/**
740	>	* setupSwitchingRadius
741	>	*
742	>	*  If the switchingRadius was explicitly set, use that value (but check it)
743	>	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
744	>	*/
745	>	void SimInfo::setupSwitchingRadius() {
746
747	<	int useLennardJones = 0;
748	<	int useElectrostatic = 0;
749	<	int useEAM = 0;
750	<	int useSC = 0;
751	<	int useCharge = 0;
752	<	int useDirectional = 0;
753	<	int useDipole = 0;
754	<	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;
747	>	if (simParams_->haveSwitchingRadius()) {
748	>	switchingRadius_ = simParams_->getSwitchingRadius();
749	>	if (switchingRadius_ > cutoffRadius_) {
750	>	sprintf(painCave.errMsg,
751	>	"SimInfo Error: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
752	>	switchingRadius_, cutoffRadius_);
753	>	painCave.isFatal = 1;
754	>	simError();
755
756	<	// set the useRF logical
757	<	useRF = 0;
758	<	useSF = 0;
756	>	}
757	>	} else {
758	>	switchingRadius_ = 0.85 * cutoffRadius_;
759	>	sprintf(painCave.errMsg,
760	>	"SimInfo Warning: No value was set for the switchingRadius.\n"
761	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
762	>	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
763	>	painCave.isFatal = 0;
764	>	simError();
765	>	}
766	>	InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
767	>	}
768
769	+	/**
770	+	* setupSkinThickness
771	+	*
772	+	*  If the skinThickness was explicitly set, use that value (but check it)
773	+	*  If the skinThickness was not explicitly set: use 1.0 angstroms
774	+	*/
775	+	void SimInfo::setupSkinThickness() {
776	+	if (simParams_->haveSkinThickness()) {
777	+	skinThickness_ = simParams_->getSkinThickness();
778	+	} else {
779	+	skinThickness_ = 1.0;
780	+	sprintf(painCave.errMsg,
781	+	"SimInfo Warning: No value was set for the skinThickness.\n"
782	+	"\tOpenMD will use a default value of %f Angstroms\n"
783	+	"\tfor this simulation\n", skinThickness_);
784	+	painCave.isFatal = 0;
785	+	simError();
786	+	}
787	+	}
788
789	<	if (simParams_->haveElectrostaticSummationMethod()) {
790	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
791	<	toUpper(myMethod);
792	<	if (myMethod == "REACTION_FIELD") {
669	<	useRF=1;
670	<	} else {
671	<	if (myMethod == "SHIFTED_FORCE") {
672	<	useSF = 1;
673	<	}
674	<	}
675	<	}
789	>	void SimInfo::setupSimType() {
790	>	set<AtomType*>::iterator i;
791	>	set<AtomType*> atomTypes;
792	>	atomTypes = getSimulatedAtomTypes();
793
794	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
795	+
796	+	int usesElectrostatic = 0;
797	+	int usesMetallic = 0;
798	+	int usesDirectional = 0;
799		//loop over all of the atom types
800		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
801	<	useLennardJones |= (*i)->isLennardJones();
802	<	useElectrostatic |= (*i)->isElectrostatic();
803	<	useEAM |= (*i)->isEAM();
682	<	useSC |= (*i)->isSC();
683	<	useCharge |= (*i)->isCharge();
684	<	useDirectional |= (*i)->isDirectional();
685	<	useDipole |= (*i)->isDipole();
686	<	useGayBerne |= (*i)->isGayBerne();
687	<	useSticky |= (*i)->isSticky();
688	<	useStickyPower |= (*i)->isStickyPower();
689	<	useShape |= (*i)->isShape();
801	>	usesElectrostatic |= (*i)->isElectrostatic();
802	>	usesMetallic |= (*i)->isMetal();
803	>	usesDirectional |= (*i)->isDirectional();
804		}
805
692	–	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
693	–	useDirectionalAtom = 1;
694	–	}
695	–
696	–	if (useCharge || useDipole) {
697	–	useElectrostatics = 1;
698	–	}
699	–
806		#ifdef IS_MPI
807		int temp;
808	<
809	<	temp = usePBC;
704	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
705	<
706	<	temp = useDirectionalAtom;
707	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
708	<
709	<	temp = useLennardJones;
710	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
711	<
712	<	temp = useElectrostatics;
713	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
714	<
715	<	temp = useCharge;
716	<	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);
808	>	temp = usesDirectional;
809	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810
811	<	temp = useSticky;
812	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
811	>	temp = usesMetallic;
812	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813
814	<	temp = useStickyPower;
815	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
726	<
727	<	temp = useGayBerne;
728	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
729	<
730	<	temp = useEAM;
731	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
732	<
733	<	temp = useSC;
734	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
735	<
736	<	temp = useShape;
737	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
738	<
739	<	temp = useFLARB;
740	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
741	<
742	<	temp = useRF;
743	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
744	<
745	<	temp = useSF;
746	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
747	<
814	>	temp = usesElectrostatic;
815	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816		#endif
817	<
818	<	fInfo_.SIM_uses_PBC = usePBC;
819	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
820	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
821	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
822	<	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;
765	<
766	<	if( myMethod == "REACTION_FIELD") {
767	<
768	<	if (simParams_->haveDielectric()) {
769	<	fInfo_.dielect = simParams_->getDielectric();
770	<	} else {
771	<	sprintf(painCave.errMsg,
772	<	"SimSetup Error: No Dielectric constant was set.\n"
773	<	"\tYou are trying to use Reaction Field without"
774	<	"\tsetting a dielectric constant!\n");
775	<	painCave.isFatal = 1;
776	<	simError();
777	<	}
778	<	}
779	<
817	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
818	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
819	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
820	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
821	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
822	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
823		}
824
825		void SimInfo::setupFortranSim() {
826		int isError;
827	<	int nExclude;
828	<	std::vector<int> fortranGlobalGroupMembership;
827	>	int nExclude, nOneTwo, nOneThree, nOneFour;
828	>	vector<int> fortranGlobalGroupMembership;
829
830	<	nExclude = exclude_.getSize();
830	>	notifyFortranSkinThickness(&skinThickness_);
831	>
832	>	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
833	>	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
834	>	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
835	>
836		isError = 0;
837
838		//globalGroupMembership_ is filled by SimCreator
#	Line 793 | Line 841 | namespace oopse {
841		}
842
843		//calculate mass ratio of cutoff group
844	<	std::vector<double> mfact;
844	>	vector<RealType> mfact;
845		SimInfo::MoleculeIterator mi;
846		Molecule* mol;
847		Molecule::CutoffGroupIterator ci;
848		CutoffGroup* cg;
849		Molecule::AtomIterator ai;
850		Atom* atom;
851	<	double totalMass;
851	>	RealType totalMass;
852
853		//to avoid memory reallocation, reserve enough space for mfact
854		mfact.reserve(getNCutoffGroups());
#	Line 816 | Line 864 | namespace oopse {
864		else
865		mfact.push_back( 1.0 );
866		}
819	–
867		}
868		}
869
870		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
871	<	std::vector<int> identArray;
871	>	vector<int> identArray;
872
873		//to avoid memory reallocation, reserve enough space identArray
874		identArray.reserve(getNAtoms());
#	Line 834 | Line 881 | namespace oopse {
881
882		//fill molMembershipArray
883		//molMembershipArray is filled by SimCreator
884	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
884	>	vector<int> molMembershipArray(nGlobalAtoms_);
885		for (int i = 0; i < nGlobalAtoms_; i++) {
886		molMembershipArray[i] = globalMolMembership_[i] + 1;
887		}
888
889		//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);
890
891	<	if( isError ){
891	>	nExclude = excludedInteractions_.getSize();
892	>	nOneTwo = oneTwoInteractions_.getSize();
893	>	nOneThree = oneThreeInteractions_.getSize();
894	>	nOneFour = oneFourInteractions_.getSize();
895
896	+	int* excludeList = excludedInteractions_.getPairList();
897	+	int* oneTwoList = oneTwoInteractions_.getPairList();
898	+	int* oneThreeList = oneThreeInteractions_.getPairList();
899	+	int* oneFourList = oneFourInteractions_.getPairList();
900	+
901	+	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
902	+	&nExclude, excludeList,
903	+	&nOneTwo, oneTwoList,
904	+	&nOneThree, oneThreeList,
905	+	&nOneFour, oneFourList,
906	+	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
907	+	&fortranGlobalGroupMembership[0], &isError);
908	+
909	+	if( isError ){
910	+
911		sprintf( painCave.errMsg,
912		"There was an error setting the simulation information in fortran.\n" );
913		painCave.isFatal = 1;
914	<	painCave.severity = OOPSE_ERROR;
914	>	painCave.severity = OPENMD_ERROR;
915		simError();
916		}
917	<
918	<	#ifdef IS_MPI
917	>
918	>
919		sprintf( checkPointMsg,
920		"succesfully sent the simulation information to fortran.\n");
921	<	MPIcheckPoint();
922	<	#endif // is_mpi
921	>
922	>	errorCheckPoint();
923	>
924	>	// Setup number of neighbors in neighbor list if present
925	>	if (simParams_->haveNeighborListNeighbors()) {
926	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
927	>	setNeighbors(&nlistNeighbors);
928	>	}
929	>
930	>
931		}
932
933
867	–	#ifdef IS_MPI
934		void SimInfo::setupFortranParallel() {
935	<
935	>	#ifdef IS_MPI
936		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
937	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
938	<	std::vector<int> localToGlobalCutoffGroupIndex;
937	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
938	>	vector<int> localToGlobalCutoffGroupIndex;
939		SimInfo::MoleculeIterator mi;
940		Molecule::AtomIterator ai;
941		Molecule::CutoffGroupIterator ci;
#	Line 916 | Line 982 | namespace oopse {
982		}
983
984		sprintf(checkPointMsg, " mpiRefresh successful.\n");
985	<	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	<	}
985	>	errorCheckPoint();
986
941	–	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
942	–	#ifdef IS_MPI
943	–	//pick the max cutoff radius among the processors
987		#endif
945	–
946	–	return maxCutoffRadius;
988		}
989
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	–	}
990
991		void SimInfo::setupSwitchingFunction() {
992		int ft = CUBIC;
993	<
993	>
994		if (simParams_->haveSwitchingFunctionType()) {
995	<	std::string funcType = simParams_->getSwitchingFunctionType();
995	>	string funcType = simParams_->getSwitchingFunctionType();
996		toUpper(funcType);
997		if (funcType == "CUBIC") {
998		ft = CUBIC;
#	Line 1122 | Line 1002 | namespace oopse {
1002		} else {
1003		// throw error
1004		sprintf( painCave.errMsg,
1005	<	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1005	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n"
1006	>	"\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".",
1007	>	funcType.c_str() );
1008		painCave.isFatal = 1;
1009		simError();
1010		}
#	Line 1134 | Line 1016 | namespace oopse {
1016
1017		}
1018
1019	+	void SimInfo::setupAccumulateBoxDipole() {
1020	+
1021	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1022	+	if ( simParams_->haveAccumulateBoxDipole() )
1023	+	if ( simParams_->getAccumulateBoxDipole() ) {
1024	+	calcBoxDipole_ = true;
1025	+	}
1026	+
1027	+	}
1028	+
1029		void SimInfo::addProperty(GenericData* genData) {
1030		properties_.addProperty(genData);
1031		}
1032
1033	<	void SimInfo::removeProperty(const std::string& propName) {
1033	>	void SimInfo::removeProperty(const string& propName) {
1034		properties_.removeProperty(propName);
1035		}
1036
#	Line 1146 | Line 1038 | namespace oopse {
1038		properties_.clearProperties();
1039		}
1040
1041	<	std::vector<std::string> SimInfo::getPropertyNames() {
1041	>	vector<string> SimInfo::getPropertyNames() {
1042		return properties_.getPropertyNames();
1043		}
1044
1045	<	std::vector<GenericData*> SimInfo::getProperties() {
1045	>	vector<GenericData*> SimInfo::getProperties() {
1046		return properties_.getProperties();
1047		}
1048
1049	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1049	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1050		return properties_.getPropertyByName(propName);
1051		}
1052
#	Line 1190 | Line 1082 | namespace oopse {
1082		Molecule* mol;
1083
1084		Vector3d comVel(0.0);
1085	<	double totalMass = 0.0;
1085	>	RealType totalMass = 0.0;
1086
1087
1088		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1089	<	double mass = mol->getMass();
1089	>	RealType mass = mol->getMass();
1090		totalMass += mass;
1091		comVel += mass * mol->getComVel();
1092		}
1093
1094		#ifdef IS_MPI
1095	<	double tmpMass = totalMass;
1095	>	RealType tmpMass = totalMass;
1096		Vector3d tmpComVel(comVel);
1097	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1098	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1097	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1098	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1099		#endif
1100
1101		comVel /= totalMass;
#	Line 1216 | Line 1108 | namespace oopse {
1108		Molecule* mol;
1109
1110		Vector3d com(0.0);
1111	<	double totalMass = 0.0;
1111	>	RealType totalMass = 0.0;
1112
1113		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1114	<	double mass = mol->getMass();
1114	>	RealType mass = mol->getMass();
1115		totalMass += mass;
1116		com += mass * mol->getCom();
1117		}
1118
1119		#ifdef IS_MPI
1120	<	double tmpMass = totalMass;
1120	>	RealType tmpMass = totalMass;
1121		Vector3d tmpCom(com);
1122	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1123	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1122	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1123	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1124		#endif
1125
1126		com /= totalMass;
#	Line 1237 | Line 1129 | namespace oopse {
1129
1130		}
1131
1132	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1132	>	ostream& operator <<(ostream& o, SimInfo& info) {
1133
1134		return o;
1135		}
#	Line 1252 | Line 1144 | namespace oopse {
1144		Molecule* mol;
1145
1146
1147	<	double totalMass = 0.0;
1147	>	RealType totalMass = 0.0;
1148
1149
1150		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1151	<	double mass = mol->getMass();
1151	>	RealType mass = mol->getMass();
1152		totalMass += mass;
1153		com += mass * mol->getCom();
1154		comVel += mass * mol->getComVel();
1155		}
1156
1157		#ifdef IS_MPI
1158	<	double tmpMass = totalMass;
1158	>	RealType tmpMass = totalMass;
1159		Vector3d tmpCom(com);
1160		Vector3d tmpComVel(comVel);
1161	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1162	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1163	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1161	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1162	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1163	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1164		#endif
1165
1166		com /= totalMass;
#	Line 1280 | Line 1172 | namespace oopse {
1172
1173
1174		[  Ixx -Ixy  -Ixz ]
1175	<	J =| -Iyx  Iyy  -Iyz |
1175	>	J =| -Iyx  Iyy  -Iyz |
1176		[ -Izx -Iyz   Izz ]
1177		*/
1178
1179		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1180
1181
1182	<	double xx = 0.0;
1183	<	double yy = 0.0;
1184	<	double zz = 0.0;
1185	<	double xy = 0.0;
1186	<	double xz = 0.0;
1187	<	double yz = 0.0;
1182	>	RealType xx = 0.0;
1183	>	RealType yy = 0.0;
1184	>	RealType zz = 0.0;
1185	>	RealType xy = 0.0;
1186	>	RealType xz = 0.0;
1187	>	RealType yz = 0.0;
1188		Vector3d com(0.0);
1189		Vector3d comVel(0.0);
1190
#	Line 1304 | Line 1196 | namespace oopse {
1196		Vector3d thisq(0.0);
1197		Vector3d thisv(0.0);
1198
1199	<	double thisMass = 0.0;
1199	>	RealType thisMass = 0.0;
1200
1201
1202
#	Line 1342 | Line 1234 | namespace oopse {
1234		#ifdef IS_MPI
1235		Mat3x3d tmpI(inertiaTensor);
1236		Vector3d tmpAngMom;
1237	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1238	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1237	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1238	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1239		#endif
1240
1241		return;
#	Line 1364 | Line 1256 | namespace oopse {
1256		Vector3d thisr(0.0);
1257		Vector3d thisp(0.0);
1258
1259	<	double thisMass;
1259	>	RealType thisMass;
1260
1261		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1262		thisMass = mol->getMass();
#	Line 1377 | Line 1269 | namespace oopse {
1269
1270		#ifdef IS_MPI
1271		Vector3d tmpAngMom;
1272	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1272	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1273		#endif
1274
1275		return angularMomentum;
1276		}
1277
1278	<
1279	<	}//end namespace oopse
1278	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1279	>	return IOIndexToIntegrableObject.at(index);
1280	>	}
1281	>
1282	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1283	>	IOIndexToIntegrableObject= v;
1284	>	}
1285
1286	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1287	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1288	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1289	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1290	+	*/
1291	+	void SimInfo::getGyrationalVolume(RealType &volume){
1292	+	Mat3x3d intTensor;
1293	+	RealType det;
1294	+	Vector3d dummyAngMom;
1295	+	RealType sysconstants;
1296	+	RealType geomCnst;
1297	+
1298	+	geomCnst = 3.0/2.0;
1299	+	/* Get the inertial tensor and angular momentum for free*/
1300	+	getInertiaTensor(intTensor,dummyAngMom);
1301	+
1302	+	det = intTensor.determinant();
1303	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1304	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1305	+	return;
1306	+	}
1307	+
1308	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1309	+	Mat3x3d intTensor;
1310	+	Vector3d dummyAngMom;
1311	+	RealType sysconstants;
1312	+	RealType geomCnst;
1313	+
1314	+	geomCnst = 3.0/2.0;
1315	+	/* Get the inertial tensor and angular momentum for free*/
1316	+	getInertiaTensor(intTensor,dummyAngMom);
1317	+
1318	+	detI = intTensor.determinant();
1319	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1320	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1321	+	return;
1322	+	}
1323	+	/*
1324	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1325	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1326	+	sdByGlobalIndex_ = v;
1327	+	}
1328	+
1329	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1330	+	//assert(index < nAtoms_ + nRigidBodies_);
1331	+	return sdByGlobalIndex_.at(index);
1332	+	}
1333	+	*/
1334	+	int SimInfo::getNGlobalConstraints() {
1335	+	int nGlobalConstraints;
1336	+	#ifdef IS_MPI
1337	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1338	+	MPI_COMM_WORLD);
1339	+	#else
1340	+	nGlobalConstraints =  nConstraints_;
1341	+	#endif
1342	+	return nGlobalConstraints;
1343	+	}
1344	+
1345	+	}//end namespace OpenMD
1346	+

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 1529 by gezelter, Mon Dec 27 18:35:59 2010 UTC

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