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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 709 by chrisfen, Wed Nov 2 20:36:15 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/fScreeningMethod.h"
58	<	#include "UseTheForce/doForces_interface.h"
59	<	#include "UseTheForce/DarkSide/electrostatic_interface.h"
60	<	#include "UseTheForce/notifyCutoffs_interface.h"
57	>	#include "primitives/StuntDouble.hpp"
58		#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60		#include "selection/SelectionManager.hpp"
61	<
61	>	#include "io/ForceFieldOptions.hpp"
62	>	#include "brains/ForceField.hpp"
63	>	#include "nonbonded/SwitchingFunction.hpp"
64		#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
68	<	#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	<
82	<
83	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
84	<	MoleculeStamp* molStamp;
85	<	int nMolWithSameStamp;
86	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
88	<	CutoffGroupStamp* cgStamp;
89	<	RigidBodyStamp* rbStamp;
90	<	int nRigidAtoms = 0;
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	<
119	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
120	<	rbStamp = molStamp->getRigidBody(j);
121	<	nAtomsInRigidBodies += rbStamp->getNMembers();
122	<	}
123	<
124	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
125	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
126	<
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();
145	<
146	<	#ifdef IS_MPI
147	<	molToProcMap_.resize(nGlobalMols_);
148	<	#endif
149	<
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
159	–	delete stamps_;
155		delete sman_;
156		delete simParams_;
157		delete forceField_;
158		}
159
165	–	int SimInfo::getNGlobalConstraints() {
166	–	int nGlobalConstraints;
167	–	#ifdef IS_MPI
168	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
169	–	MPI_COMM_WORLD);
170	–	#else
171	–	nGlobalConstraints =  nConstraints_;
172	–	#endif
173	–	return nGlobalConstraints;
174	–	}
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 210 | 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 224 | Line 211 | namespace oopse {
211		} else {
212		return false;
213		}
227	–
228	–
214		}
215
216
#	Line 241 | 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)) {
253	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
254	–	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 281 | 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)) {
296	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
297	–	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 310 | 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 323 | 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 332 | 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 457 | Line 686 | namespace oopse {
686		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
687		}
688
460	–	void SimInfo::update() {
689
690	<	setupSimType();
691	<
692	<	#ifdef IS_MPI
693	<	setupFortranParallel();
694	<	#endif
695	<
696	<	setupFortranSim();
697	<
698	<	//setup fortran force field
471	<	/** @deprecate */
472	<	int isError = 0;
473	<
474	<	setupElectrostaticSummationMethod( isError );
475	<
476	<	if(isError){
477	<	sprintf( painCave.errMsg,
478	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
479	<	painCave.isFatal = 1;
480	<	simError();
481	<	}
482	<
483	<
484	<	setupCutoff();
485	<
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();
489	–
490	–	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	<	return atomTypes;
758	<	}
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	<	void SimInfo::setupSimType() {
766	<	std::set<AtomType*>::iterator i;
767	<	std::set<AtomType*> atomTypes;
768	<	atomTypes = getUniqueAtomTypes();
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	<	int useLennardJones = 0;
775	<	int useElectrostatic = 0;
776	<	int useEAM = 0;
777	<	int useCharge = 0;
778	<	int useDirectional = 0;
779	<	int useDipole = 0;
780	<	int useGayBerne = 0;
523	<	int useSticky = 0;
524	<	int useStickyPower = 0;
525	<	int useShape = 0;
526	<	int useFLARB = 0; //it is not in AtomType yet
527	<	int useDirectionalAtom = 0;
528	<	int useElectrostatics = 0;
529	<	//usePBC and useRF are from simParams
530	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
531	<	int useRF;
532	<	int useDW;
533	<	std::string myMethod;
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	<	// set the useRF logical
783	<	useRF = 0;
537	<	useDW = 0;
782	>	return atomTypes;
783	>	}
784
785
786	<	if (simParams_->haveElectrostaticSummationMethod()) {
787	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
788	<	toUpper(myMethod);
789	<	if (myMethod == "REACTION_FIELD") {
544	<	useRF=1;
545	<	} else {
546	<	if (myMethod == "SHIFTED_POTENTIAL") {
547	<	useDW = 1;
548	<	}
549	<	}
550	<	}
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	+	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	+	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	<	useCharge |= (*i)->isCharge();
558	<	useDirectional |= (*i)->isDirectional();
559	<	useDipole |= (*i)->isDipole();
560	<	useGayBerne |= (*i)->isGayBerne();
561	<	useSticky |= (*i)->isSticky();
562	<	useStickyPower |= (*i)->isStickyPower();
563	<	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
580	–	temp = useDirectionalAtom;
581	–	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;
587	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
588	<
589	<	temp = useCharge;
590	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
591	<
592	<	temp = useDipole;
593	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
594	<
595	<	temp = useSticky;
596	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
597	<
598	<	temp = useStickyPower;
599	<	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
604	–	temp = useEAM;
605	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
875
876	<	temp = useShape;
877	<	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	<
613	<	temp = useRF;
614	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
615	<
616	<	temp = useDW;
617	<	MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
618	<
619	<	#endif
620	<
621	<	fInfo_.SIM_uses_PBC = usePBC;
622	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
623	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
624	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
625	<	fInfo_.SIM_uses_Charges = useCharge;
626	<	fInfo_.SIM_uses_Dipoles = useDipole;
627	<	fInfo_.SIM_uses_Sticky = useSticky;
628	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
629	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
630	<	fInfo_.SIM_uses_EAM = useEAM;
631	<	fInfo_.SIM_uses_Shapes = useShape;
632	<	fInfo_.SIM_uses_FLARB = useFLARB;
633	<	fInfo_.SIM_uses_RF = useRF;
634	<	fInfo_.SIM_uses_DampedWolf = useDW;
635	<
636	<	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"
644	<	"\tsetting a dielectric constant!\n");
645	<	painCave.isFatal = 1;
646	<	simError();
647	<	}
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
652	–	void SimInfo::setupFortranSim() {
653	–	int isError;
654	–	int nExclude;
655	–	std::vector<int> fortranGlobalGroupMembership;
656	–
657	–	nExclude = exclude_.getSize();
658	–	isError = 0;
896
897	<	//globalGroupMembership_ is filled by SimCreator
661	<	for (int i = 0; i < nGlobalAtoms_; i++) {
662	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
663	<	}
897	>	void SimInfo::prepareTopology() {
898
899		//calculate mass ratio of cutoff group
666	–	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		}
689	–
931		}
932		}
933
934	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
694	<	std::vector<int> identArray;
934	>	// Build the identArray_
935
936	<	//to avoid memory reallocation, reserve enough space identArray
937	<	identArray.reserve(getNAtoms());
698	<
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		}
704	–
705	–	//fill molMembershipArray
706	–	//molMembershipArray is filled by SimCreator
707	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
708	–	for (int i = 0; i < nGlobalAtoms_; i++) {
709	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
710	–	}
943
944	<	//setup fortran simulation
713	<	int nGlobalExcludes = 0;
714	<	int* globalExcludes = NULL;
715	<	int* excludeList = exclude_.getExcludeList();
716	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
717	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
718	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
719	<
720	<	if( isError ){
721	<
722	<	sprintf( painCave.errMsg,
723	<	"There was an error setting the simulation information in fortran.\n" );
724	<	painCave.isFatal = 1;
725	<	painCave.severity = OOPSE_ERROR;
726	<	simError();
727	<	}
728	<
729	<	#ifdef IS_MPI
730	<	sprintf( checkPointMsg,
731	<	"succesfully sent the simulation information to fortran.\n");
732	<	MPIcheckPoint();
733	<	#endif // is_mpi
734	<	}
735	<
736	<
737	<	#ifdef IS_MPI
738	<	void SimInfo::setupFortranParallel() {
739	<
740	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
741	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
742	<	std::vector<int> localToGlobalCutoffGroupIndex;
743	<	SimInfo::MoleculeIterator mi;
744	<	Molecule::AtomIterator ai;
745	<	Molecule::CutoffGroupIterator ci;
746	<	Molecule* mol;
747	<	Atom* atom;
748	<	CutoffGroup* cg;
749	<	mpiSimData parallelData;
750	<	int isError;
751	<
752	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
753	<
754	<	//local index(index in DataStorge) of atom is important
755	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
756	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
757	<	}
758	<
759	<	//local index of cutoff group is trivial, it only depends on the order of travesing
760	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
761	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
762	<	}
763	<
764	<	}
765	<
766	<	//fill up mpiSimData struct
767	<	parallelData.nMolGlobal = getNGlobalMolecules();
768	<	parallelData.nMolLocal = getNMolecules();
769	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
770	<	parallelData.nAtomsLocal = getNAtoms();
771	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
772	<	parallelData.nGroupsLocal = getNCutoffGroups();
773	<	parallelData.myNode = worldRank;
774	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
775	<
776	<	//pass mpiSimData struct and index arrays to fortran
777	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
778	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
779	<	&localToGlobalCutoffGroupIndex[0], &isError);
780	<
781	<	if (isError) {
782	<	sprintf(painCave.errMsg,
783	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
784	<	painCave.isFatal = 1;
785	<	simError();
786	<	}
787	<
788	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
789	<	MPIcheckPoint();
790	<
791	<
792	<	}
793	<
794	<	#endif
795	<
796	<	double SimInfo::calcMaxCutoffRadius() {
797	<
798	<
799	<	std::set<AtomType*> atomTypes;
800	<	std::set<AtomType*>::iterator i;
801	<	std::vector<double> cutoffRadius;
802	<
803	<	//get the unique atom types
804	<	atomTypes = getUniqueAtomTypes();
805	<
806	<	//query the max cutoff radius among these atom types
807	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
808	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
809	<	}
810	<
811	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
812	<	#ifdef IS_MPI
813	<	//pick the max cutoff radius among the processors
814	<	#endif
815	<
816	<	return maxCutoffRadius;
817	<	}
818	<
819	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
820	<
821	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
822	<
823	<	if (!simParams_->haveCutoffRadius()){
824	<	sprintf(painCave.errMsg,
825	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
826	<	"\tOOPSE will use a default value of 15.0 angstroms"
827	<	"\tfor the cutoffRadius.\n");
828	<	painCave.isFatal = 0;
829	<	simError();
830	<	rcut = 15.0;
831	<	} else{
832	<	rcut = simParams_->getCutoffRadius();
833	<	}
834	<
835	<	if (!simParams_->haveSwitchingRadius()){
836	<	sprintf(painCave.errMsg,
837	<	"SimCreator Warning: No value was set for switchingRadius.\n"
838	<	"\tOOPSE will use a default value of\n"
839	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
840	<	painCave.isFatal = 0;
841	<	simError();
842	<	rsw = 0.85 * rcut;
843	<	} else{
844	<	rsw = simParams_->getSwitchingRadius();
845	<	}
846	<
847	<	} else {
848	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
849	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
850	<
851	<	if (simParams_->haveCutoffRadius()) {
852	<	rcut = simParams_->getCutoffRadius();
853	<	} else {
854	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
855	<	rcut = calcMaxCutoffRadius();
856	<	}
857	<
858	<	if (simParams_->haveSwitchingRadius()) {
859	<	rsw  = simParams_->getSwitchingRadius();
860	<	} else {
861	<	rsw = rcut;
862	<	}
863	<
864	<	}
944	>	topologyDone_ = true;
945		}
946
867	–	void SimInfo::setupCutoff() {
868	–	getCutoff(rcut_, rsw_);
869	–	double rnblist = rcut_ + 1; // skin of neighbor list
870	–
871	–	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
872	–
873	–	int cp =  TRADITIONAL_CUTOFF_POLICY;
874	–	if (simParams_->haveCutoffPolicy()) {
875	–	std::string myPolicy = simParams_->getCutoffPolicy();
876	–	toUpper(myPolicy);
877	–	if (myPolicy == "MIX") {
878	–	cp = MIX_CUTOFF_POLICY;
879	–	} else {
880	–	if (myPolicy == "MAX") {
881	–	cp = MAX_CUTOFF_POLICY;
882	–	} else {
883	–	if (myPolicy == "TRADITIONAL") {
884	–	cp = TRADITIONAL_CUTOFF_POLICY;
885	–	} else {
886	–	// throw error
887	–	sprintf( painCave.errMsg,
888	–	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
889	–	painCave.isFatal = 1;
890	–	simError();
891	–	}
892	–	}
893	–	}
894	–	}
895	–
896	–
897	–	if (simParams_->haveSkinThickness()) {
898	–	double skinThickness = simParams_->getSkinThickness();
899	–	}
900	–
901	–	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
902	–	// also send cutoff notification to electrostatics
903	–	setElectrostaticCutoffRadius(&rcut_, &rsw_);
904	–	}
905	–
906	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
907	–
908	–	int errorOut;
909	–	int esm =  NONE;
910	–	int sm = UNDAMPED;
911	–	double alphaVal;
912	–	double dielectric;
913	–
914	–	errorOut = isError;
915	–	alphaVal = simParams_->getDampingAlpha();
916	–	dielectric = simParams_->getDielectric();
917	–
918	–	if (simParams_->haveElectrostaticSummationMethod()) {
919	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
920	–	toUpper(myMethod);
921	–	if (myMethod == "NONE") {
922	–	esm = NONE;
923	–	} else {
924	–	if (myMethod == "SWITCHING_FUNCTION") {
925	–	esm = SWITCHING_FUNCTION;
926	–	} else {
927	–	if (myMethod == "SHIFTED_POTENTIAL") {
928	–	esm = SHIFTED_POTENTIAL;
929	–	} else {
930	–	if (myMethod == "SHIFTED_FORCE") {
931	–	esm = SHIFTED_FORCE;
932	–	} else {
933	–	if (myMethod == "REACTION_FIELD") {
934	–	esm = REACTION_FIELD;
935	–	} else {
936	–	// throw error
937	–	sprintf( painCave.errMsg,
938	–	"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() );
939	–	painCave.isFatal = 1;
940	–	simError();
941	–	}
942	–	}
943	–	}
944	–	}
945	–	}
946	–	}
947	–
948	–	if (simParams_->haveScreeningMethod()) {
949	–	std::string myScreen = simParams_->getScreeningMethod();
950	–	toUpper(myScreen);
951	–	if (myScreen == "UNDAMPED") {
952	–	sm = UNDAMPED;
953	–	} else {
954	–	if (myScreen == "DAMPED") {
955	–	sm = DAMPED;
956	–	if (!simParams_->haveDampingAlpha()) {
957	–	//throw error
958	–	sprintf( painCave.errMsg,
959	–	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
960	–	painCave.isFatal = 0;
961	–	simError();
962	–	} else {
963	–	// throw error
964	–	sprintf( painCave.errMsg,
965	–	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
966	–	painCave.isFatal = 1;
967	–	simError();
968	–	}
969	–	}
970	–	}
971	–	}
972	–	// let's pass some summation method variables to fortran
973	–	setElectrostaticSummationMethod( &esm );
974	–	setScreeningMethod( &sm );
975	–	setDampingAlpha( &alphaVal );
976	–	setReactionFieldDielectric( &dielectric );
977	–	initFortranFF( &esm, &errorOut );
978	–	}
979	–
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 989 | 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 1011 | 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
1031	–	Vector3d SimInfo::getComVel(){
1032	–	SimInfo::MoleculeIterator i;
1033	–	Molecule* mol;
1007
1008	<	Vector3d comVel(0.0);
1036	<	double totalMass = 0.0;
1037	<
1038	<
1039	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1040	<	double mass = mol->getMass();
1041	<	totalMass += mass;
1042	<	comVel += mass * mol->getComVel();
1043	<	}
1008	>	ostream& operator <<(ostream& o, SimInfo& info) {
1009
1045	–	#ifdef IS_MPI
1046	–	double tmpMass = totalMass;
1047	–	Vector3d tmpComVel(comVel);
1048	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1049	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1050	–	#endif
1051	–
1052	–	comVel /= totalMass;
1053	–
1054	–	return comVel;
1055	–	}
1056	–
1057	–	Vector3d SimInfo::getCom(){
1058	–	SimInfo::MoleculeIterator i;
1059	–	Molecule* mol;
1060	–
1061	–	Vector3d com(0.0);
1062	–	double totalMass = 0.0;
1063	–
1064	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1065	–	double mass = mol->getMass();
1066	–	totalMass += mass;
1067	–	com += mass * mol->getCom();
1068	–	}
1069	–
1070	–	#ifdef IS_MPI
1071	–	double tmpMass = totalMass;
1072	–	Vector3d tmpCom(com);
1073	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1074	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1075	–	#endif
1076	–
1077	–	com /= totalMass;
1078	–
1079	–	return com;
1080	–
1081	–	}
1082	–
1083	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1084	–
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();
1103	<	totalMass += mass;
1104	<	com += mass * mol->getCom();
1105	<	comVel += mass * mol->getComVel();
1106	<	}
1107	<
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);
1113	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1114	<	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;
1118	<	comVel /= totalMass;
1119	<	}
1120	<
1121	<	/*
1122	<	Return intertia tensor for entire system and angular momentum Vector.
1038	>	return nGlobalConstraints;
1039	>	}
1040
1041	+	}//end namespace OpenMD
1042
1125	–	[  Ixx -Ixy  -Ixz ]
1126	–	J =| -Iyx  Iyy  -Iyz |
1127	–	[ -Izx -Iyz   Izz ]
1128	–	*/
1129	–
1130	–	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1131	–
1132	–
1133	–	double xx = 0.0;
1134	–	double yy = 0.0;
1135	–	double zz = 0.0;
1136	–	double xy = 0.0;
1137	–	double xz = 0.0;
1138	–	double yz = 0.0;
1139	–	Vector3d com(0.0);
1140	–	Vector3d comVel(0.0);
1141	–
1142	–	getComAll(com, comVel);
1143	–
1144	–	SimInfo::MoleculeIterator i;
1145	–	Molecule* mol;
1146	–
1147	–	Vector3d thisq(0.0);
1148	–	Vector3d thisv(0.0);
1149	–
1150	–	double thisMass = 0.0;
1151	–
1152	–
1153	–
1154	–
1155	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1156	–
1157	–	thisq = mol->getCom()-com;
1158	–	thisv = mol->getComVel()-comVel;
1159	–	thisMass = mol->getMass();
1160	–	// Compute moment of intertia coefficients.
1161	–	xx += thisq[0]*thisq[0]*thisMass;
1162	–	yy += thisq[1]*thisq[1]*thisMass;
1163	–	zz += thisq[2]*thisq[2]*thisMass;
1164	–
1165	–	// compute products of intertia
1166	–	xy += thisq[0]*thisq[1]*thisMass;
1167	–	xz += thisq[0]*thisq[2]*thisMass;
1168	–	yz += thisq[1]*thisq[2]*thisMass;
1169	–
1170	–	angularMomentum += cross( thisq, thisv ) * thisMass;
1171	–
1172	–	}
1173	–
1174	–
1175	–	inertiaTensor(0,0) = yy + zz;
1176	–	inertiaTensor(0,1) = -xy;
1177	–	inertiaTensor(0,2) = -xz;
1178	–	inertiaTensor(1,0) = -xy;
1179	–	inertiaTensor(1,1) = xx + zz;
1180	–	inertiaTensor(1,2) = -yz;
1181	–	inertiaTensor(2,0) = -xz;
1182	–	inertiaTensor(2,1) = -yz;
1183	–	inertiaTensor(2,2) = xx + yy;
1184	–
1185	–	#ifdef IS_MPI
1186	–	Mat3x3d tmpI(inertiaTensor);
1187	–	Vector3d tmpAngMom;
1188	–	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1189	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1190	–	#endif
1191	–
1192	–	return;
1193	–	}
1194	–
1195	–	//Returns the angular momentum of the system
1196	–	Vector3d SimInfo::getAngularMomentum(){
1197	–
1198	–	Vector3d com(0.0);
1199	–	Vector3d comVel(0.0);
1200	–	Vector3d angularMomentum(0.0);
1201	–
1202	–	getComAll(com,comVel);
1203	–
1204	–	SimInfo::MoleculeIterator i;
1205	–	Molecule* mol;
1206	–
1207	–	Vector3d thisr(0.0);
1208	–	Vector3d thisp(0.0);
1209	–
1210	–	double thisMass;
1211	–
1212	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1213	–	thisMass = mol->getMass();
1214	–	thisr = mol->getCom()-com;
1215	–	thisp = (mol->getComVel()-comVel)*thisMass;
1216	–
1217	–	angularMomentum += cross( thisr, thisp );
1218	–
1219	–	}
1220	–
1221	–	#ifdef IS_MPI
1222	–	Vector3d tmpAngMom;
1223	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1224	–	#endif
1225	–
1226	–	return angularMomentum;
1227	–	}
1228	–
1229	–
1230	–	}//end namespace oopse
1231	–

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 709 by chrisfen, Wed Nov 2 20:36:15 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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