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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 608 by chrisfen, Fri Sep 16 21:07:45 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1528 by gezelter, Fri Dec 17 20:11:05 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 48 | Line 48
48
49		#include <algorithm>
50		#include <set>
51	+	#include <map>
52
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"
58	<	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
58	>	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
59		#include "UseTheForce/doForces_interface.h"
60	<	#include "UseTheForce/notifyCutoffs_interface.h"
60	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
61	>	#include "UseTheForce/DarkSide/switcheroo_interface.h"
62		#include "utils/MemoryUtils.hpp"
63		#include "utils/simError.h"
64		#include "selection/SelectionManager.hpp"
65	+	#include "io/ForceFieldOptions.hpp"
66	+	#include "UseTheForce/ForceField.hpp"
67	+	#include "nonbonded/InteractionManager.hpp"
68
69	+
70		#ifdef IS_MPI
71		#include "UseTheForce/mpiComponentPlan.h"
72		#include "UseTheForce/DarkSide/simParallel_interface.h"
73		#endif
74
75	<	namespace oopse {
76	<
77	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
78	<	ForceField* ff, Globals* simParams) :
79	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
80	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
75	>	using namespace std;
76	>	namespace OpenMD {
77	>
78	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
79	>	forceField_(ff), simParams_(simParams),
80	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
81		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
82		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
83	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
84	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
85	<	sman_(NULL), fortranInitialized_(false) {
86	<
80	<
81	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
82	<	MoleculeStamp* molStamp;
83	<	int nMolWithSameStamp;
84	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
85	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
86	<	CutoffGroupStamp* cgStamp;
87	<	RigidBodyStamp* rbStamp;
88	<	int nRigidAtoms = 0;
83	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
84	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
85	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
86	>	calcBoxDipole_(false), useAtomicVirial_(true) {
87
88	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
89	<	molStamp = i->first;
90	<	nMolWithSameStamp = i->second;
91	<
92	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
93	<
94	<	//calculate atoms in molecules
95	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
96	<
97	<
98	<	//calculate atoms in cutoff groups
99	<	int nAtomsInGroups = 0;
100	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
101	<
102	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
103	<	cgStamp = molStamp->getCutoffGroup(j);
104	<	nAtomsInGroups += cgStamp->getNMembers();
105	<	}
106	<
107	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
108	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
109	<
110	<	//calculate atoms in rigid bodies
111	<	int nAtomsInRigidBodies = 0;
112	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
113	<
116	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
117	<	rbStamp = molStamp->getRigidBody(j);
118	<	nAtomsInRigidBodies += rbStamp->getNMembers();
119	<	}
120	<
121	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
122	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
123	<
88	>	MoleculeStamp* molStamp;
89	>	int nMolWithSameStamp;
90	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
91	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
92	>	CutoffGroupStamp* cgStamp;
93	>	RigidBodyStamp* rbStamp;
94	>	int nRigidAtoms = 0;
95	>
96	>	vector<Component*> components = simParams->getComponents();
97	>
98	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
99	>	molStamp = (*i)->getMoleculeStamp();
100	>	nMolWithSameStamp = (*i)->getNMol();
101	>
102	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
103	>
104	>	//calculate atoms in molecules
105	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
106	>
107	>	//calculate atoms in cutoff groups
108	>	int nAtomsInGroups = 0;
109	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
110	>
111	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
112	>	cgStamp = molStamp->getCutoffGroupStamp(j);
113	>	nAtomsInGroups += cgStamp->getNMembers();
114		}
115	<
116	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
117	<	//therefore the total number of cutoff groups in the system is equal to
118	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
119	<	//file plus the number of cutoff groups defined in meta-data file
120	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
121	<
122	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
123	<	//therefore the total number of  integrable objects in the system is equal to
124	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
125	<	//file plus the number of  rigid bodies defined in meta-data file
126	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
127	<
128	<	nGlobalMols_ = molStampIds_.size();
129	<
130	<	#ifdef IS_MPI
131	<	molToProcMap_.resize(nGlobalMols_);
132	<	#endif
133	<
134	<	}
135	<
115	>
116	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
117	>
118	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
119	>
120	>	//calculate atoms in rigid bodies
121	>	int nAtomsInRigidBodies = 0;
122	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
123	>
124	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
125	>	rbStamp = molStamp->getRigidBodyStamp(j);
126	>	nAtomsInRigidBodies += rbStamp->getNMembers();
127	>	}
128	>
129	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
130	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
131	>
132	>	}
133	>
134	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
135	>	//group therefore the total number of cutoff groups in the system is
136	>	//equal to the total number of atoms minus number of atoms belong to
137	>	//cutoff group defined in meta-data file plus the number of cutoff
138	>	//groups defined in meta-data file
139	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
140	>
141	>	//every free atom (atom does not belong to rigid bodies) is an
142	>	//integrable object therefore the total number of integrable objects
143	>	//in the system is equal to the total number of atoms minus number of
144	>	//atoms belong to rigid body defined in meta-data file plus the number
145	>	//of rigid bodies defined in meta-data file
146	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
147	>	+ nGlobalRigidBodies_;
148	>
149	>	nGlobalMols_ = molStampIds_.size();
150	>	molToProcMap_.resize(nGlobalMols_);
151	>	}
152	>
153		SimInfo::~SimInfo() {
154	<	std::map<int, Molecule*>::iterator i;
154	>	map<int, Molecule*>::iterator i;
155		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
156		delete i->second;
157		}
158		molecules_.clear();
159
153	–	delete stamps_;
160		delete sman_;
161		delete simParams_;
162		delete forceField_;
163		}
164
159	–	int SimInfo::getNGlobalConstraints() {
160	–	int nGlobalConstraints;
161	–	#ifdef IS_MPI
162	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
163	–	MPI_COMM_WORLD);
164	–	#else
165	–	nGlobalConstraints =  nConstraints_;
166	–	#endif
167	–	return nGlobalConstraints;
168	–	}
165
166		bool SimInfo::addMolecule(Molecule* mol) {
167		MoleculeIterator i;
168	<
168	>
169		i = molecules_.find(mol->getGlobalIndex());
170		if (i == molecules_.end() ) {
171	<
172	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
173	<
171	>
172	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
173	>
174		nAtoms_ += mol->getNAtoms();
175		nBonds_ += mol->getNBonds();
176		nBends_ += mol->getNBends();
177		nTorsions_ += mol->getNTorsions();
178	+	nInversions_ += mol->getNInversions();
179		nRigidBodies_ += mol->getNRigidBodies();
180		nIntegrableObjects_ += mol->getNIntegrableObjects();
181		nCutoffGroups_ += mol->getNCutoffGroups();
182		nConstraints_ += mol->getNConstraintPairs();
183	<
184	<	addExcludePairs(mol);
185	<
183	>
184	>	addInteractionPairs(mol);
185	>
186		return true;
187		} else {
188		return false;
189		}
190		}
191	<
191	>
192		bool SimInfo::removeMolecule(Molecule* mol) {
193		MoleculeIterator i;
194		i = molecules_.find(mol->getGlobalIndex());
#	Line 204 | Line 201 | namespace oopse {
201		nBonds_ -= mol->getNBonds();
202		nBends_ -= mol->getNBends();
203		nTorsions_ -= mol->getNTorsions();
204	+	nInversions_ -= mol->getNInversions();
205		nRigidBodies_ -= mol->getNRigidBodies();
206		nIntegrableObjects_ -= mol->getNIntegrableObjects();
207		nCutoffGroups_ -= mol->getNCutoffGroups();
208		nConstraints_ -= mol->getNConstraintPairs();
209
210	<	removeExcludePairs(mol);
210	>	removeInteractionPairs(mol);
211		molecules_.erase(mol->getGlobalIndex());
212
213		delete mol;
#	Line 218 | Line 216 | namespace oopse {
216		} else {
217		return false;
218		}
221	–
222	–
219		}
220
221
#	Line 237 | Line 233 | namespace oopse {
233		void SimInfo::calcNdf() {
234		int ndf_local;
235		MoleculeIterator i;
236	<	std::vector<StuntDouble*>::iterator j;
236	>	vector<StuntDouble*>::iterator j;
237		Molecule* mol;
238		StuntDouble* integrableObject;
239
#	Line 257 | Line 253 | namespace oopse {
253		}
254		}
255
256	<	}//end for (integrableObject)
257	<	}// end for (mol)
256	>	}
257	>	}
258
259		// n_constraints is local, so subtract them on each processor
260		ndf_local -= nConstraints_;
#	Line 275 | Line 271 | namespace oopse {
271
272		}
273
274	+	int SimInfo::getFdf() {
275	+	#ifdef IS_MPI
276	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
277	+	#else
278	+	fdf_ = fdf_local;
279	+	#endif
280	+	return fdf_;
281	+	}
282	+
283		void SimInfo::calcNdfRaw() {
284		int ndfRaw_local;
285
286		MoleculeIterator i;
287	<	std::vector<StuntDouble*>::iterator j;
287	>	vector<StuntDouble*>::iterator j;
288		Molecule* mol;
289		StuntDouble* integrableObject;
290
#	Line 326 | Line 331 | namespace oopse {
331
332		}
333
334	<	void SimInfo::addExcludePairs(Molecule* mol) {
335	<	std::vector<Bond*>::iterator bondIter;
336	<	std::vector<Bend*>::iterator bendIter;
337	<	std::vector<Torsion*>::iterator torsionIter;
334	>	void SimInfo::addInteractionPairs(Molecule* mol) {
335	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
336	>	vector<Bond*>::iterator bondIter;
337	>	vector<Bend*>::iterator bendIter;
338	>	vector<Torsion*>::iterator torsionIter;
339	>	vector<Inversion*>::iterator inversionIter;
340		Bond* bond;
341		Bend* bend;
342		Torsion* torsion;
343	+	Inversion* inversion;
344		int a;
345		int b;
346		int c;
347		int d;
348	+
349	+	// atomGroups can be used to add special interaction maps between
350	+	// groups of atoms that are in two separate rigid bodies.
351	+	// However, most site-site interactions between two rigid bodies
352	+	// are probably not special, just the ones between the physically
353	+	// bonded atoms.  Interactions *within* a single rigid body should
354	+	// always be excluded.  These are done at the bottom of this
355	+	// function.
356	+
357	+	map<int, set<int> > atomGroups;
358	+	Molecule::RigidBodyIterator rbIter;
359	+	RigidBody* rb;
360	+	Molecule::IntegrableObjectIterator ii;
361	+	StuntDouble* integrableObject;
362
363	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
363	>	for (integrableObject = mol->beginIntegrableObject(ii);
364	>	integrableObject != NULL;
365	>	integrableObject = mol->nextIntegrableObject(ii)) {
366	>
367	>	if (integrableObject->isRigidBody()) {
368	>	rb = static_cast<RigidBody*>(integrableObject);
369	>	vector<Atom*> atoms = rb->getAtoms();
370	>	set<int> rigidAtoms;
371	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
372	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
373	>	}
374	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
375	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
376	>	}
377	>	} else {
378	>	set<int> oneAtomSet;
379	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
380	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
381	>	}
382	>	}
383	>
384	>	for (bond= mol->beginBond(bondIter); bond != NULL;
385	>	bond = mol->nextBond(bondIter)) {
386	>
387		a = bond->getAtomA()->getGlobalIndex();
388	<	b = bond->getAtomB()->getGlobalIndex();
389	<	exclude_.addPair(a, b);
388	>	b = bond->getAtomB()->getGlobalIndex();
389	>
390	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
391	>	oneTwoInteractions_.addPair(a, b);
392	>	} else {
393	>	excludedInteractions_.addPair(a, b);
394	>	}
395		}
396
397	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
397	>	for (bend= mol->beginBend(bendIter); bend != NULL;
398	>	bend = mol->nextBend(bendIter)) {
399	>
400		a = bend->getAtomA()->getGlobalIndex();
401		b = bend->getAtomB()->getGlobalIndex();
402		c = bend->getAtomC()->getGlobalIndex();
403	+
404	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
405	+	oneTwoInteractions_.addPair(a, b);
406	+	oneTwoInteractions_.addPair(b, c);
407	+	} else {
408	+	excludedInteractions_.addPair(a, b);
409	+	excludedInteractions_.addPair(b, c);
410	+	}
411
412	<	exclude_.addPair(a, b);
413	<	exclude_.addPair(a, c);
414	<	exclude_.addPair(b, c);
412	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
413	>	oneThreeInteractions_.addPair(a, c);
414	>	} else {
415	>	excludedInteractions_.addPair(a, c);
416	>	}
417		}
418
419	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
419	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
420	>	torsion = mol->nextTorsion(torsionIter)) {
421	>
422		a = torsion->getAtomA()->getGlobalIndex();
423		b = torsion->getAtomB()->getGlobalIndex();
424		c = torsion->getAtomC()->getGlobalIndex();
425	<	d = torsion->getAtomD()->getGlobalIndex();
425	>	d = torsion->getAtomD()->getGlobalIndex();
426
427	<	exclude_.addPair(a, b);
428	<	exclude_.addPair(a, c);
429	<	exclude_.addPair(a, d);
430	<	exclude_.addPair(b, c);
431	<	exclude_.addPair(b, d);
432	<	exclude_.addPair(c, d);
427	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
428	>	oneTwoInteractions_.addPair(a, b);
429	>	oneTwoInteractions_.addPair(b, c);
430	>	oneTwoInteractions_.addPair(c, d);
431	>	} else {
432	>	excludedInteractions_.addPair(a, b);
433	>	excludedInteractions_.addPair(b, c);
434	>	excludedInteractions_.addPair(c, d);
435	>	}
436	>
437	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
438	>	oneThreeInteractions_.addPair(a, c);
439	>	oneThreeInteractions_.addPair(b, d);
440	>	} else {
441	>	excludedInteractions_.addPair(a, c);
442	>	excludedInteractions_.addPair(b, d);
443	>	}
444	>
445	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
446	>	oneFourInteractions_.addPair(a, d);
447	>	} else {
448	>	excludedInteractions_.addPair(a, d);
449	>	}
450		}
451
452	<	Molecule::RigidBodyIterator rbIter;
453	<	RigidBody* rb;
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) {
452	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
453	>	inversion = mol->nextInversion(inversionIter)) {
454	>
455	>	a = inversion->getAtomA()->getGlobalIndex();
456	>	b = inversion->getAtomB()->getGlobalIndex();
457	>	c = inversion->getAtomC()->getGlobalIndex();
458	>	d = inversion->getAtomD()->getGlobalIndex();
459	>
460	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
461	>	oneTwoInteractions_.addPair(a, b);
462	>	oneTwoInteractions_.addPair(a, c);
463	>	oneTwoInteractions_.addPair(a, d);
464	>	} else {
465	>	excludedInteractions_.addPair(a, b);
466	>	excludedInteractions_.addPair(a, c);
467	>	excludedInteractions_.addPair(a, d);
468	>	}
469	>
470	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
471	>	oneThreeInteractions_.addPair(b, c);
472	>	oneThreeInteractions_.addPair(b, d);
473	>	oneThreeInteractions_.addPair(c, d);
474	>	} else {
475	>	excludedInteractions_.addPair(b, c);
476	>	excludedInteractions_.addPair(b, d);
477	>	excludedInteractions_.addPair(c, d);
478	>	}
479	>	}
480	>
481	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
482	>	rb = mol->nextRigidBody(rbIter)) {
483	>	vector<Atom*> atoms = rb->getAtoms();
484	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
485	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
486		a = atoms[i]->getGlobalIndex();
487		b = atoms[j]->getGlobalIndex();
488	<	exclude_.addPair(a, b);
488	>	excludedInteractions_.addPair(a, b);
489		}
490		}
491		}
492
493		}
494
495	<	void SimInfo::removeExcludePairs(Molecule* mol) {
496	<	std::vector<Bond*>::iterator bondIter;
497	<	std::vector<Bend*>::iterator bendIter;
498	<	std::vector<Torsion*>::iterator torsionIter;
495	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
496	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
497	>	vector<Bond*>::iterator bondIter;
498	>	vector<Bend*>::iterator bendIter;
499	>	vector<Torsion*>::iterator torsionIter;
500	>	vector<Inversion*>::iterator inversionIter;
501		Bond* bond;
502		Bend* bend;
503		Torsion* torsion;
504	+	Inversion* inversion;
505		int a;
506		int b;
507		int c;
508		int d;
509	+
510	+	map<int, set<int> > atomGroups;
511	+	Molecule::RigidBodyIterator rbIter;
512	+	RigidBody* rb;
513	+	Molecule::IntegrableObjectIterator ii;
514	+	StuntDouble* integrableObject;
515
516	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
516	>	for (integrableObject = mol->beginIntegrableObject(ii);
517	>	integrableObject != NULL;
518	>	integrableObject = mol->nextIntegrableObject(ii)) {
519	>
520	>	if (integrableObject->isRigidBody()) {
521	>	rb = static_cast<RigidBody*>(integrableObject);
522	>	vector<Atom*> atoms = rb->getAtoms();
523	>	set<int> rigidAtoms;
524	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
525	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
526	>	}
527	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
528	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
529	>	}
530	>	} else {
531	>	set<int> oneAtomSet;
532	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
533	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
534	>	}
535	>	}
536	>
537	>	for (bond= mol->beginBond(bondIter); bond != NULL;
538	>	bond = mol->nextBond(bondIter)) {
539	>
540		a = bond->getAtomA()->getGlobalIndex();
541	<	b = bond->getAtomB()->getGlobalIndex();
542	<	exclude_.removePair(a, b);
541	>	b = bond->getAtomB()->getGlobalIndex();
542	>
543	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
544	>	oneTwoInteractions_.removePair(a, b);
545	>	} else {
546	>	excludedInteractions_.removePair(a, b);
547	>	}
548		}
549
550	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
550	>	for (bend= mol->beginBend(bendIter); bend != NULL;
551	>	bend = mol->nextBend(bendIter)) {
552	>
553		a = bend->getAtomA()->getGlobalIndex();
554		b = bend->getAtomB()->getGlobalIndex();
555		c = bend->getAtomC()->getGlobalIndex();
556	+
557	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
558	+	oneTwoInteractions_.removePair(a, b);
559	+	oneTwoInteractions_.removePair(b, c);
560	+	} else {
561	+	excludedInteractions_.removePair(a, b);
562	+	excludedInteractions_.removePair(b, c);
563	+	}
564
565	<	exclude_.removePair(a, b);
566	<	exclude_.removePair(a, c);
567	<	exclude_.removePair(b, c);
565	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
566	>	oneThreeInteractions_.removePair(a, c);
567	>	} else {
568	>	excludedInteractions_.removePair(a, c);
569	>	}
570		}
571
572	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
572	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
573	>	torsion = mol->nextTorsion(torsionIter)) {
574	>
575		a = torsion->getAtomA()->getGlobalIndex();
576		b = torsion->getAtomB()->getGlobalIndex();
577		c = torsion->getAtomC()->getGlobalIndex();
578	<	d = torsion->getAtomD()->getGlobalIndex();
578	>	d = torsion->getAtomD()->getGlobalIndex();
579	>
580	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
581	>	oneTwoInteractions_.removePair(a, b);
582	>	oneTwoInteractions_.removePair(b, c);
583	>	oneTwoInteractions_.removePair(c, d);
584	>	} else {
585	>	excludedInteractions_.removePair(a, b);
586	>	excludedInteractions_.removePair(b, c);
587	>	excludedInteractions_.removePair(c, d);
588	>	}
589
590	<	exclude_.removePair(a, b);
591	<	exclude_.removePair(a, c);
592	<	exclude_.removePair(a, d);
593	<	exclude_.removePair(b, c);
594	<	exclude_.removePair(b, d);
595	<	exclude_.removePair(c, d);
590	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
591	>	oneThreeInteractions_.removePair(a, c);
592	>	oneThreeInteractions_.removePair(b, d);
593	>	} else {
594	>	excludedInteractions_.removePair(a, c);
595	>	excludedInteractions_.removePair(b, d);
596	>	}
597	>
598	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
599	>	oneFourInteractions_.removePair(a, d);
600	>	} else {
601	>	excludedInteractions_.removePair(a, d);
602	>	}
603		}
604
605	<	Molecule::RigidBodyIterator rbIter;
606	<	RigidBody* rb;
607	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
608	<	std::vector<Atom*> atoms = rb->getAtoms();
609	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
610	<	for (int j = i + 1; j < atoms.size(); ++j) {
605	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
606	>	inversion = mol->nextInversion(inversionIter)) {
607	>
608	>	a = inversion->getAtomA()->getGlobalIndex();
609	>	b = inversion->getAtomB()->getGlobalIndex();
610	>	c = inversion->getAtomC()->getGlobalIndex();
611	>	d = inversion->getAtomD()->getGlobalIndex();
612	>
613	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
614	>	oneTwoInteractions_.removePair(a, b);
615	>	oneTwoInteractions_.removePair(a, c);
616	>	oneTwoInteractions_.removePair(a, d);
617	>	} else {
618	>	excludedInteractions_.removePair(a, b);
619	>	excludedInteractions_.removePair(a, c);
620	>	excludedInteractions_.removePair(a, d);
621	>	}
622	>
623	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
624	>	oneThreeInteractions_.removePair(b, c);
625	>	oneThreeInteractions_.removePair(b, d);
626	>	oneThreeInteractions_.removePair(c, d);
627	>	} else {
628	>	excludedInteractions_.removePair(b, c);
629	>	excludedInteractions_.removePair(b, d);
630	>	excludedInteractions_.removePair(c, d);
631	>	}
632	>	}
633	>
634	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
635	>	rb = mol->nextRigidBody(rbIter)) {
636	>	vector<Atom*> atoms = rb->getAtoms();
637	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
638	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
639		a = atoms[i]->getGlobalIndex();
640		b = atoms[j]->getGlobalIndex();
641	<	exclude_.removePair(a, b);
641	>	excludedInteractions_.removePair(a, b);
642		}
643		}
644		}
645	<
645	>
646		}
647	<
648	<
647	>
648	>
649		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
650		int curStampId;
651	<
651	>
652		//index from 0
653		curStampId = moleculeStamps_.size();
654
#	Line 454 | Line 659 | namespace oopse {
659		void SimInfo::update() {
660
661		setupSimType();
662	+	setupCutoffRadius();
663	+	setupSwitchingRadius();
664	+	setupCutoffMethod();
665	+	setupSkinThickness();
666	+	setupSwitchingFunction();
667	+	setupAccumulateBoxDipole();
668
669		#ifdef IS_MPI
670		setupFortranParallel();
671		#endif
461	–
672		setupFortranSim();
673	+	fortranInitialized_ = true;
674
464	–	//setup fortran force field
465	–	/** @deprecate */
466	–	int isError = 0;
467	–
468	–	setupElectrostaticSummationMethod( isError );
469	–
470	–	if(isError){
471	–	sprintf( painCave.errMsg,
472	–	"ForceField error: There was an error initializing the forceField in fortran.\n" );
473	–	painCave.isFatal = 1;
474	–	simError();
475	–	}
476	–
477	–
478	–	setupCutoff();
479	–
675		calcNdf();
676		calcNdfRaw();
677		calcNdfTrans();
483	–
484	–	fortranInitialized_ = true;
678		}
679	<
680	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
679	>
680	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
681		SimInfo::MoleculeIterator mi;
682		Molecule* mol;
683		Molecule::AtomIterator ai;
684		Atom* atom;
685	<	std::set<AtomType*> atomTypes;
686	<
685	>	set<AtomType*> atomTypes;
686	>
687		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
688	<
688	>
689		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
690		atomTypes.insert(atom->getAtomType());
691		}
692	<
692	>
693		}
694	<
694	>
695		return atomTypes;
696		}
697
698	<	void SimInfo::setupSimType() {
699	<	std::set<AtomType*>::iterator i;
700	<	std::set<AtomType*> atomTypes;
701	<	atomTypes = getUniqueAtomTypes();
698	>	/**
699	>	* setupCutoffRadius
700	>	*
701	>	*  If the cutoffRadius was explicitly set, use that value.
702	>	*  If the cutoffRadius was not explicitly set:
703	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
704	>	*      No electrostatic atoms?  Poll the atom types present in the
705	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
706	>	*      Use the maximum suggested value that was found.
707	>	*/
708	>	void SimInfo::setupCutoffRadius() {
709
710	<	int useLennardJones = 0;
711	<	int useElectrostatic = 0;
712	<	int useEAM = 0;
713	<	int useCharge = 0;
714	<	int useDirectional = 0;
715	<	int useDipole = 0;
716	<	int useGayBerne = 0;
717	<	int useSticky = 0;
718	<	int useStickyPower = 0;
719	<	int useShape = 0;
720	<	int useFLARB = 0; //it is not in AtomType yet
721	<	int useDirectionalAtom = 0;
722	<	int useElectrostatics = 0;
723	<	//usePBC and useRF are from simParams
724	<	int usePBC = simParams_->getPBC();
725	<
726	<	//loop over all of the atom types
727	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
728	<	useLennardJones |= (*i)->isLennardJones();
729	<	useElectrostatic |= (*i)->isElectrostatic();
730	<	useEAM |= (*i)->isEAM();
731	<	useCharge |= (*i)->isCharge();
732	<	useDirectional |= (*i)->isDirectional();
733	<	useDipole |= (*i)->isDipole();
734	<	useGayBerne |= (*i)->isGayBerne();
735	<	useSticky |= (*i)->isSticky();
736	<	useStickyPower |= (*i)->isStickyPower();
537	<	useShape |= (*i)->isShape();
710	>	if (simParams_->haveCutoffRadius()) {
711	>	cutoffRadius_ = simParams_->getCutoffRadius();
712	>	} else {
713	>	if (usesElectrostaticAtoms_) {
714	>	sprintf(painCave.errMsg,
715	>	"SimInfo Warning: No value was set for the cutoffRadius.\n"
716	>	"\tOpenMD will use a default value of 12.0 angstroms"
717	>	"\tfor the cutoffRadius.\n");
718	>	painCave.isFatal = 0;
719	>	simError();
720	>	cutoffRadius_ = 12.0;
721	>	} else {
722	>	RealType thisCut;
723	>	set<AtomType*>::iterator i;
724	>	set<AtomType*> atomTypes;
725	>	atomTypes = getSimulatedAtomTypes();
726	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
727	>	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
728	>	cutoffRadius_ = max(thisCut, cutoffRadius_);
729	>	}
730	>	sprintf(painCave.errMsg,
731	>	"SimInfo Warning: No value was set for the cutoffRadius.\n"
732	>	"\tOpenMD will use %lf angstroms.\n",
733	>	cutoffRadius_);
734	>	painCave.isFatal = 0;
735	>	simError();
736	>	}
737		}
738
739	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
740	<	useDirectionalAtom = 1;
741	<	}
739	>	InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
740	>	}
741	>
742	>	/**
743	>	* setupSwitchingRadius
744	>	*
745	>	*  If the switchingRadius was explicitly set, use that value (but check it)
746	>	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
747	>	*/
748	>	void SimInfo::setupSwitchingRadius() {
749	>
750	>	if (simParams_->haveSwitchingRadius()) {
751	>	switchingRadius_ = simParams_->getSwitchingRadius();
752	>	if (switchingRadius_ > cutoffRadius_) {
753	>	sprintf(painCave.errMsg,
754	>	"SimInfo Error: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
755	>	switchingRadius_, cutoffRadius_);
756	>	painCave.isFatal = 1;
757	>	simError();
758
759	<	if (useCharge || useDipole) {
760	<	useElectrostatics = 1;
761	<	}
759	>	}
760	>	} else {
761	>	switchingRadius_ = 0.85 * cutoffRadius_;
762	>	sprintf(painCave.errMsg,
763	>	"SimInfo Warning: No value was set for the switchingRadius.\n"
764	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
765	>	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
766	>	painCave.isFatal = 0;
767	>	simError();
768	>	}
769	>	InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
770	>	}
771
772	<	#ifdef IS_MPI
773	<	int temp;
772	>	/**
773	>	* setupSkinThickness
774	>	*
775	>	*  If the skinThickness was explicitly set, use that value (but check it)
776	>	*  If the skinThickness was not explicitly set: use 1.0 angstroms
777	>	*/
778	>	void SimInfo::setupSkinThickness() {
779	>	if (simParams_->haveSkinThickness()) {
780	>	skinThickness_ = simParams_->getSkinThickness();
781	>	} else {
782	>	skinThickness_ = 1.0;
783	>	sprintf(painCave.errMsg,
784	>	"SimInfo Warning: No value was set for the skinThickness.\n"
785	>	"\tOpenMD will use a default value of %f Angstroms\n"
786	>	"\tfor this simulation\n", skinThickness_);
787	>	painCave.isFatal = 0;
788	>	simError();
789	>	}
790	>	}
791
792	<	temp = usePBC;
793	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
792	>	void SimInfo::setupSimType() {
793	>	set<AtomType*>::iterator i;
794	>	set<AtomType*> atomTypes;
795	>	atomTypes = getSimulatedAtomTypes();
796
797	<	temp = useDirectionalAtom;
555	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
797	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
798
799	<	temp = useLennardJones;
800	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
799	>	int usesElectrostatic = 0;
800	>	int usesMetallic = 0;
801	>	int usesDirectional = 0;
802	>	//loop over all of the atom types
803	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
804	>	usesElectrostatic |= (*i)->isElectrostatic();
805	>	usesMetallic |= (*i)->isMetal();
806	>	usesDirectional |= (*i)->isDirectional();
807	>	}
808
809	<	temp = useElectrostatics;
810	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
811	<
812	<	temp = useCharge;
564	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
565	<
566	<	temp = useDipole;
567	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
568	<
569	<	temp = useSticky;
570	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
571	<
572	<	temp = useStickyPower;
573	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
574	<
575	<	temp = useGayBerne;
576	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
809	>	#ifdef IS_MPI
810	>	int temp;
811	>	temp = usesDirectional;
812	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813
814	<	temp = useEAM;
815	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814	>	temp = usesMetallic;
815	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816
817	<	temp = useShape;
818	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
583	<
584	<	temp = useFLARB;
585	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
586	<
817	>	temp = usesElectrostatic;
818	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819		#endif
820	<
821	<	fInfo_.SIM_uses_PBC = usePBC;
822	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
823	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
824	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
825	<	fInfo_.SIM_uses_Charges = useCharge;
594	<	fInfo_.SIM_uses_Dipoles = useDipole;
595	<	fInfo_.SIM_uses_Sticky = useSticky;
596	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
597	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
598	<	fInfo_.SIM_uses_EAM = useEAM;
599	<	fInfo_.SIM_uses_Shapes = useShape;
600	<	fInfo_.SIM_uses_FLARB = useFLARB;
601	<
602	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
603	<
604	<	if (simParams_->haveDielectric()) {
605	<	fInfo_.dielect = simParams_->getDielectric();
606	<	} else {
607	<	sprintf(painCave.errMsg,
608	<	"SimSetup Error: No Dielectric constant was set.\n"
609	<	"\tYou are trying to use Reaction Field without"
610	<	"\tsetting a dielectric constant!\n");
611	<	painCave.isFatal = 1;
612	<	simError();
613	<	}
614	<
615	<	} else {
616	<	fInfo_.dielect = 0.0;
617	<	}
618	<
820	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
821	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
822	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
823	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
824	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
825	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
826		}
827
828		void SimInfo::setupFortranSim() {
829		int isError;
830	<	int nExclude;
831	<	std::vector<int> fortranGlobalGroupMembership;
830	>	int nExclude, nOneTwo, nOneThree, nOneFour;
831	>	vector<int> fortranGlobalGroupMembership;
832
833	<	nExclude = exclude_.getSize();
833	>	notifyFortranSkinThickness(&skinThickness_);
834	>
835	>	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
836	>	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
837	>	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
838	>
839		isError = 0;
840
841		//globalGroupMembership_ is filled by SimCreator
#	Line 632 | Line 844 | namespace oopse {
844		}
845
846		//calculate mass ratio of cutoff group
847	<	std::vector<double> mfact;
847	>	vector<RealType> mfact;
848		SimInfo::MoleculeIterator mi;
849		Molecule* mol;
850		Molecule::CutoffGroupIterator ci;
851		CutoffGroup* cg;
852		Molecule::AtomIterator ai;
853		Atom* atom;
854	<	double totalMass;
854	>	RealType totalMass;
855
856		//to avoid memory reallocation, reserve enough space for mfact
857		mfact.reserve(getNCutoffGroups());
#	Line 649 | Line 861 | namespace oopse {
861
862		totalMass = cg->getMass();
863		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
864	<	mfact.push_back(atom->getMass()/totalMass);
864	>	// Check for massless groups - set mfact to 1 if true
865	>	if (totalMass != 0)
866	>	mfact.push_back(atom->getMass()/totalMass);
867	>	else
868	>	mfact.push_back( 1.0 );
869		}
654	–
870		}
871		}
872
873		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
874	<	std::vector<int> identArray;
874	>	vector<int> identArray;
875
876		//to avoid memory reallocation, reserve enough space identArray
877		identArray.reserve(getNAtoms());
#	Line 669 | Line 884 | namespace oopse {
884
885		//fill molMembershipArray
886		//molMembershipArray is filled by SimCreator
887	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
887	>	vector<int> molMembershipArray(nGlobalAtoms_);
888		for (int i = 0; i < nGlobalAtoms_; i++) {
889		molMembershipArray[i] = globalMolMembership_[i] + 1;
890		}
891
892		//setup fortran simulation
678	–	int nGlobalExcludes = 0;
679	–	int* globalExcludes = NULL;
680	–	int* excludeList = exclude_.getExcludeList();
681	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
682	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
683	–	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
893
894	<	if( isError ){
894	>	nExclude = excludedInteractions_.getSize();
895	>	nOneTwo = oneTwoInteractions_.getSize();
896	>	nOneThree = oneThreeInteractions_.getSize();
897	>	nOneFour = oneFourInteractions_.getSize();
898
899	+	int* excludeList = excludedInteractions_.getPairList();
900	+	int* oneTwoList = oneTwoInteractions_.getPairList();
901	+	int* oneThreeList = oneThreeInteractions_.getPairList();
902	+	int* oneFourList = oneFourInteractions_.getPairList();
903	+
904	+	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
905	+	&nExclude, excludeList,
906	+	&nOneTwo, oneTwoList,
907	+	&nOneThree, oneThreeList,
908	+	&nOneFour, oneFourList,
909	+	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
910	+	&fortranGlobalGroupMembership[0], &isError);
911	+
912	+	if( isError ){
913	+
914		sprintf( painCave.errMsg,
915		"There was an error setting the simulation information in fortran.\n" );
916		painCave.isFatal = 1;
917	<	painCave.severity = OOPSE_ERROR;
917	>	painCave.severity = OPENMD_ERROR;
918		simError();
919		}
920	<
921	<	#ifdef IS_MPI
920	>
921	>
922		sprintf( checkPointMsg,
923		"succesfully sent the simulation information to fortran.\n");
924	<	MPIcheckPoint();
925	<	#endif // is_mpi
924	>
925	>	errorCheckPoint();
926	>
927	>	// Setup number of neighbors in neighbor list if present
928	>	if (simParams_->haveNeighborListNeighbors()) {
929	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
930	>	setNeighbors(&nlistNeighbors);
931	>	}
932	>
933	>
934		}
935
936
702	–	#ifdef IS_MPI
937		void SimInfo::setupFortranParallel() {
938	<
938	>	#ifdef IS_MPI
939		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
940	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
941	<	std::vector<int> localToGlobalCutoffGroupIndex;
940	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
941	>	vector<int> localToGlobalCutoffGroupIndex;
942		SimInfo::MoleculeIterator mi;
943		Molecule::AtomIterator ai;
944		Molecule::CutoffGroupIterator ci;
#	Line 751 | Line 985 | namespace oopse {
985		}
986
987		sprintf(checkPointMsg, " mpiRefresh successful.\n");
988	<	MPIcheckPoint();
755	<
756	<
757	<	}
758	<
759	<	#endif
760	<
761	<	double SimInfo::calcMaxCutoffRadius() {
762	<
763	<
764	<	std::set<AtomType*> atomTypes;
765	<	std::set<AtomType*>::iterator i;
766	<	std::vector<double> cutoffRadius;
767	<
768	<	//get the unique atom types
769	<	atomTypes = getUniqueAtomTypes();
988	>	errorCheckPoint();
989
771	–	//query the max cutoff radius among these atom types
772	–	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
773	–	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
774	–	}
775	–
776	–	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
777	–	#ifdef IS_MPI
778	–	//pick the max cutoff radius among the processors
990		#endif
780	–
781	–	return maxCutoffRadius;
991		}
992
784	–	void SimInfo::getCutoff(double& rcut, double& rsw) {
785	–
786	–	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
787	–
788	–	if (!simParams_->haveRcut()){
789	–	sprintf(painCave.errMsg,
790	–	"SimCreator Warning: No value was set for the cutoffRadius.\n"
791	–	"\tOOPSE will use a default value of 15.0 angstroms"
792	–	"\tfor the cutoffRadius.\n");
793	–	painCave.isFatal = 0;
794	–	simError();
795	–	rcut = 15.0;
796	–	} else{
797	–	rcut = simParams_->getRcut();
798	–	}
993
994	<	if (!simParams_->haveRsw()){
995	<	sprintf(painCave.errMsg,
802	<	"SimCreator Warning: No value was set for switchingRadius.\n"
803	<	"\tOOPSE will use a default value of\n"
804	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
805	<	painCave.isFatal = 0;
806	<	simError();
807	<	rsw = 0.95 * rcut;
808	<	} else{
809	<	rsw = simParams_->getRsw();
810	<	}
811	<
812	<	} else {
813	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
814	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
815	<
816	<	if (simParams_->haveRcut()) {
817	<	rcut = simParams_->getRcut();
818	<	} else {
819	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
820	<	rcut = calcMaxCutoffRadius();
821	<	}
822	<
823	<	if (simParams_->haveRsw()) {
824	<	rsw  = simParams_->getRsw();
825	<	} else {
826	<	rsw = rcut;
827	<	}
994	>	void SimInfo::setupSwitchingFunction() {
995	>	int ft = CUBIC;
996
997	<	}
998	<	}
999	<
1000	<	void SimInfo::setupCutoff() {
1001	<	getCutoff(rcut_, rsw_);
834	<	double rnblist = rcut_ + 1; // skin of neighbor list
835	<
836	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
837	<
838	<	int cp =  TRADITIONAL_CUTOFF_POLICY;
839	<	if (simParams_->haveCutoffPolicy()) {
840	<	std::string myPolicy = simParams_->getCutoffPolicy();
841	<	if (myPolicy == "MIX") {
842	<	cp = MIX_CUTOFF_POLICY;
997	>	if (simParams_->haveSwitchingFunctionType()) {
998	>	string funcType = simParams_->getSwitchingFunctionType();
999	>	toUpper(funcType);
1000	>	if (funcType == "CUBIC") {
1001	>	ft = CUBIC;
1002		} else {
1003	<	if (myPolicy == "MAX") {
1004	<	cp = MAX_CUTOFF_POLICY;
1005	<	} else {
1006	<	if (myPolicy == "TRADITIONAL") {
1007	<	cp = TRADITIONAL_CUTOFF_POLICY;
1008	<	} else {
1009	<	// throw error
1010	<	sprintf( painCave.errMsg,
852	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
853	<	painCave.isFatal = 1;
854	<	simError();
855	<	}
1003	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1004	>	ft = FIFTH_ORDER_POLY;
1005	>	} else {
1006	>	// throw error
1007	>	sprintf( painCave.errMsg,
1008	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1009	>	painCave.isFatal = 1;
1010	>	simError();
1011		}
1012		}
1013		}
859	–	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
860	–	}
1014
1015	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1016	<
864	<	int errorOut;
865	<	int esm =  NONE;
866	<	double alphaVal;
1015	>	// send switching function notification to switcheroo
1016	>	setFunctionType(&ft);
1017
1018	<	errorOut = isError;
1018	>	}
1019
1020	<	if (simParams_->haveElectrostaticSummationMethod()) {
1021	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1022	<	if (myMethod == "NONE") {
1023	<	esm = NONE;
1024	<	} else {
1025	<	if (myMethod == "UNDAMPED_WOLF") {
876	<	esm = UNDAMPED_WOLF;
877	<	} else {
878	<	if (myMethod == "DAMPED_WOLF") {
879	<	esm = DAMPED_WOLF;
880	<	if (!simParams_->haveDampingAlpha()) {
881	<	//throw error
882	<	sprintf( painCave.errMsg,
883	<	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", simParams_->getDampingAlpha());
884	<	painCave.isFatal = 0;
885	<	simError();
886	<	}
887	<	alphaVal = simParams_->getDampingAlpha();
888	<	} else {
889	<	if (myMethod == "REACTION_FIELD") {
890	<	esm = REACTION_FIELD;
891	<	} else {
892	<	// throw error
893	<	sprintf( painCave.errMsg,
894	<	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"undamped_wolf\", \"damped_wolf\", or \"reaction_field\".", myMethod.c_str() );
895	<	painCave.isFatal = 1;
896	<	simError();
897	<	}
898	<	}
899	<	}
1020	>	void SimInfo::setupAccumulateBoxDipole() {
1021	>
1022	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1023	>	if ( simParams_->haveAccumulateBoxDipole() )
1024	>	if ( simParams_->getAccumulateBoxDipole() ) {
1025	>	calcBoxDipole_ = true;
1026		}
1027	<	}
902	<	initFortranFF( &esm, &alphaVal, &errorOut );
1027	>
1028		}
1029
1030		void SimInfo::addProperty(GenericData* genData) {
1031		properties_.addProperty(genData);
1032		}
1033
1034	<	void SimInfo::removeProperty(const std::string& propName) {
1034	>	void SimInfo::removeProperty(const string& propName) {
1035		properties_.removeProperty(propName);
1036		}
1037
#	Line 914 | Line 1039 | namespace oopse {
1039		properties_.clearProperties();
1040		}
1041
1042	<	std::vector<std::string> SimInfo::getPropertyNames() {
1042	>	vector<string> SimInfo::getPropertyNames() {
1043		return properties_.getPropertyNames();
1044		}
1045
1046	<	std::vector<GenericData*> SimInfo::getProperties() {
1046	>	vector<GenericData*> SimInfo::getProperties() {
1047		return properties_.getProperties();
1048		}
1049
1050	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1050	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1051		return properties_.getPropertyByName(propName);
1052		}
1053
#	Line 958 | Line 1083 | namespace oopse {
1083		Molecule* mol;
1084
1085		Vector3d comVel(0.0);
1086	<	double totalMass = 0.0;
1086	>	RealType totalMass = 0.0;
1087
1088
1089		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1090	<	double mass = mol->getMass();
1090	>	RealType mass = mol->getMass();
1091		totalMass += mass;
1092		comVel += mass * mol->getComVel();
1093		}
1094
1095		#ifdef IS_MPI
1096	<	double tmpMass = totalMass;
1096	>	RealType tmpMass = totalMass;
1097		Vector3d tmpComVel(comVel);
1098	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1099	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1098	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1099	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1100		#endif
1101
1102		comVel /= totalMass;
#	Line 984 | Line 1109 | namespace oopse {
1109		Molecule* mol;
1110
1111		Vector3d com(0.0);
1112	<	double totalMass = 0.0;
1112	>	RealType totalMass = 0.0;
1113
1114		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1115	<	double mass = mol->getMass();
1115	>	RealType mass = mol->getMass();
1116		totalMass += mass;
1117		com += mass * mol->getCom();
1118		}
1119
1120		#ifdef IS_MPI
1121	<	double tmpMass = totalMass;
1121	>	RealType tmpMass = totalMass;
1122		Vector3d tmpCom(com);
1123	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1124	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1123	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1124	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1125		#endif
1126
1127		com /= totalMass;
#	Line 1005 | Line 1130 | namespace oopse {
1130
1131		}
1132
1133	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1133	>	ostream& operator <<(ostream& o, SimInfo& info) {
1134
1135		return o;
1136		}
#	Line 1020 | Line 1145 | namespace oopse {
1145		Molecule* mol;
1146
1147
1148	<	double totalMass = 0.0;
1148	>	RealType totalMass = 0.0;
1149
1150
1151		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1152	<	double mass = mol->getMass();
1152	>	RealType mass = mol->getMass();
1153		totalMass += mass;
1154		com += mass * mol->getCom();
1155		comVel += mass * mol->getComVel();
1156		}
1157
1158		#ifdef IS_MPI
1159	<	double tmpMass = totalMass;
1159	>	RealType tmpMass = totalMass;
1160		Vector3d tmpCom(com);
1161		Vector3d tmpComVel(comVel);
1162	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1163	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1164	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1162	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1163	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1164	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1165		#endif
1166
1167		com /= totalMass;
#	Line 1048 | Line 1173 | namespace oopse {
1173
1174
1175		[  Ixx -Ixy  -Ixz ]
1176	<	J =| -Iyx  Iyy  -Iyz |
1176	>	J =| -Iyx  Iyy  -Iyz |
1177		[ -Izx -Iyz   Izz ]
1178		*/
1179
1180		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1181
1182
1183	<	double xx = 0.0;
1184	<	double yy = 0.0;
1185	<	double zz = 0.0;
1186	<	double xy = 0.0;
1187	<	double xz = 0.0;
1188	<	double yz = 0.0;
1183	>	RealType xx = 0.0;
1184	>	RealType yy = 0.0;
1185	>	RealType zz = 0.0;
1186	>	RealType xy = 0.0;
1187	>	RealType xz = 0.0;
1188	>	RealType yz = 0.0;
1189		Vector3d com(0.0);
1190		Vector3d comVel(0.0);
1191
#	Line 1072 | Line 1197 | namespace oopse {
1197		Vector3d thisq(0.0);
1198		Vector3d thisv(0.0);
1199
1200	<	double thisMass = 0.0;
1200	>	RealType thisMass = 0.0;
1201
1202
1203
#	Line 1110 | Line 1235 | namespace oopse {
1235		#ifdef IS_MPI
1236		Mat3x3d tmpI(inertiaTensor);
1237		Vector3d tmpAngMom;
1238	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1239	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1238	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1239	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1240		#endif
1241
1242		return;
#	Line 1132 | Line 1257 | namespace oopse {
1257		Vector3d thisr(0.0);
1258		Vector3d thisp(0.0);
1259
1260	<	double thisMass;
1260	>	RealType thisMass;
1261
1262		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1263		thisMass = mol->getMass();
#	Line 1145 | Line 1270 | namespace oopse {
1270
1271		#ifdef IS_MPI
1272		Vector3d tmpAngMom;
1273	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1273	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1274		#endif
1275
1276		return angularMomentum;
1277		}
1278
1279	<
1280	<	}//end namespace oopse
1279	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1280	>	return IOIndexToIntegrableObject.at(index);
1281	>	}
1282	>
1283	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1284	>	IOIndexToIntegrableObject= v;
1285	>	}
1286
1287	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1288	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1289	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1290	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1291	+	*/
1292	+	void SimInfo::getGyrationalVolume(RealType &volume){
1293	+	Mat3x3d intTensor;
1294	+	RealType det;
1295	+	Vector3d dummyAngMom;
1296	+	RealType sysconstants;
1297	+	RealType geomCnst;
1298	+
1299	+	geomCnst = 3.0/2.0;
1300	+	/* Get the inertial tensor and angular momentum for free*/
1301	+	getInertiaTensor(intTensor,dummyAngMom);
1302	+
1303	+	det = intTensor.determinant();
1304	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1305	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1306	+	return;
1307	+	}
1308	+
1309	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1310	+	Mat3x3d intTensor;
1311	+	Vector3d dummyAngMom;
1312	+	RealType sysconstants;
1313	+	RealType geomCnst;
1314	+
1315	+	geomCnst = 3.0/2.0;
1316	+	/* Get the inertial tensor and angular momentum for free*/
1317	+	getInertiaTensor(intTensor,dummyAngMom);
1318	+
1319	+	detI = intTensor.determinant();
1320	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1321	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1322	+	return;
1323	+	}
1324	+	/*
1325	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1326	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1327	+	sdByGlobalIndex_ = v;
1328	+	}
1329	+
1330	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1331	+	//assert(index < nAtoms_ + nRigidBodies_);
1332	+	return sdByGlobalIndex_.at(index);
1333	+	}
1334	+	*/
1335	+	int SimInfo::getNGlobalConstraints() {
1336	+	int nGlobalConstraints;
1337	+	#ifdef IS_MPI
1338	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1339	+	MPI_COMM_WORLD);
1340	+	#else
1341	+	nGlobalConstraints =  nConstraints_;
1342	+	#endif
1343	+	return nGlobalConstraints;
1344	+	}
1345	+
1346	+	}//end namespace OpenMD
1347	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 608 by chrisfen, Fri Sep 16 21:07:45 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1528 by gezelter, Fri Dec 17 20:11:05 2010 UTC

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