anchor.diff:  This assumes that the dynamical matrix has been calculation at the gamma point using phonopy and is stored in the files qpoints.yaml in the current directory.  There should also be a phonopy.yaml file present in the same directory.  By default the PHONOPY interface will use the atomic weights in the OUTCAR file.  It is recommended that PDielec replace these with its own internal atomic weights.  The use of 'isotope' should give results consistent with PHONOPY's own results.
   
   
  -== Command line options
  +=== Command line options
   
   .Table Command line options
   |===
   
   | Option | Default | Purpose | Repeatable? 
   
  -| -program s |  | Specifies the program used in generating the output which will be analysed. Options are *castep*, *gulp*, *abinit*, *phonopy*, *vasp*, *crystal* or *qe*| No 
  -| -method s | *maxwell* | The method is given by the string s and may be either *ap*, *maxwell* or *bruggeman*| Yes 
  +| -program s |  | Specifies the program used in generating the output which will be analysed. Options are *castep*, *gulp*, *abinit*, *phonopy*, *vasp*, *crystal*, *experiment* or *qe*| No 
  +| -method s | *maxwell* | The method is given by the string s and may be either *ap*, *maxwell*, *mie* or *bruggeman*| Yes 
   | -sphere | | The inclusion is a sphere, the default if no other shape is given | No
   | -needle h k l | | The inclusion is a needle whose unique direction is given by [hkl] | Yes 
   | -plate h k l | | The inclusion is a plate whose surface is defined by (hkl) | Yes
   | -ellipse h k l z | | The inclusion is an ellipsoid whose unique direction is given by [hkl] and the eccentricity is given by z | Yes
   | -vf z | 0.1 | z specifies the volume fraction | Yes
   | -mf z | 0.0 | z specifies the mass fraction | Yes
  +| -size z1 [z2] | 0.0 | z1 specifies the radius in microns of a sphere for the *bruggeman*, *maxwell* and *mie* methods.  If z2 is specified a log-normal distribution for the *mie* method is used | Yes
   | -matrix s | *ptfe* | The supporting matrix is defined by the string s.  Options are *ptfe*, *kbr*, *nujol*, *air*, *vacuum*, *ldpe*, *mdpe*, *hdpe* | Yes
   | -density z | 2.2 | z defines the density of the supporting matrix | No
   | -dielectric z | 2.0 | z defines the dielectric of the supporting matrix | No
  
positive.code: | -vm z | 300.0 | The final wavenumber for the frequency range | No
  | -i z | 0.2 | The increment wavenumber used to cover the frequency range | No
  | -plot s | | A plot is requested the string s can be *absorption*, *molar_absorption*, *real*, or *imaginary* | Yes
  | -csv s | | Output is sent to a comma delimited file specified by the string s | No
  | -csv_ext s | | Output is sent to 3 comma delimited files specified by the string s_frequencies.csv s_spectrum.csv and s_command.csv | No
  | -print | | Additional output is printed regarding the QM/MM program | No
  
negative.code: 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.  
  
  == Installation
  The pdielec package is written in Python and has been tested using Python 2.7 and Python 3.6.4 on Linux and in Windows 10.
  The package is available on GitHub and can be downloaded from https://github.com/JohnKendrick/PDielec
  An auxilliary program, preader, is also distributed.  This command summarises the output from the solid state packages as a csv file which can be simply read as a spread sheet.
  
   git clone https://github.com/JohnKendrick/PDielec.git
  
  === Linux
  Both Python 2.7 and Python 3 or supported.  Install Python using the package manager for your version of Linux or get your IT manager to do it for you..  In addition install python versions of yaml, numpy, scipy, pymiescatt, pyyaml, xlsxwriter, termcolor and matplotlib.  They can be installed using the pip program in Python.  If the user does not have administrator rights on the machine then the use of pip install --user will install the python modules in a user's directory.  If the user does have administrator rights and wants to install the packages for all users then the '--user' option can be omitted.
  
   pip install --user numpy
   pip install --user scipy
   pip install --user matplotlib
   pip install --user PyYaml
   pip install --user PyMieScatt
   pip install --user XlsxWriter
   pip install --user termcolor
  
  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 for me 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
    make install
  
  This copies the commands and modules to the \~/bin directory which should be included in your PATH environment variable.
  
   export PATH=~/bin;$PATH
  
   
  === Windows
  A Windows 10 installation which works for users without administrator rights involves a few steps but gives an installation which can run 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 you process choose to install the Quick Launch and Desktop icons as these make using the program easier. 
  * If you are not familar 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 replace by the Unix commands.  
  * 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 hickups 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 completed.  When this happens I kill the setup process with the task manager
  
  ==== Install make
  Once you have Git installed open the "Git bash" shell and create the following directories in your home directory;
  
    mkdir bin
    mkdir Software
  
  From the web url http://www.equation.com/servlet/equation.cmd?fa=make download the 64-bit version of make.exe and copy it into your bin/ directory.  You should find this directory in c:\users\yourusername\bin in the file manager.
  
  ==== Install Python
  * From https://www.python.org/downloads/windows/ download and run the Windows x86-64 executable installer for the latest Python 3.6 version
  * Uncheck install launcher for all users
  * Check "Add Python 3.6 to PATH"
  * Click on "Install now" button
  * Check installation ran OK by running the Idle
  
  ==== Install additional Python modules for PDielec
  Open a Git Bash Console and type;
  
   pip install numpy
   pip install scipy
   pip install matplotlib
   pip install PyYaml
   pip install PyMieScatt
   pip install XlsxWriter
   pip install termcolor
  
  ==== Install PDielec
  Open a Git Bash Console and type;
  
    cd Software
    git clone https://github.com/JohnKendrick/PDielec.git
  
  This should create a directory in Software called PDielec
  
  ==== Testing PDielec
  Open a Git Bash Console and type;
  
    cd Software/PDielec
    make test_preader
    make test_pdielec
  
  ==== Installing PDielec to run in any Git Bash Console
  Open a Git Bash Console and type;
  
    cd Software/PDielec
    export SCRIPTS=~/bin
    make install
  
  ==== Updating PDielec from the Git repository
  Open a Git Bash Console and type;
  
    cd Software/PDielec
    git pull
  
  === PDielec Directory structure
  
  * PDielec/ is the home directory and contains the `pdielec` and `preader` commands
  * PDielec/Python holds the source for the modules used by the pdielec and preader commands
  * PDielec/Examples a set of examples are 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.
  
  === Examples
  Each example directory has the relevant input data sets use to run the QM/MM program and the output files from that run which are post-processed by PDielec.  There is a file `command.sh` which contains a typical example of a PDielec command line and which has been used to create the reference output files `command.ref.out` and `csvfile.ref.csv`.  The example can be run
  
   bash command.sh
  