Add new setup for 3D flame propagation through a tube

Exec/science/flame_tube/GNUmakefile

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+PRECISION  = DOUBLE
+PROFILE    = FALSE
+
+DEBUG      = FALSE
+
+DIM        = 3
+
+COMP	   = gnu
+
+USE_MPI    = TRUE
+
+USE_GRAV   = TRUE
+USE_REACT  = TRUE
+
+USE_ROTATION  = FALSE
+USE_DIFFUSION = TRUE
+
+# define the location of the CASTRO top directory
+CASTRO_HOME  := ../../..
+
+USE_JACOBIAN_CACHING = TRUE
+USE_CXX_MODEL_PARSER = TRUE
+NUM_MODELS := 2
+
+# This sets the EOS directory in $(MICROPHYSICS_HOME)/eos
+EOS_DIR     := helmholtz
+
+# This sets the network directory in $(MICROPHYSICS_HOME)/networks
+NETWORK_DIR := aprox13
+
+INTEGRATOR_DIR := VODE
+
+CONDUCTIVITY_DIR := stellar
+
+Bpack   := ./Make.package
+Blocs   := .
+
+include $(CASTRO_HOME)/Exec/Make.Castro

Exec/science/flame_tube/Make.package

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+CEXE_headers += initial_model.H
+

Exec/science/flame_tube/README.md

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+# flame_tube
+
+This is a slightly modified version of flame_wave that models a 3-d flame
+propagating through a tube shaped domain, with a periodic boundary along the
+transverse horizontal direction (y).

Exec/science/flame_tube/_prob_params

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+
+dtemp                   real              3.81e8_rt                 y
+
+x_half_max              real              1.2e5_rt                  y
+
+x_half_width            real              3.6e4_rt                  y
+
+# cutoff mass fraction of the first species for refinement
+X_min                   real              1.e-4_rt                  y
+
+# do we dynamically refine based on density? or based on height?
+tag_by_density          integer           1                         y
+
+# used for tagging if tag_by_density = 1
+cutoff_density          real              500.e0_rt                 y
+
+# used if we are refining based on height rather than density
+refine_height           real              3600                      y
+
+dx_model                real              10.0_rt                   y
+
+T_hi                    real              5.e8_rt                   y
+
+T_star                  real              1.e8_rt                   y
+
+T_lo                    real              5.e7_rt                   y
+
+dens_base               real              2.e6_rt                   y
+
+H_star                  real              500.e0_rt                 y
+
+atm_delta               real              25.e0_rt                  y
+
+fuel1_name              character         "helium-4"                y
+
+fuel2_name              character         ""                        y
+
+fuel3_name              character         ""                        y
+
+fuel4_name              character         ""                        y
+
+ash1_name               character         "iron-56"                 y
+
+ash2_name               character         ""                        y
+
+ash3_name               character         ""                        y
+
+fuel1_frac              real              1.0_rt                    y
+
+fuel2_frac              real              0.0_rt                    y
+
+fuel3_frac              real              0.0_rt                    y
+
+fuel4_frac              real              0.0_rt                    y
+
+ash1_frac               real              1.0_rt                    y
+
+ash2_frac               real              0.0_rt                    y
+
+ash3_frac               real              0.0_rt                    y
+
+low_density_cutoff      real              1.e-4_rt                  y
+
+smallx                  real              1.e-10_rt                 y
+
+x_refine_distance       real              1.e30_rt                  y
+
+max_hse_tagging_level   integer           2                         y
+
+max_base_tagging_level  integer           1                         y

Exec/science/flame_tube/analysis/vis_3d/andes-single.submit

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+#!/bin/bash
+#SBATCH -A ast106
+#SBATCH -J flame_tube_vr
+#SBATCH -N 1
+#SBATCH -t 4:00:00
+
+set -u
+
+cd $SLURM_SUBMIT_DIR
+
+source "/ccs/proj/ast106/$USER/mambaforge_$(uname -m)/etc/profile.d/conda.sh"
+conda activate andes_yt_dev
+
+plotfiles=(run_256/flame_tube_25cm_smallplt*)
+plotfiles=(run_256_extra_plotfiles/flame_tube_25cm_smallplt0039200)
+#plotfile=flame_wave_1000Hz_25cm_smallplt207887
+#plotfile=flame_wave_1000Hz_25cm_smallplt40842
+
+#for i in flame_wave_1000Hz_25cm_smallplt*[0-9]
+todo=()
+for f in "${plotfiles[@]}"; do
+  dest=${f/run_/analysis_}
+  # check the last image generated for each plotfile
+  #if ! [[ -f "${dest}_enuc_annotated_top.png" ]]; then
+    todo+=("$f")
+  #fi
+done
+
+export OMP_NUM_THREADS=16
+if [[ ${#todo[@]} -gt 0 ]]; then
+  srun --cpu-bind=no python ~/dev/Castro/Exec/science/flame_tube/analysis/vis_3d/vol-xrb.py "${todo[@]}"
+fi
+
+echo "done!"

Exec/science/flame_tube/analysis/vis_3d/andes-slice.submit

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+#!/bin/bash
+#SBATCH -A ast106
+#SBATCH -J plots
+#SBATCH -N 1
+#SBATCH -t 8:00:00
+#SBATCH -p gpu
+
+cd $SLURM_SUBMIT_DIR
+
+#plotfile=flame_wave_1000Hz_25cm_smallplt207887
+#plotfile=flame_wave_1000Hz_25cm_smallplt40842
+
+source activate andes_env
+
+srun python slice_vertical.py flame_wave_1000Hz_25cm_smallplt174562
+
+

Exec/science/flame_tube/analysis/vis_3d/andes.submit

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+#!/bin/bash
+#SBATCH -A ast106
+#SBATCH -J plots
+#SBATCH -N 1
+#SBATCH -t 8:00:00
+
+cd $SLURM_SUBMIT_DIR
+
+source "/ccs/proj/ast106/$USER/mambaforge_$(uname -m)/etc/profile.d/conda.sh"
+conda activate andes_yt_dev
+
+plotfile=run_256_extra_plotfiles/flame_tube_25cm_smallplt0039200
+#plotfile=flame_wave_1000Hz_25cm_smallplt207887
+#plotfile=flame_wave_1000Hz_25cm_smallplt40842
+
+#for i in flame_wave_1000Hz_25cm_smallplt*[0-9]
+export OMP_NUM_THREADS=16
+for i in $plotfile; do
+  dest=${i/run_/analysis_}
+  if ! [[ -f "${dest}_abar_annotated_top.png" ]]; then
+    srun --cpu-bind=no python ~/dev/Castro/Exec/science/flame_tube/analysis/vis_3d/vol-xrb-abar.py "${i}"
+    srun --cpu-bind=no python ~/dev/Castro/Exec/science/flame_tube/analysis/vis_3d/vol-xrb-enuc.py "${i}"
+  fi
+done
+
+echo "done!"

Exec/science/flame_tube/analysis/vis_3d/slice_vertical.py

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+import argparse
+import os
+import sys
+
+import matplotlib
+import matplotlib.pyplot as plt
+import numpy as np
+from mpl_toolkits.axes_grid1 import ImageGrid
+
+import yt
+from yt.frontends.boxlib.api import CastroDataset
+# assume that our data is in CGS
+from yt.units import amu, cm
+
+matplotlib.use('agg')
+
+
+
+
+def doit(plotfiles):
+
+    plotfile = sys.argv[1]
+    ds = CastroDataset(plotfile)
+
+    xmin = ds.domain_left_edge[0]
+    xmax = ds.domain_right_edge[0]
+    xctr = 0.5 * (xmin + xmax)
+    L_x = (2./3.) * (xmax - xmin)
+
+    ymin = ds.domain_left_edge[1]
+    ymax = ds.domain_right_edge[1]
+    yctr = 0.5*(ymin + ymax)
+
+    zmin = 0.0*cm
+    zmax = 1.e4*cm
+
+    zctr = 0.5*(zmin + zmax)
+    L_z = zmax - zmin
+
+    fig = plt.figure()
+
+    grid = ImageGrid(fig, 111, nrows_ncols=(len(plotfiles), 1),
+                     axes_pad=0.25, label_mode="L",
+                     cbar_mode="single", cbar_size="0.5%")
+
+    for i, pf in enumerate(plotfiles):
+
+        ds = CastroDataset(pf)
+
+        f = "abar"
+
+        sp = yt.SlicePlot(ds, "y", f, origin="native", center=[xctr, yctr, zctr],
+                          width=[L_z, L_x], fontsize="9")
+        sp.set_buff_size((4800,4800))
+        sp.swap_axes()
+
+        sp.set_zlim(f, 4, 5)
+        sp.set_log(f, False)
+        sp.set_cmap(f, "plasma_r")
+
+        sp.set_axes_unit("cm")
+
+        sp.annotate_text((0.8, 0.9), "{:5.2f} ms".format(1000.0*float(ds.current_time.in_cgs())),
+                         coord_system="axis", text_args={"color": "black", "size": 9})
+
+        plot = sp.plots["abar"]
+        plot.figure = fig
+        plot.axes = grid[i].axes
+        plot.cax = grid.cbar_axes[i]
+        if i < len(plotfiles)-1:
+            grid[i].axes.xaxis.offsetText.set_visible(False)
+
+        sp._setup_plots()
+
+    fig.set_size_inches(10.0, 3.5)
+    fig.subplots_adjust(left=0.05, right=0.95, top=0.95, bottom=0.05)
+    fig.savefig("time_series_3D.pdf")
+
+if __name__ == "__main__":
+
+    p = argparse.ArgumentParser()
+
+    p.add_argument("--skip", type=int, default=1,
+                   help="interval between plotfiles")
+    p.add_argument("plotfiles", type=str, nargs="+",
+                   help="list of plotfiles to plot")
+
+    args = p.parse_args()
+
+    plot_prefix = args.plotfiles[0].split("plt")[0] + "plt"
+    plot_nums = sorted([p.split("plt")[1] for p in args.plotfiles], key=int)
+
+    plotfiles = []
+    for n in range(0, len(plot_nums), args.skip):
+        plotfiles.append("{}{}".format(plot_prefix, plot_nums[n]))
+
+    doit(plotfiles)