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Add script to compute vertical coordinate for initial condition #495

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Merged
mark-petersen merged 9 commits into from
Apr 2, 2020
Merged

Add script to compute vertical coordinate for initial condition #495

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0d5e14f
original script from Luke
mark-petersen Mar 30, 2020
c11d2c6
Add 64 layer to domains, add plotting, set parameters
mark-petersen Mar 30, 2020
888a13e
Switch algorithm for finding layer thicknesses
xylar Mar 31, 2020
1b70231
Add new vertical grid to all cases
mark-petersen Apr 1, 2020
e6a6aad
Remove EC60to30wISC/init/config_initial_state.xml
mark-petersen Apr 1, 2020
d4202b8
Add link for EC60to30wISC/init/config_initial_state.xml
mark-petersen Apr 1, 2020
e378b8e
Add old 60 layer to other cases
mark-petersen Apr 1, 2020
80630e9
Set 64 layer to 6000m max depth, varying from 2m to 210m
mark-petersen Apr 1, 2020
d44bb16
Add histogram plots of initial state
mark-petersen Apr 2, 2020
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6 changes: 3 additions & 3 deletions src/core_ocean/mode_init/Registry_global_ocean.xml
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description="Minimum depth where column contains all water-filled cells. The first layer with refBottomDepth greater than this value is included in whole, i.e. no partial bottom cells are used in this layer."
possible_values="Any positive real value greater than 0, but typically greater than 10 m."
/>
<nml_option name="config_global_ocean_depth_file" type="character" default_value="none" units="unitless"
<nml_option name="config_global_ocean_depth_file" type="character" default_value="vertical_grid.nc" units="unitless"
description="Path to the depth initial condition file."
possible_values="path/to/temperature/file.nc"
/>
<nml_option name="config_global_ocean_depth_dimname" type="character" default_value="none" units="unitless"
<nml_option name="config_global_ocean_depth_dimname" type="character" default_value="nVertLevels" units="unitless"
description="Name of the dimension defining the number of vertical levels in input files."
possible_values="Dim name from input files."
/>
<nml_option name="config_global_ocean_depth_varname" type="character" default_value="none" units="unitless"
<nml_option name="config_global_ocean_depth_varname" type="character" default_value="refMidDepth" units="unitless"
description="Name of the variable containing mid-depth of levels in temperature and salinity initial condition files."
possible_values="Variable name from input files."
/>
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2 changes: 1 addition & 1 deletion testing_and_setup/compass/ocean/global_ocean/ARM60to10/init/config_initial_state.xml
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../../config_files/config_initial_state_60_layers.xml
../../config_files/config_initial_state.xml
1 change: 1 addition & 0 deletions ...ng_and_setup/compass/ocean/global_ocean/ARM60to10/init/config_initial_state_60_layers.xml
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../../config_files/config_initial_state_60_layers.xml
1 change: 1 addition & 0 deletions testing_and_setup/compass/ocean/global_ocean/ARM60to10/init/define_vertical_grid.py
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../../../scripts/vertical_grid/define_vertical_grid_64_layers.py
2 changes: 1 addition & 1 deletion testing_and_setup/compass/ocean/global_ocean/ARM60to6/init/config_initial_state.xml
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../../config_files/config_initial_state_60_layers.xml
../../config_files/config_initial_state.xml
1 change: 1 addition & 0 deletions ...ing_and_setup/compass/ocean/global_ocean/ARM60to6/init/config_initial_state_60_layers.xml
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../../config_files/config_initial_state_60_layers.xml
1 change: 1 addition & 0 deletions testing_and_setup/compass/ocean/global_ocean/ARM60to6/init/define_vertical_grid.py
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../../../scripts/vertical_grid/define_vertical_grid_64_layers.py
1 change: 1 addition & 0 deletions testing_and_setup/compass/ocean/global_ocean/CUSP12/init/config_initial_state_60_layers.xml
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../../config_files/config_initial_state_60_layers.xml
1 change: 1 addition & 0 deletions testing_and_setup/compass/ocean/global_ocean/CUSP12/init/define_vertical_grid.py
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../../../scripts/vertical_grid/define_vertical_grid_64_layers.py
1 change: 1 addition & 0 deletions testing_and_setup/compass/ocean/global_ocean/CUSP8/init/config_initial_state_60_layers.xml
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../../config_files/config_initial_state_60_layers.xml
1 change: 1 addition & 0 deletions testing_and_setup/compass/ocean/global_ocean/CUSP8/init/define_vertical_grid.py
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../../../scripts/vertical_grid/define_vertical_grid_64_layers.py
53 changes: 0 additions & 53 deletions testing_and_setup/compass/ocean/global_ocean/EC60to30/init/config_initial_state.xml
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This file was deleted.

1 change: 1 addition & 0 deletions testing_and_setup/compass/ocean/global_ocean/EC60to30/init/config_initial_state.xml
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../../config_files/config_initial_state.xml
1 change: 1 addition & 0 deletions ...ing_and_setup/compass/ocean/global_ocean/EC60to30/init/config_initial_state_60_layers.xml
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../../config_files/config_initial_state_60_layers.xml
1 change: 1 addition & 0 deletions testing_and_setup/compass/ocean/global_ocean/EC60to30/init/define_vertical_grid.py
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../../../scripts/vertical_grid/define_vertical_grid_64_layers.py
60 changes: 0 additions & 60 deletions testing_and_setup/compass/ocean/global_ocean/EC60to30wISC/init/config_initial_state.xml
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1 change: 1 addition & 0 deletions testing_and_setup/compass/ocean/global_ocean/EC60to30wISC/init/config_initial_state.xml
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../../config_files_ISC/config_initial_state.xml
1 change: 1 addition & 0 deletions testing_and_setup/compass/ocean/global_ocean/EC60to30wISC/init/define_vertical_grid.py
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../../../scripts/vertical_grid/define_vertical_grid_64_layers.py
1 change: 1 addition & 0 deletions testing_and_setup/compass/ocean/global_ocean/QU240/init/config_initial_state_60_layers.xml
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../../config_files/config_initial_state_60_layers.xml
1 change: 1 addition & 0 deletions testing_and_setup/compass/ocean/global_ocean/QU240/init/define_vertical_grid.py
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../../../scripts/vertical_grid/define_vertical_grid_16_layers.py
1 change: 1 addition & 0 deletions testing_and_setup/compass/ocean/global_ocean/QU240wISC/init/define_vertical_grid.py
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../../../scripts/vertical_grid/define_vertical_grid_64_layers.py
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Collaborator

@xylar xylar Mar 31, 2020

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I think links like this are needed for a lot more test cases, right?

  • CUSP12
  • CUSP8
  • QU60
  • SO60to10wISC
  • SOQU60to15 (is this even a configuration we want to keep?)

1 change: 1 addition & 0 deletions testing_and_setup/compass/ocean/global_ocean/SO60to10wISC/init/define_vertical_grid.py
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../../../scripts/vertical_grid/define_vertical_grid_64_layers.py
2 changes: 1 addition & 1 deletion testing_and_setup/compass/ocean/global_ocean/config_files/config_base_mesh.xml
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<config case="base_mesh">

<add_link source_path="mpas_model" source="testing_and_setup/compass/ocean/jigsaw_to_MPAS" dest="jigsaw_to_MPAS"/>
<add_link source_path="script_test_dir" source="." dest="define_base_mesh"/>
<copy_file source_path="script_test_dir" source="define_base_mesh.py" dest="define_base_mesh.py"/>

<run_script name="run.py">
<step executable="python">
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19 changes: 14 additions & 5 deletions testing_and_setup/compass/ocean/global_ocean/config_files/config_initial_state.xml
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Expand Up @@ -28,7 +28,9 @@
<add_link source="../culled_mesh/culled_mesh.nc" dest="mesh.nc"/>
<add_link source="../culled_mesh/culled_graph.info" dest="graph.info"/>
<add_link source="../culled_mesh/critical_passages_mask_final.nc" dest="critical_passages.nc"/>
<add_link source_path="initial_condition_database" source="layer_depth.80Layer.180619.nc" dest="layer_depth.nc"/>
<copy_file source_path="script_test_dir" source="define_vertical_grid.py" dest="define_vertical_grid.py"/>
<add_link source_path="script_core_dir" source="scripts/vertical_grid/make_vertical_grid.py" dest="make_vertical_grid.py"/>
<add_link source_path="script_core_dir" source="scripts/plots/plot_initial_state.py" dest="plot_initial_state.py"/>
<add_link source_path="initial_condition_database" source="PTemp.Jan_p3.filled.mpas100levs.160127.nc" dest="temperature.nc"/>
<add_link source_path="initial_condition_database" source="Salt.Jan_p3.noBlackCaspian.filled.mpas100levs.160127.nc" dest="salinity.nc"/>
<add_link source_path="initial_condition_database" source="windStress.ncep_1958-2000avg.interp3600x2431.151106.nc" dest="wind_stress.nc"/>
Expand All @@ -38,7 +40,9 @@
<namelist name="namelist.ocean" mode="init">
<template file="template_initial_state.xml" path_base="script_configuration_dir"/>
<template file="template_critical_passages.xml" path_base="script_core_dir" path="global_ocean"/>
<option name="config_global_ocean_depth_file">'layer_depth.nc'</option>
<option name="config_global_ocean_depth_file">'vertical_grid.nc'</option>
<option name="config_global_ocean_depth_dimname">'nVertLevels'</option>
<option name="config_global_ocean_depth_varname">'refMidDepth'</option>
<option name="config_global_ocean_minimum_depth">10</option>
<option name="config_global_ocean_deepen_critical_passages">.false.</option>
</namelist>
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<run_script name="run.py">
<step executable="gpmetis">
<argument flag="graph.info">8</argument>
<argument flag="graph.info">4</argument>
</step>
<model_run procs="8" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
</run_script>
<step executable="./define_vertical_grid.py">
</step>
<model_run procs="4" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
<step executable="./plot_initial_state.py">
</step>
</run_script>

</config>
2 changes: 1 addition & 1 deletion testing_and_setup/compass/ocean/global_ocean/config_files/config_initial_state_60_layers.xml
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<?xml version="1.0"?>
<config case="initial_state">
<config case="initial_state_60_layer">
<get_file dest_path="initial_condition_database" file_name="Salinity.01.filled.60levels.PHC.151106.nc">
<mirror protocol="wget" url="https://web.lcrc.anl.gov/public/e3sm/mpas_standalonedata/mpas-ocean/initial_condition_database/"/>
</get_file>
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18 changes: 11 additions & 7 deletions testing_and_setup/compass/ocean/global_ocean/config_files_ISC/config_initial_state.xml
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<?xml version="1.0"?>
<config case="initial_state">
<get_file dest_path="initial_condition_database" file_name="layer_depth.80Layer.180619.nc">
<mirror protocol="wget" url="https://web.lcrc.anl.gov/public/e3sm/mpas_standalonedata/mpas-ocean/initial_condition_database/"/>
</get_file>

<get_file dest_path="initial_condition_database" file_name="PTemp.Jan_p3.filled.mpas100levs.160127.nc">
<mirror protocol="wget" url="https://web.lcrc.anl.gov/public/e3sm/mpas_standalonedata/mpas-ocean/initial_condition_database/"/>
</get_file>
Expand All @@ -28,8 +24,10 @@
<add_link source="../culled_mesh/culled_mesh.nc" dest="mesh.nc"/>
<add_link source="../culled_mesh/culled_graph.info" dest="graph.info"/>
<add_link source="../culled_mesh/critical_passages_mask_final.nc" dest="critical_passages.nc"/>
<copy_file source_path="script_test_dir" source="define_vertical_grid.py" dest="define_vertical_grid.py"/>
<add_link source="../culled_mesh/land_ice_mask.nc" dest="land_ice_mask.nc"/>
<add_link source_path="initial_condition_database" source="layer_depth.80Layer.180619.nc" dest="layer_depth.nc"/>
<add_link source_path="script_core_dir" source="scripts/vertical_grid/make_vertical_grid.py" dest="make_vertical_grid.py"/>
<add_link source_path="script_core_dir" source="scripts/plots/plot_initial_state.py" dest="plot_initial_state.py"/>
<add_link source_path="initial_condition_database" source="PTemp.Jan_p3.filled.mpas100levs.160127.nc" dest="temperature.nc"/>
<add_link source_path="initial_condition_database" source="Salt.Jan_p3.noBlackCaspian.filled.mpas100levs.160127.nc" dest="salinity.nc"/>
<add_link source_path="initial_condition_database" source="windStress.ncep_1958-2000avg.interp3600x2431.151106.nc" dest="wind_stress.nc"/>
Expand All @@ -41,7 +39,9 @@
<template file="template_critical_passages.xml" path_base="script_core_dir" path="global_ocean"/>
<template file="template_init_with_land_ice.xml" path_base="script_configuration_dir"/>
<option name="config_iterative_init_variable">'landIcePressure_from_top_density'</option>
<option name="config_global_ocean_depth_file">'layer_depth.nc'</option>
<option name="config_global_ocean_depth_file">'vertical_grid.nc'</option>
<option name="config_global_ocean_depth_dimname">'nVertLevels'</option>
<option name="config_global_ocean_depth_varname">'refMidDepth'</option>
<option name="config_global_ocean_minimum_depth">10</option>
<option name="config_global_ocean_deepen_critical_passages">.false.</option>
</namelist>
Expand All @@ -56,7 +56,11 @@
<step executable="gpmetis">
<argument flag="graph.info">4</argument>
</step>
<step executable="./define_vertical_grid.py">
</step>
<model_run procs="4" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
</run_script>
<step executable="./plot_initial_state.py">
</step>
</run_script>

</config>
2 changes: 1 addition & 1 deletion testing_and_setup/compass/ocean/global_ocean/config_files_ISC/config_ssh_adjustment.xml
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<add_link source="../initial_state/initial_state.nc" dest="init0.nc"/>

<add_link source_path="script_core_dir" source="iterative_ssh_landIcePressure_scripts/iterate_init.py" dest="iterate_init.py"/>
<add_link source_path="script_core_dir" source="scripts/plot_globalStats.py" dest="plot_globalStats.py"/>
<add_link source_path="script_core_dir" source="scripts/plots/plot_globalStats.py" dest="plot_globalStats.py"/>

<namelist name="namelist.ocean" mode="forward">
<template file="template_forward.xml" path_base="script_configuration_dir"/>
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2 changes: 1 addition & 1 deletion testing_and_setup/compass/ocean/isomip_plus/2km/Ocean0/config_adjust_ssh.xml
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<add_link source_path="script_core_dir" source="iterative_ssh_landIcePressure_scripts/iterate_init.py" dest="iterate_init.py"/>
<add_link source_path="script_core_dir" source="iterative_ssh_landIcePressure_scripts/plot_cart_ssh_landIcePressure.py" dest="plot_cart_ssh_landIcePressure.py"/>
<add_link source_path="script_core_dir" source="scripts/plot_globalStats.py" dest="plot_globalStats.py"/>
<add_link source_path="script_core_dir" source="scripts/plots/plot_globalStats.py" dest="plot_globalStats.py"/>

<namelist name="namelist.ocean" mode="forward">
<template file="template_forward.xml" path_base="script_configuration_dir"/>
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2 changes: 1 addition & 1 deletion testing_and_setup/compass/ocean/isomip_plus/2km/Ocean1/config_adjust_ssh.xml
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<add_link source_path="script_core_dir" source="iterative_ssh_landIcePressure_scripts/iterate_init.py" dest="iterate_init.py"/>
<add_link source_path="script_core_dir" source="iterative_ssh_landIcePressure_scripts/plot_cart_ssh_landIcePressure.py" dest="plot_cart_ssh_landIcePressure.py"/>
<add_link source_path="script_core_dir" source="scripts/plot_globalStats.py" dest="plot_globalStats.py"/>
<add_link source_path="script_core_dir" source="scripts/plots/plot_globalStats.py" dest="plot_globalStats.py"/>

<namelist name="namelist.ocean" mode="forward">
<template file="template_forward.xml" path_base="script_configuration_dir"/>
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2 changes: 1 addition & 1 deletion testing_and_setup/compass/ocean/isomip_plus/2km/Ocean2/config_adjust_ssh.xml
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Expand Up @@ -7,7 +7,7 @@

<add_link source_path="script_core_dir" source="iterative_ssh_landIcePressure_scripts/iterate_init.py" dest="iterate_init.py"/>
<add_link source_path="script_core_dir" source="iterative_ssh_landIcePressure_scripts/plot_cart_ssh_landIcePressure.py" dest="plot_cart_ssh_landIcePressure.py"/>
<add_link source_path="script_core_dir" source="scripts/plot_globalStats.py" dest="plot_globalStats.py"/>
<add_link source_path="script_core_dir" source="scripts/plots/plot_globalStats.py" dest="plot_globalStats.py"/>

<namelist name="namelist.ocean" mode="forward">
<template file="template_forward.xml" path_base="script_configuration_dir"/>
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2 changes: 1 addition & 1 deletion testing_and_setup/compass/ocean/isomip_plus/2km/time_varying_Ocean0/config_adjust_ssh.xml
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Expand Up @@ -7,7 +7,7 @@

<add_link source_path="script_core_dir" source="iterative_ssh_landIcePressure_scripts/iterate_init.py" dest="iterate_init.py"/>
<add_link source_path="script_core_dir" source="iterative_ssh_landIcePressure_scripts/plot_cart_ssh_landIcePressure.py" dest="plot_cart_ssh_landIcePressure.py"/>
<add_link source_path="script_core_dir" source="scripts/plot_globalStats.py" dest="plot_globalStats.py"/>
<add_link source_path="script_core_dir" source="scripts/plots/plot_globalStats.py" dest="plot_globalStats.py"/>

<namelist name="namelist.ocean" mode="forward">
<template file="template_forward.xml" path_base="script_configuration_dir"/>
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