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update scripts and input files for diffusion test #3012

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Dec 13, 2024
Merged

update scripts and input files for diffusion test #3012

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e8d96d9
fix diffusion test readme, analysis script and input filename
zhichen3 Dec 12, 2024
90b0e6f
update slice_grid script
zhichen3 Dec 13, 2024
ee20f23
add a 2d spherical geometry input file
zhichen3 Dec 13, 2024
293385a
fix
zhichen3 Dec 13, 2024
c57a25d
Merge branch 'development' into sph_diffusion_test
zhichen3 Dec 13, 2024
789e8b1
rename cyl -> axisymmetric
zhichen3 Dec 13, 2024
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2 changes: 1 addition & 1 deletion Exec/unit_tests/diffusion_test/GNUmakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ DEBUG = FALSE

DIM = 2

COMP = gnu
COMP = gnu

USE_MPI = TRUE
USE_OMP = FALSE
Expand Down
76 changes: 36 additions & 40 deletions Exec/unit_tests/diffusion_test/README.md
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Expand Up @@ -40,27 +40,27 @@ analyic solution) at the end of the simulation. This can be used
for convergence testing.


## 1-d spherical with AMR
## 2-d axisymmetric with AMR

This uses the 2nd order accurate predictor-corrector formulation of
diffusion that is used with the CTU hydrodynamics solver. A test of
the diffusion in 1-d spherical coordinates, with 2 levels of
refinement can be run as:
the diffusion in 2-d cylindrical axisymmetric coordinates,
with 2 levels of refinement can be run as:

```
./Castro2d.gnu.ex inputs.2d.sph
./Castro2d.gnu.ex inputs.2d.sph amr.n_cell=128 256
./Castro2d.gnu.ex inputs.2d.sph amr.n_cell=256 512
./Castro2d.gnu.ex inputs.2d.axisymmetric amr.n_cell=64 128
./Castro2d.gnu.ex inputs.2d.axisymmetric amr.n_cell=128 256
./Castro2d.gnu.ex inputs.2d.axisymmetric amr.n_cell=256 512
```

At the end, each run will report the norm of the error against the
analytic solution, giving:

```
base resolution L-inf error
64 0.0003707056645
128 9.414571162e-05
256 2.437072009e-05
(64 , 128) 0.0003707056645
(128, 256) 9.414571162e-05
(256, 512) 2.437072009e-05
```


Expand Down Expand Up @@ -137,15 +137,15 @@ Warning: BoxArray lengths are not the same at level 0
\begin{center}
\begin{tabular}{|cccc|} \hline
Variable & $e_{4h \rightarrow 2h}$ & Order & $e_{2h \rightarrow h}$\\
\hline
density& 0.000000e+00 & ------------ &0.000000e+00 \\
xmom& 0.000000e+00 & ------------ &0.000000e+00 \\
ymom& 0.000000e+00 & ------------ &0.000000e+00 \\
zmom& 0.000000e+00 & ------------ &0.000000e+00 \\
rho_E& 3.479414e-04 & 2.012958966 & 8.620750e-05 \\
rho_e& 3.479414e-04 & 2.012958966 & 8.620750e-05 \\
Temp& 3.479414e-04 & 2.012958966 & 8.620750e-05 \\
rho_X& 0.000000e+00 & ------------ &0.000000e+00 \\
\hline
density& 0.000000e+00 & ------------ &0.000000e+00 \\
xmom& 0.000000e+00 & ------------ &0.000000e+00 \\
ymom& 0.000000e+00 & ------------ &0.000000e+00 \\
zmom& 0.000000e+00 & ------------ &0.000000e+00 \\
rho_E& 3.479414e-04 & 2.012958966 & 8.620750e-05 \\
rho_e& 3.479414e-04 & 2.012958966 & 8.620750e-05 \\
Temp& 3.479414e-04 & 2.012958966 & 8.620750e-05 \\
rho_X& 0.000000e+00 & ------------ &0.000000e+00 \\
```

(some bits were edited out)
Expand Down Expand Up @@ -190,16 +190,16 @@ Warning: BoxArray lengths are not the same at level 0
\begin{center}
\begin{tabular}{|cccc|} \hline
Variable & $e_{4h \rightarrow 2h}$ & Order & $e_{2h \rightarrow h}$\\
\hline
density& 0.000000e+00 & ------------ &0.000000e+00 \\
xmom& 0.000000e+00 & ------------ &0.000000e+00 \\
ymom& 0.000000e+00 & ------------ &0.000000e+00 \\
zmom& 0.000000e+00 & ------------ &0.000000e+00 \\
rho_E& 1.111626e-05 & 3.948910124 & 7.198104e-07 \\
rho_e& 1.111626e-05 & 3.948910124 & 7.198104e-07 \\
Temp& 1.063477e-05 & 3.952987539 & 6.866892e-07 \\
rho_X& 0.000000e+00 & ------------ &0.000000e+00 \\
pressure& 7.410837e-06 & 3.948910124 & 4.798736e-07 \\
\hline
density& 0.000000e+00 & ------------ &0.000000e+00 \\
xmom& 0.000000e+00 & ------------ &0.000000e+00 \\
ymom& 0.000000e+00 & ------------ &0.000000e+00 \\
zmom& 0.000000e+00 & ------------ &0.000000e+00 \\
rho_E& 1.111626e-05 & 3.948910124 & 7.198104e-07 \\
rho_e& 1.111626e-05 & 3.948910124 & 7.198104e-07 \\
Temp& 1.063477e-05 & 3.952987539 & 6.866892e-07 \\
rho_X& 0.000000e+00 & ------------ &0.000000e+00 \\
pressure& 7.410837e-06 & 3.948910124 & 4.798736e-07 \\
```

e.g. we see fourth-order convergence in the temperature
Expand Down Expand Up @@ -241,18 +241,14 @@ Warning: BoxArray lengths are not the same at level 0
\begin{center}
\begin{tabular}{|cccc|} \hline
Variable & $e_{4h \rightarrow 2h}$ & Order & $e_{2h \rightarrow h}$\\
\hline
density& 0.000000e+00 & ------------ &0.000000e+00 \\
xmom& 0.000000e+00 & ------------ &0.000000e+00 \\
ymom& 0.000000e+00 & ------------ &0.000000e+00 \\
zmom& 0.000000e+00 & ------------ &0.000000e+00 \\
rho_E& 1.902161e-06 & 3.957610923 & 1.224299e-07 \\
rho_e& 1.902161e-06 & 3.957610923 & 1.224299e-07 \\
Temp& 1.770452e-06 & 3.966033724 & 1.132894e-07 \\
\hline
density& 0.000000e+00 & ------------ &0.000000e+00 \\
xmom& 0.000000e+00 & ------------ &0.000000e+00 \\
ymom& 0.000000e+00 & ------------ &0.000000e+00 \\
zmom& 0.000000e+00 & ------------ &0.000000e+00 \\
rho_E& 1.902161e-06 & 3.957610923 & 1.224299e-07 \\
rho_e& 1.902161e-06 & 3.957610923 & 1.224299e-07 \\
Temp& 1.770452e-06 & 3.966033724 & 1.132894e-07 \\
```

e.g. we see fourth-order convergence in the temperature




15 changes: 12 additions & 3 deletions Exec/unit_tests/diffusion_test/analysis/profiles.py
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Expand Up @@ -12,6 +12,8 @@
import matplotlib.pyplot as plt

import yt
from yt.frontends.boxlib.api import CastroDataset


## Define RGBA to HEX
def rgba_to_hex(rgba):
Expand All @@ -22,15 +24,22 @@ def rgba_to_hex(rgba):

def get_T_profile(plotfile):

ds = yt.load(plotfile)
ds = CastroDataset(plotfile)

time = float(ds.current_time)
ad = ds.all_data()

# Sort the ray values by 'x' so there are no discontinuities
# in the line plot
srt = np.argsort(ad['x'])
x_coord = np.array(ad['x'][srt])

coords = {"cartesian":"x",
"cylindrical":"z",
"spherical":"r"}

coord = coords[ds.geometry]

srt = np.argsort(ad[coord])
x_coord = np.array(ad[coord][srt])
temp = np.array(ad['Temp'][srt])

return time, x_coord, temp
Expand Down
26 changes: 20 additions & 6 deletions Exec/unit_tests/diffusion_test/analysis/slice_grid.py
100644 → 100755
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@@ -1,14 +1,28 @@
#!/usr/bin/env python3

import sys
import yt
from yt.frontends.boxlib.api import CastroDataset

"""
Give a temperature slice plot for 2d plot file
"""

fname = sys.argv[1]
ds = CastroDataset(fname)

ds = yt.load("diffuse_plt00147")
slice_dirs = {"cylindrical":"theta",
"spherical":"phi"}
slice_dir = slice_dirs[ds.geometry]

slc = yt.SlicePlot(ds, "theta", "Temp")
slc.annotate_grids()
slc.set_figure_size(16)
slc = yt.SlicePlot(ds, slice_dir, "Temp")
if ds.geometry == "cylindrical":
slc.annotate_grids()
slc.set_figure_size(12)
slc.set_buff_size(1600)
slc.set_font_size(64)
slc.set_font_size(24)
slc.set_cmap("Temp", "plasma_r")
slc.set_log("Temp", False)
slc.set_axes_unit("cm")

slc.save("diffusion_temp_amr.pdf")
slc.save("diffusion_temp.png")
70 changes: 70 additions & 0 deletions Exec/unit_tests/diffusion_test/inputs.2d.axisymmetric
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@@ -0,0 +1,70 @@
# ------------------ INPUTS TO MAIN PROGRAM -------------------
max_step = 50000
stop_time = 0.001

# PROBLEM SIZE & GEOMETRY
geometry.is_periodic = 0 0
geometry.coord_sys = 1 # 1 = RZ
geometry.prob_lo = 0.0 0.0
geometry.prob_hi = 0.5 1.0
amr.n_cell = 64 128

# >>>>>>>>>>>>> BC FLAGS <<<<<<<<<<<<<<<<
# 0 = Interior 3 = Symmetry
# 1 = Inflow 4 = SlipWall
# 2 = Outflow 5 = NoSlipWall
# >>>>>>>>>>>>> BC FLAGS <<<<<<<<<<<<<<<<
castro.lo_bc = 3 2
castro.hi_bc = 2 2

# WHICH PHYSICS
castro.do_hydro = 0
castro.diffuse_temp = 1
castro.do_react = 0

# TIME STEP CONTROL

castro.cfl = 0.5 # cfl number for hyperbolic system
castro.init_shrink = 0.1 # scale back initial timestep
castro.change_max = 1.1 # maximum increase in dt over successive steps

# DIAGNOSTICS & VERBOSITY
castro.sum_interval = 1 # timesteps between computing mass
castro.v = 1 # verbosity in Castro.cpp
amr.v = 1 # verbosity in Amr.cpp
#amr.grid_log = grdlog # name of grid logging file

# REFINEMENT / REGRIDDING
amr.max_level = 1 # maximum level number allowed
amr.ref_ratio = 2 2 2 2 # refinement ratio
amr.regrid_int = 2 # how often to regrid
amr.blocking_factor = 8 # block factor in grid generation
amr.max_grid_size = 32

amr.refinement_indicators = temperr tempgrad

amr.refine.temperr.value_greater = 1.1
amr.refine.temperr.field_name = Temp
amr.refine.temperr.max_level = 3

amr.refine.tempgrad.gradient = 0.1
amr.refine.tempgrad.field_name = Temp
amr.refine.tempgrad.max_level = 3

# CHECKPOINT FILES
amr.check_file = diffuse_chk # root name of checkpoint file
amr.check_int = 1000 # number of timesteps between checkpoints

# PLOTFILES
amr.plot_file = diffuse_plt
amr.plot_int = 10
amr.derive_plot_vars=ALL

# PROBLEM PARAMETERS
problem.diff_coeff = 1.0

# CONDUCTIVITY
conductivity.const_conductivity = 10.0

# EOS
eos.eos_assume_neutral = 1
18 changes: 10 additions & 8 deletions Exec/unit_tests/diffusion_test/inputs.2d.sph
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Expand Up @@ -4,20 +4,22 @@ stop_time = 0.001

# PROBLEM SIZE & GEOMETRY
geometry.is_periodic = 0 0
geometry.coord_sys = 1 # 1 = RZ
geometry.prob_lo = 0.0 0.0
geometry.prob_hi = 0.5 1.0
amr.n_cell = 64 128
geometry.coord_sys = 2 # 2 = SPHERICAL
geometry.prob_lo = 0.00001 0.0
geometry.prob_hi = 1.0 3.141592653589793238
amr.n_cell = 64 64

castro.allow_non_unit_aspect_zones = 1

# >>>>>>>>>>>>> BC FLAGS <<<<<<<<<<<<<<<<
# 0 = Interior 3 = Symmetry
# 1 = Inflow 4 = SlipWall
# 2 = Outflow 5 = NoSlipWall
# >>>>>>>>>>>>> BC FLAGS <<<<<<<<<<<<<<<<
castro.lo_bc = 3 2
castro.hi_bc = 2 2
castro.lo_bc = 3 3
castro.hi_bc = 2 3

# WHICH PHYSICS
# WHICH PHYSICS
castro.do_hydro = 0
castro.diffuse_temp = 1
castro.do_react = 0
Expand All @@ -35,7 +37,7 @@ amr.v = 1 # verbosity in Amr.cpp
#amr.grid_log = grdlog # name of grid logging file

# REFINEMENT / REGRIDDING
amr.max_level = 1 # maximum level number allowed
amr.max_level = 0 # maximum level number allowed
amr.ref_ratio = 2 2 2 2 # refinement ratio
amr.regrid_int = 2 # how often to regrid
amr.blocking_factor = 8 # block factor in grid generation
Expand Down
10 changes: 7 additions & 3 deletions Exec/unit_tests/diffusion_test/prob_util.H
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Expand Up @@ -5,7 +5,7 @@ AMREX_GPU_HOST_DEVICE AMREX_INLINE
Real analytic(const Real* r, const Real time, const int coord_type) {

Real exponent;
if (AMREX_SPACEDIM == 1 && coord_type == 2) {
if (coord_type == 2) {
// Handle spherical coordinates
exponent = 3.0_rt / 2.0_rt;
} else if (AMREX_SPACEDIM == 2 && coord_type == 1) {
Expand All @@ -16,8 +16,12 @@ Real analytic(const Real* r, const Real time, const int coord_type) {
}

Real dist2 = 0.0;
for (int d = 0; d < AMREX_SPACEDIM; d++) {
dist2 += r[d] * r[d];
if (coord_type == 2) {
dist2 = r[0]*r[0];
} else {
for (int d = 0; d < AMREX_SPACEDIM; d++) {
dist2 += r[d] * r[d];
}
}

Real temp = problem::T1 + (problem::T2 - problem::T1) *
Expand Down
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