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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 705 by chrisfen, Tue Nov 1 19:14:27 2005 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 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 46 | Line 47
47		* @version 1.0
48		*/
49
50	+	#ifdef IS_MPI
51	+	#include <mpi.h>
52	+	#endif
53		#include <algorithm>
54		#include <set>
55	+	#include <map>
56
57		#include "brains/SimInfo.hpp"
58		#include "math/Vector3.hpp"
59		#include "primitives/Molecule.hpp"
60	<	#include "UseTheForce/fCutoffPolicy.h"
56	<	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
57	<	#include "UseTheForce/doForces_interface.h"
58	<	#include "UseTheForce/DarkSide/electrostatic_interface.h"
59	<	#include "UseTheForce/notifyCutoffs_interface.h"
60	>	#include "primitives/StuntDouble.hpp"
61		#include "utils/MemoryUtils.hpp"
62		#include "utils/simError.h"
63		#include "selection/SelectionManager.hpp"
64	+	#include "io/ForceFieldOptions.hpp"
65	+	#include "brains/ForceField.hpp"
66	+	#include "nonbonded/SwitchingFunction.hpp"
67
68	<	#ifdef IS_MPI
69	<	#include "UseTheForce/mpiComponentPlan.h"
70	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
71	<	#endif
72	<
73	<	namespace oopse {
70	<
71	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
72	<	ForceField* ff, Globals* simParams) :
73	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
74	<	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	<
80	<
81	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
83	<	MoleculeStamp* molStamp;
84	<	int nMolWithSameStamp;
85	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
86	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
87	<	CutoffGroupStamp* cgStamp;
88	<	RigidBodyStamp* rbStamp;
89	<	int nRigidAtoms = 0;
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	>	nGlobalFluctuatingCharges_(0), nGlobalBonds_(0), nGlobalBends_(0),
77	>	nGlobalTorsions_(0), nGlobalInversions_(0), nAtoms_(0), nBonds_(0),
78	>	nBends_(0), nTorsions_(0), nInversions_(0), nRigidBodies_(0),
79	>	nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
80	>	nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
81	>	calcBoxDipole_(false), useAtomicVirial_(true) {
82
83	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
84	<	molStamp = i->first;
85	<	nMolWithSameStamp = i->second;
86	<
87	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
88	<
89	<	//calculate atoms in molecules
90	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
91	<
92	<
93	<	//calculate atoms in cutoff groups
94	<	int nAtomsInGroups = 0;
95	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
96	<
97	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
98	<	cgStamp = molStamp->getCutoffGroup(j);
99	<	nAtomsInGroups += cgStamp->getNMembers();
100	<	}
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->getRigidBody(j);
120	<	nAtomsInRigidBodies += rbStamp->getNMembers();
121	<	}
122	<
123	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
124	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
125	<
83	>	MoleculeStamp* molStamp;
84	>	int nMolWithSameStamp;
85	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
86	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
87	>	CutoffGroupStamp* cgStamp;
88	>	RigidBodyStamp* rbStamp;
89	>	int nRigidAtoms = 0;
90	>
91	>	vector<Component*> components = simParams->getComponents();
92	>
93	>	for (vector<Component*>::iterator i = components.begin();
94	>	i !=components.end(); ++i) {
95	>	molStamp = (*i)->getMoleculeStamp();
96	>	if ( (*i)->haveRegion() ) {
97	>	molStamp->setRegion( (*i)->getRegion() );
98	>	} else {
99	>	// set the region to a disallowed value:
100	>	molStamp->setRegion( -1 );
101		}
102
103	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
104	<	//group therefore the total number of cutoff groups in the system is
105	<	//equal to the total number of atoms minus number of atoms belong to
106	<	//cutoff group defined in meta-data file plus the number of cutoff
107	<	//groups defined in meta-data file
108	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
109	<
110	<	//every free atom (atom does not belong to rigid bodies) is an
111	<	//integrable object therefore the total number of integrable objects
112	<	//in the system is equal to the total number of atoms minus number of
113	<	//atoms belong to rigid body defined in meta-data file plus the number
114	<	//of rigid bodies defined in meta-data file
115	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
116	<	+ nGlobalRigidBodies_;
117	<
118	<	nGlobalMols_ = molStampIds_.size();
119	<
120	<	#ifdef IS_MPI
121	<	molToProcMap_.resize(nGlobalMols_);
122	<	#endif
123	<
103	>	nMolWithSameStamp = (*i)->getNMol();
104	>
105	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
106	>
107	>	//calculate atoms in molecules
108	>	nGlobalAtoms_ += molStamp->getNAtoms() * nMolWithSameStamp;
109	>	nGlobalBonds_ += molStamp->getNBonds() * nMolWithSameStamp;
110	>	nGlobalBends_ += molStamp->getNBends() * nMolWithSameStamp;
111	>	nGlobalTorsions_ += molStamp->getNTorsions() * nMolWithSameStamp;
112	>	nGlobalInversions_ += molStamp->getNInversions() * nMolWithSameStamp;
113	>
114	>	//calculate atoms in cutoff groups
115	>	int nAtomsInGroups = 0;
116	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
117	>
118	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
119	>	cgStamp = molStamp->getCutoffGroupStamp(j);
120	>	nAtomsInGroups += cgStamp->getNMembers();
121	>	}
122	>
123	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
124	>
125	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
126	>
127	>	//calculate atoms in rigid bodies
128	>	int nAtomsInRigidBodies = 0;
129	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
130	>
131	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
132	>	rbStamp = molStamp->getRigidBodyStamp(j);
133	>	nAtomsInRigidBodies += rbStamp->getNMembers();
134	>	}
135	>
136	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
137	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
138	>
139		}
140	+
141	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
142	+	//group therefore the total number of cutoff groups in the system is
143	+	//equal to the total number of atoms minus number of atoms belong to
144	+	//cutoff group defined in meta-data file plus the number of cutoff
145	+	//groups defined in meta-data file
146
147	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
148	+
149	+	//every free atom (atom does not belong to rigid bodies) is an
150	+	//integrable object therefore the total number of integrable objects
151	+	//in the system is equal to the total number of atoms minus number of
152	+	//atoms belong to rigid body defined in meta-data file plus the number
153	+	//of rigid bodies defined in meta-data file
154	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
155	+	+ nGlobalRigidBodies_;
156	+
157	+	nGlobalMols_ = molStampIds_.size();
158	+	molToProcMap_.resize(nGlobalMols_);
159	+	}
160	+
161		SimInfo::~SimInfo() {
162	<	std::map<int, Molecule*>::iterator i;
162	>	map<int, Molecule*>::iterator i;
163		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
164		delete i->second;
165		}
166		molecules_.clear();
167
158	–	delete stamps_;
168		delete sman_;
169		delete simParams_;
170		delete forceField_;
171		}
172
164	–	int SimInfo::getNGlobalConstraints() {
165	–	int nGlobalConstraints;
166	–	#ifdef IS_MPI
167	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
168	–	MPI_COMM_WORLD);
169	–	#else
170	–	nGlobalConstraints =  nConstraints_;
171	–	#endif
172	–	return nGlobalConstraints;
173	–	}
173
174		bool SimInfo::addMolecule(Molecule* mol) {
175		MoleculeIterator i;
176	<
176	>
177		i = molecules_.find(mol->getGlobalIndex());
178		if (i == molecules_.end() ) {
179	<
180	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
181	<
179	>
180	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
181	>
182		nAtoms_ += mol->getNAtoms();
183		nBonds_ += mol->getNBonds();
184		nBends_ += mol->getNBends();
185		nTorsions_ += mol->getNTorsions();
186	+	nInversions_ += mol->getNInversions();
187		nRigidBodies_ += mol->getNRigidBodies();
188		nIntegrableObjects_ += mol->getNIntegrableObjects();
189		nCutoffGroups_ += mol->getNCutoffGroups();
190		nConstraints_ += mol->getNConstraintPairs();
191	<
192	<	addExcludePairs(mol);
193	<
191	>
192	>	addInteractionPairs(mol);
193	>
194		return true;
195		} else {
196		return false;
197		}
198		}
199	<
199	>
200		bool SimInfo::removeMolecule(Molecule* mol) {
201		MoleculeIterator i;
202		i = molecules_.find(mol->getGlobalIndex());
#	Line 209 | Line 209 | namespace oopse {
209		nBonds_ -= mol->getNBonds();
210		nBends_ -= mol->getNBends();
211		nTorsions_ -= mol->getNTorsions();
212	+	nInversions_ -= mol->getNInversions();
213		nRigidBodies_ -= mol->getNRigidBodies();
214		nIntegrableObjects_ -= mol->getNIntegrableObjects();
215		nCutoffGroups_ -= mol->getNCutoffGroups();
216		nConstraints_ -= mol->getNConstraintPairs();
217
218	<	removeExcludePairs(mol);
218	>	removeInteractionPairs(mol);
219		molecules_.erase(mol->getGlobalIndex());
220
221		delete mol;
#	Line 223 | Line 224 | namespace oopse {
224		} else {
225		return false;
226		}
226	–
227	–
227		}
228
229
#	Line 240 | Line 239 | namespace oopse {
239
240
241		void SimInfo::calcNdf() {
242	<	int ndf_local;
242	>	int ndf_local, nfq_local;
243		MoleculeIterator i;
244	<	std::vector<StuntDouble*>::iterator j;
244	>	vector<StuntDouble*>::iterator j;
245	>	vector<Atom*>::iterator k;
246	>
247		Molecule* mol;
248	<	StuntDouble* integrableObject;
248	>	StuntDouble* sd;
249	>	Atom* atom;
250
251		ndf_local = 0;
252	+	nfq_local = 0;
253
254		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
252	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
253	–	integrableObject = mol->nextIntegrableObject(j)) {
255
256	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
257	+	sd = mol->nextIntegrableObject(j)) {
258	+
259		ndf_local += 3;
260
261	<	if (integrableObject->isDirectional()) {
262	<	if (integrableObject->isLinear()) {
261	>	if (sd->isDirectional()) {
262	>	if (sd->isLinear()) {
263		ndf_local += 2;
264		} else {
265		ndf_local += 3;
266		}
267		}
268	<
269	<	}//end for (integrableObject)
270	<	}// end for (mol)
268	>	}
269	>
270	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
271	>	atom = mol->nextFluctuatingCharge(k)) {
272	>	if (atom->isFluctuatingCharge()) {
273	>	nfq_local++;
274	>	}
275	>	}
276	>	}
277
278	+	ndfLocal_ = ndf_local;
279	+
280		// n_constraints is local, so subtract them on each processor
281		ndf_local -= nConstraints_;
282
283		#ifdef IS_MPI
284	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
284	>	MPI_Allreduce(&ndf_local, &ndf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
285	>	MPI_Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
286	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
287	>	// MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
288	>	// MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
289	>	//                           MPI::INT, MPI::SUM);
290		#else
291		ndf_ = ndf_local;
292	+	nGlobalFluctuatingCharges_ = nfq_local;
293		#endif
294
295		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 280 | Line 298 | namespace oopse {
298
299		}
300
301	+	int SimInfo::getFdf() {
302	+	#ifdef IS_MPI
303	+	MPI_Allreduce(&fdf_local, &fdf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
304	+	// MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
305	+	#else
306	+	fdf_ = fdf_local;
307	+	#endif
308	+	return fdf_;
309	+	}
310	+
311	+	unsigned int SimInfo::getNLocalCutoffGroups(){
312	+	int nLocalCutoffAtoms = 0;
313	+	Molecule* mol;
314	+	MoleculeIterator mi;
315	+	CutoffGroup* cg;
316	+	Molecule::CutoffGroupIterator ci;
317	+
318	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
319	+
320	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
321	+	cg = mol->nextCutoffGroup(ci)) {
322	+	nLocalCutoffAtoms += cg->getNumAtom();
323	+
324	+	}
325	+	}
326	+
327	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
328	+	}
329	+
330		void SimInfo::calcNdfRaw() {
331		int ndfRaw_local;
332
333		MoleculeIterator i;
334	<	std::vector<StuntDouble*>::iterator j;
334	>	vector<StuntDouble*>::iterator j;
335		Molecule* mol;
336	<	StuntDouble* integrableObject;
336	>	StuntDouble* sd;
337
338		// Raw degrees of freedom that we have to set
339		ndfRaw_local = 0;
340
341		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
295	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
296	–	integrableObject = mol->nextIntegrableObject(j)) {
342
343	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
344	+	sd = mol->nextIntegrableObject(j)) {
345	+
346		ndfRaw_local += 3;
347
348	<	if (integrableObject->isDirectional()) {
349	<	if (integrableObject->isLinear()) {
348	>	if (sd->isDirectional()) {
349	>	if (sd->isLinear()) {
350		ndfRaw_local += 2;
351		} else {
352		ndfRaw_local += 3;
#	Line 309 | Line 357 | namespace oopse {
357		}
358
359		#ifdef IS_MPI
360	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
360	>	MPI_Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
361	>	// MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
362		#else
363		ndfRaw_ = ndfRaw_local;
364		#endif
#	Line 322 | Line 371 | namespace oopse {
371
372
373		#ifdef IS_MPI
374	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
374	>	MPI_Allreduce(&ndfTrans_local, &ndfTrans_, 1,
375	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
376	>	// MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
377	>	//                           MPI::INT, MPI::SUM);
378		#else
379		ndfTrans_ = ndfTrans_local;
380		#endif
#	Line 331 | Line 383 | namespace oopse {
383
384		}
385
386	<	void SimInfo::addExcludePairs(Molecule* mol) {
387	<	std::vector<Bond*>::iterator bondIter;
388	<	std::vector<Bend*>::iterator bendIter;
389	<	std::vector<Torsion*>::iterator torsionIter;
386	>	void SimInfo::addInteractionPairs(Molecule* mol) {
387	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
388	>	vector<Bond*>::iterator bondIter;
389	>	vector<Bend*>::iterator bendIter;
390	>	vector<Torsion*>::iterator torsionIter;
391	>	vector<Inversion*>::iterator inversionIter;
392		Bond* bond;
393		Bend* bend;
394		Torsion* torsion;
395	+	Inversion* inversion;
396		int a;
397		int b;
398		int c;
399		int d;
400	+
401	+	// atomGroups can be used to add special interaction maps between
402	+	// groups of atoms that are in two separate rigid bodies.
403	+	// However, most site-site interactions between two rigid bodies
404	+	// are probably not special, just the ones between the physically
405	+	// bonded atoms.  Interactions *within* a single rigid body should
406	+	// always be excluded.  These are done at the bottom of this
407	+	// function.
408	+
409	+	map<int, set<int> > atomGroups;
410	+	Molecule::RigidBodyIterator rbIter;
411	+	RigidBody* rb;
412	+	Molecule::IntegrableObjectIterator ii;
413	+	StuntDouble* sd;
414
415	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
415	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
416	>	sd = mol->nextIntegrableObject(ii)) {
417	>
418	>	if (sd->isRigidBody()) {
419	>	rb = static_cast<RigidBody*>(sd);
420	>	vector<Atom*> atoms = rb->getAtoms();
421	>	set<int> rigidAtoms;
422	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
423	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
424	>	}
425	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
426	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
427	>	}
428	>	} else {
429	>	set<int> oneAtomSet;
430	>	oneAtomSet.insert(sd->getGlobalIndex());
431	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
432	>	}
433	>	}
434	>
435	>
436	>	for (bond= mol->beginBond(bondIter); bond != NULL;
437	>	bond = mol->nextBond(bondIter)) {
438	>
439		a = bond->getAtomA()->getGlobalIndex();
440	<	b = bond->getAtomB()->getGlobalIndex();
441	<	exclude_.addPair(a, b);
440	>	b = bond->getAtomB()->getGlobalIndex();
441	>
442	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
443	>	oneTwoInteractions_.addPair(a, b);
444	>	} else {
445	>	excludedInteractions_.addPair(a, b);
446	>	}
447		}
448
449	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
449	>	for (bend= mol->beginBend(bendIter); bend != NULL;
450	>	bend = mol->nextBend(bendIter)) {
451	>
452		a = bend->getAtomA()->getGlobalIndex();
453		b = bend->getAtomB()->getGlobalIndex();
454		c = bend->getAtomC()->getGlobalIndex();
455	+
456	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
457	+	oneTwoInteractions_.addPair(a, b);
458	+	oneTwoInteractions_.addPair(b, c);
459	+	} else {
460	+	excludedInteractions_.addPair(a, b);
461	+	excludedInteractions_.addPair(b, c);
462	+	}
463
464	<	exclude_.addPair(a, b);
465	<	exclude_.addPair(a, c);
466	<	exclude_.addPair(b, c);
464	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
465	>	oneThreeInteractions_.addPair(a, c);
466	>	} else {
467	>	excludedInteractions_.addPair(a, c);
468	>	}
469		}
470
471	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
471	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
472	>	torsion = mol->nextTorsion(torsionIter)) {
473	>
474		a = torsion->getAtomA()->getGlobalIndex();
475		b = torsion->getAtomB()->getGlobalIndex();
476		c = torsion->getAtomC()->getGlobalIndex();
477	<	d = torsion->getAtomD()->getGlobalIndex();
477	>	d = torsion->getAtomD()->getGlobalIndex();
478
479	<	exclude_.addPair(a, b);
480	<	exclude_.addPair(a, c);
481	<	exclude_.addPair(a, d);
482	<	exclude_.addPair(b, c);
483	<	exclude_.addPair(b, d);
484	<	exclude_.addPair(c, d);
479	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
480	>	oneTwoInteractions_.addPair(a, b);
481	>	oneTwoInteractions_.addPair(b, c);
482	>	oneTwoInteractions_.addPair(c, d);
483	>	} else {
484	>	excludedInteractions_.addPair(a, b);
485	>	excludedInteractions_.addPair(b, c);
486	>	excludedInteractions_.addPair(c, d);
487	>	}
488	>
489	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
490	>	oneThreeInteractions_.addPair(a, c);
491	>	oneThreeInteractions_.addPair(b, d);
492	>	} else {
493	>	excludedInteractions_.addPair(a, c);
494	>	excludedInteractions_.addPair(b, d);
495	>	}
496	>
497	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
498	>	oneFourInteractions_.addPair(a, d);
499	>	} else {
500	>	excludedInteractions_.addPair(a, d);
501	>	}
502		}
503
504	<	Molecule::RigidBodyIterator rbIter;
505	<	RigidBody* rb;
506	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
507	<	std::vector<Atom*> atoms = rb->getAtoms();
508	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
509	<	for (int j = i + 1; j < atoms.size(); ++j) {
504	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
505	>	inversion = mol->nextInversion(inversionIter)) {
506	>
507	>	a = inversion->getAtomA()->getGlobalIndex();
508	>	b = inversion->getAtomB()->getGlobalIndex();
509	>	c = inversion->getAtomC()->getGlobalIndex();
510	>	d = inversion->getAtomD()->getGlobalIndex();
511	>
512	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
513	>	oneTwoInteractions_.addPair(a, b);
514	>	oneTwoInteractions_.addPair(a, c);
515	>	oneTwoInteractions_.addPair(a, d);
516	>	} else {
517	>	excludedInteractions_.addPair(a, b);
518	>	excludedInteractions_.addPair(a, c);
519	>	excludedInteractions_.addPair(a, d);
520	>	}
521	>
522	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
523	>	oneThreeInteractions_.addPair(b, c);
524	>	oneThreeInteractions_.addPair(b, d);
525	>	oneThreeInteractions_.addPair(c, d);
526	>	} else {
527	>	excludedInteractions_.addPair(b, c);
528	>	excludedInteractions_.addPair(b, d);
529	>	excludedInteractions_.addPair(c, d);
530	>	}
531	>	}
532	>
533	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
534	>	rb = mol->nextRigidBody(rbIter)) {
535	>	vector<Atom*> atoms = rb->getAtoms();
536	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
537	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
538		a = atoms[i]->getGlobalIndex();
539		b = atoms[j]->getGlobalIndex();
540	<	exclude_.addPair(a, b);
540	>	excludedInteractions_.addPair(a, b);
541		}
542		}
543		}
544
545		}
546
547	<	void SimInfo::removeExcludePairs(Molecule* mol) {
548	<	std::vector<Bond*>::iterator bondIter;
549	<	std::vector<Bend*>::iterator bendIter;
550	<	std::vector<Torsion*>::iterator torsionIter;
547	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
548	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
549	>	vector<Bond*>::iterator bondIter;
550	>	vector<Bend*>::iterator bendIter;
551	>	vector<Torsion*>::iterator torsionIter;
552	>	vector<Inversion*>::iterator inversionIter;
553		Bond* bond;
554		Bend* bend;
555		Torsion* torsion;
556	+	Inversion* inversion;
557		int a;
558		int b;
559		int c;
560		int d;
561	+
562	+	map<int, set<int> > atomGroups;
563	+	Molecule::RigidBodyIterator rbIter;
564	+	RigidBody* rb;
565	+	Molecule::IntegrableObjectIterator ii;
566	+	StuntDouble* sd;
567
568	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
568	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
569	>	sd = mol->nextIntegrableObject(ii)) {
570	>
571	>	if (sd->isRigidBody()) {
572	>	rb = static_cast<RigidBody*>(sd);
573	>	vector<Atom*> atoms = rb->getAtoms();
574	>	set<int> rigidAtoms;
575	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
576	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
577	>	}
578	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
579	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
580	>	}
581	>	} else {
582	>	set<int> oneAtomSet;
583	>	oneAtomSet.insert(sd->getGlobalIndex());
584	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
585	>	}
586	>	}
587	>
588	>	for (bond= mol->beginBond(bondIter); bond != NULL;
589	>	bond = mol->nextBond(bondIter)) {
590	>
591		a = bond->getAtomA()->getGlobalIndex();
592	<	b = bond->getAtomB()->getGlobalIndex();
593	<	exclude_.removePair(a, b);
592	>	b = bond->getAtomB()->getGlobalIndex();
593	>
594	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
595	>	oneTwoInteractions_.removePair(a, b);
596	>	} else {
597	>	excludedInteractions_.removePair(a, b);
598	>	}
599		}
600
601	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
601	>	for (bend= mol->beginBend(bendIter); bend != NULL;
602	>	bend = mol->nextBend(bendIter)) {
603	>
604		a = bend->getAtomA()->getGlobalIndex();
605		b = bend->getAtomB()->getGlobalIndex();
606		c = bend->getAtomC()->getGlobalIndex();
607	+
608	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
609	+	oneTwoInteractions_.removePair(a, b);
610	+	oneTwoInteractions_.removePair(b, c);
611	+	} else {
612	+	excludedInteractions_.removePair(a, b);
613	+	excludedInteractions_.removePair(b, c);
614	+	}
615
616	<	exclude_.removePair(a, b);
617	<	exclude_.removePair(a, c);
618	<	exclude_.removePair(b, c);
616	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
617	>	oneThreeInteractions_.removePair(a, c);
618	>	} else {
619	>	excludedInteractions_.removePair(a, c);
620	>	}
621		}
622
623	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
623	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
624	>	torsion = mol->nextTorsion(torsionIter)) {
625	>
626		a = torsion->getAtomA()->getGlobalIndex();
627		b = torsion->getAtomB()->getGlobalIndex();
628		c = torsion->getAtomC()->getGlobalIndex();
629	<	d = torsion->getAtomD()->getGlobalIndex();
629	>	d = torsion->getAtomD()->getGlobalIndex();
630	>
631	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
632	>	oneTwoInteractions_.removePair(a, b);
633	>	oneTwoInteractions_.removePair(b, c);
634	>	oneTwoInteractions_.removePair(c, d);
635	>	} else {
636	>	excludedInteractions_.removePair(a, b);
637	>	excludedInteractions_.removePair(b, c);
638	>	excludedInteractions_.removePair(c, d);
639	>	}
640
641	<	exclude_.removePair(a, b);
642	<	exclude_.removePair(a, c);
643	<	exclude_.removePair(a, d);
644	<	exclude_.removePair(b, c);
645	<	exclude_.removePair(b, d);
646	<	exclude_.removePair(c, d);
641	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
642	>	oneThreeInteractions_.removePair(a, c);
643	>	oneThreeInteractions_.removePair(b, d);
644	>	} else {
645	>	excludedInteractions_.removePair(a, c);
646	>	excludedInteractions_.removePair(b, d);
647	>	}
648	>
649	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
650	>	oneFourInteractions_.removePair(a, d);
651	>	} else {
652	>	excludedInteractions_.removePair(a, d);
653	>	}
654		}
655
656	<	Molecule::RigidBodyIterator rbIter;
657	<	RigidBody* rb;
658	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
659	<	std::vector<Atom*> atoms = rb->getAtoms();
660	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
661	<	for (int j = i + 1; j < atoms.size(); ++j) {
656	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
657	>	inversion = mol->nextInversion(inversionIter)) {
658	>
659	>	a = inversion->getAtomA()->getGlobalIndex();
660	>	b = inversion->getAtomB()->getGlobalIndex();
661	>	c = inversion->getAtomC()->getGlobalIndex();
662	>	d = inversion->getAtomD()->getGlobalIndex();
663	>
664	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
665	>	oneTwoInteractions_.removePair(a, b);
666	>	oneTwoInteractions_.removePair(a, c);
667	>	oneTwoInteractions_.removePair(a, d);
668	>	} else {
669	>	excludedInteractions_.removePair(a, b);
670	>	excludedInteractions_.removePair(a, c);
671	>	excludedInteractions_.removePair(a, d);
672	>	}
673	>
674	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
675	>	oneThreeInteractions_.removePair(b, c);
676	>	oneThreeInteractions_.removePair(b, d);
677	>	oneThreeInteractions_.removePair(c, d);
678	>	} else {
679	>	excludedInteractions_.removePair(b, c);
680	>	excludedInteractions_.removePair(b, d);
681	>	excludedInteractions_.removePair(c, d);
682	>	}
683	>	}
684	>
685	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
686	>	rb = mol->nextRigidBody(rbIter)) {
687	>	vector<Atom*> atoms = rb->getAtoms();
688	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
689	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
690		a = atoms[i]->getGlobalIndex();
691		b = atoms[j]->getGlobalIndex();
692	<	exclude_.removePair(a, b);
692	>	excludedInteractions_.removePair(a, b);
693		}
694		}
695		}
696	<
696	>
697		}
698	<
699	<
698	>
699	>
700		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
701		int curStampId;
702	<
702	>
703		//index from 0
704		curStampId = moleculeStamps_.size();
705
#	Line 456 | Line 707 | namespace oopse {
707		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
708		}
709
459	–	void SimInfo::update() {
710
711	<	setupSimType();
712	<
713	<	#ifdef IS_MPI
714	<	setupFortranParallel();
715	<	#endif
716	<
717	<	setupFortranSim();
718	<
719	<	//setup fortran force field
470	<	/** @deprecate */
471	<	int isError = 0;
472	<
473	<	setupElectrostaticSummationMethod( isError );
474	<
475	<	if(isError){
476	<	sprintf( painCave.errMsg,
477	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
478	<	painCave.isFatal = 1;
479	<	simError();
480	<	}
481	<
482	<
483	<	setupCutoff();
484	<
711	>	/**
712	>	* update
713	>	*
714	>	*  Performs the global checks and variable settings after the
715	>	*  objects have been created.
716	>	*
717	>	*/
718	>	void SimInfo::update() {
719	>	setupSimVariables();
720		calcNdf();
721		calcNdfRaw();
722		calcNdfTrans();
488	–
489	–	fortranInitialized_ = true;
723		}
724	<
725	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
724	>
725	>	/**
726	>	* getSimulatedAtomTypes
727	>	*
728	>	* Returns an STL set of AtomType* that are actually present in this
729	>	* simulation.  Must query all processors to assemble this information.
730	>	*
731	>	*/
732	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
733		SimInfo::MoleculeIterator mi;
734		Molecule* mol;
735		Molecule::AtomIterator ai;
736		Atom* atom;
737	<	std::set<AtomType*> atomTypes;
738	<
737	>	set<AtomType*> atomTypes;
738	>
739		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
740	<
741	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
740	>	for(atom = mol->beginAtom(ai); atom != NULL;
741	>	atom = mol->nextAtom(ai)) {
742		atomTypes.insert(atom->getAtomType());
743	<	}
744	<
743	>	}
744	>	}
745	>
746	>	#ifdef IS_MPI
747	>
748	>	// loop over the found atom types on this processor, and add their
749	>	// numerical idents to a vector:
750	>
751	>	vector<int> foundTypes;
752	>	set<AtomType*>::iterator i;
753	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
754	>	foundTypes.push_back( (*i)->getIdent() );
755	>
756	>	// count_local holds the number of found types on this processor
757	>	int count_local = foundTypes.size();
758	>
759	>	int nproc;
760	>	MPI_Comm_size( MPI_COMM_WORLD, &nproc);
761	>	// int nproc = MPI::COMM_WORLD.Get_size();
762	>
763	>	// we need arrays to hold the counts and displacement vectors for
764	>	// all processors
765	>	vector<int> counts(nproc, 0);
766	>	vector<int> disps(nproc, 0);
767	>
768	>	// fill the counts array
769	>	MPI_Allgather(&count_local, 1, MPI_INT, &counts[0],
770	>	1, MPI_INT, MPI_COMM_WORLD);
771	>	// MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
772	>	//                           1, MPI::INT);
773	>
774	>	// use the processor counts to compute the displacement array
775	>	disps[0] = 0;
776	>	int totalCount = counts[0];
777	>	for (int iproc = 1; iproc < nproc; iproc++) {
778	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
779	>	totalCount += counts[iproc];
780		}
781
782	<	return atomTypes;
783	<	}
782	>	// we need a (possibly redundant) set of all found types:
783	>	vector<int> ftGlobal(totalCount);
784	>
785	>	// now spray out the foundTypes to all the other processors:
786	>	MPI_Allgatherv(&foundTypes[0], count_local, MPI_INT,
787	>	&ftGlobal[0], &counts[0], &disps[0],
788	>	MPI_INT, MPI_COMM_WORLD);
789	>	// MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
790	>	//                            &ftGlobal[0], &counts[0], &disps[0],
791	>	//                            MPI::INT);
792
793	<	void SimInfo::setupSimType() {
794	<	std::set<AtomType*>::iterator i;
795	<	std::set<AtomType*> atomTypes;
796	<	atomTypes = getUniqueAtomTypes();
793	>	vector<int>::iterator j;
794	>
795	>	// foundIdents is a stl set, so inserting an already found ident
796	>	// will have no effect.
797	>	set<int> foundIdents;
798	>
799	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
800	>	foundIdents.insert((*j));
801
802	<	int useLennardJones = 0;
803	<	int useElectrostatic = 0;
804	<	int useEAM = 0;
805	<	int useCharge = 0;
806	<	int useDirectional = 0;
807	<	int useDipole = 0;
808	<	int useGayBerne = 0;
522	<	int useSticky = 0;
523	<	int useStickyPower = 0;
524	<	int useShape = 0;
525	<	int useFLARB = 0; //it is not in AtomType yet
526	<	int useDirectionalAtom = 0;
527	<	int useElectrostatics = 0;
528	<	//usePBC and useRF are from simParams
529	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
530	<	int useRF;
531	<	int useDW;
532	<	std::string myMethod;
802	>	// now iterate over the foundIdents and get the actual atom types
803	>	// that correspond to these:
804	>	set<int>::iterator it;
805	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
806	>	atomTypes.insert( forceField_->getAtomType((*it)) );
807	>
808	>	#endif
809
810	<	// set the useRF logical
811	<	useRF = 0;
536	<	useDW = 0;
810	>	return atomTypes;
811	>	}
812
813
814	<	if (simParams_->haveElectrostaticSummationMethod()) {
815	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
816	<	toUpper(myMethod);
817	<	if (myMethod == "REACTION_FIELD") {
543	<	useRF=1;
544	<	} else {
545	<	if (myMethod == "DAMPED_WOLF") {
546	<	useDW = 1;
547	<	}
548	<	}
549	<	}
814	>	int getGlobalCountOfType(AtomType* atype) {
815	>	/*
816	>	set<AtomType*> atypes = getSimulatedAtomTypes();
817	>	map<AtomType*, int> counts_;
818
819	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
820	+	for(atom = mol->beginAtom(ai); atom != NULL;
821	+	atom = mol->nextAtom(ai)) {
822	+	atom->getAtomType();
823	+	}
824	+	}
825	+	*/
826	+	return 0;
827	+	}
828	+
829	+	void SimInfo::setupSimVariables() {
830	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
831	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
832	+	// parameter is true
833	+	calcBoxDipole_ = false;
834	+	if ( simParams_->haveAccumulateBoxDipole() )
835	+	if ( simParams_->getAccumulateBoxDipole() ) {
836	+	calcBoxDipole_ = true;
837	+	}
838	+
839	+	set<AtomType*>::iterator i;
840	+	set<AtomType*> atomTypes;
841	+	atomTypes = getSimulatedAtomTypes();
842	+	bool usesElectrostatic = false;
843	+	bool usesMetallic = false;
844	+	bool usesDirectional = false;
845	+	bool usesFluctuatingCharges =  false;
846		//loop over all of the atom types
847		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
848	<	useLennardJones |= (*i)->isLennardJones();
849	<	useElectrostatic |= (*i)->isElectrostatic();
850	<	useEAM |= (*i)->isEAM();
851	<	useCharge |= (*i)->isCharge();
557	<	useDirectional |= (*i)->isDirectional();
558	<	useDipole |= (*i)->isDipole();
559	<	useGayBerne |= (*i)->isGayBerne();
560	<	useSticky |= (*i)->isSticky();
561	<	useStickyPower |= (*i)->isStickyPower();
562	<	useShape |= (*i)->isShape();
848	>	usesElectrostatic |= (*i)->isElectrostatic();
849	>	usesMetallic |= (*i)->isMetal();
850	>	usesDirectional |= (*i)->isDirectional();
851	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
852		}
853
854	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
566	<	useDirectionalAtom = 1;
567	<	}
568	<
569	<	if (useCharge || useDipole) {
570	<	useElectrostatics = 1;
571	<	}
572	<
573	<	#ifdef IS_MPI
854	>	#ifdef IS_MPI
855		int temp;
856
857	<	temp = usePBC;
858	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
857	>	temp = usesDirectional;
858	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
859	>	usesDirectionalAtoms_ = (temp == 0) ? false : true;
860
861	<	temp = useDirectionalAtom;
862	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
861	>	// MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
862	>	//                           MPI::LOR);
863	>
864	>	temp = usesMetallic;
865	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
866	>	usesMetallicAtoms_ = (temp == 0) ? false : true;
867
868	<	temp = useLennardJones;
869	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
868	>	// MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
869	>	//                           MPI::LOR);
870	>
871	>	temp = usesElectrostatic;
872	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
873	>	usesElectrostaticAtoms_ = (temp == 0) ? false : true;
874
875	<	temp = useElectrostatics;
876	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
875	>	// MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
876	>	//                           MPI::LOR);
877
878	<	temp = useCharge;
879	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
878	>	temp = usesFluctuatingCharges;
879	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
880	>	usesFluctuatingCharges_ = (temp == 0) ? false : true;
881
882	<	temp = useDipole;
883	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
882	>	// MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
883	>	//                           MPI::LOR);
884
885	<	temp = useSticky;
595	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
885	>	#else
886
887	<	temp = useStickyPower;
888	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
887	>	usesDirectionalAtoms_ = usesDirectional;
888	>	usesMetallicAtoms_ = usesMetallic;
889	>	usesElectrostaticAtoms_ = usesElectrostatic;
890	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
891	>
892	>	#endif
893
894	<	temp = useGayBerne;
895	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
894	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
895	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
896	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
897	>	}
898
603	–	temp = useEAM;
604	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
899
900	<	temp = useShape;
901	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
900	>	vector<int> SimInfo::getGlobalAtomIndices() {
901	>	SimInfo::MoleculeIterator mi;
902	>	Molecule* mol;
903	>	Molecule::AtomIterator ai;
904	>	Atom* atom;
905
906	<	temp = useFLARB;
907	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
906	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
907	>
908	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
909	>
910	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
911	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
912	>	}
913	>	}
914	>	return GlobalAtomIndices;
915	>	}
916
612	–	temp = useRF;
613	–	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
917
918	<	temp = useDW;
919	<	MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
918	>	vector<int> SimInfo::getGlobalGroupIndices() {
919	>	SimInfo::MoleculeIterator mi;
920	>	Molecule* mol;
921	>	Molecule::CutoffGroupIterator ci;
922	>	CutoffGroup* cg;
923
924	<	#endif
925	<
926	<	fInfo_.SIM_uses_PBC = usePBC;
621	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
622	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
623	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
624	<	fInfo_.SIM_uses_Charges = useCharge;
625	<	fInfo_.SIM_uses_Dipoles = useDipole;
626	<	fInfo_.SIM_uses_Sticky = useSticky;
627	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
628	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
629	<	fInfo_.SIM_uses_EAM = useEAM;
630	<	fInfo_.SIM_uses_Shapes = useShape;
631	<	fInfo_.SIM_uses_FLARB = useFLARB;
632	<	fInfo_.SIM_uses_RF = useRF;
633	<	fInfo_.SIM_uses_DampedWolf = useDW;
634	<
635	<	if( myMethod == "REACTION_FIELD") {
924	>	vector<int> GlobalGroupIndices;
925	>
926	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
927
928	<	if (simParams_->haveDielectric()) {
929	<	fInfo_.dielect = simParams_->getDielectric();
930	<	} else {
931	<	sprintf(painCave.errMsg,
932	<	"SimSetup Error: No Dielectric constant was set.\n"
933	<	"\tYou are trying to use Reaction Field without"
643	<	"\tsetting a dielectric constant!\n");
644	<	painCave.isFatal = 1;
645	<	simError();
646	<	}
928	>	//local index of cutoff group is trivial, it only depends on the
929	>	//order of travesing
930	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
931	>	cg = mol->nextCutoffGroup(ci)) {
932	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
933	>	}
934		}
935	<
935	>	return GlobalGroupIndices;
936		}
937
651	–	void SimInfo::setupFortranSim() {
652	–	int isError;
653	–	int nExclude;
654	–	std::vector<int> fortranGlobalGroupMembership;
655	–
656	–	nExclude = exclude_.getSize();
657	–	isError = 0;
938
939	<	//globalGroupMembership_ is filled by SimCreator
660	<	for (int i = 0; i < nGlobalAtoms_; i++) {
661	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
662	<	}
939	>	void SimInfo::prepareTopology() {
940
941		//calculate mass ratio of cutoff group
665	–	std::vector<double> mfact;
942		SimInfo::MoleculeIterator mi;
943		Molecule* mol;
944		Molecule::CutoffGroupIterator ci;
945		CutoffGroup* cg;
946		Molecule::AtomIterator ai;
947		Atom* atom;
948	<	double totalMass;
948	>	RealType totalMass;
949
950	<	//to avoid memory reallocation, reserve enough space for mfact
951	<	mfact.reserve(getNCutoffGroups());
950	>	/**
951	>	* The mass factor is the relative mass of an atom to the total
952	>	* mass of the cutoff group it belongs to.  By default, all atoms
953	>	* are their own cutoff groups, and therefore have mass factors of
954	>	* 1.  We need some special handling for massless atoms, which
955	>	* will be treated as carrying the entire mass of the cutoff
956	>	* group.
957	>	*/
958	>	massFactors_.clear();
959	>	massFactors_.resize(getNAtoms(), 1.0);
960
961		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
962	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
962	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
963	>	cg = mol->nextCutoffGroup(ci)) {
964
965		totalMass = cg->getMass();
966		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
967		// Check for massless groups - set mfact to 1 if true
968	<	if (totalMass != 0)
969	<	mfact.push_back(atom->getMass()/totalMass);
968	>	if (totalMass != 0)
969	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
970		else
971	<	mfact.push_back( 1.0 );
971	>	massFactors_[atom->getLocalIndex()] = 1.0;
972		}
688	–
973		}
974		}
975
976	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
693	<	std::vector<int> identArray;
976	>	// Build the identArray_ and regions_
977
978	<	//to avoid memory reallocation, reserve enough space identArray
979	<	identArray.reserve(getNAtoms());
980	<
981	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
978	>	identArray_.clear();
979	>	identArray_.reserve(getNAtoms());
980	>	regions_.clear();
981	>	regions_.reserve(getNAtoms());
982	>
983	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
984	>	int reg = mol->getRegion();
985		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
986	<	identArray.push_back(atom->getIdent());
986	>	identArray_.push_back(atom->getIdent());
987	>	regions_.push_back(reg);
988		}
989		}
990	<
991	<	//fill molMembershipArray
705	<	//molMembershipArray is filled by SimCreator
706	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
707	<	for (int i = 0; i < nGlobalAtoms_; i++) {
708	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
709	<	}
710	<
711	<	//setup fortran simulation
712	<	int nGlobalExcludes = 0;
713	<	int* globalExcludes = NULL;
714	<	int* excludeList = exclude_.getExcludeList();
715	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
716	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
717	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
718	<
719	<	if( isError ){
720	<
721	<	sprintf( painCave.errMsg,
722	<	"There was an error setting the simulation information in fortran.\n" );
723	<	painCave.isFatal = 1;
724	<	painCave.severity = OOPSE_ERROR;
725	<	simError();
726	<	}
727	<
728	<	#ifdef IS_MPI
729	<	sprintf( checkPointMsg,
730	<	"succesfully sent the simulation information to fortran.\n");
731	<	MPIcheckPoint();
732	<	#endif // is_mpi
733	<	}
734	<
735	<
736	<	#ifdef IS_MPI
737	<	void SimInfo::setupFortranParallel() {
738	<
739	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
740	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
741	<	std::vector<int> localToGlobalCutoffGroupIndex;
742	<	SimInfo::MoleculeIterator mi;
743	<	Molecule::AtomIterator ai;
744	<	Molecule::CutoffGroupIterator ci;
745	<	Molecule* mol;
746	<	Atom* atom;
747	<	CutoffGroup* cg;
748	<	mpiSimData parallelData;
749	<	int isError;
750	<
751	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
752	<
753	<	//local index(index in DataStorge) of atom is important
754	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
755	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
756	<	}
757	<
758	<	//local index of cutoff group is trivial, it only depends on the order of travesing
759	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
760	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
761	<	}
762	<
763	<	}
764	<
765	<	//fill up mpiSimData struct
766	<	parallelData.nMolGlobal = getNGlobalMolecules();
767	<	parallelData.nMolLocal = getNMolecules();
768	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
769	<	parallelData.nAtomsLocal = getNAtoms();
770	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
771	<	parallelData.nGroupsLocal = getNCutoffGroups();
772	<	parallelData.myNode = worldRank;
773	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
774	<
775	<	//pass mpiSimData struct and index arrays to fortran
776	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
777	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
778	<	&localToGlobalCutoffGroupIndex[0], &isError);
779	<
780	<	if (isError) {
781	<	sprintf(painCave.errMsg,
782	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
783	<	painCave.isFatal = 1;
784	<	simError();
785	<	}
786	<
787	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
788	<	MPIcheckPoint();
789	<
790	<
791	<	}
792	<
793	<	#endif
794	<
795	<	double SimInfo::calcMaxCutoffRadius() {
796	<
797	<
798	<	std::set<AtomType*> atomTypes;
799	<	std::set<AtomType*>::iterator i;
800	<	std::vector<double> cutoffRadius;
801	<
802	<	//get the unique atom types
803	<	atomTypes = getUniqueAtomTypes();
804	<
805	<	//query the max cutoff radius among these atom types
806	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
807	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
808	<	}
809	<
810	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
811	<	#ifdef IS_MPI
812	<	//pick the max cutoff radius among the processors
813	<	#endif
814	<
815	<	return maxCutoffRadius;
816	<	}
817	<
818	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
819	<
820	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
821	<
822	<	if (!simParams_->haveCutoffRadius()){
823	<	sprintf(painCave.errMsg,
824	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
825	<	"\tOOPSE will use a default value of 15.0 angstroms"
826	<	"\tfor the cutoffRadius.\n");
827	<	painCave.isFatal = 0;
828	<	simError();
829	<	rcut = 15.0;
830	<	} else{
831	<	rcut = simParams_->getCutoffRadius();
832	<	}
833	<
834	<	if (!simParams_->haveSwitchingRadius()){
835	<	sprintf(painCave.errMsg,
836	<	"SimCreator Warning: No value was set for switchingRadius.\n"
837	<	"\tOOPSE will use a default value of\n"
838	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
839	<	painCave.isFatal = 0;
840	<	simError();
841	<	rsw = 0.85 * rcut;
842	<	} else{
843	<	rsw = simParams_->getSwitchingRadius();
844	<	}
845	<
846	<	} else {
847	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
848	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
849	<
850	<	if (simParams_->haveCutoffRadius()) {
851	<	rcut = simParams_->getCutoffRadius();
852	<	} else {
853	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
854	<	rcut = calcMaxCutoffRadius();
855	<	}
856	<
857	<	if (simParams_->haveSwitchingRadius()) {
858	<	rsw  = simParams_->getSwitchingRadius();
859	<	} else {
860	<	rsw = rcut;
861	<	}
862	<
863	<	}
990	>
991	>	topologyDone_ = true;
992		}
993
866	–	void SimInfo::setupCutoff() {
867	–	getCutoff(rcut_, rsw_);
868	–	double rnblist = rcut_ + 1; // skin of neighbor list
869	–
870	–	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
871	–
872	–	int cp =  TRADITIONAL_CUTOFF_POLICY;
873	–	if (simParams_->haveCutoffPolicy()) {
874	–	std::string myPolicy = simParams_->getCutoffPolicy();
875	–	toUpper(myPolicy);
876	–	if (myPolicy == "MIX") {
877	–	cp = MIX_CUTOFF_POLICY;
878	–	} else {
879	–	if (myPolicy == "MAX") {
880	–	cp = MAX_CUTOFF_POLICY;
881	–	} else {
882	–	if (myPolicy == "TRADITIONAL") {
883	–	cp = TRADITIONAL_CUTOFF_POLICY;
884	–	} else {
885	–	// throw error
886	–	sprintf( painCave.errMsg,
887	–	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
888	–	painCave.isFatal = 1;
889	–	simError();
890	–	}
891	–	}
892	–	}
893	–	}
894	–
895	–
896	–	if (simParams_->haveSkinThickness()) {
897	–	double skinThickness = simParams_->getSkinThickness();
898	–	}
899	–
900	–	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
901	–	// also send cutoff notification to electrostatics
902	–	setElectrostaticCutoffRadius(&rcut_, &rsw_);
903	–	}
904	–
905	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
906	–
907	–	int errorOut;
908	–	int esm =  NONE;
909	–	double alphaVal;
910	–	double dielectric;
911	–
912	–	errorOut = isError;
913	–	alphaVal = simParams_->getDampingAlpha();
914	–	dielectric = simParams_->getDielectric();
915	–
916	–	if (simParams_->haveElectrostaticSummationMethod()) {
917	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
918	–	toUpper(myMethod);
919	–	if (myMethod == "NONE") {
920	–	esm = NONE;
921	–	} else {
922	–	if (myMethod == "UNDAMPED_WOLF") {
923	–	esm = UNDAMPED_WOLF;
924	–	} else {
925	–	if (myMethod == "DAMPED_WOLF") {
926	–	esm = DAMPED_WOLF;
927	–	if (!simParams_->haveDampingAlpha()) {
928	–	//throw error
929	–	sprintf( painCave.errMsg,
930	–	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", alphaVal);
931	–	painCave.isFatal = 0;
932	–	simError();
933	–	}
934	–	} else {
935	–	if (myMethod == "REACTION_FIELD") {
936	–	esm = REACTION_FIELD;
937	–	} else {
938	–	// throw error
939	–	sprintf( painCave.errMsg,
940	–	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"undamped_wolf\", \"damped_wolf\", or \"reaction_field\".", myMethod.c_str() );
941	–	painCave.isFatal = 1;
942	–	simError();
943	–	}
944	–	}
945	–	}
946	–	}
947	–	}
948	–	// let's pass some summation method variables to fortran
949	–	setElectrostaticSummationMethod( &esm );
950	–	setDampedWolfAlpha( &alphaVal );
951	–	setReactionFieldDielectric( &dielectric );
952	–	initFortranFF( &esm, &errorOut );
953	–	}
954	–
994		void SimInfo::addProperty(GenericData* genData) {
995		properties_.addProperty(genData);
996		}
997
998	<	void SimInfo::removeProperty(const std::string& propName) {
998	>	void SimInfo::removeProperty(const string& propName) {
999		properties_.removeProperty(propName);
1000		}
1001
#	Line 964 | Line 1003 | namespace oopse {
1003		properties_.clearProperties();
1004		}
1005
1006	<	std::vector<std::string> SimInfo::getPropertyNames() {
1006	>	vector<string> SimInfo::getPropertyNames() {
1007		return properties_.getPropertyNames();
1008		}
1009
1010	<	std::vector<GenericData*> SimInfo::getProperties() {
1010	>	vector<GenericData*> SimInfo::getProperties() {
1011		return properties_.getProperties();
1012		}
1013
1014	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1014	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1015		return properties_.getPropertyByName(propName);
1016		}
1017
#	Line 983 | Line 1022 | namespace oopse {
1022		delete sman_;
1023		sman_ = sman;
1024
986	–	Molecule* mol;
987	–	RigidBody* rb;
988	–	Atom* atom;
1025		SimInfo::MoleculeIterator mi;
1026	+	Molecule::AtomIterator ai;
1027		Molecule::RigidBodyIterator rbIter;
1028	<	Molecule::AtomIterator atomIter;;
1028	>	Molecule::CutoffGroupIterator cgIter;
1029	>	Molecule::BondIterator bondIter;
1030	>	Molecule::BendIterator bendIter;
1031	>	Molecule::TorsionIterator torsionIter;
1032	>	Molecule::InversionIterator inversionIter;
1033
1034	+	Molecule* mol;
1035	+	Atom* atom;
1036	+	RigidBody* rb;
1037	+	CutoffGroup* cg;
1038	+	Bond* bond;
1039	+	Bend* bend;
1040	+	Torsion* torsion;
1041	+	Inversion* inversion;
1042	+
1043		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1044
1045	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1045	>	for (atom = mol->beginAtom(ai); atom != NULL;
1046	>	atom = mol->nextAtom(ai)) {
1047		atom->setSnapshotManager(sman_);
1048	<	}
1049	<
1050	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1048	>	}
1049	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1050	>	rb = mol->nextRigidBody(rbIter)) {
1051		rb->setSnapshotManager(sman_);
1052		}
1053	<	}
1054	<
1053	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1054	>	cg = mol->nextCutoffGroup(cgIter)) {
1055	>	cg->setSnapshotManager(sman_);
1056	>	}
1057	>	for (bond = mol->beginBond(bondIter); bond != NULL;
1058	>	bond = mol->nextBond(bondIter)) {
1059	>	bond->setSnapshotManager(sman_);
1060	>	}
1061	>	for (bend = mol->beginBend(bendIter); bend != NULL;
1062	>	bend = mol->nextBend(bendIter)) {
1063	>	bend->setSnapshotManager(sman_);
1064	>	}
1065	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
1066	>	torsion = mol->nextTorsion(torsionIter)) {
1067	>	torsion->setSnapshotManager(sman_);
1068	>	}
1069	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
1070	>	inversion = mol->nextInversion(inversionIter)) {
1071	>	inversion->setSnapshotManager(sman_);
1072	>	}
1073	>	}
1074		}
1075
1006	–	Vector3d SimInfo::getComVel(){
1007	–	SimInfo::MoleculeIterator i;
1008	–	Molecule* mol;
1076
1077	<	Vector3d comVel(0.0);
1011	<	double totalMass = 0.0;
1012	<
1013	<
1014	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1015	<	double mass = mol->getMass();
1016	<	totalMass += mass;
1017	<	comVel += mass * mol->getComVel();
1018	<	}
1077	>	ostream& operator <<(ostream& o, SimInfo& info) {
1078
1020	–	#ifdef IS_MPI
1021	–	double tmpMass = totalMass;
1022	–	Vector3d tmpComVel(comVel);
1023	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1024	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1025	–	#endif
1026	–
1027	–	comVel /= totalMass;
1028	–
1029	–	return comVel;
1030	–	}
1031	–
1032	–	Vector3d SimInfo::getCom(){
1033	–	SimInfo::MoleculeIterator i;
1034	–	Molecule* mol;
1035	–
1036	–	Vector3d com(0.0);
1037	–	double totalMass = 0.0;
1038	–
1039	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1040	–	double mass = mol->getMass();
1041	–	totalMass += mass;
1042	–	com += mass * mol->getCom();
1043	–	}
1044	–
1045	–	#ifdef IS_MPI
1046	–	double tmpMass = totalMass;
1047	–	Vector3d tmpCom(com);
1048	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1049	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1050	–	#endif
1051	–
1052	–	com /= totalMass;
1053	–
1054	–	return com;
1055	–
1056	–	}
1057	–
1058	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1059	–
1079		return o;
1080		}
1081
1082	<
1083	<	/*
1084	<	Returns center of mass and center of mass velocity in one function call.
1085	<	*/
1086	<
1087	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1088	<	SimInfo::MoleculeIterator i;
1089	<	Molecule* mol;
1090	<
1091	<
1092	<	double totalMass = 0.0;
1093	<
1082	>
1083	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1084	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1085	>	sprintf(painCave.errMsg,
1086	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1087	>	"\tindex exceeds number of known objects!\n");
1088	>	painCave.isFatal = 1;
1089	>	simError();
1090	>	return NULL;
1091	>	} else
1092	>	return IOIndexToIntegrableObject.at(index);
1093	>	}
1094	>
1095	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1096	>	IOIndexToIntegrableObject= v;
1097	>	}
1098
1099	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1100	<	double mass = mol->getMass();
1078	<	totalMass += mass;
1079	<	com += mass * mol->getCom();
1080	<	comVel += mass * mol->getComVel();
1081	<	}
1082	<
1099	>	int SimInfo::getNGlobalConstraints() {
1100	>	int nGlobalConstraints;
1101		#ifdef IS_MPI
1102	<	double tmpMass = totalMass;
1103	<	Vector3d tmpCom(com);
1104	<	Vector3d tmpComVel(comVel);
1105	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1106	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1107	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1102	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1103	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1104	>	// MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1105	>	//                           MPI::INT, MPI::SUM);
1106	>	#else
1107	>	nGlobalConstraints =  nConstraints_;
1108		#endif
1109	<
1110	<	com /= totalMass;
1093	<	comVel /= totalMass;
1094	<	}
1095	<
1096	<	/*
1097	<	Return intertia tensor for entire system and angular momentum Vector.
1109	>	return nGlobalConstraints;
1110	>	}
1111
1112	+	}//end namespace OpenMD
1113
1100	–	[  Ixx -Ixy  -Ixz ]
1101	–	J =| -Iyx  Iyy  -Iyz |
1102	–	[ -Izx -Iyz   Izz ]
1103	–	*/
1104	–
1105	–	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1106	–
1107	–
1108	–	double xx = 0.0;
1109	–	double yy = 0.0;
1110	–	double zz = 0.0;
1111	–	double xy = 0.0;
1112	–	double xz = 0.0;
1113	–	double yz = 0.0;
1114	–	Vector3d com(0.0);
1115	–	Vector3d comVel(0.0);
1116	–
1117	–	getComAll(com, comVel);
1118	–
1119	–	SimInfo::MoleculeIterator i;
1120	–	Molecule* mol;
1121	–
1122	–	Vector3d thisq(0.0);
1123	–	Vector3d thisv(0.0);
1124	–
1125	–	double thisMass = 0.0;
1126	–
1127	–
1128	–
1129	–
1130	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1131	–
1132	–	thisq = mol->getCom()-com;
1133	–	thisv = mol->getComVel()-comVel;
1134	–	thisMass = mol->getMass();
1135	–	// Compute moment of intertia coefficients.
1136	–	xx += thisq[0]*thisq[0]*thisMass;
1137	–	yy += thisq[1]*thisq[1]*thisMass;
1138	–	zz += thisq[2]*thisq[2]*thisMass;
1139	–
1140	–	// compute products of intertia
1141	–	xy += thisq[0]*thisq[1]*thisMass;
1142	–	xz += thisq[0]*thisq[2]*thisMass;
1143	–	yz += thisq[1]*thisq[2]*thisMass;
1144	–
1145	–	angularMomentum += cross( thisq, thisv ) * thisMass;
1146	–
1147	–	}
1148	–
1149	–
1150	–	inertiaTensor(0,0) = yy + zz;
1151	–	inertiaTensor(0,1) = -xy;
1152	–	inertiaTensor(0,2) = -xz;
1153	–	inertiaTensor(1,0) = -xy;
1154	–	inertiaTensor(1,1) = xx + zz;
1155	–	inertiaTensor(1,2) = -yz;
1156	–	inertiaTensor(2,0) = -xz;
1157	–	inertiaTensor(2,1) = -yz;
1158	–	inertiaTensor(2,2) = xx + yy;
1159	–
1160	–	#ifdef IS_MPI
1161	–	Mat3x3d tmpI(inertiaTensor);
1162	–	Vector3d tmpAngMom;
1163	–	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1164	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1165	–	#endif
1166	–
1167	–	return;
1168	–	}
1169	–
1170	–	//Returns the angular momentum of the system
1171	–	Vector3d SimInfo::getAngularMomentum(){
1172	–
1173	–	Vector3d com(0.0);
1174	–	Vector3d comVel(0.0);
1175	–	Vector3d angularMomentum(0.0);
1176	–
1177	–	getComAll(com,comVel);
1178	–
1179	–	SimInfo::MoleculeIterator i;
1180	–	Molecule* mol;
1181	–
1182	–	Vector3d thisr(0.0);
1183	–	Vector3d thisp(0.0);
1184	–
1185	–	double thisMass;
1186	–
1187	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1188	–	thisMass = mol->getMass();
1189	–	thisr = mol->getCom()-com;
1190	–	thisp = (mol->getComVel()-comVel)*thisMass;
1191	–
1192	–	angularMomentum += cross( thisr, thisp );
1193	–
1194	–	}
1195	–
1196	–	#ifdef IS_MPI
1197	–	Vector3d tmpAngMom;
1198	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1199	–	#endif
1200	–
1201	–	return angularMomentum;
1202	–	}
1203	–
1204	–
1205	–	}//end namespace oopse
1206	–

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 705 by chrisfen, Tue Nov 1 19:14:27 2005 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

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