DUMPCUBE

This is part of the gridtools module

Output a three dimensional grid using the Gaussian cube file format.

Suppose you have calculated the value of a function on a three dimensional grid. This function might be a HISTOGRAM or it might be a free energy energy surface that was calculated from this histogram by using CONVERT_TO_FES. Alternatively, your function might be a phase-field that was calculated using MULTICOLVARDENS. Whatever the function is, however, you obviously cannot show it using a typical contour plotting program such as gnuplot as you have three input variables.

Tools like VMD have nice features for plotting these types of three dimensional functions but typically you are required to use a Gaussian cube file format to input the data. This action thus allows you to output a function evaluated on a grid to a Gaussian cube file format.

Examples

The input below can be used to post process a trajectory. A histogram as a function of the distance between atoms 1 and 2, the distance between atom 1 and 3 and the angle between the vector connecting atoms 1 and 2 and 1 and 3 is computed using kernel density estimation. Once all the data contained in the trajectory has been read in and all the kernels have been added the resulting histogram is output to a file called histoA1.cube. This file has the Gaussian cube file format. The histogram can thus be visualized using tools such as VMD.

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

x1: DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=1,2  You cannot view the components that are calculated by each action for this input file. Sorry 
x2: DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=1,3  You cannot view the components that are calculated by each action for this input file. Sorry 
x3: ANGLE 
ATOMS
the list of atoms involved in this collective variable (either 3 or 4 atoms). 
=1,2,3  You cannot view the components that are calculated by each action for this input file. Sorry 
hA1: HISTOGRAM 
ARG
the quantities that are being used to construct the histogram 
=x1,x2,x3 
GRID_MIN
compulsory keyword ( default=auto )
the lower bounds for the grid 
=0.0,0.0,0.0 
GRID_MAX
compulsory keyword ( default=auto )
the upper bounds for the grid 
=3.0,3.0,3.0 
GRID_BIN
the number of bins for the grid 
=10,10,10 
BANDWIDTH
the bandwidths for kernel density esimtation 
=1.0,1.0,1.0  You cannot view the components that are calculated by each action for this input file. Sorry 
DUMPCUBE 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hA1 
FILE
compulsory keyword ( default=density )
the file on which to write the grid. 
=histoA1.cube  You cannot view the components that are calculated by each action for this input file. Sorry 

Glossary of keywords and components

Compulsory keywords

ARG	the label for the grid that you would like to output
STRIDE	( default=0 ) the frequency with which the grid should be output to the file. Default of zero means dump at end of calculation
FILE	( default=density ) the file on which to write the grid.

Options

PRINT_XYZ	( default=off ) output coordinates on fibonacci grid to xyz file
PRINT_ONE_FILE	( default=off ) output grids one after the other in a single file
GRID	the grid you would like to print (can also use ARG for specifying what is being printed)
FMT	the format that should be used to output real numbers