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Merged
mark-petersen merged 3 commits into from
May 9, 2019
Merged

CONUS mesh update #201

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a93f78d
Add Greenland to NAEC60to30cr8 mesh and update coastal_tools.py
Apr 8, 2019
eea24b3
remove source_path=jigsaw_to_MPAS to subdirectory of mpas_model
mark-petersen Apr 10, 2019
50b204b
Add 60 layer version of NAEC60to30cr8
Apr 10, 2019
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1 change: 0 additions & 1 deletion testing_and_setup/compass/general.config.ocean
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Expand Up @@ -48,4 +48,3 @@ jigsaw-geo-matlab = FULL_PATH_TO_JIGSAW_REPO
mesh_database = FULL_PATH_TO_LOCAL_MESH_DATABASE
initial_condition_database = FULL_PATH_TO_LOCAL_INITIAL_CONDITION_DATABASE
bathymetry_database = FULL_PATH_TO_BATHYMETRY_DATABASE
jigsaw_to_MPAS = FULL_PATH_TO_MPAS_MODEL_REPORT/testing_and_setup/compass/ocean/jigsaw_to_MPAS
16 changes: 8 additions & 8 deletions testing_and_setup/compass/ocean/global_ocean/NAEC60to30cr8/init/config_base_mesh.xml
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Expand Up @@ -4,16 +4,16 @@
<add_executable source="mesh_converter" dest="MpasMeshConverter.x"/>
<add_executable source="cell_culler" dest="MpasCellCuller.x"/>

<add_link source_path="jigsaw_to_MPAS" source="build_mesh.py" dest="build_mesh.py"/>
<add_link source_path="jigsaw_to_MPAS" source="jigsaw_driver.m" dest="jigsaw_driver.m"/>
<add_link source_path="jigsaw_to_MPAS" source="triangle_jigsaw_to_netcdf.py" dest="triangle_jigsaw_to_netcdf.py"/>
<add_link source_path="jigsaw_to_MPAS" source="mesh_definition_tools.py" dest="mesh_definition_tools.py"/>
<add_link source_path="jigsaw_to_MPAS" source="coastal_tools.py" dest="coastal_tools.py"/>
<add_link source_path="jigsaw_to_MPAS" source="inject_meshDensity.py" dest="inject_meshDensity.py"/>
<add_link source_path="jigsaw_to_MPAS" source="inject_bathymetry.py" dest="inject_bathymetry.py"/>
<add_link source_path="mpas_model" source="testing_and_setup/compass/ocean/jigsaw_to_MPAS/build_mesh.py" dest="build_mesh.py"/>
<add_link source_path="mpas_model" source="testing_and_setup/compass/ocean/jigsaw_to_MPAS/jigsaw_driver.m" dest="jigsaw_driver.m"/>
<add_link source_path="mpas_model" source="testing_and_setup/compass/ocean/jigsaw_to_MPAS/triangle_jigsaw_to_netcdf.py" dest="triangle_jigsaw_to_netcdf.py"/>
<add_link source_path="mpas_model" source="testing_and_setup/compass/ocean/jigsaw_to_MPAS/mesh_definition_tools.py" dest="mesh_definition_tools.py"/>
<add_link source_path="mpas_model" source="testing_and_setup/compass/ocean/jigsaw_to_MPAS/coastal_tools.py" dest="coastal_tools.py"/>
<add_link source_path="mpas_model" source="testing_and_setup/compass/ocean/jigsaw_to_MPAS/inject_meshDensity.py" dest="inject_meshDensity.py"/>
<add_link source_path="mpas_model" source="testing_and_setup/compass/ocean/jigsaw_to_MPAS/inject_bathymetry.py" dest="inject_bathymetry.py"/>
<add_link source_path="script_test_dir" source="define_base_mesh.py" dest="define_base_mesh.py"/>
<add_link source_path="jigsaw-geo-matlab" source="." dest="jigsaw-geo-matlab"/>
<add_link source_path="bathymetry_database" source="SRTM15_plus/earth_relief_15s.nc" dest="earth_relief_15s.nc"/>
<add_link source_path="bathymetry_database" source="SRTM15_plus/earth_relief_15s.nc" dest="earth_relief_15s.nc"/>

<run_script name="run.py">
<step executable="./build_mesh.py">
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16 changes: 12 additions & 4 deletions testing_and_setup/compass/ocean/global_ocean/NAEC60to30cr8/init/define_base_mesh.py
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Expand Up @@ -91,11 +91,18 @@ def cellWidthVsLatLon():
cell_width,lon,lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)

print "***Greenland***"
Greenland = {"include":[np.array([-49,-45,60,61])],
"exclude":[]}
params["region_box"] = Greenland
params["region_box"] = ct.Greenland
params["restrict_box"] = ct.Empty
params["trans_start"] = 900.0*km
params["trans_width"] = 600.0*km
params["trans_start"] = 275.0*km
cell_width, lon, lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)

print "***Labrador Sea***"
params["region_box"] = ct.Empty
params["restrict_box"] = ct.Empty
params["point_list"] = [np.array([-50.0,55.0])]
params["trans_width"] = 600.0*km
params["trans_start"] = 400.0*km
cell_width, lon, lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)

print"***Central America (West Coast)***"
Expand All @@ -114,6 +121,7 @@ def cellWidthVsLatLon():
"exclude":[]}
params["region_box"] = Central_America
params["restrict_box"] = ct.Empty
params["point_list"] = None
params["trans_width"] = 600.0*km
params["trans_start"] = 400.0*km
cell_width, lon, lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)
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23 changes: 23 additions & 0 deletions testing_and_setup/compass/ocean/global_ocean/NAEC60to30cr8L60/init/config_base_mesh.xml
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@@ -0,0 +1,23 @@
<?xml version="1.0"?>
<config case="base_mesh">

<add_executable source="mesh_converter" dest="MpasMeshConverter.x"/>
<add_executable source="cell_culler" dest="MpasCellCuller.x"/>

<add_link source_path="mpas_model" source="testing_and_setup/compass/ocean/jigsaw_to_MPAS/build_mesh.py" dest="build_mesh.py"/>
<add_link source_path="mpas_model" source="testing_and_setup/compass/ocean/jigsaw_to_MPAS/jigsaw_driver.m" dest="jigsaw_driver.m"/>
<add_link source_path="mpas_model" source="testing_and_setup/compass/ocean/jigsaw_to_MPAS/triangle_jigsaw_to_netcdf.py" dest="triangle_jigsaw_to_netcdf.py"/>
<add_link source_path="mpas_model" source="testing_and_setup/compass/ocean/jigsaw_to_MPAS/mesh_definition_tools.py" dest="mesh_definition_tools.py"/>
<add_link source_path="mpas_model" source="testing_and_setup/compass/ocean/jigsaw_to_MPAS/coastal_tools.py" dest="coastal_tools.py"/>
<add_link source_path="mpas_model" source="testing_and_setup/compass/ocean/jigsaw_to_MPAS/inject_meshDensity.py" dest="inject_meshDensity.py"/>
<add_link source_path="mpas_model" source="testing_and_setup/compass/ocean/jigsaw_to_MPAS/inject_bathymetry.py" dest="inject_bathymetry.py"/>
<add_link source_path="script_test_dir" source="define_base_mesh.py" dest="define_base_mesh.py"/>
<add_link source_path="jigsaw-geo-matlab" source="." dest="jigsaw-geo-matlab"/>
<add_link source_path="bathymetry_database" source="SRTM15_plus/earth_relief_15s.nc" dest="earth_relief_15s.nc"/>

<run_script name="run.py">
<step executable="./build_mesh.py">
</step>
</run_script>

</config>
1 change: 1 addition & 0 deletions testing_and_setup/compass/ocean/global_ocean/NAEC60to30cr8L60/init/config_culled_mesh.xml
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@@ -0,0 +1 @@
../../config_files/config_culled_mesh.xml
1 change: 1 addition & 0 deletions testing_and_setup/compass/ocean/global_ocean/NAEC60to30cr8L60/init/config_driver.xml
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../../config_files/config_driver_init.xml
1 change: 1 addition & 0 deletions testing_and_setup/compass/ocean/global_ocean/NAEC60to30cr8L60/init/config_initial_state.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/NAEC60to30cr8L60/init/config_mesh_metrics.xml
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../../config_files/config_mesh_metrics.xml
1 change: 1 addition & 0 deletions testing_and_setup/compass/ocean/global_ocean/NAEC60to30cr8L60/init/define_base_mesh.py
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../../NAEC60to30cr8/init/define_base_mesh.py
28 changes: 28 additions & 0 deletions testing_and_setup/compass/ocean/global_ocean/NAEC60to30cr8L60/spin_up/config_driver.xml
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<driver_script name="run_test.py">
<case name="spin_up1">
<step executable="./run.py" quiet="true" pre_message=" * Running spin_up1" post_message=" - Complete"/>
</case>
<case name="spin_up2">
<step executable="./run.py" quiet="true" pre_message=" * Running spin_up2" post_message=" - Complete"/>
</case>
<case name="spin_up3">
<step executable="./run.py" quiet="true" pre_message=" * Running spin_up3" post_message=" - Complete"/>
</case>
<case name="spin_up4">
<step executable="./run.py" quiet="true" pre_message=" * Running spin_up4" post_message=" - Complete"/>
</case>
<case name="spin_up5">
<step executable="./run.py" quiet="true" pre_message=" * Running spin_up5" post_message=" - Complete"/>
</case>
<case name="spin_up6">
<step executable="./run.py" quiet="true" pre_message=" * Running spin_up6" post_message=" - Complete"/>
</case>
<case name="test_final_settings">
<step executable="./run.py" quiet="true" pre_message=" * Running test_final_settings" post_message=" - Complete"/>
</case>
<validation>
<compare_fields file1="test_final_settings/output.nc">
<template file="prognostic_comparison.xml" path_base="script_core_dir" path="templates/validations"/>
</compare_fields>
</validation>
</driver_script>
49 changes: 49 additions & 0 deletions testing_and_setup/compass/ocean/global_ocean/NAEC60to30cr8L60/spin_up/config_spin_up1.xml
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<?xml version="1.0"?>
<config case="spin_up1">
<add_link source="../../init/initial_state/initial_state.nc" dest="init.nc"/>
<add_link source="../../init/initial_state/graph.info" dest="graph.info"/>
<add_link source="../../init/initial_state/init_mode_forcing_data.nc" dest="forcing_data.nc"/>

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

<namelist name="namelist.ocean" mode="forward">
<template file="template_forward.xml" path_base="script_configuration_dir"/>
<template file="template_forward.xml" path_base="script_resolution_dir"/>
<option name="config_run_duration">'00-00-00_06:00:00'</option>
<option name="config_dt">'00:00:30'</option>
<option name="config_btr_dt">'00:00:01.5'</option>
<option name="config_Rayleigh_friction">.true.</option>
<option name="config_Rayleigh_damping_coeff">1.0e-3</option>
<template file="global_stats.xml" path_base="script_core_dir" path="templates/analysis_members"/>
</namelist>

<streams name="streams.ocean" keep="immutable" mode="forward">
<stream name="mesh">
<attribute name="filename_template">init.nc</attribute>
</stream>
<stream name="input">
<attribute name="filename_template">init.nc</attribute>
</stream>
<template file="output.xml" path_base="script_core_dir" path="templates/streams"/>
<stream name="output">
<attribute name="output_interval">00-00-10_00:00:00</attribute>
</stream>
<stream name="restart">
<attribute name="output_interval">00-00-00_06:00:00</attribute>
</stream>

<template file="forcing_data.xml" path_base="script_core_dir" path="templates/streams"/>
<template file="shortwave_forcing_data.xml" path_base="script_core_dir" path="templates/streams"/>
<template file="global_stats.xml" path_base="script_core_dir" path="templates/analysis_members"/>

</streams>

<run_script name="run.py">
<step executable="./metis">
<argument flag="graph.info">720</argument>
</step>

<model_run procs="720" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
</run_script>
</config>
53 changes: 53 additions & 0 deletions testing_and_setup/compass/ocean/global_ocean/NAEC60to30cr8L60/spin_up/config_spin_up2.xml
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<?xml version="1.0"?>
<config case="spin_up2">
<add_link source="../../init/initial_state/initial_state.nc" dest="init.nc"/>
<add_link source="../../init/initial_state/graph.info" dest="graph.info"/>
<add_link source="../../init/initial_state/init_mode_forcing_data.nc" dest="forcing_data.nc"/>
<add_link source="../spin_up1/Restart_timestamp" dest="Restart_timestamp"/>
<add_link source="../spin_up1/restarts" dest="restarts"/>

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

<namelist name="namelist.ocean" mode="forward">
<template file="template_forward.xml" path_base="script_configuration_dir"/>
<template file="template_forward.xml" path_base="script_resolution_dir"/>
<option name="config_run_duration">'00-00-00_06:00:00'</option>
<option name="config_do_restart">.true.</option>
<option name="config_start_time">'file'</option>
<option name="config_dt">'00:01:00'</option>
<option name="config_btr_dt">'00:00:03'</option>
<option name="config_Rayleigh_friction">.true.</option>
<option name="config_Rayleigh_damping_coeff">4.0e-4</option>
<template file="global_stats.xml" path_base="script_core_dir" path="templates/analysis_members"/>
</namelist>

<streams name="streams.ocean" keep="immutable" mode="forward">
<stream name="mesh">
<attribute name="filename_template">init.nc</attribute>
</stream>
<stream name="input">
<attribute name="filename_template">init.nc</attribute>
</stream>
<template file="output.xml" path_base="script_core_dir" path="templates/streams"/>
<stream name="output">
<attribute name="output_interval">00-00-10_00:00:00</attribute>
</stream>
<stream name="restart">
<attribute name="output_interval">00-00-00_06:00:00</attribute>
</stream>

<template file="forcing_data.xml" path_base="script_core_dir" path="templates/streams"/>
<template file="shortwave_forcing_data.xml" path_base="script_core_dir" path="templates/streams"/>
<template file="global_stats.xml" path_base="script_core_dir" path="templates/analysis_members"/>

</streams>

<run_script name="run.py">
<step executable="./metis">
<argument flag="graph.info">720</argument>
</step>

<model_run procs="720" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
</run_script>
</config>
53 changes: 53 additions & 0 deletions testing_and_setup/compass/ocean/global_ocean/NAEC60to30cr8L60/spin_up/config_spin_up3.xml
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<?xml version="1.0"?>
<config case="spin_up3">
<add_link source="../../init/initial_state/initial_state.nc" dest="init.nc"/>
<add_link source="../../init/initial_state/graph.info" dest="graph.info"/>
<add_link source="../../init/initial_state/init_mode_forcing_data.nc" dest="forcing_data.nc"/>
<add_link source="../spin_up1/Restart_timestamp" dest="Restart_timestamp"/>
<add_link source="../spin_up1/restarts" dest="restarts"/>

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

<namelist name="namelist.ocean" mode="forward">
<template file="template_forward.xml" path_base="script_configuration_dir"/>
<template file="template_forward.xml" path_base="script_resolution_dir"/>
<option name="config_run_duration">'00-00-00_12:00:00'</option>
<option name="config_do_restart">.true.</option>
<option name="config_start_time">'file'</option>
<option name="config_dt">'00:02:00'</option>
<option name="config_btr_dt">'00:00:06'</option>
<option name="config_Rayleigh_friction">.true.</option>
<option name="config_Rayleigh_damping_coeff">1.0e-4</option>
<template file="global_stats.xml" path_base="script_core_dir" path="templates/analysis_members"/>
</namelist>

<streams name="streams.ocean" keep="immutable" mode="forward">
<stream name="mesh">
<attribute name="filename_template">init.nc</attribute>
</stream>
<stream name="input">
<attribute name="filename_template">init.nc</attribute>
</stream>
<template file="output.xml" path_base="script_core_dir" path="templates/streams"/>
<stream name="output">
<attribute name="output_interval">00-00-10_00:00:00</attribute>
</stream>
<stream name="restart">
<attribute name="output_interval">00-00-00_12:00:00</attribute>
</stream>

<template file="forcing_data.xml" path_base="script_core_dir" path="templates/streams"/>
<template file="shortwave_forcing_data.xml" path_base="script_core_dir" path="templates/streams"/>
<template file="global_stats.xml" path_base="script_core_dir" path="templates/analysis_members"/>

</streams>

<run_script name="run.py">
<step executable="./metis">
<argument flag="graph.info">720</argument>
</step>

<model_run procs="720" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
</run_script>
</config>
53 changes: 53 additions & 0 deletions testing_and_setup/compass/ocean/global_ocean/NAEC60to30cr8L60/spin_up/config_spin_up4.xml
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<?xml version="1.0"?>
<config case="spin_up4">
<add_link source="../../init/initial_state/initial_state.nc" dest="init.nc"/>
<add_link source="../../init/initial_state/graph.info" dest="graph.info"/>
<add_link source="../../init/initial_state/init_mode_forcing_data.nc" dest="forcing_data.nc"/>
<add_link source="../spin_up1/Restart_timestamp" dest="Restart_timestamp"/>
<add_link source="../spin_up1/restarts" dest="restarts"/>

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

<namelist name="namelist.ocean" mode="forward">
<template file="template_forward.xml" path_base="script_configuration_dir"/>
<template file="template_forward.xml" path_base="script_resolution_dir"/>
<option name="config_run_duration">'00-00-01_00:00:00'</option>
<option name="config_do_restart">.true.</option>
<option name="config_start_time">'file'</option>
<option name="config_dt">'00:03:00'</option>
<option name="config_btr_dt">'00:00:09'</option>
<option name="config_Rayleigh_friction">.true.</option>
<option name="config_Rayleigh_damping_coeff">4.0e-5</option>
<template file="global_stats.xml" path_base="script_core_dir" path="templates/analysis_members"/>
</namelist>

<streams name="streams.ocean" keep="immutable" mode="forward">
<stream name="mesh">
<attribute name="filename_template">init.nc</attribute>
</stream>
<stream name="input">
<attribute name="filename_template">init.nc</attribute>
</stream>
<template file="output.xml" path_base="script_core_dir" path="templates/streams"/>
<stream name="output">
<attribute name="output_interval">00-00-10_00:00:00</attribute>
</stream>
<stream name="restart">
<attribute name="output_interval">00-00-01_00:00:00</attribute>
</stream>

<template file="forcing_data.xml" path_base="script_core_dir" path="templates/streams"/>
<template file="shortwave_forcing_data.xml" path_base="script_core_dir" path="templates/streams"/>
<template file="global_stats.xml" path_base="script_core_dir" path="templates/analysis_members"/>

</streams>

<run_script name="run.py">
<step executable="./metis">
<argument flag="graph.info">720</argument>
</step>

<model_run procs="720" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
</run_script>
</config>
53 changes: 53 additions & 0 deletions testing_and_setup/compass/ocean/global_ocean/NAEC60to30cr8L60/spin_up/config_spin_up5.xml
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<?xml version="1.0"?>
<config case="spin_up5">
<add_link source="../../init/initial_state/initial_state.nc" dest="init.nc"/>
<add_link source="../../init/initial_state/graph.info" dest="graph.info"/>
<add_link source="../../init/initial_state/init_mode_forcing_data.nc" dest="forcing_data.nc"/>
<add_link source="../spin_up1/Restart_timestamp" dest="Restart_timestamp"/>
<add_link source="../spin_up1/restarts" dest="restarts"/>

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

<namelist name="namelist.ocean" mode="forward">
<template file="template_forward.xml" path_base="script_configuration_dir"/>
<template file="template_forward.xml" path_base="script_resolution_dir"/>
<option name="config_run_duration">'00-00-01_00:00:00'</option>
<option name="config_do_restart">.true.</option>
<option name="config_start_time">'file'</option>
<option name="config_dt">'00:05:00'</option>
<option name="config_btr_dt">'00:00:12'</option>
<option name="config_Rayleigh_friction">.true.</option>
<option name="config_Rayleigh_damping_coeff">2.0e-5</option>
<template file="global_stats.xml" path_base="script_core_dir" path="templates/analysis_members"/>
</namelist>

<streams name="streams.ocean" keep="immutable" mode="forward">
<stream name="mesh">
<attribute name="filename_template">init.nc</attribute>
</stream>
<stream name="input">
<attribute name="filename_template">init.nc</attribute>
</stream>
<template file="output.xml" path_base="script_core_dir" path="templates/streams"/>
<stream name="output">
<attribute name="output_interval">00-00-10_00:00:00</attribute>
</stream>
<stream name="restart">
<attribute name="output_interval">00-00-01_00:00:00</attribute>
</stream>

<template file="forcing_data.xml" path_base="script_core_dir" path="templates/streams"/>
<template file="shortwave_forcing_data.xml" path_base="script_core_dir" path="templates/streams"/>
<template file="global_stats.xml" path_base="script_core_dir" path="templates/analysis_members"/>

</streams>

<run_script name="run.py">
<step executable="./metis">
<argument flag="graph.info">720</argument>
</step>

<model_run procs="720" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
</run_script>
</config>
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