PYSCF-ITA

The [information-theoretic quantities](../developer/ita.ipynb) developed by Shubin Liu et al. is becoming more and more popular in predicting and understanding many chemical relevant problems, such as reactivity, regioselectivity, aromaticity, pKa and so on. See Acta Phys. -Chim. Sin., 32, 98 (2016) and WIREs Comput Mol Sci., e1461 (2019) for reviews.

PYSCF-ITA is a Python extension library of PyScf for post-processing molecular quantum chemistry calculations. So, like any other library, it can be directly imported and used in Python scripts and codes. All the information-theoretic quantities can be easily calculated by pyscf-ita, which can be freely download at https://zhaoyilin.github.io/pyscf-ita/. This document will briefly illustrate how to calculate various information-theoretic and related quantities.

Contents

USER DOCUMENTATION:

• 1. Installation
  • 1.1. Prerequisites
  • 1.2. Compiling from source code
• 2. Quick Start
  • 2.1. Molecular build
  • 2.2. Pyscf Calculation
  • 2.3. Grids
  • 2.4. Compute ITA
• 3. Examples

DEVELOPER DOCUMENTATION:

• 1. Atoms-in-Molecules
  • 1.1. Becke’s fuzzy atom approach
  • 1.2. Bader’s zero-flux AIM approach
  • 1.3. Hirshfeld’s stockholder approach
• 2. Information-Theoretic Approach
  • 2.1. Electron Density Representation
  • 2.2. Shape Function Representation
  • 2.3. Atoms-in-Molecules Representation
• 3. API
  • 3.1. pyscf.ita.promolecule module
    • ProMolecule
      • ProMolecule.build()
      • ProMolecule.electron_density()
      • ProMolecule.get_atom()
      • ProMolecule.get_method()
      • ProMolecule.get_scf()
      • ProMolecule.get_xc()
      • ProMolecule.identical_method()
      • ProMolecule.spheric_average_method()
  • 3.2. pyscf.ita.aim module
    • Becke
      • Becke.sharing_function()
    • Hirshfeld
      • Hirshfeld.build()
      • Hirshfeld.sharing_function()
  • 3.3. pyscf.ita.dens module
    • ElectronDensity
      • ElectronDensity.build()
      • ElectronDensity.density()
      • ElectronDensity.gradient()
      • ElectronDensity.gradient_norm()
      • ElectronDensity.laplacian()
      • ElectronDensity.spin_reduction()
      • ElectronDensity.tau()
    • PartitionDensity
      • PartitionDensity.density()
      • PartitionDensity.gradient()
      • PartitionDensity.gradient_norm()
      • PartitionDensity.laplacian()
      • PartitionDensity.orbital()
      • PartitionDensity.tau()
  • 3.4. pyscf.ita.ked module
    • KineticEnergyDensity
      • KineticEnergyDensity.dirac()
      • KineticEnergyDensity.general()
      • KineticEnergyDensity.gradient_expansion()
      • KineticEnergyDensity.positive_definite()
      • KineticEnergyDensity.single_particle()
      • KineticEnergyDensity.thomas_fermi()
      • KineticEnergyDensity.weizsacker()
  • 3.5. pyscf.ita.itad module
    • ItaDensity
      • ItaDensity.G1()
      • ItaDensity.G2()
      • ItaDensity.G3()
      • ItaDensity.GBP_entropy()
      • ItaDensity.alternative_fisher_information()
      • ItaDensity.fisher_information()
      • ItaDensity.relative_alternative_fisher_information()
      • ItaDensity.relative_fisher_information()
      • ItaDensity.relative_rho_power()
      • ItaDensity.relative_shannon_entropy()
      • ItaDensity.rho_power()
      • ItaDensity.shannon_entropy()
  • 3.6. pyscf.ita.ita module
    • ITA
      • ITA.G1()
      • ITA.G2()
      • ITA.G3()
      • ITA.GBP_entropy()
      • ITA.alternative_fisher_information()
      • ITA.batch_compute()
      • ITA.build()
      • ITA.fisher_information()
      • ITA.onicescu_information()
      • ITA.relative_alternative_fisher_information()
      • ITA.relative_fisher_information()
      • ITA.relative_onicescu_information()
      • ITA.relative_renyi_entropy()
      • ITA.relative_shannon_entropy()
      • ITA.relative_tsallis_entropy()
      • ITA.renyi_entropy()
      • ITA.rho_power()
      • ITA.shannon_entropy()
      • ITA.tsallis_entropy()
  • 3.7. pyscf.ita.script module
    • batch_compute()
    • section_compute()

Indices and tables

• Index

• Module Index

• Search Page