2. Installation

2.1. Anaconda

Unless you are interested in the full Anaconda 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 Anaconda 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 Anaconda can be performed on Linux, Windows, and Mac systems. However, there are no example files installed, only the executables. 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 Anaconda, 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.

2.2. PyPi

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

pip install --user pdielec
pdgui

2.3. 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. To make the program generally available to the user:

cd ~/Software/PDielec
pdmake install

This copies the commands and modules to the ~/bin directory which should be included in your PATH environment variable.:

export PATH=~/bin;$PATH

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

pyqt5
psutil
numpy
scipy
dill
matplotlib
pyopengl
openpyxl
pyyaml
xlsxwriter
termcolor
imageio
imageio-ffmpeg
scikit-learn

2.4. GitHub - Windows

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

2.4.1. Installation from repository

This Windows installation method is only needed if installation through Anaconda 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.

2.4.1.1. 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

2.4.1.2. 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 pyqt5
pip install psutil
pip install numpy
pip install scipy
pip install dill
pip install matplotlib
pip install pyopengl
pip install openpyxl
pip install pyyaml
pip install xlsxwriter
pip install termcolor
pip install imageio
pip install imageio-ffmpeg
pip install sklearn

2.4.1.3. 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.

2.4.1.4. Testing PDielec

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

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

2.4.1.5. Installing PDielec to run in any git bash console

Open a git bash console and type;:

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

2.4.1.6. Updating PDielec from the git repository

Open a git bash console and type;:

cd Software/PDielec
git pull

2.5. 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.

2.6. 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 2.1 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
QE/Cocaine	Quantum Espresso	Cocaine	Maxwel-Garnett sphere
QE/Na2SO42	Quantum Espresso	Na2(SO4)2	Maxwell-Garnett and Bruggeman on needle, ellipsoid and plate
QE/ZnO	Quantum Espresso	ZnO	Maxwell-Garnett and Bruggeman on needle, ellipsoid and plate
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
Vasp/Na2SO42	Vasp	Na2(SO4)2	Maxwell-Garnett and Bruggeman, needle, plate and needle
Vasp/ZnO	Vasp	ZnO	Maxwell-Garnett and Bruggeman, needle, plate and needle, mass fraction