another cleanup

teuben · Jun 30, 2023 · 6c91c92 · 6c91c92
1 parent 9b16124
commit 6c91c92
Showing 1 changed file with 38 additions and 19 deletions.
diff --git a/README.md b/README.md
@@ -17,15 +17,19 @@ into the executable. Some older comments on athena++ can be found below.
 
 Again, an example how to compile and run the code
 
+```bash
      git clone --recursive https://gitlab.com/theias/hpc/jmstone/athena-parthenon/athenak
      mkdir athenak/build
      cd athenak/build
      cmake ..
      make -j
+```
 
 or if you're lazy, use the Makefile in this directory:
 
+```bash
      make build
+```     
 
 this takes a bit longer than athena++,
 mostly because the kokkos library has to be compiled with).   The binary is
@@ -67,22 +71,28 @@ build/src/athena -i inputs/hydro/viscosity.athinput         -d run8
 
 First we grab and compile the code for the linear wave problem
 
+```bash
      git clone https://github.com/PrincetonUniversity/athena
      cd athena
      ./configure.py --prob linear_wave
      make clean
      make -j
+```     
 
 Compiling the code takes the most time, but on a typical laptop well under 30 seconds.
 
 After this we can run it
 
+```bash
      bin/athena  -i inputs/hydro/athinput.linear_wave1d  -d run1
+```          
 
 but the default output from that **athinput** file is the **vtk** data format, which for this demo will
 be too complex to parse. TBD. For now we switch to the ascii table format, viz.
 
+```bash
      bin/athena  -i inputs/hydro/athinput.linear_wave1d  -d run2 output2/file_type=tab
+```
 
 ### Animations
 
@@ -91,41 +101,50 @@ in each table shows the columns names:
 
 
 ```text
-  # Athena++ data at time=0.000000e+00  cycle=0  variables=prim 
-  # i       x1v         rho          press          vel1         vel2         vel3     
+# Athena++ data at time=0.000000e+00  cycle=0  variables=prim 
+# i       x1v         rho          press          vel1         vel2         vel3     
 ```
 
+this would be an animation of *x1v* vs. *vel1*
+
 ```bash
-for f in LinWave*.tab; do
-   tabplot $f xcol=2 ycol=5
-done
+     for f in LinWave*.tab; do
+        tabplot $f xcol=2 ycol=5
+     done
 ```
 
 or using our sample script
+
 ```bash
-   ../../animate1 xcol=2 ycol=5
+     ../../animate1 xcol=x1v ycol=vel1
 ```
 
 if **tkrun** is enabled, use
 
-   tkrun ../../animate1 
+```bash
+     tkrun ../../animate1
+```
+
+but this may be broken by now.
 
 
 ### Statistics
 
 The history (hst) keeps track of a number of variables of which we can obtain the statistics (agui/show_stats)
 
 ```text
-#        [1]=time     [2]=dt      [3]=mass [4]=1-mom    [5]=2-mom [6]=3-mom [7]=1-KE    [8]=2-KE [9]=3-KE [10]=tot-E [11]=max-v2
-npt:     501          501         501      501          501       501       501         501      501      501        501
-min:     0            1.31217e-05 1        -3.14329e-22 0         0         2.49497e-13 0        0        0.9        0
-max:     5            0.003125    1        3.19912e-22  0         0         2.5e-13     0        0        0.9        0
-sum:     1253.43      1.56251     501      -1.56725e-20 0         0         1.25127e-10 0        0        450.9      0
-mean:    2.50186      0.00311879  1        -3.12825e-23 0         0         2.49754e-13 0        0        0.9        0
-disp:    1.44625      0.00013889  0        8.61373e-23  0         0         1.46346e-16 0        0        0          0
-skew:    -4.15046e-05 -22.316     0        0.0211432    0         0         -0.0439997  0        0        0          0
-kurt:    -1.20002     496.002     0        0.579502     0         0         -1.23003    0        0        0          0
-min/sig: -1.72989     -22.3607    -nan     -3.28599     -nan      -nan      -1.75681    -nan     -nan     inf        -nan
-max/sig: 1.72732      0.0447214   -nan     4.07715      -nan      -nan      1.68025     -nan     -nan     inf        -nan
-median:  2.50312      0.003125    1        -3.21566e-23 0         0         2.49757e-13 0        0        0.9        0
+#col    [1]          [2]         [3]    [4]          [5]     [6]     [7]         [8]     [9]    [10]      [11]
+#name   time         dt          mass   1-mom        2-mom   3-mom   1-KE        2-KE    3-KE    tot-E     max-v2
+
+npt:    501          501         501    501          501     501     501         501     501     501       501
+min:    0            1.31217e-05 1      -3.14329e-22 0       0       2.49497e-13 0       0       0.9       0
+max:    5            0.003125    1      3.19912e-22  0       0       2.5e-13     0       0       0.9       0
+sum:    1253.43      1.56251     501    -1.56725e-20 0       0       1.25127e-10 0       0       450.9     0
+mean:   2.50186      0.00311879  1      -3.12825e-23 0       0       2.49754e-13 0       0       0.9       0
+disp:   1.44625      0.00013889  0      8.61373e-23  0       0       1.46346e-16 0       0       0         0
+skew:   -4.15046e-05 -22.316     0      0.0211432    0       0       -0.0439997  0       0       0         0
+kurt:   -1.20002     496.002     0      0.579502     0       0       -1.23003    0       0       0         0
+min:    -1.72989     -22.3607    -nan   -3.28599     -nan    -nan    -1.75681    -nan    -nan    inf       -nan
+max:    1.72732      0.0447214   -nan   4.07715      -nan    -nan    1.68025     -nan    -nan    inf       -nan
+median: 2.50312      0.003125    1      -3.21566e-23 0       0       2.49757e-13 0       0       0.9       0
 ```