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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 604 by chrisfen, Fri Sep 16 19:00:12 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1540 by gezelter, Mon Jan 17 21:34:36 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/fCutoffPolicy.h"
57	<	#include "UseTheForce/Darkside/fElectrostaticSummationMethod.h"
56	>	#include "primitives/StuntDouble.hpp"
57	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
58		#include "UseTheForce/doForces_interface.h"
58	–	#include "UseTheForce/notifyCutoffs_interface.h"
59		#include "utils/MemoryUtils.hpp"
60		#include "utils/simError.h"
61		#include "selection/SelectionManager.hpp"
62	+	#include "io/ForceFieldOptions.hpp"
63	+	#include "UseTheForce/ForceField.hpp"
64	+	#include "nonbonded/SwitchingFunction.hpp"
65
66		#ifdef IS_MPI
67		#include "UseTheForce/mpiComponentPlan.h"
68		#include "UseTheForce/DarkSide/simParallel_interface.h"
69		#endif
70
71	<	namespace oopse {
72	<
73	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
74	<	ForceField* ff, Globals* simParams) :
75	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
76	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
71	>	using namespace std;
72	>	namespace OpenMD {
73	>
74	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
75	>	forceField_(ff), simParams_(simParams),
76	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
77		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
78		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
79	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
80	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
81	<	sman_(NULL), fortranInitialized_(false) {
82	<
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;
79	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
80	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
81	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
82	>	calcBoxDipole_(false), useAtomicVirial_(true) {
83
84	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
85	<	molStamp = i->first;
86	<	nMolWithSameStamp = i->second;
87	<
88	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
89	<
90	<	//calculate atoms in molecules
91	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
92	<
93	<
94	<	//calculate atoms in cutoff groups
95	<	int nAtomsInGroups = 0;
96	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
97	<
98	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
99	<	cgStamp = molStamp->getCutoffGroup(j);
100	<	nAtomsInGroups += cgStamp->getNMembers();
101	<	}
102	<
103	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
104	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
105	<
106	<	//calculate atoms in rigid bodies
107	<	int nAtomsInRigidBodies = 0;
108	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
109	<
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	<
84	>	MoleculeStamp* molStamp;
85	>	int nMolWithSameStamp;
86	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
88	>	CutoffGroupStamp* cgStamp;
89	>	RigidBodyStamp* rbStamp;
90	>	int nRigidAtoms = 0;
91	>
92	>	vector<Component*> components = simParams->getComponents();
93	>
94	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
95	>	molStamp = (*i)->getMoleculeStamp();
96	>	nMolWithSameStamp = (*i)->getNMol();
97	>
98	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
99	>
100	>	//calculate atoms in molecules
101	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
102	>
103	>	//calculate atoms in cutoff groups
104	>	int nAtomsInGroups = 0;
105	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
106	>
107	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
108	>	cgStamp = molStamp->getCutoffGroupStamp(j);
109	>	nAtomsInGroups += cgStamp->getNMembers();
110		}
111	<
112	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
113	<	//therefore the total number of cutoff groups in the system is equal to
114	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
115	<	//file plus the number of cutoff groups defined in meta-data file
116	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
117	<
118	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
119	<	//therefore the total number of  integrable objects in the system is equal to
120	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
121	<	//file plus the number of  rigid bodies defined in meta-data file
122	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
123	<
124	<	nGlobalMols_ = molStampIds_.size();
125	<
126	<	#ifdef IS_MPI
127	<	molToProcMap_.resize(nGlobalMols_);
142	<	#endif
143	<
111	>
112	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
113	>
114	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
115	>
116	>	//calculate atoms in rigid bodies
117	>	int nAtomsInRigidBodies = 0;
118	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
119	>
120	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
121	>	rbStamp = molStamp->getRigidBodyStamp(j);
122	>	nAtomsInRigidBodies += rbStamp->getNMembers();
123	>	}
124	>
125	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
126	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
127	>
128		}
129	+
130	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
131	+	//group therefore the total number of cutoff groups in the system is
132	+	//equal to the total number of atoms minus number of atoms belong to
133	+	//cutoff group defined in meta-data file plus the number of cutoff
134	+	//groups defined in meta-data file
135	+	std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
136	+	std::cerr << "nCA = " << nCutoffAtoms << "\n";
137	+	std::cerr << "nG = " << nGroups << "\n";
138
139	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
140	+
141	+	std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
142	+
143	+	//every free atom (atom does not belong to rigid bodies) is an
144	+	//integrable object therefore the total number of integrable objects
145	+	//in the system is equal to the total number of atoms minus number of
146	+	//atoms belong to rigid body defined in meta-data file plus the number
147	+	//of rigid bodies defined in meta-data file
148	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
149	+	+ nGlobalRigidBodies_;
150	+
151	+	nGlobalMols_ = molStampIds_.size();
152	+	molToProcMap_.resize(nGlobalMols_);
153	+	}
154	+
155		SimInfo::~SimInfo() {
156	<	std::map<int, Molecule*>::iterator i;
156	>	map<int, Molecule*>::iterator i;
157		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
158		delete i->second;
159		}
160		molecules_.clear();
161
153	–	delete stamps_;
162		delete sman_;
163		delete simParams_;
164		delete forceField_;
165		}
166
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	–	}
167
168		bool SimInfo::addMolecule(Molecule* mol) {
169		MoleculeIterator i;
170	<
170	>
171		i = molecules_.find(mol->getGlobalIndex());
172		if (i == molecules_.end() ) {
173	<
174	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
175	<
173	>
174	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
175	>
176		nAtoms_ += mol->getNAtoms();
177		nBonds_ += mol->getNBonds();
178		nBends_ += mol->getNBends();
179		nTorsions_ += mol->getNTorsions();
180	+	nInversions_ += mol->getNInversions();
181		nRigidBodies_ += mol->getNRigidBodies();
182		nIntegrableObjects_ += mol->getNIntegrableObjects();
183		nCutoffGroups_ += mol->getNCutoffGroups();
184		nConstraints_ += mol->getNConstraintPairs();
185	<
186	<	addExcludePairs(mol);
187	<
185	>
186	>	addInteractionPairs(mol);
187	>
188		return true;
189		} else {
190		return false;
191		}
192		}
193	<
193	>
194		bool SimInfo::removeMolecule(Molecule* mol) {
195		MoleculeIterator i;
196		i = molecules_.find(mol->getGlobalIndex());
#	Line 204 | Line 203 | namespace oopse {
203		nBonds_ -= mol->getNBonds();
204		nBends_ -= mol->getNBends();
205		nTorsions_ -= mol->getNTorsions();
206	+	nInversions_ -= mol->getNInversions();
207		nRigidBodies_ -= mol->getNRigidBodies();
208		nIntegrableObjects_ -= mol->getNIntegrableObjects();
209		nCutoffGroups_ -= mol->getNCutoffGroups();
210		nConstraints_ -= mol->getNConstraintPairs();
211
212	<	removeExcludePairs(mol);
212	>	removeInteractionPairs(mol);
213		molecules_.erase(mol->getGlobalIndex());
214
215		delete mol;
#	Line 218 | Line 218 | namespace oopse {
218		} else {
219		return false;
220		}
221	–
222	–
221		}
222
223
#	Line 237 | Line 235 | namespace oopse {
235		void SimInfo::calcNdf() {
236		int ndf_local;
237		MoleculeIterator i;
238	<	std::vector<StuntDouble*>::iterator j;
238	>	vector<StuntDouble*>::iterator j;
239		Molecule* mol;
240		StuntDouble* integrableObject;
241
#	Line 257 | Line 255 | namespace oopse {
255		}
256		}
257
258	<	}//end for (integrableObject)
259	<	}// end for (mol)
258	>	}
259	>	}
260
261		// n_constraints is local, so subtract them on each processor
262		ndf_local -= nConstraints_;
#	Line 275 | Line 273 | namespace oopse {
273
274		}
275
276	+	int SimInfo::getFdf() {
277	+	#ifdef IS_MPI
278	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
279	+	#else
280	+	fdf_ = fdf_local;
281	+	#endif
282	+	return fdf_;
283	+	}
284	+
285		void SimInfo::calcNdfRaw() {
286		int ndfRaw_local;
287
288		MoleculeIterator i;
289	<	std::vector<StuntDouble*>::iterator j;
289	>	vector<StuntDouble*>::iterator j;
290		Molecule* mol;
291		StuntDouble* integrableObject;
292
#	Line 326 | Line 333 | namespace oopse {
333
334		}
335
336	<	void SimInfo::addExcludePairs(Molecule* mol) {
337	<	std::vector<Bond*>::iterator bondIter;
338	<	std::vector<Bend*>::iterator bendIter;
339	<	std::vector<Torsion*>::iterator torsionIter;
336	>	void SimInfo::addInteractionPairs(Molecule* mol) {
337	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
338	>	vector<Bond*>::iterator bondIter;
339	>	vector<Bend*>::iterator bendIter;
340	>	vector<Torsion*>::iterator torsionIter;
341	>	vector<Inversion*>::iterator inversionIter;
342		Bond* bond;
343		Bend* bend;
344		Torsion* torsion;
345	+	Inversion* inversion;
346		int a;
347		int b;
348		int c;
349		int d;
350	+
351	+	// atomGroups can be used to add special interaction maps between
352	+	// groups of atoms that are in two separate rigid bodies.
353	+	// However, most site-site interactions between two rigid bodies
354	+	// are probably not special, just the ones between the physically
355	+	// bonded atoms.  Interactions *within* a single rigid body should
356	+	// always be excluded.  These are done at the bottom of this
357	+	// function.
358	+
359	+	map<int, set<int> > atomGroups;
360	+	Molecule::RigidBodyIterator rbIter;
361	+	RigidBody* rb;
362	+	Molecule::IntegrableObjectIterator ii;
363	+	StuntDouble* integrableObject;
364
365	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
365	>	for (integrableObject = mol->beginIntegrableObject(ii);
366	>	integrableObject != NULL;
367	>	integrableObject = mol->nextIntegrableObject(ii)) {
368	>
369	>	if (integrableObject->isRigidBody()) {
370	>	rb = static_cast<RigidBody*>(integrableObject);
371	>	vector<Atom*> atoms = rb->getAtoms();
372	>	set<int> rigidAtoms;
373	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
374	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
375	>	}
376	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
377	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
378	>	}
379	>	} else {
380	>	set<int> oneAtomSet;
381	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
382	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
383	>	}
384	>	}
385	>
386	>	for (bond= mol->beginBond(bondIter); bond != NULL;
387	>	bond = mol->nextBond(bondIter)) {
388	>
389		a = bond->getAtomA()->getGlobalIndex();
390	<	b = bond->getAtomB()->getGlobalIndex();
391	<	exclude_.addPair(a, b);
390	>	b = bond->getAtomB()->getGlobalIndex();
391	>
392	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
393	>	oneTwoInteractions_.addPair(a, b);
394	>	} else {
395	>	excludedInteractions_.addPair(a, b);
396	>	}
397		}
398
399	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
399	>	for (bend= mol->beginBend(bendIter); bend != NULL;
400	>	bend = mol->nextBend(bendIter)) {
401	>
402		a = bend->getAtomA()->getGlobalIndex();
403		b = bend->getAtomB()->getGlobalIndex();
404		c = bend->getAtomC()->getGlobalIndex();
405	<
406	<	exclude_.addPair(a, b);
407	<	exclude_.addPair(a, c);
408	<	exclude_.addPair(b, c);
405	>
406	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
407	>	oneTwoInteractions_.addPair(a, b);
408	>	oneTwoInteractions_.addPair(b, c);
409	>	} else {
410	>	excludedInteractions_.addPair(a, b);
411	>	excludedInteractions_.addPair(b, c);
412	>	}
413	>
414	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
415	>	oneThreeInteractions_.addPair(a, c);
416	>	} else {
417	>	excludedInteractions_.addPair(a, c);
418	>	}
419		}
420
421	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
421	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
422	>	torsion = mol->nextTorsion(torsionIter)) {
423	>
424		a = torsion->getAtomA()->getGlobalIndex();
425		b = torsion->getAtomB()->getGlobalIndex();
426		c = torsion->getAtomC()->getGlobalIndex();
427	<	d = torsion->getAtomD()->getGlobalIndex();
427	>	d = torsion->getAtomD()->getGlobalIndex();
428
429	<	exclude_.addPair(a, b);
430	<	exclude_.addPair(a, c);
431	<	exclude_.addPair(a, d);
432	<	exclude_.addPair(b, c);
433	<	exclude_.addPair(b, d);
434	<	exclude_.addPair(c, d);
429	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
430	>	oneTwoInteractions_.addPair(a, b);
431	>	oneTwoInteractions_.addPair(b, c);
432	>	oneTwoInteractions_.addPair(c, d);
433	>	} else {
434	>	excludedInteractions_.addPair(a, b);
435	>	excludedInteractions_.addPair(b, c);
436	>	excludedInteractions_.addPair(c, d);
437	>	}
438	>
439	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
440	>	oneThreeInteractions_.addPair(a, c);
441	>	oneThreeInteractions_.addPair(b, d);
442	>	} else {
443	>	excludedInteractions_.addPair(a, c);
444	>	excludedInteractions_.addPair(b, d);
445	>	}
446	>
447	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
448	>	oneFourInteractions_.addPair(a, d);
449	>	} else {
450	>	excludedInteractions_.addPair(a, d);
451	>	}
452		}
453
454	<	Molecule::RigidBodyIterator rbIter;
455	<	RigidBody* rb;
456	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
457	<	std::vector<Atom*> atoms = rb->getAtoms();
458	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
459	<	for (int j = i + 1; j < atoms.size(); ++j) {
454	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
455	>	inversion = mol->nextInversion(inversionIter)) {
456	>
457	>	a = inversion->getAtomA()->getGlobalIndex();
458	>	b = inversion->getAtomB()->getGlobalIndex();
459	>	c = inversion->getAtomC()->getGlobalIndex();
460	>	d = inversion->getAtomD()->getGlobalIndex();
461	>
462	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
463	>	oneTwoInteractions_.addPair(a, b);
464	>	oneTwoInteractions_.addPair(a, c);
465	>	oneTwoInteractions_.addPair(a, d);
466	>	} else {
467	>	excludedInteractions_.addPair(a, b);
468	>	excludedInteractions_.addPair(a, c);
469	>	excludedInteractions_.addPair(a, d);
470	>	}
471	>
472	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
473	>	oneThreeInteractions_.addPair(b, c);
474	>	oneThreeInteractions_.addPair(b, d);
475	>	oneThreeInteractions_.addPair(c, d);
476	>	} else {
477	>	excludedInteractions_.addPair(b, c);
478	>	excludedInteractions_.addPair(b, d);
479	>	excludedInteractions_.addPair(c, d);
480	>	}
481	>	}
482	>
483	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
484	>	rb = mol->nextRigidBody(rbIter)) {
485	>	vector<Atom*> atoms = rb->getAtoms();
486	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
487	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
488		a = atoms[i]->getGlobalIndex();
489		b = atoms[j]->getGlobalIndex();
490	<	exclude_.addPair(a, b);
490	>	excludedInteractions_.addPair(a, b);
491		}
492		}
493		}
494
495		}
496
497	<	void SimInfo::removeExcludePairs(Molecule* mol) {
498	<	std::vector<Bond*>::iterator bondIter;
499	<	std::vector<Bend*>::iterator bendIter;
500	<	std::vector<Torsion*>::iterator torsionIter;
497	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
498	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
499	>	vector<Bond*>::iterator bondIter;
500	>	vector<Bend*>::iterator bendIter;
501	>	vector<Torsion*>::iterator torsionIter;
502	>	vector<Inversion*>::iterator inversionIter;
503		Bond* bond;
504		Bend* bend;
505		Torsion* torsion;
506	+	Inversion* inversion;
507		int a;
508		int b;
509		int c;
510		int d;
511	+
512	+	map<int, set<int> > atomGroups;
513	+	Molecule::RigidBodyIterator rbIter;
514	+	RigidBody* rb;
515	+	Molecule::IntegrableObjectIterator ii;
516	+	StuntDouble* integrableObject;
517
518	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
518	>	for (integrableObject = mol->beginIntegrableObject(ii);
519	>	integrableObject != NULL;
520	>	integrableObject = mol->nextIntegrableObject(ii)) {
521	>
522	>	if (integrableObject->isRigidBody()) {
523	>	rb = static_cast<RigidBody*>(integrableObject);
524	>	vector<Atom*> atoms = rb->getAtoms();
525	>	set<int> rigidAtoms;
526	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
527	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
528	>	}
529	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
530	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
531	>	}
532	>	} else {
533	>	set<int> oneAtomSet;
534	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
535	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
536	>	}
537	>	}
538	>
539	>	for (bond= mol->beginBond(bondIter); bond != NULL;
540	>	bond = mol->nextBond(bondIter)) {
541	>
542		a = bond->getAtomA()->getGlobalIndex();
543	<	b = bond->getAtomB()->getGlobalIndex();
544	<	exclude_.removePair(a, b);
543	>	b = bond->getAtomB()->getGlobalIndex();
544	>
545	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
546	>	oneTwoInteractions_.removePair(a, b);
547	>	} else {
548	>	excludedInteractions_.removePair(a, b);
549	>	}
550		}
551
552	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
552	>	for (bend= mol->beginBend(bendIter); bend != NULL;
553	>	bend = mol->nextBend(bendIter)) {
554	>
555		a = bend->getAtomA()->getGlobalIndex();
556		b = bend->getAtomB()->getGlobalIndex();
557		c = bend->getAtomC()->getGlobalIndex();
558	+
559	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
560	+	oneTwoInteractions_.removePair(a, b);
561	+	oneTwoInteractions_.removePair(b, c);
562	+	} else {
563	+	excludedInteractions_.removePair(a, b);
564	+	excludedInteractions_.removePair(b, c);
565	+	}
566
567	<	exclude_.removePair(a, b);
568	<	exclude_.removePair(a, c);
569	<	exclude_.removePair(b, c);
567	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
568	>	oneThreeInteractions_.removePair(a, c);
569	>	} else {
570	>	excludedInteractions_.removePair(a, c);
571	>	}
572		}
573
574	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
574	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
575	>	torsion = mol->nextTorsion(torsionIter)) {
576	>
577		a = torsion->getAtomA()->getGlobalIndex();
578		b = torsion->getAtomB()->getGlobalIndex();
579		c = torsion->getAtomC()->getGlobalIndex();
580	<	d = torsion->getAtomD()->getGlobalIndex();
580	>	d = torsion->getAtomD()->getGlobalIndex();
581	>
582	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
583	>	oneTwoInteractions_.removePair(a, b);
584	>	oneTwoInteractions_.removePair(b, c);
585	>	oneTwoInteractions_.removePair(c, d);
586	>	} else {
587	>	excludedInteractions_.removePair(a, b);
588	>	excludedInteractions_.removePair(b, c);
589	>	excludedInteractions_.removePair(c, d);
590	>	}
591
592	<	exclude_.removePair(a, b);
593	<	exclude_.removePair(a, c);
594	<	exclude_.removePair(a, d);
595	<	exclude_.removePair(b, c);
596	<	exclude_.removePair(b, d);
597	<	exclude_.removePair(c, d);
592	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
593	>	oneThreeInteractions_.removePair(a, c);
594	>	oneThreeInteractions_.removePair(b, d);
595	>	} else {
596	>	excludedInteractions_.removePair(a, c);
597	>	excludedInteractions_.removePair(b, d);
598	>	}
599	>
600	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
601	>	oneFourInteractions_.removePair(a, d);
602	>	} else {
603	>	excludedInteractions_.removePair(a, d);
604	>	}
605		}
606
607	<	Molecule::RigidBodyIterator rbIter;
608	<	RigidBody* rb;
609	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
610	<	std::vector<Atom*> atoms = rb->getAtoms();
611	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
612	<	for (int j = i + 1; j < atoms.size(); ++j) {
607	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
608	>	inversion = mol->nextInversion(inversionIter)) {
609	>
610	>	a = inversion->getAtomA()->getGlobalIndex();
611	>	b = inversion->getAtomB()->getGlobalIndex();
612	>	c = inversion->getAtomC()->getGlobalIndex();
613	>	d = inversion->getAtomD()->getGlobalIndex();
614	>
615	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
616	>	oneTwoInteractions_.removePair(a, b);
617	>	oneTwoInteractions_.removePair(a, c);
618	>	oneTwoInteractions_.removePair(a, d);
619	>	} else {
620	>	excludedInteractions_.removePair(a, b);
621	>	excludedInteractions_.removePair(a, c);
622	>	excludedInteractions_.removePair(a, d);
623	>	}
624	>
625	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
626	>	oneThreeInteractions_.removePair(b, c);
627	>	oneThreeInteractions_.removePair(b, d);
628	>	oneThreeInteractions_.removePair(c, d);
629	>	} else {
630	>	excludedInteractions_.removePair(b, c);
631	>	excludedInteractions_.removePair(b, d);
632	>	excludedInteractions_.removePair(c, d);
633	>	}
634	>	}
635	>
636	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
637	>	rb = mol->nextRigidBody(rbIter)) {
638	>	vector<Atom*> atoms = rb->getAtoms();
639	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
640	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
641		a = atoms[i]->getGlobalIndex();
642		b = atoms[j]->getGlobalIndex();
643	<	exclude_.removePair(a, b);
643	>	excludedInteractions_.removePair(a, b);
644		}
645		}
646		}
647	<
647	>
648		}
649	<
650	<
649	>
650	>
651		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
652		int curStampId;
653	<
653	>
654		//index from 0
655		curStampId = moleculeStamps_.size();
656
#	Line 451 | Line 658 | namespace oopse {
658		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
659		}
660
454	–	void SimInfo::update() {
661
662	<	setupSimType();
663	<
664	<	#ifdef IS_MPI
665	<	setupFortranParallel();
666	<	#endif
667	<
668	<	setupFortranSim();
669	<
670	<	//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	<
662	>	/**
663	>	* update
664	>	*
665	>	*  Performs the global checks and variable settings after the
666	>	*  objects have been created.
667	>	*
668	>	*/
669	>	void SimInfo::update() {
670	>	setupSimVariables();
671		calcNdf();
672		calcNdfRaw();
673		calcNdfTrans();
483	–
484	–	fortranInitialized_ = true;
674		}
675	<
676	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
675	>
676	>	/**
677	>	* getSimulatedAtomTypes
678	>	*
679	>	* Returns an STL set of AtomType* that are actually present in this
680	>	* simulation.  Must query all processors to assemble this information.
681	>	*
682	>	*/
683	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
684		SimInfo::MoleculeIterator mi;
685		Molecule* mol;
686		Molecule::AtomIterator ai;
687		Atom* atom;
688	<	std::set<AtomType*> atomTypes;
689	<
690	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
495	<
688	>	set<AtomType*> atomTypes;
689	>
690	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
691		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
692		atomTypes.insert(atom->getAtomType());
693	<	}
694	<
500	<	}
693	>	}
694	>	}
695
696	<	return atomTypes;
503	<	}
696	>	#ifdef IS_MPI
697
698	<	void SimInfo::setupSimType() {
699	<	std::set<AtomType*>::iterator i;
507	<	std::set<AtomType*> atomTypes;
508	<	atomTypes = getUniqueAtomTypes();
509	<
510	<	int useLennardJones = 0;
511	<	int useElectrostatic = 0;
512	<	int useEAM = 0;
513	<	int useCharge = 0;
514	<	int useDirectional = 0;
515	<	int useDipole = 0;
516	<	int useGayBerne = 0;
517	<	int useSticky = 0;
518	<	int useStickyPower = 0;
519	<	int useShape = 0;
520	<	int useFLARB = 0; //it is not in AtomType yet
521	<	int useDirectionalAtom = 0;
522	<	int useElectrostatics = 0;
523	<	//usePBC and useRF are from simParams
524	<	int usePBC = simParams_->getPBC();
698	>	// loop over the found atom types on this processor, and add their
699	>	// numerical idents to a vector:
700
701	<	//loop over all of the atom types
702	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
703	<	useLennardJones |= (*i)->isLennardJones();
704	<	useElectrostatic |= (*i)->isElectrostatic();
530	<	useEAM |= (*i)->isEAM();
531	<	useCharge |= (*i)->isCharge();
532	<	useDirectional |= (*i)->isDirectional();
533	<	useDipole |= (*i)->isDipole();
534	<	useGayBerne |= (*i)->isGayBerne();
535	<	useSticky |= (*i)->isSticky();
536	<	useStickyPower |= (*i)->isStickyPower();
537	<	useShape |= (*i)->isShape();
538	<	}
701	>	vector<int> foundTypes;
702	>	set<AtomType*>::iterator i;
703	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
704	>	foundTypes.push_back( (*i)->getIdent() );
705
706	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
707	<	useDirectionalAtom = 1;
542	<	}
706	>	// count_local holds the number of found types on this processor
707	>	int count_local = foundTypes.size();
708
709	<	if (useCharge || useDipole) {
710	<	useElectrostatics = 1;
711	<	}
709	>	// count holds the total number of found types on all processors
710	>	// (some will be redundant with the ones found locally):
711	>	int count;
712	>	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
713
714	<	#ifdef IS_MPI
715	<	int temp;
714	>	// create a vector to hold the globally found types, and resize it:
715	>	vector<int> ftGlobal;
716	>	ftGlobal.resize(count);
717	>	vector<int> counts;
718
719	<	temp = usePBC;
720	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
719	>	int nproc = MPI::COMM_WORLD.Get_size();
720	>	counts.resize(nproc);
721	>	vector<int> disps;
722	>	disps.resize(nproc);
723
724	<	temp = useDirectionalAtom;
555	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
556	<
557	<	temp = useLennardJones;
558	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
559	<
560	<	temp = useElectrostatics;
561	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
562	<
563	<	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);
724	>	// now spray out the foundTypes to all the other processors:
725
726	<	temp = useGayBerne;
727	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
726	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
727	>	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
728
729	<	temp = useEAM;
730	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
731	<
732	<	temp = useShape;
733	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
734	<
735	<	temp = useFLARB;
736	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
737	<
729	>	// foundIdents is a stl set, so inserting an already found ident
730	>	// will have no effect.
731	>	set<int> foundIdents;
732	>	vector<int>::iterator j;
733	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
734	>	foundIdents.insert((*j));
735	>
736	>	// now iterate over the foundIdents and get the actual atom types
737	>	// that correspond to these:
738	>	set<int>::iterator it;
739	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
740	>	atomTypes.insert( forceField_->getAtomType((*it)) );
741	>
742		#endif
743	+
744	+	return atomTypes;
745	+	}
746
747	<	fInfo_.SIM_uses_PBC = usePBC;
748	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
749	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
750	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
751	<	fInfo_.SIM_uses_Charges = useCharge;
752	<	fInfo_.SIM_uses_Dipoles = useDipole;
753	<	fInfo_.SIM_uses_Sticky = useSticky;
754	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
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) {
747	>	void SimInfo::setupSimVariables() {
748	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
749	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
750	>	calcBoxDipole_ = false;
751	>	if ( simParams_->haveAccumulateBoxDipole() )
752	>	if ( simParams_->getAccumulateBoxDipole() ) {
753	>	calcBoxDipole_ = true;
754	>	}
755
756	<	if (simParams_->haveDielectric()) {
757	<	fInfo_.dielect = simParams_->getDielectric();
758	<	} else {
759	<	sprintf(painCave.errMsg,
760	<	"SimSetup Error: No Dielectric constant was set.\n"
761	<	"\tYou are trying to use Reaction Field without"
762	<	"\tsetting a dielectric constant!\n");
763	<	painCave.isFatal = 1;
764	<	simError();
765	<	}
766	<
615	<	} else {
616	<	fInfo_.dielect = 0.0;
756	>	set<AtomType*>::iterator i;
757	>	set<AtomType*> atomTypes;
758	>	atomTypes = getSimulatedAtomTypes();
759	>	int usesElectrostatic = 0;
760	>	int usesMetallic = 0;
761	>	int usesDirectional = 0;
762	>	//loop over all of the atom types
763	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
764	>	usesElectrostatic |= (*i)->isElectrostatic();
765	>	usesMetallic |= (*i)->isMetal();
766	>	usesDirectional |= (*i)->isDirectional();
767		}
768
769	+	#ifdef IS_MPI
770	+	int temp;
771	+	temp = usesDirectional;
772	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
773	+
774	+	temp = usesMetallic;
775	+	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776	+
777	+	temp = usesElectrostatic;
778	+	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
779	+	#endif
780	+	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
781	+	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
782	+	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
783	+	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
784	+	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
785	+	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
786		}
787
788	<	void SimInfo::setupFortranSim() {
788	>	void SimInfo::setupFortran() {
789		int isError;
790	<	int nExclude;
791	<	std::vector<int> fortranGlobalGroupMembership;
790	>	int nExclude, nOneTwo, nOneThree, nOneFour;
791	>	vector<int> fortranGlobalGroupMembership;
792
626	–	nExclude = exclude_.getSize();
793		isError = 0;
794
795		//globalGroupMembership_ is filled by SimCreator
#	Line 632 | Line 798 | namespace oopse {
798		}
799
800		//calculate mass ratio of cutoff group
801	<	std::vector<double> mfact;
801	>	vector<RealType> mfact;
802		SimInfo::MoleculeIterator mi;
803		Molecule* mol;
804		Molecule::CutoffGroupIterator ci;
805		CutoffGroup* cg;
806		Molecule::AtomIterator ai;
807		Atom* atom;
808	<	double totalMass;
808	>	RealType totalMass;
809
810		//to avoid memory reallocation, reserve enough space for mfact
811		mfact.reserve(getNCutoffGroups());
#	Line 649 | Line 815 | namespace oopse {
815
816		totalMass = cg->getMass();
817		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
818	<	mfact.push_back(atom->getMass()/totalMass);
818	>	// Check for massless groups - set mfact to 1 if true
819	>	if (totalMass != 0)
820	>	mfact.push_back(atom->getMass()/totalMass);
821	>	else
822	>	mfact.push_back( 1.0 );
823		}
654	–
824		}
825		}
826
827	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
828	<	std::vector<int> identArray;
827	>	//fill ident array of local atoms (it is actually ident of
828	>	//AtomType, it is so confusing !!!)
829	>	vector<int> identArray;
830
831		//to avoid memory reallocation, reserve enough space identArray
832		identArray.reserve(getNAtoms());
#	Line 669 | Line 839 | namespace oopse {
839
840		//fill molMembershipArray
841		//molMembershipArray is filled by SimCreator
842	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
842	>	vector<int> molMembershipArray(nGlobalAtoms_);
843		for (int i = 0; i < nGlobalAtoms_; i++) {
844		molMembershipArray[i] = globalMolMembership_[i] + 1;
845		}
846
847		//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);
848
849	<	if( isError ){
849	>	nExclude = excludedInteractions_.getSize();
850	>	nOneTwo = oneTwoInteractions_.getSize();
851	>	nOneThree = oneThreeInteractions_.getSize();
852	>	nOneFour = oneFourInteractions_.getSize();
853
854	+	int* excludeList = excludedInteractions_.getPairList();
855	+	int* oneTwoList = oneTwoInteractions_.getPairList();
856	+	int* oneThreeList = oneThreeInteractions_.getPairList();
857	+	int* oneFourList = oneFourInteractions_.getPairList();
858	+
859	+	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
860	+	&nExclude, excludeList,
861	+	&nOneTwo, oneTwoList,
862	+	&nOneThree, oneThreeList,
863	+	&nOneFour, oneFourList,
864	+	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
865	+	&fortranGlobalGroupMembership[0], &isError);
866	+
867	+	if( isError ){
868	+
869		sprintf( painCave.errMsg,
870		"There was an error setting the simulation information in fortran.\n" );
871		painCave.isFatal = 1;
872	<	painCave.severity = OOPSE_ERROR;
872	>	painCave.severity = OPENMD_ERROR;
873		simError();
874		}
875	<
876	<	#ifdef IS_MPI
875	>
876	>
877		sprintf( checkPointMsg,
878		"succesfully sent the simulation information to fortran.\n");
697	–	MPIcheckPoint();
698	–	#endif // is_mpi
699	–	}
700	–
701	–
702	–	#ifdef IS_MPI
703	–	void SimInfo::setupFortranParallel() {
879
880	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
881	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
882	<	std::vector<int> localToGlobalCutoffGroupIndex;
883	<	SimInfo::MoleculeIterator mi;
884	<	Molecule::AtomIterator ai;
885	<	Molecule::CutoffGroupIterator ci;
886	<	Molecule* mol;
887	<	Atom* atom;
888	<	CutoffGroup* cg;
880	>	errorCheckPoint();
881	>
882	>	// Setup number of neighbors in neighbor list if present
883	>	if (simParams_->haveNeighborListNeighbors()) {
884	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
885	>	setNeighbors(&nlistNeighbors);
886	>	}
887	>
888	>	#ifdef IS_MPI
889	>	//SimInfo is responsible for creating localToGlobalAtomIndex and
890	>	//localToGlobalGroupIndex
891	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
892	>	vector<int> localToGlobalCutoffGroupIndex;
893		mpiSimData parallelData;
715	–	int isError;
894
895		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
896
#	Line 751 | Line 929 | namespace oopse {
929		}
930
931		sprintf(checkPointMsg, " mpiRefresh successful.\n");
932	<	MPIcheckPoint();
755	<
756	<
757	<	}
758	<
932	>	errorCheckPoint();
933		#endif
934
935	<	double SimInfo::calcMaxCutoffRadius() {
936	<
937	<
938	<	std::set<AtomType*> atomTypes;
939	<	std::set<AtomType*>::iterator i;
940	<	std::vector<double> cutoffRadius;
767	<
768	<	//get the unique atom types
769	<	atomTypes = getUniqueAtomTypes();
770	<
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));
935	>	initFortranFF(&isError);
936	>	if (isError) {
937	>	sprintf(painCave.errMsg,
938	>	"initFortranFF errror: fortran didn't like something we gave it.\n");
939	>	painCave.isFatal = 1;
940	>	simError();
941		}
942	<
776	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
777	<	#ifdef IS_MPI
778	<	//pick the max cutoff radius among the processors
779	<	#endif
780	<
781	<	return maxCutoffRadius;
942	>	fortranInitialized_ = true;
943		}
944
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	–	}
799	–
800	–	if (!simParams_->haveRsw()){
801	–	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	–	}
828	–
829	–	}
830	–	}
831	–
832	–	void SimInfo::setupCutoff() {
833	–	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;
843	–	} else {
844	–	if (myPolicy == "MAX") {
845	–	cp = MAX_CUTOFF_POLICY;
846	–	} else {
847	–	if (myPolicy == "TRADITIONAL") {
848	–	cp = TRADITIONAL_CUTOFF_POLICY;
849	–	} else {
850	–	// throw error
851	–	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	–	}
856	–	}
857	–	}
858	–	}
859	–	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
860	–	}
861	–
862	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
863	–
864	–	int errorOut;
865	–	int esm =  NONE;
866	–	double alphaVal;
867	–
868	–	errorOut = isError;
869	–
870	–	if (simParams_->haveElectrostaticSummationMethod()) {
871	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
872	–	if (myMethod == "NONE") {
873	–	esm = NONE;
874	–	} else {
875	–	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	–	}
900	–	}
901	–	}
902	–	initFortranFF( &fInfo_.SIM_uses_RF, &esm, &alphaVal, &errorOut );
903	–	}
904	–
945		void SimInfo::addProperty(GenericData* genData) {
946		properties_.addProperty(genData);
947		}
948
949	<	void SimInfo::removeProperty(const std::string& propName) {
949	>	void SimInfo::removeProperty(const string& propName) {
950		properties_.removeProperty(propName);
951		}
952
#	Line 914 | Line 954 | namespace oopse {
954		properties_.clearProperties();
955		}
956
957	<	std::vector<std::string> SimInfo::getPropertyNames() {
957	>	vector<string> SimInfo::getPropertyNames() {
958		return properties_.getPropertyNames();
959		}
960
961	<	std::vector<GenericData*> SimInfo::getProperties() {
961	>	vector<GenericData*> SimInfo::getProperties() {
962		return properties_.getProperties();
963		}
964
965	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
965	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
966		return properties_.getPropertyByName(propName);
967		}
968
#	Line 936 | Line 976 | namespace oopse {
976		Molecule* mol;
977		RigidBody* rb;
978		Atom* atom;
979	+	CutoffGroup* cg;
980		SimInfo::MoleculeIterator mi;
981		Molecule::RigidBodyIterator rbIter;
982	<	Molecule::AtomIterator atomIter;;
982	>	Molecule::AtomIterator atomIter;
983	>	Molecule::CutoffGroupIterator cgIter;
984
985		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
986
#	Line 949 | Line 991 | namespace oopse {
991		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
992		rb->setSnapshotManager(sman_);
993		}
994	+
995	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
996	+	cg->setSnapshotManager(sman_);
997	+	}
998		}
999
1000		}
#	Line 958 | Line 1004 | namespace oopse {
1004		Molecule* mol;
1005
1006		Vector3d comVel(0.0);
1007	<	double totalMass = 0.0;
1007	>	RealType totalMass = 0.0;
1008
1009
1010		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1011	<	double mass = mol->getMass();
1011	>	RealType mass = mol->getMass();
1012		totalMass += mass;
1013		comVel += mass * mol->getComVel();
1014		}
1015
1016		#ifdef IS_MPI
1017	<	double tmpMass = totalMass;
1017	>	RealType tmpMass = totalMass;
1018		Vector3d tmpComVel(comVel);
1019	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1020	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1019	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1020	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1021		#endif
1022
1023		comVel /= totalMass;
#	Line 984 | Line 1030 | namespace oopse {
1030		Molecule* mol;
1031
1032		Vector3d com(0.0);
1033	<	double totalMass = 0.0;
1033	>	RealType totalMass = 0.0;
1034
1035		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1036	<	double mass = mol->getMass();
1036	>	RealType mass = mol->getMass();
1037		totalMass += mass;
1038		com += mass * mol->getCom();
1039		}
1040
1041		#ifdef IS_MPI
1042	<	double tmpMass = totalMass;
1042	>	RealType tmpMass = totalMass;
1043		Vector3d tmpCom(com);
1044	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1045	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1044	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1045	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1046		#endif
1047
1048		com /= totalMass;
#	Line 1005 | Line 1051 | namespace oopse {
1051
1052		}
1053
1054	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1054	>	ostream& operator <<(ostream& o, SimInfo& info) {
1055
1056		return o;
1057		}
#	Line 1020 | Line 1066 | namespace oopse {
1066		Molecule* mol;
1067
1068
1069	<	double totalMass = 0.0;
1069	>	RealType totalMass = 0.0;
1070
1071
1072		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1073	<	double mass = mol->getMass();
1073	>	RealType mass = mol->getMass();
1074		totalMass += mass;
1075		com += mass * mol->getCom();
1076		comVel += mass * mol->getComVel();
1077		}
1078
1079		#ifdef IS_MPI
1080	<	double tmpMass = totalMass;
1080	>	RealType tmpMass = totalMass;
1081		Vector3d tmpCom(com);
1082		Vector3d tmpComVel(comVel);
1083	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1084	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1085	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1083	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1084	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1085	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1086		#endif
1087
1088		com /= totalMass;
#	Line 1048 | Line 1094 | namespace oopse {
1094
1095
1096		[  Ixx -Ixy  -Ixz ]
1097	<	J =| -Iyx  Iyy  -Iyz |
1097	>	J =| -Iyx  Iyy  -Iyz |
1098		[ -Izx -Iyz   Izz ]
1099		*/
1100
1101		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1102
1103
1104	<	double xx = 0.0;
1105	<	double yy = 0.0;
1106	<	double zz = 0.0;
1107	<	double xy = 0.0;
1108	<	double xz = 0.0;
1109	<	double yz = 0.0;
1104	>	RealType xx = 0.0;
1105	>	RealType yy = 0.0;
1106	>	RealType zz = 0.0;
1107	>	RealType xy = 0.0;
1108	>	RealType xz = 0.0;
1109	>	RealType yz = 0.0;
1110		Vector3d com(0.0);
1111		Vector3d comVel(0.0);
1112
#	Line 1072 | Line 1118 | namespace oopse {
1118		Vector3d thisq(0.0);
1119		Vector3d thisv(0.0);
1120
1121	<	double thisMass = 0.0;
1121	>	RealType thisMass = 0.0;
1122
1123
1124
#	Line 1110 | Line 1156 | namespace oopse {
1156		#ifdef IS_MPI
1157		Mat3x3d tmpI(inertiaTensor);
1158		Vector3d tmpAngMom;
1159	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1160	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1159	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1160	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1161		#endif
1162
1163		return;
#	Line 1132 | Line 1178 | namespace oopse {
1178		Vector3d thisr(0.0);
1179		Vector3d thisp(0.0);
1180
1181	<	double thisMass;
1181	>	RealType thisMass;
1182
1183		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1184		thisMass = mol->getMass();
#	Line 1145 | Line 1191 | namespace oopse {
1191
1192		#ifdef IS_MPI
1193		Vector3d tmpAngMom;
1194	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1194	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1195		#endif
1196
1197		return angularMomentum;
1198		}
1199
1200	<
1201	<	}//end namespace oopse
1200	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1201	>	return IOIndexToIntegrableObject.at(index);
1202	>	}
1203	>
1204	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1205	>	IOIndexToIntegrableObject= v;
1206	>	}
1207
1208	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1209	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1210	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1211	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1212	+	*/
1213	+	void SimInfo::getGyrationalVolume(RealType &volume){
1214	+	Mat3x3d intTensor;
1215	+	RealType det;
1216	+	Vector3d dummyAngMom;
1217	+	RealType sysconstants;
1218	+	RealType geomCnst;
1219	+
1220	+	geomCnst = 3.0/2.0;
1221	+	/* Get the inertial tensor and angular momentum for free*/
1222	+	getInertiaTensor(intTensor,dummyAngMom);
1223	+
1224	+	det = intTensor.determinant();
1225	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1226	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1227	+	return;
1228	+	}
1229	+
1230	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1231	+	Mat3x3d intTensor;
1232	+	Vector3d dummyAngMom;
1233	+	RealType sysconstants;
1234	+	RealType geomCnst;
1235	+
1236	+	geomCnst = 3.0/2.0;
1237	+	/* Get the inertial tensor and angular momentum for free*/
1238	+	getInertiaTensor(intTensor,dummyAngMom);
1239	+
1240	+	detI = intTensor.determinant();
1241	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1242	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1243	+	return;
1244	+	}
1245	+	/*
1246	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1247	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1248	+	sdByGlobalIndex_ = v;
1249	+	}
1250	+
1251	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1252	+	//assert(index < nAtoms_ + nRigidBodies_);
1253	+	return sdByGlobalIndex_.at(index);
1254	+	}
1255	+	*/
1256	+	int SimInfo::getNGlobalConstraints() {
1257	+	int nGlobalConstraints;
1258	+	#ifdef IS_MPI
1259	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1260	+	MPI_COMM_WORLD);
1261	+	#else
1262	+	nGlobalConstraints =  nConstraints_;
1263	+	#endif
1264	+	return nGlobalConstraints;
1265	+	}
1266	+
1267	+	}//end namespace OpenMD
1268	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 604 by chrisfen, Fri Sep 16 19:00:12 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1540 by gezelter, Mon Jan 17 21:34:36 2011 UTC

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