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Stream Class Reference

Streamlined, abstract grid generation class. More...

Public Member Functions

bool saveToFile (const char *fname, int noOfThreads)
 Generates the grid and saves it to the file with given name. More...
 
 Stream (ActiveBfShells &abs, RadialScheme *rs, real radint, int angmin, int angmax, real boxSize, bool forceCubic)
 The Stream constructor. More...
 
 ~Stream ()
 
unsigned getPointCount () const
 

Public Attributes

real boxSize
 
Dft::SparsePattern * sparsePattern
 

Protected Member Functions

bool saveAtomsRecursively (StreamSaveContext &ssc, const Box &box, unsigned cnt, const unsigned atoms[], int depth) const
 This is a recursive procedure that generates the grid points that lie in the specified bounding box. More...
 
unsigned saveAtomGridInBox (unsigned iAtom, const Box &box, BoxPartitioner &partitioner, unsigned cnt, const unsigned atoms[], int(*shlBlocks)[2], FILE *stream) const
 Method saves all grid points associated with specified atom, located in the specified box. More...
 
unsigned noOfAtoms () const
 
const AtomicGridgetAtomicGrid (unsigned i) const
 
void addAtom (const real coor[3], int charge, int atomNo)
 
void addAtom (const Atom &at, int atomNo)
 
unsigned saveBatch (unsigned batchLength, real(*coor)[3], real *weight, unsigned nBlocks, int(*shlBlocks)[2], FILE *f) const
 Saves a batch of grid points to given file. More...
 

Static Protected Member Functions

static void * saveThread (void *data)
 

Protected Attributes

bool forceCubic
 

Private Attributes

std::vector< RadialGrid * > atomTypes
 We store just one entry per atom type - there is no reason to have thousands identical copies. More...
 
std::vector< AtomicGridatoms
 
ActiveBfShellsactiveShells
 
RadialSchemeradialScheme
 
real radialThreshold
 
int angularMin
 
int angularMax
 
unsigned savedPoints
 
unsigned expectedPoints
 
int noOfThreads
 

Static Private Attributes

static pthread_mutex_t fileSaveMutex = PTHREAD_MUTEX_INITIALIZER
 

Detailed Description

Streamlined, abstract grid generation class.

This class does not depend explicitly on the representation of the basis set and molecule. All such dependence is abstracted away in case the grid generator is to be used with another program.

Constructor & Destructor Documentation

Stream::Stream ( ActiveBfShells abs,
RadialScheme rs,
real  radint,
int  angmin,
int  angmax,
real  boxSize_,
bool  forceCubic_ 
)

The Stream constructor.

Takes over the radial scheme object, which has to be allocated dynamically.

Member Function Documentation

void Stream::addAtom ( const real  coor[3],
int  charge,
int  atomNo 
)
protected
void Stream::addAtom ( const Atom at,
int  atomNo 
)
inlineprotected
const AtomicGrid & Stream::getAtomicGrid ( unsigned  i) const
protected
unsigned Stream::getPointCount ( ) const
inline
unsigned Stream::noOfAtoms ( ) const
inlineprotected
unsigned Stream::saveAtomGridInBox ( unsigned  iAtom,
const Box box,
BoxPartitioner partitioner,
unsigned  cnt,
const unsigned  relevantAtoms[],
int(*)  shlBlocks[2],
FILE *  stream 
) const
protected

Method saves all grid points associated with specified atom, located in the specified box.

It will also save the associated auxiliary information (usually a list of active orbitals) - this is why we pass an atom list. FIXME: this probably needs to be thought through: what factor decides the atom radius, really? Is it max(auxiliaryRadius, gridRadius)?

References AtomicGrid::center, Box::contains(), BoxPartitioner::coor, Box::getDistanceTo(), AtomicGrid::getRadialGrid(), Box::hi, ll_sphere(), Box::lo, RadialGrid::nAngular, RadialGrid::noOfRadPoints, BoxPartitioner::process(), RadialGrid::rad, Vector3D::v, and RadialGrid::weights.

bool Stream::saveAtomsRecursively ( StreamSaveContext ssc,
const Box box,
unsigned  atomCount,
const unsigned  atomIndices[],
int  depth 
) const
protected

This is a recursive procedure that generates the grid points that lie in the specified bounding box.

As an optimization, a list of atoms that may overlap with given grid is passed so that linear scaling can be achieved. This goal is achieved by recursive division of the bounding box until there are no atoms that can overlap with it, or the minimal size is achieved. In the latter case, all atoms are iterated over and the grid points associated with them that lie in the bounding box are saved. An associated auxiliary information is saved as well.

An atom is considered relevant for given box, if its Voronoi polyhedra (+safety margin) overlaps with the box.

Parameters
sscthe saving context containing information about selected partitioner and other grid generation specifics.
boxsave only the points within the box.
atomCountthe number of potentially relevant atoms that have grids overlapping with the box in question..
atomIndices... and their indices in the global array.
depththe recursion depth for logging purposes.

randomly chosen parameter. We need in general a better way to determing whether the voronoi polyhedra associated with a given atom overlaps with the box in question...

References StreamSaveContext::boxCount, AtomicGrid::center, Box::getMaxDim(), Box::hi, Box::lo, StreamSaveContext::myRank, Box::overlapsWith(), StreamSaveContext::partitioner, AtomicGrid::radius(), StreamSaveContext::savedPoints, StreamSaveContext::shlBlocks, Box::size(), StreamSaveContext::stream, and Vector3D::v.

Referenced by saveThread().

unsigned Stream::saveBatch ( unsigned  batchLength,
real(*)  coor[3],
real weight,
unsigned  nBlocks,
int(*)  shlBlocks[2],
FILE *  f 
) const
protected

Saves a batch of grid points to given file.

References BoxPartitioner::coor.

bool Stream::saveToFile ( const char *  fname,
int  noOfThreads 
)

Generates the grid and saves it to the file with given name.

Returns
Number of saved grid points.

References getBoundingBox(), Box::hi, and Box::lo.

Member Data Documentation

ActiveBfShells& Stream::activeShells
private

Referenced by saveThread().

int Stream::angularMax
private
int Stream::angularMin
private
std::vector<AtomicGrid> Stream::atoms
private
std::vector<RadialGrid*> Stream::atomTypes
private

We store just one entry per atom type - there is no reason to have thousands identical copies.

Referenced by ~Stream().

real Stream::boxSize
unsigned Stream::expectedPoints
private

Referenced by ~Stream().

pthread_mutex_t Stream::fileSaveMutex = PTHREAD_MUTEX_INITIALIZER
staticprivate
bool Stream::forceCubic
protected
int Stream::noOfThreads
private
RadialScheme* Stream::radialScheme
private

Referenced by ~Stream().

real Stream::radialThreshold
private
unsigned Stream::savedPoints
private

Referenced by ~Stream().

Dft::SparsePattern* Stream::sparsePattern

The documentation for this class was generated from the following file: