anchor.diff:  
   | Option | Default | Purpose | Repeatable? 
   
  -| -program s |  | Specifies the program used in generating the output which will be analysed| No 
  +| -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 
   | -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 
  
positive.code: 
  * 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 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
  
negative.code: 
   pdielec -program gulp -matrix hdpe -method ap -method maxwell -sphere -plate -1 -1 -2 -vmax 2000 -vf 0.1 calcite.gout  -csv calcite.csv
  
  The Phonopy program may also be used to generate the dynamical matrix at the gamma point.  Phonopy drives a number of programs to calculate the dynamical matrix numerically.  The pdielec interface has so far only be tested for Phonopy/VASP and requires the output of a calculation of the Born charges using VASP.
  An example of its use is;
  
   pdielec -program phonopy vasp OUTCAR -matrix hdpe -method ap -method maxwell -sphere -plate -1 -1 -2 -vmax 2000 -vf 0.1 -csv calcite.csv
  
  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.
  
  
  == Command line options
  
  .Table Command line options
  