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.):
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
faverage
Compute the lateral average of a variable in a plotfile, with optional density weighting. For 2-d, a profile \(f(y)\) is returned where the average was done over \(x\). For 3-d, a profile \(f(z)\) is returned where the average was done over \(x\) and \(y\).
How to build and run
In amrex/Tools/Plotfile, type make programs=faverage and then ./faverage.gnu.ex to run.
Typing ./faverage.gnu.ex without inputs will bring up usage and options.
Example
user@:~/AMReX/amrex/Tools/Plotfile$ ./faverage.gnu.ex -v density plt0000000
will compute the average density as a function of height, outputting a data file
plt0000000.slice.
fgradient
Compute the gradient of variables in a plotfile.
How to build and run
In amrex/Tools/Plotfile, type make programs=fgradient and then ./fgradient.gnu.ex to run.
Typing ./fgradient.gnu.ex without inputs will bring up usage and options.
Example
user@:~/AMReX/amrex/Tools/Plotfile$ ./fgradient.gnu.ex -v density plt0000000
will compute the gradient of density as a function of height, outputting a
new plotfile grad.plt0000000.