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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 720 by chrisfen, Tue Nov 8 13:32:06 2005 UTC vs.
Revision 1983 by gezelter, Tue Apr 15 20:36:19 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/DarkSide/fElectrostaticScreeningMethod.h"
58	<	#include "UseTheForce/doForces_interface.h"
59	<	#include "UseTheForce/DarkSide/electrostatic_interface.h"
60	<	#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 {
71	<
72	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
73	<	ForceField* ff, Globals* simParams) :
74	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
75	<	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;
82	<	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),
76	>	nGlobalFluctuatingCharges_(0), nGlobalBonds_(0), nGlobalBends_(0),
77	>	nGlobalTorsions_(0), nGlobalInversions_(0), nGlobalConstraints_(0),
78	>	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0),
79	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
80	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL),
81	>	topologyDone_(false), calcBoxDipole_(false), useAtomicVirial_(true),
82	>	hasNGlobalConstraints_(false) {
83
84	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
85	<	molStamp = i->first;
86	<	nMolWithSameStamp = i->second;
87	<
88	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
89	<
90	<	//calculate atoms in molecules
91	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
92	<
93	<
94	<	//calculate atoms in cutoff groups
95	<	int nAtomsInGroups = 0;
96	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
97	<
98	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
99	<	cgStamp = molStamp->getCutoffGroup(j);
100	<	nAtomsInGroups += cgStamp->getNMembers();
101	<	}
110	<
111	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
112	<
113	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
114	<
115	<	//calculate atoms in rigid bodies
116	<	int nAtomsInRigidBodies = 0;
117	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
118	<
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	<
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;
91	>
92	>	vector<Component*> components = simParams->getComponents();
93	>
94	>	for (vector<Component*>::iterator i = components.begin();
95	>	i !=components.end(); ++i) {
96	>	molStamp = (*i)->getMoleculeStamp();
97	>	if ( (*i)->haveRegion() ) {
98	>	molStamp->setRegion( (*i)->getRegion() );
99	>	} else {
100	>	// set the region to a disallowed value:
101	>	molStamp->setRegion( -1 );
102		}
103
104	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
105	<	//group therefore the total number of cutoff groups in the system is
106	<	//equal to the total number of atoms minus number of atoms belong to
107	<	//cutoff group defined in meta-data file plus the number of cutoff
108	<	//groups defined in meta-data file
109	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
110	<
111	<	//every free atom (atom does not belong to rigid bodies) is an
112	<	//integrable object therefore the total number of integrable objects
113	<	//in the system is equal to the total number of atoms minus number of
114	<	//atoms belong to rigid body defined in meta-data file plus the number
115	<	//of rigid bodies defined in meta-data file
116	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
117	<	+ nGlobalRigidBodies_;
118	<
119	<	nGlobalMols_ = molStampIds_.size();
120	<
121	<	#ifdef IS_MPI
122	<	molToProcMap_.resize(nGlobalMols_);
123	<	#endif
124	<
104	>	nMolWithSameStamp = (*i)->getNMol();
105	>
106	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
107	>
108	>	//calculate atoms in molecules
109	>	nGlobalAtoms_ += molStamp->getNAtoms() * nMolWithSameStamp;
110	>	nGlobalBonds_ += molStamp->getNBonds() * nMolWithSameStamp;
111	>	nGlobalBends_ += molStamp->getNBends() * nMolWithSameStamp;
112	>	nGlobalTorsions_ += molStamp->getNTorsions() * nMolWithSameStamp;
113	>	nGlobalInversions_ += molStamp->getNInversions() * nMolWithSameStamp;
114	>
115	>	//calculate atoms in cutoff groups
116	>	int nAtomsInGroups = 0;
117	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
118	>
119	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
120	>	cgStamp = molStamp->getCutoffGroupStamp(j);
121	>	nAtomsInGroups += cgStamp->getNMembers();
122	>	}
123	>
124	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
125	>
126	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
127	>
128	>	//calculate atoms in rigid bodies
129	>	int nAtomsInRigidBodies = 0;
130	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
131	>
132	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
133	>	rbStamp = molStamp->getRigidBodyStamp(j);
134	>	nAtomsInRigidBodies += rbStamp->getNMembers();
135	>	}
136	>
137	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
138	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
139	>
140		}
141	+
142	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
143	+	//group therefore the total number of cutoff groups in the system is
144	+	//equal to the total number of atoms minus number of atoms belong to
145	+	//cutoff group defined in meta-data file plus the number of cutoff
146	+	//groups defined in meta-data file
147
148	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
149	+
150	+	//every free atom (atom does not belong to rigid bodies) is an
151	+	//integrable object therefore the total number of integrable objects
152	+	//in the system is equal to the total number of atoms minus number of
153	+	//atoms belong to rigid body defined in meta-data file plus the number
154	+	//of rigid bodies defined in meta-data file
155	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
156	+	+ nGlobalRigidBodies_;
157	+
158	+	nGlobalMols_ = molStampIds_.size();
159	+	molToProcMap_.resize(nGlobalMols_);
160	+	}
161	+
162		SimInfo::~SimInfo() {
163	<	std::map<int, Molecule*>::iterator i;
163	>	map<int, Molecule*>::iterator i;
164		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
165		delete i->second;
166		}
167		molecules_.clear();
168
159	–	delete stamps_;
169		delete sman_;
170		delete simParams_;
171		delete forceField_;
172		}
173
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	–	}
174
175		bool SimInfo::addMolecule(Molecule* mol) {
176		MoleculeIterator i;
177	<
177	>
178		i = molecules_.find(mol->getGlobalIndex());
179		if (i == molecules_.end() ) {
180	<
181	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
182	<
180	>
181	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
182	>
183		nAtoms_ += mol->getNAtoms();
184		nBonds_ += mol->getNBonds();
185		nBends_ += mol->getNBends();
186		nTorsions_ += mol->getNTorsions();
187	+	nInversions_ += mol->getNInversions();
188		nRigidBodies_ += mol->getNRigidBodies();
189		nIntegrableObjects_ += mol->getNIntegrableObjects();
190		nCutoffGroups_ += mol->getNCutoffGroups();
191		nConstraints_ += mol->getNConstraintPairs();
192	<
193	<	addExcludePairs(mol);
194	<
192	>
193	>	addInteractionPairs(mol);
194	>
195		return true;
196		} else {
197		return false;
198		}
199		}
200	<
200	>
201		bool SimInfo::removeMolecule(Molecule* mol) {
202		MoleculeIterator i;
203		i = molecules_.find(mol->getGlobalIndex());
#	Line 210 | Line 210 | namespace oopse {
210		nBonds_ -= mol->getNBonds();
211		nBends_ -= mol->getNBends();
212		nTorsions_ -= mol->getNTorsions();
213	+	nInversions_ -= mol->getNInversions();
214		nRigidBodies_ -= mol->getNRigidBodies();
215		nIntegrableObjects_ -= mol->getNIntegrableObjects();
216		nCutoffGroups_ -= mol->getNCutoffGroups();
217		nConstraints_ -= mol->getNConstraintPairs();
218
219	<	removeExcludePairs(mol);
219	>	removeInteractionPairs(mol);
220		molecules_.erase(mol->getGlobalIndex());
221
222		delete mol;
#	Line 224 | Line 225 | namespace oopse {
225		} else {
226		return false;
227		}
227	–
228	–
228		}
229
230
#	Line 241 | Line 240 | namespace oopse {
240
241
242		void SimInfo::calcNdf() {
243	<	int ndf_local;
243	>	int ndf_local, nfq_local;
244		MoleculeIterator i;
245	<	std::vector<StuntDouble*>::iterator j;
245	>	vector<StuntDouble*>::iterator j;
246	>	vector<Atom*>::iterator k;
247	>
248		Molecule* mol;
249	<	StuntDouble* integrableObject;
249	>	StuntDouble* sd;
250	>	Atom* atom;
251
252		ndf_local = 0;
253	+	nfq_local = 0;
254
255		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
253	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
254	–	integrableObject = mol->nextIntegrableObject(j)) {
256
257	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
258	+	sd = mol->nextIntegrableObject(j)) {
259	+
260		ndf_local += 3;
261
262	<	if (integrableObject->isDirectional()) {
263	<	if (integrableObject->isLinear()) {
262	>	if (sd->isDirectional()) {
263	>	if (sd->isLinear()) {
264		ndf_local += 2;
265		} else {
266		ndf_local += 3;
267		}
268		}
269	<
270	<	}//end for (integrableObject)
271	<	}// end for (mol)
269	>	}
270	>
271	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
272	>	atom = mol->nextFluctuatingCharge(k)) {
273	>	if (atom->isFluctuatingCharge()) {
274	>	nfq_local++;
275	>	}
276	>	}
277	>	}
278
279	+	ndfLocal_ = ndf_local;
280	+
281		// n_constraints is local, so subtract them on each processor
282		ndf_local -= nConstraints_;
283
284		#ifdef IS_MPI
285	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
285	>	MPI_Allreduce(&ndf_local, &ndf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
286	>	MPI_Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
287	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
288		#else
289		ndf_ = ndf_local;
290	+	nGlobalFluctuatingCharges_ = nfq_local;
291		#endif
292
293		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 281 | Line 296 | namespace oopse {
296
297		}
298
299	+	int SimInfo::getFdf() {
300	+	#ifdef IS_MPI
301	+	MPI_Allreduce(&fdf_local, &fdf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
302	+	#else
303	+	fdf_ = fdf_local;
304	+	#endif
305	+	return fdf_;
306	+	}
307	+
308	+	unsigned int SimInfo::getNLocalCutoffGroups(){
309	+	int nLocalCutoffAtoms = 0;
310	+	Molecule* mol;
311	+	MoleculeIterator mi;
312	+	CutoffGroup* cg;
313	+	Molecule::CutoffGroupIterator ci;
314	+
315	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
316	+
317	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
318	+	cg = mol->nextCutoffGroup(ci)) {
319	+	nLocalCutoffAtoms += cg->getNumAtom();
320	+
321	+	}
322	+	}
323	+
324	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
325	+	}
326	+
327		void SimInfo::calcNdfRaw() {
328		int ndfRaw_local;
329
330		MoleculeIterator i;
331	<	std::vector<StuntDouble*>::iterator j;
331	>	vector<StuntDouble*>::iterator j;
332		Molecule* mol;
333	<	StuntDouble* integrableObject;
333	>	StuntDouble* sd;
334
335		// Raw degrees of freedom that we have to set
336		ndfRaw_local = 0;
337
338		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
296	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
297	–	integrableObject = mol->nextIntegrableObject(j)) {
339
340	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
341	+	sd = mol->nextIntegrableObject(j)) {
342	+
343		ndfRaw_local += 3;
344
345	<	if (integrableObject->isDirectional()) {
346	<	if (integrableObject->isLinear()) {
345	>	if (sd->isDirectional()) {
346	>	if (sd->isLinear()) {
347		ndfRaw_local += 2;
348		} else {
349		ndfRaw_local += 3;
#	Line 310 | Line 354 | namespace oopse {
354		}
355
356		#ifdef IS_MPI
357	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
357	>	MPI_Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
358		#else
359		ndfRaw_ = ndfRaw_local;
360		#endif
#	Line 321 | Line 365 | namespace oopse {
365
366		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
367
324	–
368		#ifdef IS_MPI
369	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
369	>	MPI_Allreduce(&ndfTrans_local, &ndfTrans_, 1, MPI_INT, MPI_SUM,
370	>	MPI_COMM_WORLD);
371		#else
372		ndfTrans_ = ndfTrans_local;
373		#endif
374
375		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
332	–
376		}
377
378	<	void SimInfo::addExcludePairs(Molecule* mol) {
379	<	std::vector<Bond*>::iterator bondIter;
380	<	std::vector<Bend*>::iterator bendIter;
381	<	std::vector<Torsion*>::iterator torsionIter;
378	>	void SimInfo::addInteractionPairs(Molecule* mol) {
379	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
380	>	vector<Bond*>::iterator bondIter;
381	>	vector<Bend*>::iterator bendIter;
382	>	vector<Torsion*>::iterator torsionIter;
383	>	vector<Inversion*>::iterator inversionIter;
384		Bond* bond;
385		Bend* bend;
386		Torsion* torsion;
387	+	Inversion* inversion;
388		int a;
389		int b;
390		int c;
391		int d;
392	+
393	+	// atomGroups can be used to add special interaction maps between
394	+	// groups of atoms that are in two separate rigid bodies.
395	+	// However, most site-site interactions between two rigid bodies
396	+	// are probably not special, just the ones between the physically
397	+	// bonded atoms.  Interactions *within* a single rigid body should
398	+	// always be excluded.  These are done at the bottom of this
399	+	// function.
400	+
401	+	map<int, set<int> > atomGroups;
402	+	Molecule::RigidBodyIterator rbIter;
403	+	RigidBody* rb;
404	+	Molecule::IntegrableObjectIterator ii;
405	+	StuntDouble* sd;
406
407	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
407	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
408	>	sd = mol->nextIntegrableObject(ii)) {
409	>
410	>	if (sd->isRigidBody()) {
411	>	rb = static_cast<RigidBody*>(sd);
412	>	vector<Atom*> atoms = rb->getAtoms();
413	>	set<int> rigidAtoms;
414	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
415	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
416	>	}
417	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
418	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
419	>	}
420	>	} else {
421	>	set<int> oneAtomSet;
422	>	oneAtomSet.insert(sd->getGlobalIndex());
423	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
424	>	}
425	>	}
426	>
427	>
428	>	for (bond= mol->beginBond(bondIter); bond != NULL;
429	>	bond = mol->nextBond(bondIter)) {
430	>
431		a = bond->getAtomA()->getGlobalIndex();
432	<	b = bond->getAtomB()->getGlobalIndex();
433	<	exclude_.addPair(a, b);
432	>	b = bond->getAtomB()->getGlobalIndex();
433	>
434	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
435	>	oneTwoInteractions_.addPair(a, b);
436	>	} else {
437	>	excludedInteractions_.addPair(a, b);
438	>	}
439		}
440
441	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
441	>	for (bend= mol->beginBend(bendIter); bend != NULL;
442	>	bend = mol->nextBend(bendIter)) {
443	>
444		a = bend->getAtomA()->getGlobalIndex();
445		b = bend->getAtomB()->getGlobalIndex();
446		c = bend->getAtomC()->getGlobalIndex();
447	+
448	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
449	+	oneTwoInteractions_.addPair(a, b);
450	+	oneTwoInteractions_.addPair(b, c);
451	+	} else {
452	+	excludedInteractions_.addPair(a, b);
453	+	excludedInteractions_.addPair(b, c);
454	+	}
455
456	<	exclude_.addPair(a, b);
457	<	exclude_.addPair(a, c);
458	<	exclude_.addPair(b, c);
456	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
457	>	oneThreeInteractions_.addPair(a, c);
458	>	} else {
459	>	excludedInteractions_.addPair(a, c);
460	>	}
461		}
462
463	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
463	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
464	>	torsion = mol->nextTorsion(torsionIter)) {
465	>
466		a = torsion->getAtomA()->getGlobalIndex();
467		b = torsion->getAtomB()->getGlobalIndex();
468		c = torsion->getAtomC()->getGlobalIndex();
469	<	d = torsion->getAtomD()->getGlobalIndex();
469	>	d = torsion->getAtomD()->getGlobalIndex();
470
471	<	exclude_.addPair(a, b);
472	<	exclude_.addPair(a, c);
473	<	exclude_.addPair(a, d);
474	<	exclude_.addPair(b, c);
475	<	exclude_.addPair(b, d);
476	<	exclude_.addPair(c, d);
471	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
472	>	oneTwoInteractions_.addPair(a, b);
473	>	oneTwoInteractions_.addPair(b, c);
474	>	oneTwoInteractions_.addPair(c, d);
475	>	} else {
476	>	excludedInteractions_.addPair(a, b);
477	>	excludedInteractions_.addPair(b, c);
478	>	excludedInteractions_.addPair(c, d);
479	>	}
480	>
481	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
482	>	oneThreeInteractions_.addPair(a, c);
483	>	oneThreeInteractions_.addPair(b, d);
484	>	} else {
485	>	excludedInteractions_.addPair(a, c);
486	>	excludedInteractions_.addPair(b, d);
487	>	}
488	>
489	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
490	>	oneFourInteractions_.addPair(a, d);
491	>	} else {
492	>	excludedInteractions_.addPair(a, d);
493	>	}
494		}
495
496	<	Molecule::RigidBodyIterator rbIter;
497	<	RigidBody* rb;
498	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
499	<	std::vector<Atom*> atoms = rb->getAtoms();
500	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
501	<	for (int j = i + 1; j < atoms.size(); ++j) {
496	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
497	>	inversion = mol->nextInversion(inversionIter)) {
498	>
499	>	a = inversion->getAtomA()->getGlobalIndex();
500	>	b = inversion->getAtomB()->getGlobalIndex();
501	>	c = inversion->getAtomC()->getGlobalIndex();
502	>	d = inversion->getAtomD()->getGlobalIndex();
503	>
504	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
505	>	oneTwoInteractions_.addPair(a, b);
506	>	oneTwoInteractions_.addPair(a, c);
507	>	oneTwoInteractions_.addPair(a, d);
508	>	} else {
509	>	excludedInteractions_.addPair(a, b);
510	>	excludedInteractions_.addPair(a, c);
511	>	excludedInteractions_.addPair(a, d);
512	>	}
513	>
514	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
515	>	oneThreeInteractions_.addPair(b, c);
516	>	oneThreeInteractions_.addPair(b, d);
517	>	oneThreeInteractions_.addPair(c, d);
518	>	} else {
519	>	excludedInteractions_.addPair(b, c);
520	>	excludedInteractions_.addPair(b, d);
521	>	excludedInteractions_.addPair(c, d);
522	>	}
523	>	}
524	>
525	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
526	>	rb = mol->nextRigidBody(rbIter)) {
527	>	vector<Atom*> atoms = rb->getAtoms();
528	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
529	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
530		a = atoms[i]->getGlobalIndex();
531		b = atoms[j]->getGlobalIndex();
532	<	exclude_.addPair(a, b);
532	>	excludedInteractions_.addPair(a, b);
533		}
534		}
535		}
536
537		}
538
539	<	void SimInfo::removeExcludePairs(Molecule* mol) {
540	<	std::vector<Bond*>::iterator bondIter;
541	<	std::vector<Bend*>::iterator bendIter;
542	<	std::vector<Torsion*>::iterator torsionIter;
539	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
540	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
541	>	vector<Bond*>::iterator bondIter;
542	>	vector<Bend*>::iterator bendIter;
543	>	vector<Torsion*>::iterator torsionIter;
544	>	vector<Inversion*>::iterator inversionIter;
545		Bond* bond;
546		Bend* bend;
547		Torsion* torsion;
548	+	Inversion* inversion;
549		int a;
550		int b;
551		int c;
552		int d;
553	+
554	+	map<int, set<int> > atomGroups;
555	+	Molecule::RigidBodyIterator rbIter;
556	+	RigidBody* rb;
557	+	Molecule::IntegrableObjectIterator ii;
558	+	StuntDouble* sd;
559
560	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
560	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
561	>	sd = mol->nextIntegrableObject(ii)) {
562	>
563	>	if (sd->isRigidBody()) {
564	>	rb = static_cast<RigidBody*>(sd);
565	>	vector<Atom*> atoms = rb->getAtoms();
566	>	set<int> rigidAtoms;
567	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
568	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
569	>	}
570	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
571	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
572	>	}
573	>	} else {
574	>	set<int> oneAtomSet;
575	>	oneAtomSet.insert(sd->getGlobalIndex());
576	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
577	>	}
578	>	}
579	>
580	>	for (bond= mol->beginBond(bondIter); bond != NULL;
581	>	bond = mol->nextBond(bondIter)) {
582	>
583		a = bond->getAtomA()->getGlobalIndex();
584	<	b = bond->getAtomB()->getGlobalIndex();
585	<	exclude_.removePair(a, b);
584	>	b = bond->getAtomB()->getGlobalIndex();
585	>
586	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
587	>	oneTwoInteractions_.removePair(a, b);
588	>	} else {
589	>	excludedInteractions_.removePair(a, b);
590	>	}
591		}
592
593	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
593	>	for (bend= mol->beginBend(bendIter); bend != NULL;
594	>	bend = mol->nextBend(bendIter)) {
595	>
596		a = bend->getAtomA()->getGlobalIndex();
597		b = bend->getAtomB()->getGlobalIndex();
598		c = bend->getAtomC()->getGlobalIndex();
599	+
600	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
601	+	oneTwoInteractions_.removePair(a, b);
602	+	oneTwoInteractions_.removePair(b, c);
603	+	} else {
604	+	excludedInteractions_.removePair(a, b);
605	+	excludedInteractions_.removePair(b, c);
606	+	}
607
608	<	exclude_.removePair(a, b);
609	<	exclude_.removePair(a, c);
610	<	exclude_.removePair(b, c);
608	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
609	>	oneThreeInteractions_.removePair(a, c);
610	>	} else {
611	>	excludedInteractions_.removePair(a, c);
612	>	}
613		}
614
615	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
615	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
616	>	torsion = mol->nextTorsion(torsionIter)) {
617	>
618		a = torsion->getAtomA()->getGlobalIndex();
619		b = torsion->getAtomB()->getGlobalIndex();
620		c = torsion->getAtomC()->getGlobalIndex();
621	<	d = torsion->getAtomD()->getGlobalIndex();
621	>	d = torsion->getAtomD()->getGlobalIndex();
622	>
623	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
624	>	oneTwoInteractions_.removePair(a, b);
625	>	oneTwoInteractions_.removePair(b, c);
626	>	oneTwoInteractions_.removePair(c, d);
627	>	} else {
628	>	excludedInteractions_.removePair(a, b);
629	>	excludedInteractions_.removePair(b, c);
630	>	excludedInteractions_.removePair(c, d);
631	>	}
632
633	<	exclude_.removePair(a, b);
634	<	exclude_.removePair(a, c);
635	<	exclude_.removePair(a, d);
636	<	exclude_.removePair(b, c);
637	<	exclude_.removePair(b, d);
638	<	exclude_.removePair(c, d);
633	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
634	>	oneThreeInteractions_.removePair(a, c);
635	>	oneThreeInteractions_.removePair(b, d);
636	>	} else {
637	>	excludedInteractions_.removePair(a, c);
638	>	excludedInteractions_.removePair(b, d);
639	>	}
640	>
641	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
642	>	oneFourInteractions_.removePair(a, d);
643	>	} else {
644	>	excludedInteractions_.removePair(a, d);
645	>	}
646		}
647
648	<	Molecule::RigidBodyIterator rbIter;
649	<	RigidBody* rb;
650	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
651	<	std::vector<Atom*> atoms = rb->getAtoms();
652	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
653	<	for (int j = i + 1; j < atoms.size(); ++j) {
648	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
649	>	inversion = mol->nextInversion(inversionIter)) {
650	>
651	>	a = inversion->getAtomA()->getGlobalIndex();
652	>	b = inversion->getAtomB()->getGlobalIndex();
653	>	c = inversion->getAtomC()->getGlobalIndex();
654	>	d = inversion->getAtomD()->getGlobalIndex();
655	>
656	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
657	>	oneTwoInteractions_.removePair(a, b);
658	>	oneTwoInteractions_.removePair(a, c);
659	>	oneTwoInteractions_.removePair(a, d);
660	>	} else {
661	>	excludedInteractions_.removePair(a, b);
662	>	excludedInteractions_.removePair(a, c);
663	>	excludedInteractions_.removePair(a, d);
664	>	}
665	>
666	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
667	>	oneThreeInteractions_.removePair(b, c);
668	>	oneThreeInteractions_.removePair(b, d);
669	>	oneThreeInteractions_.removePair(c, d);
670	>	} else {
671	>	excludedInteractions_.removePair(b, c);
672	>	excludedInteractions_.removePair(b, d);
673	>	excludedInteractions_.removePair(c, d);
674	>	}
675	>	}
676	>
677	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
678	>	rb = mol->nextRigidBody(rbIter)) {
679	>	vector<Atom*> atoms = rb->getAtoms();
680	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
681	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
682		a = atoms[i]->getGlobalIndex();
683		b = atoms[j]->getGlobalIndex();
684	<	exclude_.removePair(a, b);
684	>	excludedInteractions_.removePair(a, b);
685		}
686		}
687		}
688	<
688	>
689		}
690	<
691	<
690	>
691	>
692		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
693		int curStampId;
694	<
694	>
695		//index from 0
696		curStampId = moleculeStamps_.size();
697
#	Line 457 | Line 699 | namespace oopse {
699		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
700		}
701
460	–	void SimInfo::update() {
702
703	<	setupSimType();
704	<
705	<	#ifdef IS_MPI
706	<	setupFortranParallel();
707	<	#endif
708	<
709	<	setupFortranSim();
710	<
711	<	//setup fortran force field
712	<	/** @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	<
703	>	/**
704	>	* update
705	>	*
706	>	*  Performs the global checks and variable settings after the
707	>	*  objects have been created.
708	>	*
709	>	*/
710	>	void SimInfo::update() {
711	>	setupSimVariables();
712	>	calcNConstraints();
713		calcNdf();
714		calcNdfRaw();
715		calcNdfTrans();
489	–
490	–	fortranInitialized_ = true;
716		}
717	<
718	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
717	>
718	>	/**
719	>	* getSimulatedAtomTypes
720	>	*
721	>	* Returns an STL set of AtomType* that are actually present in this
722	>	* simulation.  Must query all processors to assemble this information.
723	>	*
724	>	*/
725	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
726		SimInfo::MoleculeIterator mi;
727		Molecule* mol;
728		Molecule::AtomIterator ai;
729		Atom* atom;
730	<	std::set<AtomType*> atomTypes;
731	<
730	>	set<AtomType*> atomTypes;
731	>
732		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
733	<
734	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
733	>	for(atom = mol->beginAtom(ai); atom != NULL;
734	>	atom = mol->nextAtom(ai)) {
735		atomTypes.insert(atom->getAtomType());
736	<	}
737	<
736	>	}
737	>	}
738	>
739	>	#ifdef IS_MPI
740	>
741	>	// loop over the found atom types on this processor, and add their
742	>	// numerical idents to a vector:
743	>
744	>	vector<int> foundTypes;
745	>	set<AtomType*>::iterator i;
746	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
747	>	foundTypes.push_back( (*i)->getIdent() );
748	>
749	>	// count_local holds the number of found types on this processor
750	>	int count_local = foundTypes.size();
751	>
752	>	int nproc;
753	>	MPI_Comm_size( MPI_COMM_WORLD, &nproc);
754	>	// int nproc = MPI::COMM_WORLD.Get_size();
755	>
756	>	// we need arrays to hold the counts and displacement vectors for
757	>	// all processors
758	>	vector<int> counts(nproc, 0);
759	>	vector<int> disps(nproc, 0);
760	>
761	>	// fill the counts array
762	>	MPI_Allgather(&count_local, 1, MPI_INT, &counts[0],
763	>	1, MPI_INT, MPI_COMM_WORLD);
764	>	// MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
765	>	//                           1, MPI::INT);
766	>
767	>	// use the processor counts to compute the displacement array
768	>	disps[0] = 0;
769	>	int totalCount = counts[0];
770	>	for (int iproc = 1; iproc < nproc; iproc++) {
771	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
772	>	totalCount += counts[iproc];
773		}
774
775	<	return atomTypes;
776	<	}
775	>	// we need a (possibly redundant) set of all found types:
776	>	vector<int> ftGlobal(totalCount);
777	>
778	>	// now spray out the foundTypes to all the other processors:
779	>	MPI_Allgatherv(&foundTypes[0], count_local, MPI_INT,
780	>	&ftGlobal[0], &counts[0], &disps[0],
781	>	MPI_INT, MPI_COMM_WORLD);
782	>	// MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
783	>	//                            &ftGlobal[0], &counts[0], &disps[0],
784	>	//                            MPI::INT);
785
786	<	void SimInfo::setupSimType() {
787	<	std::set<AtomType*>::iterator i;
788	<	std::set<AtomType*> atomTypes;
789	<	atomTypes = getUniqueAtomTypes();
786	>	vector<int>::iterator j;
787	>
788	>	// foundIdents is a stl set, so inserting an already found ident
789	>	// will have no effect.
790	>	set<int> foundIdents;
791	>
792	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
793	>	foundIdents.insert((*j));
794
795	<	int useLennardJones = 0;
796	<	int useElectrostatic = 0;
797	<	int useEAM = 0;
798	<	int useCharge = 0;
799	<	int useDirectional = 0;
800	<	int useDipole = 0;
801	<	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 useSF;
533	<	std::string myMethod;
795	>	// now iterate over the foundIdents and get the actual atom types
796	>	// that correspond to these:
797	>	set<int>::iterator it;
798	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
799	>	atomTypes.insert( forceField_->getAtomType((*it)) );
800	>
801	>	#endif
802
803	<	// set the useRF logical
804	<	useRF = 0;
537	<	useSF = 0;
803	>	return atomTypes;
804	>	}
805
806
807	<	if (simParams_->haveElectrostaticSummationMethod()) {
808	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
809	<	toUpper(myMethod);
810	<	if (myMethod == "REACTION_FIELD") {
544	<	useRF=1;
545	<	} else {
546	<	if (myMethod == "SHIFTED_FORCE") {
547	<	useSF = 1;
548	<	}
549	<	}
550	<	}
807	>	int getGlobalCountOfType(AtomType* atype) {
808	>	/*
809	>	set<AtomType*> atypes = getSimulatedAtomTypes();
810	>	map<AtomType*, int> counts_;
811
812	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
813	+	for(atom = mol->beginAtom(ai); atom != NULL;
814	+	atom = mol->nextAtom(ai)) {
815	+	atom->getAtomType();
816	+	}
817	+	}
818	+	*/
819	+	return 0;
820	+	}
821	+
822	+	void SimInfo::setupSimVariables() {
823	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
824	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
825	+	// parameter is true
826	+	calcBoxDipole_ = false;
827	+	if ( simParams_->haveAccumulateBoxDipole() )
828	+	if ( simParams_->getAccumulateBoxDipole() ) {
829	+	calcBoxDipole_ = true;
830	+	}
831	+
832	+	set<AtomType*>::iterator i;
833	+	set<AtomType*> atomTypes;
834	+	atomTypes = getSimulatedAtomTypes();
835	+	bool usesElectrostatic = false;
836	+	bool usesMetallic = false;
837	+	bool usesDirectional = false;
838	+	bool usesFluctuatingCharges =  false;
839		//loop over all of the atom types
840		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
841	<	useLennardJones |= (*i)->isLennardJones();
842	<	useElectrostatic |= (*i)->isElectrostatic();
843	<	useEAM |= (*i)->isEAM();
844	<	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();
841	>	usesElectrostatic |= (*i)->isElectrostatic();
842	>	usesMetallic |= (*i)->isMetal();
843	>	usesDirectional |= (*i)->isDirectional();
844	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
845		}
846
847	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
567	<	useDirectionalAtom = 1;
568	<	}
569	<
570	<	if (useCharge || useDipole) {
571	<	useElectrostatics = 1;
572	<	}
573	<
574	<	#ifdef IS_MPI
847	>	#ifdef IS_MPI
848		int temp;
849
850	<	temp = usePBC;
851	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
850	>	temp = usesDirectional;
851	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
852	>	usesDirectionalAtoms_ = (temp == 0) ? false : true;
853	>
854	>	temp = usesMetallic;
855	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
856	>	usesMetallicAtoms_ = (temp == 0) ? false : true;
857
858	<	temp = useDirectionalAtom;
859	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
858	>	temp = usesElectrostatic;
859	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
860	>	usesElectrostaticAtoms_ = (temp == 0) ? false : true;
861
862	<	temp = useLennardJones;
863	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
862	>	temp = usesFluctuatingCharges;
863	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
864	>	usesFluctuatingCharges_ = (temp == 0) ? false : true;
865	>	#else
866
867	<	temp = useElectrostatics;
868	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
867	>	usesDirectionalAtoms_ = usesDirectional;
868	>	usesMetallicAtoms_ = usesMetallic;
869	>	usesElectrostaticAtoms_ = usesElectrostatic;
870	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
871
872	<	temp = useCharge;
873	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
872	>	#endif
873	>
874	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
875	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
876	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
877	>	}
878
592	–	temp = useDipole;
593	–	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
879
880	<	temp = useSticky;
881	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
880	>	vector<int> SimInfo::getGlobalAtomIndices() {
881	>	SimInfo::MoleculeIterator mi;
882	>	Molecule* mol;
883	>	Molecule::AtomIterator ai;
884	>	Atom* atom;
885
886	<	temp = useStickyPower;
599	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
886	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
887
888	<	temp = useGayBerne;
889	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
888	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
889	>
890	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
891	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
892	>	}
893	>	}
894	>	return GlobalAtomIndices;
895	>	}
896
604	–	temp = useEAM;
605	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
897
898	<	temp = useShape;
899	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
898	>	vector<int> SimInfo::getGlobalGroupIndices() {
899	>	SimInfo::MoleculeIterator mi;
900	>	Molecule* mol;
901	>	Molecule::CutoffGroupIterator ci;
902	>	CutoffGroup* cg;
903
904	<	temp = useFLARB;
905	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
906	<
613	<	temp = useRF;
614	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
615	<
616	<	temp = useSF;
617	<	MPI_Allreduce(&temp, &useSF, 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_SF = useSF;
635	<
636	<	if( myMethod == "REACTION_FIELD") {
904	>	vector<int> GlobalGroupIndices;
905	>
906	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
907
908	<	if (simParams_->haveDielectric()) {
909	<	fInfo_.dielect = simParams_->getDielectric();
910	<	} else {
911	<	sprintf(painCave.errMsg,
912	<	"SimSetup Error: No Dielectric constant was set.\n"
913	<	"\tYou are trying to use Reaction Field without"
644	<	"\tsetting a dielectric constant!\n");
645	<	painCave.isFatal = 1;
646	<	simError();
647	<	}
908	>	//local index of cutoff group is trivial, it only depends on the
909	>	//order of travesing
910	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
911	>	cg = mol->nextCutoffGroup(ci)) {
912	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
913	>	}
914		}
915	<
915	>	return GlobalGroupIndices;
916		}
917
652	–	void SimInfo::setupFortranSim() {
653	–	int isError;
654	–	int nExclude;
655	–	std::vector<int> fortranGlobalGroupMembership;
656	–
657	–	nExclude = exclude_.getSize();
658	–	isError = 0;
918
919	<	//globalGroupMembership_ is filled by SimCreator
661	<	for (int i = 0; i < nGlobalAtoms_; i++) {
662	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
663	<	}
919	>	void SimInfo::prepareTopology() {
920
921		//calculate mass ratio of cutoff group
666	–	std::vector<double> mfact;
922		SimInfo::MoleculeIterator mi;
923		Molecule* mol;
924		Molecule::CutoffGroupIterator ci;
925		CutoffGroup* cg;
926		Molecule::AtomIterator ai;
927		Atom* atom;
928	<	double totalMass;
928	>	RealType totalMass;
929
930	<	//to avoid memory reallocation, reserve enough space for mfact
931	<	mfact.reserve(getNCutoffGroups());
930	>	/**
931	>	* The mass factor is the relative mass of an atom to the total
932	>	* mass of the cutoff group it belongs to.  By default, all atoms
933	>	* are their own cutoff groups, and therefore have mass factors of
934	>	* 1.  We need some special handling for massless atoms, which
935	>	* will be treated as carrying the entire mass of the cutoff
936	>	* group.
937	>	*/
938	>	massFactors_.clear();
939	>	massFactors_.resize(getNAtoms(), 1.0);
940
941		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
942	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
942	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
943	>	cg = mol->nextCutoffGroup(ci)) {
944
945		totalMass = cg->getMass();
946		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
947		// Check for massless groups - set mfact to 1 if true
948	<	if (totalMass != 0)
949	<	mfact.push_back(atom->getMass()/totalMass);
948	>	if (totalMass != 0)
949	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
950		else
951	<	mfact.push_back( 1.0 );
951	>	massFactors_[atom->getLocalIndex()] = 1.0;
952		}
689	–
953		}
954		}
955
956	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
694	<	std::vector<int> identArray;
956	>	// Build the identArray_ and regions_
957
958	<	//to avoid memory reallocation, reserve enough space identArray
959	<	identArray.reserve(getNAtoms());
960	<
961	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
958	>	identArray_.clear();
959	>	identArray_.reserve(getNAtoms());
960	>	regions_.clear();
961	>	regions_.reserve(getNAtoms());
962	>
963	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
964	>	int reg = mol->getRegion();
965		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
966	<	identArray.push_back(atom->getIdent());
966	>	identArray_.push_back(atom->getIdent());
967	>	regions_.push_back(reg);
968		}
969		}
970	<
971	<	//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	<	}
711	<
712	<	//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	<	}
865	<	}
866	<
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_);
970	>
971	>	topologyDone_ = true;
972		}
973
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_->haveElectrostaticScreeningMethod()) {
949	–	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
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	–	}
963	–	} else {
964	–	// throw error
965	–	sprintf( painCave.errMsg,
966	–	"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
967	–	painCave.isFatal = 1;
968	–	simError();
969	–	}
970	–	}
971	–	}
972	–
973	–	// let's pass some summation method variables to fortran
974	–	setElectrostaticSummationMethod( &esm );
975	–	setScreeningMethod( &sm );
976	–	setDampingAlpha( &alphaVal );
977	–	setReactionFieldDielectric( &dielectric );
978	–	initFortranFF( &esm, &errorOut );
979	–	}
980	–
974		void SimInfo::addProperty(GenericData* genData) {
975		properties_.addProperty(genData);
976		}
977
978	<	void SimInfo::removeProperty(const std::string& propName) {
978	>	void SimInfo::removeProperty(const string& propName) {
979		properties_.removeProperty(propName);
980		}
981
#	Line 990 | Line 983 | namespace oopse {
983		properties_.clearProperties();
984		}
985
986	<	std::vector<std::string> SimInfo::getPropertyNames() {
986	>	vector<string> SimInfo::getPropertyNames() {
987		return properties_.getPropertyNames();
988		}
989
990	<	std::vector<GenericData*> SimInfo::getProperties() {
990	>	vector<GenericData*> SimInfo::getProperties() {
991		return properties_.getProperties();
992		}
993
994	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
994	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
995		return properties_.getPropertyByName(propName);
996		}
997
#	Line 1009 | Line 1002 | namespace oopse {
1002		delete sman_;
1003		sman_ = sman;
1004
1012	–	Molecule* mol;
1013	–	RigidBody* rb;
1014	–	Atom* atom;
1005		SimInfo::MoleculeIterator mi;
1006	+	Molecule::AtomIterator ai;
1007		Molecule::RigidBodyIterator rbIter;
1008	<	Molecule::AtomIterator atomIter;;
1008	>	Molecule::CutoffGroupIterator cgIter;
1009	>	Molecule::BondIterator bondIter;
1010	>	Molecule::BendIterator bendIter;
1011	>	Molecule::TorsionIterator torsionIter;
1012	>	Molecule::InversionIterator inversionIter;
1013
1014	+	Molecule* mol;
1015	+	Atom* atom;
1016	+	RigidBody* rb;
1017	+	CutoffGroup* cg;
1018	+	Bond* bond;
1019	+	Bend* bend;
1020	+	Torsion* torsion;
1021	+	Inversion* inversion;
1022	+
1023		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1024
1025	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1025	>	for (atom = mol->beginAtom(ai); atom != NULL;
1026	>	atom = mol->nextAtom(ai)) {
1027		atom->setSnapshotManager(sman_);
1028	<	}
1029	<
1030	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1028	>	}
1029	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1030	>	rb = mol->nextRigidBody(rbIter)) {
1031		rb->setSnapshotManager(sman_);
1032		}
1033	<	}
1034	<
1033	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1034	>	cg = mol->nextCutoffGroup(cgIter)) {
1035	>	cg->setSnapshotManager(sman_);
1036	>	}
1037	>	for (bond = mol->beginBond(bondIter); bond != NULL;
1038	>	bond = mol->nextBond(bondIter)) {
1039	>	bond->setSnapshotManager(sman_);
1040	>	}
1041	>	for (bend = mol->beginBend(bendIter); bend != NULL;
1042	>	bend = mol->nextBend(bendIter)) {
1043	>	bend->setSnapshotManager(sman_);
1044	>	}
1045	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
1046	>	torsion = mol->nextTorsion(torsionIter)) {
1047	>	torsion->setSnapshotManager(sman_);
1048	>	}
1049	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
1050	>	inversion = mol->nextInversion(inversionIter)) {
1051	>	inversion->setSnapshotManager(sman_);
1052	>	}
1053	>	}
1054		}
1055
1032	–	Vector3d SimInfo::getComVel(){
1033	–	SimInfo::MoleculeIterator i;
1034	–	Molecule* mol;
1056
1057	<	Vector3d comVel(0.0);
1037	<	double totalMass = 0.0;
1038	<
1039	<
1040	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1041	<	double mass = mol->getMass();
1042	<	totalMass += mass;
1043	<	comVel += mass * mol->getComVel();
1044	<	}
1057	>	ostream& operator <<(ostream& o, SimInfo& info) {
1058
1046	–	#ifdef IS_MPI
1047	–	double tmpMass = totalMass;
1048	–	Vector3d tmpComVel(comVel);
1049	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1050	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1051	–	#endif
1052	–
1053	–	comVel /= totalMass;
1054	–
1055	–	return comVel;
1056	–	}
1057	–
1058	–	Vector3d SimInfo::getCom(){
1059	–	SimInfo::MoleculeIterator i;
1060	–	Molecule* mol;
1061	–
1062	–	Vector3d com(0.0);
1063	–	double totalMass = 0.0;
1064	–
1065	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1066	–	double mass = mol->getMass();
1067	–	totalMass += mass;
1068	–	com += mass * mol->getCom();
1069	–	}
1070	–
1071	–	#ifdef IS_MPI
1072	–	double tmpMass = totalMass;
1073	–	Vector3d tmpCom(com);
1074	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1075	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1076	–	#endif
1077	–
1078	–	com /= totalMass;
1079	–
1080	–	return com;
1081	–
1082	–	}
1083	–
1084	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1085	–
1059		return o;
1060		}
1061
1062	<
1063	<	/*
1064	<	Returns center of mass and center of mass velocity in one function call.
1065	<	*/
1066	<
1067	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1068	<	SimInfo::MoleculeIterator i;
1069	<	Molecule* mol;
1070	<
1071	<
1072	<	double totalMass = 0.0;
1073	<
1062	>
1063	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1064	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1065	>	sprintf(painCave.errMsg,
1066	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1067	>	"\tindex exceeds number of known objects!\n");
1068	>	painCave.isFatal = 1;
1069	>	simError();
1070	>	return NULL;
1071	>	} else
1072	>	return IOIndexToIntegrableObject.at(index);
1073	>	}
1074	>
1075	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1076	>	IOIndexToIntegrableObject= v;
1077	>	}
1078
1079	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1103	<	double mass = mol->getMass();
1104	<	totalMass += mass;
1105	<	com += mass * mol->getCom();
1106	<	comVel += mass * mol->getComVel();
1107	<	}
1108	<
1079	>	void SimInfo::calcNConstraints() {
1080		#ifdef IS_MPI
1081	<	double tmpMass = totalMass;
1082	<	Vector3d tmpCom(com);
1083	<	Vector3d tmpComVel(comVel);
1084	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1114	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1115	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1081	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints_, 1,
1082	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1083	>	#else
1084	>	nGlobalConstraints_ =  nConstraints_;
1085		#endif
1086	<
1118	<	com /= totalMass;
1119	<	comVel /= totalMass;
1120	<	}
1121	<
1122	<	/*
1123	<	Return intertia tensor for entire system and angular momentum Vector.
1086	>	}
1087
1088	+	}//end namespace OpenMD
1089
1126	–	[  Ixx -Ixy  -Ixz ]
1127	–	J =| -Iyx  Iyy  -Iyz |
1128	–	[ -Izx -Iyz   Izz ]
1129	–	*/
1130	–
1131	–	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1132	–
1133	–
1134	–	double xx = 0.0;
1135	–	double yy = 0.0;
1136	–	double zz = 0.0;
1137	–	double xy = 0.0;
1138	–	double xz = 0.0;
1139	–	double yz = 0.0;
1140	–	Vector3d com(0.0);
1141	–	Vector3d comVel(0.0);
1142	–
1143	–	getComAll(com, comVel);
1144	–
1145	–	SimInfo::MoleculeIterator i;
1146	–	Molecule* mol;
1147	–
1148	–	Vector3d thisq(0.0);
1149	–	Vector3d thisv(0.0);
1150	–
1151	–	double thisMass = 0.0;
1152	–
1153	–
1154	–
1155	–
1156	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1157	–
1158	–	thisq = mol->getCom()-com;
1159	–	thisv = mol->getComVel()-comVel;
1160	–	thisMass = mol->getMass();
1161	–	// Compute moment of intertia coefficients.
1162	–	xx += thisq[0]*thisq[0]*thisMass;
1163	–	yy += thisq[1]*thisq[1]*thisMass;
1164	–	zz += thisq[2]*thisq[2]*thisMass;
1165	–
1166	–	// compute products of intertia
1167	–	xy += thisq[0]*thisq[1]*thisMass;
1168	–	xz += thisq[0]*thisq[2]*thisMass;
1169	–	yz += thisq[1]*thisq[2]*thisMass;
1170	–
1171	–	angularMomentum += cross( thisq, thisv ) * thisMass;
1172	–
1173	–	}
1174	–
1175	–
1176	–	inertiaTensor(0,0) = yy + zz;
1177	–	inertiaTensor(0,1) = -xy;
1178	–	inertiaTensor(0,2) = -xz;
1179	–	inertiaTensor(1,0) = -xy;
1180	–	inertiaTensor(1,1) = xx + zz;
1181	–	inertiaTensor(1,2) = -yz;
1182	–	inertiaTensor(2,0) = -xz;
1183	–	inertiaTensor(2,1) = -yz;
1184	–	inertiaTensor(2,2) = xx + yy;
1185	–
1186	–	#ifdef IS_MPI
1187	–	Mat3x3d tmpI(inertiaTensor);
1188	–	Vector3d tmpAngMom;
1189	–	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1190	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1191	–	#endif
1192	–
1193	–	return;
1194	–	}
1195	–
1196	–	//Returns the angular momentum of the system
1197	–	Vector3d SimInfo::getAngularMomentum(){
1198	–
1199	–	Vector3d com(0.0);
1200	–	Vector3d comVel(0.0);
1201	–	Vector3d angularMomentum(0.0);
1202	–
1203	–	getComAll(com,comVel);
1204	–
1205	–	SimInfo::MoleculeIterator i;
1206	–	Molecule* mol;
1207	–
1208	–	Vector3d thisr(0.0);
1209	–	Vector3d thisp(0.0);
1210	–
1211	–	double thisMass;
1212	–
1213	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1214	–	thisMass = mol->getMass();
1215	–	thisr = mol->getCom()-com;
1216	–	thisp = (mol->getComVel()-comVel)*thisMass;
1217	–
1218	–	angularMomentum += cross( thisr, thisp );
1219	–
1220	–	}
1221	–
1222	–	#ifdef IS_MPI
1223	–	Vector3d tmpAngMom;
1224	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1225	–	#endif
1226	–
1227	–	return angularMomentum;
1228	–	}
1229	–
1230	–
1231	–	}//end namespace oopse
1232	–

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 720 by chrisfen, Tue Nov 8 13:32:06 2005 UTC vs.
Revision 1983 by gezelter, Tue Apr 15 20:36:19 2014 UTC

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