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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 611 by chrisfen, Mon Sep 19 23:21:46 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1544 by gezelter, Fri Mar 18 19:31:52 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/DarkSide/electrostatic_interface.h"
59	–	#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	<
81	<
82	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
83	<	MoleculeStamp* molStamp;
84	<	int nMolWithSameStamp;
85	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
86	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
87	<	CutoffGroupStamp* cgStamp;
88	<	RigidBodyStamp* rbStamp;
89	<	int nRigidAtoms = 0;
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	<
117	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
118	<	rbStamp = molStamp->getRigidBody(j);
119	<	nAtomsInRigidBodies += rbStamp->getNMembers();
120	<	}
121	<
122	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
123	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
124	<
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_);
143	<	#endif
144	<
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
154	–	delete stamps_;
162		delete sman_;
163		delete simParams_;
164		delete forceField_;
165		}
166
160	–	int SimInfo::getNGlobalConstraints() {
161	–	int nGlobalConstraints;
162	–	#ifdef IS_MPI
163	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
164	–	MPI_COMM_WORLD);
165	–	#else
166	–	nGlobalConstraints =  nConstraints_;
167	–	#endif
168	–	return nGlobalConstraints;
169	–	}
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 205 | 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 219 | Line 218 | namespace oopse {
218		} else {
219		return false;
220		}
222	–
223	–
221		}
222
223
#	Line 238 | 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 258 | 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 276 | 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 327 | 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	+	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	<	exclude_.addPair(a, b);
415	<	exclude_.addPair(a, c);
416	<	exclude_.addPair(b, c);
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 452 | Line 658 | namespace oopse {
658		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
659		}
660
455	–	void SimInfo::update() {
661
662	<	setupSimType();
663	<
664	<	#ifdef IS_MPI
665	<	setupFortranParallel();
666	<	#endif
667	<
668	<	setupFortranSim();
669	<
670	<	//setup fortran force field
466	<	/** @deprecate */
467	<	int isError = 0;
468	<
469	<	setupElectrostaticSummationMethod( isError );
470	<
471	<	if(isError){
472	<	sprintf( painCave.errMsg,
473	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
474	<	painCave.isFatal = 1;
475	<	simError();
476	<	}
477	<
478	<
479	<	setupCutoff();
480	<
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();
484	–
485	–	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)) {
496	<
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	<
695	<	}
693	>	}
694	>	}
695	>
696	>	#ifdef IS_MPI
697
698	<	return atomTypes;
699	<	}
698	>	// loop over the found atom types on this processor, and add their
699	>	// numerical idents to a vector:
700
701	<	void SimInfo::setupSimType() {
702	<	std::set<AtomType*>::iterator i;
703	<	std::set<AtomType*> atomTypes;
704	<	atomTypes = getUniqueAtomTypes();
510	<
511	<	int useLennardJones = 0;
512	<	int useElectrostatic = 0;
513	<	int useEAM = 0;
514	<	int useCharge = 0;
515	<	int useDirectional = 0;
516	<	int useDipole = 0;
517	<	int useGayBerne = 0;
518	<	int useSticky = 0;
519	<	int useStickyPower = 0;
520	<	int useShape = 0;
521	<	int useFLARB = 0; //it is not in AtomType yet
522	<	int useDirectionalAtom = 0;
523	<	int useElectrostatics = 0;
524	<	//usePBC and useRF are from simParams
525	<	int usePBC = simParams_->getPBC();
526	<	int useRF;
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	<	// set the useRF logical
707	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
530	<	if (myMethod == "REACTION_FIELD")
531	<	useRF = 1;
532	<	else
533	<	useRF = 0;
706	>	// count_local holds the number of found types on this processor
707	>	int count_local = foundTypes.size();
708
709	<	//loop over all of the atom types
710	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
711	<	useLennardJones |= (*i)->isLennardJones();
712	<	useElectrostatic |= (*i)->isElectrostatic();
539	<	useEAM |= (*i)->isEAM();
540	<	useCharge |= (*i)->isCharge();
541	<	useDirectional |= (*i)->isDirectional();
542	<	useDipole |= (*i)->isDipole();
543	<	useGayBerne |= (*i)->isGayBerne();
544	<	useSticky |= (*i)->isSticky();
545	<	useStickyPower |= (*i)->isStickyPower();
546	<	useShape |= (*i)->isShape();
547	<	}
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	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
715	<	useDirectionalAtom = 1;
716	<	}
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	<	if (useCharge || useDipole) {
720	<	useElectrostatics = 1;
721	<	}
719	>	int nproc = MPI::COMM_WORLD.Get_size();
720	>	counts.resize(nproc);
721	>	vector<int> disps;
722	>	disps.resize(nproc);
723
724	<	#ifdef IS_MPI
725	<	int temp;
724	>	// now spray out the foundTypes to all the other processors:
725	>
726	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
727	>	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
728
729	<	temp = usePBC;
730	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
731	<
732	<	temp = useDirectionalAtom;
733	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
734	<
566	<	temp = useLennardJones;
567	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
568	<
569	<	temp = useElectrostatics;
570	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
571	<
572	<	temp = useCharge;
573	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
574	<
575	<	temp = useDipole;
576	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
577	<
578	<	temp = useSticky;
579	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
580	<
581	<	temp = useStickyPower;
582	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
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	<	temp = useGayBerne;
737	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
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	<	temp = useEAM;
748	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
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	<	temp = useShape;
757	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
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	<	temp = useFLARB;
770	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
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 = useRF;
775	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
774	>	temp = usesMetallic;
775	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776
777	+	temp = usesElectrostatic;
778	+	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
779		#endif
780	<
781	<	fInfo_.SIM_uses_PBC = usePBC;
782	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
783	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
784	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
785	<	fInfo_.SIM_uses_Charges = useCharge;
606	<	fInfo_.SIM_uses_Dipoles = useDipole;
607	<	fInfo_.SIM_uses_Sticky = useSticky;
608	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
609	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
610	<	fInfo_.SIM_uses_EAM = useEAM;
611	<	fInfo_.SIM_uses_Shapes = useShape;
612	<	fInfo_.SIM_uses_FLARB = useFLARB;
613	<	fInfo_.SIM_uses_RF = useRF;
614	<
615	<	if( fInfo_.SIM_uses_Dipoles && myMethod == "REACTION_FIELD") {
616	<
617	<	if (simParams_->haveDielectric()) {
618	<	fInfo_.dielect = simParams_->getDielectric();
619	<	} else {
620	<	sprintf(painCave.errMsg,
621	<	"SimSetup Error: No Dielectric constant was set.\n"
622	<	"\tYou are trying to use Reaction Field without"
623	<	"\tsetting a dielectric constant!\n");
624	<	painCave.isFatal = 1;
625	<	simError();
626	<	}
627	<
628	<	} else {
629	<	fInfo_.dielect = 0.0;
630	<	}
631	<
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
639	–	nExclude = exclude_.getSize();
793		isError = 0;
794
795		//globalGroupMembership_ is filled by SimCreator
#	Line 645 | 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 662 | 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		}
667	–
824		}
825		}
826
827	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
672	<	std::vector<int> identArray;
827	>	// Build the identArray_
828
829	<	//to avoid memory reallocation, reserve enough space identArray
830	<	identArray.reserve(getNAtoms());
676	<
829	>	identArray_.clear();
830	>	identArray_.reserve(getNAtoms());
831		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
832		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
833	<	identArray.push_back(atom->getIdent());
833	>	identArray_.push_back(atom->getIdent());
834		}
835		}
836
837		//fill molMembershipArray
838		//molMembershipArray is filled by SimCreator
839	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
839	>	vector<int> molMembershipArray(nGlobalAtoms_);
840		for (int i = 0; i < nGlobalAtoms_; i++) {
841		molMembershipArray[i] = globalMolMembership_[i] + 1;
842		}
843
844		//setup fortran simulation
691	–	int nGlobalExcludes = 0;
692	–	int* globalExcludes = NULL;
693	–	int* excludeList = exclude_.getExcludeList();
694	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
695	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
696	–	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
845
846	<	if( isError ){
846	>	nExclude = excludedInteractions_.getSize();
847	>	nOneTwo = oneTwoInteractions_.getSize();
848	>	nOneThree = oneThreeInteractions_.getSize();
849	>	nOneFour = oneFourInteractions_.getSize();
850
851	+	int* excludeList = excludedInteractions_.getPairList();
852	+	int* oneTwoList = oneTwoInteractions_.getPairList();
853	+	int* oneThreeList = oneThreeInteractions_.getPairList();
854	+	int* oneFourList = oneFourInteractions_.getPairList();
855	+
856	+	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
857	+	&nExclude, excludeList,
858	+	&nOneTwo, oneTwoList,
859	+	&nOneThree, oneThreeList,
860	+	&nOneFour, oneFourList,
861	+	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
862	+	&fortranGlobalGroupMembership[0], &isError);
863	+
864	+	if( isError ){
865	+
866		sprintf( painCave.errMsg,
867		"There was an error setting the simulation information in fortran.\n" );
868		painCave.isFatal = 1;
869	<	painCave.severity = OOPSE_ERROR;
869	>	painCave.severity = OPENMD_ERROR;
870		simError();
871		}
872	<
873	<	#ifdef IS_MPI
872	>
873	>
874		sprintf( checkPointMsg,
875		"succesfully sent the simulation information to fortran.\n");
710	–	MPIcheckPoint();
711	–	#endif // is_mpi
712	–	}
713	–
714	–
715	–	#ifdef IS_MPI
716	–	void SimInfo::setupFortranParallel() {
876
877	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
878	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
879	<	std::vector<int> localToGlobalCutoffGroupIndex;
880	<	SimInfo::MoleculeIterator mi;
881	<	Molecule::AtomIterator ai;
882	<	Molecule::CutoffGroupIterator ci;
883	<	Molecule* mol;
884	<	Atom* atom;
885	<	CutoffGroup* cg;
877	>	errorCheckPoint();
878	>
879	>	// Setup number of neighbors in neighbor list if present
880	>	if (simParams_->haveNeighborListNeighbors()) {
881	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
882	>	setNeighbors(&nlistNeighbors);
883	>	}
884	>
885	>	#ifdef IS_MPI
886	>	//SimInfo is responsible for creating localToGlobalAtomIndex and
887	>	//localToGlobalGroupIndex
888	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
889	>	vector<int> localToGlobalCutoffGroupIndex;
890		mpiSimData parallelData;
728	–	int isError;
891
892		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
893
#	Line 764 | Line 926 | namespace oopse {
926		}
927
928		sprintf(checkPointMsg, " mpiRefresh successful.\n");
929	<	MPIcheckPoint();
768	<
769	<
770	<	}
771	<
929	>	errorCheckPoint();
930		#endif
931
932	<	double SimInfo::calcMaxCutoffRadius() {
933	<
934	<
935	<	std::set<AtomType*> atomTypes;
936	<	std::set<AtomType*>::iterator i;
937	<	std::vector<double> cutoffRadius;
780	<
781	<	//get the unique atom types
782	<	atomTypes = getUniqueAtomTypes();
783	<
784	<	//query the max cutoff radius among these atom types
785	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
786	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
932	>	initFortranFF(&isError);
933	>	if (isError) {
934	>	sprintf(painCave.errMsg,
935	>	"initFortranFF errror: fortran didn't like something we gave it.\n");
936	>	painCave.isFatal = 1;
937	>	simError();
938		}
939	<
789	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
790	<	#ifdef IS_MPI
791	<	//pick the max cutoff radius among the processors
792	<	#endif
793	<
794	<	return maxCutoffRadius;
939	>	fortranInitialized_ = true;
940		}
941
797	–	void SimInfo::getCutoff(double& rcut, double& rsw) {
798	–
799	–	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
800	–
801	–	if (!simParams_->haveRcut()){
802	–	sprintf(painCave.errMsg,
803	–	"SimCreator Warning: No value was set for the cutoffRadius.\n"
804	–	"\tOOPSE will use a default value of 15.0 angstroms"
805	–	"\tfor the cutoffRadius.\n");
806	–	painCave.isFatal = 0;
807	–	simError();
808	–	rcut = 15.0;
809	–	} else{
810	–	rcut = simParams_->getRcut();
811	–	}
812	–
813	–	if (!simParams_->haveRsw()){
814	–	sprintf(painCave.errMsg,
815	–	"SimCreator Warning: No value was set for switchingRadius.\n"
816	–	"\tOOPSE will use a default value of\n"
817	–	"\t0.95 * cutoffRadius for the switchingRadius\n");
818	–	painCave.isFatal = 0;
819	–	simError();
820	–	rsw = 0.95 * rcut;
821	–	} else{
822	–	rsw = simParams_->getRsw();
823	–	}
824	–
825	–	} else {
826	–	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
827	–	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
828	–
829	–	if (simParams_->haveRcut()) {
830	–	rcut = simParams_->getRcut();
831	–	} else {
832	–	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
833	–	rcut = calcMaxCutoffRadius();
834	–	}
835	–
836	–	if (simParams_->haveRsw()) {
837	–	rsw  = simParams_->getRsw();
838	–	} else {
839	–	rsw = rcut;
840	–	}
841	–
842	–	}
843	–	}
844	–
845	–	void SimInfo::setupCutoff() {
846	–	getCutoff(rcut_, rsw_);
847	–	double rnblist = rcut_ + 1; // skin of neighbor list
848	–
849	–	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
850	–
851	–	int cp =  TRADITIONAL_CUTOFF_POLICY;
852	–	if (simParams_->haveCutoffPolicy()) {
853	–	std::string myPolicy = simParams_->getCutoffPolicy();
854	–	if (myPolicy == "MIX") {
855	–	cp = MIX_CUTOFF_POLICY;
856	–	} else {
857	–	if (myPolicy == "MAX") {
858	–	cp = MAX_CUTOFF_POLICY;
859	–	} else {
860	–	if (myPolicy == "TRADITIONAL") {
861	–	cp = TRADITIONAL_CUTOFF_POLICY;
862	–	} else {
863	–	// throw error
864	–	sprintf( painCave.errMsg,
865	–	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
866	–	painCave.isFatal = 1;
867	–	simError();
868	–	}
869	–	}
870	–	}
871	–	}
872	–	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
873	–	// also send cutoff notification to electrostatics
874	–	setElectrostaticCutoffRadius(&rcut_);
875	–	}
876	–
877	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
878	–
879	–	int errorOut;
880	–	int esm =  NONE;
881	–	double alphaVal;
882	–	double dielectric;
883	–
884	–	errorOut = isError;
885	–	alphaVal = simParams_->getDampingAlpha();
886	–	dielectric = simParams_->getDielectric();
887	–
888	–	if (simParams_->haveElectrostaticSummationMethod()) {
889	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
890	–	if (myMethod == "NONE") {
891	–	esm = NONE;
892	–	} else {
893	–	if (myMethod == "UNDAMPED_WOLF") {
894	–	esm = UNDAMPED_WOLF;
895	–	} else {
896	–	if (myMethod == "DAMPED_WOLF") {
897	–	esm = DAMPED_WOLF;
898	–	if (!simParams_->haveDampingAlpha()) {
899	–	//throw error
900	–	sprintf( painCave.errMsg,
901	–	"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.", alphaVal);
902	–	painCave.isFatal = 0;
903	–	simError();
904	–	}
905	–	} else {
906	–	if (myMethod == "REACTION_FIELD") {
907	–	esm = REACTION_FIELD;
908	–	} else {
909	–	// throw error
910	–	sprintf( painCave.errMsg,
911	–	"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() );
912	–	painCave.isFatal = 1;
913	–	simError();
914	–	}
915	–	}
916	–	}
917	–	}
918	–	}
919	–	// let's pass some summation method variables to fortran
920	–	setElectrostaticSummationMethod( &esm );
921	–	setDampedWolfAlpha( &alphaVal );
922	–	setReactionFieldDielectric( &dielectric );
923	–	initFortranFF( &esm, &errorOut );
924	–	}
925	–
942		void SimInfo::addProperty(GenericData* genData) {
943		properties_.addProperty(genData);
944		}
945
946	<	void SimInfo::removeProperty(const std::string& propName) {
946	>	void SimInfo::removeProperty(const string& propName) {
947		properties_.removeProperty(propName);
948		}
949
#	Line 935 | Line 951 | namespace oopse {
951		properties_.clearProperties();
952		}
953
954	<	std::vector<std::string> SimInfo::getPropertyNames() {
954	>	vector<string> SimInfo::getPropertyNames() {
955		return properties_.getPropertyNames();
956		}
957
958	<	std::vector<GenericData*> SimInfo::getProperties() {
958	>	vector<GenericData*> SimInfo::getProperties() {
959		return properties_.getProperties();
960		}
961
962	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
962	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
963		return properties_.getPropertyByName(propName);
964		}
965
#	Line 957 | Line 973 | namespace oopse {
973		Molecule* mol;
974		RigidBody* rb;
975		Atom* atom;
976	+	CutoffGroup* cg;
977		SimInfo::MoleculeIterator mi;
978		Molecule::RigidBodyIterator rbIter;
979	<	Molecule::AtomIterator atomIter;;
979	>	Molecule::AtomIterator atomIter;
980	>	Molecule::CutoffGroupIterator cgIter;
981
982		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
983
#	Line 970 | Line 988 | namespace oopse {
988		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
989		rb->setSnapshotManager(sman_);
990		}
991	+
992	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
993	+	cg->setSnapshotManager(sman_);
994	+	}
995		}
996
997		}
#	Line 979 | Line 1001 | namespace oopse {
1001		Molecule* mol;
1002
1003		Vector3d comVel(0.0);
1004	<	double totalMass = 0.0;
1004	>	RealType totalMass = 0.0;
1005
1006
1007		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1008	<	double mass = mol->getMass();
1008	>	RealType mass = mol->getMass();
1009		totalMass += mass;
1010		comVel += mass * mol->getComVel();
1011		}
1012
1013		#ifdef IS_MPI
1014	<	double tmpMass = totalMass;
1014	>	RealType tmpMass = totalMass;
1015		Vector3d tmpComVel(comVel);
1016	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1017	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1016	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1017	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1018		#endif
1019
1020		comVel /= totalMass;
#	Line 1005 | Line 1027 | namespace oopse {
1027		Molecule* mol;
1028
1029		Vector3d com(0.0);
1030	<	double totalMass = 0.0;
1030	>	RealType totalMass = 0.0;
1031
1032		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1033	<	double mass = mol->getMass();
1033	>	RealType mass = mol->getMass();
1034		totalMass += mass;
1035		com += mass * mol->getCom();
1036		}
1037
1038		#ifdef IS_MPI
1039	<	double tmpMass = totalMass;
1039	>	RealType tmpMass = totalMass;
1040		Vector3d tmpCom(com);
1041	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1042	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1041	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1042	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1043		#endif
1044
1045		com /= totalMass;
#	Line 1026 | Line 1048 | namespace oopse {
1048
1049		}
1050
1051	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1051	>	ostream& operator <<(ostream& o, SimInfo& info) {
1052
1053		return o;
1054		}
#	Line 1041 | Line 1063 | namespace oopse {
1063		Molecule* mol;
1064
1065
1066	<	double totalMass = 0.0;
1066	>	RealType totalMass = 0.0;
1067
1068
1069		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1070	<	double mass = mol->getMass();
1070	>	RealType mass = mol->getMass();
1071		totalMass += mass;
1072		com += mass * mol->getCom();
1073		comVel += mass * mol->getComVel();
1074		}
1075
1076		#ifdef IS_MPI
1077	<	double tmpMass = totalMass;
1077	>	RealType tmpMass = totalMass;
1078		Vector3d tmpCom(com);
1079		Vector3d tmpComVel(comVel);
1080	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1081	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1082	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1080	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1081	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1082	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1083		#endif
1084
1085		com /= totalMass;
#	Line 1069 | Line 1091 | namespace oopse {
1091
1092
1093		[  Ixx -Ixy  -Ixz ]
1094	<	J =| -Iyx  Iyy  -Iyz |
1094	>	J =| -Iyx  Iyy  -Iyz |
1095		[ -Izx -Iyz   Izz ]
1096		*/
1097
1098		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1099
1100
1101	<	double xx = 0.0;
1102	<	double yy = 0.0;
1103	<	double zz = 0.0;
1104	<	double xy = 0.0;
1105	<	double xz = 0.0;
1106	<	double yz = 0.0;
1101	>	RealType xx = 0.0;
1102	>	RealType yy = 0.0;
1103	>	RealType zz = 0.0;
1104	>	RealType xy = 0.0;
1105	>	RealType xz = 0.0;
1106	>	RealType yz = 0.0;
1107		Vector3d com(0.0);
1108		Vector3d comVel(0.0);
1109
#	Line 1093 | Line 1115 | namespace oopse {
1115		Vector3d thisq(0.0);
1116		Vector3d thisv(0.0);
1117
1118	<	double thisMass = 0.0;
1118	>	RealType thisMass = 0.0;
1119
1120
1121
#	Line 1131 | Line 1153 | namespace oopse {
1153		#ifdef IS_MPI
1154		Mat3x3d tmpI(inertiaTensor);
1155		Vector3d tmpAngMom;
1156	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1157	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1156	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1157	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1158		#endif
1159
1160		return;
#	Line 1153 | Line 1175 | namespace oopse {
1175		Vector3d thisr(0.0);
1176		Vector3d thisp(0.0);
1177
1178	<	double thisMass;
1178	>	RealType thisMass;
1179
1180		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1181		thisMass = mol->getMass();
#	Line 1166 | Line 1188 | namespace oopse {
1188
1189		#ifdef IS_MPI
1190		Vector3d tmpAngMom;
1191	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1191	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1192		#endif
1193
1194		return angularMomentum;
1195		}
1196
1197	<
1198	<	}//end namespace oopse
1197	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1198	>	return IOIndexToIntegrableObject.at(index);
1199	>	}
1200	>
1201	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1202	>	IOIndexToIntegrableObject= v;
1203	>	}
1204
1205	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1206	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1207	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1208	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1209	+	*/
1210	+	void SimInfo::getGyrationalVolume(RealType &volume){
1211	+	Mat3x3d intTensor;
1212	+	RealType det;
1213	+	Vector3d dummyAngMom;
1214	+	RealType sysconstants;
1215	+	RealType geomCnst;
1216	+
1217	+	geomCnst = 3.0/2.0;
1218	+	/* Get the inertial tensor and angular momentum for free*/
1219	+	getInertiaTensor(intTensor,dummyAngMom);
1220	+
1221	+	det = intTensor.determinant();
1222	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1223	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1224	+	return;
1225	+	}
1226	+
1227	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1228	+	Mat3x3d intTensor;
1229	+	Vector3d dummyAngMom;
1230	+	RealType sysconstants;
1231	+	RealType geomCnst;
1232	+
1233	+	geomCnst = 3.0/2.0;
1234	+	/* Get the inertial tensor and angular momentum for free*/
1235	+	getInertiaTensor(intTensor,dummyAngMom);
1236	+
1237	+	detI = intTensor.determinant();
1238	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1239	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1240	+	return;
1241	+	}
1242	+	/*
1243	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1244	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1245	+	sdByGlobalIndex_ = v;
1246	+	}
1247	+
1248	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1249	+	//assert(index < nAtoms_ + nRigidBodies_);
1250	+	return sdByGlobalIndex_.at(index);
1251	+	}
1252	+	*/
1253	+	int SimInfo::getNGlobalConstraints() {
1254	+	int nGlobalConstraints;
1255	+	#ifdef IS_MPI
1256	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1257	+	MPI_COMM_WORLD);
1258	+	#else
1259	+	nGlobalConstraints =  nConstraints_;
1260	+	#endif
1261	+	return nGlobalConstraints;
1262	+	}
1263	+
1264	+	}//end namespace OpenMD
1265	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 611 by chrisfen, Mon Sep 19 23:21:46 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1544 by gezelter, Fri Mar 18 19:31:52 2011 UTC

#	Line 0 | Line 1
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