Merge branch 'development' into optimal_subcycling_prep

maxpkatz · Jul 4, 2023 · 62f11dc · 62f11dc
2 parents 0bc0e26 + 939f998
commit 62f11dc
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Showing 15 changed files with 105 additions and 99 deletions.
diff --git a/Docs/source/FlowChart.rst b/Docs/source/FlowChart.rst
@@ -56,8 +56,7 @@ The time-integration method used is controlled by
     order integration implemented.  At the moment, this does not support
     multilevel domains.  Note: because of differences in the interfaces with the 
     default Strang method, you must compile with ``USE_TRUE_SDC = TRUE`` for this
-    method to work (in particular, this defines ``EXTRA_THERMO`` which enables some
-    additional EOS derivatives).
+    method to work.
 
   * ``time_integration_method = 3``: this is the simplified SDC method
     described above that uses the CTU hydro advection and an ODE

diff --git a/Exec/Make.Castro b/Exec/Make.Castro
@@ -186,18 +186,6 @@ endif
 ifeq ($(USE_REACT), TRUE)
   Bdirs += Source/reactions
   DEFINES += -DREACTIONS
-
-  ifeq ($(USE_TRUE_SDC), TRUE)
-    # we need the compositional derivatives for SDC
-    DEFINES += -DEXTRA_THERMO
-  endif
-
-  ifeq ($(USE_SIMPLIFIED_SDC), TRUE)
-    # we need the compositional derivatives for SDC
-    DEFINES += -DEXTRA_THERMO
-    # we only implement this for C++ reactions
-  endif
-
 endif
 
 ifeq ($(USE_REACT_SPARSE_JACOBIAN), TRUE)

diff --git a/Exec/science/flame_wave/analysis/vis_3d/vol-xrb-abar.py b/Exec/science/flame_wave/analysis/vis_3d/vol-xrb-abar.py
@@ -1,16 +1,19 @@
 #!/usr/bin/env python
 
-import matplotlib
-matplotlib.use('agg')
-
 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')
+
+resolution = (1920, 1080)
 
 # this is for the wdconvect problem
 
@@ -56,7 +59,7 @@ def doit(plotfile):
     sc.get_source(0).transfer_function = tf
 
     cam = sc.add_camera(ds, lens_type="perspective")
-    cam.resolution = (1920, 1280)
+    cam.resolution = resolution
 
     # view 1
 
@@ -77,14 +80,24 @@ def doit(plotfile):
     cam.zoom(3.0)
     sc.camera = cam
 
-    sc.save_annotated("{}_abar_annotated_side.png".format(plotfile),
-                      sigma_clip=3.0,
+    sc.save(f"{plotfile}_abar_noaxes_side.png", sigma_clip=3.0)
+
+    sc.annotate_axes(alpha=0.005, thickness=6)
+
+    sc.save(f"{plotfile}_abar_side.png", sigma_clip=3.0)
+
+    sc.save_annotated(f"{plotfile}_abar_annotated_side.png",
+                      sigma_clip=3.0, label_fmt="%.2f",
                       text_annotate=[[(0.05, 0.05),
                                       f"t = {ds.current_time.d:7.5f} s",
                                       dict(horizontalalignment="left")]])
 
     # view 2
 
+    # remove the annotation source for now
+    print(list(sc.sources.keys()))
+    sc.sources.pop("source_01")
+
     dx = ds.domain_right_edge[0] - ds.domain_left_edge[0]
     cam.position = [0.5*(ds.domain_left_edge[0] + ds.domain_right_edge[0]) + 0.0001 * dx,
                     0.5*(ds.domain_left_edge[1] + ds.domain_right_edge[1]),
@@ -103,8 +116,13 @@ def doit(plotfile):
     cam.zoom(0.6)
     sc.camera = cam
 
+    sc.save(f"{plotfile}_abar_noaxes_top.png", sigma_clip=3.0)
+
+    sc.annotate_axes(alpha=0.005, thickness=6)
+
+    sc.save(f"{plotfile}_abar_top.png", sigma_clip=3.0)
     sc.save_annotated("{}_abar_annotated_top.png".format(plotfile),
-                      sigma_clip=3.0,
+                      sigma_clip=3.0, label_fmt="%.2f",
                       text_annotate=[[(0.05, 0.05),
                                       f"t = {ds.current_time.d:7.5f} s",
                                       dict(horizontalalignment="left")]])

diff --git a/Exec/science/subchandra/GNUmakefile b/Exec/science/subchandra/GNUmakefile
@@ -22,7 +22,7 @@ USE_SIMPLIFIED_SDC=TRUE
 EOS_DIR     := helmholtz
 
 # This sets the network directory in $(MICROPHYSICS_HOME)/networks
-NETWORK_DIR := subch_approx
+NETWORK_DIR := subch_simple
 
 INTEGRATOR_DIR := VODE
 

diff --git a/Exec/science/subchandra/inputs_2d.N14.coarse b/Exec/science/subchandra/inputs_2d.N14.coarse
@@ -62,7 +62,7 @@ castro.sponge_timescale     = 1.e-3
 castro.cfl            = 0.2     # cfl number for hyperbolic system
 castro.init_shrink    = 0.05     # scale back initial timestep by this factor
 castro.change_max     = 1.025    # factor by which dt is allowed to change each timestep
-castro.sum_interval   = 0       # timesteps between computing and printing volume averages
+castro.sum_interval   = 5       # timesteps between computing and printing volume averages
 castro.update_sources_after_reflux = 0
 castro.time_integration_method = 3
 
@@ -147,12 +147,12 @@ integrator.rtol_spec = 1.e-5
 integrator.atol_spec = 1.e-5
 integrator.rtol_enuc = 1.e-5
 integrator.atol_enuc = 1.e-5
-integrator.jacobian = 2
+integrator.jacobian = 1
 
 integrator.X_reject_buffer = 4.0
 
 # disable jacobian caching in VODE
 integrator.use_jacobian_caching = 0
 
-integrator.ode_max_steps = 500000
+integrator.ode_max_steps = 1000000