moldenViz 1.1.0

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moldenViz

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Installation

pip install moldenViz

Note

If you want to use the plotter, make sure python has access to tkinter

python3 -m tkinter

If python doesn't have access to tkinter, then you can get it from the latest python version, or

macOS

brew install python-tk

Ubuntu

sudo apt-get install python-tk

Usage

CLI

To run moldenViz with a molden file, you can do

moldenViz molden.inp

you can instead use examples

moldenViz -e co

a full list of examples can be found below.

You can also choose to only plot the molecule

moldenViz molden.inp -m

For more details, you can do

moldenViz -h

Inside python

If you don't have a molden file, you can get examples by doing

from moldenViz import Plotter
from moldenViz.examples import co

Plotter(co)

the list of examples is:

• co
• o2
• co2
• h2o
• benzene
• prismane
• pyridine
• furan
• acrolein

In the next examples, I'll be using 'molden.inp', but you can replace it with your molden file path, or one of the examples.

Plotter

You can use the plotter to plot just the molecule

from moldenViz import Plotter

Plotter('molden.inp', only_molecule=True)

or to plot the molecular orbitals

from moldenViz import Plotter

Plotter('molden.inp')

Tabulator

You can use moldenViz to tabulate the GTOs

from moldenViz import Tabulator
import numpy as np

tab = Tabulator('molden.inp')

# Using a spherical grid
tab.spherical_grid(
    r = np.linspace(0, 5, 20),
    theta = np.linspace(0, np.pi, 20),
    phi = np.linspace(0, 2 * np.pi, 40)
)

# Or a cartesian grid
tab.cartesian_grid(
    x = np.linspace(-2, 2, 20),
    y = np.linspace(-2, 2, 20),
    z = np.linspace(-2, 2, 20)
)

print(tab.grid.shape)
print(tab.gtos.shape)

And to tabulate a molecular orbital

mo_data = tab.tabulate_mos(0)

or a list

mo_data = tab.tabulate_mos([0,1,4])

or a range

mo_data = tab.tabulate_mos(range(1, 10, 2))

or all of them

mos_data = tab.tabulate_mos()

Configuration

moldenViz supports customization through configuration files. You can customize:

• Bond colors and appearance (uniform vs split coloring)
• Atom colors and radii for different elements
• Grid parameters

Create a configuration file at ~/.config/moldenViz/config.toml to customize settings. See the documentation for detailed configuration options and examples.

Documentation

You can find the documentation here.

Roadmap

• 0.1: Basic commands inside python.
  • 0.1.5: Documentation support
• 0.2: Plotter.
• 0.3: CLI.
• 1.0: Improved documentation and config file for plot settings
• 2.0: Support for cartesian functions.
• 3.0: Tabulation and plot of different quantities