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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 726 by chrisfen, Fri Nov 11 15:22:11 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/DarkSide/fElectrostaticScreeningMethod.h"
58	<	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
59	<	#include "UseTheForce/doForces_interface.h"
60	<	#include "UseTheForce/DarkSide/electrostatic_interface.h"
61	<	#include "UseTheForce/notifyCutoffs_interface.h"
62	<	#include "UseTheForce/DarkSide/switcheroo_interface.h"
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 {
73	<
74	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
75	<	ForceField* ff, Globals* simParams) :
76	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
77	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
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;
86	<	MoleculeStamp* molStamp;
87	<	int nMolWithSameStamp;
88	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
89	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
90	<	CutoffGroupStamp* cgStamp;
91	<	RigidBodyStamp* rbStamp;
92	<	int nRigidAtoms = 0;
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
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	<	}
112	<
113	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
114	<
115	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
116	<
117	<	//calculate atoms in rigid bodies
118	<	int nAtomsInRigidBodies = 0;
119	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
120	<
121	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
122	<	rbStamp = molStamp->getRigidBody(j);
123	<	nAtomsInRigidBodies += rbStamp->getNMembers();
124	<	}
125	<
126	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
127	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
128	<
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
161	–	delete stamps_;
168		delete sman_;
169		delete simParams_;
170		delete forceField_;
171		}
172
167	–	int SimInfo::getNGlobalConstraints() {
168	–	int nGlobalConstraints;
169	–	#ifdef IS_MPI
170	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
171	–	MPI_COMM_WORLD);
172	–	#else
173	–	nGlobalConstraints =  nConstraints_;
174	–	#endif
175	–	return nGlobalConstraints;
176	–	}
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 212 | 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 226 | Line 224 | namespace oopse {
224		} else {
225		return false;
226		}
229	–
230	–
227		}
228
229
#	Line 243 | 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)) {
255	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
256	–	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 283 | 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)) {
298	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
299	–	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 312 | 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 325 | 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 334 | 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 459 | Line 707 | namespace oopse {
707		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
708		}
709
710	<	void SimInfo::update() {
711	<
712	<	setupSimType();
713	<
714	<	#ifdef IS_MPI
715	<	setupFortranParallel();
716	<	#endif
717	<
718	<	setupFortranSim();
719	<
472	<	//setup fortran force field
473	<	/** @deprecate */
474	<	int isError = 0;
475	<
476	<	setupElectrostaticSummationMethod( isError );
477	<	setupSwitchingFunction();
478	<
479	<	if(isError){
480	<	sprintf( painCave.errMsg,
481	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
482	<	painCave.isFatal = 1;
483	<	simError();
484	<	}
485	<
486	<
487	<	setupCutoff();
488	<
710	>
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();
492	–
493	–	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	<
745	<	}
743	>	}
744	>	}
745	>
746	>	#ifdef IS_MPI
747
748	<	return atomTypes;
749	<	}
513	<
514	<	void SimInfo::setupSimType() {
515	<	std::set<AtomType*>::iterator i;
516	<	std::set<AtomType*> atomTypes;
517	<	atomTypes = getUniqueAtomTypes();
748	>	// loop over the found atom types on this processor, and add their
749	>	// numerical idents to a vector:
750
751	<	int useLennardJones = 0;
752	<	int useElectrostatic = 0;
753	<	int useEAM = 0;
754	<	int useCharge = 0;
523	<	int useDirectional = 0;
524	<	int useDipole = 0;
525	<	int useGayBerne = 0;
526	<	int useSticky = 0;
527	<	int useStickyPower = 0;
528	<	int useShape = 0;
529	<	int useFLARB = 0; //it is not in AtomType yet
530	<	int useDirectionalAtom = 0;
531	<	int useElectrostatics = 0;
532	<	//usePBC and useRF are from simParams
533	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
534	<	int useRF;
535	<	int useSF;
536	<	std::string myMethod;
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	<	// set the useRF logical
757	<	useRF = 0;
540	<	useSF = 0;
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	<	if (simParams_->haveElectrostaticSummationMethod()) {
764	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
765	<	toUpper(myMethod);
766	<	if (myMethod == "REACTION_FIELD") {
547	<	useRF=1;
548	<	} else {
549	<	if (myMethod == "SHIFTED_FORCE") {
550	<	useSF = 1;
551	<	}
552	<	}
553	<	}
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	<	//loop over all of the atom types
769	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
770	<	useLennardJones |= (*i)->isLennardJones();
771	<	useElectrostatic |= (*i)->isElectrostatic();
772	<	useEAM |= (*i)->isEAM();
773	<	useCharge |= (*i)->isCharge();
774	<	useDirectional |= (*i)->isDirectional();
775	<	useDipole |= (*i)->isDipole();
776	<	useGayBerne |= (*i)->isGayBerne();
777	<	useSticky |= (*i)->isSticky();
778	<	useStickyPower |= (*i)->isStickyPower();
779	<	useShape |= (*i)->isShape();
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	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
783	<	useDirectionalAtom = 1;
784	<	}
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	<	if (useCharge || useDipole) {
574	<	useElectrostatics = 1;
575	<	}
793	>	vector<int>::iterator j;
794
795	<	#ifdef IS_MPI
796	<	int temp;
795	>	// foundIdents is a stl set, so inserting an already found ident
796	>	// will have no effect.
797	>	set<int> foundIdents;
798
799	<	temp = usePBC;
800	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
799	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
800	>	foundIdents.insert((*j));
801	>
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	<	temp = useDirectionalAtom;
811	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810	>	return atomTypes;
811	>	}
812
586	–	temp = useLennardJones;
587	–	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813
814	<	temp = useElectrostatics;
815	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816	<
817	<	temp = useCharge;
593	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814	>	int getGlobalCountOfType(AtomType* atype) {
815	>	/*
816	>	set<AtomType*> atypes = getSimulatedAtomTypes();
817	>	map<AtomType*, int> counts_;
818
819	<	temp = useDipole;
820	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
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	<	temp = useSticky;
830	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
831	<
832	<	temp = useStickyPower;
833	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
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	<	temp = useGayBerne;
840	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
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	>	usesElectrostatic |= (*i)->isElectrostatic();
849	>	usesMetallic |= (*i)->isMetal();
850	>	usesDirectional |= (*i)->isDirectional();
851	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
852	>	}
853
854	<	temp = useEAM;
855	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
854	>	#ifdef IS_MPI
855	>	int temp;
856
857	<	temp = useShape;
858	<	MPI_Allreduce(&temp, &useShape, 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 = useFLARB;
862	<	MPI_Allreduce(&temp, &useFLARB, 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 = useRF;
869	<	MPI_Allreduce(&temp, &useRF, 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 = useSF;
876	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
875	>	// MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
876	>	//                           MPI::LOR);
877
878	<	#endif
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	<	fInfo_.SIM_uses_PBC = usePBC;
883	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
626	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
627	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
628	<	fInfo_.SIM_uses_Charges = useCharge;
629	<	fInfo_.SIM_uses_Dipoles = useDipole;
630	<	fInfo_.SIM_uses_Sticky = useSticky;
631	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
632	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
633	<	fInfo_.SIM_uses_EAM = useEAM;
634	<	fInfo_.SIM_uses_Shapes = useShape;
635	<	fInfo_.SIM_uses_FLARB = useFLARB;
636	<	fInfo_.SIM_uses_RF = useRF;
637	<	fInfo_.SIM_uses_SF = useSF;
882	>	// MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
883	>	//                           MPI::LOR);
884
885	<	if( myMethod == "REACTION_FIELD") {
640	<
641	<	if (simParams_->haveDielectric()) {
642	<	fInfo_.dielect = simParams_->getDielectric();
643	<	} else {
644	<	sprintf(painCave.errMsg,
645	<	"SimSetup Error: No Dielectric constant was set.\n"
646	<	"\tYou are trying to use Reaction Field without"
647	<	"\tsetting a dielectric constant!\n");
648	<	painCave.isFatal = 1;
649	<	simError();
650	<	}
651	<	}
885	>	#else
886
887	<	}
887	>	usesDirectionalAtoms_ = usesDirectional;
888	>	usesMetallicAtoms_ = usesMetallic;
889	>	usesElectrostaticAtoms_ = usesElectrostatic;
890	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
891
892	<	void SimInfo::setupFortranSim() {
656	<	int isError;
657	<	int nExclude;
658	<	std::vector<int> fortranGlobalGroupMembership;
892	>	#endif
893
894	<	nExclude = exclude_.getSize();
895	<	isError = 0;
894	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
895	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
896	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
897	>	}
898
663	–	//globalGroupMembership_ is filled by SimCreator
664	–	for (int i = 0; i < nGlobalAtoms_; i++) {
665	–	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
666	–	}
899
900	<	//calculate mass ratio of cutoff group
669	<	std::vector<double> mfact;
900	>	vector<int> SimInfo::getGlobalAtomIndices() {
901		SimInfo::MoleculeIterator mi;
902		Molecule* mol;
672	–	Molecule::CutoffGroupIterator ci;
673	–	CutoffGroup* cg;
903		Molecule::AtomIterator ai;
904		Atom* atom;
676	–	double totalMass;
905
906	<	//to avoid memory reallocation, reserve enough space for mfact
679	<	mfact.reserve(getNCutoffGroups());
906	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
907
908	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
909	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
910	<
911	<	totalMass = cg->getMass();
685	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
686	<	// Check for massless groups - set mfact to 1 if true
687	<	if (totalMass != 0)
688	<	mfact.push_back(atom->getMass()/totalMass);
689	<	else
690	<	mfact.push_back( 1.0 );
691	<	}
692	<
693	<	}
694	<	}
695	<
696	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
697	<	std::vector<int> identArray;
698	<
699	<	//to avoid memory reallocation, reserve enough space identArray
700	<	identArray.reserve(getNAtoms());
701	<
702	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
703	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
704	<	identArray.push_back(atom->getIdent());
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		}
706	–	}
707	–
708	–	//fill molMembershipArray
709	–	//molMembershipArray is filled by SimCreator
710	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
711	–	for (int i = 0; i < nGlobalAtoms_; i++) {
712	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
913		}
914	<
715	<	//setup fortran simulation
716	<	int nGlobalExcludes = 0;
717	<	int* globalExcludes = NULL;
718	<	int* excludeList = exclude_.getExcludeList();
719	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
720	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
721	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
722	<
723	<	if( isError ){
724	<
725	<	sprintf( painCave.errMsg,
726	<	"There was an error setting the simulation information in fortran.\n" );
727	<	painCave.isFatal = 1;
728	<	painCave.severity = OOPSE_ERROR;
729	<	simError();
730	<	}
731	<
732	<	#ifdef IS_MPI
733	<	sprintf( checkPointMsg,
734	<	"succesfully sent the simulation information to fortran.\n");
735	<	MPIcheckPoint();
736	<	#endif // is_mpi
914	>	return GlobalAtomIndices;
915		}
916
917
918	<	#ifdef IS_MPI
741	<	void SimInfo::setupFortranParallel() {
742	<
743	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
744	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
745	<	std::vector<int> localToGlobalCutoffGroupIndex;
918	>	vector<int> SimInfo::getGlobalGroupIndices() {
919		SimInfo::MoleculeIterator mi;
747	–	Molecule::AtomIterator ai;
748	–	Molecule::CutoffGroupIterator ci;
920		Molecule* mol;
921	<	Atom* atom;
921	>	Molecule::CutoffGroupIterator ci;
922		CutoffGroup* cg;
752	–	mpiSimData parallelData;
753	–	int isError;
923
924	+	vector<int> GlobalGroupIndices;
925	+
926		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
927	<
928	<	//local index(index in DataStorge) of atom is important
929	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
930	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
931	<	}
932	<
762	<	//local index of cutoff group is trivial, it only depends on the order of travesing
763	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
764	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
927	>
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		}
766	–
934		}
935	<
769	<	//fill up mpiSimData struct
770	<	parallelData.nMolGlobal = getNGlobalMolecules();
771	<	parallelData.nMolLocal = getNMolecules();
772	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
773	<	parallelData.nAtomsLocal = getNAtoms();
774	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
775	<	parallelData.nGroupsLocal = getNCutoffGroups();
776	<	parallelData.myNode = worldRank;
777	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
778	<
779	<	//pass mpiSimData struct and index arrays to fortran
780	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
781	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
782	<	&localToGlobalCutoffGroupIndex[0], &isError);
783	<
784	<	if (isError) {
785	<	sprintf(painCave.errMsg,
786	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
787	<	painCave.isFatal = 1;
788	<	simError();
789	<	}
790	<
791	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
792	<	MPIcheckPoint();
793	<
794	<
935	>	return GlobalGroupIndices;
936		}
937
797	–	#endif
938
939	<	double SimInfo::calcMaxCutoffRadius() {
939	>	void SimInfo::prepareTopology() {
940
941	+	//calculate mass ratio of cutoff group
942	+	SimInfo::MoleculeIterator mi;
943	+	Molecule* mol;
944	+	Molecule::CutoffGroupIterator ci;
945	+	CutoffGroup* cg;
946	+	Molecule::AtomIterator ai;
947	+	Atom* atom;
948	+	RealType totalMass;
949
950	<	std::set<AtomType*> atomTypes;
951	<	std::set<AtomType*>::iterator i;
952	<	std::vector<double> cutoffRadius;
953	<
954	<	//get the unique atom types
955	<	atomTypes = getUniqueAtomTypes();
956	<
957	<	//query the max cutoff radius among these atom types
958	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
959	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
812	<	}
813	<
814	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
815	<	#ifdef IS_MPI
816	<	//pick the max cutoff radius among the processors
817	<	#endif
818	<
819	<	return maxCutoffRadius;
820	<	}
821	<
822	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
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	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
962	<
963	<	if (!simParams_->haveCutoffRadius()){
827	<	sprintf(painCave.errMsg,
828	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
829	<	"\tOOPSE will use a default value of 15.0 angstroms"
830	<	"\tfor the cutoffRadius.\n");
831	<	painCave.isFatal = 0;
832	<	simError();
833	<	rcut = 15.0;
834	<	} else{
835	<	rcut = simParams_->getCutoffRadius();
836	<	}
961	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
962	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
963	>	cg = mol->nextCutoffGroup(ci)) {
964
965	<	if (!simParams_->haveSwitchingRadius()){
966	<	sprintf(painCave.errMsg,
967	<	"SimCreator Warning: No value was set for switchingRadius.\n"
968	<	"\tOOPSE will use a default value of\n"
969	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
970	<	painCave.isFatal = 0;
971	<	simError();
972	<	rsw = 0.85 * rcut;
973	<	} else{
847	<	rsw = simParams_->getSwitchingRadius();
848	<	}
849	<
850	<	} else {
851	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
852	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
853	<
854	<	if (simParams_->haveCutoffRadius()) {
855	<	rcut = simParams_->getCutoffRadius();
856	<	} else {
857	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
858	<	rcut = calcMaxCutoffRadius();
859	<	}
860	<
861	<	if (simParams_->haveSwitchingRadius()) {
862	<	rsw  = simParams_->getSwitchingRadius();
863	<	} else {
864	<	rsw = rcut;
865	<	}
866	<
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	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
970	>	else
971	>	massFactors_[atom->getLocalIndex()] = 1.0;
972	>	}
973	>	}
974		}
868	–	}
975
976	<	void SimInfo::setupCutoff() {
871	<	getCutoff(rcut_, rsw_);
872	<	double rnblist = rcut_ + 1; // skin of neighbor list
976	>	// Build the identArray_ and regions_
977
978	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
979	<
980	<	int cp =  TRADITIONAL_CUTOFF_POLICY;
981	<	if (simParams_->haveCutoffPolicy()) {
982	<	std::string myPolicy = simParams_->getCutoffPolicy();
983	<	toUpper(myPolicy);
984	<	if (myPolicy == "MIX") {
985	<	cp = MIX_CUTOFF_POLICY;
986	<	} else {
987	<	if (myPolicy == "MAX") {
884	<	cp = MAX_CUTOFF_POLICY;
885	<	} else {
886	<	if (myPolicy == "TRADITIONAL") {
887	<	cp = TRADITIONAL_CUTOFF_POLICY;
888	<	} else {
889	<	// throw error
890	<	sprintf( painCave.errMsg,
891	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
892	<	painCave.isFatal = 1;
893	<	simError();
894	<	}
895	<	}
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());
987	>	regions_.push_back(reg);
988		}
989	<	}
990	<
991	<
900	<	if (simParams_->haveSkinThickness()) {
901	<	double skinThickness = simParams_->getSkinThickness();
902	<	}
903	<
904	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
905	<	// also send cutoff notification to electrostatics
906	<	setElectrostaticCutoffRadius(&rcut_, &rsw_);
989	>	}
990	>
991	>	topologyDone_ = true;
992		}
993
909	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
910	–
911	–	int errorOut;
912	–	int esm =  NONE;
913	–	int sm = UNDAMPED;
914	–	double alphaVal;
915	–	double dielectric;
916	–
917	–	errorOut = isError;
918	–	alphaVal = simParams_->getDampingAlpha();
919	–	dielectric = simParams_->getDielectric();
920	–
921	–	if (simParams_->haveElectrostaticSummationMethod()) {
922	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
923	–	toUpper(myMethod);
924	–	if (myMethod == "NONE") {
925	–	esm = NONE;
926	–	} else {
927	–	if (myMethod == "SWITCHING_FUNCTION") {
928	–	esm = SWITCHING_FUNCTION;
929	–	} else {
930	–	if (myMethod == "SHIFTED_POTENTIAL") {
931	–	esm = SHIFTED_POTENTIAL;
932	–	} else {
933	–	if (myMethod == "SHIFTED_FORCE") {
934	–	esm = SHIFTED_FORCE;
935	–	} else {
936	–	if (myMethod == "REACTION_FIELD") {
937	–	esm = REACTION_FIELD;
938	–	} else {
939	–	// throw error
940	–	sprintf( painCave.errMsg,
941	–	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() );
942	–	painCave.isFatal = 1;
943	–	simError();
944	–	}
945	–	}
946	–	}
947	–	}
948	–	}
949	–	}
950	–
951	–	if (simParams_->haveElectrostaticScreeningMethod()) {
952	–	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
953	–	toUpper(myScreen);
954	–	if (myScreen == "UNDAMPED") {
955	–	sm = UNDAMPED;
956	–	} else {
957	–	if (myScreen == "DAMPED") {
958	–	sm = DAMPED;
959	–	if (!simParams_->haveDampingAlpha()) {
960	–	//throw error
961	–	sprintf( painCave.errMsg,
962	–	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
963	–	painCave.isFatal = 0;
964	–	simError();
965	–	}
966	–	} else {
967	–	// throw error
968	–	sprintf( painCave.errMsg,
969	–	"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
970	–	painCave.isFatal = 1;
971	–	simError();
972	–	}
973	–	}
974	–	}
975	–
976	–	// let's pass some summation method variables to fortran
977	–	setElectrostaticSummationMethod( &esm );
978	–	setScreeningMethod( &sm );
979	–	setDampingAlpha( &alphaVal );
980	–	setReactionFieldDielectric( &dielectric );
981	–	initFortranFF( &esm, &errorOut );
982	–	}
983	–
984	–	void SimInfo::setupSwitchingFunction() {
985	–	int ft = CUBIC;
986	–
987	–	if (simParams_->haveSwitchingFunctionType()) {
988	–	std::string funcType = simParams_->getSwitchingFunctionType();
989	–	toUpper(funcType);
990	–	if (funcType == "CUBIC") {
991	–	ft = CUBIC;
992	–	} else {
993	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
994	–	ft = FIFTH_ORDER_POLY;
995	–	} else {
996	–	// throw error
997	–	sprintf( painCave.errMsg,
998	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
999	–	painCave.isFatal = 1;
1000	–	simError();
1001	–	}
1002	–	}
1003	–	}
1004	–
1005	–	// send switching function notification to switcheroo
1006	–	setFunctionType(&ft);
1007	–
1008	–	}
1009	–
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 1019 | 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 1038 | Line 1022 | namespace oopse {
1022		delete sman_;
1023		sman_ = sman;
1024
1041	–	Molecule* mol;
1042	–	RigidBody* rb;
1043	–	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
1061	–	Vector3d SimInfo::getComVel(){
1062	–	SimInfo::MoleculeIterator i;
1063	–	Molecule* mol;
1076
1077	<	Vector3d comVel(0.0);
1066	<	double totalMass = 0.0;
1067	<
1068	<
1069	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1070	<	double mass = mol->getMass();
1071	<	totalMass += mass;
1072	<	comVel += mass * mol->getComVel();
1073	<	}
1077	>	ostream& operator <<(ostream& o, SimInfo& info) {
1078
1075	–	#ifdef IS_MPI
1076	–	double tmpMass = totalMass;
1077	–	Vector3d tmpComVel(comVel);
1078	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1079	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1080	–	#endif
1081	–
1082	–	comVel /= totalMass;
1083	–
1084	–	return comVel;
1085	–	}
1086	–
1087	–	Vector3d SimInfo::getCom(){
1088	–	SimInfo::MoleculeIterator i;
1089	–	Molecule* mol;
1090	–
1091	–	Vector3d com(0.0);
1092	–	double totalMass = 0.0;
1093	–
1094	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1095	–	double mass = mol->getMass();
1096	–	totalMass += mass;
1097	–	com += mass * mol->getCom();
1098	–	}
1099	–
1100	–	#ifdef IS_MPI
1101	–	double tmpMass = totalMass;
1102	–	Vector3d tmpCom(com);
1103	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1104	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1105	–	#endif
1106	–
1107	–	com /= totalMass;
1108	–
1109	–	return com;
1110	–
1111	–	}
1112	–
1113	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1114	–
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();
1133	<	totalMass += mass;
1134	<	com += mass * mol->getCom();
1135	<	comVel += mass * mol->getComVel();
1136	<	}
1137	<
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;
1148	<	comVel /= totalMass;
1149	<	}
1150	<
1151	<	/*
1152	<	Return intertia tensor for entire system and angular momentum Vector.
1109	>	return nGlobalConstraints;
1110	>	}
1111
1112	+	}//end namespace OpenMD
1113
1155	–	[  Ixx -Ixy  -Ixz ]
1156	–	J =| -Iyx  Iyy  -Iyz |
1157	–	[ -Izx -Iyz   Izz ]
1158	–	*/
1159	–
1160	–	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1161	–
1162	–
1163	–	double xx = 0.0;
1164	–	double yy = 0.0;
1165	–	double zz = 0.0;
1166	–	double xy = 0.0;
1167	–	double xz = 0.0;
1168	–	double yz = 0.0;
1169	–	Vector3d com(0.0);
1170	–	Vector3d comVel(0.0);
1171	–
1172	–	getComAll(com, comVel);
1173	–
1174	–	SimInfo::MoleculeIterator i;
1175	–	Molecule* mol;
1176	–
1177	–	Vector3d thisq(0.0);
1178	–	Vector3d thisv(0.0);
1179	–
1180	–	double thisMass = 0.0;
1181	–
1182	–
1183	–
1184	–
1185	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1186	–
1187	–	thisq = mol->getCom()-com;
1188	–	thisv = mol->getComVel()-comVel;
1189	–	thisMass = mol->getMass();
1190	–	// Compute moment of intertia coefficients.
1191	–	xx += thisq[0]*thisq[0]*thisMass;
1192	–	yy += thisq[1]*thisq[1]*thisMass;
1193	–	zz += thisq[2]*thisq[2]*thisMass;
1194	–
1195	–	// compute products of intertia
1196	–	xy += thisq[0]*thisq[1]*thisMass;
1197	–	xz += thisq[0]*thisq[2]*thisMass;
1198	–	yz += thisq[1]*thisq[2]*thisMass;
1199	–
1200	–	angularMomentum += cross( thisq, thisv ) * thisMass;
1201	–
1202	–	}
1203	–
1204	–
1205	–	inertiaTensor(0,0) = yy + zz;
1206	–	inertiaTensor(0,1) = -xy;
1207	–	inertiaTensor(0,2) = -xz;
1208	–	inertiaTensor(1,0) = -xy;
1209	–	inertiaTensor(1,1) = xx + zz;
1210	–	inertiaTensor(1,2) = -yz;
1211	–	inertiaTensor(2,0) = -xz;
1212	–	inertiaTensor(2,1) = -yz;
1213	–	inertiaTensor(2,2) = xx + yy;
1214	–
1215	–	#ifdef IS_MPI
1216	–	Mat3x3d tmpI(inertiaTensor);
1217	–	Vector3d tmpAngMom;
1218	–	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1219	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1220	–	#endif
1221	–
1222	–	return;
1223	–	}
1224	–
1225	–	//Returns the angular momentum of the system
1226	–	Vector3d SimInfo::getAngularMomentum(){
1227	–
1228	–	Vector3d com(0.0);
1229	–	Vector3d comVel(0.0);
1230	–	Vector3d angularMomentum(0.0);
1231	–
1232	–	getComAll(com,comVel);
1233	–
1234	–	SimInfo::MoleculeIterator i;
1235	–	Molecule* mol;
1236	–
1237	–	Vector3d thisr(0.0);
1238	–	Vector3d thisp(0.0);
1239	–
1240	–	double thisMass;
1241	–
1242	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1243	–	thisMass = mol->getMass();
1244	–	thisr = mol->getCom()-com;
1245	–	thisp = (mol->getComVel()-comVel)*thisMass;
1246	–
1247	–	angularMomentum += cross( thisr, thisp );
1248	–
1249	–	}
1250	–
1251	–	#ifdef IS_MPI
1252	–	Vector3d tmpAngMom;
1253	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1254	–	#endif
1255	–
1256	–	return angularMomentum;
1257	–	}
1258	–
1259	–
1260	–	}//end namespace oopse
1261	–

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 726 by chrisfen, Fri Nov 11 15:22:11 2005 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

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