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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 853 by chrisfen, Thu Jan 12 16:47:25 2006 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1530 by gezelter, Tue Dec 28 21:47:55 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"
59	–	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
58		#include "UseTheForce/doForces_interface.h"
59	<	#include "UseTheForce/DarkSide/electrostatic_interface.h"
62	<	#include "UseTheForce/DarkSide/switcheroo_interface.h"
59	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
60		#include "utils/MemoryUtils.hpp"
61		#include "utils/simError.h"
62		#include "selection/SelectionManager.hpp"
63		#include "io/ForceFieldOptions.hpp"
64		#include "UseTheForce/ForceField.hpp"
65	+	#include "nonbonded/SwitchingFunction.hpp"
66
67	+
68		#ifdef IS_MPI
69		#include "UseTheForce/mpiComponentPlan.h"
70		#include "UseTheForce/DarkSide/simParallel_interface.h"
71		#endif
72
73	<	namespace oopse {
74	<	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	<	}
73	>	using namespace std;
74	>	namespace OpenMD {
75
76		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
77		forceField_(ff), simParams_(simParams),
78	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
78	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
79		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
80		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
81	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
82	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
83	<	sman_(NULL), fortranInitialized_(false) {
84	<
85	<	MoleculeStamp* molStamp;
86	<	int nMolWithSameStamp;
87	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
88	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
89	<	CutoffGroupStamp* cgStamp;
90	<	RigidBodyStamp* rbStamp;
91	<	int nRigidAtoms = 0;
92	<	std::vector<Component*> components = simParams->getComponents();
81	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
82	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
83	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
84	>	calcBoxDipole_(false), useAtomicVirial_(true) {
85	>
86	>	MoleculeStamp* molStamp;
87	>	int nMolWithSameStamp;
88	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
89	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
90	>	CutoffGroupStamp* cgStamp;
91	>	RigidBodyStamp* rbStamp;
92	>	int nRigidAtoms = 0;
93	>
94	>	vector<Component*> components = simParams->getComponents();
95	>
96	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
97	>	molStamp = (*i)->getMoleculeStamp();
98	>	nMolWithSameStamp = (*i)->getNMol();
99
100	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
101	<	molStamp = (*i)->getMoleculeStamp();
102	<	nMolWithSameStamp = (*i)->getNMol();
103	<
104	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
105	<
106	<	//calculate atoms in molecules
107	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
108	<
109	<	//calculate atoms in cutoff groups
110	<	int nAtomsInGroups = 0;
111	<	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	<
100	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
101	>
102	>	//calculate atoms in molecules
103	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
104	>
105	>	//calculate atoms in cutoff groups
106	>	int nAtomsInGroups = 0;
107	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
108	>
109	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
110	>	cgStamp = molStamp->getCutoffGroupStamp(j);
111	>	nAtomsInGroups += cgStamp->getNMembers();
112		}
113	<
114	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
115	<	//group therefore the total number of cutoff groups in the system is
116	<	//equal to the total number of atoms minus number of atoms belong to
117	<	//cutoff group defined in meta-data file plus the number of cutoff
118	<	//groups defined in meta-data file
119	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
120	<
121	<	//every free atom (atom does not belong to rigid bodies) is an
122	<	//integrable object therefore the total number of integrable objects
123	<	//in the system is equal to the total number of atoms minus number of
124	<	//atoms belong to rigid body defined in meta-data file plus the number
125	<	//of rigid bodies defined in meta-data file
126	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
127	<	+ nGlobalRigidBodies_;
128	<
129	<	nGlobalMols_ = molStampIds_.size();
155	<
156	<	#ifdef IS_MPI
157	<	molToProcMap_.resize(nGlobalMols_);
158	<	#endif
159	<
113	>
114	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
115	>
116	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
117	>
118	>	//calculate atoms in rigid bodies
119	>	int nAtomsInRigidBodies = 0;
120	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
121	>
122	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
123	>	rbStamp = molStamp->getRigidBodyStamp(j);
124	>	nAtomsInRigidBodies += rbStamp->getNMembers();
125	>	}
126	>
127	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
128	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
129	>
130		}
131	<
131	>
132	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
133	>	//group therefore the total number of cutoff groups in the system is
134	>	//equal to the total number of atoms minus number of atoms belong to
135	>	//cutoff group defined in meta-data file plus the number of cutoff
136	>	//groups defined in meta-data file
137	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
138	>
139	>	//every free atom (atom does not belong to rigid bodies) is an
140	>	//integrable object therefore the total number of integrable objects
141	>	//in the system is equal to the total number of atoms minus number of
142	>	//atoms belong to rigid body defined in meta-data file plus the number
143	>	//of rigid bodies defined in meta-data file
144	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
145	>	+ nGlobalRigidBodies_;
146	>
147	>	nGlobalMols_ = molStampIds_.size();
148	>	molToProcMap_.resize(nGlobalMols_);
149	>	}
150	>
151		SimInfo::~SimInfo() {
152	<	std::map<int, Molecule*>::iterator i;
152	>	map<int, Molecule*>::iterator i;
153		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
154		delete i->second;
155		}
#	Line 171 | Line 160 | namespace oopse {
160		delete forceField_;
161		}
162
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	–	}
163
164		bool SimInfo::addMolecule(Molecule* mol) {
165		MoleculeIterator i;
166	<
166	>
167		i = molecules_.find(mol->getGlobalIndex());
168		if (i == molecules_.end() ) {
169	<
170	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
171	<
169	>
170	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
171	>
172		nAtoms_ += mol->getNAtoms();
173		nBonds_ += mol->getNBonds();
174		nBends_ += mol->getNBends();
175		nTorsions_ += mol->getNTorsions();
176	+	nInversions_ += mol->getNInversions();
177		nRigidBodies_ += mol->getNRigidBodies();
178		nIntegrableObjects_ += mol->getNIntegrableObjects();
179		nCutoffGroups_ += mol->getNCutoffGroups();
180		nConstraints_ += mol->getNConstraintPairs();
181	<
182	<	addExcludePairs(mol);
183	<
181	>
182	>	addInteractionPairs(mol);
183	>
184		return true;
185		} else {
186		return false;
187		}
188		}
189	<
189	>
190		bool SimInfo::removeMolecule(Molecule* mol) {
191		MoleculeIterator i;
192		i = molecules_.find(mol->getGlobalIndex());
#	Line 219 | Line 199 | namespace oopse {
199		nBonds_ -= mol->getNBonds();
200		nBends_ -= mol->getNBends();
201		nTorsions_ -= mol->getNTorsions();
202	+	nInversions_ -= mol->getNInversions();
203		nRigidBodies_ -= mol->getNRigidBodies();
204		nIntegrableObjects_ -= mol->getNIntegrableObjects();
205		nCutoffGroups_ -= mol->getNCutoffGroups();
206		nConstraints_ -= mol->getNConstraintPairs();
207
208	<	removeExcludePairs(mol);
208	>	removeInteractionPairs(mol);
209		molecules_.erase(mol->getGlobalIndex());
210
211		delete mol;
#	Line 233 | Line 214 | namespace oopse {
214		} else {
215		return false;
216		}
236	–
237	–
217		}
218
219
#	Line 252 | Line 231 | namespace oopse {
231		void SimInfo::calcNdf() {
232		int ndf_local;
233		MoleculeIterator i;
234	<	std::vector<StuntDouble*>::iterator j;
234	>	vector<StuntDouble*>::iterator j;
235		Molecule* mol;
236		StuntDouble* integrableObject;
237
#	Line 290 | Line 269 | namespace oopse {
269
270		}
271
272	+	int SimInfo::getFdf() {
273	+	#ifdef IS_MPI
274	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
275	+	#else
276	+	fdf_ = fdf_local;
277	+	#endif
278	+	return fdf_;
279	+	}
280	+
281		void SimInfo::calcNdfRaw() {
282		int ndfRaw_local;
283
284		MoleculeIterator i;
285	<	std::vector<StuntDouble*>::iterator j;
285	>	vector<StuntDouble*>::iterator j;
286		Molecule* mol;
287		StuntDouble* integrableObject;
288
#	Line 341 | Line 329 | namespace oopse {
329
330		}
331
332	<	void SimInfo::addExcludePairs(Molecule* mol) {
333	<	std::vector<Bond*>::iterator bondIter;
334	<	std::vector<Bend*>::iterator bendIter;
335	<	std::vector<Torsion*>::iterator torsionIter;
332	>	void SimInfo::addInteractionPairs(Molecule* mol) {
333	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
334	>	vector<Bond*>::iterator bondIter;
335	>	vector<Bend*>::iterator bendIter;
336	>	vector<Torsion*>::iterator torsionIter;
337	>	vector<Inversion*>::iterator inversionIter;
338		Bond* bond;
339		Bend* bend;
340		Torsion* torsion;
341	+	Inversion* inversion;
342		int a;
343		int b;
344		int c;
345		int d;
346
347	<	std::map<int, std::set<int> > atomGroups;
347	>	// atomGroups can be used to add special interaction maps between
348	>	// groups of atoms that are in two separate rigid bodies.
349	>	// However, most site-site interactions between two rigid bodies
350	>	// are probably not special, just the ones between the physically
351	>	// bonded atoms.  Interactions *within* a single rigid body should
352	>	// always be excluded.  These are done at the bottom of this
353	>	// function.
354
355	+	map<int, set<int> > atomGroups;
356		Molecule::RigidBodyIterator rbIter;
357		RigidBody* rb;
358		Molecule::IntegrableObjectIterator ii;
359		StuntDouble* integrableObject;
360
361	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
362	<	integrableObject = mol->nextIntegrableObject(ii)) {
363	<
361	>	for (integrableObject = mol->beginIntegrableObject(ii);
362	>	integrableObject != NULL;
363	>	integrableObject = mol->nextIntegrableObject(ii)) {
364	>
365		if (integrableObject->isRigidBody()) {
366	<	rb = static_cast<RigidBody*>(integrableObject);
367	<	std::vector<Atom*> atoms = rb->getAtoms();
368	<	std::set<int> rigidAtoms;
369	<	for (int i = 0; i < atoms.size(); ++i) {
370	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
371	<	}
372	<	for (int i = 0; i < atoms.size(); ++i) {
373	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
374	<	}
366	>	rb = static_cast<RigidBody*>(integrableObject);
367	>	vector<Atom*> atoms = rb->getAtoms();
368	>	set<int> rigidAtoms;
369	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
370	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
371	>	}
372	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
373	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
374	>	}
375		} else {
376	<	std::set<int> oneAtomSet;
376	>	set<int> oneAtomSet;
377		oneAtomSet.insert(integrableObject->getGlobalIndex());
378	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
378	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
379		}
380		}
381	+
382	+	for (bond= mol->beginBond(bondIter); bond != NULL;
383	+	bond = mol->nextBond(bondIter)) {
384
383	–
384	–
385	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
385		a = bond->getAtomA()->getGlobalIndex();
386	<	b = bond->getAtomB()->getGlobalIndex();
387	<	exclude_.addPair(a, b);
386	>	b = bond->getAtomB()->getGlobalIndex();
387	>
388	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
389	>	oneTwoInteractions_.addPair(a, b);
390	>	} else {
391	>	excludedInteractions_.addPair(a, b);
392	>	}
393		}
394
395	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
395	>	for (bend= mol->beginBend(bendIter); bend != NULL;
396	>	bend = mol->nextBend(bendIter)) {
397	>
398		a = bend->getAtomA()->getGlobalIndex();
399		b = bend->getAtomB()->getGlobalIndex();
400		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);
401
402	<	//exclude_.addPair(a, b);
403	<	//exclude_.addPair(a, c);
404	<	//exclude_.addPair(b, c);
402	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
403	>	oneTwoInteractions_.addPair(a, b);
404	>	oneTwoInteractions_.addPair(b, c);
405	>	} else {
406	>	excludedInteractions_.addPair(a, b);
407	>	excludedInteractions_.addPair(b, c);
408	>	}
409	>
410	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
411	>	oneThreeInteractions_.addPair(a, c);
412	>	} else {
413	>	excludedInteractions_.addPair(a, c);
414	>	}
415		}
416
417	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
417	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
418	>	torsion = mol->nextTorsion(torsionIter)) {
419	>
420		a = torsion->getAtomA()->getGlobalIndex();
421		b = torsion->getAtomB()->getGlobalIndex();
422		c = torsion->getAtomC()->getGlobalIndex();
423	<	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);
423	>	d = torsion->getAtomD()->getGlobalIndex();
424
425	<	exclude_.addPairs(rigidSetA, rigidSetB);
426	<	exclude_.addPairs(rigidSetA, rigidSetC);
427	<	exclude_.addPairs(rigidSetA, rigidSetD);
428	<	exclude_.addPairs(rigidSetB, rigidSetC);
429	<	exclude_.addPairs(rigidSetB, rigidSetD);
430	<	exclude_.addPairs(rigidSetC, rigidSetD);
425	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
426	>	oneTwoInteractions_.addPair(a, b);
427	>	oneTwoInteractions_.addPair(b, c);
428	>	oneTwoInteractions_.addPair(c, d);
429	>	} else {
430	>	excludedInteractions_.addPair(a, b);
431	>	excludedInteractions_.addPair(b, c);
432	>	excludedInteractions_.addPair(c, d);
433	>	}
434
435	<	/*
436	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
437	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
438	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
439	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
440	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
441	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
442	<
443	<
444	<	exclude_.addPair(a, b);
445	<	exclude_.addPair(a, c);
446	<	exclude_.addPair(a, d);
447	<	exclude_.addPair(b, c);
438	<	exclude_.addPair(b, d);
439	<	exclude_.addPair(c, d);
440	<	*/
435	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
436	>	oneThreeInteractions_.addPair(a, c);
437	>	oneThreeInteractions_.addPair(b, d);
438	>	} else {
439	>	excludedInteractions_.addPair(a, c);
440	>	excludedInteractions_.addPair(b, d);
441	>	}
442	>
443	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
444	>	oneFourInteractions_.addPair(a, d);
445	>	} else {
446	>	excludedInteractions_.addPair(a, d);
447	>	}
448		}
449
450	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
451	<	std::vector<Atom*> atoms = rb->getAtoms();
452	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
453	<	for (int j = i + 1; j < atoms.size(); ++j) {
450	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
451	>	inversion = mol->nextInversion(inversionIter)) {
452	>
453	>	a = inversion->getAtomA()->getGlobalIndex();
454	>	b = inversion->getAtomB()->getGlobalIndex();
455	>	c = inversion->getAtomC()->getGlobalIndex();
456	>	d = inversion->getAtomD()->getGlobalIndex();
457	>
458	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
459	>	oneTwoInteractions_.addPair(a, b);
460	>	oneTwoInteractions_.addPair(a, c);
461	>	oneTwoInteractions_.addPair(a, d);
462	>	} else {
463	>	excludedInteractions_.addPair(a, b);
464	>	excludedInteractions_.addPair(a, c);
465	>	excludedInteractions_.addPair(a, d);
466	>	}
467	>
468	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
469	>	oneThreeInteractions_.addPair(b, c);
470	>	oneThreeInteractions_.addPair(b, d);
471	>	oneThreeInteractions_.addPair(c, d);
472	>	} else {
473	>	excludedInteractions_.addPair(b, c);
474	>	excludedInteractions_.addPair(b, d);
475	>	excludedInteractions_.addPair(c, d);
476	>	}
477	>	}
478	>
479	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
480	>	rb = mol->nextRigidBody(rbIter)) {
481	>	vector<Atom*> atoms = rb->getAtoms();
482	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
483	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
484		a = atoms[i]->getGlobalIndex();
485		b = atoms[j]->getGlobalIndex();
486	<	exclude_.addPair(a, b);
486	>	excludedInteractions_.addPair(a, b);
487		}
488		}
489		}
490
491		}
492
493	<	void SimInfo::removeExcludePairs(Molecule* mol) {
494	<	std::vector<Bond*>::iterator bondIter;
495	<	std::vector<Bend*>::iterator bendIter;
496	<	std::vector<Torsion*>::iterator torsionIter;
493	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
494	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
495	>	vector<Bond*>::iterator bondIter;
496	>	vector<Bend*>::iterator bendIter;
497	>	vector<Torsion*>::iterator torsionIter;
498	>	vector<Inversion*>::iterator inversionIter;
499		Bond* bond;
500		Bend* bend;
501		Torsion* torsion;
502	+	Inversion* inversion;
503		int a;
504		int b;
505		int c;
506		int d;
507
508	<	std::map<int, std::set<int> > atomGroups;
469	<
508	>	map<int, set<int> > atomGroups;
509		Molecule::RigidBodyIterator rbIter;
510		RigidBody* rb;
511		Molecule::IntegrableObjectIterator ii;
512		StuntDouble* integrableObject;
513
514	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
515	<	integrableObject = mol->nextIntegrableObject(ii)) {
516	<
514	>	for (integrableObject = mol->beginIntegrableObject(ii);
515	>	integrableObject != NULL;
516	>	integrableObject = mol->nextIntegrableObject(ii)) {
517	>
518		if (integrableObject->isRigidBody()) {
519	<	rb = static_cast<RigidBody*>(integrableObject);
520	<	std::vector<Atom*> atoms = rb->getAtoms();
521	<	std::set<int> rigidAtoms;
522	<	for (int i = 0; i < atoms.size(); ++i) {
523	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
524	<	}
525	<	for (int i = 0; i < atoms.size(); ++i) {
526	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
527	<	}
519	>	rb = static_cast<RigidBody*>(integrableObject);
520	>	vector<Atom*> atoms = rb->getAtoms();
521	>	set<int> rigidAtoms;
522	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
523	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
524	>	}
525	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
526	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
527	>	}
528		} else {
529	<	std::set<int> oneAtomSet;
529	>	set<int> oneAtomSet;
530		oneAtomSet.insert(integrableObject->getGlobalIndex());
531	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
531	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
532		}
533		}
534
535	<
536	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
535	>	for (bond= mol->beginBond(bondIter); bond != NULL;
536	>	bond = mol->nextBond(bondIter)) {
537	>
538		a = bond->getAtomA()->getGlobalIndex();
539	<	b = bond->getAtomB()->getGlobalIndex();
540	<	exclude_.removePair(a, b);
539	>	b = bond->getAtomB()->getGlobalIndex();
540	>
541	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
542	>	oneTwoInteractions_.removePair(a, b);
543	>	} else {
544	>	excludedInteractions_.removePair(a, b);
545	>	}
546		}
547
548	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
548	>	for (bend= mol->beginBend(bendIter); bend != NULL;
549	>	bend = mol->nextBend(bendIter)) {
550	>
551		a = bend->getAtomA()->getGlobalIndex();
552		b = bend->getAtomB()->getGlobalIndex();
553		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);
554
555	<	//exclude_.removePair(a, b);
556	<	//exclude_.removePair(a, c);
557	<	//exclude_.removePair(b, c);
555	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
556	>	oneTwoInteractions_.removePair(a, b);
557	>	oneTwoInteractions_.removePair(b, c);
558	>	} else {
559	>	excludedInteractions_.removePair(a, b);
560	>	excludedInteractions_.removePair(b, c);
561	>	}
562	>
563	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
564	>	oneThreeInteractions_.removePair(a, c);
565	>	} else {
566	>	excludedInteractions_.removePair(a, c);
567	>	}
568		}
569
570	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
570	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
571	>	torsion = mol->nextTorsion(torsionIter)) {
572	>
573		a = torsion->getAtomA()->getGlobalIndex();
574		b = torsion->getAtomB()->getGlobalIndex();
575		c = torsion->getAtomC()->getGlobalIndex();
576	<	d = torsion->getAtomD()->getGlobalIndex();
576	>	d = torsion->getAtomD()->getGlobalIndex();
577	>
578	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
579	>	oneTwoInteractions_.removePair(a, b);
580	>	oneTwoInteractions_.removePair(b, c);
581	>	oneTwoInteractions_.removePair(c, d);
582	>	} else {
583	>	excludedInteractions_.removePair(a, b);
584	>	excludedInteractions_.removePair(b, c);
585	>	excludedInteractions_.removePair(c, d);
586	>	}
587
588	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
589	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
590	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
591	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
588	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
589	>	oneThreeInteractions_.removePair(a, c);
590	>	oneThreeInteractions_.removePair(b, d);
591	>	} else {
592	>	excludedInteractions_.removePair(a, c);
593	>	excludedInteractions_.removePair(b, d);
594	>	}
595
596	<	exclude_.removePairs(rigidSetA, rigidSetB);
597	<	exclude_.removePairs(rigidSetA, rigidSetC);
598	<	exclude_.removePairs(rigidSetA, rigidSetD);
599	<	exclude_.removePairs(rigidSetB, rigidSetC);
600	<	exclude_.removePairs(rigidSetB, rigidSetD);
601	<	exclude_.removePairs(rigidSetC, rigidSetD);
596	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
597	>	oneFourInteractions_.removePair(a, d);
598	>	} else {
599	>	excludedInteractions_.removePair(a, d);
600	>	}
601	>	}
602
603	<	/*
604	<	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());
603	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
604	>	inversion = mol->nextInversion(inversionIter)) {
605
606	<
607	<	exclude_.removePair(a, b);
608	<	exclude_.removePair(a, c);
609	<	exclude_.removePair(a, d);
610	<	exclude_.removePair(b, c);
611	<	exclude_.removePair(b, d);
612	<	exclude_.removePair(c, d);
613	<	*/
606	>	a = inversion->getAtomA()->getGlobalIndex();
607	>	b = inversion->getAtomB()->getGlobalIndex();
608	>	c = inversion->getAtomC()->getGlobalIndex();
609	>	d = inversion->getAtomD()->getGlobalIndex();
610	>
611	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
612	>	oneTwoInteractions_.removePair(a, b);
613	>	oneTwoInteractions_.removePair(a, c);
614	>	oneTwoInteractions_.removePair(a, d);
615	>	} else {
616	>	excludedInteractions_.removePair(a, b);
617	>	excludedInteractions_.removePair(a, c);
618	>	excludedInteractions_.removePair(a, d);
619	>	}
620	>
621	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
622	>	oneThreeInteractions_.removePair(b, c);
623	>	oneThreeInteractions_.removePair(b, d);
624	>	oneThreeInteractions_.removePair(c, d);
625	>	} else {
626	>	excludedInteractions_.removePair(b, c);
627	>	excludedInteractions_.removePair(b, d);
628	>	excludedInteractions_.removePair(c, d);
629	>	}
630		}
631
632	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
633	<	std::vector<Atom*> atoms = rb->getAtoms();
634	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
635	<	for (int j = i + 1; j < atoms.size(); ++j) {
632	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
633	>	rb = mol->nextRigidBody(rbIter)) {
634	>	vector<Atom*> atoms = rb->getAtoms();
635	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
636	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
637		a = atoms[i]->getGlobalIndex();
638		b = atoms[j]->getGlobalIndex();
639	<	exclude_.removePair(a, b);
639	>	excludedInteractions_.removePair(a, b);
640		}
641		}
642		}
643	<
643	>
644		}
645	<
646	<
645	>
646	>
647		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
648		int curStampId;
649	<
649	>
650		//index from 0
651		curStampId = moleculeStamps_.size();
652
#	Line 577 | Line 654 | namespace oopse {
654		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
655		}
656
657	+
658	+	/**
659	+	* update
660	+	*
661	+	*  Performs the global checks and variable settings after the objects have been
662	+	*  created.
663	+	*
664	+	*/
665		void SimInfo::update() {
666	+
667	+	setupSimVariables();
668	+	setupCutoffs();
669	+	setupSwitching();
670	+	setupElectrostatics();
671	+	setupNeighborlists();
672
582	–	setupSimType();
583	–
673		#ifdef IS_MPI
674		setupFortranParallel();
675		#endif
587	–
676		setupFortranSim();
677	+	fortranInitialized_ = true;
678
590	–	//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	–
679		calcNdf();
680		calcNdfRaw();
681		calcNdfTrans();
610	–
611	–	fortranInitialized_ = true;
682		}
683	<
684	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
683	>
684	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
685		SimInfo::MoleculeIterator mi;
686		Molecule* mol;
687		Molecule::AtomIterator ai;
688		Atom* atom;
689	<	std::set<AtomType*> atomTypes;
690	<
691	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
622	<
689	>	set<AtomType*> atomTypes;
690	>
691	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
692		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
693		atomTypes.insert(atom->getAtomType());
694	<	}
695	<
627	<	}
628	<
694	>	}
695	>	}
696		return atomTypes;
697		}
698
699	<	void SimInfo::setupSimType() {
700	<	std::set<AtomType*>::iterator i;
701	<	std::set<AtomType*> atomTypes;
702	<	atomTypes = getUniqueAtomTypes();
699	>	/**
700	>	* setupCutoffs
701	>	*
702	>	* Sets the values of cutoffRadius and cutoffMethod
703	>	*
704	>	* cutoffRadius : realType
705	>	*  If the cutoffRadius was explicitly set, use that value.
706	>	*  If the cutoffRadius was not explicitly set:
707	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
708	>	*      No electrostatic atoms?  Poll the atom types present in the
709	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
710	>	*      Use the maximum suggested value that was found.
711	>	*
712	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
713	>	*      If cutoffMethod was explicitly set, use that choice.
714	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
715	>	*/
716	>	void SimInfo::setupCutoffs() {
717
718	<	int useLennardJones = 0;
719	<	int useElectrostatic = 0;
720	<	int useEAM = 0;
721	<	int useSC = 0;
722	<	int useCharge = 0;
723	<	int useDirectional = 0;
724	<	int useDipole = 0;
725	<	int useGayBerne = 0;
726	<	int useSticky = 0;
727	<	int useStickyPower = 0;
728	<	int useShape = 0;
729	<	int useFLARB = 0; //it is not in AtomType yet
730	<	int useDirectionalAtom = 0;
731	<	int useElectrostatics = 0;
732	<	//usePBC and useRF are from simParams
733	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
734	<	int useRF;
735	<	int useSF;
736	<	std::string myMethod;
737	<
738	<	// set the useRF logical
739	<	useRF = 0;
740	<	useSF = 0;
718	>	if (simParams_->haveCutoffRadius()) {
719	>	cutoffRadius_ = simParams_->getCutoffRadius();
720	>	} else {
721	>	if (usesElectrostaticAtoms_) {
722	>	sprintf(painCave.errMsg,
723	>	"SimInfo: No value was set for the cutoffRadius.\n"
724	>	"\tOpenMD will use a default value of 12.0 angstroms"
725	>	"\tfor the cutoffRadius.\n");
726	>	painCave.isFatal = 0;
727	>	painCave.severity = OPENMD_INFO;
728	>	simError();
729	>	cutoffRadius_ = 12.0;
730	>	} else {
731	>	RealType thisCut;
732	>	set<AtomType*>::iterator i;
733	>	set<AtomType*> atomTypes;
734	>	atomTypes = getSimulatedAtomTypes();
735	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
736	>	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
737	>	cutoffRadius_ = max(thisCut, cutoffRadius_);
738	>	}
739	>	sprintf(painCave.errMsg,
740	>	"SimInfo: No value was set for the cutoffRadius.\n"
741	>	"\tOpenMD will use %lf angstroms.\n",
742	>	cutoffRadius_);
743	>	painCave.isFatal = 0;
744	>	painCave.severity = OPENMD_INFO;
745	>	simError();
746	>	}
747	>	}
748
749	+	InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
750
751	<	if (simParams_->haveElectrostaticSummationMethod()) {
752	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
753	<	toUpper(myMethod);
754	<	if (myMethod == "REACTION_FIELD") {
755	<	useRF=1;
751	>	map<string, CutoffMethod> stringToCutoffMethod;
752	>	stringToCutoffMethod["HARD"] = HARD;
753	>	stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
754	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
755	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
756	>
757	>	if (simParams_->haveCutoffMethod()) {
758	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
759	>	map<string, CutoffMethod>::iterator i;
760	>	i = stringToCutoffMethod.find(cutMeth);
761	>	if (i == stringToCutoffMethod.end()) {
762	>	sprintf(painCave.errMsg,
763	>	"SimInfo: Could not find chosen cutoffMethod %s\n"
764	>	"\tShould be one of: "
765	>	"HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
766	>	cutMeth.c_str());
767	>	painCave.isFatal = 1;
768	>	painCave.severity = OPENMD_ERROR;
769	>	simError();
770		} else {
771	<	if (myMethod == "SHIFTED_FORCE") {
669	<	useSF = 1;
670	<	}
771	>	cutoffMethod_ = i->second;
772		}
773	+	} else {
774	+	sprintf(painCave.errMsg,
775	+	"SimInfo: No value was set for the cutoffMethod.\n"
776	+	"\tOpenMD will use SHIFTED_FORCE.\n");
777	+	painCave.isFatal = 0;
778	+	painCave.severity = OPENMD_INFO;
779	+	simError();
780	+	cutoffMethod_ = SHIFTED_FORCE;
781		}
782
783	<	//loop over all of the atom types
784	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
785	<	useLennardJones |= (*i)->isLennardJones();
786	<	useElectrostatic |= (*i)->isElectrostatic();
787	<	useEAM |= (*i)->isEAM();
788	<	useSC |= (*i)->isSC();
789	<	useCharge |= (*i)->isCharge();
790	<	useDirectional |= (*i)->isDirectional();
791	<	useDipole |= (*i)->isDipole();
792	<	useGayBerne |= (*i)->isGayBerne();
793	<	useSticky |= (*i)->isSticky();
794	<	useStickyPower |= (*i)->isStickyPower();
795	<	useShape |= (*i)->isShape();
796	<	}
783	>	InteractionManager::Instance()->setCutoffMethod(cutoffMethod_);
784	>	}
785	>
786	>	/**
787	>	* setupSwitching
788	>	*
789	>	* Sets the values of switchingRadius and
790	>	*  If the switchingRadius was explicitly set, use that value (but check it)
791	>	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
792	>	*/
793	>	void SimInfo::setupSwitching() {
794	>
795	>	if (simParams_->haveSwitchingRadius()) {
796	>	switchingRadius_ = simParams_->getSwitchingRadius();
797	>	if (switchingRadius_ > cutoffRadius_) {
798	>	sprintf(painCave.errMsg,
799	>	"SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
800	>	switchingRadius_, cutoffRadius_);
801	>	painCave.isFatal = 1;
802	>	painCave.severity = OPENMD_ERROR;
803	>	simError();
804	>	}
805	>	} else {
806	>	switchingRadius_ = 0.85 * cutoffRadius_;
807	>	sprintf(painCave.errMsg,
808	>	"SimInfo: No value was set for the switchingRadius.\n"
809	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
810	>	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
811	>	painCave.isFatal = 0;
812	>	painCave.severity = OPENMD_WARNING;
813	>	simError();
814	>	}
815	>
816	>	InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
817
818	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
819	<	useDirectionalAtom = 1;
818	>	SwitchingFunctionType ft;
819	>
820	>	if (simParams_->haveSwitchingFunctionType()) {
821	>	string funcType = simParams_->getSwitchingFunctionType();
822	>	toUpper(funcType);
823	>	if (funcType == "CUBIC") {
824	>	ft = cubic;
825	>	} else {
826	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
827	>	ft = fifth_order_poly;
828	>	} else {
829	>	// throw error
830	>	sprintf( painCave.errMsg,
831	>	"SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
832	>	"\tswitchingFunctionType must be one of: "
833	>	"\"cubic\" or \"fifth_order_polynomial\".",
834	>	funcType.c_str() );
835	>	painCave.isFatal = 1;
836	>	painCave.severity = OPENMD_ERROR;
837	>	simError();
838	>	}
839	>	}
840		}
841
842	<	if (useCharge || useDipole) {
843	<	useElectrostatics = 1;
695	<	}
842	>	InteractionManager::Instance()->setSwitchingFunctionType(ft);
843	>	}
844
845	<	#ifdef IS_MPI
846	<	int temp;
845	>	/**
846	>	* setupSkinThickness
847	>	*
848	>	*  If the skinThickness was explicitly set, use that value (but check it)
849	>	*  If the skinThickness was not explicitly set: use 1.0 angstroms
850	>	*/
851	>	void SimInfo::setupSkinThickness() {
852	>	if (simParams_->haveSkinThickness()) {
853	>	skinThickness_ = simParams_->getSkinThickness();
854	>	} else {
855	>	skinThickness_ = 1.0;
856	>	sprintf(painCave.errMsg,
857	>	"SimInfo Warning: No value was set for the skinThickness.\n"
858	>	"\tOpenMD will use a default value of %f Angstroms\n"
859	>	"\tfor this simulation\n", skinThickness_);
860	>	painCave.isFatal = 0;
861	>	simError();
862	>	}
863	>	}
864
865	<	temp = usePBC;
866	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
865	>	void SimInfo::setupSimType() {
866	>	set<AtomType*>::iterator i;
867	>	set<AtomType*> atomTypes;
868	>	atomTypes = getSimulatedAtomTypes();
869
870	<	temp = useDirectionalAtom;
704	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
870	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
871
872	<	temp = useLennardJones;
873	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
874	<
875	<	temp = useElectrostatics;
876	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
877	<
878	<	temp = useCharge;
879	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
872	>	int usesElectrostatic = 0;
873	>	int usesMetallic = 0;
874	>	int usesDirectional = 0;
875	>	//loop over all of the atom types
876	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
877	>	usesElectrostatic |= (*i)->isElectrostatic();
878	>	usesMetallic |= (*i)->isMetal();
879	>	usesDirectional |= (*i)->isDirectional();
880	>	}
881
882	<	temp = useDipole;
883	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
882	>	#ifdef IS_MPI
883	>	int temp;
884	>	temp = usesDirectional;
885	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
886
887	<	temp = useSticky;
888	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
887	>	temp = usesMetallic;
888	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
889
890	<	temp = useStickyPower;
891	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
723	<
724	<	temp = useGayBerne;
725	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
726	<
727	<	temp = useEAM;
728	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
729	<
730	<	temp = useSC;
731	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
732	<
733	<	temp = useShape;
734	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
735	<
736	<	temp = useFLARB;
737	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
738	<
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	<
890	>	temp = usesElectrostatic;
891	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
892		#endif
893	<
894	<	fInfo_.SIM_uses_PBC = usePBC;
895	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
896	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
897	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
898	<	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") {
764	<
765	<	if (simParams_->haveDielectric()) {
766	<	fInfo_.dielect = simParams_->getDielectric();
767	<	} else {
768	<	sprintf(painCave.errMsg,
769	<	"SimSetup Error: No Dielectric constant was set.\n"
770	<	"\tYou are trying to use Reaction Field without"
771	<	"\tsetting a dielectric constant!\n");
772	<	painCave.isFatal = 1;
773	<	simError();
774	<	}
775	<	}
776	<
893	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
894	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
895	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
896	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
897	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
898	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
899		}
900
901		void SimInfo::setupFortranSim() {
902		int isError;
903	<	int nExclude;
904	<	std::vector<int> fortranGlobalGroupMembership;
903	>	int nExclude, nOneTwo, nOneThree, nOneFour;
904	>	vector<int> fortranGlobalGroupMembership;
905
906	<	nExclude = exclude_.getSize();
906	>	notifyFortranSkinThickness(&skinThickness_);
907	>
908	>	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
909	>	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
910	>	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
911	>
912		isError = 0;
913
914		//globalGroupMembership_ is filled by SimCreator
#	Line 790 | Line 917 | namespace oopse {
917		}
918
919		//calculate mass ratio of cutoff group
920	<	std::vector<double> mfact;
920	>	vector<RealType> mfact;
921		SimInfo::MoleculeIterator mi;
922		Molecule* mol;
923		Molecule::CutoffGroupIterator ci;
924		CutoffGroup* cg;
925		Molecule::AtomIterator ai;
926		Atom* atom;
927	<	double totalMass;
927	>	RealType totalMass;
928
929		//to avoid memory reallocation, reserve enough space for mfact
930		mfact.reserve(getNCutoffGroups());
#	Line 813 | Line 940 | namespace oopse {
940		else
941		mfact.push_back( 1.0 );
942		}
816	–
943		}
944		}
945
946		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
947	<	std::vector<int> identArray;
947	>	vector<int> identArray;
948
949		//to avoid memory reallocation, reserve enough space identArray
950		identArray.reserve(getNAtoms());
#	Line 831 | Line 957 | namespace oopse {
957
958		//fill molMembershipArray
959		//molMembershipArray is filled by SimCreator
960	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
960	>	vector<int> molMembershipArray(nGlobalAtoms_);
961		for (int i = 0; i < nGlobalAtoms_; i++) {
962		molMembershipArray[i] = globalMolMembership_[i] + 1;
963		}
964
965		//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);
966
967	<	if( isError ){
967	>	nExclude = excludedInteractions_.getSize();
968	>	nOneTwo = oneTwoInteractions_.getSize();
969	>	nOneThree = oneThreeInteractions_.getSize();
970	>	nOneFour = oneFourInteractions_.getSize();
971
972	+	int* excludeList = excludedInteractions_.getPairList();
973	+	int* oneTwoList = oneTwoInteractions_.getPairList();
974	+	int* oneThreeList = oneThreeInteractions_.getPairList();
975	+	int* oneFourList = oneFourInteractions_.getPairList();
976	+
977	+	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
978	+	&nExclude, excludeList,
979	+	&nOneTwo, oneTwoList,
980	+	&nOneThree, oneThreeList,
981	+	&nOneFour, oneFourList,
982	+	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
983	+	&fortranGlobalGroupMembership[0], &isError);
984	+
985	+	if( isError ){
986	+
987		sprintf( painCave.errMsg,
988		"There was an error setting the simulation information in fortran.\n" );
989		painCave.isFatal = 1;
990	<	painCave.severity = OOPSE_ERROR;
990	>	painCave.severity = OPENMD_ERROR;
991		simError();
992		}
993	<
994	<	#ifdef IS_MPI
993	>
994	>
995		sprintf( checkPointMsg,
996		"succesfully sent the simulation information to fortran.\n");
997	<	MPIcheckPoint();
998	<	#endif // is_mpi
997	>
998	>	errorCheckPoint();
999	>
1000	>	// Setup number of neighbors in neighbor list if present
1001	>	if (simParams_->haveNeighborListNeighbors()) {
1002	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
1003	>	setNeighbors(&nlistNeighbors);
1004	>	}
1005	>
1006	>
1007		}
1008
1009
864	–	#ifdef IS_MPI
1010		void SimInfo::setupFortranParallel() {
1011	<
1011	>	#ifdef IS_MPI
1012		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1013	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1014	<	std::vector<int> localToGlobalCutoffGroupIndex;
1013	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1014	>	vector<int> localToGlobalCutoffGroupIndex;
1015		SimInfo::MoleculeIterator mi;
1016		Molecule::AtomIterator ai;
1017		Molecule::CutoffGroupIterator ci;
#	Line 913 | Line 1058 | namespace oopse {
1058		}
1059
1060		sprintf(checkPointMsg, " mpiRefresh successful.\n");
1061	<	MPIcheckPoint();
1061	>	errorCheckPoint();
1062
1063	<
1063	>	#endif
1064		}
1065
921	–	#endif
1066
1067	<	void SimInfo::setupCutoff() {
924	<
925	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
926	<
927	<	// Check the cutoff policy
928	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
929	<
930	<	std::string myPolicy;
931	<	if (forceFieldOptions_.haveCutoffPolicy()){
932	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
933	<	}else if (simParams_->haveCutoffPolicy()) {
934	<	myPolicy = simParams_->getCutoffPolicy();
935	<	}
1067	>	void SimInfo::setupSwitchingFunction() {
1068
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	–	}
1069		}
1070
1071	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1026	<
1027	<	int errorOut;
1028	<	int esm =  NONE;
1029	<	int sm = UNDAMPED;
1030	<	double alphaVal;
1031	<	double dielectric;
1071	>	void SimInfo::setupAccumulateBoxDipole() {
1072
1073	<	errorOut = isError;
1074	<	alphaVal = simParams_->getDampingAlpha();
1075	<	dielectric = simParams_->getDielectric();
1076	<
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	<	setElectrostaticSummationMethod( &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	<	}
1073	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1074	>	if ( simParams_->haveAccumulateBoxDipole() )
1075	>	if ( simParams_->getAccumulateBoxDipole() ) {
1076	>	calcBoxDipole_ = true;
1077		}
1128	–	}
1078
1130	–	// send switching function notification to switcheroo
1131	–	setFunctionType(&ft);
1132	–
1079		}
1080
1081		void SimInfo::addProperty(GenericData* genData) {
1082		properties_.addProperty(genData);
1083		}
1084
1085	<	void SimInfo::removeProperty(const std::string& propName) {
1085	>	void SimInfo::removeProperty(const string& propName) {
1086		properties_.removeProperty(propName);
1087		}
1088
#	Line 1144 | Line 1090 | namespace oopse {
1090		properties_.clearProperties();
1091		}
1092
1093	<	std::vector<std::string> SimInfo::getPropertyNames() {
1093	>	vector<string> SimInfo::getPropertyNames() {
1094		return properties_.getPropertyNames();
1095		}
1096
1097	<	std::vector<GenericData*> SimInfo::getProperties() {
1097	>	vector<GenericData*> SimInfo::getProperties() {
1098		return properties_.getProperties();
1099		}
1100
1101	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1101	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1102		return properties_.getPropertyByName(propName);
1103		}
1104
#	Line 1188 | Line 1134 | namespace oopse {
1134		Molecule* mol;
1135
1136		Vector3d comVel(0.0);
1137	<	double totalMass = 0.0;
1137	>	RealType totalMass = 0.0;
1138
1139
1140		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1141	<	double mass = mol->getMass();
1141	>	RealType mass = mol->getMass();
1142		totalMass += mass;
1143		comVel += mass * mol->getComVel();
1144		}
1145
1146		#ifdef IS_MPI
1147	<	double tmpMass = totalMass;
1147	>	RealType tmpMass = totalMass;
1148		Vector3d tmpComVel(comVel);
1149	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1150	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1149	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1150	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1151		#endif
1152
1153		comVel /= totalMass;
#	Line 1214 | Line 1160 | namespace oopse {
1160		Molecule* mol;
1161
1162		Vector3d com(0.0);
1163	<	double totalMass = 0.0;
1163	>	RealType totalMass = 0.0;
1164
1165		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1166	<	double mass = mol->getMass();
1166	>	RealType mass = mol->getMass();
1167		totalMass += mass;
1168		com += mass * mol->getCom();
1169		}
1170
1171		#ifdef IS_MPI
1172	<	double tmpMass = totalMass;
1172	>	RealType tmpMass = totalMass;
1173		Vector3d tmpCom(com);
1174	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1175	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1174	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1175	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1176		#endif
1177
1178		com /= totalMass;
#	Line 1235 | Line 1181 | namespace oopse {
1181
1182		}
1183
1184	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1184	>	ostream& operator <<(ostream& o, SimInfo& info) {
1185
1186		return o;
1187		}
#	Line 1250 | Line 1196 | namespace oopse {
1196		Molecule* mol;
1197
1198
1199	<	double totalMass = 0.0;
1199	>	RealType totalMass = 0.0;
1200
1201
1202		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1203	<	double mass = mol->getMass();
1203	>	RealType mass = mol->getMass();
1204		totalMass += mass;
1205		com += mass * mol->getCom();
1206		comVel += mass * mol->getComVel();
1207		}
1208
1209		#ifdef IS_MPI
1210	<	double tmpMass = totalMass;
1210	>	RealType tmpMass = totalMass;
1211		Vector3d tmpCom(com);
1212		Vector3d tmpComVel(comVel);
1213	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1214	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1215	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1213	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1214	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1215	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1216		#endif
1217
1218		com /= totalMass;
#	Line 1278 | Line 1224 | namespace oopse {
1224
1225
1226		[  Ixx -Ixy  -Ixz ]
1227	<	J =| -Iyx  Iyy  -Iyz |
1227	>	J =| -Iyx  Iyy  -Iyz |
1228		[ -Izx -Iyz   Izz ]
1229		*/
1230
1231		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1232
1233
1234	<	double xx = 0.0;
1235	<	double yy = 0.0;
1236	<	double zz = 0.0;
1237	<	double xy = 0.0;
1238	<	double xz = 0.0;
1239	<	double yz = 0.0;
1234	>	RealType xx = 0.0;
1235	>	RealType yy = 0.0;
1236	>	RealType zz = 0.0;
1237	>	RealType xy = 0.0;
1238	>	RealType xz = 0.0;
1239	>	RealType yz = 0.0;
1240		Vector3d com(0.0);
1241		Vector3d comVel(0.0);
1242
#	Line 1302 | Line 1248 | namespace oopse {
1248		Vector3d thisq(0.0);
1249		Vector3d thisv(0.0);
1250
1251	<	double thisMass = 0.0;
1251	>	RealType thisMass = 0.0;
1252
1253
1254
#	Line 1340 | Line 1286 | namespace oopse {
1286		#ifdef IS_MPI
1287		Mat3x3d tmpI(inertiaTensor);
1288		Vector3d tmpAngMom;
1289	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1290	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1289	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1290	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1291		#endif
1292
1293		return;
#	Line 1362 | Line 1308 | namespace oopse {
1308		Vector3d thisr(0.0);
1309		Vector3d thisp(0.0);
1310
1311	<	double thisMass;
1311	>	RealType thisMass;
1312
1313		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1314		thisMass = mol->getMass();
#	Line 1375 | Line 1321 | namespace oopse {
1321
1322		#ifdef IS_MPI
1323		Vector3d tmpAngMom;
1324	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1324	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1325		#endif
1326
1327		return angularMomentum;
1328		}
1329
1330	<
1331	<	}//end namespace oopse
1330	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1331	>	return IOIndexToIntegrableObject.at(index);
1332	>	}
1333	>
1334	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1335	>	IOIndexToIntegrableObject= v;
1336	>	}
1337
1338	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1339	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1340	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1341	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1342	+	*/
1343	+	void SimInfo::getGyrationalVolume(RealType &volume){
1344	+	Mat3x3d intTensor;
1345	+	RealType det;
1346	+	Vector3d dummyAngMom;
1347	+	RealType sysconstants;
1348	+	RealType geomCnst;
1349	+
1350	+	geomCnst = 3.0/2.0;
1351	+	/* Get the inertial tensor and angular momentum for free*/
1352	+	getInertiaTensor(intTensor,dummyAngMom);
1353	+
1354	+	det = intTensor.determinant();
1355	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1356	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1357	+	return;
1358	+	}
1359	+
1360	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1361	+	Mat3x3d intTensor;
1362	+	Vector3d dummyAngMom;
1363	+	RealType sysconstants;
1364	+	RealType geomCnst;
1365	+
1366	+	geomCnst = 3.0/2.0;
1367	+	/* Get the inertial tensor and angular momentum for free*/
1368	+	getInertiaTensor(intTensor,dummyAngMom);
1369	+
1370	+	detI = intTensor.determinant();
1371	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1372	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1373	+	return;
1374	+	}
1375	+	/*
1376	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1377	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1378	+	sdByGlobalIndex_ = v;
1379	+	}
1380	+
1381	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1382	+	//assert(index < nAtoms_ + nRigidBodies_);
1383	+	return sdByGlobalIndex_.at(index);
1384	+	}
1385	+	*/
1386	+	int SimInfo::getNGlobalConstraints() {
1387	+	int nGlobalConstraints;
1388	+	#ifdef IS_MPI
1389	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1390	+	MPI_COMM_WORLD);
1391	+	#else
1392	+	nGlobalConstraints =  nConstraints_;
1393	+	#endif
1394	+	return nGlobalConstraints;
1395	+	}
1396	+
1397	+	}//end namespace OpenMD
1398	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 853 by chrisfen, Thu Jan 12 16:47:25 2006 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1530 by gezelter, Tue Dec 28 21:47:55 2010 UTC

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