Skip to content
PDielec is a Python package for post-processing solid state QM and MM calculations of Infrared Spectra
Python TeX Other
Branch: master
Clone or download
JohnKendrick Phonopy was giving errors on reading files via the GUI. This was down…
… to a misuse of the os.path.join command. Now fixed.
Latest commit cb2920c Jun 16, 2019
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
Documentation ding a more detailed description of using Phonopy Feb 11, 2019
Examples Updated examples for which include the air-bubble size in the scenario Feb 11, 2019
Python Phonopy was giving errors on reading files via the GUI. This was down… Jun 15, 2019
Sphinx
docs Updates to the documentation Jun 5, 2019
.gitignore Updated the documentation with information about the Fitter Tab Oct 29, 2018
.pylintrc Added more special variables Jan 7, 2017
CHANGES Small changes in the Windows version Sep 13, 2018
LICENSE.md Update LICENSE.md Nov 17, 2015
LICENSE.txt New files associated with the windows installation Feb 28, 2018
Makefile Major changes - Sep 13, 2018
README.adoc Updated documentation for the air bubbles Feb 11, 2019
ToDo.txt Modified ToDO Aug 30, 2016
after_installation.txt Minor changes to the installation files for Windows 10 Feb 28, 2018
before_installion.txt Minor changes to the installation files for Windows 10 Feb 28, 2018
checkcsv Fixed issues associated with Python2 Jan 30, 2018
checkexcel Skip a sheet if the number of rows or columns are not the same Dec 23, 2018
inno.txt New files associated with the windows installation Feb 28, 2018
p2cif New command to extract cif file and write it out May 23, 2018
p2cif.py New command to extract cif file and write it out May 23, 2018
pdcompare New command to calculte the cross correlation coefficient between spe… Aug 2, 2018
pdcompare.py Added the ATR sheet to the comparison Oct 4, 2018
pdgui First alpha release of the GUI Feb 25, 2018
pdgui.iss Updated documentation for the air bubbles Feb 11, 2019
pdgui.py Major changes - Sep 13, 2018
pdgui.spec Small changes in the Windows version Sep 13, 2018
preader First alpha release of the GUI Feb 25, 2018
preader.py Changed the order of reading QE files to .log .out .dynG This avoids … May 16, 2018

README.adoc

The PDielec package

Authors: John Kendrick and Andrew Burnett

The Python package, PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processesing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach has been published. Any use of the package should cite; PDielec: The calculation of infrared and terahertz absorption for powdered crystals John Kendrick and Andrew D. Burnett Journal of Computational Chemistry 2016, vol 27, 1491-1504 DOI: 10.1002/jcc.24344

Introduction

The molecular and solid state quantum mechanical calculations of response properties such as the frequencies and intensities of infrared (IR) and terahertz (THz) radiation absorption has become generally available in many molecular and solid state computer programs. A common approach is to assume the harmonic approximation and calculate the mass weighted force constant matrix (for molecules) or the dynamical matrix at the gamma point (for periodic solids). Diagonalisation of the matrix gives the frequencies for absorption and the normal modes (molecules) or phonon displacements (periodic solids). The calculation of the absorption intensity for each mode requires the calculation of the change in dipole moment caused by the displacement of the atoms for that mode. For solids where there is a large separation of charge, there can be a large coupling between a phonon mode and the internal field within a particle resulting from its morphology. The PDielec program is written in Python and post processes the output of solid state quantum mechanical (QM) and molecular mechanics (MM) based codes such as VASP, CASTEP, CRYSTAL14, Abinit, QuantumEspresso, Phonopy and GULP to predict the infrared absorption of crystalline insulator materials whose crystal size is small compared with the wavelength of the absorbing radiation. The package is suited for the calculation of the complex, frequency dependent permittivity and its associated absorption of infrared radiation for a finely ground crystalline material dispersed in a low loss dielectric medium such KBr or PTFE. A particular feature of the program is its ability to take into account the constant permittivity of the supporting medium and the particle shape through an effective medium theory. Calculation of ATR spectra has been included in v5.0. More details as to the theory are available here; https://johnkendrick.github.io/PDielec/

Installation

Full documentation of the program and its installation is available here; https://johnkendrick.github.io/PDielec/

You can’t perform that action at this time.