diff --git a/docs/developers_guide/framework.rst b/docs/developers_guide/framework.rst index f2e7d71d19..482db29ddd 100644 --- a/docs/developers_guide/framework.rst +++ b/docs/developers_guide/framework.rst @@ -244,7 +244,7 @@ functions. Here is a code snippet from section = config['dome'] ... levels = section.getfloat('levels') - args = ['create_landice_grid_from_generic_MPAS_grid.py', + args = ['create_landice_grid_from_generic_mpas_grid', '-i', 'mpas_grid.nc', '-o', 'landice_grid.nc', '-l', levels] @@ -253,7 +253,7 @@ functions. Here is a code snippet from ... -This example calls the script ``create_landice_grid_from_generic_MPAS_grid.py`` +This example calls the script ``create_landice_grid_from_generic_mpas_grid`` from ``mpas_tools`` with several arguments, making use of the ``logger``. .. _dev_io: diff --git a/docs/developers_guide/landice/test_groups/circular_shelf.rst b/docs/developers_guide/landice/test_groups/circular_shelf.rst index 2c5b81f055..c5a0517827 100644 --- a/docs/developers_guide/landice/test_groups/circular_shelf.rst +++ b/docs/developers_guide/landice/test_groups/circular_shelf.rst @@ -30,7 +30,7 @@ constructed at runtime (using :py:func:`mpas_tools.planar_hex.make_planar_hex_mesh()`). A MALI grid is created with the MPAS-Tools script -``create_landice_grid_from_generic_MPAS_grid.py`` and a graph file is created +``create_landice_grid_from_generic_mpas_grid`` and a graph file is created to partition the mesh before the model run. Finally, the initial condition is defined in the private function diff --git a/docs/developers_guide/landice/test_groups/dome.rst b/docs/developers_guide/landice/test_groups/dome.rst index b18e8ae87d..175c5d33c7 100644 --- a/docs/developers_guide/landice/test_groups/dome.rst +++ b/docs/developers_guide/landice/test_groups/dome.rst @@ -47,7 +47,7 @@ The variable resolution mesh is downloaded from section of the config file. A MALI grid is created with the MPAS-Tools script -``create_landice_grid_from_generic_MPAS_grid.py`` and a graph file is created +``create_landice_grid_from_generic_mpas_grid`` and a graph file is created to partition the mesh before the model run. Finally, the initial condition is defined in the private function diff --git a/docs/developers_guide/landice/test_groups/eismint2.rst b/docs/developers_guide/landice/test_groups/eismint2.rst index c46c75b7f9..43cc627470 100644 --- a/docs/developers_guide/landice/test_groups/eismint2.rst +++ b/docs/developers_guide/landice/test_groups/eismint2.rst @@ -30,7 +30,7 @@ defines a step for setting up the mesh for each test case. The horizontal mesh is constructed at runtime (using :py:func:`mpas_tools.planar_hex.make_planar_hex_mesh()`). A MALI grid is created with the MPAS-Tools script -``create_landice_grid_from_generic_MPAS_grid.py`` and a graph file is created +``create_landice_grid_from_generic_mpas_grid`` and a graph file is created to partition the mesh before the model run. run_experiment diff --git a/docs/developers_guide/landice/test_groups/enthalpy_benchmark.rst b/docs/developers_guide/landice/test_groups/enthalpy_benchmark.rst index b92809ca7c..8fd8ba91c7 100644 --- a/docs/developers_guide/landice/test_groups/enthalpy_benchmark.rst +++ b/docs/developers_guide/landice/test_groups/enthalpy_benchmark.rst @@ -34,7 +34,7 @@ defines a step for setting up the mesh for each test case. The horizontal mesh is constructed at runtime (using :py:func:`mpas_tools.planar_hex.make_planar_hex_mesh()`). Then, a MALI grid is -created with the MPAS-Tools script ``create_landice_grid_from_generic_MPAS_grid.py`` +created with the MPAS-Tools script ``create_landice_grid_from_generic_mpas_grid`` and a graph file is created to partition the mesh before the model run. Finally, the initial condition is defined in the private function diff --git a/docs/developers_guide/landice/test_groups/hydro_radial.rst b/docs/developers_guide/landice/test_groups/hydro_radial.rst index e82704b221..c63e501b62 100644 --- a/docs/developers_guide/landice/test_groups/hydro_radial.rst +++ b/docs/developers_guide/landice/test_groups/hydro_radial.rst @@ -31,7 +31,7 @@ defines a step for setting up the mesh for each test case. The horizontal mesh is constructed at runtime (using :py:func:`mpas_tools.planar_hex.make_planar_hex_mesh()`). A MALI grid is created with the MPAS-Tools script -``create_landice_grid_from_generic_MPAS_grid.py`` and a graph file is created +``create_landice_grid_from_generic_mpas_grid`` and a graph file is created to partition the mesh before the model run. Finally, the initial condition is defined in the private function diff --git a/docs/developers_guide/landice/test_groups/ismip6_forcing.rst b/docs/developers_guide/landice/test_groups/ismip6_forcing.rst index 4f9d2e88aa..da9dab1faf 100644 --- a/docs/developers_guide/landice/test_groups/ismip6_forcing.rst +++ b/docs/developers_guide/landice/test_groups/ismip6_forcing.rst @@ -9,7 +9,7 @@ atmospheric and oceanic forcing data of the Ice Sheet Model Intercomparison for CMIP6 (ISMIP6) protocol from its native polarstereo grid to the unstructure MALI mesh. The test group includes five test cases: ``atmosphere``, ``ocean_basal``, ``ocean_thermal_obs``, ``ocean_thermal`` and -``shelf_collapse``. The ``atmosphere`` test case has two steps: +``shelf_collapse``. The ``atmosphere`` test case has two steps: ``process_smb`` and ``process_smb_racmo``; the ``ocean_basal`` and ``shelf_collpase`` test cases each have one step, ``process_basal_melt`` and ``process_shelf_collpase`` (respectively); the ``ocean_thermal_obs`` and ``ocean_thermal`` @@ -34,15 +34,15 @@ create_mapfile The module :py:class:`compass.landice.tests.ismip6_forcing.create_mapfile` defines a unified framework for creating the SCRIP and mapping files from the ISMIP6 -source data files. The function +source data files. The function :py:func:`compass.landice.tests.ismip6_forcing.create_mapfile.build_mapping_file` is the common interface to build the SCRIP files and mapping files. The ``scrip_from_latlon`` keyword argument is used to call the appropriate function for generating the SCRIP file. If ``scrip_from_latlon`` is ``false`` the -``create_SCRIP_file_from_planar_rectangular_grid.py`` command line executable -from the ``MPAS_Tools`` conda package is used, otherwise the +``create_scrip_file_from_planar_rectangular_grid`` command line executable +from the ``MPAS_Tools`` conda package is used, otherwise the :py:func:`compass.landice.tests.ismip6_forcing.create_mapfile.create_scrip_from_latlon` -function is used. Multiple methods for creating SCRIP files are necessary due to +function is used. Multiple methods for creating SCRIP files are necessary due to inconsistent dimensions names across the different ISMIP6 datasets. Test cases @@ -87,4 +87,4 @@ shelf_collapse ~~~~~~~~~~~~~~ The :py:class:`compass.landice.tests.ismip6_forcing.shelf_collapse.ShelfCollapse` test case performs the processing of ice shelf collapse masks by remapping the -original ISMIP6 forcing data to MALI's unstructured grid and renaming variables. +original ISMIP6 forcing data to MALI's unstructured grid and renaming variables. diff --git a/docs/developers_guide/landice/test_groups/ismip6_run.rst b/docs/developers_guide/landice/test_groups/ismip6_run.rst index 6a79f18a4e..6f29ef68ee 100644 --- a/docs/developers_guide/landice/test_groups/ismip6_run.rst +++ b/docs/developers_guide/landice/test_groups/ismip6_run.rst @@ -28,7 +28,7 @@ excessive subdirectories. The ``configure`` method is where the experiments to be set up are determined. The config option ``exp_list`` is parsed and each experiment to be included -is set up as a step of the test case by calling the +is set up as a step of the test case by calling the ``SetUpExperiment`` constructor (``__init__``). All of the experiments are removed from ``steps_to_run``, because the experiments (steps) are not meant to be run together through the test @@ -70,7 +70,7 @@ in the comparison of post-simulation ice mass calculations from the model output To address this issue, an interim solution has been made to project the southern polar region onto the MALI planar mesh assuming a sphere (this is done by setting the lat/long in the MALI mesh using the 'aid-bedmap2-sphere' projection string in -calling the function in 'set_lat_lon_fields_in_planar_grid.py'. Thus, the resulting +calling the function in 'set_lat_lon_fields_in_planar_grid'. Thus, the resulting MALI mesh for coupled MALI-SLM simulations that are setup from this testgroup have the lat/long values based off sphere. Once the simulation outputs are generated, it is necessary to calculate and apply the scaling factors to the MALI outputs diff --git a/docs/developers_guide/landice/test_groups/mesh_modifications.rst b/docs/developers_guide/landice/test_groups/mesh_modifications.rst index f20b2c3a29..0e58e954dd 100644 --- a/docs/developers_guide/landice/test_groups/mesh_modifications.rst +++ b/docs/developers_guide/landice/test_groups/mesh_modifications.rst @@ -42,7 +42,7 @@ steps: * interpolate fields from source mesh to subdomain mesh using nearest neighbor interpolation. - This can be done either with the ``interpolate_to_mpasli_grid.py`` script + This can be done either with the ``interpolate_to_mpasli_grid`` script or using ``ncremap``. The ncremap method is slower and potentially more fragile (depends on more external tools), but if used allows the option to remap additional files (e.g. forcing files). diff --git a/docs/tutorials/dev_add_rrm.rst b/docs/tutorials/dev_add_rrm.rst index 701c6e9e50..71a415514c 100644 --- a/docs/tutorials/dev_add_rrm.rst +++ b/docs/tutorials/dev_add_rrm.rst @@ -1868,7 +1868,7 @@ run: .. code-block:: bash - paraview_vtk_field_extractor.py -m init.nc \ + paraview_vtk_field_extractor -m init.nc \ -f output.nc -v normalVelocity,temperature,salinity \ -d nVertLevels=0 diff --git a/docs/users_guide/landice/test_groups/antarctica.rst b/docs/users_guide/landice/test_groups/antarctica.rst index cef797f9ee..ec49e5f1df 100644 --- a/docs/users_guide/landice/test_groups/antarctica.rst +++ b/docs/users_guide/landice/test_groups/antarctica.rst @@ -73,19 +73,19 @@ the mesh generation options are adjusted through the config file. # path to directory containing BedMachine and Measures datasets # (default value is for Perlmutter) data_path = /global/cfs/cdirs/fanssie/standard_datasets/AIS_datasets - + # filename of the BedMachine thickness and bedTopography dataset # (default value is for Perlmutter) bedmachine_filename = BedMachineAntarctica_2020-07-15_v02_edits_floodFill_extrap_fillVostok.nc - + # filename of the MEASURES ice velocity dataset # (default value is for Perlmutter) measures_filename = antarctica_ice_velocity_450m_v2_edits_extrap.nc - + # projection of the source datasets, according to the dictionary keys - # create_SCRIP_file_from_planar_rectangular_grid.py from MPAS_Tools + # create_scrip_file_from_planar_rectangular_grid from MPAS_Tools src_proj = ais-bedmap2 - + # number of processors to use for ESMF_RegridWeightGen nProcs = 128 diff --git a/docs/users_guide/landice/test_groups/greenland.rst b/docs/users_guide/landice/test_groups/greenland.rst index 146119b909..ae0285589b 100644 --- a/docs/users_guide/landice/test_groups/greenland.rst +++ b/docs/users_guide/landice/test_groups/greenland.rst @@ -90,19 +90,19 @@ The other test cases do not use config options. # path to directory containing BedMachine and Measures datasets # (default value is for Perlmutter) data_path = /global/cfs/cdirs/fanssie/standard_datasets/GIS_datasets/ - + # filename of the BedMachine thickness and bedTopography dataset # (default value is for Perlmutter) bedmachine_filename = BedMachineGreenland-v5_edits_floodFill_extrap.nc - + # filename of the MEASURES ice velocity dataset # (default value is for Perlmutter) measures_filename = greenland_vel_mosaic500_extrap.nc - + # projection of the source datasets, according to the dictionary keys - # create_SCRIP_file_from_planar_rectangular_grid.py from MPAS_Tools + # create_scrip_file_from_planar_rectangular_grid from MPAS_Tools src_proj = gis-gimp - + # number of processors to use for ESMF_RegridWeightGen nProcs = 128 diff --git a/docs/users_guide/landice/test_groups/ismip6_run.rst b/docs/users_guide/landice/test_groups/ismip6_run.rst index ac5b3390d3..2ab1ad04f0 100644 --- a/docs/users_guide/landice/test_groups/ismip6_run.rst +++ b/docs/users_guide/landice/test_groups/ismip6_run.rst @@ -173,7 +173,7 @@ in the comparison of post-simulation ice mass calculations from the model output To address this issue, an interim solution has been made to project the southern polar region onto the MALI planar mesh assuming a sphere (this is done by setting the lat/long in the MALI mesh using the 'aid-bedmap2-sphere' projection string in -calling the function in 'set_lat_lon_fields_in_planar_grid.py'. Thus, the resulting +calling the function in 'set_lat_lon_fields_in_planar_grid'. Thus, the resulting MALI mesh for coupled MALI-SLM simulations that are setup from this testgroup have the lat/long values based off sphere. Once the simulation outputs are generated, it is necessary to calculate and apply the scaling factors to the MALI outputs diff --git a/docs/users_guide/landice/test_groups/mesh_modifications.rst b/docs/users_guide/landice/test_groups/mesh_modifications.rst index 063bd37e81..33e1dba0b4 100644 --- a/docs/users_guide/landice/test_groups/mesh_modifications.rst +++ b/docs/users_guide/landice/test_groups/mesh_modifications.rst @@ -88,7 +88,7 @@ the test case. # nstd weight file and then uses ncremap to perform remapping. # This method supports interpolating ancillary files (below) # but likely needs to be run on a compute node and is more fragile. - # 'mali_interp' uses the MALI interpolation script interpolate_to_mpasli_grid.py + # 'mali_interp' uses the MALI interpolation script interpolate_to_mpasli_grid # This method does not support ancillary files but may be more robust # and can likely be run quickly on a login node. interp_method = ncremap