moldenViz 0.2.1

No project description provided

moldenViz

---

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 install it with

macOS

brew install python-tk

Ubuntu

sudo apt-get install python-tk

Usage

If you don't have a molden file (then why are you using this package?) you can get some examples by doing

from moldenViz.examples import co

Plotter(co)

the total 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 you 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 and molecular orbitals

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_data.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()

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 options.