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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 1386 by gezelter, Fri Oct 23 18:41:09 2009 UTC vs.
Revision 1987 by gezelter, Thu Apr 17 19:07:31 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>
#	Line 54 | Line 58
58		#include "math/Vector3.hpp"
59		#include "primitives/Molecule.hpp"
60		#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"
61		#include "utils/MemoryUtils.hpp"
62		#include "utils/simError.h"
63		#include "selection/SelectionManager.hpp"
64		#include "io/ForceFieldOptions.hpp"
65	<	#include "UseTheForce/ForceField.hpp"
65	>	#include "brains/ForceField.hpp"
66	>	#include "nonbonded/SwitchingFunction.hpp"
67
68	<
69	<	#ifdef IS_MPI
73	<	#include "UseTheForce/mpiComponentPlan.h"
74	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
75	<	#endif
76	<
77	<	namespace oopse {
78	<	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),
76	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	>	nGlobalFluctuatingCharges_(0), nGlobalBonds_(0), nGlobalBends_(0),
77	>	nGlobalTorsions_(0), nGlobalInversions_(0), nGlobalConstraints_(0),
78	>	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0),
79		nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
80	<	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
81	<	calcBoxDipole_(false), useAtomicVirial_(true) {
80	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL),
81	>	topologyDone_(false), calcBoxDipole_(false), useAtomicVirial_(true),
82	>	hasNGlobalConstraints_(false) {
83	>
84	>	MoleculeStamp* molStamp;
85	>	int nMolWithSameStamp;
86	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
88	>	CutoffGroupStamp* cgStamp;
89	>	RigidBodyStamp* rbStamp;
90	>	int nRigidAtoms = 0;
91	>
92	>	vector<Component*> components = simParams->getComponents();
93	>
94	>	for (vector<Component*>::iterator i = components.begin();
95	>	i !=components.end(); ++i) {
96	>	molStamp = (*i)->getMoleculeStamp();
97	>	if ( (*i)->haveRegion() ) {
98	>	molStamp->setRegion( (*i)->getRegion() );
99	>	} else {
100	>	// set the region to a disallowed value:
101	>	molStamp->setRegion( -1 );
102	>	}
103
104	<
99	<	MoleculeStamp* molStamp;
100	<	int nMolWithSameStamp;
101	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
102	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
103	<	CutoffGroupStamp* cgStamp;
104	<	RigidBodyStamp* rbStamp;
105	<	int nRigidAtoms = 0;
106	<
107	<	std::vector<Component*> components = simParams->getComponents();
104	>	nMolWithSameStamp = (*i)->getNMol();
105
106	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
107	<	molStamp = (*i)->getMoleculeStamp();
108	<	nMolWithSameStamp = (*i)->getNMol();
109	<
110	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
111	<
112	<	//calculate atoms in molecules
113	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
114	<
115	<	//calculate atoms in cutoff groups
116	<	int nAtomsInGroups = 0;
117	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
118	<
119	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
120	<	cgStamp = molStamp->getCutoffGroupStamp(j);
121	<	nAtomsInGroups += cgStamp->getNMembers();
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	<
106	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
107	>
108	>	//calculate atoms in molecules
109	>	nGlobalAtoms_ += molStamp->getNAtoms() * nMolWithSameStamp;
110	>	nGlobalBonds_ += molStamp->getNBonds() * nMolWithSameStamp;
111	>	nGlobalBends_ += molStamp->getNBends() * nMolWithSameStamp;
112	>	nGlobalTorsions_ += molStamp->getNTorsions() * nMolWithSameStamp;
113	>	nGlobalInversions_ += molStamp->getNInversions() * nMolWithSameStamp;
114	>
115	>	//calculate atoms in cutoff groups
116	>	int nAtomsInGroups = 0;
117	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
118	>
119	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
120	>	cgStamp = molStamp->getCutoffGroupStamp(j);
121	>	nAtomsInGroups += cgStamp->getNMembers();
122		}
123	<
124	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
125	<	//group therefore the total number of cutoff groups in the system is
126	<	//equal to the total number of atoms minus number of atoms belong to
127	<	//cutoff group defined in meta-data file plus the number of cutoff
128	<	//groups defined in meta-data file
129	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
130	<
131	<	//every free atom (atom does not belong to rigid bodies) is an
132	<	//integrable object therefore the total number of integrable objects
133	<	//in the system is equal to the total number of atoms minus number of
134	<	//atoms belong to rigid body defined in meta-data file plus the number
135	<	//of rigid bodies defined in meta-data file
136	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
137	<	+ nGlobalRigidBodies_;
138	<
139	<	nGlobalMols_ = molStampIds_.size();
161	<	molToProcMap_.resize(nGlobalMols_);
123	>
124	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
125	>
126	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
127	>
128	>	//calculate atoms in rigid bodies
129	>	int nAtomsInRigidBodies = 0;
130	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
131	>
132	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
133	>	rbStamp = molStamp->getRigidBodyStamp(j);
134	>	nAtomsInRigidBodies += rbStamp->getNMembers();
135	>	}
136	>
137	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
138	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
139	>
140		}
141	+
142	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
143	+	//group therefore the total number of cutoff groups in the system is
144	+	//equal to the total number of atoms minus number of atoms belong to
145	+	//cutoff group defined in meta-data file plus the number of cutoff
146	+	//groups defined in meta-data file
147
148	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
149	+
150	+	//every free atom (atom does not belong to rigid bodies) is an
151	+	//integrable object therefore the total number of integrable objects
152	+	//in the system is equal to the total number of atoms minus number of
153	+	//atoms belong to rigid body defined in meta-data file plus the number
154	+	//of rigid bodies defined in meta-data file
155	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
156	+	+ nGlobalRigidBodies_;
157	+
158	+	nGlobalMols_ = molStampIds_.size();
159	+	molToProcMap_.resize(nGlobalMols_);
160	+	}
161	+
162		SimInfo::~SimInfo() {
163	<	std::map<int, Molecule*>::iterator i;
163	>	map<int, Molecule*>::iterator i;
164		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
165		delete i->second;
166		}
#	Line 173 | Line 171 | namespace oopse {
171		delete forceField_;
172		}
173
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	–	}
174
175		bool SimInfo::addMolecule(Molecule* mol) {
176		MoleculeIterator i;
177	<
177	>
178		i = molecules_.find(mol->getGlobalIndex());
179		if (i == molecules_.end() ) {
180	<
181	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
182	<
180	>
181	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
182	>
183		nAtoms_ += mol->getNAtoms();
184		nBonds_ += mol->getNBonds();
185		nBends_ += mol->getNBends();
#	Line 201 | Line 189 | namespace oopse {
189		nIntegrableObjects_ += mol->getNIntegrableObjects();
190		nCutoffGroups_ += mol->getNCutoffGroups();
191		nConstraints_ += mol->getNConstraintPairs();
192	<
192	>
193		addInteractionPairs(mol);
194	<
194	>
195		return true;
196		} else {
197		return false;
198		}
199		}
200	<
200	>
201		bool SimInfo::removeMolecule(Molecule* mol) {
202		MoleculeIterator i;
203		i = molecules_.find(mol->getGlobalIndex());
#	Line 237 | Line 225 | namespace oopse {
225		} else {
226		return false;
227		}
240	–
241	–
228		}
229
230
#	Line 254 | Line 240 | namespace oopse {
240
241
242		void SimInfo::calcNdf() {
243	<	int ndf_local;
243	>	int ndf_local, nfq_local;
244		MoleculeIterator i;
245	<	std::vector<StuntDouble*>::iterator j;
245	>	vector<StuntDouble*>::iterator j;
246	>	vector<Atom*>::iterator k;
247	>
248		Molecule* mol;
249	<	StuntDouble* integrableObject;
249	>	StuntDouble* sd;
250	>	Atom* atom;
251
252		ndf_local = 0;
253	+	nfq_local = 0;
254
255		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
266	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
267	–	integrableObject = mol->nextIntegrableObject(j)) {
256
257	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
258	+	sd = mol->nextIntegrableObject(j)) {
259	+
260		ndf_local += 3;
261
262	<	if (integrableObject->isDirectional()) {
263	<	if (integrableObject->isLinear()) {
262	>	if (sd->isDirectional()) {
263	>	if (sd->isLinear()) {
264		ndf_local += 2;
265		} else {
266		ndf_local += 3;
267		}
268		}
278	–
269		}
270	+
271	+	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
272	+	atom = mol->nextFluctuatingCharge(k)) {
273	+	if (atom->isFluctuatingCharge()) {
274	+	nfq_local++;
275	+	}
276	+	}
277		}
278
279	+	ndfLocal_ = ndf_local;
280	+
281		// n_constraints is local, so subtract them on each processor
282		ndf_local -= nConstraints_;
283
284		#ifdef IS_MPI
285	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
285	>	MPI_Allreduce(&ndf_local, &ndf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
286	>	MPI_Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
287	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
288		#else
289		ndf_ = ndf_local;
290	+	nGlobalFluctuatingCharges_ = nfq_local;
291		#endif
292
293		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 296 | Line 298 | namespace oopse {
298
299		int SimInfo::getFdf() {
300		#ifdef IS_MPI
301	<	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
301	>	MPI_Allreduce(&fdf_local, &fdf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
302		#else
303		fdf_ = fdf_local;
304		#endif
305		return fdf_;
306		}
307	+
308	+	unsigned int SimInfo::getNLocalCutoffGroups(){
309	+	int nLocalCutoffAtoms = 0;
310	+	Molecule* mol;
311	+	MoleculeIterator mi;
312	+	CutoffGroup* cg;
313	+	Molecule::CutoffGroupIterator ci;
314
315	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
316	+
317	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
318	+	cg = mol->nextCutoffGroup(ci)) {
319	+	nLocalCutoffAtoms += cg->getNumAtom();
320	+
321	+	}
322	+	}
323	+
324	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
325	+	}
326	+
327		void SimInfo::calcNdfRaw() {
328		int ndfRaw_local;
329
330		MoleculeIterator i;
331	<	std::vector<StuntDouble*>::iterator j;
331	>	vector<StuntDouble*>::iterator j;
332		Molecule* mol;
333	<	StuntDouble* integrableObject;
333	>	StuntDouble* sd;
334
335		// Raw degrees of freedom that we have to set
336		ndfRaw_local = 0;
337
338		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
318	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
319	–	integrableObject = mol->nextIntegrableObject(j)) {
339
340	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
341	+	sd = mol->nextIntegrableObject(j)) {
342	+
343		ndfRaw_local += 3;
344
345	<	if (integrableObject->isDirectional()) {
346	<	if (integrableObject->isLinear()) {
345	>	if (sd->isDirectional()) {
346	>	if (sd->isLinear()) {
347		ndfRaw_local += 2;
348		} else {
349		ndfRaw_local += 3;
#	Line 332 | Line 354 | namespace oopse {
354		}
355
356		#ifdef IS_MPI
357	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
357	>	MPI_Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
358		#else
359		ndfRaw_ = ndfRaw_local;
360		#endif
#	Line 342 | Line 364 | namespace oopse {
364		int ndfTrans_local;
365
366		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
345	–
367
368		#ifdef IS_MPI
369	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
369	>	MPI_Allreduce(&ndfTrans_local, &ndfTrans_, 1, MPI_INT, MPI_SUM,
370	>	MPI_COMM_WORLD);
371		#else
372		ndfTrans_ = ndfTrans_local;
373		#endif
374
375		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
354	–
376		}
377
378		void SimInfo::addInteractionPairs(Molecule* mol) {
379		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
380	<	std::vector<Bond*>::iterator bondIter;
381	<	std::vector<Bend*>::iterator bendIter;
382	<	std::vector<Torsion*>::iterator torsionIter;
383	<	std::vector<Inversion*>::iterator inversionIter;
380	>	vector<Bond*>::iterator bondIter;
381	>	vector<Bend*>::iterator bendIter;
382	>	vector<Torsion*>::iterator torsionIter;
383	>	vector<Inversion*>::iterator inversionIter;
384		Bond* bond;
385		Bend* bend;
386		Torsion* torsion;
#	Line 377 | Line 398 | namespace oopse {
398		// always be excluded.  These are done at the bottom of this
399		// function.
400
401	<	std::map<int, std::set<int> > atomGroups;
401	>	map<int, set<int> > atomGroups;
402		Molecule::RigidBodyIterator rbIter;
403		RigidBody* rb;
404		Molecule::IntegrableObjectIterator ii;
405	<	StuntDouble* integrableObject;
405	>	StuntDouble* sd;
406
407	<	for (integrableObject = mol->beginIntegrableObject(ii);
408	<	integrableObject != NULL;
388	<	integrableObject = mol->nextIntegrableObject(ii)) {
407	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
408	>	sd = mol->nextIntegrableObject(ii)) {
409
410	<	if (integrableObject->isRigidBody()) {
411	<	rb = static_cast<RigidBody*>(integrableObject);
412	<	std::vector<Atom*> atoms = rb->getAtoms();
413	<	std::set<int> rigidAtoms;
410	>	if (sd->isRigidBody()) {
411	>	rb = static_cast<RigidBody*>(sd);
412	>	vector<Atom*> atoms = rb->getAtoms();
413	>	set<int> rigidAtoms;
414		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
415		rigidAtoms.insert(atoms[i]->getGlobalIndex());
416		}
417		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
418	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
418	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
419		}
420		} else {
421	<	std::set<int> oneAtomSet;
422	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
423	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
421	>	set<int> oneAtomSet;
422	>	oneAtomSet.insert(sd->getGlobalIndex());
423	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
424		}
425		}
426	+
427
428		for (bond= mol->beginBond(bondIter); bond != NULL;
429		bond = mol->nextBond(bondIter)) {
430
431		a = bond->getAtomA()->getGlobalIndex();
432		b = bond->getAtomB()->getGlobalIndex();
433	<
433	>
434		if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
435		oneTwoInteractions_.addPair(a, b);
436		} else {
#	Line 503 | Line 524 | namespace oopse {
524
525		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
526		rb = mol->nextRigidBody(rbIter)) {
527	<	std::vector<Atom*> atoms = rb->getAtoms();
527	>	vector<Atom*> atoms = rb->getAtoms();
528		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
529		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
530		a = atoms[i]->getGlobalIndex();
#	Line 517 | Line 538 | namespace oopse {
538
539		void SimInfo::removeInteractionPairs(Molecule* mol) {
540		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
541	<	std::vector<Bond*>::iterator bondIter;
542	<	std::vector<Bend*>::iterator bendIter;
543	<	std::vector<Torsion*>::iterator torsionIter;
544	<	std::vector<Inversion*>::iterator inversionIter;
541	>	vector<Bond*>::iterator bondIter;
542	>	vector<Bend*>::iterator bendIter;
543	>	vector<Torsion*>::iterator torsionIter;
544	>	vector<Inversion*>::iterator inversionIter;
545		Bond* bond;
546		Bend* bend;
547		Torsion* torsion;
#	Line 530 | Line 551 | namespace oopse {
551		int c;
552		int d;
553
554	<	std::map<int, std::set<int> > atomGroups;
554	>	map<int, set<int> > atomGroups;
555		Molecule::RigidBodyIterator rbIter;
556		RigidBody* rb;
557		Molecule::IntegrableObjectIterator ii;
558	<	StuntDouble* integrableObject;
558	>	StuntDouble* sd;
559
560	<	for (integrableObject = mol->beginIntegrableObject(ii);
561	<	integrableObject != NULL;
541	<	integrableObject = mol->nextIntegrableObject(ii)) {
560	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
561	>	sd = mol->nextIntegrableObject(ii)) {
562
563	<	if (integrableObject->isRigidBody()) {
564	<	rb = static_cast<RigidBody*>(integrableObject);
565	<	std::vector<Atom*> atoms = rb->getAtoms();
566	<	std::set<int> rigidAtoms;
563	>	if (sd->isRigidBody()) {
564	>	rb = static_cast<RigidBody*>(sd);
565	>	vector<Atom*> atoms = rb->getAtoms();
566	>	set<int> rigidAtoms;
567		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
568		rigidAtoms.insert(atoms[i]->getGlobalIndex());
569		}
570		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
571	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
571	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
572		}
573		} else {
574	<	std::set<int> oneAtomSet;
575	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
576	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
574	>	set<int> oneAtomSet;
575	>	oneAtomSet.insert(sd->getGlobalIndex());
576	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
577		}
578		}
579
#	Line 656 | Line 676 | namespace oopse {
676
677		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
678		rb = mol->nextRigidBody(rbIter)) {
679	<	std::vector<Atom*> atoms = rb->getAtoms();
679	>	vector<Atom*> atoms = rb->getAtoms();
680		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
681		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
682		a = atoms[i]->getGlobalIndex();
#	Line 679 | Line 699 | namespace oopse {
699		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
700		}
701
682	–	void SimInfo::update() {
702
703	<	setupSimType();
704	<
705	<	#ifdef IS_MPI
706	<	setupFortranParallel();
707	<	#endif
708	<
709	<	setupFortranSim();
710	<
711	<	//setup fortran force field
712	<	/** @deprecate */
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	<
703	>	/**
704	>	* update
705	>	*
706	>	*  Performs the global checks and variable settings after the
707	>	*  objects have been created.
708	>	*
709	>	*/
710	>	void SimInfo::update() {
711	>	setupSimVariables();
712	>	calcNConstraints();
713		calcNdf();
714		calcNdfRaw();
715		calcNdfTrans();
712	–
713	–	fortranInitialized_ = true;
716		}
717	<
718	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
717	>
718	>	/**
719	>	* getSimulatedAtomTypes
720	>	*
721	>	* Returns an STL set of AtomType* that are actually present in this
722	>	* simulation.  Must query all processors to assemble this information.
723	>	*
724	>	*/
725	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
726		SimInfo::MoleculeIterator mi;
727		Molecule* mol;
728		Molecule::AtomIterator ai;
729		Atom* atom;
730	<	std::set<AtomType*> atomTypes;
731	<
730	>	set<AtomType*> atomTypes;
731	>
732		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
733	<
734	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
733	>	for(atom = mol->beginAtom(ai); atom != NULL;
734	>	atom = mol->nextAtom(ai)) {
735		atomTypes.insert(atom->getAtomType());
736	<	}
737	<
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();
736	>	}
737	>	}
738
739	<	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;
739	>	#ifdef IS_MPI
740
741	<	std::string myMethod;
742	<
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	<	}
741	>	// loop over the found atom types on this processor, and add their
742	>	// numerical idents to a vector:
743
744	<	if (simParams_->haveAccumulateBoxDipole())
745	<	if (simParams_->getAccumulateBoxDipole())
746	<	useBoxDipole = 1;
744	>	vector<int> foundTypes;
745	>	set<AtomType*>::iterator i;
746	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
747	>	foundTypes.push_back( (*i)->getIdent() );
748
749	<	useAtomicVirial_ = simParams_->getUseAtomicVirial();
749	>	// count_local holds the number of found types on this processor
750	>	int count_local = foundTypes.size();
751
752	<	//loop over all of the atom types
753	<	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	<	}
752	>	int nproc;
753	>	MPI_Comm_size( MPI_COMM_WORLD, &nproc);
754
755	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
756	<	useDirectionalAtom = 1;
757	<	}
755	>	// we need arrays to hold the counts and displacement vectors for
756	>	// all processors
757	>	vector<int> counts(nproc, 0);
758	>	vector<int> disps(nproc, 0);
759
760	<	if (useCharge || useDipole) {
761	<	useElectrostatics = 1;
760	>	// fill the counts array
761	>	MPI_Allgather(&count_local, 1, MPI_INT, &counts[0],
762	>	1, MPI_INT, MPI_COMM_WORLD);
763	>
764	>	// use the processor counts to compute the displacement array
765	>	disps[0] = 0;
766	>	int totalCount = counts[0];
767	>	for (int iproc = 1; iproc < nproc; iproc++) {
768	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
769	>	totalCount += counts[iproc];
770		}
771
772	<	#ifdef IS_MPI
773	<	int temp;
772	>	// we need a (possibly redundant) set of all found types:
773	>	vector<int> ftGlobal(totalCount);
774	>
775	>	// now spray out the foundTypes to all the other processors:
776	>	MPI_Allgatherv(&foundTypes[0], count_local, MPI_INT,
777	>	&ftGlobal[0], &counts[0], &disps[0],
778	>	MPI_INT, MPI_COMM_WORLD);
779
780	<	temp = usePBC;
814	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
780	>	vector<int>::iterator j;
781
782	<	temp = useDirectionalAtom;
783	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
782	>	// foundIdents is a stl set, so inserting an already found ident
783	>	// will have no effect.
784	>	set<int> foundIdents;
785
786	<	temp = useLennardJones;
787	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
786	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
787	>	foundIdents.insert((*j));
788	>
789	>	// now iterate over the foundIdents and get the actual atom types
790	>	// that correspond to these:
791	>	set<int>::iterator it;
792	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
793	>	atomTypes.insert( forceField_->getAtomType((*it)) );
794	>
795	>	#endif
796
797	<	temp = useElectrostatics;
798	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
797	>	return atomTypes;
798	>	}
799
825	–	temp = useCharge;
826	–	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
800
801	<	temp = useDipole;
802	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
801	>	int getGlobalCountOfType(AtomType* atype) {
802	>	/*
803	>	set<AtomType*> atypes = getSimulatedAtomTypes();
804	>	map<AtomType*, int> counts_;
805
806	<	temp = useSticky;
807	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
806	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
807	>	for(atom = mol->beginAtom(ai); atom != NULL;
808	>	atom = mol->nextAtom(ai)) {
809	>	atom->getAtomType();
810	>	}
811	>	}
812	>	*/
813	>	return 0;
814	>	}
815
816	<	temp = useStickyPower;
817	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816	>	void SimInfo::setupSimVariables() {
817	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
818	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
819	>	// parameter is true
820	>	calcBoxDipole_ = false;
821	>	if ( simParams_->haveAccumulateBoxDipole() )
822	>	if ( simParams_->getAccumulateBoxDipole() ) {
823	>	calcBoxDipole_ = true;
824	>	}
825
826	<	temp = useGayBerne;
827	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
826	>	set<AtomType*>::iterator i;
827	>	set<AtomType*> atomTypes;
828	>	atomTypes = getSimulatedAtomTypes();
829	>	bool usesElectrostatic = false;
830	>	bool usesMetallic = false;
831	>	bool usesDirectional = false;
832	>	bool usesFluctuatingCharges =  false;
833	>	//loop over all of the atom types
834	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
835	>	usesElectrostatic |= (*i)->isElectrostatic();
836	>	usesMetallic |= (*i)->isMetal();
837	>	usesDirectional |= (*i)->isDirectional();
838	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
839	>	}
840
841	<	temp = useEAM;
842	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
841	>	#ifdef IS_MPI
842	>	int temp;
843
844	<	temp = useSC;
845	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
844	>	temp = usesDirectional;
845	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
846	>	usesDirectionalAtoms_ = (temp == 0) ? false : true;
847
848	<	temp = useShape;
849	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
848	>	temp = usesMetallic;
849	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
850	>	usesMetallicAtoms_ = (temp == 0) ? false : true;
851
852	<	temp = useFLARB;
853	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
852	>	temp = usesElectrostatic;
853	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
854	>	usesElectrostaticAtoms_ = (temp == 0) ? false : true;
855
856	<	temp = useRF;
857	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
856	>	temp = usesFluctuatingCharges;
857	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
858	>	usesFluctuatingCharges_ = (temp == 0) ? false : true;
859	>	#else
860
861	<	temp = useSF;
862	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
861	>	usesDirectionalAtoms_ = usesDirectional;
862	>	usesMetallicAtoms_ = usesMetallic;
863	>	usesElectrostaticAtoms_ = usesElectrostatic;
864	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
865
866	<	temp = useSP;
867	<	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
866	>	#endif
867	>
868	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
869	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
870	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
871	>	}
872
861	–	temp = useBoxDipole;
862	–	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
873
874	<	temp = useAtomicVirial_;
875	<	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
874	>	vector<int> SimInfo::getGlobalAtomIndices() {
875	>	SimInfo::MoleculeIterator mi;
876	>	Molecule* mol;
877	>	Molecule::AtomIterator ai;
878	>	Atom* atom;
879
880	<	#endif
881	<
882	<	fInfo_.SIM_uses_PBC = usePBC;
883	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
884	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
885	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
886	<	fInfo_.SIM_uses_Charges = useCharge;
887	<	fInfo_.SIM_uses_Dipoles = useDipole;
888	<	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_;
880	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
881	>
882	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
883	>
884	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
885	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
886	>	}
887	>	}
888	>	return GlobalAtomIndices;
889		}
890
889	–	void SimInfo::setupFortranSim() {
890	–	int isError;
891	–	int nExclude, nOneTwo, nOneThree, nOneFour;
892	–	std::vector<int> fortranGlobalGroupMembership;
893	–
894	–	isError = 0;
891
892	<	//globalGroupMembership_ is filled by SimCreator
893	<	for (int i = 0; i < nGlobalAtoms_; i++) {
894	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
892	>	vector<int> SimInfo::getGlobalGroupIndices() {
893	>	SimInfo::MoleculeIterator mi;
894	>	Molecule* mol;
895	>	Molecule::CutoffGroupIterator ci;
896	>	CutoffGroup* cg;
897	>
898	>	vector<int> GlobalGroupIndices;
899	>
900	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
901	>
902	>	//local index of cutoff group is trivial, it only depends on the
903	>	//order of travesing
904	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
905	>	cg = mol->nextCutoffGroup(ci)) {
906	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
907	>	}
908		}
909	+	return GlobalGroupIndices;
910	+	}
911
912	+
913	+	void SimInfo::prepareTopology() {
914	+
915		//calculate mass ratio of cutoff group
902	–	std::vector<RealType> mfact;
916		SimInfo::MoleculeIterator mi;
917		Molecule* mol;
918		Molecule::CutoffGroupIterator ci;
#	Line 908 | Line 921 | namespace oopse {
921		Atom* atom;
922		RealType totalMass;
923
924	<	//to avoid memory reallocation, reserve enough space for mfact
925	<	mfact.reserve(getNCutoffGroups());
924	>	/**
925	>	* The mass factor is the relative mass of an atom to the total
926	>	* mass of the cutoff group it belongs to.  By default, all atoms
927	>	* are their own cutoff groups, and therefore have mass factors of
928	>	* 1.  We need some special handling for massless atoms, which
929	>	* will be treated as carrying the entire mass of the cutoff
930	>	* group.
931	>	*/
932	>	massFactors_.clear();
933	>	massFactors_.resize(getNAtoms(), 1.0);
934
935		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
936	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
936	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
937	>	cg = mol->nextCutoffGroup(ci)) {
938
939		totalMass = cg->getMass();
940		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
941		// Check for massless groups - set mfact to 1 if true
942	<	if (totalMass != 0)
943	<	mfact.push_back(atom->getMass()/totalMass);
942	>	if (totalMass != 0)
943	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
944		else
945	<	mfact.push_back( 1.0 );
945	>	massFactors_[atom->getLocalIndex()] = 1.0;
946		}
947		}
948		}
949
950	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
929	<	std::vector<int> identArray;
950	>	// Build the identArray_ and regions_
951
952	<	//to avoid memory reallocation, reserve enough space identArray
953	<	identArray.reserve(getNAtoms());
954	<
955	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
952	>	identArray_.clear();
953	>	identArray_.reserve(getNAtoms());
954	>	regions_.clear();
955	>	regions_.reserve(getNAtoms());
956	>
957	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
958	>	int reg = mol->getRegion();
959		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
960	<	identArray.push_back(atom->getIdent());
960	>	identArray_.push_back(atom->getIdent());
961	>	regions_.push_back(reg);
962		}
963		}
964	+
965	+	topologyDone_ = true;
966	+	}
967
968	<	//fill molMembershipArray
969	<	//molMembershipArray is filled by SimCreator
970	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
943	<	for (int i = 0; i < nGlobalAtoms_; i++) {
944	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
945	<	}
946	<
947	<	//setup fortran simulation
968	>	void SimInfo::addProperty(GenericData* genData) {
969	>	properties_.addProperty(genData);
970	>	}
971
972	<	nExclude = excludedInteractions_.getSize();
973	<	nOneTwo = oneTwoInteractions_.getSize();
974	<	nOneThree = oneThreeInteractions_.getSize();
952	<	nOneFour = oneFourInteractions_.getSize();
972	>	void SimInfo::removeProperty(const string& propName) {
973	>	properties_.removeProperty(propName);
974	>	}
975
976	<	int* excludeList = excludedInteractions_.getPairList();
977	<	int* oneTwoList = oneTwoInteractions_.getPairList();
978	<	int* oneThreeList = oneThreeInteractions_.getPairList();
957	<	int* oneFourList = oneFourInteractions_.getPairList();
976	>	void SimInfo::clearProperties() {
977	>	properties_.clearProperties();
978	>	}
979
980	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
981	<	&nExclude, excludeList,
982	<	&nOneTwo, oneTwoList,
962	<	&nOneThree, oneThreeList,
963	<	&nOneFour, oneFourList,
964	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
965	<	&fortranGlobalGroupMembership[0], &isError);
966	<
967	<	if( isError ){
980	>	vector<string> SimInfo::getPropertyNames() {
981	>	return properties_.getPropertyNames();
982	>	}
983
984	<	sprintf( painCave.errMsg,
985	<	"There was an error setting the simulation information in fortran.\n" );
986	<	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	<
984	>	vector<GenericData*> SimInfo::getProperties() {
985	>	return properties_.getProperties();
986	>	}
987
988	+	GenericData* SimInfo::getPropertyByName(const string& propName) {
989	+	return properties_.getPropertyByName(propName);
990		}
991
992	+	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
993	+	if (sman_ == sman) {
994	+	return;
995	+	}
996	+	delete sman_;
997	+	sman_ = sman;
998
992	–	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;
999		SimInfo::MoleculeIterator mi;
1000		Molecule::AtomIterator ai;
1001	<	Molecule::CutoffGroupIterator ci;
1001	>	Molecule::RigidBodyIterator rbIter;
1002	>	Molecule::CutoffGroupIterator cgIter;
1003	>	Molecule::BondIterator bondIter;
1004	>	Molecule::BendIterator bendIter;
1005	>	Molecule::TorsionIterator torsionIter;
1006	>	Molecule::InversionIterator inversionIter;
1007	>
1008		Molecule* mol;
1009		Atom* atom;
1010	+	RigidBody* rb;
1011		CutoffGroup* cg;
1012	<	mpiSimData parallelData;
1013	<	int isError;
1012	>	Bond* bond;
1013	>	Bend* bend;
1014	>	Torsion* torsion;
1015	>	Inversion* inversion;
1016
1017	<	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	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1018
1019	<	}
1020	<
1021	<	//fill up mpiSimData struct
1022	<	parallelData.nMolGlobal = getNGlobalMolecules();
1023	<	parallelData.nMolLocal = getNMolecules();
1024	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
1025	<	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
1046	<	}
1047	<
1048	<	void SimInfo::setupCutoff() {
1049	<
1050	<	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	<	}
1019	>	for (atom = mol->beginAtom(ai); atom != NULL;
1020	>	atom = mol->nextAtom(ai)) {
1021	>	atom->setSnapshotManager(sman_);
1022	>	}
1023	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1024	>	rb = mol->nextRigidBody(rbIter)) {
1025	>	rb->setSnapshotManager(sman_);
1026		}
1027	<	}
1028	<	notifyFortranCutoffPolicy(&cp);
1029	<
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	<	}
1027	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1028	>	cg = mol->nextCutoffGroup(cgIter)) {
1029	>	cg->setSnapshotManager(sman_);
1030		}
1031	<
1032	<	if (simParams_->haveElectrostaticSummationMethod()) {
1033	<	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	<	}
1031	>	for (bond = mol->beginBond(bondIter); bond != NULL;
1032	>	bond = mol->nextBond(bondIter)) {
1033	>	bond->setSnapshotManager(sman_);
1034		}
1035	<
1036	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1037	<
1136	<	} else {
1137	<
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	<
1035	>	for (bend = mol->beginBend(bendIter); bend != NULL;
1036	>	bend = mol->nextBend(bendIter)) {
1037	>	bend->setSnapshotManager(sman_);
1038		}
1039	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
1040	+	torsion = mol->nextTorsion(torsionIter)) {
1041	+	torsion->setSnapshotManager(sman_);
1042	+	}
1043	+	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
1044	+	inversion = mol->nextInversion(inversionIter)) {
1045	+	inversion->setSnapshotManager(sman_);
1046	+	}
1047		}
1048		}
1049
1195	–	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;
1050
1051	<	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;
1051	>	ostream& operator <<(ostream& o, SimInfo& info) {
1052
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) {
1353	–	return properties_.getPropertyByName(propName);
1354	–	}
1355	–
1356	–	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1357	–	if (sman_ == sman) {
1358	–	return;
1359	–	}
1360	–	delete sman_;
1361	–	sman_ = sman;
1362	–
1363	–	Molecule* mol;
1364	–	RigidBody* rb;
1365	–	Atom* atom;
1366	–	SimInfo::MoleculeIterator mi;
1367	–	Molecule::RigidBodyIterator rbIter;
1368	–	Molecule::AtomIterator atomIter;;
1369	–
1370	–	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1371	–
1372	–	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1373	–	atom->setSnapshotManager(sman_);
1374	–	}
1375	–
1376	–	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1377	–	rb->setSnapshotManager(sman_);
1378	–	}
1379	–	}
1380	–
1381	–	}
1382	–
1383	–	Vector3d SimInfo::getComVel(){
1384	–	SimInfo::MoleculeIterator i;
1385	–	Molecule* mol;
1386	–
1387	–	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	–	}
1396	–
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	–
1053		return o;
1054		}
1055
1056	<
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	<
1056	>
1057		StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1058	<	return IOIndexToIntegrableObject.at(index);
1058	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1059	>	sprintf(painCave.errMsg,
1060	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1061	>	"\tindex exceeds number of known objects!\n");
1062	>	painCave.isFatal = 1;
1063	>	simError();
1064	>	return NULL;
1065	>	} else
1066	>	return IOIndexToIntegrableObject.at(index);
1067		}
1068
1069	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1069	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1070		IOIndexToIntegrableObject= v;
1071		}
1072
1073	<	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1074	<	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1075	<	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1076	<	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1077	<	*/
1078	<	void SimInfo::getGyrationalVolume(RealType &volume){
1079	<	Mat3x3d intTensor;
1596	<	RealType det;
1597	<	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;
1073	>	void SimInfo::calcNConstraints() {
1074	>	#ifdef IS_MPI
1075	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints_, 1,
1076	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1077	>	#else
1078	>	nGlobalConstraints_ =  nConstraints_;
1079	>	#endif
1080		}
1081
1082	<	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1612	<	Mat3x3d intTensor;
1613	<	Vector3d dummyAngMom;
1614	<	RealType sysconstants;
1615	<	RealType geomCnst;
1082	>	}//end namespace OpenMD
1083
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.
Revision 1987 by gezelter, Thu Apr 17 19:07:31 2014 UTC

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