Introduced automated tests for EnzoMethodGrackle

A section was also added to the website documentation to describe these tests.

doc/source/tests/grackle.rst

@@ -0,0 +1,34 @@
+----------------
+Grackle Tests
+----------------
+
+Tests for the method that invokes Grackle. These tests set up a
+cooling test without hydrodynamics to run many one-zone models in
+Grackle, fully sampling the density, temperature, and metallicity
+parameter space over which the chemistry and cooling/heating tables
+are valid.
+
+method_grackle_general
+======================
+
+This test compares the summary statistics computed for several grackle
+fields after a certain period of time to previously archived values.
+The simulation timesteps are much larger that the cooling/heating
+timescales, to help improve detection of problems related to SMP mode.
+
+This test is somewhat fragile given that upgrading Grackle versions could
+conceivably alter the field values. In the future it would be better to
+replace this with a test that:
+
+1. checks out and builds a previous commit of Enzo-E
+2. runs the simulation and saves the exact field values after running the simulations
+3. checks out and builds a newer commit of Enzo-E (while leaving the build of Grackle unchanged)
+4. runs the simulation and confirms that the Grackle related field values are identical to the field values from the earlier simulation.
+
+method_grackle_cooling_dt
+=========================
+
+This test runs Grackle for a fixed number of cycles, and compares the
+final simulation time to a reference value. Each simulation timestep
+is set fraction of the minimum magnitude of the cooling/heating
+timestep.

doc/source/tests/index.rst

@@ -14,6 +14,7 @@ This testing section describes tests on enzo-e program
    collapse
    cosmology
    gravity
+   grackle
    heat
    helloworld
    hierarchy

input/Grackle/grackle.incl

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+#
+#  Grackle Test Problem:
+#
+#  Sets up a cooling test without hydrodynamics to run many
+#  one-zone models in Grackle, fully sampling the density,
+#  temperature, and metallicity parameter space over which 
+#  the chemistry and cooling/heating tables are valid.
+#
+#  When including this file to launch a simulation, be sure to:
+#    - overwrite the entry in Method:grackle:data_file parameter
+#    - specify a stopping condition
+#    - specify an output schedule for the "data" output fileset
+#      (or drop that fileset from the output list)
+
+ Boundary {
+     type = "reflecting";
+ }
+
+ Domain {
+     lower = [ 0.0, 0.0, 0.0];
+     upper = [ 1.0, 1.0, 1.0];
+ }
+
+ Units {
+    density = 1.6726219E-24;  # m_H in grams... so n = 1.0 cm^-3 for pure hydrogen
+    time    = 3.15576E13;     # 1 Myr in seconds
+    length  = 3.086E16;       # 1 pc in cm - does not actually matter
+ }
+
+ Field {
+     alignment = 8;
+     gamma = 1.400;
+     ghost_depth = 3;
+     list = [ "density", 
+              "internal_energy",
+              "total_energy",
+              "velocity_x",
+              "velocity_y",
+              "velocity_z",
+# purposefully commenting these out to test automatic
+# creation of needed fields
+#              "HI_density",
+#              "HII_density",
+              "HM_density",
+              "HeI_density",
+              "HeII_density",
+              "HeIII_density",
+              "H2I_density",
+              "H2II_density",
+              "DI_density",
+              "DII_density",
+              "HDI_density",
+              "e_density",
+              "metal_density",
+              "cooling_time",  
+              "temperature",
+              "pressure",
+              "gamma"
+     ];
+
+     padding = 0;
+ }
+
+ Group {
+   list = ["color", "derived"];
+
+   # fields that should be advected by hydro MUST be defined
+   # as color here. This is handled automatically in 
+   # EnzoMethodGrackle for the Grackle-specific fields (species)
+   # but not everything
+    color {
+       field_list = [
+              "HI_density",
+              "HII_density",
+              "HM_density",
+              "HeI_density",
+              "HeII_density",
+              "HeIII_density",
+              "H2I_density",
+              "H2II_density",
+              "DI_density",
+              "DII_density",
+              "HDI_density",
+              "e_density",
+              "metal_density",
+              "cooling_time",
+              "temperature",
+              "pressure",
+              "gamma" ];
+    }
+
+# derived fields grouping enables Enzo-E to ensure
+#  that all derived fields are updated prior to output
+#  In order for this to work, these MUST have their own
+#  compute classes.
+    derived {
+        field_list = ["temperature",
+                      "pressure",
+                      "cooling_time"];
+    }
+ }
+
+ Initial {
+   list = ["grackle_test"];
+   grackle_test {
+      # See note in "Mesh" on running in < 3D
+
+      minimum_H_number_density = 0.0001;
+      maximum_H_number_density = 1000.0;
+      minimum_metallicity      = 1.0;
+      maximum_metallicity      = 1.0;
+      minimum_temperature      = 10.0;
+      maximum_temperature      = 1.0E8;
+
+      # Keep temperature constant with changing mu?
+      reset_energies           = 0;
+
+      dt = 100.0;
+   }
+ }
+
+ Mesh {
+     #   This test problem varies density, temperature,
+     #   and metallicity over x, y, and z dimensions 
+     #   respectively. For smaller problems you can 
+     #   run in 1 or 2 dimensions by changing the below
+     #   accordingly and setting the min/max values in
+     #   initialization to be the same. Currently cannot
+     #   pick which value goes in which dimension,
+     #   so 2D can only be density and temperature,
+     #   1D can only vary density.
+
+     #root_blocks = [ 4, 4];
+     #root_rank = 2;
+     #root_size = [128, 128];
+
+     # 3D test example:
+     root_blocks = [ 4, 4, 4];
+     root_rank = 3;
+     root_size = [32, 32, 32];
+
+ }
+
+ Method {
+      list = [ "grackle", "null"];
+
+     grackle {
+        courant = 0.40; # meaningless unless use_cooling_timestep = true;
+
+        data_file = "CloudyData_UVB=HM2012_shielded.h5";
+
+        with_radiative_cooling = 1;
+        primordial_chemistry   = 3;  # 1, 2, or 3
+        metal_cooling          = 1;  # 0 or 1 (off/on)
+        UVbackground           = 1;  # on or off
+        self_shielding_method  = 3;  # 0 - 3 (0 or 3 recommended)
+
+        HydrogenFractionByMass = 0.73;
+
+        # set this to true to limit the maximum timestep to the product of the
+        # minimum cooling/heating time and courant.
+        use_cooling_timestep = false; # default is false
+     }
+
+     # use this to limit maximum timestep if grackle::use_cooling_timestep is
+     # set to false and Grackle crashes due to max iteration limit - this is
+     # not needed generally in a real simulation as hydro timestep will
+     # be small (usually)
+     null { dt = 100.0; }
+
+ }
+
+ Output {
+     list = ["data"];
+
+     data {
+         field_list = [ "density",
+              "internal_energy",
+              "total_energy",
+              "velocity_x",
+              "velocity_y",
+              "velocity_z",
+              "HI_density",
+              "HII_density",
+              "HM_density",
+              "HeI_density",
+              "HeII_density",
+              "HeIII_density",
+              "H2I_density",
+              "H2II_density",
+              "DI_density",
+              "DII_density",
+              "HDI_density",
+              "e_density",
+              "metal_density",
+              "cooling_time",
+              "temperature",
+              "pressure",
+              "gamma"
+               ];
+
+         dir   = ["GRACKLE_TEST_%03d","cycle"];
+         name = [ "method_grackle-1-%03d.h5", "proc" ];
+         schedule {
+             var = "time";
+             step = 1000.0;
+             start = 0.0;
+         }
+         type = "data";
+     }
+
+ }
+

input/Grackle/method_grackle_cooling_dt.in

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+# this file is used for a test where the cooling time is used to limit
+# the size of the timestep
+#
+# The automated test will also overwrite the entry in
+# Method:grackle:data_file parameter with a valid path
+
+include "input/Grackle/grackle.incl"
+
+Output { list = []; } # don't write any outputs
+
+Method {
+    list = [ "grackle" ]; # intentionally omit "null"
+    grackle {
+        courant = 0.40;
+        use_cooling_timestep = true;
+    }
+}
+
+Testing {
+    time_final  = [0.00201833123232718];
+    time_tolerance = 1.0e-4;
+}
+
+Stopping { cycle = 20; }

input/Grackle/method_grackle_general.in

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+# this file is used for checking general consistency of grackle results
+# (without using a timestep based on the minimum cooling time)
+#
+# The automated test will also overwrite the entry in
+# Method:grackle:data_file parameter with a valid path
+
+include "input/Grackle/grackle.incl"
+
+Output {
+    data {
+        dir = ["GeneralGrackle-%06.2f", "time"];
+        schedule {
+            var = "time";
+            list = [500.0];
+        }
+    }
+}
+
+Stopping { time = 500.0; }