Installation#

Conda#

Unless you are interested in the full conda package, a miniconda installation should be sufficient for installing the rest of the modules needed for the PDielec installation. Miniconda is the recommended environment for installing PDielec. On Windows, it is necessary to run the commands in an conda command terminal, which will be added to the user’s menu when miniconda is installed.

PDielec is available on the conda-forge channel and installation using conda can be performed on Linux, Windows, and Mac systems. However, in a conda installation, there are no example files installed, only the executables and python files. Example files for each of the DFT packages supported can be downloaded from the Git repository.

The conda-forge package has a Python 3 environment included in the package. After installation of miniconda or conda, a new environment should be created in which to install the package:

conda create  --name pdielec
conda activate pdielec
conda config --add channels conda-forge
conda install -c conda-forge pdielec
pdgui

If at a later stage, you want to update PDielec to the latest version from conda-forge, you should be able to update the environment in the following way:

conda activate pdielec
conda update pdielec

This only works if the conda-forge channel has been added to the channel list for the environment.

If the full GitHub installation is required to run the examples for instance, then this can be downloaded from

PyPi#

If you do not want to use conda or miniconda, PDielec is available on pypi.org and can be installed using pip.:

pip install --user pdielec
pdgui

Sometimes a pip install my fail because there isn’t a wheel (compiled) version of a required package and the compilation is not possible because the necessary tools have not been installed. In this case it is necessary to look to see what versions of the whl files are available on PyPi and ensure that the version of Python running is compatible. Sometimes downgrading the Python version is enough to install all the software requirements from wheels, thereby avoiding recompilation.

GitHub - Linux#

The package is available on GitHub and can be downloaded from https://github.com/JohnKendrick/PDielec. cd to a directory where PDielec will be installed and use git to clone a copy of the program. I use a ‘Software/’ directory in my home directory to store programs, so the commands to obtain PDielec would look like this.:

cd ~/Software
git clone https://github.com/JohnKendrick/PDielec.git

This will create a directory ~/Software/PDielec.

As part of the installation, you will have to install several Python packages into your environment. The full list of packages is as follows;

dill
imageio
imageio-ffmpeg
matplotlib
numpy
openpyxl
psutil
PyOpenGL
PyYAML
QtPy
scikit_learn
scipy
setuptools
spglib
termcolor
XlsxWriter
scikit-learn

GitHub - Windows#

An conda installation is the recommended way of installing on a Windows machine. See the section on conda above. If the user still wishes to proceed with a local installation based purely on the GitHub releases, see below.

Installation from repository#

This Windows installation method is only needed if installation through conda is not possible. A Windows 10 installation from the git repository which works for users without administrator rights involves a few steps but gives an installation that runs all the test cases. In the following instructions replace ‘yourusername’ with your user name.

Install git#

First of all, install a Windows version of git from www.git-scm.com. A 64-bit version of Windows 10 will be assumed for the following instructions.

  • From the download page download and run the 64-bit Git for Windows setup.

  • During the installation install the Quick Launch and Desktop icons as these make using the program easier.

  • If you are not familiar with the vi or vim editor, it is probably best to use the Nano editor, although if you wish you can install Notepad++ and use that as the default editor.

  • In the section concerning the PATH environment, I would recommend the last option “Use git and optional Unix tools from the Windows Command prompt”. This option will mean that some Windows commands eg. find and sort will be replaced by the Unix commands, so be careful.

  • Leave the https certificate choice as the default, namely the OpenSSL library.

  • Line endings are best left to the default setting of Windows-style for checkout and Unix-style for check-in.

  • The Console I use is the MinTTY console it has a larger scrolling buffer than the Windows console.

  • Under the “Configuring extra options” I leave everything as the default.

I have seen a few hiccups in the installation of Git. Occasionally I have to do the installation twice and occasionally I am left with the Setup Installing window indicating that I should wait, when in fact the installation has been completed. When this happens I kill the setup process with the task manager

Install Python#

  • From https://www.python.org/downloads/windows/ download and run the Windows x86-64 executable installer for the latest Python 3.x version

  • Uncheck the “Install launcher” for all users

  • Check “Add Python 3.x to PATH”

  • Click on the “Install now” button

  • Check installation ran OK by running the Idle Python environment

Open a git bash console and type;

pip install dill
pip install imageio
pip install imageio-ffmpeg
pip install matplotlib
pip install mkl
pip install numpy
pip install openpyxl
pip install psutil
pip install PyOpenGL
pip install PyYAML
pip install QtPy
pip install scikit_learn
pip install scipy
pip install setuptools
pip install spglib
pip install termcolor
pip install XlsxWriter
pip install scikit-learn

Install PDielec#

Open a git bash console and type;:

cd Software
git clone -c core.symlinks=true https://github.com/JohnKendrick/PDielec.git

This should create a directory in Software called PDielec. The “-c core.symlinks=true” means that the commands; pdgui and preader are treated as windows symlinks to their equivalent .py file.

Testing PDielec#

Open a git bash console. If you have installed Python using conda then you need to ‘source activate’ the environment you have established before typing;:

cd Software/PDielec
pdmake test-preader
pdmake test-pdgui

Installing PDielec to run in any git bash console#

Open a git bash console and type;:

cd Software/PDielec
export SCRIPTS=~/bin
pdmake install

Updating PDielec from the git repository#

Open a git bash console and type;:

cd Software/PDielec
git pull

GitHub - PDielec directory structure#

  • PDielec/ - The home directory that contains the pdgui and preader commands

  • PDielec/PDielec - Holds the source for the modules used by the pdielec and preader commands

  • PDielec/PDielec/GUI - Holds the Python code for PDGui

  • PDielec/Examples - A set of examples is available for Abinit, Crystal14, CASTEP, GULP, Phonopy, Mie, and VASP. Each example directory holds the input files to the QM/MM program and the relevant output files which are post-processed by PDielec. For each program there is also a preader directory which holds test output for the preader command.

  • PDielec/Sphinx - Holds the documentation as restructured text documents (.rst). Sphinx can be used to build the documentation in either HTML or PDF format.

  • PDielec/docs - Holds the final HTML documentation.

Examples#

Each example directory has the relevant input data sets used to run the QM/MM program and the output files from that run, which are post-processed by PDielec. There is a file script.py which which has been used to create the reference output file results.ref.xlsx. The example can be run interactively:

pdmake view

The output can be compared with the reference data to see if the program is working correctly. The checkexcel command can be used to do this automatically. A complete set of tests for the system can be run using:

pdmake tests

This will run each example automatically and compare the output compared with the reference files. To remove the intermediate files after running the tests, type pdmake clean.

A benchmark can be run for comparison of the performance of PDielec on different platforms by typing;

pdmake benchmarks

This runs a range of calculations on different systems and provides a real-world view of the performance. An indication of the likely performance of the program is given in the Performance section of the documentation.

A summary of the different examples and their purpose is shown below;

Table 1 Summary of the Examples available in the Examples/ directory#

Directory

Program

Molecule

Description

ATR/AlAs

AbInit

AlAs

Maxwell Garnett calculation of the ATR spectrum of an ellipsoid along [001]. The incident angle varies from 0 to 80 degrees.

ATR/Na2SO42

Vasp

Na2(SO4)2

Maxwell-Garnett calculation of the ATR spectrum, changes the S polarisation component from 0 to 100%

ATR/Na2SO42_fit

Vasp

Na2(SO4)2

Maxwell-Garnett calculation of the ATR spectrum, an example of fitting the spectrum to experiment

AbInit/AlAs

AbInit

AlAs

Average permittivity and Maxwell-Garnett calculation of sphere, plate and ellipsoid

AbInit/BaTiO3

AbInit

BaTiO3

Average permittivity and Maxwell-Garnett calculations of sphere, plate and ellipsoid, using average isotope masses

AbInit/BaTiO3-phonana

AbInit

BaTiO3

Average permittivity and Maxwell-Garnett calculations of sphere, plate and ellipsoid, using program-defined masses

AbInit/Na2SO42

AbInit

Na2(SO4)2

Average permittivity and Maxwell-Garnett calculations of Na2(SO4)2, sphere, plate and ellipsoid, using program-defined masses

Castep/AsparticAcid

Castep

Aspartic Acid

Average permittivity and Maxwell-Garnett calculations of sphere, plate and ellipsoid, using program-defined masses

Castep/Bubbles

Castep

MgO

Maxwell-Garnett calculation showing the effect of air bubbles at 24% volume fraction and 30 micron radius

Castep/Castep17

Castep

beta-Lactose

Castep 17, Maxwell-Garnett sphere and plates with 3 surfaces

Castep/Isoleucine

Castep

Isoleucine

Maxwell-Garnett sphere

Castep/MgO

Castep

MgO

Comparison of MG, Bruggeman and AP methods changing shapes and volume fractions

Castep/Na2SO42

Castep

Na2(SO4)2

Comparison of MG and Bruggeman, for needle, ellipsoid and plate shapes

Crystal/Leucine

Crystal

Leuscine

Comparison of MG, plates and ellipsoids

Crystal/Na2SO42

Crystal

Na2(SO4)2

Comparison of MG for needle, ellipsoid and plate shapes

Crystal/Na2SO42_C17

Crystal

Na2(SO4)2

Comparison of MG for needle, ellipsoid and plate shapes, reading output from Crystal 17

Crystal/Quartz

Crystal

Quartz

Comparison of MG for needle, ellipsoid and plate shapes

Crystal/ZnO/CPHF

Crystal

ZnO

Coupled Hartree-Fock, Maxwell-Garnett Sphere, Needle and Plate

Crystal/ZnO/Default

Crystal

ZnO

Default Crystal calculation of IR spectrum, Maxwell-Garnett Sphere, Needle and Plate

Crystal/ZnO/NoEckart

Crystal

ZnO

As above, but no Eckart projection in Crystal, Maxwell-Garnett Sphere, Needle and Plate

Experiment/Forsterite

Experiment

Forsterite

Single crystal calculations of a thick slab, for a, b and c axis alignments with polarisation direction. Uses FPSQ model for permittivity.

Experiment/Mayerhofer

Experiment

Toy model

Example of a Drude Lorentz model permittivity

Experiment/constant

Experiment

Constant

Example of a constant permittivity with loss

Experiment/drude-lorentz

Experiment

MgO

A Drude-Lorentz model for MgO, varying the angle of incidence

Experiment/fpsq

Experiment

Quartz

An FPSQ model for Quartz, showing polarisation on along different axes and different incident angles.

Experiment/interpolation

Experiment

Quartz

An example of an interpolation model

Experiment/AlN

Experiment

AlN

Aluminium Nitride multi-layer system including SiC and Si

Experiment/Sapphire

Experiment

Sapphire

Sapphire example and test of the materials database

Gulp/Na2SO42

Gulp

Na2(SO4)2

Maxwell-Garnett and Bruggeman on needle, ellipsoid and plate

Gulp/calcite

Gulp

Calcite

Maxwell-Garnett method on Sphere and Plate

Mie/MgO

Castep

MgO

Mie method with varying volume fractions and sphere sizes

Mie/MgO_lognormal

Castep

MgO

Mie method with varying volume fractions and sphere size distributions

Phonopy/Na2SO42

Phonopy

Na2(SO4)2

Maxwell-Garnett and Bruggeman method for needle, ellipsoid and plate shapes, with varying volume fractions

Phonopy/ZnO

Phonopy

ZnO

Maxwell-Garnett and Bruggeman method for needle, ellipsoid and plate shapes

Phonopy/Crystal

Phonopy/Crystal

Urea

Powder and single crystal Phonopy example using Crystal

Phonopy/QE

Phonopy/QE

Urea

Powder and single crystal Phonopy example using QE

Phonopy/Vasp

Phonopy/Vasp

Urea

Powder and single crystal Phonopy example using Vasp

QE/Cocaine

Quantum Espresso

Cocaine

Maxwel-Garnett sphere, using QE 4.1

QE/Na2SO42

Quantum Espresso

Na2(SO4)2

Maxwell-Garnett and Bruggeman on needle, ellipsoid and plate, using QE 5.1

QE/Na2SO42-v7

Quantum Espresso

Na2(SO4)2

Maxwell-Garnett and Bruggeman on needle, ellipsoid and plate, using QE 7.3.1

QE/Urea

Quantum Espresso

Urea

Maxwell-Garnett and single crystal, using QE 7.3.1

QE/ZnO

Quantum Espresso

ZnO

Maxwell-Garnett and Bruggeman on needle, ellipsoid and plate, using QE 5.4.0

SingleCrystal/Bi2Se3

Vasp

Bi2Se3

Single crystal example of thick slab, angle of incidence varies from 0 to 90

SingleCrystal/Bi2Se3_film

Vasp

Bi2Se3

Single crystal example of thin film, angle of incidence varies from 0 to 90

SingleCrystal/L-Alanine

Crystal

L-Alanine

Explores single crystal calculations on L-Alanine and compares the results with experiment

SizeEffects/BaTiO3

Abinit

BaTiO3

Exploration of size effects in Bruggeman effective medium theory

SizeEffects/MgO

Castep

MgO

Exploration of size effects in Bruggeman and Maxwell-Garnett effective medium theories

SizeEffects/ZnO

Vasp

ZnO

Exploration of size effects in Maxwell-Garnett effective medium theory

Vasp/F-Apatite

Vasp

F-Apatite

Maxwell-Garnett, sphere plates and needles, using Vasp 5.3.5

Vasp/Na2SO42

Vasp

Na2(SO4)2

Maxwell-Garnett and Bruggeman, needle, plate and needle, using Vasp 5.3.5

Vasp/Urea

Vasp

Urea

Powder and single crystal exampl, using Vasp 5.4.4

Vasp/ZnO

Vasp

ZnO

Maxwell-Garnett and Bruggeman, needle, plate and needle, mass fraction, using Vasp 5.3.5