Shallow water and Barotropic Vorticity equation code

.gitignore

@@ -79,6 +79,8 @@ coverage.xml
 .pytest_cache/
 test/.cache
 test/results.xml
+*.sh.e*
+*.sh.o*
 
 # Translations
 *.mo

exp/test_cases/MiMA/MiMA_test_case.py

@@ -19,8 +19,6 @@
 # is used to load the correct compilers.  The env file is always loaded from
 # $GFDL_BASE and not the checked out git repo.
 
-cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
-
 # create an Experiment object to handle the configuration of model parameters
 # and output diagnostics
 exp = Experiment('mima_test_experiment', codebase=cb)
@@ -174,6 +172,9 @@
 })
 #Lets do a run!
 if __name__=="__main__":
+
+    cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
+
     exp.run(1, use_restart=False, num_cores=NCORES)
     for i in range(2,121):
         exp.run(i, num_cores=NCORES)

exp/test_cases/axisymmetric/axisymmetric_test_case.py

@@ -19,8 +19,6 @@
 # is used to load the correct compilers.  The env file is always loaded from
 # $GFDL_BASE and not the checked out git repo.
 
-cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
-
 # create an Experiment object to handle the configuration of model parameters
 # and output diagnostics
 exp = Experiment('axisymmetric_test_case', codebase=cb)
@@ -141,7 +139,7 @@
     'rrtm_radiation_nml': {
         'do_read_ozone':True,
         'ozone_file':'ozone_1990',
-        'dt_rad': 3600. #Set RRTM radiation timestep to 3600 seconds, meaning it runs every 5 atmospheric timesteps
+        'dt_rad': 3600, #Set RRTM radiation timestep to 3600 seconds, meaning it runs every 5 atmospheric timesteps
     },
 
     # FMS Framework configuration
@@ -181,6 +179,9 @@
 
 #Lets do a run!
 if __name__=="__main__":
+
+    cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
+
     exp.run(1, use_restart=False, num_cores=NCORES)
     for i in range(2,121):
         exp.run(i, num_cores=NCORES)

exp/test_cases/barotropic_vorticity_equation/barotropic_vor_eq_stirring_test.py

@@ -0,0 +1,117 @@
+import os
+
+import numpy as np
+
+from isca import BarotropicCodeBase, DiagTable, Experiment, Namelist, GFDL_BASE
+
+NCORES = 8
+base_dir = os.path.dirname(os.path.realpath(__file__))
+# a CodeBase can be a directory on the computer,
+# useful for iterative development
+cb = BarotropicCodeBase.from_directory(GFDL_BASE)
+
+# or it can point to a specific git repo and commit id.
+# This method should ensure future, independent, reproducibility of results.
+# cb = DryCodeBase.from_repo(repo='https://github.com/isca/isca', commit='isca1.1')
+
+# compilation depends on computer specific settings.  The $GFDL_ENV
+# environment variable is used to determine which `$GFDL_BASE/src/extra/env` file
+# is used to load the correct compilers.  The env file is always loaded from
+# $GFDL_BASE and not the checked out git repo.
+
+# create an Experiment object to handle the configuration of model parameters
+# and output diagnostics
+exp = Experiment('barotropic_stirring_test_experiment', codebase=cb)
+
+#Tell model how to write diagnostics
+diag = DiagTable()
+diag.add_file('atmos_monthly', 30, 'days', time_units='days')
+
+#Tell model which diagnostics to write
+diag.add_field('barotropic_diagnostics', 'ucomp', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'vcomp', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'vor', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'pv', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'stream', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'trs', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'tr', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'eddy_vor', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'delta_u', time_avg=True)
+diag.add_field('stirring_mod', 'stirring', time_avg=True)
+diag.add_field('stirring_mod', 'stirring_amp', time_avg=True)
+diag.add_field('stirring_mod', 'stirring_sqr', time_avg=True)
+
+exp.diag_table = diag
+
+#Empty the run directory ready to run
+exp.clear_rundir()
+
+#Define values for the 'core' namelist
+exp.namelist = namelist = Namelist({
+    'main_nml':{
+     'days'   : 30,
+     'hours'  : 0,
+     'minutes': 0,
+     'seconds': 0,
+     'dt_atmos': 1200,
+     'calendar': 'no_calendar',
+    },
+
+ 'atmosphere_nml':{
+   'print_interval': 86400,
+    },
+
+'fms_io_nml':{
+   'threading_write' :'single',
+   'fileset_write': 'single'
+    },
+
+ 'fms_nml':{
+   'print_memory_usage':True,
+   'domains_stack_size': 200000,
+    },
+
+ 'barotropic_dynamics_nml':{
+   'triang_trunc'   : True,
+   'num_lat'        : 128,
+   'num_lon'        : 256,
+   'num_fourier'    : 85,
+   'num_spherical'  : 86,
+   'fourier_inc'    : 1,
+   'damping_option' : 'resolution_dependent',
+   'damping_order'  : 2,
+   'damping_coeff'  : 1.157E-4,
+   'damping_coeff_r': 1.929E-6,
+   'grid_tracer'    : True,
+   'spec_tracer'    : True,
+   'm_0'            : 6,
+   'zeta_0'         : 0.0,
+   'eddy_lat'       : 45.0,
+   'eddy_width'     : 10.0,
+   'robert_coeff'   : 0.04,
+   'initial_zonal_wind' : 'zero',
+    },
+
+ 'barotropic_physics_nml':{
+   },
+
+ 'stirring_nml': {
+   'decay_time':172800,
+   'amplitude':3.e-11,
+   'lat0':45.,
+   'lon0':180.,
+   'widthy':12.,
+   'widthx':45.,
+   'B':1.0,
+   },
+
+})
+
+#Lets do a run!
+if __name__=="__main__":
+
+    cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
+
+    exp.run(1, use_restart=False, num_cores=NCORES)
+    for i in range(2,121):
+      exp.run(i, num_cores=NCORES)

exp/test_cases/barotropic_vorticity_equation/barotropic_vor_eq_test.py

@@ -0,0 +1,101 @@
+import os
+
+import numpy as np
+
+from isca import BarotropicCodeBase, DiagTable, Experiment, Namelist, GFDL_BASE
+
+NCORES = 8
+base_dir = os.path.dirname(os.path.realpath(__file__))
+# a CodeBase can be a directory on the computer,
+# useful for iterative development
+cb = BarotropicCodeBase.from_directory(GFDL_BASE)
+
+# or it can point to a specific git repo and commit id.
+# This method should ensure future, independent, reproducibility of results.
+# cb = DryCodeBase.from_repo(repo='https://github.com/isca/isca', commit='isca1.1')
+
+# compilation depends on computer specific settings.  The $GFDL_ENV
+# environment variable is used to determine which `$GFDL_BASE/src/extra/env` file
+# is used to load the correct compilers.  The env file is always loaded from
+# $GFDL_BASE and not the checked out git repo.
+
+# create an Experiment object to handle the configuration of model parameters
+# and output diagnostics
+exp = Experiment('barotropic_test_experiment', codebase=cb)
+
+#Tell model how to write diagnostics
+diag = DiagTable()
+diag.add_file('atmos_monthly', 30, 'days', time_units='days')
+
+#Tell model which diagnostics to write
+diag.add_field('barotropic_diagnostics', 'ucomp', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'vcomp', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'vor', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'pv', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'stream', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'trs', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'tr', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'eddy_vor', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'delta_u', time_avg=True)
+
+exp.diag_table = diag
+
+#Empty the run directory ready to run
+exp.clear_rundir()
+
+#Define values for the 'core' namelist
+exp.namelist = namelist = Namelist({
+    'main_nml':{
+     'days'   : 30,
+     'hours'  : 0,
+     'minutes': 0,
+     'seconds': 0,
+     'dt_atmos': 1200,
+     'calendar': 'no_calendar',
+    },
+
+ 'atmosphere_nml':{
+   'print_interval': 86400,
+    },
+
+'fms_io_nml':{
+   'threading_write' :'single',
+   'fileset_write': 'single'
+    },
+
+ 'fms_nml':{
+   'print_memory_usage':True,
+   'domains_stack_size': 200000,
+    },
+
+ 'barotropic_dynamics_nml':{
+   'triang_trunc'   : True,
+   'num_lat'        : 128,
+   'num_lon'        : 256,
+   'num_fourier'    : 85,
+   'num_spherical'  : 86,
+   'fourier_inc'    : 1,
+   'damping_option' : 'resolution_dependent',
+   'damping_order'  : 4,
+   'damping_coeff'  : 1.e-04,
+   'grid_tracer'    : True,
+   'spec_tracer'    : True,
+   'm_0'            : 4,
+   'zeta_0'         : 8.e-05,
+   'eddy_lat'       : 45.0,
+   'eddy_width'     : 15.0,
+   'robert_coeff'   : 0.04,
+    },
+
+ 'barotropic_physics_nml':{
+   },
+})
+
+#Lets do a run!
+if __name__=="__main__":
+
+    cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
+
+    exp.run(1, use_restart=False, num_cores=NCORES)
+    for i in range(2,121):
+        exp.run(i, num_cores=NCORES)

exp/test_cases/bucket_hydrology/bucket_model_test_case.py

@@ -19,8 +19,6 @@
 # is used to load the correct compilers.  The env file is always loaded from
 # $GFDL_BASE and not the checked out git repo.
 
-cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
-
 # create an Experiment object to handle the configuration of model parameters
 # and output diagnostics
 exp = Experiment('bucket_test_experiment', codebase=cb)
@@ -179,6 +177,8 @@
 
 #Lets do a run!
 if __name__=="__main__":
+    cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
+
     exp.run(1, use_restart=False, num_cores=NCORES)
     for i in range(2,121):
         exp.run(i, num_cores=NCORES)

exp/test_cases/frierson/frierson_test_case.py

@@ -19,8 +19,6 @@
 # is used to load the correct compilers.  The env file is always loaded from
 # $GFDL_BASE and not the checked out git repo.
 
-cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
-
 # create an Experiment object to handle the configuration of model parameters
 # and output diagnostics
 exp = Experiment('frierson_test_experiment', codebase=cb)
@@ -173,6 +171,8 @@
 
 #Lets do a run!
 if __name__=="__main__":
+    cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
+
     exp.run(1, use_restart=False, num_cores=NCORES)
     for i in range(2,121):
         exp.run(i, num_cores=NCORES)

exp/test_cases/giant_planet/giant_planet_test_case.py

@@ -19,8 +19,6 @@
 # is used to load the correct compilers.  The env file is always loaded from
 # $GFDL_BASE and not the checked out git repo.
 
-cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
-
 # create an Experiment object to handle the configuration of model parameters
 # and output diagnostics
 exp = Experiment('giant_planet_test_experiment', codebase=cb)
@@ -207,6 +205,8 @@
 
 #Lets do a run!
 if __name__=="__main__":
+    cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
+
     exp.run(1, use_restart=False, num_cores=NCORES)
     for i in range(2,121):
         exp.run(i, num_cores=NCORES)

exp/test_cases/held_suarez/held_suarez_test_case.py

@@ -18,8 +18,6 @@
 # is used to load the correct compilers.  The env file is always loaded from
 # $GFDL_BASE and not the checked out git repo.
 
-cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
-
 # create an Experiment object to handle the configuration of model parameters
 # and output diagnostics
 
@@ -104,6 +102,9 @@
 
 #Lets do a run!
 if __name__ == '__main__':
+
+    cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
+
     exp.run(1, num_cores=NCORES, use_restart=False)
     for i in range(2, 13):
         exp.run(i, num_cores=NCORES)  # use the restart i-1 by default

exp/test_cases/realistic_continents/realistic_continents_fixed_sst_test_case.py

@@ -21,8 +21,6 @@
 # is used to load the correct compilers.  The env file is always loaded from
 # $GFDL_BASE and not the checked out git repo.
 
-cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
-
 # create an Experiment object to handle the configuration of model parameters
 # and output diagnostics
 exp = Experiment('realistic_continents_fixed_sst_test_experiment', codebase=cb)
@@ -72,6 +70,8 @@
 
 #Lets do a run!
 if __name__=="__main__":
+    cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
+
     exp.run(1, use_restart=False, num_cores=NCORES)
     for i in range(2,121):
         exp.run(i, num_cores=NCORES)

exp/test_cases/realistic_continents/realistic_continents_variable_qflux_test_case.py

@@ -21,8 +21,6 @@
 # is used to load the correct compilers.  The env file is always loaded from
 # $GFDL_BASE and not the checked out git repo.
 
-cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
-
 # create an Experiment object to handle the configuration of model parameters
 # and output diagnostics
 exp = Experiment('realistic_continents_qflux_test_experiment', codebase=cb)
@@ -72,6 +70,8 @@
 
 #Lets do a run!
 if __name__=="__main__":
+    cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
+
     exp.run(1, use_restart=False, num_cores=NCORES)
     for i in range(2,121):
         exp.run(i, num_cores=NCORES)