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https://github.com/jjgoings/two-component_cubes
Python script to prepare complex, two-component Gaussian cube files to be read by GaussView or Pymol, etc.
https://github.com/jjgoings/two-component_cubes
cube-files gaussian ghf magnetization plot
Last synced: about 1 month ago
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Python script to prepare complex, two-component Gaussian cube files to be read by GaussView or Pymol, etc.
- Host: GitHub
- URL: https://github.com/jjgoings/two-component_cubes
- Owner: jjgoings
- Created: 2016-06-16T17:47:50.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2016-12-07T22:51:31.000Z (almost 8 years ago)
- Last Synced: 2023-10-20T20:46:33.965Z (about 1 year ago)
- Topics: cube-files, gaussian, ghf, magnetization, plot
- Language: Python
- Size: 25.2 MB
- Stars: 1
- Watchers: 2
- Forks: 4
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Cubes
## Basic use
This is a python class to read and write out Gaussian cube files,
with a particular emphasisis on extracting complex and two-component molecular
orbitals.
Example:
Say you have a complex 2c MO cube called `twoc.cube`.
If you have `cube.py` in the same directory, you could write a script like
```python
from cube import Cube
twoc = Cube('twoc.cube')
twoc.write_out('twoc_ra.cube',data='RA')
twoc.write_out('twoc_ia.cube',data='IA')
twoc.write_out('twoc_rb.cube',data='RB')
twoc.write_out('twoc_ib.cube',data='IB')
```
Or, if you just cloned the whole directory you can run `cube.py` as-is
```
$ python cube.py
```
(You can modify the behavior of cube.py underneath the `if__name__ ==
'__main__()':`)
This would create an object called `twoc`, which you could then dump out new
cube files that are readable by GaussView corresponding to the real alpha
(`data='RA'`), real beta (`data='RB'`), imaginary alpha (`data='IA'`), and
imaginary beta (`data='IB'`). The default for `write_out` is real alpha.
The code should be smart enough to distinguish between MO and density cube
files.
Usually there is no problem using GaussView for RHF and UHF anyway, so the code
isn't yet generalized to all cases, but I'll work that out when I have time.
## Vector quantities: Getting magnetization densities and electrostatic field gradients
If you generated your GHF cubes using the VSPIN (in the development version only of `cubegen`, I believe), you can also write out magnetization densities.
So, for example you ran the following:
```
cubegen 0 vspin ghf-vspin-example.fchk ghf-vspin-example.cube 40 h
```
Then you could do, e.g.
```
magnetization = Cube('ghf-vspin-example.cube',vspin=True)
magnetization.write_out('Mz.cube',data='Mz')
```
This would dump the z-component of the magnetization density to a new cube called `Mz.cube`. You can do this for the norm of the magnetization `data='N'`, as well as the x and y components of the magnetization (`data='Mx'` and `data='My'`, respectively). Densitites are always real.
There is also a new function to plot some vector quantities, if you have Mayavi installed. These are handled through the `plot_property` method. So continuing the example above,
```
magnetization = Cube('ghf-vspin-example.cube',vspin=True)
magnetization.plot_property('MAG')
```
would plot the magnetization vector at different points in 3D space. It's in beta, so you may need to fiddle around with the source to get it to do what you want.
Similarly, if you have an electrostatic potential generated by, for example,
```
cubegen 0 potential=scf esp-example.fchk esp-example.cube 80 h
```
Then you can do
```
ESP = Cube('esp-example.cube')
ESP.plot_property('ESP')
```
which will plot the *gradient* (a vector) of your electrostatic potential. This is helpful for visualizing the electric field generated by a molecule with a dipole moment, for example.