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Support standalone MPAS runs #306
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3929ac0
Parse file-name templates from streams
xylar 57c66aa
Use template to parse dates from monthly mean files
xylar b1064cd
Create symlinks to timeSeriesStatsMonthly output
xylar 7034195
Document setup for standalone MPAS
xylar e0dc22c
Update CI test based on recent changes
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,19 @@ | ||
| Main Authors | ||
| ============ | ||
| * Xylar Asay-Davis | ||
| * Milena Veniziani | ||
| * Philip Wolfram | ||
|
|
||
| Contributors | ||
| ============ | ||
| * Luke Van Roekel | ||
| * Greg Streletz | ||
| * Mark Petersen | ||
| * Stephen Price | ||
| * Joseph Kennedy | ||
| * Adrian Turner | ||
| * Matthew Hoffman | ||
| * Jeremy Fyke | ||
|
|
||
| For a list of all the contributions: | ||
| https://github.com/MPAS-Dev/MPAS-Analysis/graphs/contributors |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,20 @@ | ||
| E3SM | ||
| ==== | ||
|
|
||
| The Energy Exascale Earth System Model (E3SM) project, previously known as | ||
| ACME, is central to ESM as well as many of the Climate and Environmental | ||
| Sciences Division activities, as it is developing a computationally advanced | ||
| coupled climate-energy model to investigate the challenges posed by the | ||
| interactions of weather-climate scale variability with energy and related | ||
| sectors. | ||
|
|
||
| A Full description of E3SM is available at: | ||
| https://climatemodeling.science.energy.gov/projects/energy-exascale-earth-system-model | ||
|
|
||
| Setting up E3SM runs | ||
| -------------------- | ||
|
|
||
| All online analysis and output stream within MPAS components (MPAS-O and | ||
| MPAS-SeaIce) are configured to support MPAS-Analysis without any modifications | ||
| to namelists or streams files. | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,63 @@ | ||
| MPAS Sea Ice | ||
| ============ | ||
|
|
||
| The Model for Prediction Across Scales Sea Ice (MPAS Sea Ice, sometimes called | ||
| MPAS-CICE because of the physics it has inherited from the CICE sea-ice model) | ||
| is designed for the simulations of sea ice on unstructured grids supported by | ||
| the MPAS framework. The model has not yet been publicly released and does not | ||
| have public documentation. | ||
|
|
||
| Setting up Standalone MPAS Sea Ice Runs | ||
| --------------------------------------- | ||
|
|
||
| In order to support all sea=ice analysis tasks from MPAS-Analysis, certain | ||
| "analysis members", Fortran modules that perform analysis during the | ||
| simulation, need to be enabled. | ||
|
|
||
| The following is a list of suggested values for namelist options, typically | ||
| found in ``namelist.cice`` or ``mpas-cice_in``:: | ||
|
|
||
| config_AM_timeSeriesStatsMonthly_enable = .true. | ||
|
|
||
| Additionally, the duration of the run should be set to at least two years and | ||
| typically longer before most analysis is useful:: | ||
|
|
||
| config_run_duration = '0002-00-00_00:00:00' | ||
|
|
||
| Several streams must be defined in the streams file, typically | ||
| ``streams.cice``, (even if they will not be written out -- | ||
| ``output_interval=="none"``):: | ||
|
|
||
| <stream name="timeSeriesStatsMonthlyRestart" | ||
| type="input;output" | ||
| io_type="pnetcdf" | ||
| filename_template="mpascice.rst.am.timeSeriesStatsMonthly.$Y-$M-$D_$S.nc" | ||
| filename_interval="output_interval" | ||
| clobber_mode="truncate" | ||
| packages="timeSeriesStatsMonthlyAMPKG" | ||
| input_interval="initial_only" | ||
| output_interval="stream:restart:output_interval"> | ||
| </stream> | ||
|
|
||
| <stream name="timeSeriesStatsMonthlyOutput" | ||
| type="output" | ||
| io_type="pnetcdf" | ||
| filename_template="mpascice.hist.am.timeSeriesStatsMonthly.$Y-$M-$D.nc" | ||
| filename_interval="00-01-00_00:00:00" | ||
| output_interval="00-01-00_00:00:00" | ||
| clobber_mode="truncate" | ||
| packages="timeSeriesStatsMonthlyAMPKG"> | ||
|
|
||
| <var name="icePresent"/> | ||
| <var name="iceAreaCell"/> | ||
| <var name="iceVolumeCell"/> | ||
| <var name="xtime"/> | ||
| </stream> | ||
|
|
||
| The ``filename_tempalate`` can be modified as desired (these are the defalult | ||
| values from E3SM). For the ``timeSeriesStatsMonthlyOutput`` stream, both the | ||
| filename_interval and the output_interval must currently be monthly | ||
| (``"0000-01-00_00:00:00"``). | ||
|
|
||
| Additional fields can be included in the ``timeSeriesStatsMonthlyOutput`` | ||
| streams. These are the minimum that allow the analysis to run successfully. |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,156 @@ | ||
| MPAS Ocean | ||
| ========== | ||
|
|
||
| The Model for Prediction Across Scales Ocean (MPAS-O) is designed for the | ||
| simulation of the ocean system from time scales of months to millenia and | ||
| spatial scales from sub 1 km to global circulations. | ||
|
|
||
| MPAS-O has demonstrated the ability to accurately reproduce mesoscale ocean | ||
| activity with a local mesh refinement strategy. | ||
|
|
||
| In addition to faciliating the study of multiscale phenomena within the ocean | ||
| system, MPAS-O is intended for the study of anthropogenic climate change as | ||
| the ocean component of climate system models. | ||
|
|
||
|
|
||
| Full documentaiton is available at: | ||
| https://mpas-dev.github.io/ocean/ocean.html | ||
|
|
||
| Setting up Standalone MPAS-O Runs | ||
| --------------------------------- | ||
|
|
||
| In order to support all ocean analysis tasks from MPAS-Analysis, certain | ||
| "analysis members", Fortran modules that perform analysis during the | ||
| simulation, need to be enabled. | ||
|
|
||
| The following is a list of suggested values for namelist options, typically | ||
| found in ``namelist.ocean`` or ``mpas-o_in``:: | ||
|
|
||
| config_AM_surfaceAreaWeightedAverages_enable = .true. | ||
| config_AM_surfaceAreaWeightedAverages_compute_interval = '0000-00-00_01:00:00' | ||
| config_AM_layerVolumeWeightedAverage_enable = .true. | ||
| config_AM_layerVolumeWeightedAverage_compute_interval = '0000-00-00_01:00:00' | ||
| config_AM_meridionalHeatTransport_enable = .true. | ||
| config_AM_meridionalHeatTransport_compute_interval = '0000-00-00_01:00:00' | ||
| config_AM_mixedLayerDepths_enable = .true. | ||
| config_AM_timeSeriesStatsMonthly_enable = .true. | ||
|
|
||
| Additionally, the duration of the run should be set to at least two years and | ||
| typically longer before most analysis is useful:: | ||
|
|
||
| config_run_duration = '0002-00-00_00:00:00' | ||
|
|
||
| Several streams must be defined in the streams file, typically | ||
| ``streams.ocean``, (even if they will not be written out -- | ||
| ``output_intervale=="none"``):: | ||
|
|
||
| <stream name="timeSeriesStatsMonthlyRestart" | ||
| type="input;output" | ||
| filename_template="restarts/restart.AM.timeSeriesStatsMonthly.$Y-$M-$D_$h.$m.$s.nc" | ||
| filename_interval="output_interval" | ||
| reference_time="0001-01-01_00:00:00" | ||
| clobber_mode="truncate" | ||
| packages="timeSeriesStatsMonthlyAMPKG" | ||
| input_interval="initial_only" | ||
| output_interval="stream:restart:output_interval" > | ||
| </stream> | ||
|
|
||
| <stream name="timeSeriesStatsMonthlyOutput" | ||
| type="output" | ||
| filename_template="analysis_members/timeSeriesStatsMonthly.$Y-$M.nc" | ||
| filename_interval="0000-01-00_00:00:00" | ||
| reference_time="0001-01-01_00:00:00" | ||
| clobber_mode="truncate" | ||
| packages="timeSeriesStatsMonthlyAMPKG" | ||
| output_interval="00-01-00_00:00:00" > | ||
|
|
||
| <var_array name="activeTracers"/> | ||
| <var name="normalVelocity"/> | ||
| <var name="vertVelocityTop"/> | ||
| <var_array name="avgValueWithinOceanRegion"/> | ||
| <var_array name="avgValueWithinOceanLayerRegion"/> | ||
| <var name="dThreshMLD"/> | ||
| <var name="meridionalHeatTransportLatZ"/> | ||
| <var name="meridionalHeatTransportLat"/> | ||
| <var name="binBoundaryMerHeatTrans"/> | ||
| <var name="xtime"/> | ||
| </stream> | ||
|
|
||
| <stream name="layerVolumeWeightedAverageOutput" | ||
| type="output" | ||
| io_type="pnetcdf" | ||
| filename_template="mpaso.hist.am.layerVolumeWeightedAverage.$Y-$M-$D.nc" | ||
| filename_interval="00-01-00_00:00:00" | ||
| output_interval="none" | ||
| clobber_mode="truncate" | ||
| packages="layerVolumeWeightedAverageAMPKG"> | ||
|
|
||
| <var name="xtime"/> | ||
| <var name="daysSinceStartOfSim"/> | ||
| <var_array name="minValueWithinOceanLayerRegion"/> | ||
| <var_array name="maxValueWithinOceanLayerRegion"/> | ||
| <var_array name="avgValueWithinOceanLayerRegion"/> | ||
| <var_array name="minValueWithinOceanVolumeRegion"/> | ||
| <var_array name="maxValueWithinOceanVolumeRegion"/> | ||
| <var_array name="avgValueWithinOceanVolumeRegion"/> | ||
| </stream> | ||
|
|
||
| <stream name="meridionalHeatTransportOutput" | ||
| type="output" | ||
| io_type="pnetcdf" | ||
| filename_template="mpaso.hist.am.meridionalHeatTransport.$Y-$M-$D.nc" | ||
| filename_interval="00-01-00_00:00:00" | ||
| output_interval="none" | ||
| clobber_mode="truncate" | ||
| packages="meridionalHeatTransportAMPKG"> | ||
|
|
||
| <var name="xtime"/> | ||
| <var name="daysSinceStartOfSim"/> | ||
| <var name="binBoundaryMerHeatTrans"/> | ||
| <var name="meridionalHeatTransportLatZ"/> | ||
| <var name="meridionalHeatTransportLat"/> | ||
| <var name="refZMid"/> | ||
| <var name="refBottomDepth"/> | ||
| </stream> | ||
|
|
||
| <stream name="surfaceAreaWeightedAveragesOutput" | ||
| type="output" | ||
| io_type="netcdf" | ||
| filename_template="mpaso.hist.am.surfaceAreaWeightedAverages.$Y-$M-$D.nc" | ||
| filename_interval="00-01-00_00:00:00" | ||
| output_interval="none" | ||
| clobber_mode="truncate" | ||
| packages="surfaceAreaWeightedAveragesAMPKG"> | ||
|
|
||
| <var name="xtime"/> | ||
| <var name="daysSinceStartOfSim"/> | ||
| <var_array name="minValueWithinOceanRegion"/> | ||
| <var_array name="maxValueWithinOceanRegion"/> | ||
| <var_array name="avgValueWithinOceanRegion"/> | ||
| </stream> | ||
|
|
||
| <stream name="mixedLayerDepthsOutput" | ||
| type="output" | ||
| io_type="pnetcdf" | ||
| filename_template="mpaso.hist.am.mixedLayerDepths.$Y-$M-$D.nc" | ||
| filename_interval="00-01-00_00:00:00" | ||
| output_interval="none" | ||
| clobber_mode="truncate" | ||
| packages="mixedLayerDepthsAMPKG"> | ||
|
|
||
| <var name="xtime"/> | ||
| <var name="daysSinceStartOfSim"/> | ||
| <stream name="mesh"/> | ||
| <var name="tThreshMLD"/> | ||
| <var name="dThreshMLD"/> | ||
| <var name="tGradMLD"/> | ||
| <var name="dGradMLD"/> | ||
| </stream> | ||
|
|
||
| The ``filename_tempalate`` can be modified as desired (in most cases, these are | ||
| the defalult values from E3SM). For the ``timeSeriesStatsMonthlyOutput`` | ||
| stream, both the filename_interval and the output_interval must currently be | ||
| monthly (``"0000-01-00_00:00:00"``). | ||
|
|
||
| Additional fields can be included in the ``timeSeriesStatsMonthlyOutput`` | ||
| streams. These are the minimum that allow the analysis to run successfully. | ||
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I'm assuming this is from the wiki we used in this process. Thanks for including it here!
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These will become pages in the official documentation on ReadTheDocs as soon as this is merged.