This is part of the gridtools module |
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.
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.
x: DISTANCEATOMS=1,2 hA1: HISTOGRAMthe pair of atom that we are calculating the distance between.ARG=xthe quantity that is being averagedGRID_MIN=0.0compulsory keyword ( default=auto ) the lower bounds for the gridGRID_MAX=3.0compulsory keyword ( default=auto ) the upper bounds for the gridGRID_BIN=100the number of bins for the gridBANDWIDTH=0.1 ii: INTERPOLATE_GRIDthe bandwidths for kernel density esimtationGRID=hA1could not find this keywordGRID_BIN=200 DUMPGRIDthe number of bins for the gridGRID=iithe grid you would like to print (can also use ARG for specifying what is being printed)FILE=histo.datcompulsory keyword ( default=density ) the file on which to write the grid.
INTERPOLATION_TYPE | ( default=spline ) the method to use for interpolation. Can be spline, linear, ceiling or floor. |
SERIAL | ( default=off ) do the calculation in serial. Do not parallelize |
MIDPOINTS | ( default=off ) interpolate the values of the function at the midpoints of the grid coordinates of the input grid |
ZERO_OUTSIDE_GRID_RANGE | ( default=off ) if we are asked to evaluate the function for a number that is outside the range of the grid set it to zero |
GRID_BIN | the number of bins for the grid |
ARG | the input for this action is the scalar output from one or more other actions. The particular scalars that you will use are referenced using the label of the action. If the label appears on its own then it is assumed that the Action calculates a single scalar value. The value of this scalar is thus used as the input to this new action. If * or *.* appears the scalars calculated by all the proceeding actions in the input file are taken. Some actions have multi-component outputs and each component of the output has a specific label. For example a DISTANCE action labelled dist may have three components x, y and z. To take just the x component you should use dist.x, if you wish to take all three components then use dist.*.More information on the referencing of Actions can be found in the section of the manual on the PLUMED Getting Started. Scalar values can also be referenced using POSIX regular expressions as detailed in the section on Regular Expressions. To use this feature you you must compile PLUMED with the appropriate flag.. You can use multiple instances of this keyword i.e. ARG1, ARG2, ARG3... |
GRID_SPACING | the approximate grid spacing (to be used as an alternative or together with GRID_BIN) |