Skip to content
A Python script for rendering cube files generated by Psi4
Python Shell
Branch: master
Clone or download

Latest commit

Fetching latest commit…
Cannot retrieve the latest commit at this time.

Files

Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
example
LICENSE
README.md
vmd_cube.py
vmd_cube_color_schemes.png
vmd_cube_multiple_surfaces.png

README.md

vmd_cube

A Python script for rendering cube files generated by Psi4

Adaptive isocontour values

If the cube files are generated with Psi4, vmd_cube will automatically use the adaptive isocontour values reported in the comment section:

Psi4 Gaussian Cube File.
Property: Psi_a_1_1-Ag. Isocontour range for 85% of the density: (0.0535039,0)

These isocountour values capture 85% of the probability density using the least amount of grid points.

Alternatively, the isocontour range can be set with the --iso option. For example, --iso 0.03 -0.03. If vmd_cube is not provided isocountour values, it will use the default ([0.05,-0.05]).

Color schemes

The vmd_cube color scheme is customizable using the --color1/--color2 options. Alternatively the user can request one of the following color schemes (Emory is the default one).

vmd_cube color schemes

Specifying arbitrary isosurface values/colors

vmd_cube can plot an arbitrary number of isosrufaces. This can be specified with the options --isovalue and --isocolor. For example, to draw three surfaces with values [0.03,0.04,0.05] call vmd_cube with the following argument --isovalue 0.03 0.04 0.05 --isocolor 3 23 12. Note that the number of arguments passed to --isovalue and --isocolor must be the same.

The following is an example of a plot containing three isosurfaces

vmd_cube.py --isovalue -0.03 -0.06 -0.12 --isocolor 3 3 3 --opacity=0.3 --rx=0 --ry=90 --rz=0

vmd_cube color schemes

vmd_cube options

>>> ./vmd_cube.py --help
usage: vmd_cube.py [-h] [--isovalue [<isovalue> [<isovalue> ...]]]
                   [--isocolor [<integer> [<integer> ...]]] [--rx [<angle>]]
                   [--ry [<angle>]] [--rz [<angle>]] [--tx [<length>]]
                   [--ty [<length>]] [--tz [<length>]] [--opacity [<opacity>]]
                   [--scale [<factor>]] [--no-montage] [--no-labels]
                   [--imagew [<integer>]] [--imageh [<integer>]]
                   [--fontsize [<integer>]] [--interactive] [--gzip]
                   [--national_scheme] [--silver_scheme] [--bright_scheme]
                   [--electron_scheme]
                   [<cubefile dir>]

vmd_cube is a script to render cube files with vmd. To generate cube files
with Psi4 add the command cubeprop() at the end of your input file.

positional arguments:
  <cubefile dir>        The directory containing the cube files.

optional arguments:
  -h, --help            show this help message and exit
  --isovalue [<isovalue> [<isovalue> ...]]
                        a list of isosurface values (a list of floats, default
                        = [0.05,-0.05])
  --isocolor [<integer> [<integer> ...]]
                        a list of isosurface color IDs (a list of integers,
                        default = [3,23])
  --rx [<angle>]        the x-axis rotation angle (float, default = 30.0)
  --ry [<angle>]        the y-axis rotation angle (float, default = 40.0)
  --rz [<angle>]        the z-axis rotation angle (float, default = 15.0)
  --tx [<length>]       the x-axis translation (float, default = 0.0)
  --ty [<length>]       the y-axis translation (float, default = 0.0)
  --tz [<length>]       the z-axis translation (float, default = 0.0)
  --opacity [<opacity>]
                        opacity of the isosurface (float, default = 1.0)
  --scale [<factor>]    the scaling factor (float, default = 1.0)
  --no-montage          call montage to combine images. (string, default =
                        false)
  --no-labels           do not add labels to images. (string, default = false)
  --imagew [<integer>]  the width of images (integer, default = 250)
  --imageh [<integer>]  the height of images (integer, default = 250)
  --fontsize [<integer>]
                        the font size (integer, default = 20)
  --interactive         run in interactive mode (default = false)
  --gzip                gzip cube files (default = false)
  --national_scheme     use a red/blue color scheme. (string, default = false)
  --silver_scheme       use a gray/white color scheme. (string, default =
                        false)
  --bright_scheme       use a soft yellow/blue color scheme. (string, default
                        = false)
  --electron_scheme     use a purple/green color scheme. (string, default =
                        false)
You can’t perform that action at this time.