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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 726 by chrisfen, Fri Nov 11 15:22:11 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1581 by gezelter, Mon Jun 13 22:13:12 2011 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 48 | Line 48
48
49		#include <algorithm>
50		#include <set>
51	+	#include <map>
52
53		#include "brains/SimInfo.hpp"
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56	<	#include "UseTheForce/fCutoffPolicy.h"
56	<	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
57	<	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
58	<	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
59	<	#include "UseTheForce/doForces_interface.h"
60	<	#include "UseTheForce/DarkSide/electrostatic_interface.h"
61	<	#include "UseTheForce/notifyCutoffs_interface.h"
62	<	#include "UseTheForce/DarkSide/switcheroo_interface.h"
56	>	#include "primitives/StuntDouble.hpp"
57		#include "utils/MemoryUtils.hpp"
58		#include "utils/simError.h"
59		#include "selection/SelectionManager.hpp"
60	+	#include "io/ForceFieldOptions.hpp"
61	+	#include "UseTheForce/ForceField.hpp"
62	+	#include "nonbonded/SwitchingFunction.hpp"
63
64	<	#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
67	<	#endif
68	<
69	<	namespace oopse {
73	<
74	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
75	<	ForceField* ff, Globals* simParams) :
76	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
77	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
64	>	using namespace std;
65	>	namespace OpenMD {
66	>
67	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
68	>	forceField_(ff), simParams_(simParams),
69	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
70		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
71		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
72	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
73	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
74	<	sman_(NULL), fortranInitialized_(false) {
75	<
84	<
85	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
86	<	MoleculeStamp* molStamp;
87	<	int nMolWithSameStamp;
88	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
89	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
90	<	CutoffGroupStamp* cgStamp;
91	<	RigidBodyStamp* rbStamp;
92	<	int nRigidAtoms = 0;
72	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
73	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
74	>	nConstraints_(0), sman_(NULL), topologyDone_(false),
75	>	calcBoxDipole_(false), useAtomicVirial_(true) {
76
77	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
78	<	molStamp = i->first;
79	<	nMolWithSameStamp = i->second;
80	<
81	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
82	<
83	<	//calculate atoms in molecules
84	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
85	<
86	<
87	<	//calculate atoms in cutoff groups
88	<	int nAtomsInGroups = 0;
89	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
90	<
91	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
92	<	cgStamp = molStamp->getCutoffGroup(j);
93	<	nAtomsInGroups += cgStamp->getNMembers();
94	<	}
95	<
96	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
97	<
98	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
99	<
100	<	//calculate atoms in rigid bodies
101	<	int nAtomsInRigidBodies = 0;
102	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
120	<
121	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
122	<	rbStamp = molStamp->getRigidBody(j);
123	<	nAtomsInRigidBodies += rbStamp->getNMembers();
124	<	}
125	<
126	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
127	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
128	<
77	>	MoleculeStamp* molStamp;
78	>	int nMolWithSameStamp;
79	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
80	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
81	>	CutoffGroupStamp* cgStamp;
82	>	RigidBodyStamp* rbStamp;
83	>	int nRigidAtoms = 0;
84	>
85	>	vector<Component*> components = simParams->getComponents();
86	>
87	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
88	>	molStamp = (*i)->getMoleculeStamp();
89	>	nMolWithSameStamp = (*i)->getNMol();
90	>
91	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
92	>
93	>	//calculate atoms in molecules
94	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
95	>
96	>	//calculate atoms in cutoff groups
97	>	int nAtomsInGroups = 0;
98	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
99	>
100	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
101	>	cgStamp = molStamp->getCutoffGroupStamp(j);
102	>	nAtomsInGroups += cgStamp->getNMembers();
103		}
104	<
105	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
106	<	//group therefore the total number of cutoff groups in the system is
107	<	//equal to the total number of atoms minus number of atoms belong to
108	<	//cutoff group defined in meta-data file plus the number of cutoff
109	<	//groups defined in meta-data file
110	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
111	<
112	<	//every free atom (atom does not belong to rigid bodies) is an
113	<	//integrable object therefore the total number of integrable objects
114	<	//in the system is equal to the total number of atoms minus number of
115	<	//atoms belong to rigid body defined in meta-data file plus the number
116	<	//of rigid bodies defined in meta-data file
117	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
118	<	+ nGlobalRigidBodies_;
119	<
120	<	nGlobalMols_ = molStampIds_.size();
147	<
148	<	#ifdef IS_MPI
149	<	molToProcMap_.resize(nGlobalMols_);
150	<	#endif
151	<
104	>
105	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
106	>
107	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
108	>
109	>	//calculate atoms in rigid bodies
110	>	int nAtomsInRigidBodies = 0;
111	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
112	>
113	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
114	>	rbStamp = molStamp->getRigidBodyStamp(j);
115	>	nAtomsInRigidBodies += rbStamp->getNMembers();
116	>	}
117	>
118	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
119	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
120	>
121		}
122	+
123	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
124	+	//group therefore the total number of cutoff groups in the system is
125	+	//equal to the total number of atoms minus number of atoms belong to
126	+	//cutoff group defined in meta-data file plus the number of cutoff
127	+	//groups defined in meta-data file
128
129	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
130	+
131	+	//every free atom (atom does not belong to rigid bodies) is an
132	+	//integrable object therefore the total number of integrable objects
133	+	//in the system is equal to the total number of atoms minus number of
134	+	//atoms belong to rigid body defined in meta-data file plus the number
135	+	//of rigid bodies defined in meta-data file
136	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
137	+	+ nGlobalRigidBodies_;
138	+
139	+	nGlobalMols_ = molStampIds_.size();
140	+	molToProcMap_.resize(nGlobalMols_);
141	+	}
142	+
143		SimInfo::~SimInfo() {
144	<	std::map<int, Molecule*>::iterator i;
144	>	map<int, Molecule*>::iterator i;
145		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
146		delete i->second;
147		}
148		molecules_.clear();
149
161	–	delete stamps_;
150		delete sman_;
151		delete simParams_;
152		delete forceField_;
153		}
154
167	–	int SimInfo::getNGlobalConstraints() {
168	–	int nGlobalConstraints;
169	–	#ifdef IS_MPI
170	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
171	–	MPI_COMM_WORLD);
172	–	#else
173	–	nGlobalConstraints =  nConstraints_;
174	–	#endif
175	–	return nGlobalConstraints;
176	–	}
155
156		bool SimInfo::addMolecule(Molecule* mol) {
157		MoleculeIterator i;
158	<
158	>
159		i = molecules_.find(mol->getGlobalIndex());
160		if (i == molecules_.end() ) {
161	<
162	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
163	<
161	>
162	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
163	>
164		nAtoms_ += mol->getNAtoms();
165		nBonds_ += mol->getNBonds();
166		nBends_ += mol->getNBends();
167		nTorsions_ += mol->getNTorsions();
168	+	nInversions_ += mol->getNInversions();
169		nRigidBodies_ += mol->getNRigidBodies();
170		nIntegrableObjects_ += mol->getNIntegrableObjects();
171		nCutoffGroups_ += mol->getNCutoffGroups();
172		nConstraints_ += mol->getNConstraintPairs();
173	<
174	<	addExcludePairs(mol);
175	<
173	>
174	>	addInteractionPairs(mol);
175	>
176		return true;
177		} else {
178		return false;
179		}
180		}
181	<
181	>
182		bool SimInfo::removeMolecule(Molecule* mol) {
183		MoleculeIterator i;
184		i = molecules_.find(mol->getGlobalIndex());
#	Line 212 | Line 191 | namespace oopse {
191		nBonds_ -= mol->getNBonds();
192		nBends_ -= mol->getNBends();
193		nTorsions_ -= mol->getNTorsions();
194	+	nInversions_ -= mol->getNInversions();
195		nRigidBodies_ -= mol->getNRigidBodies();
196		nIntegrableObjects_ -= mol->getNIntegrableObjects();
197		nCutoffGroups_ -= mol->getNCutoffGroups();
198		nConstraints_ -= mol->getNConstraintPairs();
199
200	<	removeExcludePairs(mol);
200	>	removeInteractionPairs(mol);
201		molecules_.erase(mol->getGlobalIndex());
202
203		delete mol;
#	Line 226 | Line 206 | namespace oopse {
206		} else {
207		return false;
208		}
229	–
230	–
209		}
210
211
#	Line 245 | Line 223 | namespace oopse {
223		void SimInfo::calcNdf() {
224		int ndf_local;
225		MoleculeIterator i;
226	<	std::vector<StuntDouble*>::iterator j;
226	>	vector<StuntDouble*>::iterator j;
227		Molecule* mol;
228		StuntDouble* integrableObject;
229
#	Line 265 | Line 243 | namespace oopse {
243		}
244		}
245
246	<	}//end for (integrableObject)
247	<	}// end for (mol)
246	>	}
247	>	}
248
249		// n_constraints is local, so subtract them on each processor
250		ndf_local -= nConstraints_;
#	Line 283 | Line 261 | namespace oopse {
261
262		}
263
264	+	int SimInfo::getFdf() {
265	+	#ifdef IS_MPI
266	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
267	+	#else
268	+	fdf_ = fdf_local;
269	+	#endif
270	+	return fdf_;
271	+	}
272	+
273	+	unsigned int SimInfo::getNLocalCutoffGroups(){
274	+	int nLocalCutoffAtoms = 0;
275	+	Molecule* mol;
276	+	MoleculeIterator mi;
277	+	CutoffGroup* cg;
278	+	Molecule::CutoffGroupIterator ci;
279	+
280	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
281	+
282	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
283	+	cg = mol->nextCutoffGroup(ci)) {
284	+	nLocalCutoffAtoms += cg->getNumAtom();
285	+
286	+	}
287	+	}
288	+
289	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
290	+	}
291	+
292		void SimInfo::calcNdfRaw() {
293		int ndfRaw_local;
294
295		MoleculeIterator i;
296	<	std::vector<StuntDouble*>::iterator j;
296	>	vector<StuntDouble*>::iterator j;
297		Molecule* mol;
298		StuntDouble* integrableObject;
299
#	Line 334 | Line 340 | namespace oopse {
340
341		}
342
343	<	void SimInfo::addExcludePairs(Molecule* mol) {
344	<	std::vector<Bond*>::iterator bondIter;
345	<	std::vector<Bend*>::iterator bendIter;
346	<	std::vector<Torsion*>::iterator torsionIter;
343	>	void SimInfo::addInteractionPairs(Molecule* mol) {
344	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
345	>	vector<Bond*>::iterator bondIter;
346	>	vector<Bend*>::iterator bendIter;
347	>	vector<Torsion*>::iterator torsionIter;
348	>	vector<Inversion*>::iterator inversionIter;
349		Bond* bond;
350		Bend* bend;
351		Torsion* torsion;
352	+	Inversion* inversion;
353		int a;
354		int b;
355		int c;
356		int d;
357	<
358	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
359	<	a = bond->getAtomA()->getGlobalIndex();
360	<	b = bond->getAtomB()->getGlobalIndex();
361	<	exclude_.addPair(a, b);
357	>
358	>	// atomGroups can be used to add special interaction maps between
359	>	// groups of atoms that are in two separate rigid bodies.
360	>	// However, most site-site interactions between two rigid bodies
361	>	// are probably not special, just the ones between the physically
362	>	// bonded atoms.  Interactions *within* a single rigid body should
363	>	// always be excluded.  These are done at the bottom of this
364	>	// function.
365	>
366	>	map<int, set<int> > atomGroups;
367	>	Molecule::RigidBodyIterator rbIter;
368	>	RigidBody* rb;
369	>	Molecule::IntegrableObjectIterator ii;
370	>	StuntDouble* integrableObject;
371	>
372	>	for (integrableObject = mol->beginIntegrableObject(ii);
373	>	integrableObject != NULL;
374	>	integrableObject = mol->nextIntegrableObject(ii)) {
375	>
376	>	if (integrableObject->isRigidBody()) {
377	>	rb = static_cast<RigidBody*>(integrableObject);
378	>	vector<Atom*> atoms = rb->getAtoms();
379	>	set<int> rigidAtoms;
380	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
381	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
382	>	}
383	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
384	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
385	>	}
386	>	} else {
387	>	set<int> oneAtomSet;
388	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
389	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
390	>	}
391	>	}
392	>
393	>	for (bond= mol->beginBond(bondIter); bond != NULL;
394	>	bond = mol->nextBond(bondIter)) {
395	>
396	>	a = bond->getAtomA()->getGlobalIndex();
397	>	b = bond->getAtomB()->getGlobalIndex();
398	>
399	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
400	>	oneTwoInteractions_.addPair(a, b);
401	>	} else {
402	>	excludedInteractions_.addPair(a, b);
403	>	}
404		}
405
406	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
406	>	for (bend= mol->beginBend(bendIter); bend != NULL;
407	>	bend = mol->nextBend(bendIter)) {
408	>
409		a = bend->getAtomA()->getGlobalIndex();
410		b = bend->getAtomB()->getGlobalIndex();
411		c = bend->getAtomC()->getGlobalIndex();
412	+
413	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
414	+	oneTwoInteractions_.addPair(a, b);
415	+	oneTwoInteractions_.addPair(b, c);
416	+	} else {
417	+	excludedInteractions_.addPair(a, b);
418	+	excludedInteractions_.addPair(b, c);
419	+	}
420
421	<	exclude_.addPair(a, b);
422	<	exclude_.addPair(a, c);
423	<	exclude_.addPair(b, c);
421	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
422	>	oneThreeInteractions_.addPair(a, c);
423	>	} else {
424	>	excludedInteractions_.addPair(a, c);
425	>	}
426		}
427
428	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
428	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
429	>	torsion = mol->nextTorsion(torsionIter)) {
430	>
431		a = torsion->getAtomA()->getGlobalIndex();
432		b = torsion->getAtomB()->getGlobalIndex();
433		c = torsion->getAtomC()->getGlobalIndex();
434	<	d = torsion->getAtomD()->getGlobalIndex();
434	>	d = torsion->getAtomD()->getGlobalIndex();
435
436	<	exclude_.addPair(a, b);
437	<	exclude_.addPair(a, c);
438	<	exclude_.addPair(a, d);
439	<	exclude_.addPair(b, c);
440	<	exclude_.addPair(b, d);
441	<	exclude_.addPair(c, d);
436	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
437	>	oneTwoInteractions_.addPair(a, b);
438	>	oneTwoInteractions_.addPair(b, c);
439	>	oneTwoInteractions_.addPair(c, d);
440	>	} else {
441	>	excludedInteractions_.addPair(a, b);
442	>	excludedInteractions_.addPair(b, c);
443	>	excludedInteractions_.addPair(c, d);
444	>	}
445	>
446	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
447	>	oneThreeInteractions_.addPair(a, c);
448	>	oneThreeInteractions_.addPair(b, d);
449	>	} else {
450	>	excludedInteractions_.addPair(a, c);
451	>	excludedInteractions_.addPair(b, d);
452	>	}
453	>
454	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
455	>	oneFourInteractions_.addPair(a, d);
456	>	} else {
457	>	excludedInteractions_.addPair(a, d);
458	>	}
459		}
460
461	<	Molecule::RigidBodyIterator rbIter;
462	<	RigidBody* rb;
463	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
464	<	std::vector<Atom*> atoms = rb->getAtoms();
465	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
466	<	for (int j = i + 1; j < atoms.size(); ++j) {
461	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
462	>	inversion = mol->nextInversion(inversionIter)) {
463	>
464	>	a = inversion->getAtomA()->getGlobalIndex();
465	>	b = inversion->getAtomB()->getGlobalIndex();
466	>	c = inversion->getAtomC()->getGlobalIndex();
467	>	d = inversion->getAtomD()->getGlobalIndex();
468	>
469	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
470	>	oneTwoInteractions_.addPair(a, b);
471	>	oneTwoInteractions_.addPair(a, c);
472	>	oneTwoInteractions_.addPair(a, d);
473	>	} else {
474	>	excludedInteractions_.addPair(a, b);
475	>	excludedInteractions_.addPair(a, c);
476	>	excludedInteractions_.addPair(a, d);
477	>	}
478	>
479	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
480	>	oneThreeInteractions_.addPair(b, c);
481	>	oneThreeInteractions_.addPair(b, d);
482	>	oneThreeInteractions_.addPair(c, d);
483	>	} else {
484	>	excludedInteractions_.addPair(b, c);
485	>	excludedInteractions_.addPair(b, d);
486	>	excludedInteractions_.addPair(c, d);
487	>	}
488	>	}
489	>
490	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
491	>	rb = mol->nextRigidBody(rbIter)) {
492	>	vector<Atom*> atoms = rb->getAtoms();
493	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
494	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
495		a = atoms[i]->getGlobalIndex();
496		b = atoms[j]->getGlobalIndex();
497	<	exclude_.addPair(a, b);
497	>	excludedInteractions_.addPair(a, b);
498		}
499		}
500		}
501
502		}
503
504	<	void SimInfo::removeExcludePairs(Molecule* mol) {
505	<	std::vector<Bond*>::iterator bondIter;
506	<	std::vector<Bend*>::iterator bendIter;
507	<	std::vector<Torsion*>::iterator torsionIter;
504	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
505	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
506	>	vector<Bond*>::iterator bondIter;
507	>	vector<Bend*>::iterator bendIter;
508	>	vector<Torsion*>::iterator torsionIter;
509	>	vector<Inversion*>::iterator inversionIter;
510		Bond* bond;
511		Bend* bend;
512		Torsion* torsion;
513	+	Inversion* inversion;
514		int a;
515		int b;
516		int c;
517		int d;
518	+
519	+	map<int, set<int> > atomGroups;
520	+	Molecule::RigidBodyIterator rbIter;
521	+	RigidBody* rb;
522	+	Molecule::IntegrableObjectIterator ii;
523	+	StuntDouble* integrableObject;
524
525	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
525	>	for (integrableObject = mol->beginIntegrableObject(ii);
526	>	integrableObject != NULL;
527	>	integrableObject = mol->nextIntegrableObject(ii)) {
528	>
529	>	if (integrableObject->isRigidBody()) {
530	>	rb = static_cast<RigidBody*>(integrableObject);
531	>	vector<Atom*> atoms = rb->getAtoms();
532	>	set<int> rigidAtoms;
533	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
534	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
535	>	}
536	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
537	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
538	>	}
539	>	} else {
540	>	set<int> oneAtomSet;
541	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
542	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
543	>	}
544	>	}
545	>
546	>	for (bond= mol->beginBond(bondIter); bond != NULL;
547	>	bond = mol->nextBond(bondIter)) {
548	>
549		a = bond->getAtomA()->getGlobalIndex();
550	<	b = bond->getAtomB()->getGlobalIndex();
551	<	exclude_.removePair(a, b);
550	>	b = bond->getAtomB()->getGlobalIndex();
551	>
552	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
553	>	oneTwoInteractions_.removePair(a, b);
554	>	} else {
555	>	excludedInteractions_.removePair(a, b);
556	>	}
557		}
558
559	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
559	>	for (bend= mol->beginBend(bendIter); bend != NULL;
560	>	bend = mol->nextBend(bendIter)) {
561	>
562		a = bend->getAtomA()->getGlobalIndex();
563		b = bend->getAtomB()->getGlobalIndex();
564		c = bend->getAtomC()->getGlobalIndex();
565	+
566	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
567	+	oneTwoInteractions_.removePair(a, b);
568	+	oneTwoInteractions_.removePair(b, c);
569	+	} else {
570	+	excludedInteractions_.removePair(a, b);
571	+	excludedInteractions_.removePair(b, c);
572	+	}
573
574	<	exclude_.removePair(a, b);
575	<	exclude_.removePair(a, c);
576	<	exclude_.removePair(b, c);
574	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
575	>	oneThreeInteractions_.removePair(a, c);
576	>	} else {
577	>	excludedInteractions_.removePair(a, c);
578	>	}
579		}
580
581	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
581	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
582	>	torsion = mol->nextTorsion(torsionIter)) {
583	>
584		a = torsion->getAtomA()->getGlobalIndex();
585		b = torsion->getAtomB()->getGlobalIndex();
586		c = torsion->getAtomC()->getGlobalIndex();
587	<	d = torsion->getAtomD()->getGlobalIndex();
587	>	d = torsion->getAtomD()->getGlobalIndex();
588	>
589	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
590	>	oneTwoInteractions_.removePair(a, b);
591	>	oneTwoInteractions_.removePair(b, c);
592	>	oneTwoInteractions_.removePair(c, d);
593	>	} else {
594	>	excludedInteractions_.removePair(a, b);
595	>	excludedInteractions_.removePair(b, c);
596	>	excludedInteractions_.removePair(c, d);
597	>	}
598
599	<	exclude_.removePair(a, b);
600	<	exclude_.removePair(a, c);
601	<	exclude_.removePair(a, d);
602	<	exclude_.removePair(b, c);
603	<	exclude_.removePair(b, d);
604	<	exclude_.removePair(c, d);
599	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
600	>	oneThreeInteractions_.removePair(a, c);
601	>	oneThreeInteractions_.removePair(b, d);
602	>	} else {
603	>	excludedInteractions_.removePair(a, c);
604	>	excludedInteractions_.removePair(b, d);
605	>	}
606	>
607	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
608	>	oneFourInteractions_.removePair(a, d);
609	>	} else {
610	>	excludedInteractions_.removePair(a, d);
611	>	}
612		}
613
614	<	Molecule::RigidBodyIterator rbIter;
615	<	RigidBody* rb;
616	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
617	<	std::vector<Atom*> atoms = rb->getAtoms();
618	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
619	<	for (int j = i + 1; j < atoms.size(); ++j) {
614	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
615	>	inversion = mol->nextInversion(inversionIter)) {
616	>
617	>	a = inversion->getAtomA()->getGlobalIndex();
618	>	b = inversion->getAtomB()->getGlobalIndex();
619	>	c = inversion->getAtomC()->getGlobalIndex();
620	>	d = inversion->getAtomD()->getGlobalIndex();
621	>
622	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
623	>	oneTwoInteractions_.removePair(a, b);
624	>	oneTwoInteractions_.removePair(a, c);
625	>	oneTwoInteractions_.removePair(a, d);
626	>	} else {
627	>	excludedInteractions_.removePair(a, b);
628	>	excludedInteractions_.removePair(a, c);
629	>	excludedInteractions_.removePair(a, d);
630	>	}
631	>
632	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
633	>	oneThreeInteractions_.removePair(b, c);
634	>	oneThreeInteractions_.removePair(b, d);
635	>	oneThreeInteractions_.removePair(c, d);
636	>	} else {
637	>	excludedInteractions_.removePair(b, c);
638	>	excludedInteractions_.removePair(b, d);
639	>	excludedInteractions_.removePair(c, d);
640	>	}
641	>	}
642	>
643	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
644	>	rb = mol->nextRigidBody(rbIter)) {
645	>	vector<Atom*> atoms = rb->getAtoms();
646	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
647	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
648		a = atoms[i]->getGlobalIndex();
649		b = atoms[j]->getGlobalIndex();
650	<	exclude_.removePair(a, b);
650	>	excludedInteractions_.removePair(a, b);
651		}
652		}
653		}
654	<
654	>
655		}
656	<
657	<
656	>
657	>
658		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
659		int curStampId;
660	<
660	>
661		//index from 0
662		curStampId = moleculeStamps_.size();
663
#	Line 459 | Line 665 | namespace oopse {
665		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
666		}
667
462	–	void SimInfo::update() {
668
669	<	setupSimType();
670	<
671	<	#ifdef IS_MPI
672	<	setupFortranParallel();
673	<	#endif
674	<
675	<	setupFortranSim();
676	<
677	<	//setup fortran force field
473	<	/** @deprecate */
474	<	int isError = 0;
475	<
476	<	setupElectrostaticSummationMethod( isError );
477	<	setupSwitchingFunction();
478	<
479	<	if(isError){
480	<	sprintf( painCave.errMsg,
481	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
482	<	painCave.isFatal = 1;
483	<	simError();
484	<	}
485	<
486	<
487	<	setupCutoff();
488	<
669	>	/**
670	>	* update
671	>	*
672	>	*  Performs the global checks and variable settings after the
673	>	*  objects have been created.
674	>	*
675	>	*/
676	>	void SimInfo::update() {
677	>	setupSimVariables();
678		calcNdf();
679		calcNdfRaw();
680		calcNdfTrans();
492	–
493	–	fortranInitialized_ = true;
681		}
682	<
683	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
682	>
683	>	/**
684	>	* getSimulatedAtomTypes
685	>	*
686	>	* Returns an STL set of AtomType* that are actually present in this
687	>	* simulation.  Must query all processors to assemble this information.
688	>	*
689	>	*/
690	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
691		SimInfo::MoleculeIterator mi;
692		Molecule* mol;
693		Molecule::AtomIterator ai;
694		Atom* atom;
695	<	std::set<AtomType*> atomTypes;
696	<
697	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
504	<
695	>	set<AtomType*> atomTypes;
696	>
697	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
698		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
699		atomTypes.insert(atom->getAtomType());
700	<	}
701	<
509	<	}
700	>	}
701	>	}
702
703	<	return atomTypes;
512	<	}
703	>	#ifdef IS_MPI
704
705	<	void SimInfo::setupSimType() {
706	<	std::set<AtomType*>::iterator i;
516	<	std::set<AtomType*> atomTypes;
517	<	atomTypes = getUniqueAtomTypes();
518	<
519	<	int useLennardJones = 0;
520	<	int useElectrostatic = 0;
521	<	int useEAM = 0;
522	<	int useCharge = 0;
523	<	int useDirectional = 0;
524	<	int useDipole = 0;
525	<	int useGayBerne = 0;
526	<	int useSticky = 0;
527	<	int useStickyPower = 0;
528	<	int useShape = 0;
529	<	int useFLARB = 0; //it is not in AtomType yet
530	<	int useDirectionalAtom = 0;
531	<	int useElectrostatics = 0;
532	<	//usePBC and useRF are from simParams
533	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
534	<	int useRF;
535	<	int useSF;
536	<	std::string myMethod;
705	>	// loop over the found atom types on this processor, and add their
706	>	// numerical idents to a vector:
707
708	<	// set the useRF logical
709	<	useRF = 0;
710	<	useSF = 0;
708	>	vector<int> foundTypes;
709	>	set<AtomType*>::iterator i;
710	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
711	>	foundTypes.push_back( (*i)->getIdent() );
712
713	+	// count_local holds the number of found types on this processor
714	+	int count_local = foundTypes.size();
715
716	<	if (simParams_->haveElectrostaticSummationMethod()) {
717	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
718	<	toUpper(myMethod);
719	<	if (myMethod == "REACTION_FIELD") {
720	<	useRF=1;
721	<	} else {
722	<	if (myMethod == "SHIFTED_FORCE") {
723	<	useSF = 1;
724	<	}
725	<	}
726	<	}
716	>	// count holds the total number of found types on all processors
717	>	// (some will be redundant with the ones found locally):
718	>	int count;
719	>	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
720	>
721	>	// create a vector to hold the globally found types, and resize it:
722	>	vector<int> ftGlobal;
723	>	ftGlobal.resize(count);
724	>	vector<int> counts;
725	>
726	>	int nproc = MPI::COMM_WORLD.Get_size();
727	>	counts.resize(nproc);
728	>	vector<int> disps;
729	>	disps.resize(nproc);
730	>
731	>	// now spray out the foundTypes to all the other processors:
732	>
733	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
734	>	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
735
736	+	// foundIdents is a stl set, so inserting an already found ident
737	+	// will have no effect.
738	+	set<int> foundIdents;
739	+	vector<int>::iterator j;
740	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
741	+	foundIdents.insert((*j));
742	+
743	+	// now iterate over the foundIdents and get the actual atom types
744	+	// that correspond to these:
745	+	set<int>::iterator it;
746	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
747	+	atomTypes.insert( forceField_->getAtomType((*it)) );
748	+
749	+	#endif
750	+
751	+	return atomTypes;
752	+	}
753	+
754	+	void SimInfo::setupSimVariables() {
755	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
756	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
757	+	calcBoxDipole_ = false;
758	+	if ( simParams_->haveAccumulateBoxDipole() )
759	+	if ( simParams_->getAccumulateBoxDipole() ) {
760	+	calcBoxDipole_ = true;
761	+	}
762	+
763	+	set<AtomType*>::iterator i;
764	+	set<AtomType*> atomTypes;
765	+	atomTypes = getSimulatedAtomTypes();
766	+	int usesElectrostatic = 0;
767	+	int usesMetallic = 0;
768	+	int usesDirectional = 0;
769		//loop over all of the atom types
770		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
771	<	useLennardJones |= (*i)->isLennardJones();
772	<	useElectrostatic |= (*i)->isElectrostatic();
773	<	useEAM |= (*i)->isEAM();
560	<	useCharge |= (*i)->isCharge();
561	<	useDirectional |= (*i)->isDirectional();
562	<	useDipole |= (*i)->isDipole();
563	<	useGayBerne |= (*i)->isGayBerne();
564	<	useSticky |= (*i)->isSticky();
565	<	useStickyPower |= (*i)->isStickyPower();
566	<	useShape |= (*i)->isShape();
771	>	usesElectrostatic |= (*i)->isElectrostatic();
772	>	usesMetallic |= (*i)->isMetal();
773	>	usesDirectional |= (*i)->isDirectional();
774		}
775
569	–	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
570	–	useDirectionalAtom = 1;
571	–	}
572	–
573	–	if (useCharge || useDipole) {
574	–	useElectrostatics = 1;
575	–	}
576	–
776		#ifdef IS_MPI
777		int temp;
778	+	temp = usesDirectional;
779	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
780
781	<	temp = usePBC;
782	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
781	>	temp = usesMetallic;
782	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
783
784	<	temp = useDirectionalAtom;
785	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
784	>	temp = usesElectrostatic;
785	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
786	>	#endif
787	>	}
788
586	–	temp = useLennardJones;
587	–	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
789
790	<	temp = useElectrostatics;
791	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
790	>	vector<int> SimInfo::getGlobalAtomIndices() {
791	>	SimInfo::MoleculeIterator mi;
792	>	Molecule* mol;
793	>	Molecule::AtomIterator ai;
794	>	Atom* atom;
795
796	<	temp = useCharge;
593	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
594	<
595	<	temp = useDipole;
596	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
597	<
598	<	temp = useSticky;
599	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
600	<
601	<	temp = useStickyPower;
602	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
796	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
797
798	<	temp = useGayBerne;
799	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
798	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
799	>
800	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
801	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
802	>	}
803	>	}
804	>	return GlobalAtomIndices;
805	>	}
806
607	–	temp = useEAM;
608	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
807
808	<	temp = useShape;
809	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
808	>	vector<int> SimInfo::getGlobalGroupIndices() {
809	>	SimInfo::MoleculeIterator mi;
810	>	Molecule* mol;
811	>	Molecule::CutoffGroupIterator ci;
812	>	CutoffGroup* cg;
813
814	<	temp = useFLARB;
815	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816	<
616	<	temp = useRF;
617	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
618	<
619	<	temp = useSF;
620	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
621	<
622	<	#endif
623	<
624	<	fInfo_.SIM_uses_PBC = usePBC;
625	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
626	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
627	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
628	<	fInfo_.SIM_uses_Charges = useCharge;
629	<	fInfo_.SIM_uses_Dipoles = useDipole;
630	<	fInfo_.SIM_uses_Sticky = useSticky;
631	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
632	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
633	<	fInfo_.SIM_uses_EAM = useEAM;
634	<	fInfo_.SIM_uses_Shapes = useShape;
635	<	fInfo_.SIM_uses_FLARB = useFLARB;
636	<	fInfo_.SIM_uses_RF = useRF;
637	<	fInfo_.SIM_uses_SF = useSF;
638	<
639	<	if( myMethod == "REACTION_FIELD") {
814	>	vector<int> GlobalGroupIndices;
815	>
816	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
817
818	<	if (simParams_->haveDielectric()) {
819	<	fInfo_.dielect = simParams_->getDielectric();
820	<	} else {
821	<	sprintf(painCave.errMsg,
822	<	"SimSetup Error: No Dielectric constant was set.\n"
823	<	"\tYou are trying to use Reaction Field without"
647	<	"\tsetting a dielectric constant!\n");
648	<	painCave.isFatal = 1;
649	<	simError();
650	<	}
818	>	//local index of cutoff group is trivial, it only depends on the
819	>	//order of travesing
820	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
821	>	cg = mol->nextCutoffGroup(ci)) {
822	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
823	>	}
824		}
825	<
825	>	return GlobalGroupIndices;
826		}
827
655	–	void SimInfo::setupFortranSim() {
656	–	int isError;
657	–	int nExclude;
658	–	std::vector<int> fortranGlobalGroupMembership;
659	–
660	–	nExclude = exclude_.getSize();
661	–	isError = 0;
828
829	<	//globalGroupMembership_ is filled by SimCreator
830	<	for (int i = 0; i < nGlobalAtoms_; i++) {
665	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
666	<	}
829	>	void SimInfo::prepareTopology() {
830	>	int nExclude, nOneTwo, nOneThree, nOneFour;
831
832		//calculate mass ratio of cutoff group
669	–	std::vector<double> mfact;
833		SimInfo::MoleculeIterator mi;
834		Molecule* mol;
835		Molecule::CutoffGroupIterator ci;
836		CutoffGroup* cg;
837		Molecule::AtomIterator ai;
838		Atom* atom;
839	<	double totalMass;
839	>	RealType totalMass;
840
841	<	//to avoid memory reallocation, reserve enough space for mfact
842	<	mfact.reserve(getNCutoffGroups());
841	>	/**
842	>	* The mass factor is the relative mass of an atom to the total
843	>	* mass of the cutoff group it belongs to.  By default, all atoms
844	>	* are their own cutoff groups, and therefore have mass factors of
845	>	* 1.  We need some special handling for massless atoms, which
846	>	* will be treated as carrying the entire mass of the cutoff
847	>	* group.
848	>	*/
849	>	massFactors_.clear();
850	>	massFactors_.resize(getNAtoms(), 1.0);
851
852		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
853	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
853	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
854	>	cg = mol->nextCutoffGroup(ci)) {
855
856		totalMass = cg->getMass();
857		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
858		// Check for massless groups - set mfact to 1 if true
859	<	if (totalMass != 0)
860	<	mfact.push_back(atom->getMass()/totalMass);
859	>	if (totalMass != 0)
860	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
861		else
862	<	mfact.push_back( 1.0 );
862	>	massFactors_[atom->getLocalIndex()] = 1.0;
863		}
692	–
864		}
865		}
866
867	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
697	<	std::vector<int> identArray;
867	>	// Build the identArray_
868
869	<	//to avoid memory reallocation, reserve enough space identArray
870	<	identArray.reserve(getNAtoms());
701	<
869	>	identArray_.clear();
870	>	identArray_.reserve(getNAtoms());
871		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
872		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
873	<	identArray.push_back(atom->getIdent());
873	>	identArray_.push_back(atom->getIdent());
874		}
875		}
707	–
708	–	//fill molMembershipArray
709	–	//molMembershipArray is filled by SimCreator
710	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
711	–	for (int i = 0; i < nGlobalAtoms_; i++) {
712	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
713	–	}
876
877	<	//setup fortran simulation
716	<	int nGlobalExcludes = 0;
717	<	int* globalExcludes = NULL;
718	<	int* excludeList = exclude_.getExcludeList();
719	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
720	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
721	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
877	>	//scan topology
878
879	<	if( isError ){
879	>	nExclude = excludedInteractions_.getSize();
880	>	nOneTwo = oneTwoInteractions_.getSize();
881	>	nOneThree = oneThreeInteractions_.getSize();
882	>	nOneFour = oneFourInteractions_.getSize();
883
884	<	sprintf( painCave.errMsg,
885	<	"There was an error setting the simulation information in fortran.\n" );
886	<	painCave.isFatal = 1;
887	<	painCave.severity = OOPSE_ERROR;
729	<	simError();
730	<	}
884	>	int* excludeList = excludedInteractions_.getPairList();
885	>	int* oneTwoList = oneTwoInteractions_.getPairList();
886	>	int* oneThreeList = oneThreeInteractions_.getPairList();
887	>	int* oneFourList = oneFourInteractions_.getPairList();
888
889	<	#ifdef IS_MPI
733	<	sprintf( checkPointMsg,
734	<	"succesfully sent the simulation information to fortran.\n");
735	<	MPIcheckPoint();
736	<	#endif // is_mpi
737	<	}
738	<
739	<
740	<	#ifdef IS_MPI
741	<	void SimInfo::setupFortranParallel() {
742	<
743	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
744	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
745	<	std::vector<int> localToGlobalCutoffGroupIndex;
746	<	SimInfo::MoleculeIterator mi;
747	<	Molecule::AtomIterator ai;
748	<	Molecule::CutoffGroupIterator ci;
749	<	Molecule* mol;
750	<	Atom* atom;
751	<	CutoffGroup* cg;
752	<	mpiSimData parallelData;
753	<	int isError;
754	<
755	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
756	<
757	<	//local index(index in DataStorge) of atom is important
758	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
759	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
760	<	}
761	<
762	<	//local index of cutoff group is trivial, it only depends on the order of travesing
763	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
764	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
765	<	}
766	<
767	<	}
768	<
769	<	//fill up mpiSimData struct
770	<	parallelData.nMolGlobal = getNGlobalMolecules();
771	<	parallelData.nMolLocal = getNMolecules();
772	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
773	<	parallelData.nAtomsLocal = getNAtoms();
774	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
775	<	parallelData.nGroupsLocal = getNCutoffGroups();
776	<	parallelData.myNode = worldRank;
777	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
778	<
779	<	//pass mpiSimData struct and index arrays to fortran
780	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
781	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
782	<	&localToGlobalCutoffGroupIndex[0], &isError);
783	<
784	<	if (isError) {
785	<	sprintf(painCave.errMsg,
786	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
787	<	painCave.isFatal = 1;
788	<	simError();
789	<	}
790	<
791	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
792	<	MPIcheckPoint();
793	<
794	<
795	<	}
796	<
797	<	#endif
798	<
799	<	double SimInfo::calcMaxCutoffRadius() {
800	<
801	<
802	<	std::set<AtomType*> atomTypes;
803	<	std::set<AtomType*>::iterator i;
804	<	std::vector<double> cutoffRadius;
805	<
806	<	//get the unique atom types
807	<	atomTypes = getUniqueAtomTypes();
808	<
809	<	//query the max cutoff radius among these atom types
810	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
811	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
812	<	}
813	<
814	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
815	<	#ifdef IS_MPI
816	<	//pick the max cutoff radius among the processors
817	<	#endif
818	<
819	<	return maxCutoffRadius;
820	<	}
821	<
822	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
823	<
824	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
825	<
826	<	if (!simParams_->haveCutoffRadius()){
827	<	sprintf(painCave.errMsg,
828	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
829	<	"\tOOPSE will use a default value of 15.0 angstroms"
830	<	"\tfor the cutoffRadius.\n");
831	<	painCave.isFatal = 0;
832	<	simError();
833	<	rcut = 15.0;
834	<	} else{
835	<	rcut = simParams_->getCutoffRadius();
836	<	}
837	<
838	<	if (!simParams_->haveSwitchingRadius()){
839	<	sprintf(painCave.errMsg,
840	<	"SimCreator Warning: No value was set for switchingRadius.\n"
841	<	"\tOOPSE will use a default value of\n"
842	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
843	<	painCave.isFatal = 0;
844	<	simError();
845	<	rsw = 0.85 * rcut;
846	<	} else{
847	<	rsw = simParams_->getSwitchingRadius();
848	<	}
849	<
850	<	} else {
851	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
852	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
853	<
854	<	if (simParams_->haveCutoffRadius()) {
855	<	rcut = simParams_->getCutoffRadius();
856	<	} else {
857	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
858	<	rcut = calcMaxCutoffRadius();
859	<	}
860	<
861	<	if (simParams_->haveSwitchingRadius()) {
862	<	rsw  = simParams_->getSwitchingRadius();
863	<	} else {
864	<	rsw = rcut;
865	<	}
866	<
867	<	}
868	<	}
869	<
870	<	void SimInfo::setupCutoff() {
871	<	getCutoff(rcut_, rsw_);
872	<	double rnblist = rcut_ + 1; // skin of neighbor list
873	<
874	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
875	<
876	<	int cp =  TRADITIONAL_CUTOFF_POLICY;
877	<	if (simParams_->haveCutoffPolicy()) {
878	<	std::string myPolicy = simParams_->getCutoffPolicy();
879	<	toUpper(myPolicy);
880	<	if (myPolicy == "MIX") {
881	<	cp = MIX_CUTOFF_POLICY;
882	<	} else {
883	<	if (myPolicy == "MAX") {
884	<	cp = MAX_CUTOFF_POLICY;
885	<	} else {
886	<	if (myPolicy == "TRADITIONAL") {
887	<	cp = TRADITIONAL_CUTOFF_POLICY;
888	<	} else {
889	<	// throw error
890	<	sprintf( painCave.errMsg,
891	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
892	<	painCave.isFatal = 1;
893	<	simError();
894	<	}
895	<	}
896	<	}
897	<	}
898	<
899	<
900	<	if (simParams_->haveSkinThickness()) {
901	<	double skinThickness = simParams_->getSkinThickness();
902	<	}
903	<
904	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
905	<	// also send cutoff notification to electrostatics
906	<	setElectrostaticCutoffRadius(&rcut_, &rsw_);
907	<	}
908	<
909	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
910	<
911	<	int errorOut;
912	<	int esm =  NONE;
913	<	int sm = UNDAMPED;
914	<	double alphaVal;
915	<	double dielectric;
916	<
917	<	errorOut = isError;
918	<	alphaVal = simParams_->getDampingAlpha();
919	<	dielectric = simParams_->getDielectric();
920	<
921	<	if (simParams_->haveElectrostaticSummationMethod()) {
922	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
923	<	toUpper(myMethod);
924	<	if (myMethod == "NONE") {
925	<	esm = NONE;
926	<	} else {
927	<	if (myMethod == "SWITCHING_FUNCTION") {
928	<	esm = SWITCHING_FUNCTION;
929	<	} else {
930	<	if (myMethod == "SHIFTED_POTENTIAL") {
931	<	esm = SHIFTED_POTENTIAL;
932	<	} else {
933	<	if (myMethod == "SHIFTED_FORCE") {
934	<	esm = SHIFTED_FORCE;
935	<	} else {
936	<	if (myMethod == "REACTION_FIELD") {
937	<	esm = REACTION_FIELD;
938	<	} else {
939	<	// throw error
940	<	sprintf( painCave.errMsg,
941	<	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() );
942	<	painCave.isFatal = 1;
943	<	simError();
944	<	}
945	<	}
946	<	}
947	<	}
948	<	}
949	<	}
950	<
951	<	if (simParams_->haveElectrostaticScreeningMethod()) {
952	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
953	<	toUpper(myScreen);
954	<	if (myScreen == "UNDAMPED") {
955	<	sm = UNDAMPED;
956	<	} else {
957	<	if (myScreen == "DAMPED") {
958	<	sm = DAMPED;
959	<	if (!simParams_->haveDampingAlpha()) {
960	<	//throw error
961	<	sprintf( painCave.errMsg,
962	<	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
963	<	painCave.isFatal = 0;
964	<	simError();
965	<	}
966	<	} else {
967	<	// throw error
968	<	sprintf( painCave.errMsg,
969	<	"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
970	<	painCave.isFatal = 1;
971	<	simError();
972	<	}
973	<	}
974	<	}
975	<
976	<	// let's pass some summation method variables to fortran
977	<	setElectrostaticSummationMethod( &esm );
978	<	setScreeningMethod( &sm );
979	<	setDampingAlpha( &alphaVal );
980	<	setReactionFieldDielectric( &dielectric );
981	<	initFortranFF( &esm, &errorOut );
982	<	}
983	<
984	<	void SimInfo::setupSwitchingFunction() {
985	<	int ft = CUBIC;
986	<
987	<	if (simParams_->haveSwitchingFunctionType()) {
988	<	std::string funcType = simParams_->getSwitchingFunctionType();
989	<	toUpper(funcType);
990	<	if (funcType == "CUBIC") {
991	<	ft = CUBIC;
992	<	} else {
993	<	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
994	<	ft = FIFTH_ORDER_POLY;
995	<	} else {
996	<	// throw error
997	<	sprintf( painCave.errMsg,
998	<	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
999	<	painCave.isFatal = 1;
1000	<	simError();
1001	<	}
1002	<	}
1003	<	}
1004	<
1005	<	// send switching function notification to switcheroo
1006	<	setFunctionType(&ft);
1007	<
889	>	topologyDone_ = true;
890		}
891
892		void SimInfo::addProperty(GenericData* genData) {
893		properties_.addProperty(genData);
894		}
895
896	<	void SimInfo::removeProperty(const std::string& propName) {
896	>	void SimInfo::removeProperty(const string& propName) {
897		properties_.removeProperty(propName);
898		}
899
#	Line 1019 | Line 901 | namespace oopse {
901		properties_.clearProperties();
902		}
903
904	<	std::vector<std::string> SimInfo::getPropertyNames() {
904	>	vector<string> SimInfo::getPropertyNames() {
905		return properties_.getPropertyNames();
906		}
907
908	<	std::vector<GenericData*> SimInfo::getProperties() {
908	>	vector<GenericData*> SimInfo::getProperties() {
909		return properties_.getProperties();
910		}
911
912	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
912	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
913		return properties_.getPropertyByName(propName);
914		}
915
#	Line 1041 | Line 923 | namespace oopse {
923		Molecule* mol;
924		RigidBody* rb;
925		Atom* atom;
926	+	CutoffGroup* cg;
927		SimInfo::MoleculeIterator mi;
928		Molecule::RigidBodyIterator rbIter;
929	<	Molecule::AtomIterator atomIter;;
929	>	Molecule::AtomIterator atomIter;
930	>	Molecule::CutoffGroupIterator cgIter;
931
932		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
933
#	Line 1054 | Line 938 | namespace oopse {
938		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
939		rb->setSnapshotManager(sman_);
940		}
941	+
942	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
943	+	cg->setSnapshotManager(sman_);
944	+	}
945		}
946
947		}
#	Line 1063 | Line 951 | namespace oopse {
951		Molecule* mol;
952
953		Vector3d comVel(0.0);
954	<	double totalMass = 0.0;
954	>	RealType totalMass = 0.0;
955
956
957		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
958	<	double mass = mol->getMass();
958	>	RealType mass = mol->getMass();
959		totalMass += mass;
960		comVel += mass * mol->getComVel();
961		}
962
963		#ifdef IS_MPI
964	<	double tmpMass = totalMass;
964	>	RealType tmpMass = totalMass;
965		Vector3d tmpComVel(comVel);
966	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
967	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
966	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
967	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
968		#endif
969
970		comVel /= totalMass;
#	Line 1089 | Line 977 | namespace oopse {
977		Molecule* mol;
978
979		Vector3d com(0.0);
980	<	double totalMass = 0.0;
980	>	RealType totalMass = 0.0;
981
982		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
983	<	double mass = mol->getMass();
983	>	RealType mass = mol->getMass();
984		totalMass += mass;
985		com += mass * mol->getCom();
986		}
987
988		#ifdef IS_MPI
989	<	double tmpMass = totalMass;
989	>	RealType tmpMass = totalMass;
990		Vector3d tmpCom(com);
991	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
992	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
991	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
992	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
993		#endif
994
995		com /= totalMass;
#	Line 1110 | Line 998 | namespace oopse {
998
999		}
1000
1001	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1001	>	ostream& operator <<(ostream& o, SimInfo& info) {
1002
1003		return o;
1004		}
#	Line 1125 | Line 1013 | namespace oopse {
1013		Molecule* mol;
1014
1015
1016	<	double totalMass = 0.0;
1016	>	RealType totalMass = 0.0;
1017
1018
1019		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1020	<	double mass = mol->getMass();
1020	>	RealType mass = mol->getMass();
1021		totalMass += mass;
1022		com += mass * mol->getCom();
1023		comVel += mass * mol->getComVel();
1024		}
1025
1026		#ifdef IS_MPI
1027	<	double tmpMass = totalMass;
1027	>	RealType tmpMass = totalMass;
1028		Vector3d tmpCom(com);
1029		Vector3d tmpComVel(comVel);
1030	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1031	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1032	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1030	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1031	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1032	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1033		#endif
1034
1035		com /= totalMass;
#	Line 1153 | Line 1041 | namespace oopse {
1041
1042
1043		[  Ixx -Ixy  -Ixz ]
1044	<	J =| -Iyx  Iyy  -Iyz |
1044	>	J =| -Iyx  Iyy  -Iyz |
1045		[ -Izx -Iyz   Izz ]
1046		*/
1047
1048		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1049
1050
1051	<	double xx = 0.0;
1052	<	double yy = 0.0;
1053	<	double zz = 0.0;
1054	<	double xy = 0.0;
1055	<	double xz = 0.0;
1056	<	double yz = 0.0;
1051	>	RealType xx = 0.0;
1052	>	RealType yy = 0.0;
1053	>	RealType zz = 0.0;
1054	>	RealType xy = 0.0;
1055	>	RealType xz = 0.0;
1056	>	RealType yz = 0.0;
1057		Vector3d com(0.0);
1058		Vector3d comVel(0.0);
1059
#	Line 1177 | Line 1065 | namespace oopse {
1065		Vector3d thisq(0.0);
1066		Vector3d thisv(0.0);
1067
1068	<	double thisMass = 0.0;
1068	>	RealType thisMass = 0.0;
1069
1070
1071
#	Line 1215 | Line 1103 | namespace oopse {
1103		#ifdef IS_MPI
1104		Mat3x3d tmpI(inertiaTensor);
1105		Vector3d tmpAngMom;
1106	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1107	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1106	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1107	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1108		#endif
1109
1110		return;
#	Line 1237 | Line 1125 | namespace oopse {
1125		Vector3d thisr(0.0);
1126		Vector3d thisp(0.0);
1127
1128	<	double thisMass;
1128	>	RealType thisMass;
1129
1130		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1131		thisMass = mol->getMass();
#	Line 1250 | Line 1138 | namespace oopse {
1138
1139		#ifdef IS_MPI
1140		Vector3d tmpAngMom;
1141	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1141	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1142		#endif
1143
1144		return angularMomentum;
1145		}
1146
1147	<
1148	<	}//end namespace oopse
1147	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1148	>	return IOIndexToIntegrableObject.at(index);
1149	>	}
1150	>
1151	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1152	>	IOIndexToIntegrableObject= v;
1153	>	}
1154
1155	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1156	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1157	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1158	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1159	+	*/
1160	+	void SimInfo::getGyrationalVolume(RealType &volume){
1161	+	Mat3x3d intTensor;
1162	+	RealType det;
1163	+	Vector3d dummyAngMom;
1164	+	RealType sysconstants;
1165	+	RealType geomCnst;
1166	+
1167	+	geomCnst = 3.0/2.0;
1168	+	/* Get the inertial tensor and angular momentum for free*/
1169	+	getInertiaTensor(intTensor,dummyAngMom);
1170	+
1171	+	det = intTensor.determinant();
1172	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1173	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1174	+	return;
1175	+	}
1176	+
1177	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1178	+	Mat3x3d intTensor;
1179	+	Vector3d dummyAngMom;
1180	+	RealType sysconstants;
1181	+	RealType geomCnst;
1182	+
1183	+	geomCnst = 3.0/2.0;
1184	+	/* Get the inertial tensor and angular momentum for free*/
1185	+	getInertiaTensor(intTensor,dummyAngMom);
1186	+
1187	+	detI = intTensor.determinant();
1188	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1189	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1190	+	return;
1191	+	}
1192	+	/*
1193	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1194	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1195	+	sdByGlobalIndex_ = v;
1196	+	}
1197	+
1198	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1199	+	//assert(index < nAtoms_ + nRigidBodies_);
1200	+	return sdByGlobalIndex_.at(index);
1201	+	}
1202	+	*/
1203	+	int SimInfo::getNGlobalConstraints() {
1204	+	int nGlobalConstraints;
1205	+	#ifdef IS_MPI
1206	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1207	+	MPI_COMM_WORLD);
1208	+	#else
1209	+	nGlobalConstraints =  nConstraints_;
1210	+	#endif
1211	+	return nGlobalConstraints;
1212	+	}
1213	+
1214	+	}//end namespace OpenMD
1215	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 726 by chrisfen, Fri Nov 11 15:22:11 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1581 by gezelter, Mon Jun 13 22:13:12 2011 UTC

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