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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 557 by chuckv, Tue May 31 22:31:54 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 48 | Line 49
49
50		#include <algorithm>
51		#include <set>
52	+	#include <map>
53
54		#include "brains/SimInfo.hpp"
55		#include "math/Vector3.hpp"
56		#include "primitives/Molecule.hpp"
57	<	#include "UseTheForce/doForces_interface.h"
56	<	#include "UseTheForce/notifyCutoffs_interface.h"
57	>	#include "primitives/StuntDouble.hpp"
58		#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60		#include "selection/SelectionManager.hpp"
61	<
61	>	#include "io/ForceFieldOptions.hpp"
62	>	#include "brains/ForceField.hpp"
63	>	#include "nonbonded/SwitchingFunction.hpp"
64		#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
64	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68	<	namespace oopse {
69	<
70	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
71	<	ForceField* ff, Globals* simParams) :
72	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
73	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
68	>	using namespace std;
69	>	namespace OpenMD {
70	>
71	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72	>	forceField_(ff), simParams_(simParams),
73	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
77	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
78	<	sman_(NULL), fortranInitialized_(false) {
79	<
78	<
79	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
80	<	MoleculeStamp* molStamp;
81	<	int nMolWithSameStamp;
82	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
83	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
84	<	CutoffGroupStamp* cgStamp;
85	<	RigidBodyStamp* rbStamp;
86	<	int nRigidAtoms = 0;
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0),
76	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79	>	calcBoxDipole_(false), useAtomicVirial_(true) {
80
81	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
82	<	molStamp = i->first;
83	<	nMolWithSameStamp = i->second;
84	<
85	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
86	<
87	<	//calculate atoms in molecules
88	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
89	<
90	<
91	<	//calculate atoms in cutoff groups
92	<	int nAtomsInGroups = 0;
93	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
94	<
95	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
96	<	cgStamp = molStamp->getCutoffGroup(j);
97	<	nAtomsInGroups += cgStamp->getNMembers();
98	<	}
99	<
100	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
101	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
102	<
103	<	//calculate atoms in rigid bodies
104	<	int nAtomsInRigidBodies = 0;
105	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
106	<
114	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
115	<	rbStamp = molStamp->getRigidBody(j);
116	<	nAtomsInRigidBodies += rbStamp->getNMembers();
117	<	}
118	<
119	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
120	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
121	<
81	>	MoleculeStamp* molStamp;
82	>	int nMolWithSameStamp;
83	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
85	>	CutoffGroupStamp* cgStamp;
86	>	RigidBodyStamp* rbStamp;
87	>	int nRigidAtoms = 0;
88	>
89	>	vector<Component*> components = simParams->getComponents();
90	>
91	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
92	>	molStamp = (*i)->getMoleculeStamp();
93	>	nMolWithSameStamp = (*i)->getNMol();
94	>
95	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
96	>
97	>	//calculate atoms in molecules
98	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
99	>
100	>	//calculate atoms in cutoff groups
101	>	int nAtomsInGroups = 0;
102	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
103	>
104	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
105	>	cgStamp = molStamp->getCutoffGroupStamp(j);
106	>	nAtomsInGroups += cgStamp->getNMembers();
107		}
108	<
109	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
110	<	//therefore the total number of cutoff groups in the system is equal to
111	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
112	<	//file plus the number of cutoff groups defined in meta-data file
113	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
114	<
115	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
116	<	//therefore the total number of  integrable objects in the system is equal to
117	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
118	<	//file plus the number of  rigid bodies defined in meta-data file
119	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
120	<
121	<	nGlobalMols_ = molStampIds_.size();
122	<
123	<	#ifdef IS_MPI
124	<	molToProcMap_.resize(nGlobalMols_);
140	<	#endif
141	<
108	>
109	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
110	>
111	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
112	>
113	>	//calculate atoms in rigid bodies
114	>	int nAtomsInRigidBodies = 0;
115	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
116	>
117	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
118	>	rbStamp = molStamp->getRigidBodyStamp(j);
119	>	nAtomsInRigidBodies += rbStamp->getNMembers();
120	>	}
121	>
122	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
123	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
124	>
125		}
126	+
127	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
128	+	//group therefore the total number of cutoff groups in the system is
129	+	//equal to the total number of atoms minus number of atoms belong to
130	+	//cutoff group defined in meta-data file plus the number of cutoff
131	+	//groups defined in meta-data file
132
133	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134	+
135	+	//every free atom (atom does not belong to rigid bodies) is an
136	+	//integrable object therefore the total number of integrable objects
137	+	//in the system is equal to the total number of atoms minus number of
138	+	//atoms belong to rigid body defined in meta-data file plus the number
139	+	//of rigid bodies defined in meta-data file
140	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
141	+	+ nGlobalRigidBodies_;
142	+
143	+	nGlobalMols_ = molStampIds_.size();
144	+	molToProcMap_.resize(nGlobalMols_);
145	+	}
146	+
147		SimInfo::~SimInfo() {
148	<	std::map<int, Molecule*>::iterator i;
148	>	map<int, Molecule*>::iterator i;
149		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
150		delete i->second;
151		}
152		molecules_.clear();
153
151	–	delete stamps_;
154		delete sman_;
155		delete simParams_;
156		delete forceField_;
157		}
158
157	–	int SimInfo::getNGlobalConstraints() {
158	–	int nGlobalConstraints;
159	–	#ifdef IS_MPI
160	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
161	–	MPI_COMM_WORLD);
162	–	#else
163	–	nGlobalConstraints =  nConstraints_;
164	–	#endif
165	–	return nGlobalConstraints;
166	–	}
159
160		bool SimInfo::addMolecule(Molecule* mol) {
161		MoleculeIterator i;
162	<
162	>
163		i = molecules_.find(mol->getGlobalIndex());
164		if (i == molecules_.end() ) {
165	<
166	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
167	<
165	>
166	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
167	>
168		nAtoms_ += mol->getNAtoms();
169		nBonds_ += mol->getNBonds();
170		nBends_ += mol->getNBends();
171		nTorsions_ += mol->getNTorsions();
172	+	nInversions_ += mol->getNInversions();
173		nRigidBodies_ += mol->getNRigidBodies();
174		nIntegrableObjects_ += mol->getNIntegrableObjects();
175		nCutoffGroups_ += mol->getNCutoffGroups();
176		nConstraints_ += mol->getNConstraintPairs();
177	<
178	<	addExcludePairs(mol);
179	<
177	>
178	>	addInteractionPairs(mol);
179	>
180		return true;
181		} else {
182		return false;
183		}
184		}
185	<
185	>
186		bool SimInfo::removeMolecule(Molecule* mol) {
187		MoleculeIterator i;
188		i = molecules_.find(mol->getGlobalIndex());
#	Line 202 | Line 195 | namespace oopse {
195		nBonds_ -= mol->getNBonds();
196		nBends_ -= mol->getNBends();
197		nTorsions_ -= mol->getNTorsions();
198	+	nInversions_ -= mol->getNInversions();
199		nRigidBodies_ -= mol->getNRigidBodies();
200		nIntegrableObjects_ -= mol->getNIntegrableObjects();
201		nCutoffGroups_ -= mol->getNCutoffGroups();
202		nConstraints_ -= mol->getNConstraintPairs();
203
204	<	removeExcludePairs(mol);
204	>	removeInteractionPairs(mol);
205		molecules_.erase(mol->getGlobalIndex());
206
207		delete mol;
#	Line 216 | Line 210 | namespace oopse {
210		} else {
211		return false;
212		}
219	–
220	–
213		}
214
215
#	Line 233 | Line 225 | namespace oopse {
225
226
227		void SimInfo::calcNdf() {
228	<	int ndf_local;
228	>	int ndf_local, nfq_local;
229		MoleculeIterator i;
230	<	std::vector<StuntDouble*>::iterator j;
230	>	vector<StuntDouble*>::iterator j;
231	>	vector<Atom*>::iterator k;
232	>
233		Molecule* mol;
234		StuntDouble* integrableObject;
235	+	Atom* atom;
236
237		ndf_local = 0;
238	+	nfq_local = 0;
239
240		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
241		for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
#	Line 254 | Line 250 | namespace oopse {
250		ndf_local += 3;
251		}
252		}
253	<
254	<	}//end for (integrableObject)
255	<	}// end for (mol)
253	>	}
254	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
255	>	atom = mol->nextFluctuatingCharge(k)) {
256	>	if (atom->isFluctuatingCharge()) {
257	>	nfq_local++;
258	>	}
259	>	}
260	>	}
261
262	+	ndfLocal_ = ndf_local;
263	+
264		// n_constraints is local, so subtract them on each processor
265		ndf_local -= nConstraints_;
266
267		#ifdef IS_MPI
268		MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
269	+	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
270		#else
271		ndf_ = ndf_local;
272	+	nGlobalFluctuatingCharges_ = nfq_local;
273		#endif
274
275		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 273 | Line 278 | namespace oopse {
278
279		}
280
281	+	int SimInfo::getFdf() {
282	+	#ifdef IS_MPI
283	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
284	+	#else
285	+	fdf_ = fdf_local;
286	+	#endif
287	+	return fdf_;
288	+	}
289	+
290	+	unsigned int SimInfo::getNLocalCutoffGroups(){
291	+	int nLocalCutoffAtoms = 0;
292	+	Molecule* mol;
293	+	MoleculeIterator mi;
294	+	CutoffGroup* cg;
295	+	Molecule::CutoffGroupIterator ci;
296	+
297	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
298	+
299	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
300	+	cg = mol->nextCutoffGroup(ci)) {
301	+	nLocalCutoffAtoms += cg->getNumAtom();
302	+
303	+	}
304	+	}
305	+
306	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
307	+	}
308	+
309		void SimInfo::calcNdfRaw() {
310		int ndfRaw_local;
311
312		MoleculeIterator i;
313	<	std::vector<StuntDouble*>::iterator j;
313	>	vector<StuntDouble*>::iterator j;
314		Molecule* mol;
315		StuntDouble* integrableObject;
316
#	Line 324 | Line 357 | namespace oopse {
357
358		}
359
360	<	void SimInfo::addExcludePairs(Molecule* mol) {
361	<	std::vector<Bond*>::iterator bondIter;
362	<	std::vector<Bend*>::iterator bendIter;
363	<	std::vector<Torsion*>::iterator torsionIter;
360	>	void SimInfo::addInteractionPairs(Molecule* mol) {
361	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
362	>	vector<Bond*>::iterator bondIter;
363	>	vector<Bend*>::iterator bendIter;
364	>	vector<Torsion*>::iterator torsionIter;
365	>	vector<Inversion*>::iterator inversionIter;
366		Bond* bond;
367		Bend* bend;
368		Torsion* torsion;
369	+	Inversion* inversion;
370		int a;
371		int b;
372		int c;
373		int d;
374	+
375	+	// atomGroups can be used to add special interaction maps between
376	+	// groups of atoms that are in two separate rigid bodies.
377	+	// However, most site-site interactions between two rigid bodies
378	+	// are probably not special, just the ones between the physically
379	+	// bonded atoms.  Interactions *within* a single rigid body should
380	+	// always be excluded.  These are done at the bottom of this
381	+	// function.
382	+
383	+	map<int, set<int> > atomGroups;
384	+	Molecule::RigidBodyIterator rbIter;
385	+	RigidBody* rb;
386	+	Molecule::IntegrableObjectIterator ii;
387	+	StuntDouble* integrableObject;
388
389	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
389	>	for (integrableObject = mol->beginIntegrableObject(ii);
390	>	integrableObject != NULL;
391	>	integrableObject = mol->nextIntegrableObject(ii)) {
392	>
393	>	if (integrableObject->isRigidBody()) {
394	>	rb = static_cast<RigidBody*>(integrableObject);
395	>	vector<Atom*> atoms = rb->getAtoms();
396	>	set<int> rigidAtoms;
397	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
398	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
399	>	}
400	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
401	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
402	>	}
403	>	} else {
404	>	set<int> oneAtomSet;
405	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
406	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
407	>	}
408	>	}
409	>
410	>	for (bond= mol->beginBond(bondIter); bond != NULL;
411	>	bond = mol->nextBond(bondIter)) {
412	>
413		a = bond->getAtomA()->getGlobalIndex();
414	<	b = bond->getAtomB()->getGlobalIndex();
415	<	exclude_.addPair(a, b);
414	>	b = bond->getAtomB()->getGlobalIndex();
415	>
416	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
417	>	oneTwoInteractions_.addPair(a, b);
418	>	} else {
419	>	excludedInteractions_.addPair(a, b);
420	>	}
421		}
422
423	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
423	>	for (bend= mol->beginBend(bendIter); bend != NULL;
424	>	bend = mol->nextBend(bendIter)) {
425	>
426		a = bend->getAtomA()->getGlobalIndex();
427		b = bend->getAtomB()->getGlobalIndex();
428		c = bend->getAtomC()->getGlobalIndex();
429	+
430	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
431	+	oneTwoInteractions_.addPair(a, b);
432	+	oneTwoInteractions_.addPair(b, c);
433	+	} else {
434	+	excludedInteractions_.addPair(a, b);
435	+	excludedInteractions_.addPair(b, c);
436	+	}
437
438	<	exclude_.addPair(a, b);
439	<	exclude_.addPair(a, c);
440	<	exclude_.addPair(b, c);
438	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
439	>	oneThreeInteractions_.addPair(a, c);
440	>	} else {
441	>	excludedInteractions_.addPair(a, c);
442	>	}
443		}
444
445	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
445	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
446	>	torsion = mol->nextTorsion(torsionIter)) {
447	>
448		a = torsion->getAtomA()->getGlobalIndex();
449		b = torsion->getAtomB()->getGlobalIndex();
450		c = torsion->getAtomC()->getGlobalIndex();
451	<	d = torsion->getAtomD()->getGlobalIndex();
451	>	d = torsion->getAtomD()->getGlobalIndex();
452
453	<	exclude_.addPair(a, b);
454	<	exclude_.addPair(a, c);
455	<	exclude_.addPair(a, d);
456	<	exclude_.addPair(b, c);
457	<	exclude_.addPair(b, d);
458	<	exclude_.addPair(c, d);
453	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
454	>	oneTwoInteractions_.addPair(a, b);
455	>	oneTwoInteractions_.addPair(b, c);
456	>	oneTwoInteractions_.addPair(c, d);
457	>	} else {
458	>	excludedInteractions_.addPair(a, b);
459	>	excludedInteractions_.addPair(b, c);
460	>	excludedInteractions_.addPair(c, d);
461	>	}
462	>
463	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
464	>	oneThreeInteractions_.addPair(a, c);
465	>	oneThreeInteractions_.addPair(b, d);
466	>	} else {
467	>	excludedInteractions_.addPair(a, c);
468	>	excludedInteractions_.addPair(b, d);
469	>	}
470	>
471	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
472	>	oneFourInteractions_.addPair(a, d);
473	>	} else {
474	>	excludedInteractions_.addPair(a, d);
475	>	}
476		}
477
478	<	Molecule::RigidBodyIterator rbIter;
479	<	RigidBody* rb;
480	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
481	<	std::vector<Atom*> atoms = rb->getAtoms();
482	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
483	<	for (int j = i + 1; j < atoms.size(); ++j) {
478	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
479	>	inversion = mol->nextInversion(inversionIter)) {
480	>
481	>	a = inversion->getAtomA()->getGlobalIndex();
482	>	b = inversion->getAtomB()->getGlobalIndex();
483	>	c = inversion->getAtomC()->getGlobalIndex();
484	>	d = inversion->getAtomD()->getGlobalIndex();
485	>
486	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
487	>	oneTwoInteractions_.addPair(a, b);
488	>	oneTwoInteractions_.addPair(a, c);
489	>	oneTwoInteractions_.addPair(a, d);
490	>	} else {
491	>	excludedInteractions_.addPair(a, b);
492	>	excludedInteractions_.addPair(a, c);
493	>	excludedInteractions_.addPair(a, d);
494	>	}
495	>
496	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
497	>	oneThreeInteractions_.addPair(b, c);
498	>	oneThreeInteractions_.addPair(b, d);
499	>	oneThreeInteractions_.addPair(c, d);
500	>	} else {
501	>	excludedInteractions_.addPair(b, c);
502	>	excludedInteractions_.addPair(b, d);
503	>	excludedInteractions_.addPair(c, d);
504	>	}
505	>	}
506	>
507	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
508	>	rb = mol->nextRigidBody(rbIter)) {
509	>	vector<Atom*> atoms = rb->getAtoms();
510	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
511	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
512		a = atoms[i]->getGlobalIndex();
513		b = atoms[j]->getGlobalIndex();
514	<	exclude_.addPair(a, b);
514	>	excludedInteractions_.addPair(a, b);
515		}
516		}
517		}
518
519		}
520
521	<	void SimInfo::removeExcludePairs(Molecule* mol) {
522	<	std::vector<Bond*>::iterator bondIter;
523	<	std::vector<Bend*>::iterator bendIter;
524	<	std::vector<Torsion*>::iterator torsionIter;
521	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
522	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
523	>	vector<Bond*>::iterator bondIter;
524	>	vector<Bend*>::iterator bendIter;
525	>	vector<Torsion*>::iterator torsionIter;
526	>	vector<Inversion*>::iterator inversionIter;
527		Bond* bond;
528		Bend* bend;
529		Torsion* torsion;
530	+	Inversion* inversion;
531		int a;
532		int b;
533		int c;
534		int d;
535	+
536	+	map<int, set<int> > atomGroups;
537	+	Molecule::RigidBodyIterator rbIter;
538	+	RigidBody* rb;
539	+	Molecule::IntegrableObjectIterator ii;
540	+	StuntDouble* integrableObject;
541
542	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
542	>	for (integrableObject = mol->beginIntegrableObject(ii);
543	>	integrableObject != NULL;
544	>	integrableObject = mol->nextIntegrableObject(ii)) {
545	>
546	>	if (integrableObject->isRigidBody()) {
547	>	rb = static_cast<RigidBody*>(integrableObject);
548	>	vector<Atom*> atoms = rb->getAtoms();
549	>	set<int> rigidAtoms;
550	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
551	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
552	>	}
553	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
554	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
555	>	}
556	>	} else {
557	>	set<int> oneAtomSet;
558	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
559	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
560	>	}
561	>	}
562	>
563	>	for (bond= mol->beginBond(bondIter); bond != NULL;
564	>	bond = mol->nextBond(bondIter)) {
565	>
566		a = bond->getAtomA()->getGlobalIndex();
567	<	b = bond->getAtomB()->getGlobalIndex();
568	<	exclude_.removePair(a, b);
567	>	b = bond->getAtomB()->getGlobalIndex();
568	>
569	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
570	>	oneTwoInteractions_.removePair(a, b);
571	>	} else {
572	>	excludedInteractions_.removePair(a, b);
573	>	}
574		}
575
576	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
576	>	for (bend= mol->beginBend(bendIter); bend != NULL;
577	>	bend = mol->nextBend(bendIter)) {
578	>
579		a = bend->getAtomA()->getGlobalIndex();
580		b = bend->getAtomB()->getGlobalIndex();
581		c = bend->getAtomC()->getGlobalIndex();
582	+
583	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
584	+	oneTwoInteractions_.removePair(a, b);
585	+	oneTwoInteractions_.removePair(b, c);
586	+	} else {
587	+	excludedInteractions_.removePair(a, b);
588	+	excludedInteractions_.removePair(b, c);
589	+	}
590
591	<	exclude_.removePair(a, b);
592	<	exclude_.removePair(a, c);
593	<	exclude_.removePair(b, c);
591	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
592	>	oneThreeInteractions_.removePair(a, c);
593	>	} else {
594	>	excludedInteractions_.removePair(a, c);
595	>	}
596		}
597
598	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
598	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
599	>	torsion = mol->nextTorsion(torsionIter)) {
600	>
601		a = torsion->getAtomA()->getGlobalIndex();
602		b = torsion->getAtomB()->getGlobalIndex();
603		c = torsion->getAtomC()->getGlobalIndex();
604	<	d = torsion->getAtomD()->getGlobalIndex();
604	>	d = torsion->getAtomD()->getGlobalIndex();
605	>
606	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
607	>	oneTwoInteractions_.removePair(a, b);
608	>	oneTwoInteractions_.removePair(b, c);
609	>	oneTwoInteractions_.removePair(c, d);
610	>	} else {
611	>	excludedInteractions_.removePair(a, b);
612	>	excludedInteractions_.removePair(b, c);
613	>	excludedInteractions_.removePair(c, d);
614	>	}
615
616	<	exclude_.removePair(a, b);
617	<	exclude_.removePair(a, c);
618	<	exclude_.removePair(a, d);
619	<	exclude_.removePair(b, c);
620	<	exclude_.removePair(b, d);
621	<	exclude_.removePair(c, d);
616	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
617	>	oneThreeInteractions_.removePair(a, c);
618	>	oneThreeInteractions_.removePair(b, d);
619	>	} else {
620	>	excludedInteractions_.removePair(a, c);
621	>	excludedInteractions_.removePair(b, d);
622	>	}
623	>
624	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
625	>	oneFourInteractions_.removePair(a, d);
626	>	} else {
627	>	excludedInteractions_.removePair(a, d);
628	>	}
629		}
630
631	<	Molecule::RigidBodyIterator rbIter;
632	<	RigidBody* rb;
633	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
634	<	std::vector<Atom*> atoms = rb->getAtoms();
635	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
636	<	for (int j = i + 1; j < atoms.size(); ++j) {
631	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
632	>	inversion = mol->nextInversion(inversionIter)) {
633	>
634	>	a = inversion->getAtomA()->getGlobalIndex();
635	>	b = inversion->getAtomB()->getGlobalIndex();
636	>	c = inversion->getAtomC()->getGlobalIndex();
637	>	d = inversion->getAtomD()->getGlobalIndex();
638	>
639	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
640	>	oneTwoInteractions_.removePair(a, b);
641	>	oneTwoInteractions_.removePair(a, c);
642	>	oneTwoInteractions_.removePair(a, d);
643	>	} else {
644	>	excludedInteractions_.removePair(a, b);
645	>	excludedInteractions_.removePair(a, c);
646	>	excludedInteractions_.removePair(a, d);
647	>	}
648	>
649	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
650	>	oneThreeInteractions_.removePair(b, c);
651	>	oneThreeInteractions_.removePair(b, d);
652	>	oneThreeInteractions_.removePair(c, d);
653	>	} else {
654	>	excludedInteractions_.removePair(b, c);
655	>	excludedInteractions_.removePair(b, d);
656	>	excludedInteractions_.removePair(c, d);
657	>	}
658	>	}
659	>
660	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
661	>	rb = mol->nextRigidBody(rbIter)) {
662	>	vector<Atom*> atoms = rb->getAtoms();
663	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
664	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
665		a = atoms[i]->getGlobalIndex();
666		b = atoms[j]->getGlobalIndex();
667	<	exclude_.removePair(a, b);
667	>	excludedInteractions_.removePair(a, b);
668		}
669		}
670		}
671	<
671	>
672		}
673	<
674	<
673	>
674	>
675		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
676		int curStampId;
677	<
677	>
678		//index from 0
679		curStampId = moleculeStamps_.size();
680
#	Line 449 | Line 682 | namespace oopse {
682		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
683		}
684
452	–	void SimInfo::update() {
685
686	<	setupSimType();
687	<
688	<	#ifdef IS_MPI
689	<	setupFortranParallel();
690	<	#endif
691	<
692	<	setupFortranSim();
693	<
694	<	//setup fortran force field
463	<	/** @deprecate */
464	<	int isError = 0;
465	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
466	<	if(isError){
467	<	sprintf( painCave.errMsg,
468	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
469	<	painCave.isFatal = 1;
470	<	simError();
471	<	}
472	<
473	<
474	<	setupCutoff();
475	<
686	>	/**
687	>	* update
688	>	*
689	>	*  Performs the global checks and variable settings after the
690	>	*  objects have been created.
691	>	*
692	>	*/
693	>	void SimInfo::update() {
694	>	setupSimVariables();
695		calcNdf();
696		calcNdfRaw();
697		calcNdfTrans();
479	–
480	–	fortranInitialized_ = true;
698		}
699	<
700	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
699	>
700	>	/**
701	>	* getSimulatedAtomTypes
702	>	*
703	>	* Returns an STL set of AtomType* that are actually present in this
704	>	* simulation.  Must query all processors to assemble this information.
705	>	*
706	>	*/
707	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
708		SimInfo::MoleculeIterator mi;
709		Molecule* mol;
710		Molecule::AtomIterator ai;
711		Atom* atom;
712	<	std::set<AtomType*> atomTypes;
713	<
712	>	set<AtomType*> atomTypes;
713	>
714		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
715	<
716	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
715	>	for(atom = mol->beginAtom(ai); atom != NULL;
716	>	atom = mol->nextAtom(ai)) {
717		atomTypes.insert(atom->getAtomType());
718	<	}
719	<
718	>	}
719	>	}
720	>
721	>	#ifdef IS_MPI
722	>
723	>	// loop over the found atom types on this processor, and add their
724	>	// numerical idents to a vector:
725	>
726	>	vector<int> foundTypes;
727	>	set<AtomType*>::iterator i;
728	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
729	>	foundTypes.push_back( (*i)->getIdent() );
730	>
731	>	// count_local holds the number of found types on this processor
732	>	int count_local = foundTypes.size();
733	>
734	>	int nproc = MPI::COMM_WORLD.Get_size();
735	>
736	>	// we need arrays to hold the counts and displacement vectors for
737	>	// all processors
738	>	vector<int> counts(nproc, 0);
739	>	vector<int> disps(nproc, 0);
740	>
741	>	// fill the counts array
742	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
743	>	1, MPI::INT);
744	>
745	>	// use the processor counts to compute the displacement array
746	>	disps[0] = 0;
747	>	int totalCount = counts[0];
748	>	for (int iproc = 1; iproc < nproc; iproc++) {
749	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
750	>	totalCount += counts[iproc];
751		}
752
753	+	// we need a (possibly redundant) set of all found types:
754	+	vector<int> ftGlobal(totalCount);
755	+
756	+	// now spray out the foundTypes to all the other processors:
757	+	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
758	+	&ftGlobal[0], &counts[0], &disps[0],
759	+	MPI::INT);
760	+
761	+	vector<int>::iterator j;
762	+
763	+	// foundIdents is a stl set, so inserting an already found ident
764	+	// will have no effect.
765	+	set<int> foundIdents;
766	+
767	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
768	+	foundIdents.insert((*j));
769	+
770	+	// now iterate over the foundIdents and get the actual atom types
771	+	// that correspond to these:
772	+	set<int>::iterator it;
773	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
774	+	atomTypes.insert( forceField_->getAtomType((*it)) );
775	+
776	+	#endif
777	+
778		return atomTypes;
779		}
780
781	<	void SimInfo::setupSimType() {
782	<	std::set<AtomType*>::iterator i;
783	<	std::set<AtomType*> atomTypes;
784	<	atomTypes = getUniqueAtomTypes();
781	>	void SimInfo::setupSimVariables() {
782	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
783	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
784	>	calcBoxDipole_ = false;
785	>	if ( simParams_->haveAccumulateBoxDipole() )
786	>	if ( simParams_->getAccumulateBoxDipole() ) {
787	>	calcBoxDipole_ = true;
788	>	}
789
790	<	int useLennardJones = 0;
791	<	int useElectrostatic = 0;
792	<	int useEAM = 0;
793	<	int useCharge = 0;
794	<	int useDirectional = 0;
795	<	int useDipole = 0;
796	<	int useGayBerne = 0;
513	<	int useSticky = 0;
514	<	int useStickyPower = 0;
515	<	int useShape = 0;
516	<	int useFLARB = 0; //it is not in AtomType yet
517	<	int useDirectionalAtom = 0;
518	<	int useElectrostatics = 0;
519	<	//usePBC and useRF are from simParams
520	<	int usePBC = simParams_->getPBC();
521	<	int useRF = simParams_->getUseRF();
522	<
790	>	set<AtomType*>::iterator i;
791	>	set<AtomType*> atomTypes;
792	>	atomTypes = getSimulatedAtomTypes();
793	>	bool usesElectrostatic = false;
794	>	bool usesMetallic = false;
795	>	bool usesDirectional = false;
796	>	bool usesFluctuatingCharges =  false;
797		//loop over all of the atom types
798		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
799	<	useLennardJones |= (*i)->isLennardJones();
800	<	useElectrostatic |= (*i)->isElectrostatic();
801	<	useEAM |= (*i)->isEAM();
802	<	useCharge |= (*i)->isCharge();
529	<	useDirectional |= (*i)->isDirectional();
530	<	useDipole |= (*i)->isDipole();
531	<	useGayBerne |= (*i)->isGayBerne();
532	<	useSticky |= (*i)->isSticky();
533	<	useStickyPower |= (*i)->isStickyPower();
534	<	useShape |= (*i)->isShape();
799	>	usesElectrostatic |= (*i)->isElectrostatic();
800	>	usesMetallic |= (*i)->isMetal();
801	>	usesDirectional |= (*i)->isDirectional();
802	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
803		}
804
805	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
806	<	useDirectionalAtom = 1;
807	<	}
805	>	#ifdef IS_MPI
806	>	bool temp;
807	>	temp = usesDirectional;
808	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
809	>	MPI::LOR);
810	>
811	>	temp = usesMetallic;
812	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
813	>	MPI::LOR);
814	>
815	>	temp = usesElectrostatic;
816	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
817	>	MPI::LOR);
818
819	<	if (useCharge || useDipole) {
820	<	useElectrostatics = 1;
821	<	}
819	>	temp = usesFluctuatingCharges;
820	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
821	>	MPI::LOR);
822	>	#else
823
824	<	#ifdef IS_MPI
825	<	int temp;
824	>	usesDirectionalAtoms_ = usesDirectional;
825	>	usesMetallicAtoms_ = usesMetallic;
826	>	usesElectrostaticAtoms_ = usesElectrostatic;
827	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
828
829	<	temp = usePBC;
549	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
550	<
551	<	temp = useDirectionalAtom;
552	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
553	<
554	<	temp = useLennardJones;
555	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
556	<
557	<	temp = useElectrostatics;
558	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
559	<
560	<	temp = useCharge;
561	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
562	<
563	<	temp = useDipole;
564	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
565	<
566	<	temp = useSticky;
567	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
568	<
569	<	temp = useStickyPower;
570	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
829	>	#endif
830
831	<	temp = useGayBerne;
832	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
831	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
832	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
833	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
834	>	}
835
575	–	temp = useEAM;
576	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
836
837	<	temp = useShape;
838	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
837	>	vector<int> SimInfo::getGlobalAtomIndices() {
838	>	SimInfo::MoleculeIterator mi;
839	>	Molecule* mol;
840	>	Molecule::AtomIterator ai;
841	>	Atom* atom;
842
843	<	temp = useFLARB;
582	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
583	<
584	<	temp = useRF;
585	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
843	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
844
845	<	#endif
845	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
846	>
847	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
848	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
849	>	}
850	>	}
851	>	return GlobalAtomIndices;
852	>	}
853
589	–	fInfo_.SIM_uses_PBC = usePBC;
590	–	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
591	–	fInfo_.SIM_uses_LennardJones = useLennardJones;
592	–	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
593	–	fInfo_.SIM_uses_Charges = useCharge;
594	–	fInfo_.SIM_uses_Dipoles = useDipole;
595	–	fInfo_.SIM_uses_Sticky = useSticky;
596	–	fInfo_.SIM_uses_StickyPower = useStickyPower;
597	–	fInfo_.SIM_uses_GayBerne = useGayBerne;
598	–	fInfo_.SIM_uses_EAM = useEAM;
599	–	fInfo_.SIM_uses_Shapes = useShape;
600	–	fInfo_.SIM_uses_FLARB = useFLARB;
601	–	fInfo_.SIM_uses_RF = useRF;
854
855	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
855	>	vector<int> SimInfo::getGlobalGroupIndices() {
856	>	SimInfo::MoleculeIterator mi;
857	>	Molecule* mol;
858	>	Molecule::CutoffGroupIterator ci;
859	>	CutoffGroup* cg;
860
861	<	if (simParams_->haveDielectric()) {
862	<	fInfo_.dielect = simParams_->getDielectric();
863	<	} else {
864	<	sprintf(painCave.errMsg,
865	<	"SimSetup Error: No Dielectric constant was set.\n"
866	<	"\tYou are trying to use Reaction Field without"
867	<	"\tsetting a dielectric constant!\n");
868	<	painCave.isFatal = 1;
869	<	simError();
870	<	}
615	<
616	<	} else {
617	<	fInfo_.dielect = 0.0;
861	>	vector<int> GlobalGroupIndices;
862	>
863	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
864	>
865	>	//local index of cutoff group is trivial, it only depends on the
866	>	//order of travesing
867	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
868	>	cg = mol->nextCutoffGroup(ci)) {
869	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
870	>	}
871		}
872	<
872	>	return GlobalGroupIndices;
873		}
874
622	–	void SimInfo::setupFortranSim() {
623	–	int isError;
624	–	int nExclude;
625	–	std::vector<int> fortranGlobalGroupMembership;
626	–
627	–	nExclude = exclude_.getSize();
628	–	isError = 0;
875
876	<	//globalGroupMembership_ is filled by SimCreator
877	<	for (int i = 0; i < nGlobalAtoms_; i++) {
632	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
633	<	}
876	>	void SimInfo::prepareTopology() {
877	>	int nExclude, nOneTwo, nOneThree, nOneFour;
878
879		//calculate mass ratio of cutoff group
636	–	std::vector<double> mfact;
880		SimInfo::MoleculeIterator mi;
881		Molecule* mol;
882		Molecule::CutoffGroupIterator ci;
883		CutoffGroup* cg;
884		Molecule::AtomIterator ai;
885		Atom* atom;
886	<	double totalMass;
886	>	RealType totalMass;
887
888	<	//to avoid memory reallocation, reserve enough space for mfact
889	<	mfact.reserve(getNCutoffGroups());
888	>	/**
889	>	* The mass factor is the relative mass of an atom to the total
890	>	* mass of the cutoff group it belongs to.  By default, all atoms
891	>	* are their own cutoff groups, and therefore have mass factors of
892	>	* 1.  We need some special handling for massless atoms, which
893	>	* will be treated as carrying the entire mass of the cutoff
894	>	* group.
895	>	*/
896	>	massFactors_.clear();
897	>	massFactors_.resize(getNAtoms(), 1.0);
898
899		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
900	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
900	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
901	>	cg = mol->nextCutoffGroup(ci)) {
902
903		totalMass = cg->getMass();
904		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
905	<	mfact.push_back(atom->getMass()/totalMass);
905	>	// Check for massless groups - set mfact to 1 if true
906	>	if (totalMass != 0)
907	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
908	>	else
909	>	massFactors_[atom->getLocalIndex()] = 1.0;
910		}
655	–
911		}
912		}
913
914	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
660	<	std::vector<int> identArray;
914	>	// Build the identArray_
915
916	<	//to avoid memory reallocation, reserve enough space identArray
917	<	identArray.reserve(getNAtoms());
664	<
916	>	identArray_.clear();
917	>	identArray_.reserve(getNAtoms());
918		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
919		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
920	<	identArray.push_back(atom->getIdent());
920	>	identArray_.push_back(atom->getIdent());
921		}
922		}
670	–
671	–	//fill molMembershipArray
672	–	//molMembershipArray is filled by SimCreator
673	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
674	–	for (int i = 0; i < nGlobalAtoms_; i++) {
675	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
676	–	}
923
924	<	//setup fortran simulation
679	<	int nGlobalExcludes = 0;
680	<	int* globalExcludes = NULL;
681	<	int* excludeList = exclude_.getExcludeList();
682	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
683	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
684	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
924	>	//scan topology
925
926	<	if( isError ){
927	<
928	<	sprintf( painCave.errMsg,
929	<	"There was an error setting the simulation information in fortran.\n" );
690	<	painCave.isFatal = 1;
691	<	painCave.severity = OOPSE_ERROR;
692	<	simError();
693	<	}
694	<
695	<	#ifdef IS_MPI
696	<	sprintf( checkPointMsg,
697	<	"succesfully sent the simulation information to fortran.\n");
698	<	MPIcheckPoint();
699	<	#endif // is_mpi
700	<	}
701	<
702	<
703	<	#ifdef IS_MPI
704	<	void SimInfo::setupFortranParallel() {
705	<
706	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
707	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
708	<	std::vector<int> localToGlobalCutoffGroupIndex;
709	<	SimInfo::MoleculeIterator mi;
710	<	Molecule::AtomIterator ai;
711	<	Molecule::CutoffGroupIterator ci;
712	<	Molecule* mol;
713	<	Atom* atom;
714	<	CutoffGroup* cg;
715	<	mpiSimData parallelData;
716	<	int isError;
717	<
718	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
719	<
720	<	//local index(index in DataStorge) of atom is important
721	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
722	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
723	<	}
724	<
725	<	//local index of cutoff group is trivial, it only depends on the order of travesing
726	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
727	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
728	<	}
729	<
730	<	}
731	<
732	<	//fill up mpiSimData struct
733	<	parallelData.nMolGlobal = getNGlobalMolecules();
734	<	parallelData.nMolLocal = getNMolecules();
735	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
736	<	parallelData.nAtomsLocal = getNAtoms();
737	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
738	<	parallelData.nGroupsLocal = getNCutoffGroups();
739	<	parallelData.myNode = worldRank;
740	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
741	<
742	<	//pass mpiSimData struct and index arrays to fortran
743	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
744	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
745	<	&localToGlobalCutoffGroupIndex[0], &isError);
746	<
747	<	if (isError) {
748	<	sprintf(painCave.errMsg,
749	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
750	<	painCave.isFatal = 1;
751	<	simError();
752	<	}
753	<
754	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
755	<	MPIcheckPoint();
756	<
757	<
758	<	}
759	<
760	<	#endif
761	<
762	<	double SimInfo::calcMaxCutoffRadius() {
926	>	nExclude = excludedInteractions_.getSize();
927	>	nOneTwo = oneTwoInteractions_.getSize();
928	>	nOneThree = oneThreeInteractions_.getSize();
929	>	nOneFour = oneFourInteractions_.getSize();
930
931	+	int* excludeList = excludedInteractions_.getPairList();
932	+	int* oneTwoList = oneTwoInteractions_.getPairList();
933	+	int* oneThreeList = oneThreeInteractions_.getPairList();
934	+	int* oneFourList = oneFourInteractions_.getPairList();
935
936	<	std::set<AtomType*> atomTypes;
766	<	std::set<AtomType*>::iterator i;
767	<	std::vector<double> cutoffRadius;
768	<
769	<	//get the unique atom types
770	<	atomTypes = getUniqueAtomTypes();
771	<
772	<	//query the max cutoff radius among these atom types
773	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
774	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
775	<	}
776	<
777	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
778	<	#ifdef IS_MPI
779	<	//pick the max cutoff radius among the processors
780	<	#endif
781	<
782	<	return maxCutoffRadius;
936	>	topologyDone_ = true;
937		}
938
785	–	void SimInfo::getCutoff(double& rcut, double& rsw) {
786	–
787	–	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
788	–
789	–	if (!simParams_->haveRcut()){
790	–	sprintf(painCave.errMsg,
791	–	"SimCreator Warning: No value was set for the cutoffRadius.\n"
792	–	"\tOOPSE will use a default value of 15.0 angstroms"
793	–	"\tfor the cutoffRadius.\n");
794	–	painCave.isFatal = 0;
795	–	simError();
796	–	rcut = 15.0;
797	–	} else{
798	–	rcut = simParams_->getRcut();
799	–	}
800	–
801	–	if (!simParams_->haveRsw()){
802	–	sprintf(painCave.errMsg,
803	–	"SimCreator Warning: No value was set for switchingRadius.\n"
804	–	"\tOOPSE will use a default value of\n"
805	–	"\t0.95 * cutoffRadius for the switchingRadius\n");
806	–	painCave.isFatal = 0;
807	–	simError();
808	–	rsw = 0.95 * rcut;
809	–	} else{
810	–	rsw = simParams_->getRsw();
811	–	}
812	–
813	–	} else {
814	–	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
815	–	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
816	–
817	–	if (simParams_->haveRcut()) {
818	–	rcut = simParams_->getRcut();
819	–	} else {
820	–	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
821	–	rcut = calcMaxCutoffRadius();
822	–	}
823	–
824	–	if (simParams_->haveRsw()) {
825	–	rsw  = simParams_->getRsw();
826	–	} else {
827	–	rsw = rcut;
828	–	}
829	–
830	–	}
831	–	}
832	–
833	–	void SimInfo::setupCutoff() {
834	–	getCutoff(rcut_, rsw_);
835	–	double rnblist = rcut_ + 1; // skin of neighbor list
836	–
837	–	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
838	–	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
839	–	}
840	–
939		void SimInfo::addProperty(GenericData* genData) {
940		properties_.addProperty(genData);
941		}
942
943	<	void SimInfo::removeProperty(const std::string& propName) {
943	>	void SimInfo::removeProperty(const string& propName) {
944		properties_.removeProperty(propName);
945		}
946
#	Line 850 | Line 948 | namespace oopse {
948		properties_.clearProperties();
949		}
950
951	<	std::vector<std::string> SimInfo::getPropertyNames() {
951	>	vector<string> SimInfo::getPropertyNames() {
952		return properties_.getPropertyNames();
953		}
954
955	<	std::vector<GenericData*> SimInfo::getProperties() {
955	>	vector<GenericData*> SimInfo::getProperties() {
956		return properties_.getProperties();
957		}
958
959	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
959	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
960		return properties_.getPropertyByName(propName);
961		}
962
#	Line 872 | Line 970 | namespace oopse {
970		Molecule* mol;
971		RigidBody* rb;
972		Atom* atom;
973	+	CutoffGroup* cg;
974		SimInfo::MoleculeIterator mi;
975		Molecule::RigidBodyIterator rbIter;
976	<	Molecule::AtomIterator atomIter;;
976	>	Molecule::AtomIterator atomIter;
977	>	Molecule::CutoffGroupIterator cgIter;
978
979		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
980
#	Line 885 | Line 985 | namespace oopse {
985		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
986		rb->setSnapshotManager(sman_);
987		}
988	+
989	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
990	+	cg->setSnapshotManager(sman_);
991	+	}
992		}
993
994		}
995
892	–	Vector3d SimInfo::getComVel(){
893	–	SimInfo::MoleculeIterator i;
894	–	Molecule* mol;
996
997	<	Vector3d comVel(0.0);
897	<	double totalMass = 0.0;
898	<
899	<
900	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
901	<	double mass = mol->getMass();
902	<	totalMass += mass;
903	<	comVel += mass * mol->getComVel();
904	<	}
997	>	ostream& operator <<(ostream& o, SimInfo& info) {
998
906	–	#ifdef IS_MPI
907	–	double tmpMass = totalMass;
908	–	Vector3d tmpComVel(comVel);
909	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
910	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
911	–	#endif
912	–
913	–	comVel /= totalMass;
914	–
915	–	return comVel;
916	–	}
917	–
918	–	Vector3d SimInfo::getCom(){
919	–	SimInfo::MoleculeIterator i;
920	–	Molecule* mol;
921	–
922	–	Vector3d com(0.0);
923	–	double totalMass = 0.0;
924	–
925	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
926	–	double mass = mol->getMass();
927	–	totalMass += mass;
928	–	com += mass * mol->getCom();
929	–	}
930	–
931	–	#ifdef IS_MPI
932	–	double tmpMass = totalMass;
933	–	Vector3d tmpCom(com);
934	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
935	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
936	–	#endif
937	–
938	–	com /= totalMass;
939	–
940	–	return com;
941	–
942	–	}
943	–
944	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
945	–
999		return o;
1000		}
1001
1002	<
1003	<	/*
1004	<	Returns center of mass and center of mass velocity in one function call.
1005	<	*/
1006	<
1007	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1008	<	SimInfo::MoleculeIterator i;
1009	<	Molecule* mol;
1010	<
1011	<
1012	<	double totalMass = 0.0;
1013	<
1002	>
1003	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1004	>	return IOIndexToIntegrableObject.at(index);
1005	>	}
1006	>
1007	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1008	>	IOIndexToIntegrableObject= v;
1009	>	}
1010	>	/*
1011	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1012	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1013	>	sdByGlobalIndex_ = v;
1014	>	}
1015
1016	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1017	<	double mass = mol->getMass();
1018	<	totalMass += mass;
1019	<	com += mass * mol->getCom();
1020	<	comVel += mass * mol->getComVel();
1021	<	}
1022	<
1016	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1017	>	//assert(index < nAtoms_ + nRigidBodies_);
1018	>	return sdByGlobalIndex_.at(index);
1019	>	}
1020	>	*/
1021	>	int SimInfo::getNGlobalConstraints() {
1022	>	int nGlobalConstraints;
1023		#ifdef IS_MPI
1024	<	double tmpMass = totalMass;
1025	<	Vector3d tmpCom(com);
1026	<	Vector3d tmpComVel(comVel);
1027	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
974	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
975	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1024	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1025	>	MPI_COMM_WORLD);
1026	>	#else
1027	>	nGlobalConstraints =  nConstraints_;
1028		#endif
1029	<
1030	<	com /= totalMass;
979	<	comVel /= totalMass;
980	<	}
981	<
982	<	/*
983	<	Return intertia tensor for entire system and angular momentum Vector.
1029	>	return nGlobalConstraints;
1030	>	}
1031
1032	+	}//end namespace OpenMD
1033
986	–	[  Ixx -Ixy  -Ixz ]
987	–	J =| -Iyx  Iyy  -Iyz |
988	–	[ -Izx -Iyz   Izz ]
989	–	*/
990	–
991	–	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
992	–
993	–
994	–	double xx = 0.0;
995	–	double yy = 0.0;
996	–	double zz = 0.0;
997	–	double xy = 0.0;
998	–	double xz = 0.0;
999	–	double yz = 0.0;
1000	–	Vector3d com(0.0);
1001	–	Vector3d comVel(0.0);
1002	–
1003	–	getComAll(com, comVel);
1004	–
1005	–	SimInfo::MoleculeIterator i;
1006	–	Molecule* mol;
1007	–
1008	–	Vector3d thisq(0.0);
1009	–	Vector3d thisv(0.0);
1010	–
1011	–	double thisMass = 0.0;
1012	–
1013	–
1014	–
1015	–
1016	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1017	–
1018	–	thisq = mol->getCom()-com;
1019	–	thisv = mol->getComVel()-comVel;
1020	–	thisMass = mol->getMass();
1021	–	// Compute moment of intertia coefficients.
1022	–	xx += thisq[0]*thisq[0]*thisMass;
1023	–	yy += thisq[1]*thisq[1]*thisMass;
1024	–	zz += thisq[2]*thisq[2]*thisMass;
1025	–
1026	–	// compute products of intertia
1027	–	xy += thisq[0]*thisq[1]*thisMass;
1028	–	xz += thisq[0]*thisq[2]*thisMass;
1029	–	yz += thisq[1]*thisq[2]*thisMass;
1030	–
1031	–	angularMomentum += cross( thisq, thisv ) * thisMass;
1032	–
1033	–	}
1034	–
1035	–
1036	–	inertiaTensor(0,0) = yy + zz;
1037	–	inertiaTensor(0,1) = -xy;
1038	–	inertiaTensor(0,2) = -xz;
1039	–	inertiaTensor(1,0) = -xy;
1040	–	inertiaTensor(1,1) = xx + zz;
1041	–	inertiaTensor(1,2) = -yz;
1042	–	inertiaTensor(2,0) = -xz;
1043	–	inertiaTensor(2,1) = -yz;
1044	–	inertiaTensor(2,2) = xx + yy;
1045	–
1046	–	#ifdef IS_MPI
1047	–	Mat3x3d tmpI(inertiaTensor);
1048	–	Vector3d tmpAngMom;
1049	–	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1050	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1051	–	#endif
1052	–
1053	–	return;
1054	–	}
1055	–
1056	–	//Returns the angular momentum of the system
1057	–	Vector3d SimInfo::getAngularMomentum(){
1058	–
1059	–	Vector3d com(0.0);
1060	–	Vector3d comVel(0.0);
1061	–	Vector3d angularMomentum(0.0);
1062	–
1063	–	getComAll(com,comVel);
1064	–
1065	–	SimInfo::MoleculeIterator i;
1066	–	Molecule* mol;
1067	–
1068	–	Vector3d thisr(0.0);
1069	–	Vector3d thisp(0.0);
1070	–
1071	–	double thisMass;
1072	–
1073	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1074	–	thisMass = mol->getMass();
1075	–	thisr = mol->getCom()-com;
1076	–	thisp = (mol->getComVel()-comVel)*thisMass;
1077	–
1078	–	angularMomentum += cross( thisr, thisp );
1079	–
1080	–	}
1081	–
1082	–	#ifdef IS_MPI
1083	–	Vector3d tmpAngMom;
1084	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1085	–	#endif
1086	–
1087	–	return angularMomentum;
1088	–	}
1089	–
1090	–
1091	–	}//end namespace oopse
1092	–

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 557 by chuckv, Tue May 31 22:31:54 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC

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