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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 1386 by gezelter, Fri Oct 23 18:41:09 2009 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 54 | Line 55
55		#include "math/Vector3.hpp"
56		#include "primitives/Molecule.hpp"
57		#include "primitives/StuntDouble.hpp"
57	–	#include "UseTheForce/fCutoffPolicy.h"
58	–	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	–	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60	–	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61	–	#include "UseTheForce/doForces_interface.h"
62	–	#include "UseTheForce/DarkSide/neighborLists_interface.h"
63	–	#include "UseTheForce/DarkSide/electrostatic_interface.h"
64	–	#include "UseTheForce/DarkSide/switcheroo_interface.h"
58		#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60		#include "selection/SelectionManager.hpp"
61		#include "io/ForceFieldOptions.hpp"
62	<	#include "UseTheForce/ForceField.hpp"
63	<
71	<
62	>	#include "brains/ForceField.hpp"
63	>	#include "nonbonded/SwitchingFunction.hpp"
64		#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
75	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68	<	namespace oopse {
69	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79	<	std::map<int, std::set<int> >::iterator i = container.find(index);
80	<	std::set<int> result;
81	<	if (i != container.end()) {
82	<	result = i->second;
83	<	}
84	<
85	<	return result;
86	<	}
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),
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0),
76		nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77		nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78	<	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
79	<	calcBoxDipole_(false), useAtomicVirial_(true) {
80	<
81	<
82	<	MoleculeStamp* molStamp;
83	<	int nMolWithSameStamp;
84	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
85	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
86	<	CutoffGroupStamp* cgStamp;
87	<	RigidBodyStamp* rbStamp;
88	<	int nRigidAtoms = 0;
89	<
90	<	std::vector<Component*> components = simParams->getComponents();
78	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79	>	calcBoxDipole_(false), useAtomicVirial_(true) {
80	>
81	>	MoleculeStamp* molStamp;
82	>	int nMolWithSameStamp;
83	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
85	>	CutoffGroupStamp* cgStamp;
86	>	RigidBodyStamp* rbStamp;
87	>	int nRigidAtoms = 0;
88	>
89	>	vector<Component*> components = simParams->getComponents();
90	>
91	>	for (vector<Component*>::iterator i = components.begin();
92	>	i !=components.end(); ++i) {
93	>	molStamp = (*i)->getMoleculeStamp();
94	>	nMolWithSameStamp = (*i)->getNMol();
95
96	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
97	<	molStamp = (*i)->getMoleculeStamp();
98	<	nMolWithSameStamp = (*i)->getNMol();
99	<
100	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
101	<
102	<	//calculate atoms in molecules
103	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
104	<
105	<	//calculate atoms in cutoff groups
106	<	int nAtomsInGroups = 0;
107	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
121	<
122	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
123	<	cgStamp = molStamp->getCutoffGroupStamp(j);
124	<	nAtomsInGroups += cgStamp->getNMembers();
125	<	}
126	<
127	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
128	<
129	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
130	<
131	<	//calculate atoms in rigid bodies
132	<	int nAtomsInRigidBodies = 0;
133	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
134	<
135	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
136	<	rbStamp = molStamp->getRigidBodyStamp(j);
137	<	nAtomsInRigidBodies += rbStamp->getNMembers();
138	<	}
139	<
140	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
141	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
142	<
96	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
97	>
98	>	//calculate atoms in molecules
99	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
100	>
101	>	//calculate atoms in cutoff groups
102	>	int nAtomsInGroups = 0;
103	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
104	>
105	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
106	>	cgStamp = molStamp->getCutoffGroupStamp(j);
107	>	nAtomsInGroups += cgStamp->getNMembers();
108		}
109	<
110	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
111	<	//group therefore the total number of cutoff groups in the system is
112	<	//equal to the total number of atoms minus number of atoms belong to
113	<	//cutoff group defined in meta-data file plus the number of cutoff
114	<	//groups defined in meta-data file
115	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
116	<
117	<	//every free atom (atom does not belong to rigid bodies) is an
118	<	//integrable object therefore the total number of integrable objects
119	<	//in the system is equal to the total number of atoms minus number of
120	<	//atoms belong to rigid body defined in meta-data file plus the number
121	<	//of rigid bodies defined in meta-data file
122	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
123	<	+ nGlobalRigidBodies_;
124	<
125	<	nGlobalMols_ = molStampIds_.size();
161	<	molToProcMap_.resize(nGlobalMols_);
109	>
110	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
111	>
112	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
113	>
114	>	//calculate atoms in rigid bodies
115	>	int nAtomsInRigidBodies = 0;
116	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
117	>
118	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
119	>	rbStamp = molStamp->getRigidBodyStamp(j);
120	>	nAtomsInRigidBodies += rbStamp->getNMembers();
121	>	}
122	>
123	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
124	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
125	>
126		}
127	+
128	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
129	+	//group therefore the total number of cutoff groups in the system is
130	+	//equal to the total number of atoms minus number of atoms belong to
131	+	//cutoff group defined in meta-data file plus the number of cutoff
132	+	//groups defined in meta-data file
133
134	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
135	+
136	+	//every free atom (atom does not belong to rigid bodies) is an
137	+	//integrable object therefore the total number of integrable objects
138	+	//in the system is equal to the total number of atoms minus number of
139	+	//atoms belong to rigid body defined in meta-data file plus the number
140	+	//of rigid bodies defined in meta-data file
141	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
142	+	+ nGlobalRigidBodies_;
143	+
144	+	nGlobalMols_ = molStampIds_.size();
145	+	molToProcMap_.resize(nGlobalMols_);
146	+	}
147	+
148		SimInfo::~SimInfo() {
149	<	std::map<int, Molecule*>::iterator i;
149	>	map<int, Molecule*>::iterator i;
150		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
151		delete i->second;
152		}
#	Line 173 | Line 157 | namespace oopse {
157		delete forceField_;
158		}
159
176	–	int SimInfo::getNGlobalConstraints() {
177	–	int nGlobalConstraints;
178	–	#ifdef IS_MPI
179	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
180	–	MPI_COMM_WORLD);
181	–	#else
182	–	nGlobalConstraints =  nConstraints_;
183	–	#endif
184	–	return nGlobalConstraints;
185	–	}
160
161		bool SimInfo::addMolecule(Molecule* mol) {
162		MoleculeIterator i;
163	<
163	>
164		i = molecules_.find(mol->getGlobalIndex());
165		if (i == molecules_.end() ) {
166	<
167	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
168	<
166	>
167	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
168	>
169		nAtoms_ += mol->getNAtoms();
170		nBonds_ += mol->getNBonds();
171		nBends_ += mol->getNBends();
#	Line 201 | Line 175 | namespace oopse {
175		nIntegrableObjects_ += mol->getNIntegrableObjects();
176		nCutoffGroups_ += mol->getNCutoffGroups();
177		nConstraints_ += mol->getNConstraintPairs();
178	<
178	>
179		addInteractionPairs(mol);
180	<
180	>
181		return true;
182		} else {
183		return false;
184		}
185		}
186	<
186	>
187		bool SimInfo::removeMolecule(Molecule* mol) {
188		MoleculeIterator i;
189		i = molecules_.find(mol->getGlobalIndex());
#	Line 237 | Line 211 | namespace oopse {
211		} else {
212		return false;
213		}
240	–
241	–
214		}
215
216
#	Line 254 | Line 226 | namespace oopse {
226
227
228		void SimInfo::calcNdf() {
229	<	int ndf_local;
229	>	int ndf_local, nfq_local;
230		MoleculeIterator i;
231	<	std::vector<StuntDouble*>::iterator j;
231	>	vector<StuntDouble*>::iterator j;
232	>	vector<Atom*>::iterator k;
233	>
234		Molecule* mol;
235	<	StuntDouble* integrableObject;
235	>	StuntDouble* sd;
236	>	Atom* atom;
237
238		ndf_local = 0;
239	+	nfq_local = 0;
240
241		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
266	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
267	–	integrableObject = mol->nextIntegrableObject(j)) {
242
243	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
244	+	sd = mol->nextIntegrableObject(j)) {
245	+
246		ndf_local += 3;
247
248	<	if (integrableObject->isDirectional()) {
249	<	if (integrableObject->isLinear()) {
248	>	if (sd->isDirectional()) {
249	>	if (sd->isLinear()) {
250		ndf_local += 2;
251		} else {
252		ndf_local += 3;
253		}
254		}
278	–
255		}
256	+
257	+	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
258	+	atom = mol->nextFluctuatingCharge(k)) {
259	+	if (atom->isFluctuatingCharge()) {
260	+	nfq_local++;
261	+	}
262	+	}
263		}
264
265	+	ndfLocal_ = ndf_local;
266	+
267		// n_constraints is local, so subtract them on each processor
268		ndf_local -= nConstraints_;
269
270		#ifdef IS_MPI
271	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
271	>	MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
272	>	MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
273	>	MPI::INT, MPI::SUM);
274		#else
275		ndf_ = ndf_local;
276	+	nGlobalFluctuatingCharges_ = nfq_local;
277		#endif
278
279		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 296 | Line 284 | namespace oopse {
284
285		int SimInfo::getFdf() {
286		#ifdef IS_MPI
287	<	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
287	>	MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
288		#else
289		fdf_ = fdf_local;
290		#endif
291		return fdf_;
292		}
293	+
294	+	unsigned int SimInfo::getNLocalCutoffGroups(){
295	+	int nLocalCutoffAtoms = 0;
296	+	Molecule* mol;
297	+	MoleculeIterator mi;
298	+	CutoffGroup* cg;
299	+	Molecule::CutoffGroupIterator ci;
300
301	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
302	+
303	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
304	+	cg = mol->nextCutoffGroup(ci)) {
305	+	nLocalCutoffAtoms += cg->getNumAtom();
306	+
307	+	}
308	+	}
309	+
310	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
311	+	}
312	+
313		void SimInfo::calcNdfRaw() {
314		int ndfRaw_local;
315
316		MoleculeIterator i;
317	<	std::vector<StuntDouble*>::iterator j;
317	>	vector<StuntDouble*>::iterator j;
318		Molecule* mol;
319	<	StuntDouble* integrableObject;
319	>	StuntDouble* sd;
320
321		// Raw degrees of freedom that we have to set
322		ndfRaw_local = 0;
323
324		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
318	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
319	–	integrableObject = mol->nextIntegrableObject(j)) {
325
326	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
327	+	sd = mol->nextIntegrableObject(j)) {
328	+
329		ndfRaw_local += 3;
330
331	<	if (integrableObject->isDirectional()) {
332	<	if (integrableObject->isLinear()) {
331	>	if (sd->isDirectional()) {
332	>	if (sd->isLinear()) {
333		ndfRaw_local += 2;
334		} else {
335		ndfRaw_local += 3;
#	Line 332 | Line 340 | namespace oopse {
340		}
341
342		#ifdef IS_MPI
343	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
343	>	MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
344		#else
345		ndfRaw_ = ndfRaw_local;
346		#endif
#	Line 345 | Line 353 | namespace oopse {
353
354
355		#ifdef IS_MPI
356	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
356	>	MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
357	>	MPI::INT, MPI::SUM);
358		#else
359		ndfTrans_ = ndfTrans_local;
360		#endif
#	Line 356 | Line 365 | namespace oopse {
365
366		void SimInfo::addInteractionPairs(Molecule* mol) {
367		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
368	<	std::vector<Bond*>::iterator bondIter;
369	<	std::vector<Bend*>::iterator bendIter;
370	<	std::vector<Torsion*>::iterator torsionIter;
371	<	std::vector<Inversion*>::iterator inversionIter;
368	>	vector<Bond*>::iterator bondIter;
369	>	vector<Bend*>::iterator bendIter;
370	>	vector<Torsion*>::iterator torsionIter;
371	>	vector<Inversion*>::iterator inversionIter;
372		Bond* bond;
373		Bend* bend;
374		Torsion* torsion;
#	Line 377 | Line 386 | namespace oopse {
386		// always be excluded.  These are done at the bottom of this
387		// function.
388
389	<	std::map<int, std::set<int> > atomGroups;
389	>	map<int, set<int> > atomGroups;
390		Molecule::RigidBodyIterator rbIter;
391		RigidBody* rb;
392		Molecule::IntegrableObjectIterator ii;
393	<	StuntDouble* integrableObject;
393	>	StuntDouble* sd;
394
395	<	for (integrableObject = mol->beginIntegrableObject(ii);
396	<	integrableObject != NULL;
388	<	integrableObject = mol->nextIntegrableObject(ii)) {
395	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
396	>	sd = mol->nextIntegrableObject(ii)) {
397
398	<	if (integrableObject->isRigidBody()) {
399	<	rb = static_cast<RigidBody*>(integrableObject);
400	<	std::vector<Atom*> atoms = rb->getAtoms();
401	<	std::set<int> rigidAtoms;
398	>	if (sd->isRigidBody()) {
399	>	rb = static_cast<RigidBody*>(sd);
400	>	vector<Atom*> atoms = rb->getAtoms();
401	>	set<int> rigidAtoms;
402		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
403		rigidAtoms.insert(atoms[i]->getGlobalIndex());
404		}
405		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
406	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
406	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
407		}
408		} else {
409	<	std::set<int> oneAtomSet;
410	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
411	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
409	>	set<int> oneAtomSet;
410	>	oneAtomSet.insert(sd->getGlobalIndex());
411	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
412		}
413		}
414
#	Line 503 | Line 511 | namespace oopse {
511
512		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
513		rb = mol->nextRigidBody(rbIter)) {
514	<	std::vector<Atom*> atoms = rb->getAtoms();
514	>	vector<Atom*> atoms = rb->getAtoms();
515		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
516		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
517		a = atoms[i]->getGlobalIndex();
#	Line 517 | Line 525 | namespace oopse {
525
526		void SimInfo::removeInteractionPairs(Molecule* mol) {
527		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
528	<	std::vector<Bond*>::iterator bondIter;
529	<	std::vector<Bend*>::iterator bendIter;
530	<	std::vector<Torsion*>::iterator torsionIter;
531	<	std::vector<Inversion*>::iterator inversionIter;
528	>	vector<Bond*>::iterator bondIter;
529	>	vector<Bend*>::iterator bendIter;
530	>	vector<Torsion*>::iterator torsionIter;
531	>	vector<Inversion*>::iterator inversionIter;
532		Bond* bond;
533		Bend* bend;
534		Torsion* torsion;
#	Line 530 | Line 538 | namespace oopse {
538		int c;
539		int d;
540
541	<	std::map<int, std::set<int> > atomGroups;
541	>	map<int, set<int> > atomGroups;
542		Molecule::RigidBodyIterator rbIter;
543		RigidBody* rb;
544		Molecule::IntegrableObjectIterator ii;
545	<	StuntDouble* integrableObject;
545	>	StuntDouble* sd;
546
547	<	for (integrableObject = mol->beginIntegrableObject(ii);
548	<	integrableObject != NULL;
541	<	integrableObject = mol->nextIntegrableObject(ii)) {
547	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
548	>	sd = mol->nextIntegrableObject(ii)) {
549
550	<	if (integrableObject->isRigidBody()) {
551	<	rb = static_cast<RigidBody*>(integrableObject);
552	<	std::vector<Atom*> atoms = rb->getAtoms();
553	<	std::set<int> rigidAtoms;
550	>	if (sd->isRigidBody()) {
551	>	rb = static_cast<RigidBody*>(sd);
552	>	vector<Atom*> atoms = rb->getAtoms();
553	>	set<int> rigidAtoms;
554		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
555		rigidAtoms.insert(atoms[i]->getGlobalIndex());
556		}
557		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
558	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
558	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
559		}
560		} else {
561	<	std::set<int> oneAtomSet;
562	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
563	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
561	>	set<int> oneAtomSet;
562	>	oneAtomSet.insert(sd->getGlobalIndex());
563	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
564		}
565		}
566
#	Line 656 | Line 663 | namespace oopse {
663
664		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
665		rb = mol->nextRigidBody(rbIter)) {
666	<	std::vector<Atom*> atoms = rb->getAtoms();
666	>	vector<Atom*> atoms = rb->getAtoms();
667		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
668		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
669		a = atoms[i]->getGlobalIndex();
#	Line 679 | Line 686 | namespace oopse {
686		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
687		}
688
682	–	void SimInfo::update() {
689
690	<	setupSimType();
691	<
692	<	#ifdef IS_MPI
693	<	setupFortranParallel();
694	<	#endif
695	<
696	<	setupFortranSim();
697	<
698	<	//setup fortran force field
693	<	/** @deprecate */
694	<	int isError = 0;
695	<
696	<	setupCutoff();
697	<
698	<	setupElectrostaticSummationMethod( isError );
699	<	setupSwitchingFunction();
700	<	setupAccumulateBoxDipole();
701	<
702	<	if(isError){
703	<	sprintf( painCave.errMsg,
704	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
705	<	painCave.isFatal = 1;
706	<	simError();
707	<	}
708	<
690	>	/**
691	>	* update
692	>	*
693	>	*  Performs the global checks and variable settings after the
694	>	*  objects have been created.
695	>	*
696	>	*/
697	>	void SimInfo::update() {
698	>	setupSimVariables();
699		calcNdf();
700		calcNdfRaw();
701		calcNdfTrans();
712	–
713	–	fortranInitialized_ = true;
702		}
703	<
704	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
703	>
704	>	/**
705	>	* getSimulatedAtomTypes
706	>	*
707	>	* Returns an STL set of AtomType* that are actually present in this
708	>	* simulation.  Must query all processors to assemble this information.
709	>	*
710	>	*/
711	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
712		SimInfo::MoleculeIterator mi;
713		Molecule* mol;
714		Molecule::AtomIterator ai;
715		Atom* atom;
716	<	std::set<AtomType*> atomTypes;
717	<
716	>	set<AtomType*> atomTypes;
717	>
718		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
719	<
720	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
719	>	for(atom = mol->beginAtom(ai); atom != NULL;
720	>	atom = mol->nextAtom(ai)) {
721		atomTypes.insert(atom->getAtomType());
722	<	}
723	<
729	<	}
730	<
731	<	return atomTypes;
732	<	}
733	<
734	<	void SimInfo::setupSimType() {
735	<	std::set<AtomType*>::iterator i;
736	<	std::set<AtomType*> atomTypes;
737	<	atomTypes = getUniqueAtomTypes();
722	>	}
723	>	}
724
725	<	int useLennardJones = 0;
740	<	int useElectrostatic = 0;
741	<	int useEAM = 0;
742	<	int useSC = 0;
743	<	int useCharge = 0;
744	<	int useDirectional = 0;
745	<	int useDipole = 0;
746	<	int useGayBerne = 0;
747	<	int useSticky = 0;
748	<	int useStickyPower = 0;
749	<	int useShape = 0;
750	<	int useFLARB = 0; //it is not in AtomType yet
751	<	int useDirectionalAtom = 0;
752	<	int useElectrostatics = 0;
753	<	//usePBC and useRF are from simParams
754	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
755	<	int useRF;
756	<	int useSF;
757	<	int useSP;
758	<	int useBoxDipole;
725	>	#ifdef IS_MPI
726
727	<	std::string myMethod;
728	<
762	<	// set the useRF logical
763	<	useRF = 0;
764	<	useSF = 0;
765	<	useSP = 0;
766	<	useBoxDipole = 0;
767	<
768	<
769	<	if (simParams_->haveElectrostaticSummationMethod()) {
770	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
771	<	toUpper(myMethod);
772	<	if (myMethod == "REACTION_FIELD"){
773	<	useRF = 1;
774	<	} else if (myMethod == "SHIFTED_FORCE"){
775	<	useSF = 1;
776	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
777	<	useSP = 1;
778	<	}
779	<	}
727	>	// loop over the found atom types on this processor, and add their
728	>	// numerical idents to a vector:
729
730	<	if (simParams_->haveAccumulateBoxDipole())
731	<	if (simParams_->getAccumulateBoxDipole())
732	<	useBoxDipole = 1;
730	>	vector<int> foundTypes;
731	>	set<AtomType*>::iterator i;
732	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
733	>	foundTypes.push_back( (*i)->getIdent() );
734
735	<	useAtomicVirial_ = simParams_->getUseAtomicVirial();
735	>	// count_local holds the number of found types on this processor
736	>	int count_local = foundTypes.size();
737
738	<	//loop over all of the atom types
788	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
789	<	useLennardJones |= (*i)->isLennardJones();
790	<	useElectrostatic |= (*i)->isElectrostatic();
791	<	useEAM |= (*i)->isEAM();
792	<	useSC |= (*i)->isSC();
793	<	useCharge |= (*i)->isCharge();
794	<	useDirectional |= (*i)->isDirectional();
795	<	useDipole |= (*i)->isDipole();
796	<	useGayBerne |= (*i)->isGayBerne();
797	<	useSticky |= (*i)->isSticky();
798	<	useStickyPower |= (*i)->isStickyPower();
799	<	useShape |= (*i)->isShape();
800	<	}
738	>	int nproc = MPI::COMM_WORLD.Get_size();
739
740	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
741	<	useDirectionalAtom = 1;
742	<	}
740	>	// we need arrays to hold the counts and displacement vectors for
741	>	// all processors
742	>	vector<int> counts(nproc, 0);
743	>	vector<int> disps(nproc, 0);
744
745	<	if (useCharge || useDipole) {
746	<	useElectrostatics = 1;
745	>	// fill the counts array
746	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
747	>	1, MPI::INT);
748	>
749	>	// use the processor counts to compute the displacement array
750	>	disps[0] = 0;
751	>	int totalCount = counts[0];
752	>	for (int iproc = 1; iproc < nproc; iproc++) {
753	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
754	>	totalCount += counts[iproc];
755		}
756
757	<	#ifdef IS_MPI
758	<	int temp;
757	>	// we need a (possibly redundant) set of all found types:
758	>	vector<int> ftGlobal(totalCount);
759	>
760	>	// now spray out the foundTypes to all the other processors:
761	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
762	>	&ftGlobal[0], &counts[0], &disps[0],
763	>	MPI::INT);
764
765	<	temp = usePBC;
814	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
765	>	vector<int>::iterator j;
766
767	<	temp = useDirectionalAtom;
768	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767	>	// foundIdents is a stl set, so inserting an already found ident
768	>	// will have no effect.
769	>	set<int> foundIdents;
770
771	<	temp = useLennardJones;
772	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
771	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
772	>	foundIdents.insert((*j));
773	>
774	>	// now iterate over the foundIdents and get the actual atom types
775	>	// that correspond to these:
776	>	set<int>::iterator it;
777	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
778	>	atomTypes.insert( forceField_->getAtomType((*it)) );
779	>
780	>	#endif
781
782	<	temp = useElectrostatics;
783	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
782	>	return atomTypes;
783	>	}
784
825	–	temp = useCharge;
826	–	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
785
786	<	temp = useDipole;
787	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
786	>	int getGlobalCountOfType(AtomType* atype) {
787	>	/*
788	>	set<AtomType*> atypes = getSimulatedAtomTypes();
789	>	map<AtomType*, int> counts_;
790
791	<	temp = useSticky;
792	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
791	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
792	>	for(atom = mol->beginAtom(ai); atom != NULL;
793	>	atom = mol->nextAtom(ai)) {
794	>	atom->getAtomType();
795	>	}
796	>	}
797	>	*/
798	>	return 0;
799	>	}
800
801	<	temp = useStickyPower;
802	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
801	>	void SimInfo::setupSimVariables() {
802	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
803	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
804	>	// parameter is true
805	>	calcBoxDipole_ = false;
806	>	if ( simParams_->haveAccumulateBoxDipole() )
807	>	if ( simParams_->getAccumulateBoxDipole() ) {
808	>	calcBoxDipole_ = true;
809	>	}
810
811	<	temp = useGayBerne;
812	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
811	>	set<AtomType*>::iterator i;
812	>	set<AtomType*> atomTypes;
813	>	atomTypes = getSimulatedAtomTypes();
814	>	bool usesElectrostatic = false;
815	>	bool usesMetallic = false;
816	>	bool usesDirectional = false;
817	>	bool usesFluctuatingCharges =  false;
818	>	//loop over all of the atom types
819	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
820	>	usesElectrostatic |= (*i)->isElectrostatic();
821	>	usesMetallic |= (*i)->isMetal();
822	>	usesDirectional |= (*i)->isDirectional();
823	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
824	>	}
825
826	<	temp = useEAM;
827	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
828	<
829	<	temp = useSC;
830	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
826	>	#ifdef IS_MPI
827	>	bool temp;
828	>	temp = usesDirectional;
829	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
830	>	MPI::LOR);
831	>
832	>	temp = usesMetallic;
833	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
834	>	MPI::LOR);
835
836	<	temp = useShape;
837	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
836	>	temp = usesElectrostatic;
837	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
838	>	MPI::LOR);
839
840	<	temp = useFLARB;
841	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
840	>	temp = usesFluctuatingCharges;
841	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
842	>	MPI::LOR);
843	>	#else
844
845	<	temp = useRF;
846	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
845	>	usesDirectionalAtoms_ = usesDirectional;
846	>	usesMetallicAtoms_ = usesMetallic;
847	>	usesElectrostaticAtoms_ = usesElectrostatic;
848	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
849
850	<	temp = useSF;
851	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
850	>	#endif
851	>
852	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
853	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
854	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
855	>	}
856
858	–	temp = useSP;
859	–	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
857
858	<	temp = useBoxDipole;
859	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
858	>	vector<int> SimInfo::getGlobalAtomIndices() {
859	>	SimInfo::MoleculeIterator mi;
860	>	Molecule* mol;
861	>	Molecule::AtomIterator ai;
862	>	Atom* atom;
863
864	<	temp = useAtomicVirial_;
865	<	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
864	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
865	>
866	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
867	>
868	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
869	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
870	>	}
871	>	}
872	>	return GlobalAtomIndices;
873	>	}
874
867	–	#endif
875
876	<	fInfo_.SIM_uses_PBC = usePBC;
877	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
878	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
879	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
880	<	fInfo_.SIM_uses_Charges = useCharge;
874	<	fInfo_.SIM_uses_Dipoles = useDipole;
875	<	fInfo_.SIM_uses_Sticky = useSticky;
876	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
877	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
878	<	fInfo_.SIM_uses_EAM = useEAM;
879	<	fInfo_.SIM_uses_SC = useSC;
880	<	fInfo_.SIM_uses_Shapes = useShape;
881	<	fInfo_.SIM_uses_FLARB = useFLARB;
882	<	fInfo_.SIM_uses_RF = useRF;
883	<	fInfo_.SIM_uses_SF = useSF;
884	<	fInfo_.SIM_uses_SP = useSP;
885	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
886	<	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
887	<	}
876	>	vector<int> SimInfo::getGlobalGroupIndices() {
877	>	SimInfo::MoleculeIterator mi;
878	>	Molecule* mol;
879	>	Molecule::CutoffGroupIterator ci;
880	>	CutoffGroup* cg;
881
882	<	void SimInfo::setupFortranSim() {
890	<	int isError;
891	<	int nExclude, nOneTwo, nOneThree, nOneFour;
892	<	std::vector<int> fortranGlobalGroupMembership;
882	>	vector<int> GlobalGroupIndices;
883
884	<	isError = 0;
885	<
886	<	//globalGroupMembership_ is filled by SimCreator
887	<	for (int i = 0; i < nGlobalAtoms_; i++) {
888	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
884	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
885	>
886	>	//local index of cutoff group is trivial, it only depends on the
887	>	//order of travesing
888	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
889	>	cg = mol->nextCutoffGroup(ci)) {
890	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
891	>	}
892		}
893	+	return GlobalGroupIndices;
894	+	}
895
896	+
897	+	void SimInfo::prepareTopology() {
898	+
899		//calculate mass ratio of cutoff group
902	–	std::vector<RealType> mfact;
900		SimInfo::MoleculeIterator mi;
901		Molecule* mol;
902		Molecule::CutoffGroupIterator ci;
#	Line 908 | Line 905 | namespace oopse {
905		Atom* atom;
906		RealType totalMass;
907
908	<	//to avoid memory reallocation, reserve enough space for mfact
909	<	mfact.reserve(getNCutoffGroups());
908	>	/**
909	>	* The mass factor is the relative mass of an atom to the total
910	>	* mass of the cutoff group it belongs to.  By default, all atoms
911	>	* are their own cutoff groups, and therefore have mass factors of
912	>	* 1.  We need some special handling for massless atoms, which
913	>	* will be treated as carrying the entire mass of the cutoff
914	>	* group.
915	>	*/
916	>	massFactors_.clear();
917	>	massFactors_.resize(getNAtoms(), 1.0);
918
919		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
920	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
920	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
921	>	cg = mol->nextCutoffGroup(ci)) {
922
923		totalMass = cg->getMass();
924		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
925		// Check for massless groups - set mfact to 1 if true
926	<	if (totalMass != 0)
927	<	mfact.push_back(atom->getMass()/totalMass);
926	>	if (totalMass != 0)
927	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
928		else
929	<	mfact.push_back( 1.0 );
929	>	massFactors_[atom->getLocalIndex()] = 1.0;
930		}
931		}
932		}
933
934	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
929	<	std::vector<int> identArray;
934	>	// Build the identArray_
935
936	<	//to avoid memory reallocation, reserve enough space identArray
937	<	identArray.reserve(getNAtoms());
933	<
936	>	identArray_.clear();
937	>	identArray_.reserve(getNAtoms());
938		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
939		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
940	<	identArray.push_back(atom->getIdent());
940	>	identArray_.push_back(atom->getIdent());
941		}
942		}
939	–
940	–	//fill molMembershipArray
941	–	//molMembershipArray is filled by SimCreator
942	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
943	–	for (int i = 0; i < nGlobalAtoms_; i++) {
944	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
945	–	}
943
944	<	//setup fortran simulation
944	>	topologyDone_ = true;
945	>	}
946
947	<	nExclude = excludedInteractions_.getSize();
948	<	nOneTwo = oneTwoInteractions_.getSize();
949	<	nOneThree = oneThreeInteractions_.getSize();
952	<	nOneFour = oneFourInteractions_.getSize();
947	>	void SimInfo::addProperty(GenericData* genData) {
948	>	properties_.addProperty(genData);
949	>	}
950
951	<	int* excludeList = excludedInteractions_.getPairList();
952	<	int* oneTwoList = oneTwoInteractions_.getPairList();
956	<	int* oneThreeList = oneThreeInteractions_.getPairList();
957	<	int* oneFourList = oneFourInteractions_.getPairList();
958	<
959	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
960	<	&nExclude, excludeList,
961	<	&nOneTwo, oneTwoList,
962	<	&nOneThree, oneThreeList,
963	<	&nOneFour, oneFourList,
964	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
965	<	&fortranGlobalGroupMembership[0], &isError);
966	<
967	<	if( isError ){
968	<
969	<	sprintf( painCave.errMsg,
970	<	"There was an error setting the simulation information in fortran.\n" );
971	<	painCave.isFatal = 1;
972	<	painCave.severity = OOPSE_ERROR;
973	<	simError();
974	<	}
975	<
976	<
977	<	sprintf( checkPointMsg,
978	<	"succesfully sent the simulation information to fortran.\n");
979	<
980	<	errorCheckPoint();
981	<
982	<	// Setup number of neighbors in neighbor list if present
983	<	if (simParams_->haveNeighborListNeighbors()) {
984	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
985	<	setNeighbors(&nlistNeighbors);
986	<	}
987	<
988	<
951	>	void SimInfo::removeProperty(const string& propName) {
952	>	properties_.removeProperty(propName);
953		}
954
955	<
956	<	void SimInfo::setupFortranParallel() {
993	<	#ifdef IS_MPI
994	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
995	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
996	<	std::vector<int> localToGlobalCutoffGroupIndex;
997	<	SimInfo::MoleculeIterator mi;
998	<	Molecule::AtomIterator ai;
999	<	Molecule::CutoffGroupIterator ci;
1000	<	Molecule* mol;
1001	<	Atom* atom;
1002	<	CutoffGroup* cg;
1003	<	mpiSimData parallelData;
1004	<	int isError;
1005	<
1006	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1007	<
1008	<	//local index(index in DataStorge) of atom is important
1009	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1010	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1011	<	}
1012	<
1013	<	//local index of cutoff group is trivial, it only depends on the order of travesing
1014	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1015	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1016	<	}
1017	<
1018	<	}
1019	<
1020	<	//fill up mpiSimData struct
1021	<	parallelData.nMolGlobal = getNGlobalMolecules();
1022	<	parallelData.nMolLocal = getNMolecules();
1023	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
1024	<	parallelData.nAtomsLocal = getNAtoms();
1025	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1026	<	parallelData.nGroupsLocal = getNCutoffGroups();
1027	<	parallelData.myNode = worldRank;
1028	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1029	<
1030	<	//pass mpiSimData struct and index arrays to fortran
1031	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1032	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1033	<	&localToGlobalCutoffGroupIndex[0], &isError);
1034	<
1035	<	if (isError) {
1036	<	sprintf(painCave.errMsg,
1037	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1038	<	painCave.isFatal = 1;
1039	<	simError();
1040	<	}
1041	<
1042	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
1043	<	errorCheckPoint();
1044	<
1045	<	#endif
955	>	void SimInfo::clearProperties() {
956	>	properties_.clearProperties();
957		}
958
959	<	void SimInfo::setupCutoff() {
960	<
961	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1051	<
1052	<	// Check the cutoff policy
1053	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1054	<
1055	<	// Set LJ shifting bools to false
1056	<	ljsp_ = 0;
1057	<	ljsf_ = 0;
1058	<
1059	<	std::string myPolicy;
1060	<	if (forceFieldOptions_.haveCutoffPolicy()){
1061	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
1062	<	}else if (simParams_->haveCutoffPolicy()) {
1063	<	myPolicy = simParams_->getCutoffPolicy();
1064	<	}
1065	<
1066	<	if (!myPolicy.empty()){
1067	<	toUpper(myPolicy);
1068	<	if (myPolicy == "MIX") {
1069	<	cp = MIX_CUTOFF_POLICY;
1070	<	} else {
1071	<	if (myPolicy == "MAX") {
1072	<	cp = MAX_CUTOFF_POLICY;
1073	<	} else {
1074	<	if (myPolicy == "TRADITIONAL") {
1075	<	cp = TRADITIONAL_CUTOFF_POLICY;
1076	<	} else {
1077	<	// throw error
1078	<	sprintf( painCave.errMsg,
1079	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1080	<	painCave.isFatal = 1;
1081	<	simError();
1082	<	}
1083	<	}
1084	<	}
1085	<	}
1086	<	notifyFortranCutoffPolicy(&cp);
1087	<
1088	<	// Check the Skin Thickness for neighborlists
1089	<	RealType skin;
1090	<	if (simParams_->haveSkinThickness()) {
1091	<	skin = simParams_->getSkinThickness();
1092	<	notifyFortranSkinThickness(&skin);
1093	<	}
1094	<
1095	<	// Check if the cutoff was set explicitly:
1096	<	if (simParams_->haveCutoffRadius()) {
1097	<	rcut_ = simParams_->getCutoffRadius();
1098	<	if (simParams_->haveSwitchingRadius()) {
1099	<	rsw_  = simParams_->getSwitchingRadius();
1100	<	} else {
1101	<	if (fInfo_.SIM_uses_Charges |
1102	<	fInfo_.SIM_uses_Dipoles |
1103	<	fInfo_.SIM_uses_RF) {
1104	<
1105	<	rsw_ = 0.85 * rcut_;
1106	<	sprintf(painCave.errMsg,
1107	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1108	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1109	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1110	<	painCave.isFatal = 0;
1111	<	simError();
1112	<	} else {
1113	<	rsw_ = rcut_;
1114	<	sprintf(painCave.errMsg,
1115	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1116	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
1117	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1118	<	painCave.isFatal = 0;
1119	<	simError();
1120	<	}
1121	<	}
1122	<
1123	<	if (simParams_->haveElectrostaticSummationMethod()) {
1124	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1125	<	toUpper(myMethod);
1126	<
1127	<	if (myMethod == "SHIFTED_POTENTIAL") {
1128	<	ljsp_ = 1;
1129	<	} else if (myMethod == "SHIFTED_FORCE") {
1130	<	ljsf_ = 1;
1131	<	}
1132	<	}
1133	<
1134	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
959	>	vector<string> SimInfo::getPropertyNames() {
960	>	return properties_.getPropertyNames();
961	>	}
962
963	<	} else {
964	<
1138	<	// For electrostatic atoms, we'll assume a large safe value:
1139	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1140	<	sprintf(painCave.errMsg,
1141	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1142	<	"\tOOPSE will use a default value of 15.0 angstroms"
1143	<	"\tfor the cutoffRadius.\n");
1144	<	painCave.isFatal = 0;
1145	<	simError();
1146	<	rcut_ = 15.0;
1147	<
1148	<	if (simParams_->haveElectrostaticSummationMethod()) {
1149	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1150	<	toUpper(myMethod);
1151	<
1152	<	// For the time being, we're tethering the LJ shifted behavior to the
1153	<	// electrostaticSummationMethod keyword options
1154	<	if (myMethod == "SHIFTED_POTENTIAL") {
1155	<	ljsp_ = 1;
1156	<	} else if (myMethod == "SHIFTED_FORCE") {
1157	<	ljsf_ = 1;
1158	<	}
1159	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1160	<	if (simParams_->haveSwitchingRadius()){
1161	<	sprintf(painCave.errMsg,
1162	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1163	<	"\teven though the electrostaticSummationMethod was\n"
1164	<	"\tset to %s\n", myMethod.c_str());
1165	<	painCave.isFatal = 1;
1166	<	simError();
1167	<	}
1168	<	}
1169	<	}
1170	<
1171	<	if (simParams_->haveSwitchingRadius()){
1172	<	rsw_ = simParams_->getSwitchingRadius();
1173	<	} else {
1174	<	sprintf(painCave.errMsg,
1175	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1176	<	"\tOOPSE will use a default value of\n"
1177	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1178	<	painCave.isFatal = 0;
1179	<	simError();
1180	<	rsw_ = 0.85 * rcut_;
1181	<	}
1182	<
1183	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1184	<
1185	<	} else {
1186	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1187	<	// We'll punt and let fortran figure out the cutoffs later.
1188	<
1189	<	notifyFortranYouAreOnYourOwn();
1190	<
1191	<	}
1192	<	}
963	>	vector<GenericData*> SimInfo::getProperties() {
964	>	return properties_.getProperties();
965		}
966
967	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1196	<
1197	<	int errorOut;
1198	<	int esm =  NONE;
1199	<	int sm = UNDAMPED;
1200	<	RealType alphaVal;
1201	<	RealType dielectric;
1202	<
1203	<	errorOut = isError;
1204	<
1205	<	if (simParams_->haveElectrostaticSummationMethod()) {
1206	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1207	<	toUpper(myMethod);
1208	<	if (myMethod == "NONE") {
1209	<	esm = NONE;
1210	<	} else {
1211	<	if (myMethod == "SWITCHING_FUNCTION") {
1212	<	esm = SWITCHING_FUNCTION;
1213	<	} else {
1214	<	if (myMethod == "SHIFTED_POTENTIAL") {
1215	<	esm = SHIFTED_POTENTIAL;
1216	<	} else {
1217	<	if (myMethod == "SHIFTED_FORCE") {
1218	<	esm = SHIFTED_FORCE;
1219	<	} else {
1220	<	if (myMethod == "REACTION_FIELD") {
1221	<	esm = REACTION_FIELD;
1222	<	dielectric = simParams_->getDielectric();
1223	<	if (!simParams_->haveDielectric()) {
1224	<	// throw warning
1225	<	sprintf( painCave.errMsg,
1226	<	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1227	<	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1228	<	painCave.isFatal = 0;
1229	<	simError();
1230	<	}
1231	<	} else {
1232	<	// throw error
1233	<	sprintf( painCave.errMsg,
1234	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1235	<	"\t(Input file specified %s .)\n"
1236	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1237	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1238	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1239	<	painCave.isFatal = 1;
1240	<	simError();
1241	<	}
1242	<	}
1243	<	}
1244	<	}
1245	<	}
1246	<	}
1247	<
1248	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1249	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1250	<	toUpper(myScreen);
1251	<	if (myScreen == "UNDAMPED") {
1252	<	sm = UNDAMPED;
1253	<	} else {
1254	<	if (myScreen == "DAMPED") {
1255	<	sm = DAMPED;
1256	<	if (!simParams_->haveDampingAlpha()) {
1257	<	// first set a cutoff dependent alpha value
1258	<	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1259	<	alphaVal = 0.5125 - rcut_* 0.025;
1260	<	// for values rcut > 20.5, alpha is zero
1261	<	if (alphaVal < 0) alphaVal = 0;
1262	<
1263	<	// throw warning
1264	<	sprintf( painCave.errMsg,
1265	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1266	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1267	<	painCave.isFatal = 0;
1268	<	simError();
1269	<	} else {
1270	<	alphaVal = simParams_->getDampingAlpha();
1271	<	}
1272	<
1273	<	} else {
1274	<	// throw error
1275	<	sprintf( painCave.errMsg,
1276	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1277	<	"\t(Input file specified %s .)\n"
1278	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1279	<	"or \"damped\".\n", myScreen.c_str() );
1280	<	painCave.isFatal = 1;
1281	<	simError();
1282	<	}
1283	<	}
1284	<	}
1285	<
1286	<	// let's pass some summation method variables to fortran
1287	<	setElectrostaticSummationMethod( &esm );
1288	<	setFortranElectrostaticMethod( &esm );
1289	<	setScreeningMethod( &sm );
1290	<	setDampingAlpha( &alphaVal );
1291	<	setReactionFieldDielectric( &dielectric );
1292	<	initFortranFF( &errorOut );
1293	<	}
1294	<
1295	<	void SimInfo::setupSwitchingFunction() {
1296	<	int ft = CUBIC;
1297	<
1298	<	if (simParams_->haveSwitchingFunctionType()) {
1299	<	std::string funcType = simParams_->getSwitchingFunctionType();
1300	<	toUpper(funcType);
1301	<	if (funcType == "CUBIC") {
1302	<	ft = CUBIC;
1303	<	} else {
1304	<	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1305	<	ft = FIFTH_ORDER_POLY;
1306	<	} else {
1307	<	// throw error
1308	<	sprintf( painCave.errMsg,
1309	<	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1310	<	painCave.isFatal = 1;
1311	<	simError();
1312	<	}
1313	<	}
1314	<	}
1315	<
1316	<	// send switching function notification to switcheroo
1317	<	setFunctionType(&ft);
1318	<
1319	<	}
1320	<
1321	<	void SimInfo::setupAccumulateBoxDipole() {
1322	<
1323	<	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1324	<	if ( simParams_->haveAccumulateBoxDipole() )
1325	<	if ( simParams_->getAccumulateBoxDipole() ) {
1326	<	setAccumulateBoxDipole();
1327	<	calcBoxDipole_ = true;
1328	<	}
1329	<
1330	<	}
1331	<
1332	<	void SimInfo::addProperty(GenericData* genData) {
1333	<	properties_.addProperty(genData);
1334	<	}
1335	<
1336	<	void SimInfo::removeProperty(const std::string& propName) {
1337	<	properties_.removeProperty(propName);
1338	<	}
1339	<
1340	<	void SimInfo::clearProperties() {
1341	<	properties_.clearProperties();
1342	<	}
1343	<
1344	<	std::vector<std::string> SimInfo::getPropertyNames() {
1345	<	return properties_.getPropertyNames();
1346	<	}
1347	<
1348	<	std::vector<GenericData*> SimInfo::getProperties() {
1349	<	return properties_.getProperties();
1350	<	}
1351	<
1352	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
967	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
968		return properties_.getPropertyByName(propName);
969		}
970
#	Line 1363 | Line 978 | namespace oopse {
978		Molecule* mol;
979		RigidBody* rb;
980		Atom* atom;
981	+	CutoffGroup* cg;
982		SimInfo::MoleculeIterator mi;
983		Molecule::RigidBodyIterator rbIter;
984	<	Molecule::AtomIterator atomIter;;
984	>	Molecule::AtomIterator atomIter;
985	>	Molecule::CutoffGroupIterator cgIter;
986
987		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
988
989	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
989	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
990	>	atom = mol->nextAtom(atomIter)) {
991		atom->setSnapshotManager(sman_);
992		}
993
994	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
994	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
995	>	rb = mol->nextRigidBody(rbIter)) {
996		rb->setSnapshotManager(sman_);
997		}
998	+
999	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1000	+	cg = mol->nextCutoffGroup(cgIter)) {
1001	+	cg->setSnapshotManager(sman_);
1002	+	}
1003		}
1004
1005		}
1006
1383	–	Vector3d SimInfo::getComVel(){
1384	–	SimInfo::MoleculeIterator i;
1385	–	Molecule* mol;
1007
1008	<	Vector3d comVel(0.0);
1388	<	RealType totalMass = 0.0;
1389	<
1390	<
1391	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1392	<	RealType mass = mol->getMass();
1393	<	totalMass += mass;
1394	<	comVel += mass * mol->getComVel();
1395	<	}
1008	>	ostream& operator <<(ostream& o, SimInfo& info) {
1009
1397	–	#ifdef IS_MPI
1398	–	RealType tmpMass = totalMass;
1399	–	Vector3d tmpComVel(comVel);
1400	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1401	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1402	–	#endif
1403	–
1404	–	comVel /= totalMass;
1405	–
1406	–	return comVel;
1407	–	}
1408	–
1409	–	Vector3d SimInfo::getCom(){
1410	–	SimInfo::MoleculeIterator i;
1411	–	Molecule* mol;
1412	–
1413	–	Vector3d com(0.0);
1414	–	RealType totalMass = 0.0;
1415	–
1416	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1417	–	RealType mass = mol->getMass();
1418	–	totalMass += mass;
1419	–	com += mass * mol->getCom();
1420	–	}
1421	–
1422	–	#ifdef IS_MPI
1423	–	RealType tmpMass = totalMass;
1424	–	Vector3d tmpCom(com);
1425	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1426	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1427	–	#endif
1428	–
1429	–	com /= totalMass;
1430	–
1431	–	return com;
1432	–
1433	–	}
1434	–
1435	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1436	–
1010		return o;
1011		}
1012
1013	<
1441	<	/*
1442	<	Returns center of mass and center of mass velocity in one function call.
1443	<	*/
1444	<
1445	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1446	<	SimInfo::MoleculeIterator i;
1447	<	Molecule* mol;
1448	<
1449	<
1450	<	RealType totalMass = 0.0;
1451	<
1452	<
1453	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1454	<	RealType mass = mol->getMass();
1455	<	totalMass += mass;
1456	<	com += mass * mol->getCom();
1457	<	comVel += mass * mol->getComVel();
1458	<	}
1459	<
1460	<	#ifdef IS_MPI
1461	<	RealType tmpMass = totalMass;
1462	<	Vector3d tmpCom(com);
1463	<	Vector3d tmpComVel(comVel);
1464	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1465	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1466	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1467	<	#endif
1468	<
1469	<	com /= totalMass;
1470	<	comVel /= totalMass;
1471	<	}
1472	<
1473	<	/*
1474	<	Return intertia tensor for entire system and angular momentum Vector.
1475	<
1476	<
1477	<	[  Ixx -Ixy  -Ixz ]
1478	<	J =| -Iyx  Iyy  -Iyz |
1479	<	[ -Izx -Iyz   Izz ]
1480	<	*/
1481	<
1482	<	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1483	<
1484	<
1485	<	RealType xx = 0.0;
1486	<	RealType yy = 0.0;
1487	<	RealType zz = 0.0;
1488	<	RealType xy = 0.0;
1489	<	RealType xz = 0.0;
1490	<	RealType yz = 0.0;
1491	<	Vector3d com(0.0);
1492	<	Vector3d comVel(0.0);
1493	<
1494	<	getComAll(com, comVel);
1495	<
1496	<	SimInfo::MoleculeIterator i;
1497	<	Molecule* mol;
1498	<
1499	<	Vector3d thisq(0.0);
1500	<	Vector3d thisv(0.0);
1501	<
1502	<	RealType thisMass = 0.0;
1503	<
1504	<
1505	<
1506	<
1507	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1508	<
1509	<	thisq = mol->getCom()-com;
1510	<	thisv = mol->getComVel()-comVel;
1511	<	thisMass = mol->getMass();
1512	<	// Compute moment of intertia coefficients.
1513	<	xx += thisq[0]*thisq[0]*thisMass;
1514	<	yy += thisq[1]*thisq[1]*thisMass;
1515	<	zz += thisq[2]*thisq[2]*thisMass;
1516	<
1517	<	// compute products of intertia
1518	<	xy += thisq[0]*thisq[1]*thisMass;
1519	<	xz += thisq[0]*thisq[2]*thisMass;
1520	<	yz += thisq[1]*thisq[2]*thisMass;
1521	<
1522	<	angularMomentum += cross( thisq, thisv ) * thisMass;
1523	<
1524	<	}
1525	<
1526	<
1527	<	inertiaTensor(0,0) = yy + zz;
1528	<	inertiaTensor(0,1) = -xy;
1529	<	inertiaTensor(0,2) = -xz;
1530	<	inertiaTensor(1,0) = -xy;
1531	<	inertiaTensor(1,1) = xx + zz;
1532	<	inertiaTensor(1,2) = -yz;
1533	<	inertiaTensor(2,0) = -xz;
1534	<	inertiaTensor(2,1) = -yz;
1535	<	inertiaTensor(2,2) = xx + yy;
1536	<
1537	<	#ifdef IS_MPI
1538	<	Mat3x3d tmpI(inertiaTensor);
1539	<	Vector3d tmpAngMom;
1540	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1541	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1542	<	#endif
1543	<
1544	<	return;
1545	<	}
1546	<
1547	<	//Returns the angular momentum of the system
1548	<	Vector3d SimInfo::getAngularMomentum(){
1549	<
1550	<	Vector3d com(0.0);
1551	<	Vector3d comVel(0.0);
1552	<	Vector3d angularMomentum(0.0);
1553	<
1554	<	getComAll(com,comVel);
1555	<
1556	<	SimInfo::MoleculeIterator i;
1557	<	Molecule* mol;
1558	<
1559	<	Vector3d thisr(0.0);
1560	<	Vector3d thisp(0.0);
1561	<
1562	<	RealType thisMass;
1563	<
1564	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1565	<	thisMass = mol->getMass();
1566	<	thisr = mol->getCom()-com;
1567	<	thisp = (mol->getComVel()-comVel)*thisMass;
1568	<
1569	<	angularMomentum += cross( thisr, thisp );
1570	<
1571	<	}
1572	<
1573	<	#ifdef IS_MPI
1574	<	Vector3d tmpAngMom;
1575	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1576	<	#endif
1577	<
1578	<	return angularMomentum;
1579	<	}
1580	<
1013	>
1014		StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1015	<	return IOIndexToIntegrableObject.at(index);
1015	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1016	>	sprintf(painCave.errMsg,
1017	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1018	>	"\tindex exceeds number of known objects!\n");
1019	>	painCave.isFatal = 1;
1020	>	simError();
1021	>	return NULL;
1022	>	} else
1023	>	return IOIndexToIntegrableObject.at(index);
1024		}
1025
1026	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1026	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1027		IOIndexToIntegrableObject= v;
1028		}
1029
1030	<	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1031	<	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1032	<	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1033	<	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1034	<	*/
1035	<	void SimInfo::getGyrationalVolume(RealType &volume){
1036	<	Mat3x3d intTensor;
1037	<	RealType det;
1038	<	Vector3d dummyAngMom;
1598	<	RealType sysconstants;
1599	<	RealType geomCnst;
1600	<
1601	<	geomCnst = 3.0/2.0;
1602	<	/* Get the inertial tensor and angular momentum for free*/
1603	<	getInertiaTensor(intTensor,dummyAngMom);
1604	<
1605	<	det = intTensor.determinant();
1606	<	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1607	<	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1608	<	return;
1030	>	int SimInfo::getNGlobalConstraints() {
1031	>	int nGlobalConstraints;
1032	>	#ifdef IS_MPI
1033	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1034	>	MPI::INT, MPI::SUM);
1035	>	#else
1036	>	nGlobalConstraints =  nConstraints_;
1037	>	#endif
1038	>	return nGlobalConstraints;
1039		}
1040
1041	<	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1612	<	Mat3x3d intTensor;
1613	<	Vector3d dummyAngMom;
1614	<	RealType sysconstants;
1615	<	RealType geomCnst;
1041	>	}//end namespace OpenMD
1042
1617	–	geomCnst = 3.0/2.0;
1618	–	/* Get the inertial tensor and angular momentum for free*/
1619	–	getInertiaTensor(intTensor,dummyAngMom);
1620	–
1621	–	detI = intTensor.determinant();
1622	–	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1623	–	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1624	–	return;
1625	–	}
1626	–	/*
1627	–	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1628	–	assert( v.size() == nAtoms_ + nRigidBodies_);
1629	–	sdByGlobalIndex_ = v;
1630	–	}
1631	–
1632	–	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1633	–	//assert(index < nAtoms_ + nRigidBodies_);
1634	–	return sdByGlobalIndex_.at(index);
1635	–	}
1636	–	*/
1637	–	}//end namespace oopse
1638	–

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 1386 by gezelter, Fri Oct 23 18:41:09 2009 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

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