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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 834 by chuckv, Fri Dec 30 23:15:59 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1549 by gezelter, Wed Apr 27 18:38:15 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"
56	>	#include "primitives/StuntDouble.hpp"
57	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
58		#include "UseTheForce/doForces_interface.h"
61	–	#include "UseTheForce/DarkSide/electrostatic_interface.h"
62	–	#include "UseTheForce/DarkSide/switcheroo_interface.h"
59		#include "utils/MemoryUtils.hpp"
60		#include "utils/simError.h"
61		#include "selection/SelectionManager.hpp"
62		#include "io/ForceFieldOptions.hpp"
63		#include "UseTheForce/ForceField.hpp"
64	+	#include "nonbonded/SwitchingFunction.hpp"
65
66		#ifdef IS_MPI
67		#include "UseTheForce/mpiComponentPlan.h"
68		#include "UseTheForce/DarkSide/simParallel_interface.h"
69		#endif
70
71	<	namespace oopse {
72	<	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	<	}
71	>	using namespace std;
72	>	namespace OpenMD {
73
74		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
75		forceField_(ff), simParams_(simParams),
76	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
76	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
77		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
78		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
79	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
80	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
81	<	sman_(NULL), fortranInitialized_(false) {
82	<
83	<	MoleculeStamp* molStamp;
84	<	int nMolWithSameStamp;
85	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
86	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
87	<	CutoffGroupStamp* cgStamp;
88	<	RigidBodyStamp* rbStamp;
89	<	int nRigidAtoms = 0;
90	<	std::vector<Component*> components = simParams->getComponents();
79	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
80	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
81	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
82	>	calcBoxDipole_(false), useAtomicVirial_(true) {
83	>
84	>	MoleculeStamp* molStamp;
85	>	int nMolWithSameStamp;
86	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
88	>	CutoffGroupStamp* cgStamp;
89	>	RigidBodyStamp* rbStamp;
90	>	int nRigidAtoms = 0;
91	>
92	>	vector<Component*> components = simParams->getComponents();
93	>
94	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
95	>	molStamp = (*i)->getMoleculeStamp();
96	>	nMolWithSameStamp = (*i)->getNMol();
97
98	<	for (std::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();
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	<
98	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
99	>
100	>	//calculate atoms in molecules
101	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
102	>
103	>	//calculate atoms in cutoff groups
104	>	int nAtomsInGroups = 0;
105	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
106	>
107	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
108	>	cgStamp = molStamp->getCutoffGroupStamp(j);
109	>	nAtomsInGroups += cgStamp->getNMembers();
110		}
111	+
112	+	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
113	+
114	+	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
115	+
116	+	//calculate atoms in rigid bodies
117	+	int nAtomsInRigidBodies = 0;
118	+	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
119	+
120	+	for (int j=0; j < nRigidBodiesInStamp; j++) {
121	+	rbStamp = molStamp->getRigidBodyStamp(j);
122	+	nAtomsInRigidBodies += rbStamp->getNMembers();
123	+	}
124	+
125	+	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
126	+	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
127	+
128	+	}
129	+
130	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
131	+	//group therefore the total number of cutoff groups in the system is
132	+	//equal to the total number of atoms minus number of atoms belong to
133	+	//cutoff group defined in meta-data file plus the number of cutoff
134	+	//groups defined in meta-data file
135	+	std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
136	+	std::cerr << "nCA = " << nCutoffAtoms << "\n";
137	+	std::cerr << "nG = " << nGroups << "\n";
138
139	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
140	<	//group therefore the total number of cutoff groups in the system is
141	<	//equal to the total number of atoms minus number of atoms belong to
142	<	//cutoff group defined in meta-data file plus the number of cutoff
143	<	//groups defined in meta-data file
144	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
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_;
141	>	std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
142	>
143	>	//every free atom (atom does not belong to rigid bodies) is an
144	>	//integrable object therefore the total number of integrable objects
145	>	//in the system is equal to the total number of atoms minus number of
146	>	//atoms belong to rigid body defined in meta-data file plus the number
147	>	//of rigid bodies defined in meta-data file
148	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
149	>	+ nGlobalRigidBodies_;
150	>
151	>	nGlobalMols_ = molStampIds_.size();
152	>	molToProcMap_.resize(nGlobalMols_);
153	>	}
154
154	–	nGlobalMols_ = molStampIds_.size();
155	–
156	–	#ifdef IS_MPI
157	–	molToProcMap_.resize(nGlobalMols_);
158	–	#endif
159	–
160	–	}
161	–
155		SimInfo::~SimInfo() {
156	<	std::map<int, Molecule*>::iterator i;
156	>	map<int, Molecule*>::iterator i;
157		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
158		delete i->second;
159		}
#	Line 171 | Line 164 | namespace oopse {
164		delete forceField_;
165		}
166
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	–	}
167
168		bool SimInfo::addMolecule(Molecule* mol) {
169		MoleculeIterator i;
170	<
170	>
171		i = molecules_.find(mol->getGlobalIndex());
172		if (i == molecules_.end() ) {
173	<
174	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
175	<
173	>
174	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
175	>
176		nAtoms_ += mol->getNAtoms();
177		nBonds_ += mol->getNBonds();
178		nBends_ += mol->getNBends();
179		nTorsions_ += mol->getNTorsions();
180	+	nInversions_ += mol->getNInversions();
181		nRigidBodies_ += mol->getNRigidBodies();
182		nIntegrableObjects_ += mol->getNIntegrableObjects();
183		nCutoffGroups_ += mol->getNCutoffGroups();
184		nConstraints_ += mol->getNConstraintPairs();
185	<
186	<	addExcludePairs(mol);
187	<
185	>
186	>	addInteractionPairs(mol);
187	>
188		return true;
189		} else {
190		return false;
191		}
192		}
193	<
193	>
194		bool SimInfo::removeMolecule(Molecule* mol) {
195		MoleculeIterator i;
196		i = molecules_.find(mol->getGlobalIndex());
#	Line 219 | Line 203 | namespace oopse {
203		nBonds_ -= mol->getNBonds();
204		nBends_ -= mol->getNBends();
205		nTorsions_ -= mol->getNTorsions();
206	+	nInversions_ -= mol->getNInversions();
207		nRigidBodies_ -= mol->getNRigidBodies();
208		nIntegrableObjects_ -= mol->getNIntegrableObjects();
209		nCutoffGroups_ -= mol->getNCutoffGroups();
210		nConstraints_ -= mol->getNConstraintPairs();
211
212	<	removeExcludePairs(mol);
212	>	removeInteractionPairs(mol);
213		molecules_.erase(mol->getGlobalIndex());
214
215		delete mol;
#	Line 233 | Line 218 | namespace oopse {
218		} else {
219		return false;
220		}
236	–
237	–
221		}
222
223
#	Line 252 | Line 235 | namespace oopse {
235		void SimInfo::calcNdf() {
236		int ndf_local;
237		MoleculeIterator i;
238	<	std::vector<StuntDouble*>::iterator j;
238	>	vector<StuntDouble*>::iterator j;
239		Molecule* mol;
240		StuntDouble* integrableObject;
241
#	Line 290 | Line 273 | namespace oopse {
273
274		}
275
276	+	int SimInfo::getFdf() {
277	+	#ifdef IS_MPI
278	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
279	+	#else
280	+	fdf_ = fdf_local;
281	+	#endif
282	+	return fdf_;
283	+	}
284	+
285		void SimInfo::calcNdfRaw() {
286		int ndfRaw_local;
287
288		MoleculeIterator i;
289	<	std::vector<StuntDouble*>::iterator j;
289	>	vector<StuntDouble*>::iterator j;
290		Molecule* mol;
291		StuntDouble* integrableObject;
292
#	Line 341 | Line 333 | namespace oopse {
333
334		}
335
336	<	void SimInfo::addExcludePairs(Molecule* mol) {
337	<	std::vector<Bond*>::iterator bondIter;
338	<	std::vector<Bend*>::iterator bendIter;
339	<	std::vector<Torsion*>::iterator torsionIter;
336	>	void SimInfo::addInteractionPairs(Molecule* mol) {
337	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
338	>	vector<Bond*>::iterator bondIter;
339	>	vector<Bend*>::iterator bendIter;
340	>	vector<Torsion*>::iterator torsionIter;
341	>	vector<Inversion*>::iterator inversionIter;
342		Bond* bond;
343		Bend* bend;
344		Torsion* torsion;
345	+	Inversion* inversion;
346		int a;
347		int b;
348		int c;
349		int d;
350
351	<	std::map<int, std::set<int> > atomGroups;
351	>	// atomGroups can be used to add special interaction maps between
352	>	// groups of atoms that are in two separate rigid bodies.
353	>	// However, most site-site interactions between two rigid bodies
354	>	// are probably not special, just the ones between the physically
355	>	// bonded atoms.  Interactions *within* a single rigid body should
356	>	// always be excluded.  These are done at the bottom of this
357	>	// function.
358
359	+	map<int, set<int> > atomGroups;
360		Molecule::RigidBodyIterator rbIter;
361		RigidBody* rb;
362		Molecule::IntegrableObjectIterator ii;
363		StuntDouble* integrableObject;
364
365	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
366	<	integrableObject = mol->nextIntegrableObject(ii)) {
367	<
365	>	for (integrableObject = mol->beginIntegrableObject(ii);
366	>	integrableObject != NULL;
367	>	integrableObject = mol->nextIntegrableObject(ii)) {
368	>
369		if (integrableObject->isRigidBody()) {
370	<	rb = static_cast<RigidBody*>(integrableObject);
371	<	std::vector<Atom*> atoms = rb->getAtoms();
372	<	std::set<int> rigidAtoms;
373	<	for (int i = 0; i < atoms.size(); ++i) {
374	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
375	<	}
376	<	for (int i = 0; i < atoms.size(); ++i) {
377	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
378	<	}
370	>	rb = static_cast<RigidBody*>(integrableObject);
371	>	vector<Atom*> atoms = rb->getAtoms();
372	>	set<int> rigidAtoms;
373	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
374	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
375	>	}
376	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
377	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
378	>	}
379		} else {
380	<	std::set<int> oneAtomSet;
380	>	set<int> oneAtomSet;
381		oneAtomSet.insert(integrableObject->getGlobalIndex());
382	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
382	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
383		}
384		}
385	+
386	+	for (bond= mol->beginBond(bondIter); bond != NULL;
387	+	bond = mol->nextBond(bondIter)) {
388
383	–
384	–
385	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
389		a = bond->getAtomA()->getGlobalIndex();
390	<	b = bond->getAtomB()->getGlobalIndex();
391	<	exclude_.addPair(a, b);
390	>	b = bond->getAtomB()->getGlobalIndex();
391	>
392	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
393	>	oneTwoInteractions_.addPair(a, b);
394	>	} else {
395	>	excludedInteractions_.addPair(a, b);
396	>	}
397		}
398
399	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
399	>	for (bend= mol->beginBend(bendIter); bend != NULL;
400	>	bend = mol->nextBend(bendIter)) {
401	>
402		a = bend->getAtomA()->getGlobalIndex();
403		b = bend->getAtomB()->getGlobalIndex();
404		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);
405
406	<	//exclude_.addPair(a, b);
407	<	//exclude_.addPair(a, c);
408	<	//exclude_.addPair(b, c);
406	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
407	>	oneTwoInteractions_.addPair(a, b);
408	>	oneTwoInteractions_.addPair(b, c);
409	>	} else {
410	>	excludedInteractions_.addPair(a, b);
411	>	excludedInteractions_.addPair(b, c);
412	>	}
413	>
414	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
415	>	oneThreeInteractions_.addPair(a, c);
416	>	} else {
417	>	excludedInteractions_.addPair(a, c);
418	>	}
419		}
420
421	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
421	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
422	>	torsion = mol->nextTorsion(torsionIter)) {
423	>
424		a = torsion->getAtomA()->getGlobalIndex();
425		b = torsion->getAtomB()->getGlobalIndex();
426		c = torsion->getAtomC()->getGlobalIndex();
427	<	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);
427	>	d = torsion->getAtomD()->getGlobalIndex();
428
429	<	exclude_.addPairs(rigidSetA, rigidSetB);
430	<	exclude_.addPairs(rigidSetA, rigidSetC);
431	<	exclude_.addPairs(rigidSetA, rigidSetD);
432	<	exclude_.addPairs(rigidSetB, rigidSetC);
433	<	exclude_.addPairs(rigidSetB, rigidSetD);
434	<	exclude_.addPairs(rigidSetC, rigidSetD);
429	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
430	>	oneTwoInteractions_.addPair(a, b);
431	>	oneTwoInteractions_.addPair(b, c);
432	>	oneTwoInteractions_.addPair(c, d);
433	>	} else {
434	>	excludedInteractions_.addPair(a, b);
435	>	excludedInteractions_.addPair(b, c);
436	>	excludedInteractions_.addPair(c, d);
437	>	}
438
439	<	/*
440	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
441	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
442	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
443	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
444	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
445	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
446	<
447	<
448	<	exclude_.addPair(a, b);
449	<	exclude_.addPair(a, c);
450	<	exclude_.addPair(a, d);
451	<	exclude_.addPair(b, c);
438	<	exclude_.addPair(b, d);
439	<	exclude_.addPair(c, d);
440	<	*/
439	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
440	>	oneThreeInteractions_.addPair(a, c);
441	>	oneThreeInteractions_.addPair(b, d);
442	>	} else {
443	>	excludedInteractions_.addPair(a, c);
444	>	excludedInteractions_.addPair(b, d);
445	>	}
446	>
447	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
448	>	oneFourInteractions_.addPair(a, d);
449	>	} else {
450	>	excludedInteractions_.addPair(a, d);
451	>	}
452		}
453
454	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
455	<	std::vector<Atom*> atoms = rb->getAtoms();
456	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
457	<	for (int j = i + 1; j < atoms.size(); ++j) {
454	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
455	>	inversion = mol->nextInversion(inversionIter)) {
456	>
457	>	a = inversion->getAtomA()->getGlobalIndex();
458	>	b = inversion->getAtomB()->getGlobalIndex();
459	>	c = inversion->getAtomC()->getGlobalIndex();
460	>	d = inversion->getAtomD()->getGlobalIndex();
461	>
462	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
463	>	oneTwoInteractions_.addPair(a, b);
464	>	oneTwoInteractions_.addPair(a, c);
465	>	oneTwoInteractions_.addPair(a, d);
466	>	} else {
467	>	excludedInteractions_.addPair(a, b);
468	>	excludedInteractions_.addPair(a, c);
469	>	excludedInteractions_.addPair(a, d);
470	>	}
471	>
472	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
473	>	oneThreeInteractions_.addPair(b, c);
474	>	oneThreeInteractions_.addPair(b, d);
475	>	oneThreeInteractions_.addPair(c, d);
476	>	} else {
477	>	excludedInteractions_.addPair(b, c);
478	>	excludedInteractions_.addPair(b, d);
479	>	excludedInteractions_.addPair(c, d);
480	>	}
481	>	}
482	>
483	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
484	>	rb = mol->nextRigidBody(rbIter)) {
485	>	vector<Atom*> atoms = rb->getAtoms();
486	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
487	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
488		a = atoms[i]->getGlobalIndex();
489		b = atoms[j]->getGlobalIndex();
490	<	exclude_.addPair(a, b);
490	>	excludedInteractions_.addPair(a, b);
491		}
492		}
493		}
494
495		}
496
497	<	void SimInfo::removeExcludePairs(Molecule* mol) {
498	<	std::vector<Bond*>::iterator bondIter;
499	<	std::vector<Bend*>::iterator bendIter;
500	<	std::vector<Torsion*>::iterator torsionIter;
497	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
498	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
499	>	vector<Bond*>::iterator bondIter;
500	>	vector<Bend*>::iterator bendIter;
501	>	vector<Torsion*>::iterator torsionIter;
502	>	vector<Inversion*>::iterator inversionIter;
503		Bond* bond;
504		Bend* bend;
505		Torsion* torsion;
506	+	Inversion* inversion;
507		int a;
508		int b;
509		int c;
510		int d;
511
512	<	std::map<int, std::set<int> > atomGroups;
469	<
512	>	map<int, set<int> > atomGroups;
513		Molecule::RigidBodyIterator rbIter;
514		RigidBody* rb;
515		Molecule::IntegrableObjectIterator ii;
516		StuntDouble* integrableObject;
517
518	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
519	<	integrableObject = mol->nextIntegrableObject(ii)) {
520	<
518	>	for (integrableObject = mol->beginIntegrableObject(ii);
519	>	integrableObject != NULL;
520	>	integrableObject = mol->nextIntegrableObject(ii)) {
521	>
522		if (integrableObject->isRigidBody()) {
523	<	rb = static_cast<RigidBody*>(integrableObject);
524	<	std::vector<Atom*> atoms = rb->getAtoms();
525	<	std::set<int> rigidAtoms;
526	<	for (int i = 0; i < atoms.size(); ++i) {
527	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
528	<	}
529	<	for (int i = 0; i < atoms.size(); ++i) {
530	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
531	<	}
523	>	rb = static_cast<RigidBody*>(integrableObject);
524	>	vector<Atom*> atoms = rb->getAtoms();
525	>	set<int> rigidAtoms;
526	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
527	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
528	>	}
529	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
530	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
531	>	}
532		} else {
533	<	std::set<int> oneAtomSet;
533	>	set<int> oneAtomSet;
534		oneAtomSet.insert(integrableObject->getGlobalIndex());
535	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
535	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
536		}
537		}
538
539	<
540	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
539	>	for (bond= mol->beginBond(bondIter); bond != NULL;
540	>	bond = mol->nextBond(bondIter)) {
541	>
542		a = bond->getAtomA()->getGlobalIndex();
543	<	b = bond->getAtomB()->getGlobalIndex();
544	<	exclude_.removePair(a, b);
543	>	b = bond->getAtomB()->getGlobalIndex();
544	>
545	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
546	>	oneTwoInteractions_.removePair(a, b);
547	>	} else {
548	>	excludedInteractions_.removePair(a, b);
549	>	}
550		}
551
552	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
552	>	for (bend= mol->beginBend(bendIter); bend != NULL;
553	>	bend = mol->nextBend(bendIter)) {
554	>
555		a = bend->getAtomA()->getGlobalIndex();
556		b = bend->getAtomB()->getGlobalIndex();
557		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);
558
559	<	//exclude_.removePair(a, b);
560	<	//exclude_.removePair(a, c);
561	<	//exclude_.removePair(b, c);
559	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
560	>	oneTwoInteractions_.removePair(a, b);
561	>	oneTwoInteractions_.removePair(b, c);
562	>	} else {
563	>	excludedInteractions_.removePair(a, b);
564	>	excludedInteractions_.removePair(b, c);
565	>	}
566	>
567	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
568	>	oneThreeInteractions_.removePair(a, c);
569	>	} else {
570	>	excludedInteractions_.removePair(a, c);
571	>	}
572		}
573
574	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
574	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
575	>	torsion = mol->nextTorsion(torsionIter)) {
576	>
577		a = torsion->getAtomA()->getGlobalIndex();
578		b = torsion->getAtomB()->getGlobalIndex();
579		c = torsion->getAtomC()->getGlobalIndex();
580	<	d = torsion->getAtomD()->getGlobalIndex();
580	>	d = torsion->getAtomD()->getGlobalIndex();
581	>
582	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
583	>	oneTwoInteractions_.removePair(a, b);
584	>	oneTwoInteractions_.removePair(b, c);
585	>	oneTwoInteractions_.removePair(c, d);
586	>	} else {
587	>	excludedInteractions_.removePair(a, b);
588	>	excludedInteractions_.removePair(b, c);
589	>	excludedInteractions_.removePair(c, d);
590	>	}
591
592	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
593	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
594	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
595	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
592	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
593	>	oneThreeInteractions_.removePair(a, c);
594	>	oneThreeInteractions_.removePair(b, d);
595	>	} else {
596	>	excludedInteractions_.removePair(a, c);
597	>	excludedInteractions_.removePair(b, d);
598	>	}
599
600	<	exclude_.removePairs(rigidSetA, rigidSetB);
601	<	exclude_.removePairs(rigidSetA, rigidSetC);
602	<	exclude_.removePairs(rigidSetA, rigidSetD);
603	<	exclude_.removePairs(rigidSetB, rigidSetC);
604	<	exclude_.removePairs(rigidSetB, rigidSetD);
605	<	exclude_.removePairs(rigidSetC, rigidSetD);
600	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
601	>	oneFourInteractions_.removePair(a, d);
602	>	} else {
603	>	excludedInteractions_.removePair(a, d);
604	>	}
605	>	}
606
607	<	/*
608	<	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());
607	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
608	>	inversion = mol->nextInversion(inversionIter)) {
609
610	<
611	<	exclude_.removePair(a, b);
612	<	exclude_.removePair(a, c);
613	<	exclude_.removePair(a, d);
614	<	exclude_.removePair(b, c);
615	<	exclude_.removePair(b, d);
616	<	exclude_.removePair(c, d);
617	<	*/
610	>	a = inversion->getAtomA()->getGlobalIndex();
611	>	b = inversion->getAtomB()->getGlobalIndex();
612	>	c = inversion->getAtomC()->getGlobalIndex();
613	>	d = inversion->getAtomD()->getGlobalIndex();
614	>
615	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
616	>	oneTwoInteractions_.removePair(a, b);
617	>	oneTwoInteractions_.removePair(a, c);
618	>	oneTwoInteractions_.removePair(a, d);
619	>	} else {
620	>	excludedInteractions_.removePair(a, b);
621	>	excludedInteractions_.removePair(a, c);
622	>	excludedInteractions_.removePair(a, d);
623	>	}
624	>
625	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
626	>	oneThreeInteractions_.removePair(b, c);
627	>	oneThreeInteractions_.removePair(b, d);
628	>	oneThreeInteractions_.removePair(c, d);
629	>	} else {
630	>	excludedInteractions_.removePair(b, c);
631	>	excludedInteractions_.removePair(b, d);
632	>	excludedInteractions_.removePair(c, d);
633	>	}
634		}
635
636	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
637	<	std::vector<Atom*> atoms = rb->getAtoms();
638	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
639	<	for (int j = i + 1; j < atoms.size(); ++j) {
636	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
637	>	rb = mol->nextRigidBody(rbIter)) {
638	>	vector<Atom*> atoms = rb->getAtoms();
639	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
640	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
641		a = atoms[i]->getGlobalIndex();
642		b = atoms[j]->getGlobalIndex();
643	<	exclude_.removePair(a, b);
643	>	excludedInteractions_.removePair(a, b);
644		}
645		}
646		}
647	<
647	>
648		}
649	<
650	<
649	>
650	>
651		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
652		int curStampId;
653	<
653	>
654		//index from 0
655		curStampId = moleculeStamps_.size();
656
#	Line 577 | Line 658 | namespace oopse {
658		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
659		}
660
580	–	void SimInfo::update() {
661
662	<	setupSimType();
663	<
664	<	#ifdef IS_MPI
665	<	setupFortranParallel();
666	<	#endif
667	<
668	<	setupFortranSim();
669	<
670	<	//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	<
662	>	/**
663	>	* update
664	>	*
665	>	*  Performs the global checks and variable settings after the
666	>	*  objects have been created.
667	>	*
668	>	*/
669	>	void SimInfo::update() {
670	>	setupSimVariables();
671		calcNdf();
672		calcNdfRaw();
673		calcNdfTrans();
610	–
611	–	fortranInitialized_ = true;
674		}
675	<
676	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
675	>
676	>	/**
677	>	* getSimulatedAtomTypes
678	>	*
679	>	* Returns an STL set of AtomType* that are actually present in this
680	>	* simulation.  Must query all processors to assemble this information.
681	>	*
682	>	*/
683	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
684		SimInfo::MoleculeIterator mi;
685		Molecule* mol;
686		Molecule::AtomIterator ai;
687		Atom* atom;
688	<	std::set<AtomType*> atomTypes;
689	<
690	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
622	<
688	>	set<AtomType*> atomTypes;
689	>
690	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
691		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
692		atomTypes.insert(atom->getAtomType());
693	<	}
694	<
627	<	}
693	>	}
694	>	}
695
696	<	return atomTypes;
630	<	}
696	>	#ifdef IS_MPI
697
698	<	void SimInfo::setupSimType() {
699	<	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;
698	>	// loop over the found atom types on this processor, and add their
699	>	// numerical idents to a vector:
700
701	<	// set the useRF logical
702	<	useRF = 0;
703	<	useSF = 0;
701	>	vector<int> foundTypes;
702	>	set<AtomType*>::iterator i;
703	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
704	>	foundTypes.push_back( (*i)->getIdent() );
705
706	+	// count_local holds the number of found types on this processor
707	+	int count_local = foundTypes.size();
708
709	<	if (simParams_->haveElectrostaticSummationMethod()) {
710	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
711	<	toUpper(myMethod);
712	<	if (myMethod == "REACTION_FIELD") {
713	<	useRF=1;
714	<	} else {
715	<	if (myMethod == "SHIFTED_FORCE") {
716	<	useSF = 1;
717	<	}
709	>	// count holds the total number of found types on all processors
710	>	// (some will be redundant with the ones found locally):
711	>	int count;
712	>	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
713	>
714	>	// create a vector to hold the globally found types, and resize it:
715	>	vector<int> ftGlobal;
716	>	ftGlobal.resize(count);
717	>	vector<int> counts;
718	>
719	>	int nproc = MPI::COMM_WORLD.Get_size();
720	>	counts.resize(nproc);
721	>	vector<int> disps;
722	>	disps.resize(nproc);
723	>
724	>	// now spray out the foundTypes to all the other processors:
725	>
726	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
727	>	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
728	>
729	>	// foundIdents is a stl set, so inserting an already found ident
730	>	// will have no effect.
731	>	set<int> foundIdents;
732	>	vector<int>::iterator j;
733	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
734	>	foundIdents.insert((*j));
735	>
736	>	// now iterate over the foundIdents and get the actual atom types
737	>	// that correspond to these:
738	>	set<int>::iterator it;
739	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
740	>	atomTypes.insert( forceField_->getAtomType((*it)) );
741	>
742	>	#endif
743	>
744	>	return atomTypes;
745	>	}
746	>
747	>	void SimInfo::setupSimVariables() {
748	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
749	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
750	>	calcBoxDipole_ = false;
751	>	if ( simParams_->haveAccumulateBoxDipole() )
752	>	if ( simParams_->getAccumulateBoxDipole() ) {
753	>	calcBoxDipole_ = true;
754		}
672	–	}
755
756	+	set<AtomType*>::iterator i;
757	+	set<AtomType*> atomTypes;
758	+	atomTypes = getSimulatedAtomTypes();
759	+	int usesElectrostatic = 0;
760	+	int usesMetallic = 0;
761	+	int usesDirectional = 0;
762		//loop over all of the atom types
763		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
764	<	useLennardJones |= (*i)->isLennardJones();
765	<	useElectrostatic |= (*i)->isElectrostatic();
766	<	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();
764	>	usesElectrostatic |= (*i)->isElectrostatic();
765	>	usesMetallic |= (*i)->isMetal();
766	>	usesDirectional |= (*i)->isDirectional();
767		}
768
689	–	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
690	–	useDirectionalAtom = 1;
691	–	}
692	–
693	–	if (useCharge || useDipole) {
694	–	useElectrostatics = 1;
695	–	}
696	–
769		#ifdef IS_MPI
770		int temp;
771	+	temp = usesDirectional;
772	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
773
774	<	temp = usePBC;
775	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
774	>	temp = usesMetallic;
775	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776
777	<	temp = useDirectionalAtom;
778	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
777	>	temp = usesElectrostatic;
778	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
779	>	#endif
780	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
781	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
782	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
783	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
784	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
785	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
786	>	}
787
706	–	temp = useLennardJones;
707	–	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
788
789	<	temp = useElectrostatics;
790	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
789	>	vector<int> SimInfo::getGlobalAtomIndices() {
790	>	SimInfo::MoleculeIterator mi;
791	>	Molecule* mol;
792	>	Molecule::AtomIterator ai;
793	>	Atom* atom;
794
795	<	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);
795	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
796
797	<	temp = useGayBerne;
798	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
797	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
798	>
799	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
800	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
801	>	}
802	>	}
803	>	return GlobalAtomIndices;
804	>	}
805
727	–	temp = useEAM;
728	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
806
807	<	temp = useSC;
808	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
809	<
810	<	temp = useShape;
811	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
812	<
813	<	temp = useFLARB;
814	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
815	<
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") {
807	>	vector<int> SimInfo::getGlobalGroupIndices() {
808	>	SimInfo::MoleculeIterator mi;
809	>	Molecule* mol;
810	>	Molecule::CutoffGroupIterator ci;
811	>	CutoffGroup* cg;
812	>
813	>	vector<int> GlobalGroupIndices;
814	>
815	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
816
817	<	if (simParams_->haveDielectric()) {
818	<	fInfo_.dielect = simParams_->getDielectric();
819	<	} else {
820	<	sprintf(painCave.errMsg,
821	<	"SimSetup Error: No Dielectric constant was set.\n"
822	<	"\tYou are trying to use Reaction Field without"
771	<	"\tsetting a dielectric constant!\n");
772	<	painCave.isFatal = 1;
773	<	simError();
774	<	}
817	>	//local index of cutoff group is trivial, it only depends on the
818	>	//order of travesing
819	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
820	>	cg = mol->nextCutoffGroup(ci)) {
821	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
822	>	}
823		}
824	<
824	>	return GlobalGroupIndices;
825		}
826
827	<	void SimInfo::setupFortranSim() {
827	>
828	>	void SimInfo::setupFortran() {
829		int isError;
830	<	int nExclude;
831	<	std::vector<int> fortranGlobalGroupMembership;
830	>	int nExclude, nOneTwo, nOneThree, nOneFour;
831	>	vector<int> fortranGlobalGroupMembership;
832
784	–	nExclude = exclude_.getSize();
833		isError = 0;
834
835		//globalGroupMembership_ is filled by SimCreator
#	Line 790 | Line 838 | namespace oopse {
838		}
839
840		//calculate mass ratio of cutoff group
841	<	std::vector<double> mfact;
841	>	vector<RealType> mfact;
842		SimInfo::MoleculeIterator mi;
843		Molecule* mol;
844		Molecule::CutoffGroupIterator ci;
845		CutoffGroup* cg;
846		Molecule::AtomIterator ai;
847		Atom* atom;
848	<	double totalMass;
848	>	RealType totalMass;
849
850		//to avoid memory reallocation, reserve enough space for mfact
851		mfact.reserve(getNCutoffGroups());
#	Line 813 | Line 861 | namespace oopse {
861		else
862		mfact.push_back( 1.0 );
863		}
816	–
864		}
865		}
866
867	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
821	<	std::vector<int> identArray;
867	>	// Build the identArray_
868
869	<	//to avoid memory reallocation, reserve enough space identArray
870	<	identArray.reserve(getNAtoms());
825	<
869	>	identArray_.clear();
870	>	identArray_.reserve(getNAtoms());
871		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
872		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
873	<	identArray.push_back(atom->getIdent());
873	>	identArray_.push_back(atom->getIdent());
874		}
875		}
876
877		//fill molMembershipArray
878		//molMembershipArray is filled by SimCreator
879	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
879	>	vector<int> molMembershipArray(nGlobalAtoms_);
880		for (int i = 0; i < nGlobalAtoms_; i++) {
881		molMembershipArray[i] = globalMolMembership_[i] + 1;
882		}
883
884		//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);
885
886	<	if( isError ){
886	>	nExclude = excludedInteractions_.getSize();
887	>	nOneTwo = oneTwoInteractions_.getSize();
888	>	nOneThree = oneThreeInteractions_.getSize();
889	>	nOneFour = oneFourInteractions_.getSize();
890
891	+	int* excludeList = excludedInteractions_.getPairList();
892	+	int* oneTwoList = oneTwoInteractions_.getPairList();
893	+	int* oneThreeList = oneThreeInteractions_.getPairList();
894	+	int* oneFourList = oneFourInteractions_.getPairList();
895	+
896	+	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0],
897	+	&nExclude, excludeList,
898	+	&nOneTwo, oneTwoList,
899	+	&nOneThree, oneThreeList,
900	+	&nOneFour, oneFourList,
901	+	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
902	+	&fortranGlobalGroupMembership[0], &isError);
903	+
904	+	if( isError ){
905	+
906		sprintf( painCave.errMsg,
907		"There was an error setting the simulation information in fortran.\n" );
908		painCave.isFatal = 1;
909	<	painCave.severity = OOPSE_ERROR;
909	>	painCave.severity = OPENMD_ERROR;
910		simError();
911		}
912	<
913	<	#ifdef IS_MPI
912	>
913	>
914		sprintf( checkPointMsg,
915		"succesfully sent the simulation information to fortran.\n");
859	–	MPIcheckPoint();
860	–	#endif // is_mpi
861	–	}
862	–
863	–
864	–	#ifdef IS_MPI
865	–	void SimInfo::setupFortranParallel() {
916
917	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
918	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
919	<	std::vector<int> localToGlobalCutoffGroupIndex;
920	<	SimInfo::MoleculeIterator mi;
921	<	Molecule::AtomIterator ai;
922	<	Molecule::CutoffGroupIterator ci;
923	<	Molecule* mol;
924	<	Atom* atom;
925	<	CutoffGroup* cg;
917	>	errorCheckPoint();
918	>
919	>	// Setup number of neighbors in neighbor list if present
920	>	if (simParams_->haveNeighborListNeighbors()) {
921	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
922	>	setNeighbors(&nlistNeighbors);
923	>	}
924	>
925	>	#ifdef IS_MPI
926		mpiSimData parallelData;
877	–	int isError;
927
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	–
928		//fill up mpiSimData struct
929		parallelData.nMolGlobal = getNGlobalMolecules();
930		parallelData.nMolLocal = getNMolecules();
#	Line 901 | Line 936 | namespace oopse {
936		MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
937
938		//pass mpiSimData struct and index arrays to fortran
939	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
940	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
941	<	&localToGlobalCutoffGroupIndex[0], &isError);
939	>	//setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
940	>	//                &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
941	>	//                &localToGlobalCutoffGroupIndex[0], &isError);
942
943		if (isError) {
944		sprintf(painCave.errMsg,
#	Line 913 | Line 948 | namespace oopse {
948		}
949
950		sprintf(checkPointMsg, " mpiRefresh successful.\n");
951	<	MPIcheckPoint();
917	<
918	<
919	<	}
920	<
951	>	errorCheckPoint();
952		#endif
953
954	<	void SimInfo::setupCutoff() {
955	<
956	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
957	<
958	<	// Check the cutoff policy
959	<	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();
954	>	initFortranFF(&isError);
955	>	if (isError) {
956	>	sprintf(painCave.errMsg,
957	>	"initFortranFF errror: fortran didn't like something we gave it.\n");
958	>	painCave.isFatal = 1;
959	>	simError();
960		}
961	<
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	<	rsw_ = rcut_;
973	<	}
974	<	notifyFortranCutoffs(&rcut_, &rsw_);
975	<
976	<	} else {
977	<
978	<	// For electrostatic atoms, we'll assume a large safe value:
979	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
980	<	sprintf(painCave.errMsg,
981	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
982	<	"\tOOPSE will use a default value of 15.0 angstroms"
983	<	"\tfor the cutoffRadius.\n");
984	<	painCave.isFatal = 0;
985	<	simError();
986	<	rcut_ = 15.0;
987	<
988	<	if (simParams_->haveElectrostaticSummationMethod()) {
989	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
990	<	toUpper(myMethod);
991	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
992	<	if (simParams_->haveSwitchingRadius()){
993	<	sprintf(painCave.errMsg,
994	<	"SimInfo Warning: A value was set for the switchingRadius\n"
995	<	"\teven though the electrostaticSummationMethod was\n"
996	<	"\tset to %s\n", myMethod.c_str());
997	<	painCave.isFatal = 1;
998	<	simError();
999	<	}
1000	<	}
1001	<	}
1002	<
1003	<	if (simParams_->haveSwitchingRadius()){
1004	<	rsw_ = simParams_->getSwitchingRadius();
1005	<	} else {
1006	<	sprintf(painCave.errMsg,
1007	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1008	<	"\tOOPSE will use a default value of\n"
1009	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1010	<	painCave.isFatal = 0;
1011	<	simError();
1012	<	rsw_ = 0.85 * rcut_;
1013	<	}
1014	<	notifyFortranCutoffs(&rcut_, &rsw_);
1015	<	} else {
1016	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1017	<	// We'll punt and let fortran figure out the cutoffs later.
1018	<
1019	<	notifyFortranYouAreOnYourOwn();
1020	<
1021	<	}
1022	<	}
1023	<	}
1024	<
1025	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1026	<
1027	<	int errorOut;
1028	<	int esm =  NONE;
1029	<	int sm = UNDAMPED;
1030	<	double alphaVal;
1031	<	double dielectric;
1032	<
1033	<	errorOut = isError;
1034	<	alphaVal = simParams_->getDampingAlpha();
1035	<	dielectric = simParams_->getDielectric();
1036	<
1037	<	if (simParams_->haveElectrostaticSummationMethod()) {
1038	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1039	<	toUpper(myMethod);
1040	<	if (myMethod == "NONE") {
1041	<	esm = NONE;
1042	<	} else {
1043	<	if (myMethod == "SWITCHING_FUNCTION") {
1044	<	esm = SWITCHING_FUNCTION;
1045	<	} else {
1046	<	if (myMethod == "SHIFTED_POTENTIAL") {
1047	<	esm = SHIFTED_POTENTIAL;
1048	<	} else {
1049	<	if (myMethod == "SHIFTED_FORCE") {
1050	<	esm = SHIFTED_FORCE;
1051	<	} else {
1052	<	if (myMethod == "REACTION_FIELD") {
1053	<	esm = REACTION_FIELD;
1054	<	} else {
1055	<	// throw error
1056	<	sprintf( painCave.errMsg,
1057	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1058	<	"\t(Input file specified %s .)\n"
1059	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1060	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1061	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1062	<	painCave.isFatal = 1;
1063	<	simError();
1064	<	}
1065	<	}
1066	<	}
1067	<	}
1068	<	}
1069	<	}
1070	<
1071	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1072	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1073	<	toUpper(myScreen);
1074	<	if (myScreen == "UNDAMPED") {
1075	<	sm = UNDAMPED;
1076	<	} else {
1077	<	if (myScreen == "DAMPED") {
1078	<	sm = DAMPED;
1079	<	if (!simParams_->haveDampingAlpha()) {
1080	<	//throw error
1081	<	sprintf( painCave.errMsg,
1082	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1083	<	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1084	<	painCave.isFatal = 0;
1085	<	simError();
1086	<	}
1087	<	} else {
1088	<	// throw error
1089	<	sprintf( painCave.errMsg,
1090	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1091	<	"\t(Input file specified %s .)\n"
1092	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1093	<	"or \"damped\".\n", myScreen.c_str() );
1094	<	painCave.isFatal = 1;
1095	<	simError();
1096	<	}
1097	<	}
1098	<	}
1099	<
1100	<	// let's pass some summation method variables to fortran
1101	<	setElectrostaticSumMethod( &esm );
1102	<	setFortranElectrostaticMethod( &esm );
1103	<	setScreeningMethod( &sm );
1104	<	setDampingAlpha( &alphaVal );
1105	<	setReactionFieldDielectric( &dielectric );
1106	<	initFortranFF( &errorOut );
1107	<	}
1108	<
1109	<	void SimInfo::setupSwitchingFunction() {
1110	<	int ft = CUBIC;
1111	<
1112	<	if (simParams_->haveSwitchingFunctionType()) {
1113	<	std::string funcType = simParams_->getSwitchingFunctionType();
1114	<	toUpper(funcType);
1115	<	if (funcType == "CUBIC") {
1116	<	ft = CUBIC;
1117	<	} else {
1118	<	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1119	<	ft = FIFTH_ORDER_POLY;
1120	<	} else {
1121	<	// throw error
1122	<	sprintf( painCave.errMsg,
1123	<	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1124	<	painCave.isFatal = 1;
1125	<	simError();
1126	<	}
1127	<	}
1128	<	}
1129	<
1130	<	// send switching function notification to switcheroo
1131	<	setFunctionType(&ft);
1132	<
961	>	fortranInitialized_ = true;
962		}
963
964		void SimInfo::addProperty(GenericData* genData) {
965		properties_.addProperty(genData);
966		}
967
968	<	void SimInfo::removeProperty(const std::string& propName) {
968	>	void SimInfo::removeProperty(const string& propName) {
969		properties_.removeProperty(propName);
970		}
971
#	Line 1144 | Line 973 | namespace oopse {
973		properties_.clearProperties();
974		}
975
976	<	std::vector<std::string> SimInfo::getPropertyNames() {
976	>	vector<string> SimInfo::getPropertyNames() {
977		return properties_.getPropertyNames();
978		}
979
980	<	std::vector<GenericData*> SimInfo::getProperties() {
980	>	vector<GenericData*> SimInfo::getProperties() {
981		return properties_.getProperties();
982		}
983
984	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
984	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
985		return properties_.getPropertyByName(propName);
986		}
987
#	Line 1166 | Line 995 | namespace oopse {
995		Molecule* mol;
996		RigidBody* rb;
997		Atom* atom;
998	+	CutoffGroup* cg;
999		SimInfo::MoleculeIterator mi;
1000		Molecule::RigidBodyIterator rbIter;
1001	<	Molecule::AtomIterator atomIter;;
1001	>	Molecule::AtomIterator atomIter;
1002	>	Molecule::CutoffGroupIterator cgIter;
1003
1004		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1005
#	Line 1179 | Line 1010 | namespace oopse {
1010		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1011		rb->setSnapshotManager(sman_);
1012		}
1013	+
1014	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
1015	+	cg->setSnapshotManager(sman_);
1016	+	}
1017		}
1018
1019		}
#	Line 1188 | Line 1023 | namespace oopse {
1023		Molecule* mol;
1024
1025		Vector3d comVel(0.0);
1026	<	double totalMass = 0.0;
1026	>	RealType totalMass = 0.0;
1027
1028
1029		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1030	<	double mass = mol->getMass();
1030	>	RealType mass = mol->getMass();
1031		totalMass += mass;
1032		comVel += mass * mol->getComVel();
1033		}
1034
1035		#ifdef IS_MPI
1036	<	double tmpMass = totalMass;
1036	>	RealType tmpMass = totalMass;
1037		Vector3d tmpComVel(comVel);
1038	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1039	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1038	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1039	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1040		#endif
1041
1042		comVel /= totalMass;
#	Line 1214 | Line 1049 | namespace oopse {
1049		Molecule* mol;
1050
1051		Vector3d com(0.0);
1052	<	double totalMass = 0.0;
1052	>	RealType totalMass = 0.0;
1053
1054		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1055	<	double mass = mol->getMass();
1055	>	RealType mass = mol->getMass();
1056		totalMass += mass;
1057		com += mass * mol->getCom();
1058		}
1059
1060		#ifdef IS_MPI
1061	<	double tmpMass = totalMass;
1061	>	RealType tmpMass = totalMass;
1062		Vector3d tmpCom(com);
1063	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1064	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1063	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1064	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1065		#endif
1066
1067		com /= totalMass;
#	Line 1235 | Line 1070 | namespace oopse {
1070
1071		}
1072
1073	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1073	>	ostream& operator <<(ostream& o, SimInfo& info) {
1074
1075		return o;
1076		}
#	Line 1250 | Line 1085 | namespace oopse {
1085		Molecule* mol;
1086
1087
1088	<	double totalMass = 0.0;
1088	>	RealType totalMass = 0.0;
1089
1090
1091		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1092	<	double mass = mol->getMass();
1092	>	RealType mass = mol->getMass();
1093		totalMass += mass;
1094		com += mass * mol->getCom();
1095		comVel += mass * mol->getComVel();
1096		}
1097
1098		#ifdef IS_MPI
1099	<	double tmpMass = totalMass;
1099	>	RealType tmpMass = totalMass;
1100		Vector3d tmpCom(com);
1101		Vector3d tmpComVel(comVel);
1102	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1103	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1104	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1102	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1103	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1104	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1105		#endif
1106
1107		com /= totalMass;
#	Line 1278 | Line 1113 | namespace oopse {
1113
1114
1115		[  Ixx -Ixy  -Ixz ]
1116	<	J =| -Iyx  Iyy  -Iyz |
1116	>	J =| -Iyx  Iyy  -Iyz |
1117		[ -Izx -Iyz   Izz ]
1118		*/
1119
1120		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1121
1122
1123	<	double xx = 0.0;
1124	<	double yy = 0.0;
1125	<	double zz = 0.0;
1126	<	double xy = 0.0;
1127	<	double xz = 0.0;
1128	<	double yz = 0.0;
1123	>	RealType xx = 0.0;
1124	>	RealType yy = 0.0;
1125	>	RealType zz = 0.0;
1126	>	RealType xy = 0.0;
1127	>	RealType xz = 0.0;
1128	>	RealType yz = 0.0;
1129		Vector3d com(0.0);
1130		Vector3d comVel(0.0);
1131
#	Line 1302 | Line 1137 | namespace oopse {
1137		Vector3d thisq(0.0);
1138		Vector3d thisv(0.0);
1139
1140	<	double thisMass = 0.0;
1140	>	RealType thisMass = 0.0;
1141
1142
1143
#	Line 1340 | Line 1175 | namespace oopse {
1175		#ifdef IS_MPI
1176		Mat3x3d tmpI(inertiaTensor);
1177		Vector3d tmpAngMom;
1178	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1179	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1178	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1179	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1180		#endif
1181
1182		return;
#	Line 1362 | Line 1197 | namespace oopse {
1197		Vector3d thisr(0.0);
1198		Vector3d thisp(0.0);
1199
1200	<	double thisMass;
1200	>	RealType thisMass;
1201
1202		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1203		thisMass = mol->getMass();
#	Line 1375 | Line 1210 | namespace oopse {
1210
1211		#ifdef IS_MPI
1212		Vector3d tmpAngMom;
1213	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1213	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1214		#endif
1215
1216		return angularMomentum;
1217		}
1218
1219	<
1220	<	}//end namespace oopse
1219	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1220	>	return IOIndexToIntegrableObject.at(index);
1221	>	}
1222	>
1223	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1224	>	IOIndexToIntegrableObject= v;
1225	>	}
1226
1227	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1228	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1229	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1230	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1231	+	*/
1232	+	void SimInfo::getGyrationalVolume(RealType &volume){
1233	+	Mat3x3d intTensor;
1234	+	RealType det;
1235	+	Vector3d dummyAngMom;
1236	+	RealType sysconstants;
1237	+	RealType geomCnst;
1238	+
1239	+	geomCnst = 3.0/2.0;
1240	+	/* Get the inertial tensor and angular momentum for free*/
1241	+	getInertiaTensor(intTensor,dummyAngMom);
1242	+
1243	+	det = intTensor.determinant();
1244	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1245	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1246	+	return;
1247	+	}
1248	+
1249	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1250	+	Mat3x3d intTensor;
1251	+	Vector3d dummyAngMom;
1252	+	RealType sysconstants;
1253	+	RealType geomCnst;
1254	+
1255	+	geomCnst = 3.0/2.0;
1256	+	/* Get the inertial tensor and angular momentum for free*/
1257	+	getInertiaTensor(intTensor,dummyAngMom);
1258	+
1259	+	detI = intTensor.determinant();
1260	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1261	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1262	+	return;
1263	+	}
1264	+	/*
1265	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1266	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1267	+	sdByGlobalIndex_ = v;
1268	+	}
1269	+
1270	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1271	+	//assert(index < nAtoms_ + nRigidBodies_);
1272	+	return sdByGlobalIndex_.at(index);
1273	+	}
1274	+	*/
1275	+	int SimInfo::getNGlobalConstraints() {
1276	+	int nGlobalConstraints;
1277	+	#ifdef IS_MPI
1278	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1279	+	MPI_COMM_WORLD);
1280	+	#else
1281	+	nGlobalConstraints =  nConstraints_;
1282	+	#endif
1283	+	return nGlobalConstraints;
1284	+	}
1285	+
1286	+	}//end namespace OpenMD
1287	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 834 by chuckv, Fri Dec 30 23:15:59 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1549 by gezelter, Wed Apr 27 18:38:15 2011 UTC

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