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Add JM and Wright 1997 EOS test cases to ISOMIP+ configuration #7

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Add JM and Wright 1997 EOS test cases to ISOMIP+ configuration #7

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d55cc03
Add ISOMIP+ Ocean0 test case with JM EOS
xylar Jul 2, 2019
56587fc
Add in situ density to ISOMIP+ viz
xylar Jul 2, 2019
276dc37
Add version of ISOMIP+ Ocean0 test case with Wright EOS
xylar Jul 1, 2019
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44 changes: 44 additions & 0 deletions ocean/isomip_plus/2km/jm_eos_Ocean0/config_adjust_ssh.xml
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<?xml version="1.0"?>
<config case="adjust_ssh">
<add_link source="../init_step2/graph.info" dest="graph.info"/>
<add_link source="../init_step2/ocean.nc" dest="init0.nc"/>

<add_executable source="model" dest="ocean_model"/>

<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"/>

<namelist name="namelist.ocean" mode="forward">
<template file="template_forward.xml" path_base="script_configuration_dir"/>
<template file="global_stats.xml" path_base="script_core_dir" path="templates/analysis_members"/>
<template file="template_adjust_ssh.xml" path_base="script_configuration_dir"/>
<option name="config_pio_num_iotasks">1</option>
<option name="config_pio_stride">4</option>
<option name="config_pressure_gradient_type">'Jacobian_from_TS'</option>
<option name="config_eos_type">'jm'</option>
</namelist>

<streams name="streams.ocean" keep="immutable" mode="forward">
<template file="template_adjust_ssh.xml" path_base="script_configuration_dir"/>
<template file="global_stats.xml" path_base="script_core_dir" path="templates/analysis_members"/>
<stream name="globalStatsOutput">
<attribute name="clobber_mode">truncate</attribute>
<attribute name="output_interval">0000_00:00:01</attribute>
</stream>
</streams>

<run_script name="run.py">
<step executable="gpmetis">
<argument flag="graph.info">4</argument>
</step>
<step executable="./iterate_init.py">
<argument flag="--iteration_count">10</argument>
<argument flag="--variable_to_modify">landIcePressure</argument>
</step>
</run_script>

<run_script name="run_model.py">
<model_run procs="4" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
</run_script>
</config>
22 changes: 22 additions & 0 deletions ocean/isomip_plus/2km/jm_eos_Ocean0/config_driver.xml
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<driver_script name="run_test.py">
<case name="init_step1">
<step executable="./run.py" quiet="true" pre_message=" * Running init_step1" post_message=" Complete"/>
</case>
<case name="init_step2">
<step executable="./run.py" quiet="true" pre_message=" * Running init_step2" post_message=" Complete"/>
</case>
<case name="adjust_ssh">
<step executable="./run.py" quiet="true" pre_message=" * Running adjust_ssh" post_message=" Complete"/>
</case>
<case name="forward_short">
<step executable="./run.py" quiet="true" pre_message=" * Running forward_short" post_message=" Complete"/>
</case>
<validation>
<compare_fields file1="forward_short/output.nc">
<template file="prognostic_comparison.xml" path_base="script_core_dir" path="templates/validations"/>
</compare_fields>
<compare_fields file1="forward_short/land_ice_fluxes.nc">
<template file="land_ice_flux_comparison.xml" path_base="script_core_dir" path="templates/validations"/>
</compare_fields>
</validation>
</driver_script>
38 changes: 38 additions & 0 deletions ocean/isomip_plus/2km/jm_eos_Ocean0/config_forward.xml
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<?xml version="1.0"?>
<config case="forward">
<add_link source="../init_step2/graph.info" dest="graph.info"/>
<add_link source="../init_step2/init_mode_forcing_data.nc" dest="forcing_data_init.nc"/>
<add_link source="../adjust_ssh/init.nc" dest="init.nc"/>
<add_link source="forcing_data_init.nc" dest="forcing_data.nc"/>

<add_executable source="model" dest="ocean_model"/>

<add_link source_path="script_configuration_dir" source="viz" dest="viz"/>
<add_link source_path="script_configuration_dir" source="update_evaporationFlux.py" dest="update_evaporationFlux.py"/>
<add_link source_path="utility_scripts" source="setup_restart.py" dest="setup_restart.py"/>
<add_link source_path="utility_scripts" source="check_progress.py" dest="check_progress.py"/>

<namelist name="namelist.ocean" mode="forward">
<template file="template_forward.xml" path_base="script_configuration_dir"/>
<template file="global_stats.xml" path_base="script_core_dir" path="templates/analysis_members"/>
<option name="config_pressure_gradient_type">'Jacobian_from_TS'</option>
<option name="config_eos_type">'jm'</option>
</namelist>

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

<run_script name="run.py">
<step executable="gpmetis">
<argument flag="graph.info">136</argument>
</step>
<model_run procs="136" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
<step executable="./update_evaporationFlux.py">
<argument flag="--in_forcing_file">forcing_data_init.nc</argument>
<argument flag="--out_forcing_file">forcing_data_updated.nc</argument>
<argument flag="--out_forcing_link">forcing_data.nc</argument>
<argument flag="--avg_months">3</argument>
</step>
</run_script>
</config>
41 changes: 41 additions & 0 deletions ocean/isomip_plus/2km/jm_eos_Ocean0/config_forward_short.xml
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<?xml version="1.0"?>
<config case="forward_short">
<add_link source="../init_step2/graph.info" dest="graph.info"/>
<add_link source="../init_step2/init_mode_forcing_data.nc" dest="forcing_data_init.nc"/>
<add_link source="../adjust_ssh/init.nc" dest="init.nc"/>
<add_link source="forcing_data_init.nc" dest="forcing_data.nc"/>

<add_executable source="model" dest="ocean_model"/>

<namelist name="namelist.ocean" mode="forward">
<template file="template_forward.xml" path_base="script_configuration_dir"/>
<template file="global_stats.xml" path_base="script_core_dir" path="templates/analysis_members"/>
<option name="config_run_duration">'0000-00-00_01:00:00'</option>
<option name="config_pio_num_iotasks">1</option>
<option name="config_pio_stride">4</option>
<option name="config_pressure_gradient_type">'Jacobian_from_TS'</option>
<option name="config_eos_type">'jm'</option>
</namelist>

<streams name="streams.ocean" keep="immutable" mode="forward">
<template file="template_forward.xml" path_base="script_configuration_dir"/>
<stream name="output">
<attribute name="output_interval">0000_01:00:00</attribute>
</stream>
<template file="land_ice_fluxes.xml" path_base="script_core_dir" path="templates/streams"/>
<stream name="land_ice_fluxes">
<attribute name="clobber_mode">overwrite</attribute>
<attribute name="output_interval">0000_01:00:00</attribute>
</stream>
<stream name="globalStatsOutput">
<attribute name="output_interval">0000_00:00:01</attribute>
</stream>
</streams>

<run_script name="run.py">
<step executable="gpmetis">
<argument flag="graph.info">4</argument>
</step>
<model_run procs="4" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
</run_script>
</config>
58 changes: 58 additions & 0 deletions ocean/isomip_plus/2km/jm_eos_Ocean0/config_init1.xml
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<?xml version="1.0"?>
<config case="init_step1">

<get_file hash="kpqjir3tne" dest_path="mesh_database" file_name="doubly_periodic_2km_488x87km_planar.151226.nc">
<mirror protocol="wget" url="http://oceans11.lanl.gov/mpas_data/mesh_database/"/>
</get_file>

<get_file dest_path="initial_condition_database" file_name="Ocean1_input_geom_v1.01.nc">
<mirror protocol="wget" url="http://portal.nersc.gov/project/iceocean/isomip+/inputGeometry/"/>
</get_file>

<add_link source_path="mesh_database" source="doubly_periodic_2km_488x87km_planar.151226.nc" dest="base_mesh.nc"/>
<add_link source_path="initial_condition_database" source="Ocean1_input_geom_v1.01.nc" dest="input_geometry.nc"/>

<add_executable source="model" dest="ocean_model"/>
<add_link source_path="script_configuration_dir" source="processInputGeometry.py" dest="processInputGeometry.py"/>
<add_link source_path="script_configuration_dir" source="removePeriodic.py" dest="removePeriodic.py"/>

<namelist name="namelist.ocean" mode="init">
<template file="template_init.xml" path_base="script_configuration_dir"/>
<option name="config_pressure_gradient_type">'Jacobian_from_TS'</option>
<option name="config_eos_type">'jm'</option>
<option name="config_write_cull_cell_mask">.true.</option>
<option name="config_isomip_plus_init_bot_temp">1.0</option>
<option name="config_isomip_plus_init_bot_sal">34.7</option>
<option name="config_isomip_plus_restore_evap_rate">200.0</option>
</namelist>

<streams name="streams.ocean" keep="immutable" mode="init">
<template file="template_init.xml" path_base="script_configuration_dir"/>
</streams>

<run_script name="run.py">
<step executable="./processInputGeometry.py">
<argument flag="-i">input_geometry.nc</argument>
<argument flag="-o">input_geometry_processed.nc</argument>
<argument flag="-s">2.0</argument>
<argument flag="-m">100.0</argument>
</step>

<step executable="MpasMeshConverter.x">
<argument flag="">base_mesh.nc</argument>
<argument flag="">mesh.nc</argument>
</step>
<step executable="gpmetis">
<argument flag="graph.info">4</argument>
</step>

<model_run procs="4" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>

<step executable="MpasCellCuller.x">
<argument flag="">ocean.nc</argument>
</step>
<step executable="./removePeriodic.py">
<argument flag="">culled_mesh.nc</argument>
</step>
</run_script>
</config>
31 changes: 31 additions & 0 deletions ocean/isomip_plus/2km/jm_eos_Ocean0/config_init2.xml
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<?xml version="1.0"?>
<config case="init_step2">
<add_link source="../init_step1/culled_mesh.nc" dest="mesh.nc"/>
<add_link source="../init_step1/culled_graph.info" dest="graph.info"/>
<add_link source="../init_step1/input_geometry_processed.nc" dest="input_geometry_processed.nc"/>

<add_executable source="model" dest="ocean_model"/>

<namelist name="namelist.ocean" mode="init">
<template file="template_init.xml" path_base="script_configuration_dir"/>
<option name="config_pressure_gradient_type">'Jacobian_from_TS'</option>
<option name="config_eos_type">'jm'</option>
<option name="config_write_cull_cell_mask">.false.</option>
<option name="config_isomip_plus_init_bot_temp">1.0</option>
<option name="config_isomip_plus_init_bot_sal">34.7</option>
<option name="config_isomip_plus_restore_evap_rate">200.0</option>
</namelist>

<streams name="streams.ocean" keep="immutable" mode="init">
<template file="template_init.xml" path_base="script_configuration_dir"/>
</streams>

<run_script name="run.py">
<step executable="gpmetis">
<argument flag="graph.info">4</argument>
</step>

<model_run procs="4" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
</run_script>

</config>
44 changes: 44 additions & 0 deletions ocean/isomip_plus/2km/wright_eos_Ocean0/config_adjust_ssh.xml
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<?xml version="1.0"?>
<config case="adjust_ssh">
<add_link source="../init_step2/graph.info" dest="graph.info"/>
<add_link source="../init_step2/ocean.nc" dest="init0.nc"/>

<add_executable source="model" dest="ocean_model"/>

<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"/>

<namelist name="namelist.ocean" mode="forward">
<template file="template_forward.xml" path_base="script_configuration_dir"/>
<template file="global_stats.xml" path_base="script_core_dir" path="templates/analysis_members"/>
<template file="template_adjust_ssh.xml" path_base="script_configuration_dir"/>
<option name="config_pio_num_iotasks">1</option>
<option name="config_pio_stride">4</option>
<option name="config_pressure_gradient_type">'Jacobian_from_TS'</option>
<option name="config_eos_type">'wright'</option>
</namelist>

<streams name="streams.ocean" keep="immutable" mode="forward">
<template file="template_adjust_ssh.xml" path_base="script_configuration_dir"/>
<template file="global_stats.xml" path_base="script_core_dir" path="templates/analysis_members"/>
<stream name="globalStatsOutput">
<attribute name="clobber_mode">truncate</attribute>
<attribute name="output_interval">0000_00:00:01</attribute>
</stream>
</streams>

<run_script name="run.py">
<step executable="gpmetis">
<argument flag="graph.info">4</argument>
</step>
<step executable="./iterate_init.py">
<argument flag="--iteration_count">10</argument>
<argument flag="--variable_to_modify">landIcePressure</argument>
</step>
</run_script>

<run_script name="run_model.py">
<model_run procs="4" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
</run_script>
</config>
22 changes: 22 additions & 0 deletions ocean/isomip_plus/2km/wright_eos_Ocean0/config_driver.xml
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<driver_script name="run_test.py">
<case name="init_step1">
<step executable="./run.py" quiet="true" pre_message=" * Running init_step1" post_message=" Complete"/>
</case>
<case name="init_step2">
<step executable="./run.py" quiet="true" pre_message=" * Running init_step2" post_message=" Complete"/>
</case>
<case name="adjust_ssh">
<step executable="./run.py" quiet="true" pre_message=" * Running adjust_ssh" post_message=" Complete"/>
</case>
<case name="forward_short">
<step executable="./run.py" quiet="true" pre_message=" * Running forward_short" post_message=" Complete"/>
</case>
<validation>
<compare_fields file1="forward_short/output.nc">
<template file="prognostic_comparison.xml" path_base="script_core_dir" path="templates/validations"/>
</compare_fields>
<compare_fields file1="forward_short/land_ice_fluxes.nc">
<template file="land_ice_flux_comparison.xml" path_base="script_core_dir" path="templates/validations"/>
</compare_fields>
</validation>
</driver_script>
38 changes: 38 additions & 0 deletions ocean/isomip_plus/2km/wright_eos_Ocean0/config_forward.xml
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<?xml version="1.0"?>
<config case="forward">
<add_link source="../init_step2/graph.info" dest="graph.info"/>
<add_link source="../init_step2/init_mode_forcing_data.nc" dest="forcing_data_init.nc"/>
<add_link source="../adjust_ssh/init.nc" dest="init.nc"/>
<add_link source="forcing_data_init.nc" dest="forcing_data.nc"/>

<add_executable source="model" dest="ocean_model"/>

<add_link source_path="script_configuration_dir" source="viz" dest="viz"/>
<add_link source_path="script_configuration_dir" source="update_evaporationFlux.py" dest="update_evaporationFlux.py"/>
<add_link source_path="utility_scripts" source="setup_restart.py" dest="setup_restart.py"/>
<add_link source_path="utility_scripts" source="check_progress.py" dest="check_progress.py"/>

<namelist name="namelist.ocean" mode="forward">
<template file="template_forward.xml" path_base="script_configuration_dir"/>
<template file="global_stats.xml" path_base="script_core_dir" path="templates/analysis_members"/>
<option name="config_pressure_gradient_type">'Jacobian_from_TS'</option>
<option name="config_eos_type">'wright'</option>
</namelist>

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

<run_script name="run.py">
<step executable="gpmetis">
<argument flag="graph.info">136</argument>
</step>
<model_run procs="136" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
<step executable="./update_evaporationFlux.py">
<argument flag="--in_forcing_file">forcing_data_init.nc</argument>
<argument flag="--out_forcing_file">forcing_data_updated.nc</argument>
<argument flag="--out_forcing_link">forcing_data.nc</argument>
<argument flag="--avg_months">3</argument>
</step>
</run_script>
</config>
41 changes: 41 additions & 0 deletions ocean/isomip_plus/2km/wright_eos_Ocean0/config_forward_short.xml
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<?xml version="1.0"?>
<config case="forward_short">
<add_link source="../init_step2/graph.info" dest="graph.info"/>
<add_link source="../init_step2/init_mode_forcing_data.nc" dest="forcing_data_init.nc"/>
<add_link source="../adjust_ssh/init.nc" dest="init.nc"/>
<add_link source="forcing_data_init.nc" dest="forcing_data.nc"/>

<add_executable source="model" dest="ocean_model"/>

<namelist name="namelist.ocean" mode="forward">
<template file="template_forward.xml" path_base="script_configuration_dir"/>
<template file="global_stats.xml" path_base="script_core_dir" path="templates/analysis_members"/>
<option name="config_run_duration">'0000-00-00_01:00:00'</option>
<option name="config_pio_num_iotasks">1</option>
<option name="config_pio_stride">4</option>
<option name="config_pressure_gradient_type">'Jacobian_from_TS'</option>
<option name="config_eos_type">'wright'</option>
</namelist>

<streams name="streams.ocean" keep="immutable" mode="forward">
<template file="template_forward.xml" path_base="script_configuration_dir"/>
<stream name="output">
<attribute name="output_interval">0000_01:00:00</attribute>
</stream>
<template file="land_ice_fluxes.xml" path_base="script_core_dir" path="templates/streams"/>
<stream name="land_ice_fluxes">
<attribute name="clobber_mode">overwrite</attribute>
<attribute name="output_interval">0000_01:00:00</attribute>
</stream>
<stream name="globalStatsOutput">
<attribute name="output_interval">0000_00:00:01</attribute>
</stream>
</streams>

<run_script name="run.py">
<step executable="gpmetis">
<argument flag="graph.info">4</argument>
</step>
<model_run procs="4" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
</run_script>
</config>
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