update subchandra volume rendering scripts

Exec/science/subchandra/analysis/subch_slice_3d.py

@@ -0,0 +1,102 @@
+#!/usr/bin/env python3
+
+import os
+import sys
+from functools import reduce
+
+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')
+
+
+
+
+plotfile = sys.argv[1]
+ds = CastroDataset(plotfile)
+
+domain_frac = 0.2
+
+xmin = ds.domain_left_edge[0]
+xmax = ds.domain_right_edge[0]
+xctr = 0.5 * (xmin + xmax)
+L_x = xmax - xmin
+xmin = xctr - 0.5 * domain_frac * L_x
+xmax = xctr + 0.5 * domain_frac * L_x
+L_x = xmax - xmin
+
+ymin = ds.domain_left_edge[1]
+ymax = ds.domain_right_edge[1]
+yctr = 0.5 * (ymin + ymax)
+L_y = ymax - ymin
+ymin = yctr - 0.5 * domain_frac * L_y
+ymax = yctr + 0.5 * domain_frac * L_y
+L_y = ymax - ymin
+
+zmin = ds.domain_left_edge[2]
+zmax = ds.domain_right_edge[2]
+zctr = 0.5 * (zmin + zmax)
+L_z = zmax - zmin
+zmin = zctr - 0.5 * domain_frac * L_z
+zmax = zctr + 0.5 * domain_frac * L_z
+L_z = zmax - zmin
+
+fig = plt.figure()
+
+
+fields = ["Temp", "abar", "enuc"]
+
+grid = ImageGrid(fig, 111, nrows_ncols=(1, len(fields)),
+                 axes_pad=0.75, cbar_pad=0.05, label_mode="L", cbar_mode="each")
+
+
+for i, f in enumerate(fields):
+
+    sp = yt.SlicePlot(ds, "y", f,
+                      center=[xctr, yctr, zctr], width=[L_x, L_z],
+                      fontsize="12")
+
+    sp.set_buff_size((2400,2400))
+    sp.swap_axes()
+
+    if f == "Temp":
+        sp.set_zlim(f, 5.e7, 4e9)
+        sp.set_cmap(f, "magma_r")
+    elif f == "enuc":
+        sp.set_log(f, True, linthresh=1.e18)
+        sp.set_zlim(f, -1.e22, 1.e22)
+        sp.set_cmap(f, "bwr")
+    elif f == "density":
+        sp.set_zlim(f, 1.e-3, 5.e8)
+    elif f == "z_velocity":
+        sp.set_zlim(f, -2.e8, 2.e8)
+        sp.set_log(f, False)
+        sp.set_cmap(f, "bwr")
+    elif f == "abar":
+        sp.set_zlim(f, 4, 28)
+        sp.set_log(f, False)
+        sp.set_cmap(f, "plasma_r")
+
+    sp.set_axes_unit("cm")
+
+    plot = sp.plots[f]
+    plot.figure = fig
+    plot.axes = grid[i].axes
+    plot.cax = grid.cbar_axes[i]
+    if i < len(fields)-1:
+        grid[i].axes.xaxis.offsetText.set_visible(False)
+
+    sp._setup_plots()
+
+fig.text(0.02, 0.02, "time = {:8.5f} s".format(float(ds.current_time)), transform=fig.transFigure)
+
+fig.set_size_inches(19.2, 10.8)
+plt.tight_layout()
+plt.savefig("{}_slice.png".format(os.path.basename(plotfile)))

Exec/science/subchandra/analysis/vol-abar-subch.py

@@ -1,20 +1,20 @@
 #!/usr/bin/env python
 
-import matplotlib
-matplotlib.use('agg')
-
-import numpy as np
+# render Abar for the subchandra problem setup
 
 import sys
 
+import matplotlib
+import numpy as np
+
 import yt
 from yt.frontends.boxlib.api import CastroDataset
-import numpy as np
-#from yt.visualization.volume_rendering.render_source import VolumeSource
-from yt.visualization.volume_rendering.api import create_volume_source, Scene
 from yt.units import cm
+#from yt.visualization.volume_rendering.render_source import VolumeSource
+from yt.visualization.volume_rendering.api import Scene, create_volume_source
+
+matplotlib.use('agg')
 
-# this is for the wdconvect problem
 
 def doit(plotfile):
 
@@ -26,13 +26,6 @@ def doit(plotfile):
 
     sc = Scene()
 
-
-    # add a volume: select a sphere
-    #center = (0, 0, 0)
-    #R = (5.e8, 'cm')
-
-    #dd = ds.sphere(center, R)
-
     vol = create_volume_source(ds.all_data(), field=field)
     sc.add_source(vol)
 
@@ -71,14 +64,16 @@ def doit(plotfile):
 
     cam.switch_orientation(normal_vector=normal, north_vector=[0., 0., 1.])
     cam.set_width(ds.domain_width)
-    #cam.zoom(3.0)
+    cam.zoom(3.0)
     sc.camera = cam
 
     sc.save_annotated("{}_abar_annotated.png".format(plotfile),
+                      label_fontsize="18", label_fmt="%.1f",
+                      sigma_clip=3,
                       text_annotate=[[(0.05, 0.05),
-                                      "t = {}".format(ds.current_time.d),
-                                      dict(horizontalalignment="left")],
-                                     [(0.5,0.95),
+                                      f"t = {ds.current_time.d:6.3f}",
+                                      dict(horizontalalignment="left", fontsize="18")],
+                                     [(0.5, 0.95),
                                       "Castro simulation of double detonation SN Ia",
                                       dict(color="y", fontsize="24",
                                            horizontalalignment="center")]])

Exec/science/subchandra/analysis/vol-enuc-pos-subch.py

@@ -44,7 +44,7 @@ def doit(plotfile):
     ds._get_field_info(field).take_log = True
 
     vol = create_volume_source(ds.all_data(), field=field)
-    vol.use_ghost_zones = True
+    #vol.use_ghost_zones = True
 
     vals = [18.0, 18.5, 19.0, 19.5, 20.0, 20.5, 21.0, 21.5, 22.0]
     sigma = 0.1

Exec/science/subchandra/analysis/vol-enuc-subch.py

@@ -1,20 +1,19 @@
 #!/usr/bin/env python
 
-import matplotlib
-matplotlib.use('agg')
-
-import numpy as np
+# render enuc for the subchandra problem setup
 
 import sys
 
+import matplotlib
+import numpy as np
+
 import yt
 from yt.frontends.boxlib.api import CastroDataset
-import numpy as np
-#from yt.visualization.volume_rendering.render_source import VolumeSource
-from yt.visualization.volume_rendering.api import create_volume_source, Scene
 from yt.units import cm
+from yt.visualization.volume_rendering.api import Scene, create_volume_source
+
+matplotlib.use('agg')
 
-# this is for the wdconvect problem
 
 def _enuc_symlog(field, data):
     f = np.log10(np.abs(data["boxlib", "enuc"]))
@@ -40,12 +39,6 @@ def doit(plotfile):
     sc = Scene()
 
 
-    # add a volume: select a sphere
-    #center = (0, 0, 0)
-    #R = (5.e8, 'cm')
-
-    #dd = ds.sphere(center, R)
-
     vol = create_volume_source(ds.all_data(), field=field)
     sc.add_source(vol)
 
@@ -84,14 +77,16 @@ def doit(plotfile):
 
     cam.switch_orientation(normal_vector=normal, north_vector=[0., 0., 1.])
     cam.set_width(ds.domain_width)
-    #cam.zoom(3.0)
+    cam.zoom(3.0)
     sc.camera = cam
 
     sc.save_annotated("{}_enuc_annotated.png".format(plotfile),
+                      label_fontsize="18",
+                      sigma_clip=3,
                       text_annotate=[[(0.05, 0.05),
-                                      "t = {}".format(ds.current_time.d),
-                                      dict(horizontalalignment="left")],
-                                     [(0.5,0.95),
+                                      f"t = {ds.current_time.d:6.3f}",
+                                      dict(horizontalalignment="left", fontsize="18")],
+                                     [(0.5, 0.95),
                                       "Castro simulation of double detonation SN Ia",
                                       dict(color="y", fontsize="24",
                                            horizontalalignment="center")]])

Exec/science/subchandra/analysis/vol-subch.py → Exec/science/subchandra/analysis/vol-temp-subch.py

@@ -1,20 +1,20 @@
 #!/usr/bin/env python
 
-import matplotlib
-matplotlib.use('agg')
-
-import numpy as np
+# render Temperature for the subchandra problem setup
 
 import sys
 
+import matplotlib
+import numpy as np
+
 import yt
 from yt.frontends.boxlib.api import CastroDataset
-import numpy as np
-#from yt.visualization.volume_rendering.render_source import VolumeSource
-from yt.visualization.volume_rendering.api import create_volume_source, Scene
 from yt.units import cm
+#from yt.visualization.volume_rendering.render_source import VolumeSource
+from yt.visualization.volume_rendering.api import Scene, create_volume_source
+
+matplotlib.use('agg')
 
-# this is for the wdconvect problem
 
 def doit(plotfile):
 
@@ -26,38 +26,30 @@ def doit(plotfile):
 
     sc = Scene()
 
-
-    # add a volume: select a sphere
-    #center = (0, 0, 0)
-    #R = (5.e8, 'cm')
-
-    #dd = ds.sphere(center, R)
-
     vol = create_volume_source(ds.all_data(), field=field)
+    #vol.use_ghost_zones = True
+
     sc.add_source(vol)
 
 
     # transfer function
-    vals_tmp = [5.e7, 1.e8, 5.e8, 1.e9, 2.e9, 2.5e9, 3.e9]
+    _vals = [1.e8, 2.e8, 5.e8, 1.e9, 2.e9, 5.e9]
     vals = []
-    for v in vals_tmp:
+    for v in _vals:
         vals.append(np.log10(v))
 
+    alpha = [0.05, 0.2, 0.3, 0.3, 0.4, 0.5]
+
     sigma = 0.05
 
     tf =  yt.ColorTransferFunction((min(vals), max(vals)))
 
     tf.clear()
 
-    cmap = "viridis"
-
-    for v in vals:
-        if v < 9.01:
-            alpha = 0.25
-        else:
-            alpha = 0.75
+    cmap = "Oranges"
 
-        tf.sample_colormap(v, sigma**2, alpha=alpha, colormap=cmap)
+    for v, a in zip(vals, alpha):
+        tf.sample_colormap(v, sigma**2, alpha=a, colormap=cmap)
 
     sc.get_source(0).transfer_function = tf
 
@@ -79,14 +71,16 @@ def doit(plotfile):
 
     cam.switch_orientation(normal_vector=normal, north_vector=[0., 0., 1.])
     cam.set_width(ds.domain_width)
-    #cam.zoom(3.0)
+    cam.zoom(3.0)
     sc.camera = cam
 
-    sc.save_annotated("{}_Hnuc_annotated.png".format(plotfile),
+    sc.save_annotated("{}_Temp_annotated.png".format(plotfile),
+                      label_fontsize="18",
+                      sigma_clip=3,
                       text_annotate=[[(0.05, 0.05),
-                                      "t = {}".format(ds.current_time.d),
-                                      dict(horizontalalignment="left")],
-                                     [(0.5,0.95),
+                                      f"t = {ds.current_time.d:6.3f}",
+                                      dict(horizontalalignment="left", fontsize="18")],
+                                     [(0.5, 0.95),
                                       "Castro simulation of double detonation SN Ia",
                                       dict(color="y", fontsize="24",
                                            horizontalalignment="center")]])