INTERPOLATE_GRID

Interpolate a smooth function stored on a grid onto a grid with a smaller grid spacing.

This action takes a function evaluated on a grid as input and can be used to interpolate the values of that function on to a finer grained grid. The interpolation within this algorithm is done using splines.

Examples

The input below can be used to post process a trajectory. It calculates a HISTOGRAM as a function the distance between atoms 1 and 2 using kernel density estimation. During the calculation the values of the kernels are evaluated at 100 points on a uniform grid between 0.0 and 3.0. Prior to outputting this function at the end of the simulation this function is interpolated onto a finer grid of 200 points between 0.0 and 3.0.

Click on the labels of the actions for more information on what each action computes

x: DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=1,2 The DISTANCE action with label x calculates a single scalar value
hA1: HISTOGRAM 
ARG
the input for this action is the scalar output from one or more other actions. 
=x 
GRID_MIN
compulsory keyword 
the lower bounds for the grid 
=0.0 
GRID_MAX
compulsory keyword 
the upper bounds for the grid 
=3.0 
GRID_BIN
the number of bins for the grid 
=100 
BANDWIDTH
compulsory keyword 
the bandwidths for kernel density estimation 
=0.1 The HISTOGRAM action with label hA1
ii: INTERPOLATE_GRID 
GRID
compulsory keyword 
the action that creates the input grid you would like to use 
=hA1 
GRID_BIN
the number of bins for the grid 
=200 The INTERPOLATE_GRID action with label ii
DUMPGRID 
GRID
compulsory keyword 
the action that creates the grid you would like to output 
=ii 
FILE
compulsory keyword ( default=density )
the file on which to write the grid. 
=histo.dat The DUMPGRID action with label 

Glossary of keywords and components

Compulsory keywords

STRIDE	( default=1 ) the frequency with which the data should be collected and added to the quantity being averaged
CLEAR	( default=0 ) the frequency with which to clear all the accumulated data. The default value of 0 implies that all the data will be used and that the grid will never be cleared
NORMALIZATION	( default=true ) This controls how the data is normalized it can be set equal to true, false or ndata. The differences between these options are explained in the manual page for HISTOGRAM
GRID	the action that creates the input grid you would like to use

Options

SERIAL	( default=off ) do the calculation in serial. Do not use MPI
LOWMEM	( default=off ) lower the memory requirements
TIMINGS	( default=off ) output information on the timings of the various parts of the calculation
LOGWEIGHTS	list of actions that calculates log weights that should be used to weight configurations when calculating averages
CONCENTRATION	the concentration parameter for Von Mises-Fisher distributions
COMPONENT	if your input is a vector field use this to specify the component of the input vector field for which you wish to use
GRID_BIN	the number of bins for the grid
GRID_SPACING	the approximate grid spacing (to be used as an alternative or together with GRID_BIN)