https://github.com/fevangelista/vmd_cube

A Python script for rendering cube files generated by Psi4
https://github.com/fevangelista/vmd_cube

Last synced: 3 months ago
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A Python script for rendering cube files generated by Psi4

• Host: GitHub
• URL: https://github.com/fevangelista/vmd_cube
• Owner: fevangelista
• License: mit
• Created: 2017-01-21T01:00:37.000Z (almost 8 years ago)
• Default Branch: master
• Last Pushed: 2024-06-23T02:57:42.000Z (5 months ago)
• Last Synced: 2024-06-29T13:33:27.830Z (5 months ago)
• Language: Python
• Size: 491 KB
• Stars: 16
• Watchers: 2
• Forks: 6
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# 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](/vmd_cube_color_schemes.png?raw=true "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_multiple_surfaces.png?raw=true "Color Schemes")

## vmd_cube options

```

>>> ./vmd_cube.py --help

usage: vmd_cube.py [-h] [--isovalue [ [ ...]]]

                   [--isocolor [ [ ...]]] [--rx []]

                   [--ry []] [--rz []] [--tx []]

                   [--ty []] [--tz []] [--opacity []]

                   [--scale []] [--no-montage] [--no-labels]

                   [--imagew []] [--imageh []]

                   [--fontsize []] [--interactive] [--gzip]

                   [--national_scheme] [--silver_scheme] [--bright_scheme]

                   [--electron_scheme]

                   []

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:

          The directory containing the cube files.

optional arguments:

  -h, --help            show this help message and exit

  --isovalue [ [ ...]]

                        a list of isosurface values (a list of floats, default

                        = [0.05,-0.05])

  --isocolor [ [ ...]]

                        a list of isosurface color IDs (a list of integers,

                        default = [3,23])

  --rx []        the x-axis rotation angle (float, default = 30.0)

  --ry []        the y-axis rotation angle (float, default = 40.0)

  --rz []        the z-axis rotation angle (float, default = 15.0)

  --tx []       the x-axis translation (float, default = 0.0)

  --ty []       the y-axis translation (float, default = 0.0)

  --tz []       the z-axis translation (float, default = 0.0)

  --opacity []

                        opacity of the isosurface (float, default = 1.0)

  --scale []    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 []  the width of images (integer, default = 250)

  --imageh []  the height of images (integer, default = 250)

  --fontsize []

                        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)

```