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. After reading in the plotfile to a MultiFab, the program copies the data into a separate MultiFab with one large grid to make writing the data out sequentially an easier task.

In amrex/Tools/Postprocessing/C_Src, edit GNUMakefile to read EBASE = WritePlotfileToASCII and NEEDS_f90_SRC = FALSE and then make to generate an executable. To run the executable, <executable> infile=<plotfilename>. 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 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

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:

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 ./fcompare.gnu.ex to run. Typing ./fcompare.gnu.ex without inputs will bring up usage and options.

Example

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

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

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

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.

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.

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.

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.):

_images/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

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

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