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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 665 by tim, Thu Oct 13 22:26:47 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1725 by gezelter, Sat May 26 18:13:43 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/fCutoffPolicy.h"
56	<	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
57	<	#include "UseTheForce/doForces_interface.h"
58	<	#include "UseTheForce/DarkSide/electrostatic_interface.h"
59	<	#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"
67	<	#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	<
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;
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	<
102	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
103	<
104	<	//calculate atoms in rigid bodies
105	<	int nAtomsInRigidBodies = 0;
106	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
117	<
118	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
119	<	rbStamp = molStamp->getRigidBody(j);
120	<	nAtomsInRigidBodies += rbStamp->getNMembers();
121	<	}
122	<
123	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
124	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
125	<
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
110	<	//group therefore the total number of cutoff groups in the system is
111	<	//equal to the total number of atoms minus number of atoms belong to
112	<	//cutoff group defined in meta-data file plus the number of cutoff
113	<	//groups defined in meta-data file
114	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
115	<
116	<	//every free atom (atom does not belong to rigid bodies) is an
117	<	//integrable object therefore the total number of integrable objects
118	<	//in the system is equal to the total number of atoms minus number of
119	<	//atoms belong to rigid body defined in meta-data file plus the number
120	<	//of rigid bodies defined in meta-data file
121	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
122	<	+ nGlobalRigidBodies_;
123	<
124	<	nGlobalMols_ = molStampIds_.size();
144	<
145	<	#ifdef IS_MPI
146	<	molToProcMap_.resize(nGlobalMols_);
147	<	#endif
148	<
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
158	–	delete stamps_;
154		delete sman_;
155		delete simParams_;
156		delete forceField_;
157		}
158
164	–	int SimInfo::getNGlobalConstraints() {
165	–	int nGlobalConstraints;
166	–	#ifdef IS_MPI
167	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
168	–	MPI_COMM_WORLD);
169	–	#else
170	–	nGlobalConstraints =  nConstraints_;
171	–	#endif
172	–	return nGlobalConstraints;
173	–	}
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 209 | 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 223 | Line 210 | namespace oopse {
210		} else {
211		return false;
212		}
226	–
227	–
213		}
214
215
#	Line 240 | 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 261 | 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		// n_constraints is local, so subtract them on each processor
263		ndf_local -= nConstraints_;
264
265		#ifdef IS_MPI
266		MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
267	+	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
268		#else
269		ndf_ = ndf_local;
270	+	nGlobalFluctuatingCharges_ = nfq_local;
271		#endif
272
273		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 280 | Line 276 | namespace oopse {
276
277		}
278
279	+	int SimInfo::getFdf() {
280	+	#ifdef IS_MPI
281	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
282	+	#else
283	+	fdf_ = fdf_local;
284	+	#endif
285	+	return fdf_;
286	+	}
287	+
288	+	unsigned int SimInfo::getNLocalCutoffGroups(){
289	+	int nLocalCutoffAtoms = 0;
290	+	Molecule* mol;
291	+	MoleculeIterator mi;
292	+	CutoffGroup* cg;
293	+	Molecule::CutoffGroupIterator ci;
294	+
295	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
296	+
297	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
298	+	cg = mol->nextCutoffGroup(ci)) {
299	+	nLocalCutoffAtoms += cg->getNumAtom();
300	+
301	+	}
302	+	}
303	+
304	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
305	+	}
306	+
307		void SimInfo::calcNdfRaw() {
308		int ndfRaw_local;
309
310		MoleculeIterator i;
311	<	std::vector<StuntDouble*>::iterator j;
311	>	vector<StuntDouble*>::iterator j;
312		Molecule* mol;
313		StuntDouble* integrableObject;
314
#	Line 331 | Line 355 | namespace oopse {
355
356		}
357
358	<	void SimInfo::addExcludePairs(Molecule* mol) {
359	<	std::vector<Bond*>::iterator bondIter;
360	<	std::vector<Bend*>::iterator bendIter;
361	<	std::vector<Torsion*>::iterator torsionIter;
358	>	void SimInfo::addInteractionPairs(Molecule* mol) {
359	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
360	>	vector<Bond*>::iterator bondIter;
361	>	vector<Bend*>::iterator bendIter;
362	>	vector<Torsion*>::iterator torsionIter;
363	>	vector<Inversion*>::iterator inversionIter;
364		Bond* bond;
365		Bend* bend;
366		Torsion* torsion;
367	+	Inversion* inversion;
368		int a;
369		int b;
370		int c;
371		int d;
372	+
373	+	// atomGroups can be used to add special interaction maps between
374	+	// groups of atoms that are in two separate rigid bodies.
375	+	// However, most site-site interactions between two rigid bodies
376	+	// are probably not special, just the ones between the physically
377	+	// bonded atoms.  Interactions *within* a single rigid body should
378	+	// always be excluded.  These are done at the bottom of this
379	+	// function.
380	+
381	+	map<int, set<int> > atomGroups;
382	+	Molecule::RigidBodyIterator rbIter;
383	+	RigidBody* rb;
384	+	Molecule::IntegrableObjectIterator ii;
385	+	StuntDouble* integrableObject;
386
387	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
387	>	for (integrableObject = mol->beginIntegrableObject(ii);
388	>	integrableObject != NULL;
389	>	integrableObject = mol->nextIntegrableObject(ii)) {
390	>
391	>	if (integrableObject->isRigidBody()) {
392	>	rb = static_cast<RigidBody*>(integrableObject);
393	>	vector<Atom*> atoms = rb->getAtoms();
394	>	set<int> rigidAtoms;
395	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
396	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
397	>	}
398	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
399	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
400	>	}
401	>	} else {
402	>	set<int> oneAtomSet;
403	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
404	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
405	>	}
406	>	}
407	>
408	>	for (bond= mol->beginBond(bondIter); bond != NULL;
409	>	bond = mol->nextBond(bondIter)) {
410	>
411		a = bond->getAtomA()->getGlobalIndex();
412	<	b = bond->getAtomB()->getGlobalIndex();
413	<	exclude_.addPair(a, b);
412	>	b = bond->getAtomB()->getGlobalIndex();
413	>
414	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
415	>	oneTwoInteractions_.addPair(a, b);
416	>	} else {
417	>	excludedInteractions_.addPair(a, b);
418	>	}
419		}
420
421	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
421	>	for (bend= mol->beginBend(bendIter); bend != NULL;
422	>	bend = mol->nextBend(bendIter)) {
423	>
424		a = bend->getAtomA()->getGlobalIndex();
425		b = bend->getAtomB()->getGlobalIndex();
426		c = bend->getAtomC()->getGlobalIndex();
427	+
428	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
429	+	oneTwoInteractions_.addPair(a, b);
430	+	oneTwoInteractions_.addPair(b, c);
431	+	} else {
432	+	excludedInteractions_.addPair(a, b);
433	+	excludedInteractions_.addPair(b, c);
434	+	}
435
436	<	exclude_.addPair(a, b);
437	<	exclude_.addPair(a, c);
438	<	exclude_.addPair(b, c);
436	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
437	>	oneThreeInteractions_.addPair(a, c);
438	>	} else {
439	>	excludedInteractions_.addPair(a, c);
440	>	}
441		}
442
443	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
443	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
444	>	torsion = mol->nextTorsion(torsionIter)) {
445	>
446		a = torsion->getAtomA()->getGlobalIndex();
447		b = torsion->getAtomB()->getGlobalIndex();
448		c = torsion->getAtomC()->getGlobalIndex();
449	<	d = torsion->getAtomD()->getGlobalIndex();
449	>	d = torsion->getAtomD()->getGlobalIndex();
450
451	<	exclude_.addPair(a, b);
452	<	exclude_.addPair(a, c);
453	<	exclude_.addPair(a, d);
454	<	exclude_.addPair(b, c);
455	<	exclude_.addPair(b, d);
456	<	exclude_.addPair(c, d);
451	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
452	>	oneTwoInteractions_.addPair(a, b);
453	>	oneTwoInteractions_.addPair(b, c);
454	>	oneTwoInteractions_.addPair(c, d);
455	>	} else {
456	>	excludedInteractions_.addPair(a, b);
457	>	excludedInteractions_.addPair(b, c);
458	>	excludedInteractions_.addPair(c, d);
459	>	}
460	>
461	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
462	>	oneThreeInteractions_.addPair(a, c);
463	>	oneThreeInteractions_.addPair(b, d);
464	>	} else {
465	>	excludedInteractions_.addPair(a, c);
466	>	excludedInteractions_.addPair(b, d);
467	>	}
468	>
469	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
470	>	oneFourInteractions_.addPair(a, d);
471	>	} else {
472	>	excludedInteractions_.addPair(a, d);
473	>	}
474		}
475
476	<	Molecule::RigidBodyIterator rbIter;
477	<	RigidBody* rb;
478	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
479	<	std::vector<Atom*> atoms = rb->getAtoms();
480	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
481	<	for (int j = i + 1; j < atoms.size(); ++j) {
476	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
477	>	inversion = mol->nextInversion(inversionIter)) {
478	>
479	>	a = inversion->getAtomA()->getGlobalIndex();
480	>	b = inversion->getAtomB()->getGlobalIndex();
481	>	c = inversion->getAtomC()->getGlobalIndex();
482	>	d = inversion->getAtomD()->getGlobalIndex();
483	>
484	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
485	>	oneTwoInteractions_.addPair(a, b);
486	>	oneTwoInteractions_.addPair(a, c);
487	>	oneTwoInteractions_.addPair(a, d);
488	>	} else {
489	>	excludedInteractions_.addPair(a, b);
490	>	excludedInteractions_.addPair(a, c);
491	>	excludedInteractions_.addPair(a, d);
492	>	}
493	>
494	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
495	>	oneThreeInteractions_.addPair(b, c);
496	>	oneThreeInteractions_.addPair(b, d);
497	>	oneThreeInteractions_.addPair(c, d);
498	>	} else {
499	>	excludedInteractions_.addPair(b, c);
500	>	excludedInteractions_.addPair(b, d);
501	>	excludedInteractions_.addPair(c, d);
502	>	}
503	>	}
504	>
505	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
506	>	rb = mol->nextRigidBody(rbIter)) {
507	>	vector<Atom*> atoms = rb->getAtoms();
508	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
509	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
510		a = atoms[i]->getGlobalIndex();
511		b = atoms[j]->getGlobalIndex();
512	<	exclude_.addPair(a, b);
512	>	excludedInteractions_.addPair(a, b);
513		}
514		}
515		}
516
517		}
518
519	<	void SimInfo::removeExcludePairs(Molecule* mol) {
520	<	std::vector<Bond*>::iterator bondIter;
521	<	std::vector<Bend*>::iterator bendIter;
522	<	std::vector<Torsion*>::iterator torsionIter;
519	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
520	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
521	>	vector<Bond*>::iterator bondIter;
522	>	vector<Bend*>::iterator bendIter;
523	>	vector<Torsion*>::iterator torsionIter;
524	>	vector<Inversion*>::iterator inversionIter;
525		Bond* bond;
526		Bend* bend;
527		Torsion* torsion;
528	+	Inversion* inversion;
529		int a;
530		int b;
531		int c;
532		int d;
533	+
534	+	map<int, set<int> > atomGroups;
535	+	Molecule::RigidBodyIterator rbIter;
536	+	RigidBody* rb;
537	+	Molecule::IntegrableObjectIterator ii;
538	+	StuntDouble* integrableObject;
539
540	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
540	>	for (integrableObject = mol->beginIntegrableObject(ii);
541	>	integrableObject != NULL;
542	>	integrableObject = mol->nextIntegrableObject(ii)) {
543	>
544	>	if (integrableObject->isRigidBody()) {
545	>	rb = static_cast<RigidBody*>(integrableObject);
546	>	vector<Atom*> atoms = rb->getAtoms();
547	>	set<int> rigidAtoms;
548	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
549	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
550	>	}
551	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
552	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
553	>	}
554	>	} else {
555	>	set<int> oneAtomSet;
556	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
557	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
558	>	}
559	>	}
560	>
561	>	for (bond= mol->beginBond(bondIter); bond != NULL;
562	>	bond = mol->nextBond(bondIter)) {
563	>
564		a = bond->getAtomA()->getGlobalIndex();
565	<	b = bond->getAtomB()->getGlobalIndex();
566	<	exclude_.removePair(a, b);
565	>	b = bond->getAtomB()->getGlobalIndex();
566	>
567	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
568	>	oneTwoInteractions_.removePair(a, b);
569	>	} else {
570	>	excludedInteractions_.removePair(a, b);
571	>	}
572		}
573
574	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
574	>	for (bend= mol->beginBend(bendIter); bend != NULL;
575	>	bend = mol->nextBend(bendIter)) {
576	>
577		a = bend->getAtomA()->getGlobalIndex();
578		b = bend->getAtomB()->getGlobalIndex();
579		c = bend->getAtomC()->getGlobalIndex();
580	+
581	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
582	+	oneTwoInteractions_.removePair(a, b);
583	+	oneTwoInteractions_.removePair(b, c);
584	+	} else {
585	+	excludedInteractions_.removePair(a, b);
586	+	excludedInteractions_.removePair(b, c);
587	+	}
588
589	<	exclude_.removePair(a, b);
590	<	exclude_.removePair(a, c);
591	<	exclude_.removePair(b, c);
589	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
590	>	oneThreeInteractions_.removePair(a, c);
591	>	} else {
592	>	excludedInteractions_.removePair(a, c);
593	>	}
594		}
595
596	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
596	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
597	>	torsion = mol->nextTorsion(torsionIter)) {
598	>
599		a = torsion->getAtomA()->getGlobalIndex();
600		b = torsion->getAtomB()->getGlobalIndex();
601		c = torsion->getAtomC()->getGlobalIndex();
602	<	d = torsion->getAtomD()->getGlobalIndex();
602	>	d = torsion->getAtomD()->getGlobalIndex();
603	>
604	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
605	>	oneTwoInteractions_.removePair(a, b);
606	>	oneTwoInteractions_.removePair(b, c);
607	>	oneTwoInteractions_.removePair(c, d);
608	>	} else {
609	>	excludedInteractions_.removePair(a, b);
610	>	excludedInteractions_.removePair(b, c);
611	>	excludedInteractions_.removePair(c, d);
612	>	}
613
614	<	exclude_.removePair(a, b);
615	<	exclude_.removePair(a, c);
616	<	exclude_.removePair(a, d);
617	<	exclude_.removePair(b, c);
618	<	exclude_.removePair(b, d);
619	<	exclude_.removePair(c, d);
614	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
615	>	oneThreeInteractions_.removePair(a, c);
616	>	oneThreeInteractions_.removePair(b, d);
617	>	} else {
618	>	excludedInteractions_.removePair(a, c);
619	>	excludedInteractions_.removePair(b, d);
620	>	}
621	>
622	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
623	>	oneFourInteractions_.removePair(a, d);
624	>	} else {
625	>	excludedInteractions_.removePair(a, d);
626	>	}
627		}
628
629	<	Molecule::RigidBodyIterator rbIter;
630	<	RigidBody* rb;
631	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
632	<	std::vector<Atom*> atoms = rb->getAtoms();
633	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
634	<	for (int j = i + 1; j < atoms.size(); ++j) {
629	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
630	>	inversion = mol->nextInversion(inversionIter)) {
631	>
632	>	a = inversion->getAtomA()->getGlobalIndex();
633	>	b = inversion->getAtomB()->getGlobalIndex();
634	>	c = inversion->getAtomC()->getGlobalIndex();
635	>	d = inversion->getAtomD()->getGlobalIndex();
636	>
637	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
638	>	oneTwoInteractions_.removePair(a, b);
639	>	oneTwoInteractions_.removePair(a, c);
640	>	oneTwoInteractions_.removePair(a, d);
641	>	} else {
642	>	excludedInteractions_.removePair(a, b);
643	>	excludedInteractions_.removePair(a, c);
644	>	excludedInteractions_.removePair(a, d);
645	>	}
646	>
647	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
648	>	oneThreeInteractions_.removePair(b, c);
649	>	oneThreeInteractions_.removePair(b, d);
650	>	oneThreeInteractions_.removePair(c, d);
651	>	} else {
652	>	excludedInteractions_.removePair(b, c);
653	>	excludedInteractions_.removePair(b, d);
654	>	excludedInteractions_.removePair(c, d);
655	>	}
656	>	}
657	>
658	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
659	>	rb = mol->nextRigidBody(rbIter)) {
660	>	vector<Atom*> atoms = rb->getAtoms();
661	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
662	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
663		a = atoms[i]->getGlobalIndex();
664		b = atoms[j]->getGlobalIndex();
665	<	exclude_.removePair(a, b);
665	>	excludedInteractions_.removePair(a, b);
666		}
667		}
668		}
669	<
669	>
670		}
671	<
672	<
671	>
672	>
673		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
674		int curStampId;
675	<
675	>
676		//index from 0
677		curStampId = moleculeStamps_.size();
678
#	Line 456 | Line 680 | namespace oopse {
680		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
681		}
682
459	–	void SimInfo::update() {
683
684	<	setupSimType();
685	<
686	<	#ifdef IS_MPI
687	<	setupFortranParallel();
688	<	#endif
689	<
690	<	setupFortranSim();
691	<
692	<	//setup fortran force field
470	<	/** @deprecate */
471	<	int isError = 0;
472	<
473	<	setupElectrostaticSummationMethod( isError );
474	<
475	<	if(isError){
476	<	sprintf( painCave.errMsg,
477	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
478	<	painCave.isFatal = 1;
479	<	simError();
480	<	}
481	<
482	<
483	<	setupCutoff();
484	<
684	>	/**
685	>	* update
686	>	*
687	>	*  Performs the global checks and variable settings after the
688	>	*  objects have been created.
689	>	*
690	>	*/
691	>	void SimInfo::update() {
692	>	setupSimVariables();
693		calcNdf();
694		calcNdfRaw();
695		calcNdfTrans();
488	–
489	–	fortranInitialized_ = true;
696		}
697	<
698	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
697	>
698	>	/**
699	>	* getSimulatedAtomTypes
700	>	*
701	>	* Returns an STL set of AtomType* that are actually present in this
702	>	* simulation.  Must query all processors to assemble this information.
703	>	*
704	>	*/
705	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
706		SimInfo::MoleculeIterator mi;
707		Molecule* mol;
708		Molecule::AtomIterator ai;
709		Atom* atom;
710	<	std::set<AtomType*> atomTypes;
711	<
710	>	set<AtomType*> atomTypes;
711	>
712		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
713	<
714	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
713	>	for(atom = mol->beginAtom(ai); atom != NULL;
714	>	atom = mol->nextAtom(ai)) {
715		atomTypes.insert(atom->getAtomType());
716	<	}
717	<
718	<	}
716	>	}
717	>	}
718	>
719	>	#ifdef IS_MPI
720
721	<	return atomTypes;
722	<	}
509	<
510	<	void SimInfo::setupSimType() {
511	<	std::set<AtomType*>::iterator i;
512	<	std::set<AtomType*> atomTypes;
513	<	atomTypes = getUniqueAtomTypes();
721	>	// loop over the found atom types on this processor, and add their
722	>	// numerical idents to a vector:
723
724	<	int useLennardJones = 0;
725	<	int useElectrostatic = 0;
726	<	int useEAM = 0;
727	<	int useCharge = 0;
519	<	int useDirectional = 0;
520	<	int useDipole = 0;
521	<	int useGayBerne = 0;
522	<	int useSticky = 0;
523	<	int useStickyPower = 0;
524	<	int useShape = 0;
525	<	int useFLARB = 0; //it is not in AtomType yet
526	<	int useDirectionalAtom = 0;
527	<	int useElectrostatics = 0;
528	<	//usePBC and useRF are from simParams
529	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
530	<	int useRF;
531	<	std::string myMethod;
724	>	vector<int> foundTypes;
725	>	set<AtomType*>::iterator i;
726	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
727	>	foundTypes.push_back( (*i)->getIdent() );
728
729	<	// set the useRF logical
730	<	useRF = 0;
535	<	if (simParams_->haveElectrostaticSummationMethod()) {
536	<	myMethod = simParams_->getElectrostaticSummationMethod();
537	<	if (myMethod == "REACTION_FIELD")
538	<	useRF = 1;
539	<	}
729	>	// count_local holds the number of found types on this processor
730	>	int count_local = foundTypes.size();
731
732	<	//loop over all of the atom types
542	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
543	<	useLennardJones |= (*i)->isLennardJones();
544	<	useElectrostatic |= (*i)->isElectrostatic();
545	<	useEAM |= (*i)->isEAM();
546	<	useCharge |= (*i)->isCharge();
547	<	useDirectional |= (*i)->isDirectional();
548	<	useDipole |= (*i)->isDipole();
549	<	useGayBerne |= (*i)->isGayBerne();
550	<	useSticky |= (*i)->isSticky();
551	<	useStickyPower |= (*i)->isStickyPower();
552	<	useShape |= (*i)->isShape();
553	<	}
732	>	int nproc = MPI::COMM_WORLD.Get_size();
733
734	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
735	<	useDirectionalAtom = 1;
736	<	}
734	>	// we need arrays to hold the counts and displacement vectors for
735	>	// all processors
736	>	vector<int> counts(nproc, 0);
737	>	vector<int> disps(nproc, 0);
738
739	<	if (useCharge || useDipole) {
740	<	useElectrostatics = 1;
739	>	// fill the counts array
740	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
741	>	1, MPI::INT);
742	>
743	>	// use the processor counts to compute the displacement array
744	>	disps[0] = 0;
745	>	int totalCount = counts[0];
746	>	for (int iproc = 1; iproc < nproc; iproc++) {
747	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
748	>	totalCount += counts[iproc];
749		}
750
751	<	#ifdef IS_MPI
752	<	int temp;
751	>	// we need a (possibly redundant) set of all found types:
752	>	vector<int> ftGlobal(totalCount);
753	>
754	>	// now spray out the foundTypes to all the other processors:
755	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
756	>	&ftGlobal[0], &counts[0], &disps[0],
757	>	MPI::INT);
758
759	<	temp = usePBC;
567	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
759	>	vector<int>::iterator j;
760
761	<	temp = useDirectionalAtom;
762	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
761	>	// foundIdents is a stl set, so inserting an already found ident
762	>	// will have no effect.
763	>	set<int> foundIdents;
764
765	<	temp = useLennardJones;
766	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
765	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
766	>	foundIdents.insert((*j));
767	>
768	>	// now iterate over the foundIdents and get the actual atom types
769	>	// that correspond to these:
770	>	set<int>::iterator it;
771	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
772	>	atomTypes.insert( forceField_->getAtomType((*it)) );
773	>
774	>	#endif
775
776	<	temp = useElectrostatics;
777	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776	>	return atomTypes;
777	>	}
778
779	<	temp = useCharge;
780	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
781	<
782	<	temp = useDipole;
783	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
784	<
785	<	temp = useSticky;
786	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
586	<
587	<	temp = useStickyPower;
588	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
779	>	void SimInfo::setupSimVariables() {
780	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
781	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
782	>	calcBoxDipole_ = false;
783	>	if ( simParams_->haveAccumulateBoxDipole() )
784	>	if ( simParams_->getAccumulateBoxDipole() ) {
785	>	calcBoxDipole_ = true;
786	>	}
787
788	<	temp = useGayBerne;
789	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
788	>	set<AtomType*>::iterator i;
789	>	set<AtomType*> atomTypes;
790	>	atomTypes = getSimulatedAtomTypes();
791	>	int usesElectrostatic = 0;
792	>	int usesMetallic = 0;
793	>	int usesDirectional = 0;
794	>	int usesFluctuatingCharges =  0;
795	>	//loop over all of the atom types
796	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
797	>	usesElectrostatic |= (*i)->isElectrostatic();
798	>	usesMetallic |= (*i)->isMetal();
799	>	usesDirectional |= (*i)->isDirectional();
800	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
801	>	}
802	>
803	>	#ifdef IS_MPI
804	>	int temp;
805	>	temp = usesDirectional;
806	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
807	>
808	>	temp = usesMetallic;
809	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810	>
811	>	temp = usesElectrostatic;
812	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813
814	<	temp = useEAM;
815	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814	>	temp = usesFluctuatingCharges;
815	>	MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816	>	#else
817
818	<	temp = useShape;
819	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
818	>	usesDirectionalAtoms_ = usesDirectional;
819	>	usesMetallicAtoms_ = usesMetallic;
820	>	usesElectrostaticAtoms_ = usesElectrostatic;
821	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
822
599	–	temp = useFLARB;
600	–	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
601	–
602	–	temp = useRF;
603	–	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
604	–
823		#endif
824	+
825	+	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
826	+	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
827	+	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
828	+	}
829
607	–	fInfo_.SIM_uses_PBC = usePBC;
608	–	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
609	–	fInfo_.SIM_uses_LennardJones = useLennardJones;
610	–	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
611	–	fInfo_.SIM_uses_Charges = useCharge;
612	–	fInfo_.SIM_uses_Dipoles = useDipole;
613	–	fInfo_.SIM_uses_Sticky = useSticky;
614	–	fInfo_.SIM_uses_StickyPower = useStickyPower;
615	–	fInfo_.SIM_uses_GayBerne = useGayBerne;
616	–	fInfo_.SIM_uses_EAM = useEAM;
617	–	fInfo_.SIM_uses_Shapes = useShape;
618	–	fInfo_.SIM_uses_FLARB = useFLARB;
619	–	fInfo_.SIM_uses_RF = useRF;
830
831	<	if( fInfo_.SIM_uses_Dipoles && myMethod == "REACTION_FIELD") {
831	>	vector<int> SimInfo::getGlobalAtomIndices() {
832	>	SimInfo::MoleculeIterator mi;
833	>	Molecule* mol;
834	>	Molecule::AtomIterator ai;
835	>	Atom* atom;
836
837	<	if (simParams_->haveDielectric()) {
838	<	fInfo_.dielect = simParams_->getDielectric();
839	<	} else {
840	<	sprintf(painCave.errMsg,
841	<	"SimSetup Error: No Dielectric constant was set.\n"
842	<	"\tYou are trying to use Reaction Field without"
629	<	"\tsetting a dielectric constant!\n");
630	<	painCave.isFatal = 1;
631	<	simError();
837	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
838	>
839	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
840	>
841	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
842	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
843		}
633	–
634	–	} else {
635	–	fInfo_.dielect = 0.0;
844		}
845	<
845	>	return GlobalAtomIndices;
846		}
847
640	–	void SimInfo::setupFortranSim() {
641	–	int isError;
642	–	int nExclude;
643	–	std::vector<int> fortranGlobalGroupMembership;
644	–
645	–	nExclude = exclude_.getSize();
646	–	isError = 0;
848
849	<	//globalGroupMembership_ is filled by SimCreator
850	<	for (int i = 0; i < nGlobalAtoms_; i++) {
851	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
849	>	vector<int> SimInfo::getGlobalGroupIndices() {
850	>	SimInfo::MoleculeIterator mi;
851	>	Molecule* mol;
852	>	Molecule::CutoffGroupIterator ci;
853	>	CutoffGroup* cg;
854	>
855	>	vector<int> GlobalGroupIndices;
856	>
857	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
858	>
859	>	//local index of cutoff group is trivial, it only depends on the
860	>	//order of travesing
861	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
862	>	cg = mol->nextCutoffGroup(ci)) {
863	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
864	>	}
865		}
866	+	return GlobalGroupIndices;
867	+	}
868
869	+
870	+	void SimInfo::prepareTopology() {
871	+	int nExclude, nOneTwo, nOneThree, nOneFour;
872	+
873		//calculate mass ratio of cutoff group
654	–	std::vector<double> mfact;
874		SimInfo::MoleculeIterator mi;
875		Molecule* mol;
876		Molecule::CutoffGroupIterator ci;
877		CutoffGroup* cg;
878		Molecule::AtomIterator ai;
879		Atom* atom;
880	<	double totalMass;
880	>	RealType totalMass;
881
882	<	//to avoid memory reallocation, reserve enough space for mfact
883	<	mfact.reserve(getNCutoffGroups());
882	>	/**
883	>	* The mass factor is the relative mass of an atom to the total
884	>	* mass of the cutoff group it belongs to.  By default, all atoms
885	>	* are their own cutoff groups, and therefore have mass factors of
886	>	* 1.  We need some special handling for massless atoms, which
887	>	* will be treated as carrying the entire mass of the cutoff
888	>	* group.
889	>	*/
890	>	massFactors_.clear();
891	>	massFactors_.resize(getNAtoms(), 1.0);
892
893		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
894	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
894	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
895	>	cg = mol->nextCutoffGroup(ci)) {
896
897		totalMass = cg->getMass();
898		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
899		// Check for massless groups - set mfact to 1 if true
900	<	if (totalMass != 0)
901	<	mfact.push_back(atom->getMass()/totalMass);
900	>	if (totalMass != 0)
901	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
902		else
903	<	mfact.push_back( 1.0 );
903	>	massFactors_[atom->getLocalIndex()] = 1.0;
904		}
677	–
905		}
906		}
907
908	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
682	<	std::vector<int> identArray;
908	>	// Build the identArray_
909
910	<	//to avoid memory reallocation, reserve enough space identArray
911	<	identArray.reserve(getNAtoms());
686	<
910	>	identArray_.clear();
911	>	identArray_.reserve(getNAtoms());
912		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
913		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
914	<	identArray.push_back(atom->getIdent());
914	>	identArray_.push_back(atom->getIdent());
915		}
916		}
692	–
693	–	//fill molMembershipArray
694	–	//molMembershipArray is filled by SimCreator
695	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
696	–	for (int i = 0; i < nGlobalAtoms_; i++) {
697	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
698	–	}
917
918	<	//setup fortran simulation
701	<	int nGlobalExcludes = 0;
702	<	int* globalExcludes = NULL;
703	<	int* excludeList = exclude_.getExcludeList();
704	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
705	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
706	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
918	>	//scan topology
919
920	<	if( isError ){
920	>	nExclude = excludedInteractions_.getSize();
921	>	nOneTwo = oneTwoInteractions_.getSize();
922	>	nOneThree = oneThreeInteractions_.getSize();
923	>	nOneFour = oneFourInteractions_.getSize();
924
925	<	sprintf( painCave.errMsg,
926	<	"There was an error setting the simulation information in fortran.\n" );
927	<	painCave.isFatal = 1;
928	<	painCave.severity = OOPSE_ERROR;
714	<	simError();
715	<	}
716	<
717	<	#ifdef IS_MPI
718	<	sprintf( checkPointMsg,
719	<	"succesfully sent the simulation information to fortran.\n");
720	<	MPIcheckPoint();
721	<	#endif // is_mpi
722	<	}
723	<
724	<
725	<	#ifdef IS_MPI
726	<	void SimInfo::setupFortranParallel() {
727	<
728	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
729	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
730	<	std::vector<int> localToGlobalCutoffGroupIndex;
731	<	SimInfo::MoleculeIterator mi;
732	<	Molecule::AtomIterator ai;
733	<	Molecule::CutoffGroupIterator ci;
734	<	Molecule* mol;
735	<	Atom* atom;
736	<	CutoffGroup* cg;
737	<	mpiSimData parallelData;
738	<	int isError;
739	<
740	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
741	<
742	<	//local index(index in DataStorge) of atom is important
743	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
744	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
745	<	}
746	<
747	<	//local index of cutoff group is trivial, it only depends on the order of travesing
748	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
749	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
750	<	}
751	<
752	<	}
753	<
754	<	//fill up mpiSimData struct
755	<	parallelData.nMolGlobal = getNGlobalMolecules();
756	<	parallelData.nMolLocal = getNMolecules();
757	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
758	<	parallelData.nAtomsLocal = getNAtoms();
759	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
760	<	parallelData.nGroupsLocal = getNCutoffGroups();
761	<	parallelData.myNode = worldRank;
762	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
763	<
764	<	//pass mpiSimData struct and index arrays to fortran
765	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
766	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
767	<	&localToGlobalCutoffGroupIndex[0], &isError);
925	>	int* excludeList = excludedInteractions_.getPairList();
926	>	int* oneTwoList = oneTwoInteractions_.getPairList();
927	>	int* oneThreeList = oneThreeInteractions_.getPairList();
928	>	int* oneFourList = oneFourInteractions_.getPairList();
929
930	<	if (isError) {
770	<	sprintf(painCave.errMsg,
771	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
772	<	painCave.isFatal = 1;
773	<	simError();
774	<	}
775	<
776	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
777	<	MPIcheckPoint();
778	<
779	<
780	<	}
781	<
782	<	#endif
783	<
784	<	double SimInfo::calcMaxCutoffRadius() {
785	<
786	<
787	<	std::set<AtomType*> atomTypes;
788	<	std::set<AtomType*>::iterator i;
789	<	std::vector<double> cutoffRadius;
790	<
791	<	//get the unique atom types
792	<	atomTypes = getUniqueAtomTypes();
793	<
794	<	//query the max cutoff radius among these atom types
795	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
796	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
797	<	}
798	<
799	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
800	<	#ifdef IS_MPI
801	<	//pick the max cutoff radius among the processors
802	<	#endif
803	<
804	<	return maxCutoffRadius;
805	<	}
806	<
807	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
808	<
809	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
810	<
811	<	if (!simParams_->haveCutoffRadius()){
812	<	sprintf(painCave.errMsg,
813	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
814	<	"\tOOPSE will use a default value of 15.0 angstroms"
815	<	"\tfor the cutoffRadius.\n");
816	<	painCave.isFatal = 0;
817	<	simError();
818	<	rcut = 15.0;
819	<	} else{
820	<	rcut = simParams_->getCutoffRadius();
821	<	}
822	<
823	<	if (!simParams_->haveSwitchingRadius()){
824	<	sprintf(painCave.errMsg,
825	<	"SimCreator Warning: No value was set for switchingRadius.\n"
826	<	"\tOOPSE will use a default value of\n"
827	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
828	<	painCave.isFatal = 0;
829	<	simError();
830	<	rsw = 0.95 * rcut;
831	<	} else{
832	<	rsw = simParams_->getSwitchingRadius();
833	<	}
834	<
835	<	} else {
836	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
837	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
838	<
839	<	if (simParams_->haveCutoffRadius()) {
840	<	rcut = simParams_->getCutoffRadius();
841	<	} else {
842	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
843	<	rcut = calcMaxCutoffRadius();
844	<	}
845	<
846	<	if (simParams_->haveSwitchingRadius()) {
847	<	rsw  = simParams_->getSwitchingRadius();
848	<	} else {
849	<	rsw = rcut;
850	<	}
851	<
852	<	}
853	<	}
854	<
855	<	void SimInfo::setupCutoff() {
856	<	getCutoff(rcut_, rsw_);
857	<	double rnblist = rcut_ + 1; // skin of neighbor list
858	<
859	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
860	<
861	<	int cp =  TRADITIONAL_CUTOFF_POLICY;
862	<	if (simParams_->haveCutoffPolicy()) {
863	<	std::string myPolicy = simParams_->getCutoffPolicy();
864	<	toUpper(myPolicy);
865	<	if (myPolicy == "MIX") {
866	<	cp = MIX_CUTOFF_POLICY;
867	<	} else {
868	<	if (myPolicy == "MAX") {
869	<	cp = MAX_CUTOFF_POLICY;
870	<	} else {
871	<	if (myPolicy == "TRADITIONAL") {
872	<	cp = TRADITIONAL_CUTOFF_POLICY;
873	<	} else {
874	<	// throw error
875	<	sprintf( painCave.errMsg,
876	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
877	<	painCave.isFatal = 1;
878	<	simError();
879	<	}
880	<	}
881	<	}
882	<	}
883	<
884	<
885	<	if (simParams_->haveSkinThickness()) {
886	<	double skinThickness = simParams_->getSkinThickness();
887	<	}
888	<
889	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
890	<	// also send cutoff notification to electrostatics
891	<	setElectrostaticCutoffRadius(&rcut_);
892	<	}
893	<
894	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
895	<
896	<	int errorOut;
897	<	int esm =  NONE;
898	<	double alphaVal;
899	<	double dielectric;
900	<
901	<	errorOut = isError;
902	<	alphaVal = simParams_->getDampingAlpha();
903	<	dielectric = simParams_->getDielectric();
904	<
905	<	if (simParams_->haveElectrostaticSummationMethod()) {
906	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
907	<	toUpper(myMethod);
908	<	if (myMethod == "NONE") {
909	<	esm = NONE;
910	<	} else {
911	<	if (myMethod == "UNDAMPED_WOLF") {
912	<	esm = UNDAMPED_WOLF;
913	<	} else {
914	<	if (myMethod == "DAMPED_WOLF") {
915	<	esm = DAMPED_WOLF;
916	<	if (!simParams_->haveDampingAlpha()) {
917	<	//throw error
918	<	sprintf( painCave.errMsg,
919	<	"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);
920	<	painCave.isFatal = 0;
921	<	simError();
922	<	}
923	<	} else {
924	<	if (myMethod == "REACTION_FIELD") {
925	<	esm = REACTION_FIELD;
926	<	} else {
927	<	// throw error
928	<	sprintf( painCave.errMsg,
929	<	"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() );
930	<	painCave.isFatal = 1;
931	<	simError();
932	<	}
933	<	}
934	<	}
935	<	}
936	<	}
937	<	// let's pass some summation method variables to fortran
938	<	setElectrostaticSummationMethod( &esm );
939	<	setDampedWolfAlpha( &alphaVal );
940	<	setReactionFieldDielectric( &dielectric );
941	<	initFortranFF( &esm, &errorOut );
930	>	topologyDone_ = true;
931		}
932
933		void SimInfo::addProperty(GenericData* genData) {
934		properties_.addProperty(genData);
935		}
936
937	<	void SimInfo::removeProperty(const std::string& propName) {
937	>	void SimInfo::removeProperty(const string& propName) {
938		properties_.removeProperty(propName);
939		}
940
#	Line 953 | Line 942 | namespace oopse {
942		properties_.clearProperties();
943		}
944
945	<	std::vector<std::string> SimInfo::getPropertyNames() {
945	>	vector<string> SimInfo::getPropertyNames() {
946		return properties_.getPropertyNames();
947		}
948
949	<	std::vector<GenericData*> SimInfo::getProperties() {
949	>	vector<GenericData*> SimInfo::getProperties() {
950		return properties_.getProperties();
951		}
952
953	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
953	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
954		return properties_.getPropertyByName(propName);
955		}
956
#	Line 975 | Line 964 | namespace oopse {
964		Molecule* mol;
965		RigidBody* rb;
966		Atom* atom;
967	+	CutoffGroup* cg;
968		SimInfo::MoleculeIterator mi;
969		Molecule::RigidBodyIterator rbIter;
970	<	Molecule::AtomIterator atomIter;;
970	>	Molecule::AtomIterator atomIter;
971	>	Molecule::CutoffGroupIterator cgIter;
972
973		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
974
#	Line 988 | Line 979 | namespace oopse {
979		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
980		rb->setSnapshotManager(sman_);
981		}
982	+
983	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
984	+	cg->setSnapshotManager(sman_);
985	+	}
986		}
987
988		}
#	Line 997 | Line 992 | namespace oopse {
992		Molecule* mol;
993
994		Vector3d comVel(0.0);
995	<	double totalMass = 0.0;
995	>	RealType totalMass = 0.0;
996
997
998		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
999	<	double mass = mol->getMass();
999	>	RealType mass = mol->getMass();
1000		totalMass += mass;
1001		comVel += mass * mol->getComVel();
1002		}
1003
1004		#ifdef IS_MPI
1005	<	double tmpMass = totalMass;
1005	>	RealType tmpMass = totalMass;
1006		Vector3d tmpComVel(comVel);
1007	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1008	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1007	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1008	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1009		#endif
1010
1011		comVel /= totalMass;
#	Line 1023 | Line 1018 | namespace oopse {
1018		Molecule* mol;
1019
1020		Vector3d com(0.0);
1021	<	double totalMass = 0.0;
1021	>	RealType totalMass = 0.0;
1022
1023		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1024	<	double mass = mol->getMass();
1024	>	RealType mass = mol->getMass();
1025		totalMass += mass;
1026		com += mass * mol->getCom();
1027		}
1028
1029		#ifdef IS_MPI
1030	<	double tmpMass = totalMass;
1030	>	RealType tmpMass = totalMass;
1031		Vector3d tmpCom(com);
1032	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1033	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1032	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1033	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1034		#endif
1035
1036		com /= totalMass;
#	Line 1044 | Line 1039 | namespace oopse {
1039
1040		}
1041
1042	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1042	>	ostream& operator <<(ostream& o, SimInfo& info) {
1043
1044		return o;
1045		}
#	Line 1059 | Line 1054 | namespace oopse {
1054		Molecule* mol;
1055
1056
1057	<	double totalMass = 0.0;
1057	>	RealType totalMass = 0.0;
1058
1059
1060		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1061	<	double mass = mol->getMass();
1061	>	RealType mass = mol->getMass();
1062		totalMass += mass;
1063		com += mass * mol->getCom();
1064		comVel += mass * mol->getComVel();
1065		}
1066
1067		#ifdef IS_MPI
1068	<	double tmpMass = totalMass;
1068	>	RealType tmpMass = totalMass;
1069		Vector3d tmpCom(com);
1070		Vector3d tmpComVel(comVel);
1071	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1072	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1073	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1071	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1072	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1073	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1074		#endif
1075
1076		com /= totalMass;
#	Line 1087 | Line 1082 | namespace oopse {
1082
1083
1084		[  Ixx -Ixy  -Ixz ]
1085	<	J =| -Iyx  Iyy  -Iyz |
1085	>	J =| -Iyx  Iyy  -Iyz |
1086		[ -Izx -Iyz   Izz ]
1087		*/
1088
1089		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1090
1091
1092	<	double xx = 0.0;
1093	<	double yy = 0.0;
1094	<	double zz = 0.0;
1095	<	double xy = 0.0;
1096	<	double xz = 0.0;
1097	<	double yz = 0.0;
1092	>	RealType xx = 0.0;
1093	>	RealType yy = 0.0;
1094	>	RealType zz = 0.0;
1095	>	RealType xy = 0.0;
1096	>	RealType xz = 0.0;
1097	>	RealType yz = 0.0;
1098		Vector3d com(0.0);
1099		Vector3d comVel(0.0);
1100
#	Line 1111 | Line 1106 | namespace oopse {
1106		Vector3d thisq(0.0);
1107		Vector3d thisv(0.0);
1108
1109	<	double thisMass = 0.0;
1109	>	RealType thisMass = 0.0;
1110
1111
1112
#	Line 1149 | Line 1144 | namespace oopse {
1144		#ifdef IS_MPI
1145		Mat3x3d tmpI(inertiaTensor);
1146		Vector3d tmpAngMom;
1147	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1148	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1147	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1148	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1149		#endif
1150
1151		return;
#	Line 1171 | Line 1166 | namespace oopse {
1166		Vector3d thisr(0.0);
1167		Vector3d thisp(0.0);
1168
1169	<	double thisMass;
1169	>	RealType thisMass;
1170
1171		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1172		thisMass = mol->getMass();
#	Line 1184 | Line 1179 | namespace oopse {
1179
1180		#ifdef IS_MPI
1181		Vector3d tmpAngMom;
1182	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1182	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1183		#endif
1184
1185		return angularMomentum;
1186		}
1187
1188	<
1189	<	}//end namespace oopse
1188	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1189	>	return IOIndexToIntegrableObject.at(index);
1190	>	}
1191	>
1192	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1193	>	IOIndexToIntegrableObject= v;
1194	>	}
1195
1196	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1197	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1198	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1199	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1200	+	*/
1201	+	void SimInfo::getGyrationalVolume(RealType &volume){
1202	+	Mat3x3d intTensor;
1203	+	RealType det;
1204	+	Vector3d dummyAngMom;
1205	+	RealType sysconstants;
1206	+	RealType geomCnst;
1207	+
1208	+	geomCnst = 3.0/2.0;
1209	+	/* Get the inertial tensor and angular momentum for free*/
1210	+	getInertiaTensor(intTensor,dummyAngMom);
1211	+
1212	+	det = intTensor.determinant();
1213	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1214	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1215	+	return;
1216	+	}
1217	+
1218	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1219	+	Mat3x3d intTensor;
1220	+	Vector3d dummyAngMom;
1221	+	RealType sysconstants;
1222	+	RealType geomCnst;
1223	+
1224	+	geomCnst = 3.0/2.0;
1225	+	/* Get the inertial tensor and angular momentum for free*/
1226	+	getInertiaTensor(intTensor,dummyAngMom);
1227	+
1228	+	detI = intTensor.determinant();
1229	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1230	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1231	+	return;
1232	+	}
1233	+	/*
1234	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1235	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1236	+	sdByGlobalIndex_ = v;
1237	+	}
1238	+
1239	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1240	+	//assert(index < nAtoms_ + nRigidBodies_);
1241	+	return sdByGlobalIndex_.at(index);
1242	+	}
1243	+	*/
1244	+	int SimInfo::getNGlobalConstraints() {
1245	+	int nGlobalConstraints;
1246	+	#ifdef IS_MPI
1247	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1248	+	MPI_COMM_WORLD);
1249	+	#else
1250	+	nGlobalConstraints =  nConstraints_;
1251	+	#endif
1252	+	return nGlobalConstraints;
1253	+	}
1254	+
1255	+	}//end namespace OpenMD
1256	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 665 by tim, Thu Oct 13 22:26:47 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1725 by gezelter, Sat May 26 18:13:43 2012 UTC

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