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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 555 by chuckv, Mon May 30 14:01:52 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 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 "UseTheForce/doForces_interface.h"
56	<	#include "UseTheForce/notifyCutoffs_interface.h"
56	>	#include "primitives/StuntDouble.hpp"
57		#include "utils/MemoryUtils.hpp"
58		#include "utils/simError.h"
59		#include "selection/SelectionManager.hpp"
60	+	#include "io/ForceFieldOptions.hpp"
61	+	#include "UseTheForce/ForceField.hpp"
62	+	#include "nonbonded/SwitchingFunction.hpp"
63
64	<	#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
67	<	#endif
68	<
69	<	namespace oopse {
67	<
68	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
69	<	ForceField* ff, Globals* simParams) :
70	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
71	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
64	>	using namespace std;
65	>	namespace OpenMD {
66	>
67	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
68	>	forceField_(ff), simParams_(simParams),
69	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
70		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
71		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
72	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
73	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
74	<	sman_(NULL), fortranInitialized_(false) {
75	<
78	<
79	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
80	<	MoleculeStamp* molStamp;
81	<	int nMolWithSameStamp;
82	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
83	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
84	<	CutoffGroupStamp* cgStamp;
85	<	RigidBodyStamp* rbStamp;
86	<	int nRigidAtoms = 0;
72	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
73	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
74	>	nConstraints_(0), sman_(NULL), topologyDone_(false),
75	>	calcBoxDipole_(false), useAtomicVirial_(true) {
76
77	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
78	<	molStamp = i->first;
79	<	nMolWithSameStamp = i->second;
80	<
81	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
82	<
83	<	//calculate atoms in molecules
84	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
85	<
86	<
87	<	//calculate atoms in cutoff groups
88	<	int nAtomsInGroups = 0;
89	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
90	<
91	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
92	<	cgStamp = molStamp->getCutoffGroup(j);
93	<	nAtomsInGroups += cgStamp->getNMembers();
94	<	}
95	<
96	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
97	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
98	<
99	<	//calculate atoms in rigid bodies
100	<	int nAtomsInRigidBodies = 0;
101	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
102	<
114	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
115	<	rbStamp = molStamp->getRigidBody(j);
116	<	nAtomsInRigidBodies += rbStamp->getNMembers();
117	<	}
118	<
119	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
120	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
121	<
77	>	MoleculeStamp* molStamp;
78	>	int nMolWithSameStamp;
79	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
80	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
81	>	CutoffGroupStamp* cgStamp;
82	>	RigidBodyStamp* rbStamp;
83	>	int nRigidAtoms = 0;
84	>
85	>	vector<Component*> components = simParams->getComponents();
86	>
87	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
88	>	molStamp = (*i)->getMoleculeStamp();
89	>	nMolWithSameStamp = (*i)->getNMol();
90	>
91	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
92	>
93	>	//calculate atoms in molecules
94	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
95	>
96	>	//calculate atoms in cutoff groups
97	>	int nAtomsInGroups = 0;
98	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
99	>
100	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
101	>	cgStamp = molStamp->getCutoffGroupStamp(j);
102	>	nAtomsInGroups += cgStamp->getNMembers();
103		}
104	<
105	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
106	<	//therefore the total number of cutoff groups in the system is equal to
107	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
108	<	//file plus the number of cutoff groups defined in meta-data file
109	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
110	<
111	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
112	<	//therefore the total number of  integrable objects in the system is equal to
113	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
114	<	//file plus the number of  rigid bodies defined in meta-data file
115	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
116	<
117	<	nGlobalMols_ = molStampIds_.size();
118	<
119	<	#ifdef IS_MPI
120	<	molToProcMap_.resize(nGlobalMols_);
140	<	#endif
141	<
104	>
105	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
106	>
107	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
108	>
109	>	//calculate atoms in rigid bodies
110	>	int nAtomsInRigidBodies = 0;
111	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
112	>
113	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
114	>	rbStamp = molStamp->getRigidBodyStamp(j);
115	>	nAtomsInRigidBodies += rbStamp->getNMembers();
116	>	}
117	>
118	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
119	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
120	>
121		}
122	+
123	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
124	+	//group therefore the total number of cutoff groups in the system is
125	+	//equal to the total number of atoms minus number of atoms belong to
126	+	//cutoff group defined in meta-data file plus the number of cutoff
127	+	//groups defined in meta-data file
128	+	std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
129	+	std::cerr << "nCA = " << nCutoffAtoms << "\n";
130	+	std::cerr << "nG = " << nGroups << "\n";
131
132	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
133	+
134	+	std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
135	+
136	+	//every free atom (atom does not belong to rigid bodies) is an
137	+	//integrable object therefore the total number of integrable objects
138	+	//in the system is equal to the total number of atoms minus number of
139	+	//atoms belong to rigid body defined in meta-data file plus the number
140	+	//of rigid bodies defined in meta-data file
141	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
142	+	+ nGlobalRigidBodies_;
143	+
144	+	nGlobalMols_ = molStampIds_.size();
145	+	molToProcMap_.resize(nGlobalMols_);
146	+	}
147	+
148		SimInfo::~SimInfo() {
149	<	std::map<int, Molecule*>::iterator i;
149	>	map<int, Molecule*>::iterator i;
150		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
151		delete i->second;
152		}
153		molecules_.clear();
154
151	–	delete stamps_;
155		delete sman_;
156		delete simParams_;
157		delete forceField_;
158		}
159
157	–	int SimInfo::getNGlobalConstraints() {
158	–	int nGlobalConstraints;
159	–	#ifdef IS_MPI
160	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
161	–	MPI_COMM_WORLD);
162	–	#else
163	–	nGlobalConstraints =  nConstraints_;
164	–	#endif
165	–	return nGlobalConstraints;
166	–	}
160
161		bool SimInfo::addMolecule(Molecule* mol) {
162		MoleculeIterator i;
163	<
163	>
164		i = molecules_.find(mol->getGlobalIndex());
165		if (i == molecules_.end() ) {
166	<
167	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
168	<
166	>
167	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
168	>
169		nAtoms_ += mol->getNAtoms();
170		nBonds_ += mol->getNBonds();
171		nBends_ += mol->getNBends();
172		nTorsions_ += mol->getNTorsions();
173	+	nInversions_ += mol->getNInversions();
174		nRigidBodies_ += mol->getNRigidBodies();
175		nIntegrableObjects_ += mol->getNIntegrableObjects();
176		nCutoffGroups_ += mol->getNCutoffGroups();
177		nConstraints_ += mol->getNConstraintPairs();
178	<
179	<	addExcludePairs(mol);
180	<
178	>
179	>	addInteractionPairs(mol);
180	>
181		return true;
182		} else {
183		return false;
184		}
185		}
186	<
186	>
187		bool SimInfo::removeMolecule(Molecule* mol) {
188		MoleculeIterator i;
189		i = molecules_.find(mol->getGlobalIndex());
#	Line 202 | Line 196 | namespace oopse {
196		nBonds_ -= mol->getNBonds();
197		nBends_ -= mol->getNBends();
198		nTorsions_ -= mol->getNTorsions();
199	+	nInversions_ -= mol->getNInversions();
200		nRigidBodies_ -= mol->getNRigidBodies();
201		nIntegrableObjects_ -= mol->getNIntegrableObjects();
202		nCutoffGroups_ -= mol->getNCutoffGroups();
203		nConstraints_ -= mol->getNConstraintPairs();
204
205	<	removeExcludePairs(mol);
205	>	removeInteractionPairs(mol);
206		molecules_.erase(mol->getGlobalIndex());
207
208		delete mol;
#	Line 216 | Line 211 | namespace oopse {
211		} else {
212		return false;
213		}
219	–
220	–
214		}
215
216
#	Line 235 | Line 228 | namespace oopse {
228		void SimInfo::calcNdf() {
229		int ndf_local;
230		MoleculeIterator i;
231	<	std::vector<StuntDouble*>::iterator j;
231	>	vector<StuntDouble*>::iterator j;
232		Molecule* mol;
233		StuntDouble* integrableObject;
234
#	Line 255 | Line 248 | namespace oopse {
248		}
249		}
250
251	<	}//end for (integrableObject)
252	<	}// end for (mol)
251	>	}
252	>	}
253
254		// n_constraints is local, so subtract them on each processor
255		ndf_local -= nConstraints_;
#	Line 273 | Line 266 | namespace oopse {
266
267		}
268
269	+	int SimInfo::getFdf() {
270	+	#ifdef IS_MPI
271	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
272	+	#else
273	+	fdf_ = fdf_local;
274	+	#endif
275	+	return fdf_;
276	+	}
277	+
278		void SimInfo::calcNdfRaw() {
279		int ndfRaw_local;
280
281		MoleculeIterator i;
282	<	std::vector<StuntDouble*>::iterator j;
282	>	vector<StuntDouble*>::iterator j;
283		Molecule* mol;
284		StuntDouble* integrableObject;
285
#	Line 324 | Line 326 | namespace oopse {
326
327		}
328
329	<	void SimInfo::addExcludePairs(Molecule* mol) {
330	<	std::vector<Bond*>::iterator bondIter;
331	<	std::vector<Bend*>::iterator bendIter;
332	<	std::vector<Torsion*>::iterator torsionIter;
329	>	void SimInfo::addInteractionPairs(Molecule* mol) {
330	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
331	>	vector<Bond*>::iterator bondIter;
332	>	vector<Bend*>::iterator bendIter;
333	>	vector<Torsion*>::iterator torsionIter;
334	>	vector<Inversion*>::iterator inversionIter;
335		Bond* bond;
336		Bend* bend;
337		Torsion* torsion;
338	+	Inversion* inversion;
339		int a;
340		int b;
341		int c;
342		int d;
343	+
344	+	// atomGroups can be used to add special interaction maps between
345	+	// groups of atoms that are in two separate rigid bodies.
346	+	// However, most site-site interactions between two rigid bodies
347	+	// are probably not special, just the ones between the physically
348	+	// bonded atoms.  Interactions *within* a single rigid body should
349	+	// always be excluded.  These are done at the bottom of this
350	+	// function.
351	+
352	+	map<int, set<int> > atomGroups;
353	+	Molecule::RigidBodyIterator rbIter;
354	+	RigidBody* rb;
355	+	Molecule::IntegrableObjectIterator ii;
356	+	StuntDouble* integrableObject;
357
358	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
358	>	for (integrableObject = mol->beginIntegrableObject(ii);
359	>	integrableObject != NULL;
360	>	integrableObject = mol->nextIntegrableObject(ii)) {
361	>
362	>	if (integrableObject->isRigidBody()) {
363	>	rb = static_cast<RigidBody*>(integrableObject);
364	>	vector<Atom*> atoms = rb->getAtoms();
365	>	set<int> rigidAtoms;
366	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
367	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
368	>	}
369	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
370	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
371	>	}
372	>	} else {
373	>	set<int> oneAtomSet;
374	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
375	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
376	>	}
377	>	}
378	>
379	>	for (bond= mol->beginBond(bondIter); bond != NULL;
380	>	bond = mol->nextBond(bondIter)) {
381	>
382		a = bond->getAtomA()->getGlobalIndex();
383	<	b = bond->getAtomB()->getGlobalIndex();
384	<	exclude_.addPair(a, b);
383	>	b = bond->getAtomB()->getGlobalIndex();
384	>
385	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
386	>	oneTwoInteractions_.addPair(a, b);
387	>	} else {
388	>	excludedInteractions_.addPair(a, b);
389	>	}
390		}
391
392	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
392	>	for (bend= mol->beginBend(bendIter); bend != NULL;
393	>	bend = mol->nextBend(bendIter)) {
394	>
395		a = bend->getAtomA()->getGlobalIndex();
396		b = bend->getAtomB()->getGlobalIndex();
397		c = bend->getAtomC()->getGlobalIndex();
398	+
399	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
400	+	oneTwoInteractions_.addPair(a, b);
401	+	oneTwoInteractions_.addPair(b, c);
402	+	} else {
403	+	excludedInteractions_.addPair(a, b);
404	+	excludedInteractions_.addPair(b, c);
405	+	}
406
407	<	exclude_.addPair(a, b);
408	<	exclude_.addPair(a, c);
409	<	exclude_.addPair(b, c);
407	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
408	>	oneThreeInteractions_.addPair(a, c);
409	>	} else {
410	>	excludedInteractions_.addPair(a, c);
411	>	}
412		}
413
414	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
414	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
415	>	torsion = mol->nextTorsion(torsionIter)) {
416	>
417		a = torsion->getAtomA()->getGlobalIndex();
418		b = torsion->getAtomB()->getGlobalIndex();
419		c = torsion->getAtomC()->getGlobalIndex();
420	<	d = torsion->getAtomD()->getGlobalIndex();
420	>	d = torsion->getAtomD()->getGlobalIndex();
421
422	<	exclude_.addPair(a, b);
423	<	exclude_.addPair(a, c);
424	<	exclude_.addPair(a, d);
425	<	exclude_.addPair(b, c);
426	<	exclude_.addPair(b, d);
427	<	exclude_.addPair(c, d);
422	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
423	>	oneTwoInteractions_.addPair(a, b);
424	>	oneTwoInteractions_.addPair(b, c);
425	>	oneTwoInteractions_.addPair(c, d);
426	>	} else {
427	>	excludedInteractions_.addPair(a, b);
428	>	excludedInteractions_.addPair(b, c);
429	>	excludedInteractions_.addPair(c, d);
430	>	}
431	>
432	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
433	>	oneThreeInteractions_.addPair(a, c);
434	>	oneThreeInteractions_.addPair(b, d);
435	>	} else {
436	>	excludedInteractions_.addPair(a, c);
437	>	excludedInteractions_.addPair(b, d);
438	>	}
439	>
440	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
441	>	oneFourInteractions_.addPair(a, d);
442	>	} else {
443	>	excludedInteractions_.addPair(a, d);
444	>	}
445		}
446
447	<	Molecule::RigidBodyIterator rbIter;
448	<	RigidBody* rb;
449	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
450	<	std::vector<Atom*> atoms = rb->getAtoms();
451	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
452	<	for (int j = i + 1; j < atoms.size(); ++j) {
447	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
448	>	inversion = mol->nextInversion(inversionIter)) {
449	>
450	>	a = inversion->getAtomA()->getGlobalIndex();
451	>	b = inversion->getAtomB()->getGlobalIndex();
452	>	c = inversion->getAtomC()->getGlobalIndex();
453	>	d = inversion->getAtomD()->getGlobalIndex();
454	>
455	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
456	>	oneTwoInteractions_.addPair(a, b);
457	>	oneTwoInteractions_.addPair(a, c);
458	>	oneTwoInteractions_.addPair(a, d);
459	>	} else {
460	>	excludedInteractions_.addPair(a, b);
461	>	excludedInteractions_.addPair(a, c);
462	>	excludedInteractions_.addPair(a, d);
463	>	}
464	>
465	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
466	>	oneThreeInteractions_.addPair(b, c);
467	>	oneThreeInteractions_.addPair(b, d);
468	>	oneThreeInteractions_.addPair(c, d);
469	>	} else {
470	>	excludedInteractions_.addPair(b, c);
471	>	excludedInteractions_.addPair(b, d);
472	>	excludedInteractions_.addPair(c, d);
473	>	}
474	>	}
475	>
476	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
477	>	rb = mol->nextRigidBody(rbIter)) {
478	>	vector<Atom*> atoms = rb->getAtoms();
479	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
480	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
481		a = atoms[i]->getGlobalIndex();
482		b = atoms[j]->getGlobalIndex();
483	<	exclude_.addPair(a, b);
483	>	excludedInteractions_.addPair(a, b);
484		}
485		}
486		}
487
488		}
489
490	<	void SimInfo::removeExcludePairs(Molecule* mol) {
491	<	std::vector<Bond*>::iterator bondIter;
492	<	std::vector<Bend*>::iterator bendIter;
493	<	std::vector<Torsion*>::iterator torsionIter;
490	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
491	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
492	>	vector<Bond*>::iterator bondIter;
493	>	vector<Bend*>::iterator bendIter;
494	>	vector<Torsion*>::iterator torsionIter;
495	>	vector<Inversion*>::iterator inversionIter;
496		Bond* bond;
497		Bend* bend;
498		Torsion* torsion;
499	+	Inversion* inversion;
500		int a;
501		int b;
502		int c;
503		int d;
504	+
505	+	map<int, set<int> > atomGroups;
506	+	Molecule::RigidBodyIterator rbIter;
507	+	RigidBody* rb;
508	+	Molecule::IntegrableObjectIterator ii;
509	+	StuntDouble* integrableObject;
510
511	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
511	>	for (integrableObject = mol->beginIntegrableObject(ii);
512	>	integrableObject != NULL;
513	>	integrableObject = mol->nextIntegrableObject(ii)) {
514	>
515	>	if (integrableObject->isRigidBody()) {
516	>	rb = static_cast<RigidBody*>(integrableObject);
517	>	vector<Atom*> atoms = rb->getAtoms();
518	>	set<int> rigidAtoms;
519	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
520	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
521	>	}
522	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
523	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
524	>	}
525	>	} else {
526	>	set<int> oneAtomSet;
527	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
528	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
529	>	}
530	>	}
531	>
532	>	for (bond= mol->beginBond(bondIter); bond != NULL;
533	>	bond = mol->nextBond(bondIter)) {
534	>
535		a = bond->getAtomA()->getGlobalIndex();
536	<	b = bond->getAtomB()->getGlobalIndex();
537	<	exclude_.removePair(a, b);
536	>	b = bond->getAtomB()->getGlobalIndex();
537	>
538	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
539	>	oneTwoInteractions_.removePair(a, b);
540	>	} else {
541	>	excludedInteractions_.removePair(a, b);
542	>	}
543		}
544
545	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
545	>	for (bend= mol->beginBend(bendIter); bend != NULL;
546	>	bend = mol->nextBend(bendIter)) {
547	>
548		a = bend->getAtomA()->getGlobalIndex();
549		b = bend->getAtomB()->getGlobalIndex();
550		c = bend->getAtomC()->getGlobalIndex();
551	+
552	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
553	+	oneTwoInteractions_.removePair(a, b);
554	+	oneTwoInteractions_.removePair(b, c);
555	+	} else {
556	+	excludedInteractions_.removePair(a, b);
557	+	excludedInteractions_.removePair(b, c);
558	+	}
559
560	<	exclude_.removePair(a, b);
561	<	exclude_.removePair(a, c);
562	<	exclude_.removePair(b, c);
560	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
561	>	oneThreeInteractions_.removePair(a, c);
562	>	} else {
563	>	excludedInteractions_.removePair(a, c);
564	>	}
565		}
566
567	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
567	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
568	>	torsion = mol->nextTorsion(torsionIter)) {
569	>
570		a = torsion->getAtomA()->getGlobalIndex();
571		b = torsion->getAtomB()->getGlobalIndex();
572		c = torsion->getAtomC()->getGlobalIndex();
573	<	d = torsion->getAtomD()->getGlobalIndex();
573	>	d = torsion->getAtomD()->getGlobalIndex();
574	>
575	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
576	>	oneTwoInteractions_.removePair(a, b);
577	>	oneTwoInteractions_.removePair(b, c);
578	>	oneTwoInteractions_.removePair(c, d);
579	>	} else {
580	>	excludedInteractions_.removePair(a, b);
581	>	excludedInteractions_.removePair(b, c);
582	>	excludedInteractions_.removePair(c, d);
583	>	}
584
585	<	exclude_.removePair(a, b);
586	<	exclude_.removePair(a, c);
587	<	exclude_.removePair(a, d);
588	<	exclude_.removePair(b, c);
589	<	exclude_.removePair(b, d);
590	<	exclude_.removePair(c, d);
585	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
586	>	oneThreeInteractions_.removePair(a, c);
587	>	oneThreeInteractions_.removePair(b, d);
588	>	} else {
589	>	excludedInteractions_.removePair(a, c);
590	>	excludedInteractions_.removePair(b, d);
591	>	}
592	>
593	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
594	>	oneFourInteractions_.removePair(a, d);
595	>	} else {
596	>	excludedInteractions_.removePair(a, d);
597	>	}
598		}
599
600	<	Molecule::RigidBodyIterator rbIter;
601	<	RigidBody* rb;
602	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
603	<	std::vector<Atom*> atoms = rb->getAtoms();
604	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
605	<	for (int j = i + 1; j < atoms.size(); ++j) {
600	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
601	>	inversion = mol->nextInversion(inversionIter)) {
602	>
603	>	a = inversion->getAtomA()->getGlobalIndex();
604	>	b = inversion->getAtomB()->getGlobalIndex();
605	>	c = inversion->getAtomC()->getGlobalIndex();
606	>	d = inversion->getAtomD()->getGlobalIndex();
607	>
608	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
609	>	oneTwoInteractions_.removePair(a, b);
610	>	oneTwoInteractions_.removePair(a, c);
611	>	oneTwoInteractions_.removePair(a, d);
612	>	} else {
613	>	excludedInteractions_.removePair(a, b);
614	>	excludedInteractions_.removePair(a, c);
615	>	excludedInteractions_.removePair(a, d);
616	>	}
617	>
618	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
619	>	oneThreeInteractions_.removePair(b, c);
620	>	oneThreeInteractions_.removePair(b, d);
621	>	oneThreeInteractions_.removePair(c, d);
622	>	} else {
623	>	excludedInteractions_.removePair(b, c);
624	>	excludedInteractions_.removePair(b, d);
625	>	excludedInteractions_.removePair(c, d);
626	>	}
627	>	}
628	>
629	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
630	>	rb = mol->nextRigidBody(rbIter)) {
631	>	vector<Atom*> atoms = rb->getAtoms();
632	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
633	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
634		a = atoms[i]->getGlobalIndex();
635		b = atoms[j]->getGlobalIndex();
636	<	exclude_.removePair(a, b);
636	>	excludedInteractions_.removePair(a, b);
637		}
638		}
639		}
640	<
640	>
641		}
642	<
643	<
642	>
643	>
644		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
645		int curStampId;
646	<
646	>
647		//index from 0
648		curStampId = moleculeStamps_.size();
649
#	Line 449 | Line 651 | namespace oopse {
651		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
652		}
653
452	–	void SimInfo::update() {
654
655	<	setupSimType();
656	<
657	<	#ifdef IS_MPI
658	<	setupFortranParallel();
659	<	#endif
660	<
661	<	setupFortranSim();
662	<
663	<	//setup fortran force field
463	<	/** @deprecate */
464	<	int isError = 0;
465	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
466	<	if(isError){
467	<	sprintf( painCave.errMsg,
468	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
469	<	painCave.isFatal = 1;
470	<	simError();
471	<	}
472	<
473	<
474	<	setupCutoff();
475	<
655	>	/**
656	>	* update
657	>	*
658	>	*  Performs the global checks and variable settings after the
659	>	*  objects have been created.
660	>	*
661	>	*/
662	>	void SimInfo::update() {
663	>	setupSimVariables();
664		calcNdf();
665		calcNdfRaw();
666		calcNdfTrans();
479	–
480	–	fortranInitialized_ = true;
667		}
668	<
669	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
668	>
669	>	/**
670	>	* getSimulatedAtomTypes
671	>	*
672	>	* Returns an STL set of AtomType* that are actually present in this
673	>	* simulation.  Must query all processors to assemble this information.
674	>	*
675	>	*/
676	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
677		SimInfo::MoleculeIterator mi;
678		Molecule* mol;
679		Molecule::AtomIterator ai;
680		Atom* atom;
681	<	std::set<AtomType*> atomTypes;
682	<
683	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
491	<
681	>	set<AtomType*> atomTypes;
682	>
683	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
684		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
685		atomTypes.insert(atom->getAtomType());
686	<	}
687	<
688	<	}
686	>	}
687	>	}
688	>
689	>	#ifdef IS_MPI
690	>
691	>	// loop over the found atom types on this processor, and add their
692	>	// numerical idents to a vector:
693	>
694	>	vector<int> foundTypes;
695	>	set<AtomType*>::iterator i;
696	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
697	>	foundTypes.push_back( (*i)->getIdent() );
698	>
699	>	// count_local holds the number of found types on this processor
700	>	int count_local = foundTypes.size();
701
702	+	// count holds the total number of found types on all processors
703	+	// (some will be redundant with the ones found locally):
704	+	int count;
705	+	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
706	+
707	+	// create a vector to hold the globally found types, and resize it:
708	+	vector<int> ftGlobal;
709	+	ftGlobal.resize(count);
710	+	vector<int> counts;
711	+
712	+	int nproc = MPI::COMM_WORLD.Get_size();
713	+	counts.resize(nproc);
714	+	vector<int> disps;
715	+	disps.resize(nproc);
716	+
717	+	// now spray out the foundTypes to all the other processors:
718	+
719	+	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
720	+	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
721	+
722	+	// foundIdents is a stl set, so inserting an already found ident
723	+	// will have no effect.
724	+	set<int> foundIdents;
725	+	vector<int>::iterator j;
726	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
727	+	foundIdents.insert((*j));
728	+
729	+	// now iterate over the foundIdents and get the actual atom types
730	+	// that correspond to these:
731	+	set<int>::iterator it;
732	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
733	+	atomTypes.insert( forceField_->getAtomType((*it)) );
734	+
735	+	#endif
736	+
737		return atomTypes;
738		}
739
740	<	void SimInfo::setupSimType() {
741	<	std::set<AtomType*>::iterator i;
742	<	std::set<AtomType*> atomTypes;
743	<	atomTypes = getUniqueAtomTypes();
744	<
745	<	int useLennardJones = 0;
746	<	int useElectrostatic = 0;
747	<	int useEAM = 0;
509	<	int useCharge = 0;
510	<	int useDirectional = 0;
511	<	int useDipole = 0;
512	<	int useGayBerne = 0;
513	<	int useSticky = 0;
514	<	int useStickyPower = 0;
515	<	int useShape = 0;
516	<	int useFLARB = 0; //it is not in AtomType yet
517	<	int useDirectionalAtom = 0;
518	<	int useElectrostatics = 0;
519	<	//usePBC and useRF are from simParams
520	<	int usePBC = simParams_->getPBC();
521	<	int useRF = simParams_->getUseRF();
740	>	void SimInfo::setupSimVariables() {
741	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
742	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
743	>	calcBoxDipole_ = false;
744	>	if ( simParams_->haveAccumulateBoxDipole() )
745	>	if ( simParams_->getAccumulateBoxDipole() ) {
746	>	calcBoxDipole_ = true;
747	>	}
748
749	+	set<AtomType*>::iterator i;
750	+	set<AtomType*> atomTypes;
751	+	atomTypes = getSimulatedAtomTypes();
752	+	int usesElectrostatic = 0;
753	+	int usesMetallic = 0;
754	+	int usesDirectional = 0;
755		//loop over all of the atom types
756		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
757	<	useLennardJones |= (*i)->isLennardJones();
758	<	useElectrostatic |= (*i)->isElectrostatic();
759	<	useEAM |= (*i)->isEAM();
528	<	useCharge |= (*i)->isCharge();
529	<	useDirectional |= (*i)->isDirectional();
530	<	useDipole |= (*i)->isDipole();
531	<	useGayBerne |= (*i)->isGayBerne();
532	<	useSticky |= (*i)->isSticky();
533	<	useStickyPower |= (*i)->isStickyPower();
534	<	useShape |= (*i)->isShape();
757	>	usesElectrostatic |= (*i)->isElectrostatic();
758	>	usesMetallic |= (*i)->isMetal();
759	>	usesDirectional |= (*i)->isDirectional();
760		}
761
537	–	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
538	–	useDirectionalAtom = 1;
539	–	}
540	–
541	–	if (useCharge || useDipole) {
542	–	useElectrostatics = 1;
543	–	}
544	–
762		#ifdef IS_MPI
763		int temp;
764	+	temp = usesDirectional;
765	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766
767	<	temp = usePBC;
768	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767	>	temp = usesMetallic;
768	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769
770	<	temp = useDirectionalAtom;
771	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770	>	temp = usesElectrostatic;
771	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
772	>	#endif
773	>	}
774
554	–	temp = useLennardJones;
555	–	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
775
776	<	temp = useElectrostatics;
777	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776	>	vector<int> SimInfo::getGlobalAtomIndices() {
777	>	SimInfo::MoleculeIterator mi;
778	>	Molecule* mol;
779	>	Molecule::AtomIterator ai;
780	>	Atom* atom;
781
782	<	temp = useCharge;
561	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
562	<
563	<	temp = useDipole;
564	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
565	<
566	<	temp = useSticky;
567	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
568	<
569	<	temp = useStickyPower;
570	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
782	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
783
784	<	temp = useGayBerne;
785	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
784	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
785	>
786	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
787	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
788	>	}
789	>	}
790	>	return GlobalAtomIndices;
791	>	}
792
575	–	temp = useEAM;
576	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
793
794	<	temp = useShape;
795	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
794	>	vector<int> SimInfo::getGlobalGroupIndices() {
795	>	SimInfo::MoleculeIterator mi;
796	>	Molecule* mol;
797	>	Molecule::CutoffGroupIterator ci;
798	>	CutoffGroup* cg;
799
800	<	temp = useFLARB;
582	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
583	<
584	<	temp = useRF;
585	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
800	>	vector<int> GlobalGroupIndices;
801
802	<	#endif
803	<
804	<	fInfo_.SIM_uses_PBC = usePBC;
805	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
806	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
807	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
808	<	fInfo_.SIM_uses_Charges = useCharge;
809	<	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	<	fInfo_.SIM_uses_RF = useRF;
602	<
603	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
604	<
605	<	if (simParams_->haveDielectric()) {
606	<	fInfo_.dielect = simParams_->getDielectric();
607	<	} else {
608	<	sprintf(painCave.errMsg,
609	<	"SimSetup Error: No Dielectric constant was set.\n"
610	<	"\tYou are trying to use Reaction Field without"
611	<	"\tsetting a dielectric constant!\n");
612	<	painCave.isFatal = 1;
613	<	simError();
614	<	}
615	<
616	<	} else {
617	<	fInfo_.dielect = 0.0;
802	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
803	>
804	>	//local index of cutoff group is trivial, it only depends on the
805	>	//order of travesing
806	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
807	>	cg = mol->nextCutoffGroup(ci)) {
808	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
809	>	}
810		}
811	<
811	>	return GlobalGroupIndices;
812		}
813
622	–	void SimInfo::setupFortranSim() {
623	–	int isError;
624	–	int nExclude;
625	–	std::vector<int> fortranGlobalGroupMembership;
626	–
627	–	nExclude = exclude_.getSize();
628	–	isError = 0;
814
815	<	//globalGroupMembership_ is filled by SimCreator
816	<	for (int i = 0; i < nGlobalAtoms_; i++) {
632	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
633	<	}
815	>	void SimInfo::prepareTopology() {
816	>	int nExclude, nOneTwo, nOneThree, nOneFour;
817
818		//calculate mass ratio of cutoff group
636	–	std::vector<double> mfact;
819		SimInfo::MoleculeIterator mi;
820		Molecule* mol;
821		Molecule::CutoffGroupIterator ci;
822		CutoffGroup* cg;
823		Molecule::AtomIterator ai;
824		Atom* atom;
825	<	double totalMass;
825	>	RealType totalMass;
826
827	<	//to avoid memory reallocation, reserve enough space for mfact
828	<	mfact.reserve(getNCutoffGroups());
827	>	//to avoid memory reallocation, reserve enough space for massFactors_
828	>	massFactors_.clear();
829	>	massFactors_.reserve(getNCutoffGroups());
830
831		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
832	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
832	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
833	>	cg = mol->nextCutoffGroup(ci)) {
834
835		totalMass = cg->getMass();
836		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
837	<	mfact.push_back(atom->getMass()/totalMass);
837	>	// Check for massless groups - set mfact to 1 if true
838	>	if (totalMass != 0)
839	>	massFactors_.push_back(atom->getMass()/totalMass);
840	>	else
841	>	massFactors_.push_back( 1.0 );
842		}
655	–
843		}
844		}
845
846	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
660	<	std::vector<int> identArray;
846	>	// Build the identArray_
847
848	<	//to avoid memory reallocation, reserve enough space identArray
849	<	identArray.reserve(getNAtoms());
664	<
848	>	identArray_.clear();
849	>	identArray_.reserve(getNAtoms());
850		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
851		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
852	<	identArray.push_back(atom->getIdent());
852	>	identArray_.push_back(atom->getIdent());
853		}
854		}
670	–
671	–	//fill molMembershipArray
672	–	//molMembershipArray is filled by SimCreator
673	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
674	–	for (int i = 0; i < nGlobalAtoms_; i++) {
675	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
676	–	}
855
856	<	//setup fortran simulation
679	<	int nGlobalExcludes = 0;
680	<	int* globalExcludes = NULL;
681	<	int* excludeList = exclude_.getExcludeList();
682	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
683	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
684	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
856	>	//scan topology
857
858	<	if( isError ){
858	>	nExclude = excludedInteractions_.getSize();
859	>	nOneTwo = oneTwoInteractions_.getSize();
860	>	nOneThree = oneThreeInteractions_.getSize();
861	>	nOneFour = oneFourInteractions_.getSize();
862
863	<	sprintf( painCave.errMsg,
864	<	"There was an error setting the simulation information in fortran.\n" );
865	<	painCave.isFatal = 1;
866	<	painCave.severity = OOPSE_ERROR;
692	<	simError();
693	<	}
863	>	int* excludeList = excludedInteractions_.getPairList();
864	>	int* oneTwoList = oneTwoInteractions_.getPairList();
865	>	int* oneThreeList = oneThreeInteractions_.getPairList();
866	>	int* oneFourList = oneFourInteractions_.getPairList();
867
868	<	#ifdef IS_MPI
869	<	sprintf( checkPointMsg,
870	<	"succesfully sent the simulation information to fortran.\n");
871	<	MPIcheckPoint();
872	<	#endif // is_mpi
873	<	}
874	<
702	<
703	<	#ifdef IS_MPI
704	<	void SimInfo::setupFortranParallel() {
868	>	//setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0],
869	>	//               &nExclude, excludeList,
870	>	//               &nOneTwo, oneTwoList,
871	>	//               &nOneThree, oneThreeList,
872	>	//               &nOneFour, oneFourList,
873	>	//               &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
874	>	//               &fortranGlobalGroupMembership[0], &isError);
875
876	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
707	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
708	<	std::vector<int> localToGlobalCutoffGroupIndex;
709	<	SimInfo::MoleculeIterator mi;
710	<	Molecule::AtomIterator ai;
711	<	Molecule::CutoffGroupIterator ci;
712	<	Molecule* mol;
713	<	Atom* atom;
714	<	CutoffGroup* cg;
715	<	mpiSimData parallelData;
716	<	int isError;
717	<
718	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
719	<
720	<	//local index(index in DataStorge) of atom is important
721	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
722	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
723	<	}
724	<
725	<	//local index of cutoff group is trivial, it only depends on the order of travesing
726	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
727	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
728	<	}
729	<
730	<	}
731	<
732	<	//fill up mpiSimData struct
733	<	parallelData.nMolGlobal = getNGlobalMolecules();
734	<	parallelData.nMolLocal = getNMolecules();
735	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
736	<	parallelData.nAtomsLocal = getNAtoms();
737	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
738	<	parallelData.nGroupsLocal = getNCutoffGroups();
739	<	parallelData.myNode = worldRank;
740	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
741	<
742	<	//pass mpiSimData struct and index arrays to fortran
743	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
744	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
745	<	&localToGlobalCutoffGroupIndex[0], &isError);
746	<
747	<	if (isError) {
748	<	sprintf(painCave.errMsg,
749	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
750	<	painCave.isFatal = 1;
751	<	simError();
752	<	}
753	<
754	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
755	<	MPIcheckPoint();
756	<
757	<
876	>	topologyDone_ = true;
877		}
878
760	–	#endif
761	–
762	–	double SimInfo::calcMaxCutoffRadius() {
763	–
764	–
765	–	std::set<AtomType*> atomTypes;
766	–	std::set<AtomType*>::iterator i;
767	–	std::vector<double> cutoffRadius;
768	–
769	–	//get the unique atom types
770	–	atomTypes = getUniqueAtomTypes();
771	–
772	–	//query the max cutoff radius among these atom types
773	–	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
774	–	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
775	–	}
776	–
777	–	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
778	–	#ifdef IS_MPI
779	–	//pick the max cutoff radius among the processors
780	–	#endif
781	–
782	–	return maxCutoffRadius;
783	–	}
784	–
785	–	void SimInfo::getCutoff(double& rcut, double& rsw) {
786	–
787	–	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
788	–
789	–	if (!simParams_->haveRcut()){
790	–	sprintf(painCave.errMsg,
791	–	"SimCreator Warning: No value was set for the cutoffRadius.\n"
792	–	"\tOOPSE will use a default value of 15.0 angstroms"
793	–	"\tfor the cutoffRadius.\n");
794	–	painCave.isFatal = 0;
795	–	simError();
796	–	rcut = 15.0;
797	–	} else{
798	–	rcut = simParams_->getRcut();
799	–	}
800	–
801	–	if (!simParams_->haveRsw()){
802	–	sprintf(painCave.errMsg,
803	–	"SimCreator Warning: No value was set for switchingRadius.\n"
804	–	"\tOOPSE will use a default value of\n"
805	–	"\t0.95 * cutoffRadius for the switchingRadius\n");
806	–	painCave.isFatal = 0;
807	–	simError();
808	–	rsw = 0.95 * rcut;
809	–	} else{
810	–	rsw = simParams_->getRsw();
811	–	}
812	–
813	–	} else {
814	–	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
815	–	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
816	–
817	–	if (simParams_->haveRcut()) {
818	–	rcut = simParams_->getRcut();
819	–	} else {
820	–	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
821	–	rcut = calcMaxCutoffRadius();
822	–	}
823	–
824	–	if (simParams_->haveRsw()) {
825	–	rsw  = simParams_->getRsw();
826	–	} else {
827	–	rsw = rcut;
828	–	}
829	–
830	–	}
831	–	}
832	–
833	–	void SimInfo::setupCutoff() {
834	–	getCutoff(rcut_, rsw_);
835	–	double rnblist = rcut_ + 1; // skin of neighbor list
836	–
837	–	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
838	–	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
839	–	}
840	–
879		void SimInfo::addProperty(GenericData* genData) {
880		properties_.addProperty(genData);
881		}
882
883	<	void SimInfo::removeProperty(const std::string& propName) {
883	>	void SimInfo::removeProperty(const string& propName) {
884		properties_.removeProperty(propName);
885		}
886
#	Line 850 | Line 888 | namespace oopse {
888		properties_.clearProperties();
889		}
890
891	<	std::vector<std::string> SimInfo::getPropertyNames() {
891	>	vector<string> SimInfo::getPropertyNames() {
892		return properties_.getPropertyNames();
893		}
894
895	<	std::vector<GenericData*> SimInfo::getProperties() {
895	>	vector<GenericData*> SimInfo::getProperties() {
896		return properties_.getProperties();
897		}
898
899	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
899	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
900		return properties_.getPropertyByName(propName);
901		}
902
#	Line 872 | Line 910 | namespace oopse {
910		Molecule* mol;
911		RigidBody* rb;
912		Atom* atom;
913	+	CutoffGroup* cg;
914		SimInfo::MoleculeIterator mi;
915		Molecule::RigidBodyIterator rbIter;
916	<	Molecule::AtomIterator atomIter;;
916	>	Molecule::AtomIterator atomIter;
917	>	Molecule::CutoffGroupIterator cgIter;
918
919		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
920
#	Line 885 | Line 925 | namespace oopse {
925		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
926		rb->setSnapshotManager(sman_);
927		}
928	+
929	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
930	+	cg->setSnapshotManager(sman_);
931	+	}
932		}
933
934		}
#	Line 894 | Line 938 | namespace oopse {
938		Molecule* mol;
939
940		Vector3d comVel(0.0);
941	<	double totalMass = 0.0;
941	>	RealType totalMass = 0.0;
942
943
944		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
945	<	double mass = mol->getMass();
945	>	RealType mass = mol->getMass();
946		totalMass += mass;
947		comVel += mass * mol->getComVel();
948		}
949
950		#ifdef IS_MPI
951	<	double tmpMass = totalMass;
951	>	RealType tmpMass = totalMass;
952		Vector3d tmpComVel(comVel);
953	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
954	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
953	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
954	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
955		#endif
956
957		comVel /= totalMass;
#	Line 920 | Line 964 | namespace oopse {
964		Molecule* mol;
965
966		Vector3d com(0.0);
967	<	double totalMass = 0.0;
967	>	RealType totalMass = 0.0;
968
969		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
970	<	double mass = mol->getMass();
970	>	RealType mass = mol->getMass();
971		totalMass += mass;
972		com += mass * mol->getCom();
973		}
974
975		#ifdef IS_MPI
976	<	double tmpMass = totalMass;
976	>	RealType tmpMass = totalMass;
977		Vector3d tmpCom(com);
978	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
979	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
978	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
979	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
980		#endif
981
982		com /= totalMass;
#	Line 941 | Line 985 | namespace oopse {
985
986		}
987
988	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
988	>	ostream& operator <<(ostream& o, SimInfo& info) {
989
990		return o;
991		}
#	Line 956 | Line 1000 | namespace oopse {
1000		Molecule* mol;
1001
1002
1003	<	double totalMass = 0.0;
1003	>	RealType totalMass = 0.0;
1004
1005
1006		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1007	<	double mass = mol->getMass();
1007	>	RealType mass = mol->getMass();
1008		totalMass += mass;
1009		com += mass * mol->getCom();
1010		comVel += mass * mol->getComVel();
1011		}
1012
1013		#ifdef IS_MPI
1014	<	double tmpMass = totalMass;
1014	>	RealType tmpMass = totalMass;
1015		Vector3d tmpCom(com);
1016		Vector3d tmpComVel(comVel);
1017	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1018	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1019	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1017	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1018	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1019	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1020		#endif
1021
1022		com /= totalMass;
#	Line 981 | Line 1025 | namespace oopse {
1025
1026		/*
1027		Return intertia tensor for entire system and angular momentum Vector.
1028	+
1029	+
1030	+	[  Ixx -Ixy  -Ixz ]
1031	+	J =| -Iyx  Iyy  -Iyz |
1032	+	[ -Izx -Iyz   Izz ]
1033		*/
1034
1035		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1036
1037
1038	<	double xx = 0.0;
1039	<	double yy = 0.0;
1040	<	double zz = 0.0;
1041	<	double xy = 0.0;
1042	<	double xz = 0.0;
1043	<	double yz = 0.0;
1038	>	RealType xx = 0.0;
1039	>	RealType yy = 0.0;
1040	>	RealType zz = 0.0;
1041	>	RealType xy = 0.0;
1042	>	RealType xz = 0.0;
1043	>	RealType yz = 0.0;
1044		Vector3d com(0.0);
1045		Vector3d comVel(0.0);
1046
#	Line 1003 | Line 1052 | namespace oopse {
1052		Vector3d thisq(0.0);
1053		Vector3d thisv(0.0);
1054
1055	<	double thisMass = 0.0;
1055	>	RealType thisMass = 0.0;
1056
1057
1058
#	Line 1032 | Line 1081 | namespace oopse {
1081		inertiaTensor(0,1) = -xy;
1082		inertiaTensor(0,2) = -xz;
1083		inertiaTensor(1,0) = -xy;
1084	<	inertiaTensor(2,0) = xx + zz;
1084	>	inertiaTensor(1,1) = xx + zz;
1085		inertiaTensor(1,2) = -yz;
1086		inertiaTensor(2,0) = -xz;
1087		inertiaTensor(2,1) = -yz;
#	Line 1041 | Line 1090 | namespace oopse {
1090		#ifdef IS_MPI
1091		Mat3x3d tmpI(inertiaTensor);
1092		Vector3d tmpAngMom;
1093	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1094	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1093	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1094	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1095		#endif
1096
1097		return;
#	Line 1060 | Line 1109 | namespace oopse {
1109		SimInfo::MoleculeIterator i;
1110		Molecule* mol;
1111
1112	<	Vector3d thisq(0.0);
1113	<	Vector3d thisv(0.0);
1112	>	Vector3d thisr(0.0);
1113	>	Vector3d thisp(0.0);
1114
1115	<	double thisMass = 0.0;
1115	>	RealType thisMass;
1116
1117		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1118	<	thisq = mol->getCom()-com;
1119	<	thisv = mol->getComVel()-comVel;
1120	<	thisMass = mol->getMass();
1072	<	angularMomentum += cross( thisq, thisv ) * thisMass;
1118	>	thisMass = mol->getMass();
1119	>	thisr = mol->getCom()-com;
1120	>	thisp = (mol->getComVel()-comVel)*thisMass;
1121
1122	+	angularMomentum += cross( thisr, thisp );
1123	+
1124		}
1125
1126		#ifdef IS_MPI
1127		Vector3d tmpAngMom;
1128	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1128	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1129		#endif
1130
1131		return angularMomentum;
1132		}
1133
1134	<
1135	<	}//end namespace oopse
1134	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1135	>	return IOIndexToIntegrableObject.at(index);
1136	>	}
1137	>
1138	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1139	>	IOIndexToIntegrableObject= v;
1140	>	}
1141
1142	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1143	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1144	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1145	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1146	+	*/
1147	+	void SimInfo::getGyrationalVolume(RealType &volume){
1148	+	Mat3x3d intTensor;
1149	+	RealType det;
1150	+	Vector3d dummyAngMom;
1151	+	RealType sysconstants;
1152	+	RealType geomCnst;
1153	+
1154	+	geomCnst = 3.0/2.0;
1155	+	/* Get the inertial tensor and angular momentum for free*/
1156	+	getInertiaTensor(intTensor,dummyAngMom);
1157	+
1158	+	det = intTensor.determinant();
1159	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1160	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1161	+	return;
1162	+	}
1163	+
1164	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1165	+	Mat3x3d intTensor;
1166	+	Vector3d dummyAngMom;
1167	+	RealType sysconstants;
1168	+	RealType geomCnst;
1169	+
1170	+	geomCnst = 3.0/2.0;
1171	+	/* Get the inertial tensor and angular momentum for free*/
1172	+	getInertiaTensor(intTensor,dummyAngMom);
1173	+
1174	+	detI = intTensor.determinant();
1175	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1176	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1177	+	return;
1178	+	}
1179	+	/*
1180	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1181	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1182	+	sdByGlobalIndex_ = v;
1183	+	}
1184	+
1185	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1186	+	//assert(index < nAtoms_ + nRigidBodies_);
1187	+	return sdByGlobalIndex_.at(index);
1188	+	}
1189	+	*/
1190	+	int SimInfo::getNGlobalConstraints() {
1191	+	int nGlobalConstraints;
1192	+	#ifdef IS_MPI
1193	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1194	+	MPI_COMM_WORLD);
1195	+	#else
1196	+	nGlobalConstraints =  nConstraints_;
1197	+	#endif
1198	+	return nGlobalConstraints;
1199	+	}
1200	+
1201	+	}//end namespace OpenMD
1202	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 555 by chuckv, Mon May 30 14:01:52 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC

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