Merge branch 'development' into 2d_spherical_rotation

AMReX-Astro · Oct 24, 2024 · 1261061 · 1261061
2 parents eb83e4e + de4d8d9
commit 1261061
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diff --git a/Docs/source/mhd.rst b/Docs/source/mhd.rst
@@ -17,6 +17,9 @@ supported by MHD.
 
 .. note::
 
+   The MHD solver is still under development and should not be used
+   for science simulations.  See the issues in the github repo.
+
    The MHD solver supports 3-d only.
 
    Currently the MHD solver is single-level only.  AMR support is forthcoming.

diff --git a/Exec/science/flame_wave/ci-benchmarks/grid_diag.out b/Exec/science/flame_wave/ci-benchmarks/grid_diag.out
@@ -1,5 +1,5 @@
 #   COLUMN 1                        2                        3                        4                        5                        6                        7                        8                        9                       10                       11                       12                       13                       14                       15                       16                       17                       18                       19                       20                       21                       22                       23
 #   TIMESTEP                     TIME                     MASS                     XMOM                     YMOM                     ZMOM              ANG. MOM. X              ANG. MOM. Y              ANG. MOM. Z              KIN. ENERGY              INT. ENERGY               GAS ENERGY             GRAV. ENERGY             TOTAL ENERGY     CENTER OF MASS X-LOC     CENTER OF MASS Y-LOC     CENTER OF MASS Z-LOC     CENTER OF MASS X-VEL     CENTER OF MASS Y-VEL     CENTER OF MASS Z-VEL      MAXIMUM TEMPERATURE          MAXIMUM DENSITY        MAXIMUM T_S / T_E
            0   0.0000000000000000e+00   1.4700685690736437e+20   0.0000000000000000e+00   0.0000000000000000e+00   0.0000000000000000e+00   0.0000000000000000e+00   0.0000000000000000e+00   0.0000000000000000e+00   0.0000000000000000e+00   2.9163021935541997e+37   2.9163021935541997e+37   0.0000000000000000e+00   2.9163021935541997e+37   2.7306641645125415e+04   6.8087525965685256e+02   0.0000000000000000e+00   0.0000000000000000e+00   0.0000000000000000e+00   0.0000000000000000e+00   1.3928678114307070e+09   3.0715027784567930e+07   0.0000000000000000e+00
-           1   5.9806047036494849e-08   1.4700700110495903e+20   3.3564221217849212e+23   7.2876252590226133e+23   1.2612378556916341e+20   3.1318391966955516e+23  -2.7141686347841742e+24   1.9066097493127676e+28   7.8605324800324878e+29   2.9163081863790706e+37   2.9163082649843738e+37   0.0000000000000000e+00   2.9163082649843738e+37   2.7306641717925955e+04   6.8087482283157317e+02   0.0000000000000000e+00   2.2831716153358752e+03   4.9573321027203638e+03   8.5794407491595881e-01   1.3929561431310942e+09   3.0715326643212341e+07   3.3873763041849706e-04
-           2   1.2559269877663918e-07   1.4700717750115462e+20   7.0484895445039834e+23   1.5304335700823335e+24   5.5619061962888426e+20   1.3810900989697918e+24  -1.1969287484132617e+25   4.0039912979259806e+28   3.0853275723280981e+30   2.9163145904135894e+37   2.9163148989463411e+37   0.0000000000000000e+00   2.9163148989463411e+37   2.7306641954244522e+04   6.8087461718998338e+02   0.0000000000000000e+00   4.7946567401095926e+03   1.0410604407871944e+04   3.7834249257966728e+00   1.3933944939675827e+09   3.0715562157563787e+07   3.3857586854903492e-04
+           1   5.9806047036494849e-08   1.4700700110495903e+20   3.3564221215590610e+23   7.2876252589700228e+23   1.2612378556594561e+20   3.1318391966786556e+23  -2.7141686347838510e+24   1.9066097493139366e+28   7.8605324800584047e+29   2.9163081863790706e+37   2.9163082649843738e+37   0.0000000000000000e+00   2.9163082649843738e+37   2.7306641717925955e+04   6.8087482283158556e+02   0.0000000000000000e+00   2.2831716151822361e+03   4.9573321026845897e+03   8.5794407489407010e-01   1.3929529135508094e+09   3.0715326539046615e+07   3.3873763041849706e-04
+           2   1.2559269877663918e-07   1.4700717750115462e+20   7.0484895413073359e+23   1.5304335700221490e+24   5.5619061951241526e+20   1.3810900989051759e+24  -1.1969287484120623e+25   4.0039912979436722e+28   3.0853275724059276e+30   2.9163145904135894e+37   2.9163148989463416e+37   0.0000000000000000e+00   2.9163148989463416e+37   2.7306641954244522e+04   6.8087461719003727e+02   0.0000000000000000e+00   4.7946567379351090e+03   1.0410604407462544e+04   3.7834249250044056e+00   1.3933796339641171e+09   3.0715561813912578e+07   3.3857586854903492e-04
diff --git a/Exec/science/flame_wave/ci-benchmarks/species_diag.out b/Exec/science/flame_wave/ci-benchmarks/species_diag.out
@@ -1,5 +1,5 @@
 #   COLUMN 1                        2                        3                        4                        5                        6                        7                        8                        9                       10                       11                       12                       13                       14                       15
 #   TIMESTEP                     TIME                 Mass He4                 Mass C12                 Mass O16                Mass Ne20                Mass Mg24                Mass Si28                 Mass S32                Mass Ar36                Mass Ca40                Mass Ti44                Mass Cr48                Mass Fe52                Mass Ni56
            0   0.0000000000000000e+00   2.8142378112400895e-15   7.3932235330395157e-24   7.3932235330395157e-24   7.3932235330395157e-24   7.3932235330395157e-24   7.3932235330395157e-24   7.3932235330395157e-24   7.3932235330395157e-24   7.3932235330395157e-24   7.3932235330395157e-24   7.3932235330395157e-24   7.3932235330395157e-24   7.1117997526547418e-14
-           1   5.9806047036494849e-08   2.8142323856670446e-15   5.4329394398418374e-21   7.4194443455948811e-24   7.3934514829832856e-24   7.3935541949306949e-24   7.3933935989353088e-24   7.3932321468740865e-24   7.3932312019180345e-24   7.3932308328287333e-24   7.3932307869392985e-24   7.3932307850741519e-24   7.3932307849933044e-24   7.1118070045957103e-14
-           2   1.2559269877663918e-07   2.8142264165381050e-15   1.1401993450709496e-20   7.4929528148974785e-24   7.3944694290388374e-24   7.3939305042586412e-24   7.3935838894001731e-24   7.3932425308122493e-24   7.3932405326301655e-24   7.3932397568503098e-24   7.3932396603620498e-24   7.3932396564405566e-24   7.3932396562705492e-24   7.1118158758588142e-14
+           1   5.9806047036494849e-08   2.8142323856670446e-15   5.4329394398523593e-21   7.4194443428333686e-24   7.3934514828234477e-24   7.3935541949253214e-24   7.3933935989348298e-24   7.3932321468740835e-24   7.3932312019180345e-24   7.3932308328287333e-24   7.3932307869392985e-24   7.3932307850741519e-24   7.3932307849933044e-24   7.1118070045957103e-14
+           2   1.2559269877663918e-07   2.8142264165381050e-15   1.1401993450700379e-20   7.4929526498089992e-24   7.3944694218302123e-24   7.3939305039811099e-24   7.3935838893792728e-24   7.3932425308121303e-24   7.3932405326301640e-24   7.3932397568503098e-24   7.3932396603620498e-24   7.3932396564405580e-24   7.3932396562705492e-24   7.1118158758588142e-14
diff --git a/Exec/science/flame_wave/inputs.1d b/Exec/science/flame_wave/inputs.1d
@@ -0,0 +1,156 @@
+# ------------------  INPUTS TO MAIN PROGRAM  -------------------
+max_step = 250000000
+stop_time =  3.0
+
+# PROBLEM SIZE & GEOMETRY
+geometry.is_periodic = 0       0        0
+geometry.prob_lo     = 0       0       0
+
+geometry.coord_sys   = 0                  # 0 => cart, 1 => RZ  2=>spherical
+
+  geometry.prob_hi     = 2.4576e4
+  amr.n_cell           = 192
+
+  # >>>>>>>>>>>>>  BC FLAGS <<<<<<<<<<<<<<<<
+  # 0 = Interior           3 = Symmetry
+  # 1 = Inflow             4 = SlipWall
+  # 2 = Outflow            5 = NoSlipWall
+  # >>>>>>>>>>>>>  BC FLAGS <<<<<<<<<<<<<<<<
+  castro.lo_bc       =  3
+  castro.hi_bc       =  2
+
+  castro.fill_ambient_bc = 1
+  castro.ambient_fill_dir = 0
+  castro.ambient_outflow_vel = 1
+
+#castro.allow_non_unit_aspect_zones = 1
+
+castro.domain_is_plane_parallel = 1
+
+# WHICH PHYSICS
+castro.do_hydro = 1
+castro.do_react = 1
+castro.do_rotation = 0
+castro.do_grav = 1
+castro.do_sponge = 1
+
+castro.small_temp = 1.e6
+castro.small_dens = 1.e-5
+
+castro.ppm_type = 1
+castro.grav_source_type = 2
+castro.use_pslope = 1
+castro.pslope_cutoff_density = 1.e4
+
+gravity.gravity_type = ConstantGrav
+gravity.const_grav   = -1.5e14
+
+castro.rotational_period = 0.0
+castro.rotation_include_centrifugal = 0
+
+castro.diffuse_temp = 0
+castro.diffuse_cutoff_density_hi = 5.e4
+castro.diffuse_cutoff_density = 2.e4
+
+castro.diffuse_cond_scale_fac = 1.0
+
+castro.react_rho_min = 1.e2
+castro.react_rho_max = 5.e6
+
+castro.react_T_min = 6.e7
+
+castro.sponge_upper_density = 1.e2
+castro.sponge_lower_density = 1.e0
+castro.sponge_timescale     = 1.e-7
+
+# GPU options
+castro.hydro_memory_footprint_ratio = 3
+
+# TIME STEP CONTROL
+castro.cfl            = 0.8     # cfl number for hyperbolic system
+castro.init_shrink    = 0.1     # scale back initial timestep
+castro.change_max     = 1.1     # max time step growth
+
+castro.use_retry      = 1
+castro.max_subcycles = 16
+
+castro.retry_small_density_cutoff = 10.0
+
+castro.abundance_failure_tolerance = 0.1
+castro.abundance_failure_rho_cutoff = 1.0
+
+# DIAGNOSTICS & VERBOSITY
+castro.sum_interval   = 10       # timesteps between computing mass
+castro.v              = 1       # verbosity in Castro.cpp
+amr.v                 = 1       # verbosity in Amr.cpp
+
+# REFINEMENT / REGRIDDING
+amr.max_level       = 2       # maximum level number allowed
+amr.ref_ratio       = 4 2 2 2 # refinement ratio
+amr.regrid_int      = 0       # static grids ftw
+amr.blocking_factor = 32       # block factor in grid generation
+amr.max_grid_size   = 128
+amr.n_error_buf     = 2 2 2 2 # number of buffer cells in error est
+
+# CHECKPOINT FILES
+amr.check_file      = flame_wave_1000Hz_25cm_chk        # root name of checkpoint file
+#if AMREX_SPACEDIM == 3
+amr.check_int       = 25        # number of timesteps between checkpoints
+#elif AMREX_SPACEDIM == 2
+amr.check_int       = 250        # number of timesteps between checkpoints
+#endif
+
+amr.checkpoint_files_output = 1
+
+# PLOTFILES
+amr.plot_file        = flame_wave_1000Hz_25cm_plt        # root name of plotfile
+amr.plot_per         = 5.e-3      # number of seconds between plotfiles
+amr.derive_plot_vars = ALL
+amr.plot_files_output = 1
+
+amr.small_plot_file        = flame_wave_1000Hz_25cm_smallplt        # root name of plotfile
+amr.small_plot_per         = 5.e-4      # number of seconds between plotfiles
+amr.small_plot_vars = density Temp
+
+#if AMREX_SPACEDIM == 3
+  amr.derive_small_plot_vars = abar magvel enuc
+#elif AMREX_SPACEDIM == 2
+  amr.derive_small_plot_vars = abar x_velocity y_velocity z_velocity enuc
+#endif
+
+fab.format = NATIVE_32
+
+
+# problem initialization
+
+problem.dtemp = 1.2e9
+problem.x_half_max = 2.56e4
+problem.x_half_width = 2048.e0
+
+problem.dens_base = 3.43e6
+
+problem.T_star = 2.e8
+problem.T_hi = 2.e8
+problem.T_lo = 8.e6
+
+problem.H_star = 2000.e0
+problem.atm_delta  = 50.0
+
+problem.fuel1_name = "helium-4"
+problem.fuel1_frac = 1.0
+
+problem.ash1_name  = "nickel-56"
+problem.ash1_frac = 1.0
+
+problem.low_density_cutoff = 1.e-4
+
+problem.tag_by_density = 0
+problem.refine_height = 3600.0
+problem.max_base_tagging_level = 3
+
+# Microphysics
+
+integrator.rtol_spec = 1.e-6
+integrator.atol_spec = 1.e-6
+
+network.use_tables = 1
diff --git a/Exec/science/flame_wave/problem_initialize.H b/Exec/science/flame_wave/problem_initialize.H
@@ -190,6 +190,10 @@ void problem_initialize ()
         problem::center[d] = 0.5_rt * (problo[d] + probhi[d]);
     }
 
+#if AMREX_SPACEDIM == 1
+    problem::center[0] = 0.0_rt;
+#endif
+
 #if AMREX_SPACEDIM == 2
     // for axisymmetry, put the x-center on the x-axis
     // and the y-center at 0, so the height computation is okay

diff --git a/Exec/science/massive_star/analysis/massive_star_multi.py b/Exec/science/massive_star/analysis/massive_star_multi.py
@@ -13,7 +13,8 @@
 
 matplotlib.use('agg')
 
-
+ANNOTATE_O16 = False
+ANNOTATE_NSE = True
 
 
 def make_plot(plotfile, prefix="plot", width_frac=0.1,
@@ -25,8 +26,8 @@ def make_plot(plotfile, prefix="plot", width_frac=0.1,
     t_drive = 0.0
     if "[*] castro.drive_initial_convection_tmax" in ds.parameters:
         t_drive = ds.parameters["[*] castro.drive_initial_convection_tmax"]
-    elif "castro.drive_initial_convection_tmax" in ds.parameters:
-        t_drive = ds.parameters["castro.drive_initial_convection_tmax"]
+    elif "[*] castro.drive_initial_convection_tmax" in ds.parameters:
+        t_drive = ds.parameters["[*] castro.drive_initial_convection_tmax"]
     print(t_drive)
 
     xmin = ds.domain_left_edge[0]
@@ -75,27 +76,34 @@ def make_plot(plotfile, prefix="plot", width_frac=0.1,
             sp.set_cmap(f, "magma")
             sp.set_zlim(f, 1.e-2, 5)
 
-        if f == "enuc":
-            # now do a contour of NSE
-            if ("boxlib", "in_nse") in ds.derived_field_list:
-                sp.annotate_contour("in_nse", ncont=1, clim=(0.5, 0.5), take_log=False,
-                                    plot_args={"colors": "k", "linewidths": 2})
+
+    # now do a contour of O
+    if ANNOTATE_O16:
+        sp.annotate_contour(("boxlib", "X(O16)"), ncont=1, clim=(0.5, 0.5), factor=32, take_log=False,
+                            plot_args={"colors": "0.5", "linewidths": 2})
+
+    # now do a contour of NSE
+    if ANNOTATE_NSE:
+        if ("boxlib", "in_nse") in ds.derived_field_list:
+            sp.annotate_contour("in_nse", levels=1, clim=(0.5, 0.5), take_log=False,
+                                plot_args={"colors": "k", "linewidths": 2})
+
 
     sp.set_axes_unit("cm")
 
     fig = sp.export_to_mpl_figure((layout[0], layout[1]), axes_pad=(1.0, 0.4),
                                   cbar_location=cbar_location, cbar_pad="2%")
 
-    fig.subplots_adjust(left=0.05, right=0.95, bottom=0.025, top=0.975)
-    fig.text(0.02, 0.02, f"$t - \\tau_\\mathrm{{drive}}$ = {float(ds.current_time) - t_drive:6.1f} s",
+    fig.subplots_adjust(left=0.05, right=0.95, bottom=0.035, top=0.975)
+    fig.text(0.02, 0.01, f"$t - \\tau_\\mathrm{{drive}}$ = {float(ds.current_time) - t_drive:6.1f} s",
              transform=fig.transFigure)
     fig.set_size_inches(size)
     fig.tight_layout()
     extra = ""
     if layout[0] >= layout[1]:
         extra = "_vertical"
 
-    fig.savefig(f"{prefix}_{os.path.basename(plotfile)}_w{width_frac:04.2f}{extra}.pdf", pad_inches=0.1, bbox_inches="tight")
+    fig.savefig(f"{prefix}_{os.path.basename(plotfile)}_w{width_frac:04.2f}{extra}.pdf", pad_inches=0.1) #, bbox_inches="tight")
 
 
 if __name__ == "__main__":
@@ -112,7 +120,7 @@ def make_plot(plotfile, prefix="plot", width_frac=0.1,
     plotfile = args.plotfile[0]
 
     if args.vertical:
-        size = (7.5, 11.0)
+        size = (7.0, 10.0)
         layout = (2, 2)
     else:
         size = (19.2, 8.5)

diff --git a/Exec/science/massive_star/analysis/massive_star_sequence.py b/Exec/science/massive_star/analysis/massive_star_sequence.py
@@ -15,7 +15,7 @@
 
 matplotlib.use('agg')
 
-times = [50, 100, 150, 200, 250]
+times = [50, 100, 150, 200, 250, 300]
 
 def find_files(plist):
 
@@ -60,8 +60,8 @@ def make_plot(field, pfiles, *,
     t_drive = 0.0
     if "[*] castro.drive_initial_convection_tmax" in ds.parameters:
         t_drive = ds.parameters["[*] castro.drive_initial_convection_tmax"]
-    elif "castro.drive_initial_convection_tmax" in ds.parameters:
-        t_drive = ds.parameters["castro.drive_initial_convection_tmax"]
+    elif "[*] castro.drive_initial_convection_tmax" in ds.parameters:
+        t_drive = ds.parameters["[*] castro.drive_initial_convection_tmax"]
     print(t_drive)
 
     xmin = ds.domain_left_edge[0]
@@ -127,11 +127,10 @@ def make_plot(field, pfiles, *,
             sp.set_cmap(f, "magma")
             sp.set_zlim(f, 1.e-2, 5)
 
-        if f == "enuc":
-            # now do a contour of NSE
-            if ("boxlib", "in_nse") in ds.derived_field_list:
-                sp.annotate_contour("in_nse", levels=1, clim=(0.5, 0.5), take_log=False,
-                                    plot_args={"colors": "k", "linewidths": 2})
+        # now do a contour of NSE
+        if ("boxlib", "in_nse") in ds.derived_field_list:
+            sp.annotate_contour("in_nse", levels=1, clim=(0.5, 0.5), take_log=False,
+                                plot_args={"colors": "k", "linewidths": 2})
 
         sp.set_axes_unit("cm")
 
@@ -168,7 +167,7 @@ def make_plot(field, pfiles, *,
     args = p.parse_args()
 
     if args.vertical:
-        size = (7.5, 8.5)
+        size = (7.0, 8.0)
     else:
         size = (19.2, 8.5)