kimrojas / cube-toolz

Python tool to manipulate Gaussian cube files

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Cube Toolz

A python library and tool to read in and manipulate Gaussian cube files. This code allows you to:

• Read and write Gaussian cube files
• Translate and rotate cube data
• Integrate around a particular atom
• Integrate around a sphere
• Integrate around the whole cube file
• Take the planar average
• Add/subtract/multiply cube files

Planar averages are outputted as a column of distance and electrons. It is normalized to give the total number of electrons.

Integrating around an atom or reference point requires xyz coordinates as an input. They must be given as Angstroms. This holds true for the chosen reference point too.

Requires numpy and scipy. If you have pip, you can just run

pip install git+https://github.com/funkymunkycool/Cube-Toolz.git

to install the cube_tools module and an executable of the same name into the currently preferred Python package installation directories.

Alternatively, you can clone the repository manually and run

pip install -r requirements.txt

to install all the requirements.

This is designed to be used either as a library, or to be run from the command line. If you decide to run it from the command line, here are the required arguments:

positional arguments: Files Cube files used in program

optional arguments:

• -h, --help show this help message and exit
• -a, --add Add two or more cube files together
• -s, --subtract Subtract two or more cube files together
• -M, --multiply Multiply two or more cube files together
• -p [POWER], --power [POWER] Raise the cube file to a certain power. Any number of cube files can be specified and they will all be raised to the power defined. Default is to square the cube file(s).
• -t TRANSLATE TRANSLATE TRANSLATE, --translate TRANSLATE TRANSLATE TRANSLATE Translate a cube file. Requires a translation vector as an argument.
• -i INTEGRATE, --integrate INTEGRATE Integrate over the entire cube file.
• -ia INTEGRATE, --integrate INTEGRATE atomId Radius Integrate a sphere around an atom. Requires atom ID and the radius of the sphere
• -ir INTEGRATE, --integrate INTEGRATE x y z Radius Integrate a sphere around a point. Requires x y z coordinate of point and the radius of the sphere
• -e EXPAND EXPAND EXPAND, --expand EXPAND EXPAND EXPAND Make a supercell of the specified cube file
• -m MEAN, --mean MEAN Calculate planar average of a cube file along a particular axis. Normalized to give the total number of electrons (particles). Arguments are necessarily x,y or z.

usage: cube_tools.py [-h] [-a] [-s] [-p [POWER]] [-t TRANSLATE TRANSLATE TRANSLATE] Files [Files ...]