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Add v3 LR Documenation Page (#67)
* add v3 LR doc structure * add generated v3 data table * add citation * add instruction for using sqlite to query index.db for archive content * add HPSS url column to data table * refinement * deactivate ESGF links for now
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‎docs/source/index.rst‎

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v1/index
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v2/index
2020
v2.1/index
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v3/index
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SCREAMv0/index
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SCREAMv1/index
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‎docs/source/v2/WaterCycle/simulation_data/index.rst‎

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@@ -42,6 +42,12 @@ For more information, refer to `zstash usage <https://e3sm-project.github.io/zst
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`web interface <https://portal.nersc.gov/archive/home/projects/e3sm/www/WaterCycle/E3SMv2>`_.
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Note that this will be slow and inefficient since you'll have to download the tar files.
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**Tip for users without NERSC access**: Before downloading large tar files, you can first download the ``index.db`` file and use sqlite to check the archive contents: ::
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sqlite3 index.db "SELECT tar,name,size from files;" > archive_contents.txt
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This will help you identify which specific tar files contain the data you need before downloading.
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**v2.LR** simulations data has been archived on NERSC HPSS under: ::
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/home/projects/e3sm/www/WaterCycle/E3SMv2/LR

‎docs/source/v3/CoupledSystem/index.rst‎

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E3SMv3
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================
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The simulation campaign for E3SMv3 was performed initially with the
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**v3.LR** (lower resolution) model configuration.
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If you use data from this simulation campaign, please cite the relevant overview
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manuscripts.
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* For a general E3SMv3 overview and v3.LR simulations:
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* Xie et al. (2025). The Energy Exascale Earth System Model Version 3. Part I: Overview of the Atmospheric Component. Accepted by JAMES. DOI to follow.
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* Golaz et al. (2025). The Energy Exascale Earth System Model Version 3. Part II: Overview of the Coupled system. Submitted to JAMES.
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For information on how to access and use the simulation data, see :doc:`here <../../v2/WaterCycle/simulation_data/index>`.
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.. toctree::
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:maxdepth: 2
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:caption: Contents:
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simulation_data/index

‎docs/source/v3/CoupledSystem/simulation_data/index.rst‎

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Simulation Data
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===============
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.. toctree::
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:maxdepth: 2
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simulation_table

‎docs/source/v3/CoupledSystem/simulation_data/simulation_table.rst‎

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‎docs/source/v3/index.rst‎

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v3.LR
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==========================================
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.. toctree::
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:maxdepth: 2
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:caption: Contents:
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CoupledSystem/index

‎machine_readable_data/v3_CoupledSystem_simulations.csv‎

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Simulation,Data Size (TB),ESGF Links,HPSS Path,HPSS URL
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v3.LR.piControl,69,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piControl,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piControl
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v3.LR.abrupt-4xCO2_0101_bcdt15m,15,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.abrupt-4xCO2_0101_bcdt15m,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.abrupt-4xCO2_0101_bcdt15m
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v3.LR.1pctCO2_0101_bcdt15m,16,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.1pctCO2_0101_bcdt15m,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.1pctCO2_0101_bcdt15m
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v3.LR.historical_0051,19,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.historical_0051,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.historical_0051
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v3.LR.historical_0101,19,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.historical_0101,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.historical_0101
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v3.LR.historical_0151,19,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.historical_0151,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.historical_0151
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v3.LR.historical_0201,19,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.historical_0201,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.historical_0201
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v3.LR.historical_0251,19,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.historical_0251,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.historical_0251
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v3.LR.hist-GHG_0101,20,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.hist-GHG_0101,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.hist-GHG_0101
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v3.LR.hist-GHG_0151,20,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.hist-GHG_0151,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.hist-GHG_0151
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v3.LR.hist-GHG_0201,20,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.hist-GHG_0201,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.hist-GHG_0201
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v3.LR.hist-aer_0101,19,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.hist-aer_0101,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.hist-aer_0101
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v3.LR.hist-aer_0151,19,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.hist-aer_0151,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.hist-aer_0151
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v3.LR.hist-aer_0201,19,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.hist-aer_0201,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.hist-aer_0201
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v3.LR.hist-xGHG-xaer_0101,19,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.hist-xGHG-xaer_0101,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.hist-xGHG-xaer_0101
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v3.LR.hist-xGHG-xaer_0151,20,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.hist-xGHG-xaer_0151,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.hist-xGHG-xaer_0151
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v3.LR.hist-xGHG-xaer_0201,19,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.hist-xGHG-xaer_0201,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.hist-xGHG-xaer_0201
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v3.LR.amip_0101,8,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.amip_0101,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.amip_0101
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v3.LR.amip_0151,6,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.amip_0151,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.amip_0151
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v3.LR.amip_0201,6,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.amip_0201,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.amip_0201
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v3.LR.piClim-control-iceini,3,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piClim-control-iceini,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piClim-control-iceini
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v3.LR.piClim-histall/v3.LR.piClim-histall_0101,9,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piClim-histall/v3.LR.piClim-histall_0101,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piClim-histall/v3.LR.piClim-histall_0101
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v3.LR.piClim-histall/v3.LR.piClim-histall_0151,9,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piClim-histall/v3.LR.piClim-histall_0151,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piClim-histall/v3.LR.piClim-histall_0151
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v3.LR.piClim-histall/v3.LR.piClim-histall_0201,9,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piClim-histall/v3.LR.piClim-histall_0201,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piClim-histall/v3.LR.piClim-histall_0201
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v3.LR.piClim-histGHG/v3.LR.piClim-histGHG_0101,9,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piClim-histGHG/v3.LR.piClim-histGHG_0101,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piClim-histGHG/v3.LR.piClim-histGHG_0101
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v3.LR.piClim-histGHG/v3.LR.piClim-histGHG_0151,9,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piClim-histGHG/v3.LR.piClim-histGHG_0151,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piClim-histGHG/v3.LR.piClim-histGHG_0151
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v3.LR.piClim-histGHG/v3.LR.piClim-histGHG_0201,9,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piClim-histGHG/v3.LR.piClim-histGHG_0201,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piClim-histGHG/v3.LR.piClim-histGHG_0201
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v3.LR.piClim-histaer/v3.LR.piClim-histaer_0101,8,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piClim-histaer/v3.LR.piClim-histaer_0101,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piClim-histaer/v3.LR.piClim-histaer_0101
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v3.LR.piClim-histaer/v3.LR.piClim-histaer_0151,8,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piClim-histaer/v3.LR.piClim-histaer_0151,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piClim-histaer/v3.LR.piClim-histaer_0151
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v3.LR.piClim-histaer/v3.LR.piClim-histaer_0201,9,,/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piClim-histaer/v3.LR.piClim-histaer_0201,https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piClim-histaer/v3.LR.piClim-histaer_0201

‎utils/generate_tables.py‎

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self.esgf = get_esgf(self.model_version, self.resolution, self.simulation_name, self.experiment, self.ensemble_num, self.link_type, self.node)
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# Generate web interface URL from HPSS path
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self.web_interface = self.get_web_interface_url()
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self.run_script_original = get_run_script_original(self.model_version, self.simulation_name)
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self.run_script_reproduction = get_run_script_reproduction(self.model_version, self.simulation_name)
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if not self.run_script_original:
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self.run_script_original = "N/A"
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def get_web_interface_url(self) -> str:
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"""Generate web interface URL from HPSS path"""
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if self.hpss and self.data_size:
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# Convert HPSS path to web interface URL
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# /home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piControl -> https://portal.nersc.gov/archive/home/projects/e3sm/www/CoupledSystem/E3SMv3/LR/v3.LR.piControl
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hpss_clean = self.hpss.replace("(symlink) ", "") # Remove symlink prefix if present
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# Use the full path - each simulation gets its own distinct URL
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web_url = f"https://portal.nersc.gov/archive{hpss_clean}"
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return f"`HPSS URL <{web_url}>`_"
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return ""
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def get_row(self, output_file, minimal_content: bool = False) -> List[str]:
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if "simulation" in output_file:
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row = [self.simulation_name, self.data_size, self.esgf, self.hpss]
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row = [self.simulation_name, self.data_size, self.esgf, self.hpss, self.web_interface]
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if minimal_content:
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match_object: re.Match = re.match("`.*<(.*)>`_", self.esgf)
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if match_object:
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# Since we don't want that in the csv output,
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# which a computer reads.
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row[3] = row[3].replace("(symlink) ", "")
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# Extract web interface URL for CSV
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web_match: re.Match = re.match("`.*<(.*)>`_", self.web_interface)
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if web_match:
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row[4] = web_match.group(1) # Extract URL from the web interface link
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return row
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elif "reproduction" in output_file:
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return [self.simulation_name, self.machine, self.checksum, self.run_script_reproduction, self.run_script_original]
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simulation_dict["link_type"] = "both"
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elif simulation_dict["cmip_only"] == "cmip_only":
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simulation_dict["link_type"] = "cmip"
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elif simulation_dict["cmip_only"] == "none":
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simulation_dict["link_type"] = "none"
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else:
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raise ValueError(f"Invalid cmip_only={simulation_dict['cmip_only']}")
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simulation_dicts.append(simulation_dict)
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return string
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def generate_table(page_type: str, resolutions: OrderedDict[str, Category], header_cells: List[str], output_file: str, cell_paddings: List[int]):
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# Create output directory if it doesn't exist
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os.makedirs(os.path.dirname(output_file), exist_ok=True)
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with open(output_file, "w") as file_write:
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# Page Title
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file_write.write("**********************************\n")
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def construct_pages(csv_file: str, model_version: str, group_name: str, include_reproduction_scripts: bool = False):
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versions: OrderedDict[str, ModelVersion] = read_simulations(csv_file)
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resolutions: OrderedDict[str, Category] = versions[model_version].groups[group_name].resolutions
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header_cells: List[str] = ["Simulation", "Data Size (TB)", "ESGF Links", "HPSS Path"]
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header_cells: List[str] = ["Simulation", "Data Size (TB)", "ESGF Links", "HPSS Path", "HPSS URL"]
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construct_output_csv(resolutions, header_cells, f"../machine_readable_data/{model_version}_{group_name}_simulations.csv")
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print(f"csv of the simulations will be available at https://github.com/E3SM-Project/e3sm_data_docs/blob/main/machine_readable_data/{model_version}_{group_name}_simulations.csv")
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# TODO: add proper subdirs and index.rst files in docs/
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resolutions,
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header_cells,
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f"../docs/source/{model_version}/{group_name}/simulation_data/simulation_table.rst",
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[85, 15, 400, 140]
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[65, 15, 220, 120, 140]
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)
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if include_reproduction_scripts:
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header_cells_reproduction: List[str] = ["Simulation", "Machine", "10 day checksum", "Reproduction Script", "Original Script (requires significant changes to run!!)",]
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# Sources for v1 data
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# https://acme-climate.atlassian.net/wiki/spaces/ED/pages/4495441922/V1+Simulation+backfill+WIP
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# https://acme-climate.atlassian.net/wiki/spaces/DOC/pages/1271169273/v1+High+Res+Coupled+Run+Output+HPSS+Archive
386-
construct_pages("input/simulations_v1_water_cycle.csv", "v1", "WaterCycle")
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# construct_pages("input/simulations_v1_water_cycle.csv", "v1", "WaterCycle")
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construct_pages("input/simulations_v3_LR_coupled.csv", "v3", "CoupledSystem")

‎utils/input/simulations_v3_LR_coupled.csv‎

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model_version, group, resolution, category, simulation_name, machine, checksum, experiment, ensemble_num, cmip_only,
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v3, CoupledSystem, LR, DECK, v3.LR.piControl, chrysalis, , piControl, 1, none,
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v3, CoupledSystem, LR, DECK, v3.LR.abrupt-4xCO2_0101_bcdt15m, chrysalis, , abrupt-4xCO2, 1, none,
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v3, CoupledSystem, LR, DECK, v3.LR.1pctCO2_0101_bcdt15m, chrysalis, , 1pctCO2, 1, none,
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v3, CoupledSystem, LR, Historical, v3.LR.historical_0051, chrysalis, , historical, 1, none,
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v3, CoupledSystem, LR, Historical, v3.LR.historical_0101, chrysalis, , historical, 2, none,
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v3, CoupledSystem, LR, Historical, v3.LR.historical_0151, chrysalis, , historical, 3, none,
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v3, CoupledSystem, LR, Historical, v3.LR.historical_0201, chrysalis, , historical, 4, none,
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v3, CoupledSystem, LR, Historical, v3.LR.historical_0251, chrysalis, , historical, 5, none,
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v3, CoupledSystem, LR, Single-forcing (DAMIP-like), v3.LR.hist-GHG_0101, chrysalis, , hist-GHG, 1, none,
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v3, CoupledSystem, LR, Single-forcing (DAMIP-like), v3.LR.hist-GHG_0151, chrysalis, , hist-GHG, 2, none,
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v3, CoupledSystem, LR, Single-forcing (DAMIP-like), v3.LR.hist-GHG_0201, chrysalis, , hist-GHG, 3, none,
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v3, CoupledSystem, LR, Single-forcing (DAMIP-like), v3.LR.hist-aer_0101, chrysalis, , hist-aer, 1, none,
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v3, CoupledSystem, LR, Single-forcing (DAMIP-like), v3.LR.hist-aer_0151, chrysalis, , hist-aer, 2, none,
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v3, CoupledSystem, LR, Single-forcing (DAMIP-like), v3.LR.hist-aer_0201, chrysalis, , hist-aer, 3, none,
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v3, CoupledSystem, LR, Single-forcing (DAMIP-like), v3.LR.hist-xGHG-xaer_0101, chrysalis, , hist-nat, 1, none,
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v3, CoupledSystem, LR, Single-forcing (DAMIP-like), v3.LR.hist-xGHG-xaer_0151, chrysalis, , hist-nat, 2, none,
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v3, CoupledSystem, LR, Single-forcing (DAMIP-like), v3.LR.hist-xGHG-xaer_0201, chrysalis, , hist-nat, 3, none,
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v3, CoupledSystem, LR, AMIP, v3.LR.amip_0101, chrysalis, , amip, 1, none,
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v3, CoupledSystem, LR, AMIP, v3.LR.amip_0151, chrysalis, , amip, 2, none,
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v3, CoupledSystem, LR, AMIP, v3.LR.amip_0201, chrysalis, , amip, 3, none,
22+
v3, CoupledSystem, LR, RFMIP, v3.LR.piClim-control-iceini, chrysalis, , piClim-control, 1, none,
23+
v3, CoupledSystem, LR, RFMIP, v3.LR.piClim-histall/v3.LR.piClim-histall_0101, chrysalis, , piClim-histall, 1, none,
24+
v3, CoupledSystem, LR, RFMIP, v3.LR.piClim-histall/v3.LR.piClim-histall_0151, chrysalis, , piClim-histall, 2, none,
25+
v3, CoupledSystem, LR, RFMIP, v3.LR.piClim-histall/v3.LR.piClim-histall_0201, chrysalis, , piClim-histall, 3, none,
26+
v3, CoupledSystem, LR, RFMIP, v3.LR.piClim-histGHG/v3.LR.piClim-histGHG_0101, chrysalis, , piClim-histGHG, 1, none,
27+
v3, CoupledSystem, LR, RFMIP, v3.LR.piClim-histGHG/v3.LR.piClim-histGHG_0151, chrysalis, , piClim-histGHG, 2, none,
28+
v3, CoupledSystem, LR, RFMIP, v3.LR.piClim-histGHG/v3.LR.piClim-histGHG_0201, chrysalis, , piClim-histGHG, 3, none,
29+
v3, CoupledSystem, LR, RFMIP, v3.LR.piClim-histaer/v3.LR.piClim-histaer_0101, chrysalis, , piClim-histaer, 1, none,
30+
v3, CoupledSystem, LR, RFMIP, v3.LR.piClim-histaer/v3.LR.piClim-histaer_0151, chrysalis, , piClim-histaer, 2, none,
31+
v3, CoupledSystem, LR, RFMIP, v3.LR.piClim-histaer/v3.LR.piClim-histaer_0201, chrysalis, , piClim-histaer, 3, none,

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