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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 734 by chuckv, Tue Nov 15 16:05:38 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1874 by gezelter, Wed May 15 15:09:35 2013 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, 234107 (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/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"
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"
70	<	#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	<
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;
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();
107	<
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	<
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();
92	>	i !=components.end(); ++i) {
93	>	molStamp = (*i)->getMoleculeStamp();
94	>	nMolWithSameStamp = (*i)->getNMol();
95	>
96	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
97	>
98	>	//calculate atoms in molecules
99	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
100	>
101	>	//calculate atoms in cutoff groups
102	>	int nAtomsInGroups = 0;
103	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
104	>
105	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
106	>	cgStamp = molStamp->getCutoffGroupStamp(j);
107	>	nAtomsInGroups += cgStamp->getNMembers();
108		}
109	<
110	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
111	<	//group therefore the total number of cutoff groups in the system is
112	<	//equal to the total number of atoms minus number of atoms belong to
113	<	//cutoff group defined in meta-data file plus the number of cutoff
114	<	//groups defined in meta-data file
115	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
116	<
117	<	//every free atom (atom does not belong to rigid bodies) is an
118	<	//integrable object therefore the total number of integrable objects
119	<	//in the system is equal to the total number of atoms minus number of
120	<	//atoms belong to rigid body defined in meta-data file plus the number
121	<	//of rigid bodies defined in meta-data file
122	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
123	<	+ nGlobalRigidBodies_;
124	<
125	<	nGlobalMols_ = molStampIds_.size();
147	<
148	<	#ifdef IS_MPI
149	<	molToProcMap_.resize(nGlobalMols_);
150	<	#endif
151	<
109	>
110	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
111	>
112	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
113	>
114	>	//calculate atoms in rigid bodies
115	>	int nAtomsInRigidBodies = 0;
116	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
117	>
118	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
119	>	rbStamp = molStamp->getRigidBodyStamp(j);
120	>	nAtomsInRigidBodies += rbStamp->getNMembers();
121	>	}
122	>
123	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
124	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
125	>
126		}
127	+
128	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
129	+	//group therefore the total number of cutoff groups in the system is
130	+	//equal to the total number of atoms minus number of atoms belong to
131	+	//cutoff group defined in meta-data file plus the number of cutoff
132	+	//groups defined in meta-data file
133
134	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
135	+
136	+	//every free atom (atom does not belong to rigid bodies) is an
137	+	//integrable object therefore the total number of integrable objects
138	+	//in the system is equal to the total number of atoms minus number of
139	+	//atoms belong to rigid body defined in meta-data file plus the number
140	+	//of rigid bodies defined in meta-data file
141	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
142	+	+ nGlobalRigidBodies_;
143	+
144	+	nGlobalMols_ = molStampIds_.size();
145	+	molToProcMap_.resize(nGlobalMols_);
146	+	}
147	+
148		SimInfo::~SimInfo() {
149	<	std::map<int, Molecule*>::iterator i;
149	>	map<int, Molecule*>::iterator i;
150		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
151		delete i->second;
152		}
153		molecules_.clear();
154
161	–	delete stamps_;
155		delete sman_;
156		delete simParams_;
157		delete forceField_;
158		}
159
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	–	}
160
161		bool SimInfo::addMolecule(Molecule* mol) {
162		MoleculeIterator i;
163	<
163	>
164		i = molecules_.find(mol->getGlobalIndex());
165		if (i == molecules_.end() ) {
166	<
167	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
168	<
166	>
167	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
168	>
169		nAtoms_ += mol->getNAtoms();
170		nBonds_ += mol->getNBonds();
171		nBends_ += mol->getNBends();
172		nTorsions_ += mol->getNTorsions();
173	+	nInversions_ += mol->getNInversions();
174		nRigidBodies_ += mol->getNRigidBodies();
175		nIntegrableObjects_ += mol->getNIntegrableObjects();
176		nCutoffGroups_ += mol->getNCutoffGroups();
177		nConstraints_ += mol->getNConstraintPairs();
178	<
179	<	addExcludePairs(mol);
180	<
178	>
179	>	addInteractionPairs(mol);
180	>
181		return true;
182		} else {
183		return false;
184		}
185		}
186	<
186	>
187		bool SimInfo::removeMolecule(Molecule* mol) {
188		MoleculeIterator i;
189		i = molecules_.find(mol->getGlobalIndex());
#	Line 212 | Line 196 | namespace oopse {
196		nBonds_ -= mol->getNBonds();
197		nBends_ -= mol->getNBends();
198		nTorsions_ -= mol->getNTorsions();
199	+	nInversions_ -= mol->getNInversions();
200		nRigidBodies_ -= mol->getNRigidBodies();
201		nIntegrableObjects_ -= mol->getNIntegrableObjects();
202		nCutoffGroups_ -= mol->getNCutoffGroups();
203		nConstraints_ -= mol->getNConstraintPairs();
204
205	<	removeExcludePairs(mol);
205	>	removeInteractionPairs(mol);
206		molecules_.erase(mol->getGlobalIndex());
207
208		delete mol;
#	Line 226 | Line 211 | namespace oopse {
211		} else {
212		return false;
213		}
229	–
230	–
214		}
215
216
#	Line 243 | Line 226 | namespace oopse {
226
227
228		void SimInfo::calcNdf() {
229	<	int ndf_local;
229	>	int ndf_local, nfq_local;
230		MoleculeIterator i;
231	<	std::vector<StuntDouble*>::iterator j;
231	>	vector<StuntDouble*>::iterator j;
232	>	vector<Atom*>::iterator k;
233	>
234		Molecule* mol;
235	<	StuntDouble* integrableObject;
235	>	StuntDouble* sd;
236	>	Atom* atom;
237
238		ndf_local = 0;
239	+	nfq_local = 0;
240
241		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
255	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
256	–	integrableObject = mol->nextIntegrableObject(j)) {
242
243	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
244	+	sd = mol->nextIntegrableObject(j)) {
245	+
246		ndf_local += 3;
247
248	<	if (integrableObject->isDirectional()) {
249	<	if (integrableObject->isLinear()) {
248	>	if (sd->isDirectional()) {
249	>	if (sd->isLinear()) {
250		ndf_local += 2;
251		} else {
252		ndf_local += 3;
253		}
254		}
255	<
256	<	}//end for (integrableObject)
257	<	}// end for (mol)
255	>	}
256	>
257	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
258	>	atom = mol->nextFluctuatingCharge(k)) {
259	>	if (atom->isFluctuatingCharge()) {
260	>	nfq_local++;
261	>	}
262	>	}
263	>	}
264
265	+	ndfLocal_ = ndf_local;
266	+
267		// n_constraints is local, so subtract them on each processor
268		ndf_local -= nConstraints_;
269
270		#ifdef IS_MPI
271	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
271	>	MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
272	>	MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
273	>	MPI::INT, MPI::SUM);
274		#else
275		ndf_ = ndf_local;
276	+	nGlobalFluctuatingCharges_ = nfq_local;
277		#endif
278
279		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 283 | Line 282 | namespace oopse {
282
283		}
284
285	+	int SimInfo::getFdf() {
286	+	#ifdef IS_MPI
287	+	MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
288	+	#else
289	+	fdf_ = fdf_local;
290	+	#endif
291	+	return fdf_;
292	+	}
293	+
294	+	unsigned int SimInfo::getNLocalCutoffGroups(){
295	+	int nLocalCutoffAtoms = 0;
296	+	Molecule* mol;
297	+	MoleculeIterator mi;
298	+	CutoffGroup* cg;
299	+	Molecule::CutoffGroupIterator ci;
300	+
301	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
302	+
303	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
304	+	cg = mol->nextCutoffGroup(ci)) {
305	+	nLocalCutoffAtoms += cg->getNumAtom();
306	+
307	+	}
308	+	}
309	+
310	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
311	+	}
312	+
313		void SimInfo::calcNdfRaw() {
314		int ndfRaw_local;
315
316		MoleculeIterator i;
317	<	std::vector<StuntDouble*>::iterator j;
317	>	vector<StuntDouble*>::iterator j;
318		Molecule* mol;
319	<	StuntDouble* integrableObject;
319	>	StuntDouble* sd;
320
321		// Raw degrees of freedom that we have to set
322		ndfRaw_local = 0;
323
324		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
298	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
299	–	integrableObject = mol->nextIntegrableObject(j)) {
325
326	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
327	+	sd = mol->nextIntegrableObject(j)) {
328	+
329		ndfRaw_local += 3;
330
331	<	if (integrableObject->isDirectional()) {
332	<	if (integrableObject->isLinear()) {
331	>	if (sd->isDirectional()) {
332	>	if (sd->isLinear()) {
333		ndfRaw_local += 2;
334		} else {
335		ndfRaw_local += 3;
#	Line 312 | Line 340 | namespace oopse {
340		}
341
342		#ifdef IS_MPI
343	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
343	>	MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
344		#else
345		ndfRaw_ = ndfRaw_local;
346		#endif
#	Line 325 | Line 353 | namespace oopse {
353
354
355		#ifdef IS_MPI
356	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
356	>	MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
357	>	MPI::INT, MPI::SUM);
358		#else
359		ndfTrans_ = ndfTrans_local;
360		#endif
#	Line 334 | Line 363 | namespace oopse {
363
364		}
365
366	<	void SimInfo::addExcludePairs(Molecule* mol) {
367	<	std::vector<Bond*>::iterator bondIter;
368	<	std::vector<Bend*>::iterator bendIter;
369	<	std::vector<Torsion*>::iterator torsionIter;
366	>	void SimInfo::addInteractionPairs(Molecule* mol) {
367	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
368	>	vector<Bond*>::iterator bondIter;
369	>	vector<Bend*>::iterator bendIter;
370	>	vector<Torsion*>::iterator torsionIter;
371	>	vector<Inversion*>::iterator inversionIter;
372		Bond* bond;
373		Bend* bend;
374		Torsion* torsion;
375	+	Inversion* inversion;
376		int a;
377		int b;
378		int c;
379		int d;
380	+
381	+	// atomGroups can be used to add special interaction maps between
382	+	// groups of atoms that are in two separate rigid bodies.
383	+	// However, most site-site interactions between two rigid bodies
384	+	// are probably not special, just the ones between the physically
385	+	// bonded atoms.  Interactions *within* a single rigid body should
386	+	// always be excluded.  These are done at the bottom of this
387	+	// function.
388	+
389	+	map<int, set<int> > atomGroups;
390	+	Molecule::RigidBodyIterator rbIter;
391	+	RigidBody* rb;
392	+	Molecule::IntegrableObjectIterator ii;
393	+	StuntDouble* sd;
394
395	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
395	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
396	>	sd = mol->nextIntegrableObject(ii)) {
397	>
398	>	if (sd->isRigidBody()) {
399	>	rb = static_cast<RigidBody*>(sd);
400	>	vector<Atom*> atoms = rb->getAtoms();
401	>	set<int> rigidAtoms;
402	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
403	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
404	>	}
405	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
406	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
407	>	}
408	>	} else {
409	>	set<int> oneAtomSet;
410	>	oneAtomSet.insert(sd->getGlobalIndex());
411	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
412	>	}
413	>	}
414	>
415	>	for (bond= mol->beginBond(bondIter); bond != NULL;
416	>	bond = mol->nextBond(bondIter)) {
417	>
418		a = bond->getAtomA()->getGlobalIndex();
419	<	b = bond->getAtomB()->getGlobalIndex();
420	<	exclude_.addPair(a, b);
419	>	b = bond->getAtomB()->getGlobalIndex();
420	>
421	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
422	>	oneTwoInteractions_.addPair(a, b);
423	>	} else {
424	>	excludedInteractions_.addPair(a, b);
425	>	}
426		}
427
428	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
428	>	for (bend= mol->beginBend(bendIter); bend != NULL;
429	>	bend = mol->nextBend(bendIter)) {
430	>
431		a = bend->getAtomA()->getGlobalIndex();
432		b = bend->getAtomB()->getGlobalIndex();
433		c = bend->getAtomC()->getGlobalIndex();
434	+
435	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
436	+	oneTwoInteractions_.addPair(a, b);
437	+	oneTwoInteractions_.addPair(b, c);
438	+	} else {
439	+	excludedInteractions_.addPair(a, b);
440	+	excludedInteractions_.addPair(b, c);
441	+	}
442
443	<	exclude_.addPair(a, b);
444	<	exclude_.addPair(a, c);
445	<	exclude_.addPair(b, c);
443	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
444	>	oneThreeInteractions_.addPair(a, c);
445	>	} else {
446	>	excludedInteractions_.addPair(a, c);
447	>	}
448		}
449
450	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
450	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
451	>	torsion = mol->nextTorsion(torsionIter)) {
452	>
453		a = torsion->getAtomA()->getGlobalIndex();
454		b = torsion->getAtomB()->getGlobalIndex();
455		c = torsion->getAtomC()->getGlobalIndex();
456	<	d = torsion->getAtomD()->getGlobalIndex();
456	>	d = torsion->getAtomD()->getGlobalIndex();
457
458	<	exclude_.addPair(a, b);
459	<	exclude_.addPair(a, c);
460	<	exclude_.addPair(a, d);
461	<	exclude_.addPair(b, c);
462	<	exclude_.addPair(b, d);
463	<	exclude_.addPair(c, d);
458	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
459	>	oneTwoInteractions_.addPair(a, b);
460	>	oneTwoInteractions_.addPair(b, c);
461	>	oneTwoInteractions_.addPair(c, d);
462	>	} else {
463	>	excludedInteractions_.addPair(a, b);
464	>	excludedInteractions_.addPair(b, c);
465	>	excludedInteractions_.addPair(c, d);
466	>	}
467	>
468	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
469	>	oneThreeInteractions_.addPair(a, c);
470	>	oneThreeInteractions_.addPair(b, d);
471	>	} else {
472	>	excludedInteractions_.addPair(a, c);
473	>	excludedInteractions_.addPair(b, d);
474	>	}
475	>
476	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
477	>	oneFourInteractions_.addPair(a, d);
478	>	} else {
479	>	excludedInteractions_.addPair(a, d);
480	>	}
481		}
482
483	<	Molecule::RigidBodyIterator rbIter;
484	<	RigidBody* rb;
485	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
486	<	std::vector<Atom*> atoms = rb->getAtoms();
487	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
488	<	for (int j = i + 1; j < atoms.size(); ++j) {
483	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
484	>	inversion = mol->nextInversion(inversionIter)) {
485	>
486	>	a = inversion->getAtomA()->getGlobalIndex();
487	>	b = inversion->getAtomB()->getGlobalIndex();
488	>	c = inversion->getAtomC()->getGlobalIndex();
489	>	d = inversion->getAtomD()->getGlobalIndex();
490	>
491	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
492	>	oneTwoInteractions_.addPair(a, b);
493	>	oneTwoInteractions_.addPair(a, c);
494	>	oneTwoInteractions_.addPair(a, d);
495	>	} else {
496	>	excludedInteractions_.addPair(a, b);
497	>	excludedInteractions_.addPair(a, c);
498	>	excludedInteractions_.addPair(a, d);
499	>	}
500	>
501	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
502	>	oneThreeInteractions_.addPair(b, c);
503	>	oneThreeInteractions_.addPair(b, d);
504	>	oneThreeInteractions_.addPair(c, d);
505	>	} else {
506	>	excludedInteractions_.addPair(b, c);
507	>	excludedInteractions_.addPair(b, d);
508	>	excludedInteractions_.addPair(c, d);
509	>	}
510	>	}
511	>
512	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
513	>	rb = mol->nextRigidBody(rbIter)) {
514	>	vector<Atom*> atoms = rb->getAtoms();
515	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
516	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
517		a = atoms[i]->getGlobalIndex();
518		b = atoms[j]->getGlobalIndex();
519	<	exclude_.addPair(a, b);
519	>	excludedInteractions_.addPair(a, b);
520		}
521		}
522		}
523
524		}
525
526	<	void SimInfo::removeExcludePairs(Molecule* mol) {
527	<	std::vector<Bond*>::iterator bondIter;
528	<	std::vector<Bend*>::iterator bendIter;
529	<	std::vector<Torsion*>::iterator torsionIter;
526	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
527	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
528	>	vector<Bond*>::iterator bondIter;
529	>	vector<Bend*>::iterator bendIter;
530	>	vector<Torsion*>::iterator torsionIter;
531	>	vector<Inversion*>::iterator inversionIter;
532		Bond* bond;
533		Bend* bend;
534		Torsion* torsion;
535	+	Inversion* inversion;
536		int a;
537		int b;
538		int c;
539		int d;
540	+
541	+	map<int, set<int> > atomGroups;
542	+	Molecule::RigidBodyIterator rbIter;
543	+	RigidBody* rb;
544	+	Molecule::IntegrableObjectIterator ii;
545	+	StuntDouble* sd;
546
547	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
547	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
548	>	sd = mol->nextIntegrableObject(ii)) {
549	>
550	>	if (sd->isRigidBody()) {
551	>	rb = static_cast<RigidBody*>(sd);
552	>	vector<Atom*> atoms = rb->getAtoms();
553	>	set<int> rigidAtoms;
554	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
555	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
556	>	}
557	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
558	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
559	>	}
560	>	} else {
561	>	set<int> oneAtomSet;
562	>	oneAtomSet.insert(sd->getGlobalIndex());
563	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
564	>	}
565	>	}
566	>
567	>	for (bond= mol->beginBond(bondIter); bond != NULL;
568	>	bond = mol->nextBond(bondIter)) {
569	>
570		a = bond->getAtomA()->getGlobalIndex();
571	<	b = bond->getAtomB()->getGlobalIndex();
572	<	exclude_.removePair(a, b);
571	>	b = bond->getAtomB()->getGlobalIndex();
572	>
573	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
574	>	oneTwoInteractions_.removePair(a, b);
575	>	} else {
576	>	excludedInteractions_.removePair(a, b);
577	>	}
578		}
579
580	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
580	>	for (bend= mol->beginBend(bendIter); bend != NULL;
581	>	bend = mol->nextBend(bendIter)) {
582	>
583		a = bend->getAtomA()->getGlobalIndex();
584		b = bend->getAtomB()->getGlobalIndex();
585		c = bend->getAtomC()->getGlobalIndex();
586	+
587	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
588	+	oneTwoInteractions_.removePair(a, b);
589	+	oneTwoInteractions_.removePair(b, c);
590	+	} else {
591	+	excludedInteractions_.removePair(a, b);
592	+	excludedInteractions_.removePair(b, c);
593	+	}
594
595	<	exclude_.removePair(a, b);
596	<	exclude_.removePair(a, c);
597	<	exclude_.removePair(b, c);
595	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
596	>	oneThreeInteractions_.removePair(a, c);
597	>	} else {
598	>	excludedInteractions_.removePair(a, c);
599	>	}
600		}
601
602	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
602	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
603	>	torsion = mol->nextTorsion(torsionIter)) {
604	>
605		a = torsion->getAtomA()->getGlobalIndex();
606		b = torsion->getAtomB()->getGlobalIndex();
607		c = torsion->getAtomC()->getGlobalIndex();
608	<	d = torsion->getAtomD()->getGlobalIndex();
608	>	d = torsion->getAtomD()->getGlobalIndex();
609	>
610	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
611	>	oneTwoInteractions_.removePair(a, b);
612	>	oneTwoInteractions_.removePair(b, c);
613	>	oneTwoInteractions_.removePair(c, d);
614	>	} else {
615	>	excludedInteractions_.removePair(a, b);
616	>	excludedInteractions_.removePair(b, c);
617	>	excludedInteractions_.removePair(c, d);
618	>	}
619
620	<	exclude_.removePair(a, b);
621	<	exclude_.removePair(a, c);
622	<	exclude_.removePair(a, d);
623	<	exclude_.removePair(b, c);
624	<	exclude_.removePair(b, d);
625	<	exclude_.removePair(c, d);
620	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
621	>	oneThreeInteractions_.removePair(a, c);
622	>	oneThreeInteractions_.removePair(b, d);
623	>	} else {
624	>	excludedInteractions_.removePair(a, c);
625	>	excludedInteractions_.removePair(b, d);
626	>	}
627	>
628	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
629	>	oneFourInteractions_.removePair(a, d);
630	>	} else {
631	>	excludedInteractions_.removePair(a, d);
632	>	}
633		}
634
635	<	Molecule::RigidBodyIterator rbIter;
636	<	RigidBody* rb;
637	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
638	<	std::vector<Atom*> atoms = rb->getAtoms();
639	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
640	<	for (int j = i + 1; j < atoms.size(); ++j) {
635	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
636	>	inversion = mol->nextInversion(inversionIter)) {
637	>
638	>	a = inversion->getAtomA()->getGlobalIndex();
639	>	b = inversion->getAtomB()->getGlobalIndex();
640	>	c = inversion->getAtomC()->getGlobalIndex();
641	>	d = inversion->getAtomD()->getGlobalIndex();
642	>
643	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
644	>	oneTwoInteractions_.removePair(a, b);
645	>	oneTwoInteractions_.removePair(a, c);
646	>	oneTwoInteractions_.removePair(a, d);
647	>	} else {
648	>	excludedInteractions_.removePair(a, b);
649	>	excludedInteractions_.removePair(a, c);
650	>	excludedInteractions_.removePair(a, d);
651	>	}
652	>
653	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
654	>	oneThreeInteractions_.removePair(b, c);
655	>	oneThreeInteractions_.removePair(b, d);
656	>	oneThreeInteractions_.removePair(c, d);
657	>	} else {
658	>	excludedInteractions_.removePair(b, c);
659	>	excludedInteractions_.removePair(b, d);
660	>	excludedInteractions_.removePair(c, d);
661	>	}
662	>	}
663	>
664	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
665	>	rb = mol->nextRigidBody(rbIter)) {
666	>	vector<Atom*> atoms = rb->getAtoms();
667	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
668	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
669		a = atoms[i]->getGlobalIndex();
670		b = atoms[j]->getGlobalIndex();
671	<	exclude_.removePair(a, b);
671	>	excludedInteractions_.removePair(a, b);
672		}
673		}
674		}
675	<
675	>
676		}
677	<
678	<
677	>
678	>
679		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
680		int curStampId;
681	<
681	>
682		//index from 0
683		curStampId = moleculeStamps_.size();
684
#	Line 459 | Line 686 | namespace oopse {
686		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
687		}
688
462	–	void SimInfo::update() {
689
690	<	setupSimType();
691	<
692	<	#ifdef IS_MPI
693	<	setupFortranParallel();
694	<	#endif
695	<
696	<	setupFortranSim();
697	<
698	<	//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	<
690	>	/**
691	>	* update
692	>	*
693	>	*  Performs the global checks and variable settings after the
694	>	*  objects have been created.
695	>	*
696	>	*/
697	>	void SimInfo::update() {
698	>	setupSimVariables();
699		calcNdf();
700		calcNdfRaw();
701		calcNdfTrans();
492	–
493	–	fortranInitialized_ = true;
702		}
703	<
704	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
703	>
704	>	/**
705	>	* getSimulatedAtomTypes
706	>	*
707	>	* Returns an STL set of AtomType* that are actually present in this
708	>	* simulation.  Must query all processors to assemble this information.
709	>	*
710	>	*/
711	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
712		SimInfo::MoleculeIterator mi;
713		Molecule* mol;
714		Molecule::AtomIterator ai;
715		Atom* atom;
716	<	std::set<AtomType*> atomTypes;
717	<
716	>	set<AtomType*> atomTypes;
717	>
718		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
719	<
720	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
719	>	for(atom = mol->beginAtom(ai); atom != NULL;
720	>	atom = mol->nextAtom(ai)) {
721		atomTypes.insert(atom->getAtomType());
722	<	}
723	<
722	>	}
723	>	}
724	>
725	>	#ifdef IS_MPI
726	>
727	>	// loop over the found atom types on this processor, and add their
728	>	// numerical idents to a vector:
729	>
730	>	vector<int> foundTypes;
731	>	set<AtomType*>::iterator i;
732	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
733	>	foundTypes.push_back( (*i)->getIdent() );
734	>
735	>	// count_local holds the number of found types on this processor
736	>	int count_local = foundTypes.size();
737	>
738	>	int nproc = MPI::COMM_WORLD.Get_size();
739	>
740	>	// we need arrays to hold the counts and displacement vectors for
741	>	// all processors
742	>	vector<int> counts(nproc, 0);
743	>	vector<int> disps(nproc, 0);
744	>
745	>	// fill the counts array
746	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
747	>	1, MPI::INT);
748	>
749	>	// use the processor counts to compute the displacement array
750	>	disps[0] = 0;
751	>	int totalCount = counts[0];
752	>	for (int iproc = 1; iproc < nproc; iproc++) {
753	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
754	>	totalCount += counts[iproc];
755		}
756
757	+	// we need a (possibly redundant) set of all found types:
758	+	vector<int> ftGlobal(totalCount);
759	+
760	+	// now spray out the foundTypes to all the other processors:
761	+	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
762	+	&ftGlobal[0], &counts[0], &disps[0],
763	+	MPI::INT);
764	+
765	+	vector<int>::iterator j;
766	+
767	+	// foundIdents is a stl set, so inserting an already found ident
768	+	// will have no effect.
769	+	set<int> foundIdents;
770	+
771	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
772	+	foundIdents.insert((*j));
773	+
774	+	// now iterate over the foundIdents and get the actual atom types
775	+	// that correspond to these:
776	+	set<int>::iterator it;
777	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
778	+	atomTypes.insert( forceField_->getAtomType((*it)) );
779	+
780	+	#endif
781	+
782		return atomTypes;
783		}
784
514	–	void SimInfo::setupSimType() {
515	–	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 useSC = 0;
523	–	int useCharge = 0;
524	–	int useDirectional = 0;
525	–	int useDipole = 0;
526	–	int useGayBerne = 0;
527	–	int useSticky = 0;
528	–	int useStickyPower = 0;
529	–	int useShape = 0;
530	–	int useFLARB = 0; //it is not in AtomType yet
531	–	int useDirectionalAtom = 0;
532	–	int useElectrostatics = 0;
533	–	//usePBC and useRF are from simParams
534	–	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
535	–	int useRF;
536	–	int useSF;
537	–	std::string myMethod;
785
786	<	// set the useRF logical
787	<	useRF = 0;
788	<	useSF = 0;
786	>	int getGlobalCountOfType(AtomType* atype) {
787	>	/*
788	>	set<AtomType*> atypes = getSimulatedAtomTypes();
789	>	map<AtomType*, int> counts_;
790
791	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
792	+	for(atom = mol->beginAtom(ai); atom != NULL;
793	+	atom = mol->nextAtom(ai)) {
794	+	atom->getAtomType();
795	+	}
796	+	}
797	+	*/
798	+	return 0;
799	+	}
800
801	<	if (simParams_->haveElectrostaticSummationMethod()) {
802	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
803	<	toUpper(myMethod);
804	<	if (myMethod == "REACTION_FIELD") {
805	<	useRF=1;
806	<	} else {
807	<	if (myMethod == "SHIFTED_FORCE") {
808	<	useSF = 1;
552	<	}
801	>	void SimInfo::setupSimVariables() {
802	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
803	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
804	>	// parameter is true
805	>	calcBoxDipole_ = false;
806	>	if ( simParams_->haveAccumulateBoxDipole() )
807	>	if ( simParams_->getAccumulateBoxDipole() ) {
808	>	calcBoxDipole_ = true;
809		}
810	<	}
811	<
810	>
811	>	set<AtomType*>::iterator i;
812	>	set<AtomType*> atomTypes;
813	>	atomTypes = getSimulatedAtomTypes();
814	>	bool usesElectrostatic = false;
815	>	bool usesMetallic = false;
816	>	bool usesDirectional = false;
817	>	bool usesFluctuatingCharges =  false;
818		//loop over all of the atom types
819		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
820	<	useLennardJones |= (*i)->isLennardJones();
821	<	useElectrostatic |= (*i)->isElectrostatic();
822	<	useEAM |= (*i)->isEAM();
823	<	useSC |= (*i)->isSC();
562	<	useCharge |= (*i)->isCharge();
563	<	useDirectional |= (*i)->isDirectional();
564	<	useDipole |= (*i)->isDipole();
565	<	useGayBerne |= (*i)->isGayBerne();
566	<	useSticky |= (*i)->isSticky();
567	<	useStickyPower |= (*i)->isStickyPower();
568	<	useShape |= (*i)->isShape();
820	>	usesElectrostatic |= (*i)->isElectrostatic();
821	>	usesMetallic |= (*i)->isMetal();
822	>	usesDirectional |= (*i)->isDirectional();
823	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
824		}
825
826	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
827	<	useDirectionalAtom = 1;
828	<	}
826	>	#ifdef IS_MPI
827	>	bool temp;
828	>	temp = usesDirectional;
829	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
830	>	MPI::LOR);
831	>
832	>	temp = usesMetallic;
833	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
834	>	MPI::LOR);
835	>
836	>	temp = usesElectrostatic;
837	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
838	>	MPI::LOR);
839
840	<	if (useCharge || useDipole) {
841	<	useElectrostatics = 1;
842	<	}
840	>	temp = usesFluctuatingCharges;
841	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
842	>	MPI::LOR);
843	>	#else
844
845	<	#ifdef IS_MPI
846	<	int temp;
845	>	usesDirectionalAtoms_ = usesDirectional;
846	>	usesMetallicAtoms_ = usesMetallic;
847	>	usesElectrostaticAtoms_ = usesElectrostatic;
848	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
849
850	<	temp = usePBC;
851	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
850	>	#endif
851	>
852	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
853	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
854	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
855	>	}
856
585	–	temp = useDirectionalAtom;
586	–	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
857
858	<	temp = useLennardJones;
859	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
858	>	vector<int> SimInfo::getGlobalAtomIndices() {
859	>	SimInfo::MoleculeIterator mi;
860	>	Molecule* mol;
861	>	Molecule::AtomIterator ai;
862	>	Atom* atom;
863
864	<	temp = useElectrostatics;
592	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
593	<
594	<	temp = useCharge;
595	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
596	<
597	<	temp = useDipole;
598	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
599	<
600	<	temp = useSticky;
601	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
602	<
603	<	temp = useStickyPower;
604	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
864	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
865
866	<	temp = useGayBerne;
867	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
866	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
867	>
868	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
869	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
870	>	}
871	>	}
872	>	return GlobalAtomIndices;
873	>	}
874
609	–	temp = useEAM;
610	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
875
876	<	temp = useSC;
877	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
878	<
879	<	temp = useShape;
880	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
876	>	vector<int> SimInfo::getGlobalGroupIndices() {
877	>	SimInfo::MoleculeIterator mi;
878	>	Molecule* mol;
879	>	Molecule::CutoffGroupIterator ci;
880	>	CutoffGroup* cg;
881
882	<	temp = useFLARB;
883	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
884	<
621	<	temp = useRF;
622	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
623	<
624	<	temp = useSF;
625	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
626	<
627	<	#endif
628	<
629	<	fInfo_.SIM_uses_PBC = usePBC;
630	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
631	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
632	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
633	<	fInfo_.SIM_uses_Charges = useCharge;
634	<	fInfo_.SIM_uses_Dipoles = useDipole;
635	<	fInfo_.SIM_uses_Sticky = useSticky;
636	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
637	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
638	<	fInfo_.SIM_uses_EAM = useEAM;
639	<	fInfo_.SIM_uses_SC = useSC;
640	<	fInfo_.SIM_uses_Shapes = useShape;
641	<	fInfo_.SIM_uses_FLARB = useFLARB;
642	<	fInfo_.SIM_uses_RF = useRF;
643	<	fInfo_.SIM_uses_SF = useSF;
644	<
645	<	if( myMethod == "REACTION_FIELD") {
882	>	vector<int> GlobalGroupIndices;
883	>
884	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
885
886	<	if (simParams_->haveDielectric()) {
887	<	fInfo_.dielect = simParams_->getDielectric();
888	<	} else {
889	<	sprintf(painCave.errMsg,
890	<	"SimSetup Error: No Dielectric constant was set.\n"
891	<	"\tYou are trying to use Reaction Field without"
653	<	"\tsetting a dielectric constant!\n");
654	<	painCave.isFatal = 1;
655	<	simError();
656	<	}
886	>	//local index of cutoff group is trivial, it only depends on the
887	>	//order of travesing
888	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
889	>	cg = mol->nextCutoffGroup(ci)) {
890	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
891	>	}
892		}
893	<
893	>	return GlobalGroupIndices;
894		}
895
661	–	void SimInfo::setupFortranSim() {
662	–	int isError;
663	–	int nExclude;
664	–	std::vector<int> fortranGlobalGroupMembership;
665	–
666	–	nExclude = exclude_.getSize();
667	–	isError = 0;
896
897	<	//globalGroupMembership_ is filled by SimCreator
670	<	for (int i = 0; i < nGlobalAtoms_; i++) {
671	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
672	<	}
897	>	void SimInfo::prepareTopology() {
898
899		//calculate mass ratio of cutoff group
675	–	std::vector<double> mfact;
900		SimInfo::MoleculeIterator mi;
901		Molecule* mol;
902		Molecule::CutoffGroupIterator ci;
903		CutoffGroup* cg;
904		Molecule::AtomIterator ai;
905		Atom* atom;
906	<	double totalMass;
906	>	RealType totalMass;
907
908	<	//to avoid memory reallocation, reserve enough space for mfact
909	<	mfact.reserve(getNCutoffGroups());
908	>	/**
909	>	* The mass factor is the relative mass of an atom to the total
910	>	* mass of the cutoff group it belongs to.  By default, all atoms
911	>	* are their own cutoff groups, and therefore have mass factors of
912	>	* 1.  We need some special handling for massless atoms, which
913	>	* will be treated as carrying the entire mass of the cutoff
914	>	* group.
915	>	*/
916	>	massFactors_.clear();
917	>	massFactors_.resize(getNAtoms(), 1.0);
918
919		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
920	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
920	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
921	>	cg = mol->nextCutoffGroup(ci)) {
922
923		totalMass = cg->getMass();
924		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
925		// Check for massless groups - set mfact to 1 if true
926	<	if (totalMass != 0)
927	<	mfact.push_back(atom->getMass()/totalMass);
926	>	if (totalMass != 0)
927	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
928		else
929	<	mfact.push_back( 1.0 );
929	>	massFactors_[atom->getLocalIndex()] = 1.0;
930		}
698	–
931		}
932		}
933
934	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
703	<	std::vector<int> identArray;
934	>	// Build the identArray_
935
936	<	//to avoid memory reallocation, reserve enough space identArray
937	<	identArray.reserve(getNAtoms());
707	<
936	>	identArray_.clear();
937	>	identArray_.reserve(getNAtoms());
938		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
939		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
940	<	identArray.push_back(atom->getIdent());
940	>	identArray_.push_back(atom->getIdent());
941		}
942		}
713	–
714	–	//fill molMembershipArray
715	–	//molMembershipArray is filled by SimCreator
716	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
717	–	for (int i = 0; i < nGlobalAtoms_; i++) {
718	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
719	–	}
943
944	<	//setup fortran simulation
722	<	int nGlobalExcludes = 0;
723	<	int* globalExcludes = NULL;
724	<	int* excludeList = exclude_.getExcludeList();
725	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
726	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
727	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
728	<
729	<	if( isError ){
730	<
731	<	sprintf( painCave.errMsg,
732	<	"There was an error setting the simulation information in fortran.\n" );
733	<	painCave.isFatal = 1;
734	<	painCave.severity = OOPSE_ERROR;
735	<	simError();
736	<	}
737	<
738	<	#ifdef IS_MPI
739	<	sprintf( checkPointMsg,
740	<	"succesfully sent the simulation information to fortran.\n");
741	<	MPIcheckPoint();
742	<	#endif // is_mpi
743	<	}
744	<
745	<
746	<	#ifdef IS_MPI
747	<	void SimInfo::setupFortranParallel() {
748	<
749	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
750	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
751	<	std::vector<int> localToGlobalCutoffGroupIndex;
752	<	SimInfo::MoleculeIterator mi;
753	<	Molecule::AtomIterator ai;
754	<	Molecule::CutoffGroupIterator ci;
755	<	Molecule* mol;
756	<	Atom* atom;
757	<	CutoffGroup* cg;
758	<	mpiSimData parallelData;
759	<	int isError;
760	<
761	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
762	<
763	<	//local index(index in DataStorge) of atom is important
764	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
765	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
766	<	}
767	<
768	<	//local index of cutoff group is trivial, it only depends on the order of travesing
769	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
770	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
771	<	}
772	<
773	<	}
774	<
775	<	//fill up mpiSimData struct
776	<	parallelData.nMolGlobal = getNGlobalMolecules();
777	<	parallelData.nMolLocal = getNMolecules();
778	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
779	<	parallelData.nAtomsLocal = getNAtoms();
780	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
781	<	parallelData.nGroupsLocal = getNCutoffGroups();
782	<	parallelData.myNode = worldRank;
783	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
784	<
785	<	//pass mpiSimData struct and index arrays to fortran
786	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
787	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
788	<	&localToGlobalCutoffGroupIndex[0], &isError);
789	<
790	<	if (isError) {
791	<	sprintf(painCave.errMsg,
792	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
793	<	painCave.isFatal = 1;
794	<	simError();
795	<	}
796	<
797	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
798	<	MPIcheckPoint();
799	<
800	<
801	<	}
802	<
803	<	#endif
804	<
805	<	double SimInfo::calcMaxCutoffRadius() {
806	<
807	<
808	<	std::set<AtomType*> atomTypes;
809	<	std::set<AtomType*>::iterator i;
810	<	std::vector<double> cutoffRadius;
811	<
812	<	//get the unique atom types
813	<	atomTypes = getUniqueAtomTypes();
814	<
815	<	//query the max cutoff radius among these atom types
816	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
817	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
818	<	}
819	<
820	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
821	<	#ifdef IS_MPI
822	<	//pick the max cutoff radius among the processors
823	<	#endif
824	<
825	<	return maxCutoffRadius;
826	<	}
827	<
828	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
829	<
830	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
831	<
832	<	if (!simParams_->haveCutoffRadius()){
833	<	sprintf(painCave.errMsg,
834	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
835	<	"\tOOPSE will use a default value of 15.0 angstroms"
836	<	"\tfor the cutoffRadius.\n");
837	<	painCave.isFatal = 0;
838	<	simError();
839	<	rcut = 15.0;
840	<	} else{
841	<	rcut = simParams_->getCutoffRadius();
842	<	}
843	<
844	<	if (!simParams_->haveSwitchingRadius()){
845	<	sprintf(painCave.errMsg,
846	<	"SimCreator Warning: No value was set for switchingRadius.\n"
847	<	"\tOOPSE will use a default value of\n"
848	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
849	<	painCave.isFatal = 0;
850	<	simError();
851	<	rsw = 0.85 * rcut;
852	<	} else{
853	<	rsw = simParams_->getSwitchingRadius();
854	<	}
855	<
856	<	} else {
857	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
858	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
859	<
860	<	if (simParams_->haveCutoffRadius()) {
861	<	rcut = simParams_->getCutoffRadius();
862	<	} else {
863	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
864	<	rcut = calcMaxCutoffRadius();
865	<	}
866	<
867	<	if (simParams_->haveSwitchingRadius()) {
868	<	rsw  = simParams_->getSwitchingRadius();
869	<	} else {
870	<	rsw = rcut;
871	<	}
872	<
873	<	}
874	<	}
875	<
876	<	void SimInfo::setupCutoff() {
877	<	getCutoff(rcut_, rsw_);
878	<	double rnblist = rcut_ + 1; // skin of neighbor list
879	<
880	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
881	<
882	<	int cp =  TRADITIONAL_CUTOFF_POLICY;
883	<	if (simParams_->haveCutoffPolicy()) {
884	<	std::string myPolicy = simParams_->getCutoffPolicy();
885	<	toUpper(myPolicy);
886	<	if (myPolicy == "MIX") {
887	<	cp = MIX_CUTOFF_POLICY;
888	<	} else {
889	<	if (myPolicy == "MAX") {
890	<	cp = MAX_CUTOFF_POLICY;
891	<	} else {
892	<	if (myPolicy == "TRADITIONAL") {
893	<	cp = TRADITIONAL_CUTOFF_POLICY;
894	<	} else {
895	<	// throw error
896	<	sprintf( painCave.errMsg,
897	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
898	<	painCave.isFatal = 1;
899	<	simError();
900	<	}
901	<	}
902	<	}
903	<	}
904	<
905	<
906	<	if (simParams_->haveSkinThickness()) {
907	<	double skinThickness = simParams_->getSkinThickness();
908	<	}
909	<
910	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
911	<	// also send cutoff notification to electrostatics
912	<	setElectrostaticCutoffRadius(&rcut_, &rsw_);
944	>	topologyDone_ = true;
945		}
946
915	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
916	–
917	–	int errorOut;
918	–	int esm =  NONE;
919	–	int sm = UNDAMPED;
920	–	double alphaVal;
921	–	double dielectric;
922	–
923	–	errorOut = isError;
924	–	alphaVal = simParams_->getDampingAlpha();
925	–	dielectric = simParams_->getDielectric();
926	–
927	–	if (simParams_->haveElectrostaticSummationMethod()) {
928	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
929	–	toUpper(myMethod);
930	–	if (myMethod == "NONE") {
931	–	esm = NONE;
932	–	} else {
933	–	if (myMethod == "SWITCHING_FUNCTION") {
934	–	esm = SWITCHING_FUNCTION;
935	–	} else {
936	–	if (myMethod == "SHIFTED_POTENTIAL") {
937	–	esm = SHIFTED_POTENTIAL;
938	–	} else {
939	–	if (myMethod == "SHIFTED_FORCE") {
940	–	esm = SHIFTED_FORCE;
941	–	} else {
942	–	if (myMethod == "REACTION_FIELD") {
943	–	esm = REACTION_FIELD;
944	–	} else {
945	–	// throw error
946	–	sprintf( painCave.errMsg,
947	–	"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() );
948	–	painCave.isFatal = 1;
949	–	simError();
950	–	}
951	–	}
952	–	}
953	–	}
954	–	}
955	–	}
956	–
957	–	if (simParams_->haveElectrostaticScreeningMethod()) {
958	–	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
959	–	toUpper(myScreen);
960	–	if (myScreen == "UNDAMPED") {
961	–	sm = UNDAMPED;
962	–	} else {
963	–	if (myScreen == "DAMPED") {
964	–	sm = DAMPED;
965	–	if (!simParams_->haveDampingAlpha()) {
966	–	//throw error
967	–	sprintf( painCave.errMsg,
968	–	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
969	–	painCave.isFatal = 0;
970	–	simError();
971	–	}
972	–	} else {
973	–	// throw error
974	–	sprintf( painCave.errMsg,
975	–	"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
976	–	painCave.isFatal = 1;
977	–	simError();
978	–	}
979	–	}
980	–	}
981	–
982	–	// let's pass some summation method variables to fortran
983	–	setElectrostaticSummationMethod( &esm );
984	–	setScreeningMethod( &sm );
985	–	setDampingAlpha( &alphaVal );
986	–	setReactionFieldDielectric( &dielectric );
987	–	initFortranFF( &esm, &errorOut );
988	–	}
989	–
990	–	void SimInfo::setupSwitchingFunction() {
991	–	int ft = CUBIC;
992	–
993	–	if (simParams_->haveSwitchingFunctionType()) {
994	–	std::string funcType = simParams_->getSwitchingFunctionType();
995	–	toUpper(funcType);
996	–	if (funcType == "CUBIC") {
997	–	ft = CUBIC;
998	–	} else {
999	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1000	–	ft = FIFTH_ORDER_POLY;
1001	–	} else {
1002	–	// throw error
1003	–	sprintf( painCave.errMsg,
1004	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1005	–	painCave.isFatal = 1;
1006	–	simError();
1007	–	}
1008	–	}
1009	–	}
1010	–
1011	–	// send switching function notification to switcheroo
1012	–	setFunctionType(&ft);
1013	–
1014	–	}
1015	–
947		void SimInfo::addProperty(GenericData* genData) {
948		properties_.addProperty(genData);
949		}
950
951	<	void SimInfo::removeProperty(const std::string& propName) {
951	>	void SimInfo::removeProperty(const string& propName) {
952		properties_.removeProperty(propName);
953		}
954
#	Line 1025 | Line 956 | namespace oopse {
956		properties_.clearProperties();
957		}
958
959	<	std::vector<std::string> SimInfo::getPropertyNames() {
959	>	vector<string> SimInfo::getPropertyNames() {
960		return properties_.getPropertyNames();
961		}
962
963	<	std::vector<GenericData*> SimInfo::getProperties() {
963	>	vector<GenericData*> SimInfo::getProperties() {
964		return properties_.getProperties();
965		}
966
967	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
967	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
968		return properties_.getPropertyByName(propName);
969		}
970
#	Line 1047 | Line 978 | namespace oopse {
978		Molecule* mol;
979		RigidBody* rb;
980		Atom* atom;
981	+	CutoffGroup* cg;
982		SimInfo::MoleculeIterator mi;
983		Molecule::RigidBodyIterator rbIter;
984	<	Molecule::AtomIterator atomIter;;
984	>	Molecule::AtomIterator atomIter;
985	>	Molecule::CutoffGroupIterator cgIter;
986
987		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
988
989	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
989	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
990	>	atom = mol->nextAtom(atomIter)) {
991		atom->setSnapshotManager(sman_);
992		}
993
994	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
994	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
995	>	rb = mol->nextRigidBody(rbIter)) {
996		rb->setSnapshotManager(sman_);
997		}
998	+
999	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1000	+	cg = mol->nextCutoffGroup(cgIter)) {
1001	+	cg->setSnapshotManager(sman_);
1002	+	}
1003		}
1004
1005		}
1006
1067	–	Vector3d SimInfo::getComVel(){
1068	–	SimInfo::MoleculeIterator i;
1069	–	Molecule* mol;
1007
1008	<	Vector3d comVel(0.0);
1072	<	double totalMass = 0.0;
1073	<
1074	<
1075	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1076	<	double mass = mol->getMass();
1077	<	totalMass += mass;
1078	<	comVel += mass * mol->getComVel();
1079	<	}
1008	>	ostream& operator <<(ostream& o, SimInfo& info) {
1009
1081	–	#ifdef IS_MPI
1082	–	double tmpMass = totalMass;
1083	–	Vector3d tmpComVel(comVel);
1084	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1085	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1086	–	#endif
1087	–
1088	–	comVel /= totalMass;
1089	–
1090	–	return comVel;
1091	–	}
1092	–
1093	–	Vector3d SimInfo::getCom(){
1094	–	SimInfo::MoleculeIterator i;
1095	–	Molecule* mol;
1096	–
1097	–	Vector3d com(0.0);
1098	–	double totalMass = 0.0;
1099	–
1100	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1101	–	double mass = mol->getMass();
1102	–	totalMass += mass;
1103	–	com += mass * mol->getCom();
1104	–	}
1105	–
1106	–	#ifdef IS_MPI
1107	–	double tmpMass = totalMass;
1108	–	Vector3d tmpCom(com);
1109	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1110	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1111	–	#endif
1112	–
1113	–	com /= totalMass;
1114	–
1115	–	return com;
1116	–
1117	–	}
1118	–
1119	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1120	–
1010		return o;
1011		}
1012
1013	<
1014	<	/*
1015	<	Returns center of mass and center of mass velocity in one function call.
1016	<	*/
1017	<
1018	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1019	<	SimInfo::MoleculeIterator i;
1020	<	Molecule* mol;
1021	<
1022	<
1023	<	double totalMass = 0.0;
1024	<
1013	>
1014	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1015	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1016	>	sprintf(painCave.errMsg,
1017	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1018	>	"\tindex exceeds number of known objects!\n");
1019	>	painCave.isFatal = 1;
1020	>	simError();
1021	>	return NULL;
1022	>	} else
1023	>	return IOIndexToIntegrableObject.at(index);
1024	>	}
1025	>
1026	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1027	>	IOIndexToIntegrableObject= v;
1028	>	}
1029
1030	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1031	<	double mass = mol->getMass();
1139	<	totalMass += mass;
1140	<	com += mass * mol->getCom();
1141	<	comVel += mass * mol->getComVel();
1142	<	}
1143	<
1030	>	int SimInfo::getNGlobalConstraints() {
1031	>	int nGlobalConstraints;
1032		#ifdef IS_MPI
1033	<	double tmpMass = totalMass;
1034	<	Vector3d tmpCom(com);
1035	<	Vector3d tmpComVel(comVel);
1036	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1149	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1150	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1033	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1034	>	MPI::INT, MPI::SUM);
1035	>	#else
1036	>	nGlobalConstraints =  nConstraints_;
1037		#endif
1038	<
1039	<	com /= totalMass;
1154	<	comVel /= totalMass;
1155	<	}
1156	<
1157	<	/*
1158	<	Return intertia tensor for entire system and angular momentum Vector.
1038	>	return nGlobalConstraints;
1039	>	}
1040
1041	+	}//end namespace OpenMD
1042
1161	–	[  Ixx -Ixy  -Ixz ]
1162	–	J =| -Iyx  Iyy  -Iyz |
1163	–	[ -Izx -Iyz   Izz ]
1164	–	*/
1165	–
1166	–	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1167	–
1168	–
1169	–	double xx = 0.0;
1170	–	double yy = 0.0;
1171	–	double zz = 0.0;
1172	–	double xy = 0.0;
1173	–	double xz = 0.0;
1174	–	double yz = 0.0;
1175	–	Vector3d com(0.0);
1176	–	Vector3d comVel(0.0);
1177	–
1178	–	getComAll(com, comVel);
1179	–
1180	–	SimInfo::MoleculeIterator i;
1181	–	Molecule* mol;
1182	–
1183	–	Vector3d thisq(0.0);
1184	–	Vector3d thisv(0.0);
1185	–
1186	–	double thisMass = 0.0;
1187	–
1188	–
1189	–
1190	–
1191	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1192	–
1193	–	thisq = mol->getCom()-com;
1194	–	thisv = mol->getComVel()-comVel;
1195	–	thisMass = mol->getMass();
1196	–	// Compute moment of intertia coefficients.
1197	–	xx += thisq[0]*thisq[0]*thisMass;
1198	–	yy += thisq[1]*thisq[1]*thisMass;
1199	–	zz += thisq[2]*thisq[2]*thisMass;
1200	–
1201	–	// compute products of intertia
1202	–	xy += thisq[0]*thisq[1]*thisMass;
1203	–	xz += thisq[0]*thisq[2]*thisMass;
1204	–	yz += thisq[1]*thisq[2]*thisMass;
1205	–
1206	–	angularMomentum += cross( thisq, thisv ) * thisMass;
1207	–
1208	–	}
1209	–
1210	–
1211	–	inertiaTensor(0,0) = yy + zz;
1212	–	inertiaTensor(0,1) = -xy;
1213	–	inertiaTensor(0,2) = -xz;
1214	–	inertiaTensor(1,0) = -xy;
1215	–	inertiaTensor(1,1) = xx + zz;
1216	–	inertiaTensor(1,2) = -yz;
1217	–	inertiaTensor(2,0) = -xz;
1218	–	inertiaTensor(2,1) = -yz;
1219	–	inertiaTensor(2,2) = xx + yy;
1220	–
1221	–	#ifdef IS_MPI
1222	–	Mat3x3d tmpI(inertiaTensor);
1223	–	Vector3d tmpAngMom;
1224	–	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1225	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1226	–	#endif
1227	–
1228	–	return;
1229	–	}
1230	–
1231	–	//Returns the angular momentum of the system
1232	–	Vector3d SimInfo::getAngularMomentum(){
1233	–
1234	–	Vector3d com(0.0);
1235	–	Vector3d comVel(0.0);
1236	–	Vector3d angularMomentum(0.0);
1237	–
1238	–	getComAll(com,comVel);
1239	–
1240	–	SimInfo::MoleculeIterator i;
1241	–	Molecule* mol;
1242	–
1243	–	Vector3d thisr(0.0);
1244	–	Vector3d thisp(0.0);
1245	–
1246	–	double thisMass;
1247	–
1248	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1249	–	thisMass = mol->getMass();
1250	–	thisr = mol->getCom()-com;
1251	–	thisp = (mol->getComVel()-comVel)*thisMass;
1252	–
1253	–	angularMomentum += cross( thisr, thisp );
1254	–
1255	–	}
1256	–
1257	–	#ifdef IS_MPI
1258	–	Vector3d tmpAngMom;
1259	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1260	–	#endif
1261	–
1262	–	return angularMomentum;
1263	–	}
1264	–
1265	–
1266	–	}//end namespace oopse
1267	–

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 734 by chuckv, Tue Nov 15 16:05:38 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

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