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Add Docs for fboxinfo, fcompare, fextract, etc. to Post-Process…
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273 changes: 270 additions & 3 deletions Docs/sphinx_documentation/source/Post_Processing.rst
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.. _sec:postprocessing:

Post-Processing
===============

The following is a list of tools you may find useful for processing
plotfile data generated by AMReX codes.


WritePlotfileToASCII
====================
--------------------

This basic routine reads in a single-level plotfile and writes the entire contents
to the standard output, one line at a time for each data value.
Expand All @@ -18,14 +25,274 @@ to generate an executable. To run the executable, ``<executable> infile=<plotfi
You can modify the cpp file to write out on certain components, coordinates,
row/column formatting, etc.

|
fextract
========
--------

This basic routine reads in a single-level plotfile and extracts selected contents
along a 1-D axis to an ascii file.

**How to build and run**

In ``amrex/Tools/Plotfile``, just type ``make``
to generate an executable. To run the executable, execute ``fextract.gnu.ex`` to see the full command line
to generate an executable. To run the executable, execute ``./fextract.gnu.ex`` to see the full command line
and all the available options.
It is possible to select the axis (``-d`` flag) where the data are collected. By default the axis is taken at the center of the domain.
A generic ASCII file is generated by default, which contains many details of the simulation. However data can be exported in a raw csv file with the command ``-csv``.

**Example**

.. code-block:: console
user@machine:~/AMReX/amrex/Tools/Plotfile(postproc_docs)$ ./fextract.gnu.ex \
> ~/AMReX/FHDeX/exec/multispec/Reg_Equil_2d_Bench/plt0000003
slicing along x-direction at coarse grid (j,k)=(16,0) and output to /home/user/AMReX/FHDeX/exec/multispec/Reg_Equil_2d_Bench/plt0000003.slice
This produces an ascii file of the form:

.. code-block::
user@machine:~/AMReX/FHDeX/exec/multispec/Reg_Equil_2d_Bench(main)$ cat plt0000003.slice
# 1-d slice in x-direction, file: /home/user/AMReX/FHDeX/exec/multispec/Reg_Equil_2d_Bench/plt0000003
# time = 0.30000000000000004
# x rho rho1 rho2
0.5 2.9993686498953114 0.60059557892152249 1.0502705977511799
1.5 3.0003554204928884 0.59935306004478783 1.0508550827449006
2.5 3.0008794559257246 0.5990345897671786 1.0500559828760208
3.5 2.9997442287698322 0.60001913923213179 1.0508294996618532
4.5 3.0001395958111967 0.60021852440041579 1.0487977074444519
5.5 3.0000989976613459 0.60022830117083248 1.0489080268816791
|
fcompare
--------

Compares two plotfiles, zone by zone, to machine precision
and reports the maximum absolute and relative errors for each
variable.

**How to build and run**

In ``amrex/Tools/Plotfile``, type ``make`` and then ``./fextract.gnu.ex`` to run.
Typing ``./fextract.gnu.ex`` without inputs will bring up usage and options.


**Example**

.. code-block:: console
user@machine:~/AMReX/amrex/Tools/Plotfile$ ./fcompare.gnu.ex \
> ~/AMReX/FHDeX/exec/multispec/Reg_DetBubble_2d_Bench/plt0000000 \
> ~/AMReX/FHDeX/exec/multispec/Reg_DetBubble_2d_Bench/plt0000003
variable name absolute error relative error
(||A - B||) (||A - B||/||A||)
----------------------------------------------------------------------------
level = 0
rho 0.020039805 0.00845645443
rho1 0.01703166127 0.01450634203
rho2 0.01737072831 0.01479513491
rho3 0.01436258458 0.01436258458
c1 0.003022939351 0.00610148453
c2 0.003167240107 0.006392740399
c3 0.006190179458 0.006190179458
averaged_velx 0.0001120979347 0.02141254606
averaged_vely 0.0001120979347 0.02141254606
shifted_velx 0.0001151524563 0.02145887678
shifted_vely 0.0001151524563 0.02145887678
pres 0.05687549245 1.797693135e+308
|
fboxinfo
--------

Displays information about AMR levels and boxes. Works with
1-, 2- or 3-dimensional datasets.

**How to build and run**

In ``amrex/Tools/Plotfile``, type ``make`` and then ``./fboxinfo.gnu.ex`` to run.
Typing ``./fboxinfo.gnu.ex`` without inputs will bring up usage and options.

**Example**

.. code-block:: console
user@machine:~/AMReX/amrex/Tools/Plotfile$ ./fboxinfo.gnu.ex \
> ~/AMReX/FHDeX/exec/multispec/Reg_DetBubble_2d_Bench/plt0000000
plotfile: /home/user/AMReX/FHDeX/exec/multispec/Reg_DetBubble_2d_Bench/plt0000000
level 0: number of boxes = 4, volume = 100.00%
maximum zones = 64 x 64
|
fvarnames
---------

Takes a single plotfile and displays a list of the variables present.

**How to build and run**

In ``amrex/Tools/Plotfile``, type ``make`` and then ``./fvarnames.gnu.ex`` to run.
Typing ``./fvarnames.gnu.ex`` without inputs will bring up usage and description.

**Example**

.. code-block:: console
user@machine:~/AMReX/amrex/Tools/Plotfile$ ./fvarnames.gnu.ex \
> ~/AMReX/FHDeX/exec/multispec/Reg_DetBubble_2d_Bench/plt0000000
0 rho
1 rho1
2 rho2
3 rho3
4 c1
5 c2
6 c3
7 averaged_velx
8 averaged_vely
9 shifted_velx
10 shifted_vely
11 pres
|
ftime
-----

Takes a whitespace separated list of plotfiles and returns the time
for each plotfile.

**How to build and run**

In ``amrex/Tools/Plotfile``, type ``make`` and then ``./ftime.gnu.ex`` to run.
Typing ``./ftime.gnu.ex`` without inputs will bring up usage and description.

**Example**

.. code-block:: console
user@machine :~/AMReX/amrex/Tools/Plotfile$ ./ftime.gnu.ex \
> ~/AMReX/FHDeX/exec/multispec/Spinodal_Charges_2d_Bench/plt0000000 \
> ~/AMReX/FHDeX/exec/multispec/Spinodal_Charges_2d_Bench/plt0000002 \
> ~/AMReX/FHDeX/exec/multispec/Spinodal_Charges_2d_Bench/plt0000004 \
> ~/AMReX/FHDeX/exec/multispec/Spinodal_Charges_2d_Bench/plt0000006
/home/user/AMReX/FHDeX/exec/multispec/Spinodal_Charges_2d_Bench/plt0000000 0
/home/user/AMReX/FHDeX/exec/multispec/Spinodal_Charges_2d_Bench/plt0000002 4.0000000000000001e-13
/home/user/AMReX/FHDeX/exec/multispec/Spinodal_Charges_2d_Bench/plt0000004 8.0000000000000002e-13
/home/user/AMReX/FHDeX/exec/multispec/Spinodal_Charges_2d_Bench/plt0000006 1.1999999999999999e-12
|
fsnapshot
---------

Produces an image of a 2-d plotfile, or a slice of a 3-d plotfile.

**How to build and run**

In ``amrex/Tools/Plotfile``, type ``make`` and then ``./fsnapshot.gnu.ex`` to run.
Typing ``./fsnapshot.gnu.ex`` without inputs will bring up usage and options.

**Example**

In this example an image of the data from the 2-d plotfile ``plt0000003`` is created.

.. code-block:: console
user@silentm:~/AMReX/amrex/Tools/Plotfile$ ./fsnapshot.gnu.ex \
> -v rho -p Palette ~/AMReX/FHDeX/exec/multispec/Reg_DetBubble_2d_Bench/plt0000003
plotfile variable maximum = 2.349724636
plotfile variable minimum = 1
This command tells ``fsnapshot`` to plot the variable ``rho`` using the palette
``Palette`` which is available in the current directory, ``amrex/Tools/Plotfile``.
The image is created in the same directory as the plotfile folder.

.. code-block:: console
user@machine:~/AMReX/amrex/Tools/Plotfile$ ls ~/AMReX/FHDeX/exec/multispec/Reg_DetBubble_2d_Bench/
plt0000000 plt0000003 plt0000003.rho.ppm
The image is produced in the portable pixmap format (.ppm). It can be displayed using
the command ``display`` from `ImageMagick`_ as seen below.

.. _`ImageMagick`: https://imagemagick.org/index.php

.. code-block:: console
user@machine:~/AMReX/amrex/Tools/Plotfile$ display \
> ~/AMReX/FHDeX/exec/multispec/Reg_DetBubble_2d_Bench/plt0000003.rho.ppm
This should produce a window to view the image. (The example here is enlarged for clarity.):

.. image:: figs/ex_fsnapshot_resize.png


|
fnan
----

Takes a single plot file and reports whether each variable contains
NaN values.

**How to build and run**

In ``amrex/Tools/Plotfile``, type ``make`` and then ``./fnan.gnu.ex`` to run.
Typing ``./fnan.gnu.ex`` without inputs will bring up usage and description.

**Example**

.. code-block:: console
user@machine:~/AMReX/amrex/Tools/Plotfile$ ./fnan.gnu.ex \
> ~/AMReX/FHDeX/exec/multispec/Reg_DetBubble_2d_Bench/plt0000003
rho : clean
rho1 : clean
rho2 : clean
rho3 : clean
c1 : clean
c2 : clean
c3 : clean
averaged_velx : clean
averaged_vely : clean
shifted_velx : clean
shifted_vely : clean
pres : clean
In this example, there were no NaN values found in the variable data.

|
fextrema
--------

Report the extrema (min/max) for each variable in a plotfile.

**How to build and run**

In ``amrex/Tools/Plotfile``, type ``make`` and then ``./fextrema.gnu.ex`` to run.
Typing ``./fextrema.gnu.ex`` without inputs will bring up usage and options.

**Example**

.. code-block:: console
user@:~/AMReX/amrex/Tools/Plotfile(postproc_docs)$ ./fextrema.gnu.ex \
> ~/AMReX/FHDeX/exec/multispec/Reg_DetBubble_2d_Bench/plt0000000 \
> ~/AMReX/FHDeX/exec/multispec/Reg_DetBubble_2d_Bench/plt0000003
# time |rho |rho1 |rho2 |rho3 |c1 |c2 |c3 |averaged_velx |averaged_vely |shifted_velx |shifted_vely |pres |
# | min max | min max | min max | min max | min max | min max | min max | min max | min max | min max | min max | min max |
0 1 2.369764441 8.277319027e-17 1.174083806 8.277319027e-17 1.174083806 0.02159682815 1 8.277319027e-17 0.4954432542 8.277319027e-17 0.4954432542 0.009113491527 1 -0.005235152063 0.005235152063 -0.005235152063 0.005235152063 -0.005366192156 0.005366192156 -0.005366192156 0.005366192156 0 0
0.03 1 2.349724636 8.277319027e-17 1.157052145 8.277319027e-17 1.156713078 0.03595941273 1 8.277319027e-17 0.4924203149 8.277319027e-17 0.4922760141 0.01530367099 1 -0.005172583789 0.005172583789 -0.005172583789 0.005172583789 -0.005287367803 0.005287367803 -0.005287367803 0.005287367803 -0.004924487345 0.05687549245
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