Example Script

The following script can be found in the package.

It contains each of the examples in the tutorials.

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Notes
-----

This script contains the examples presented throughout the tutorial.
"""

import rgmol
import rgmol.examples

if __name__=="__main__":
  ##For each of these examples, just change False to True

  ## Visualization of chloromethane from an ADF output
  if False:
    file = rgmol.examples.adf_CH3Cl
    mol = rgmol.extract_adf.extract(file)
    mol.plot_radius()

  ## Visualization of a property : the dual
  if False:
    file = rgmol.examples.adf_CH3Cl
    mol = rgmol.extract_adf.extract(file)
    mol.plot_property("dual",factor=2)

  ## Visualization of a condensed kernel : condensed linear response
  if False:
    file = rgmol.examples.adf_CH3Cl
    mol = rgmol.extract_adf.extract(file)
    mol.plot_condensed_kernel("condensed linear response",factor=.5)

  ## Visualization of a diagonalized condensed kernel : condensed linear response
  if False:
    file = rgmol.examples.adf_CH3Cl
    mol = rgmol.extract_adf.extract(file)
    mol.plot_diagonalized_condensed_kernel("condensed linear response")

  ## Visualization of a cube file
  if False:
    file = rgmol.examples.cube_H2CO_MO59
    mol = rgmol.extract_cube.extract(file,do_order_bonds=1)
    mol.plot_isodensity()

  ## Visualization of Atomic Orbitals
  if False:
    file = rgmol.examples.molden_H2CO
    mol = rgmol.extract_molden.extract(file,do_order_bonds=1)
    mol.plot_AO()

  ## Visualization of Molecular Orbitals
  if False:
    file = rgmol.examples.molden_H2CO
    mol = rgmol.extract_molden.extract(file,do_order_bonds=1)
    mol.plot_MO()

  ## Visualization of Transition Densities
  if False:
    file = rgmol.examples.molden_H2CO
    mol = rgmol.extract_molden.extract(file,do_order_bonds=1)
    rgmol.extract_orca.extract_properties(rgmol.examples.orca_H2CO,mol=mol)
    mol.plot_transition_density()

  ## Visualization of Diagonalized Non-Condensed Kernel : Linear response function
  if False:
    file = rgmol.examples.molden_H2CO
    mol = rgmol.extract_molden.extract(file,do_order_bonds=1)
    rgmol.extract_orca.extract_properties(rgmol.examples.orca_H2CO,mol=mol)
    mol.plot_diagonalized_kernel(kernel="linear_response_function")

  ## Visualization of Diagonalized Non-Condensed Kernel : Softness kernel
  if False:
    file = rgmol.examples.molden_H2CO
    mol = rgmol.extract_molden.extract(file,do_order_bonds=1)
    rgmol.extract_orca.extract_properties(rgmol.examples.orca_H2CO,mol=mol)

    file_m = rgmol.examples.molden_H2CO_m
    mol_m = rgmol.extract_molden.extract(file_m)

    mol.plot_diagonalized_kernel(kernel="softness_kernel",mol_m=mol_m,fukui_type="f-")

  ## Visualization of Dipole moments
  if False:
    file = rgmol.examples.orca_CHFClBr
    mol = rgmol.extract_orca.extract(file,do_order_bonds=1)
    mol.plot_dipole_moment()