Added post proc scripts

[arn-all]

Script to process raw files.

[arn-all]

I organized the post-processing scripts I use the most in a CLI interface. It is installable for easier use (pip install -e .). I added plenty of options to make it very customizable and flexible for my use.
Functionalities are also available from python of course.

Gallery

NEB Relaxation with inter-replica energy spacing (pafi_plot neb log.lammps -E. -E flag is to add the right panel)

Energy profile at the final stage of a NEB, plotted in terminal using plotext (flags -ft). Most functionalities are compatible with this backend.

Simple plot of a PAFI run (default settings with s mode)

Same profile along with an histograp of error and a plot of std, directly inside the terminal ( -t --hist --std)

Evolution of the free energy versus temperature. Files are caught using a glob expression, an arbitrary value of 0.45 is added for 0K, and a linear model is fitted to the data up to 200K (pafi_plot pafi --mode m "T*/pafi/raw*" --H0 0.45 --harmonic-limit 200)

General

usage: pafi_plot [-h] {neb,NEB,pafi,PAFI} ...

options:
  -h, --help           show this help message and exit

Available modes:
  {neb,NEB,pafi,PAFI}
    neb (NEB)          Plot the energy profile from a NEB log.lammps file.
    pafi (PAFI)        Plot the free energy profile from a PAFI run using a
                       raw_ensemble_output file.

NEB Mode

usage: pafi_plot neb [-h] [-f] [-C N] [-n] [-N] [-E] [-R] [--print-profile]
                     [-t] [-s SAVE] [-q] [--size SIZE]
                     log_lammps

positional arguments:
  log_lammps            log.lammps file from a NEB run

options:
  -h, --help            show this help message and exit
  -f, --final           Only display the final stage of the relaxation.
                        Otherwise, profiles at the initial and pre-climb
                        stages are also shown.
  -C N, --cut-at-image N
                        If N is specified, only the first N images will be
                        shown.
  -n, --normalize-r     Normalize r such that its maximum value is 1.0
  -N, --image-number    Show image number instead of reaction coordinate on
                        the x axis
  -E, --energy_diff     Add a subplot showing the spacing of points on the
                        Energy axis. Useful to spot large gaps in energy that
                        would cause a large error for PAFI integration.
  -R, --rcdiff          Add a subplot showing the spacing of points on the r
                        axis. Useful to spot large gaps in reaction
                        coordinate.
  --print-profile       Print NEB profile raw data to terminal.
  -t, --terminal        Experimental: use plotext as backend for display in
                        terminal.
  -s SAVE, --save SAVE  name of a file destination (e.g. "plot.pdf",
                        "plot.png")
  -q, --quiet           Do not open matplotlib popup nor display in terminal.
  --size SIZE           Scaling factor of the figure passed to matplotlib
                        (default is 4).

PAFI Mode

usage: pafi_plot pafi [-h] [--mode {s,m}] [--H0 H0] [--no-fit] [--hist]
                      [--std] [--harmonic-limit HARMONIC_LIMIT] [-t] [-s SAVE]
                      [-q] [--size SIZE]
                      file

positional arguments:
  file                  A PAFI raw_ensemble_output file, or a glob expression
                        that matches a list of raw_ensemble_output files.

options:
  -h, --help            show this help message and exit
  --mode {s,m}          either plot a single or multiple raw files.
  --H0 H0, --zero H0    A value for 0K, e.g obtained from NEB.
  --no-fit              Disable fitting DeltaS on the harmonic domain.
  --hist                Plot an histogram of dF.
  --std                 Plot std for each hyperplane.
  --harmonic-limit HARMONIC_LIMIT
                        The upper temperature limit above which the entropy is
                        considered non-linear. System dependant.
  -t, --terminal        Experimental: use plotext as backend for display in
                        terminal.
  -s SAVE, --save SAVE  name of a file destination (e.g. "plot.pdf",
                        "plot.png")
  -q, --quiet           Do not open matplotlib popup nor display in terminal.
  --size SIZE           Scaling factor of the figure passed to matplotlib
                        (default is 4).