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Changes after rename of CCPPStandardNames --> ESMStandardNames (#98)
 - Remove references to CCPP except where relevant - Cherry-pick changes to tools/write_standard_name_table.py from release branch that allows for subsections in standard names and markdown table - Group CCPP-specific variables into a dedicated section - Change some long_name descriptions to remove CCPP-specific wording - A few more details in README.md
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‎Metadata-standard-names.md‎

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@@ -1,4 +1,4 @@
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# CCPP Standard Name Library
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# Earth System Modeling Standard Name Library
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#### Table of Contents
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* [dimensions](#dimensions)
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* [constants](#constants)
@@ -8,9 +8,8 @@
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* [diagnostics](#diagnostics)
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* [atmospheric_composition](#atmospheric_composition)
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* [atmospheric_composition: GOCART aerosols](#atmospheric_composition-gocart-aerosols)
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* [emissions: Community Emissions Data System (CEDS)](#emissions-community-emissions-data-system-ceds)
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* [required framework-provided variables](#required-framework-provided-variables)
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* [optional framework-provided variables](#optional-framework-provided-variables)
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* [emissions](#emissions)
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* [Application-specific variables](#application-specific-variables)
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* [system variables](#system-variables)
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* [GFS_typedefs_GFS_control_type](#gfs_typedefs_gfs_control_type)
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* [GFS_typedefs_GFS_interstitial_type](#gfs_typedefs_gfs_interstitial_type)
@@ -62,10 +61,8 @@ Currently, the only dimension which supports all six dimension types is horizont
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* `integer`: units = index
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* `vertical_index_at_top_interface`: Vertical index at top interface
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* `integer`: units = index
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* `number_of_openmp_threads`: Total number of thread blocks which the host model may use to call CCPP physics run groups during the CCPP run phase.
64+
* `number_of_openmp_threads`: Total number of thread blocks OpenMP (shared-memory) parallel threads.
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* `integer`: units = count
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* `ccpp_thread_number`: Number of current thread block. This variable may only be used during CCPP run phase
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* `integer`: units = index
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## constants
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* `avogadro_number`: Avogadro number
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* `real(kind=kind_phys)`: units = molecules mol-1
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* `real(kind=kind_phys)`: units = m-1
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* `volume_extinction_in_air_due_to_aerosol_particles_lambda3`: Aerosol extinction at wavelength3
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* `real(kind=kind_phys)`: units = m-1
455-
## emissions: Community Emissions Data System (CEDS)
452+
## emissions
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Emissions variables, contributed for the Community Emissions Data System (CEDS)
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* `emissions_of_co_due_to_anthropogenic`: Carbon monoxide emissions from anthropogenic sources, total
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* `real(kind=kind_phys)`: units = kg m-2 s-1
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* `emissions_of_no_due_to_anthropogenic`: Nitric oxide emissions from anthropogenic sources, total
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* `real(kind=kind_phys)`: units = kg m-2 s-1
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* `emissions_of_hcho_due_to_anthropogenic_waste`: Formaldehyde emissions from anthropogenic waste disposal and handling
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* `real(kind=kind_phys)`: units = kg m-2 s-1
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## required framework-provided variables
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## Application-specific variables
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Variable names only for use with a specific application
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### required framework-provided variables
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Required CCPP framework-provided variables
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* `ccpp_error_message`: Error message for error handling in CCPP
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* `character(kind=len=512)`: units = none
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* `ccpp_error_code`: Error code for error handling in CCPP
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* `integer(kind=)`: units = 1
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## optional framework-provided variables
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### optional framework-provided variables
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Optional CCPP framework-provided variables
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* `scheme_name`: CCPP physics scheme name
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* `character(kind=len=64)`: units = none
@@ -525,6 +525,12 @@ Optional CCPP framework-provided variables
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* `real(kind=kind_phys)`: units = none
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* `number_of_ccpp_constituents`: Number of constituents managed by CCPP Framework
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* `integer(kind=)`: units = count
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* `ccpp_block_count`: Ccpp block count
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* `integer(kind=)`: units = count
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* `ccpp_block_sizes`: Ccpp block sizes
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* `integer(kind=)`: units = count
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* `ccpp_thread_number`: Number of current thread block. This variable may only be used during CCPP run phase
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* `integer`: units = index
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## system variables
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Variables related to the compute environment
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* `flag_for_mpi_root`: Flag for MPI root
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* `real(kind=kind_phys)`: units = m2 s-1
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* `sigma_pressure_hybrid_coordinate_b_coefficient`: Sigma pressure hybrid coordinate b coefficient
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* `real(kind=kind_phys)`: units = 1
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* `ccpp_block_count`: Ccpp block count
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* `integer(kind=)`: units = count
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* `ccpp_block_sizes`: Ccpp block sizes
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* `integer(kind=)`: units = count
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* `cellular_automata_finer_grid`: Cellular automata finer grid
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* `integer(kind=)`: units = count
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* `cellular_automata_lifetime`: Cellular automata lifetime

‎README.md‎

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# CCPPStandardNames
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# ESMStandardNames
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The CCPPStandardNames Repository contains community-accepted CCPP
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The Earth System Modeling Standard Names Repository contains community-accepted
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Standard Names, publishing tools, and search tools.
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A Markdown file describing the standard names
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[is included](https://github.com/ESCOMP/CCPPStandardNames/blob/master/Metadata-standard-names.md).
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[is included](https://github.com/ESCOMP/ESMStandardNames/blob/main/Metadata-standard-names.md).
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Rules governing the designation and format of standard names can be found in [StandardNamesRules.rst](https://github.com/ESCOMP/ESMStandardNames/blob/main/StandardNamesRules.rst)
89

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To regenerate the standard name Markdown file, run:
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Edits to standard names should be made in the xml file, using the included python tools to generate
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the human-readable standard name Markdown file:
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```
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tools/write_standard_name_table.py standard_names.xml
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```

‎StandardNamesRules.rst‎

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<br />
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*******************
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CCPP Standard Names
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Earth System Modeling Standard Names
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*******************
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This document contains information about the rules used to create Standard Names
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for use with the Common Community Physics Package (CCPP). It describes the
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for use with Earth System Models. It describes the
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* CCPP Standard Name rules
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* ESM Standard Name rules
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* Standard Name qualifiers
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* Other common standard name components
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* Acronyms, abbreviations, and aliases
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* Units
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.. _Rules
2020
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CCPP Standard Name Rules
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ESM Standard Name Rules
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========================
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#. Standard names should be identical to those from the latest version

‎standard_names.xml‎

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<standard_names name="CCPP Standard Name Library" version="1.0">
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<standard_names name="Earth System Modeling Standard Name Library" version="1.0">
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<section name="dimensions"
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comment="Dimension standard names may come in sets of six
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related standard names for each dimension:\n
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<type units="index">integer</type>
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</standard_name>
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<standard_name name="number_of_openmp_threads"
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long_name="Total number of thread blocks which the host model may use to call CCPP physics run groups during the CCPP run phase.">
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long_name="Total number of thread blocks OpenMP (shared-memory) parallel threads.">
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<type units="count">integer</type>
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</standard_name>
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<standard_name name="ccpp_thread_number"
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long_name="Number of current thread block. This variable may only be used during CCPP run phase">
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<type units="index">integer</type>
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</standard_name>
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</section>
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<section name="constants">
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<standard_name name="avogadro_number">
@@ -791,7 +787,8 @@
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<type kind="kind_phys" units="m-1">real</type>
792788
</standard_name>
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</section>
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<section name="emissions: Community Emissions Data System (CEDS)">
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<section name="emissions"
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comment="Emissions variables, contributed for the Community Emissions Data System (CEDS)">
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<standard_name name="emissions_of_co_due_to_anthropogenic"
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long_name="Carbon monoxide emissions from anthropogenic sources, total">
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<type kind="kind_phys" units="kg m-2 s-1">real</type>
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901898
<type kind="kind_phys" units="kg m-2 s-1">real</type>
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</standard_name>
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</section>
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<section name="required framework-provided variables"
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comment="Required CCPP framework-provided variables">
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<standard_name name="ccpp_error_message"
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long_name="Error message for error handling in CCPP">
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<type kind="len=512" units="none">character</type>
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</standard_name>
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<standard_name name="ccpp_error_code"
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long_name="Error code for error handling in CCPP">
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<type kind="" units="1">integer</type>
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</standard_name>
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</section>
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<section name="optional framework-provided variables"
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comment="Optional CCPP framework-provided variables">
917-
<standard_name name="scheme_name"
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long_name="CCPP physics scheme name">
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<type kind="len=64" units="none">character</type>
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</standard_name>
921-
<standard_name name="ccpp_constituent_properties"
922-
long_name="CCPP Constituent Properties">
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<type kind="" units="none">ccpp_constituent_prop_ptr_t</type>
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</standard_name>
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<standard_name name="ccpp_constituents"
926-
long_name="Array of constituents managed by CCPP Framework">
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<type kind="kind_phys" units="none">real</type>
928-
</standard_name>
929-
<standard_name name="ccpp_constituent_minimum_values"
930-
long_name="CCPP constituent minimum values">
931-
<type kind="kind_phys" units="none">real</type>
932-
</standard_name>
933-
<standard_name name="number_of_ccpp_constituents"
934-
long_name="Number of constituents managed by CCPP Framework">
935-
<type kind="" units="count">integer</type>
936-
</standard_name>
901+
<section name="Application-specific variables"
902+
comment="Variable names only for use with a specific application">
903+
<section name="required framework-provided variables"
904+
comment="Required CCPP framework-provided variables">
905+
<standard_name name="ccpp_error_message"
906+
long_name="Error message for error handling in CCPP">
907+
<type kind="len=512" units="none">character</type>
908+
</standard_name>
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<standard_name name="ccpp_error_code"
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long_name="Error code for error handling in CCPP">
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<type kind="" units="1">integer</type>
912+
</standard_name>
913+
</section>
914+
<section name="optional framework-provided variables"
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comment="Optional CCPP framework-provided variables">
916+
<standard_name name="scheme_name"
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long_name="CCPP physics scheme name">
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<type kind="len=64" units="none">character</type>
919+
</standard_name>
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<standard_name name="ccpp_constituent_properties"
921+
long_name="CCPP Constituent Properties">
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<type kind="" units="none">ccpp_constituent_prop_ptr_t</type>
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</standard_name>
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<standard_name name="ccpp_constituents"
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long_name="Array of constituents managed by CCPP Framework">
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<type kind="kind_phys" units="none">real</type>
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</standard_name>
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<standard_name name="ccpp_constituent_minimum_values"
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long_name="CCPP constituent minimum values">
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<type kind="kind_phys" units="none">real</type>
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</standard_name>
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<standard_name name="number_of_ccpp_constituents"
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long_name="Number of constituents managed by CCPP Framework">
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<type kind="" units="count">integer</type>
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</standard_name>
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<standard_name name="ccpp_block_count">
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<type kind="" units="count">integer</type>
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</standard_name>
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<standard_name name="ccpp_block_sizes">
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<type kind="" units="count">integer</type>
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</standard_name>
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<standard_name name="ccpp_thread_number"
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long_name="Number of current thread block. This variable may only be used during CCPP run phase">
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<type units="index">integer</type>
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</standard_name>
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</section>
937947
</section>
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<section name="system variables"
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comment="Variables related to the compute environment">
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983993
<standard_name name="sigma_pressure_hybrid_coordinate_b_coefficient">
984994
<type kind="kind_phys" units="1">real</type>
985995
</standard_name>
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<standard_name name="ccpp_block_count">
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<type kind="" units="count">integer</type>
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</standard_name>
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<standard_name name="ccpp_block_sizes">
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<type kind="" units="count">integer</type>
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</standard_name>
992996
<standard_name name="cellular_automata_finer_grid">
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<type kind="" units="count">integer</type>
994998
</standard_name>

tools/meta_stdname_check.py renamed to tools/ccpp_meta_stdname_check.py

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from collections import OrderedDict
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################################################
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#Add CCPP framework (lib) modules to python path
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# Add lib modules to python path
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################################################
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_CURR_DIR = os.path.dirname(os.path.abspath(__file__))

‎tools/check_name_rules.py‎

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import re
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################################################
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#Add CCPP framework (lib) modules to python path
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# Add lib modules to python path
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################################################
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_CURR_DIR = os.path.dirname(os.path.abspath(__file__))

‎tools/check_xml_unique.py‎

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import copy
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################################################
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#Add CCPP framework (lib) modules to python path
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# Add lib modules to python path
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################################################
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_CURR_DIR = os.path.dirname(os.path.abspath(__file__))

‎tools/write_standard_name_table.py‎

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import re
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################################################
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#Add CCPP framework (lib) modules to python path
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# Add lib modules to python path
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################################################
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_CURR_DIR = os.path.dirname(os.path.abspath(__file__))
@@ -63,21 +63,20 @@ def convert_text_to_link(text_str):
6363
def standard_name_to_long_name(prop_dict, context=None):
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########################################################################
6565
"""Translate a standard_name to its default long_name
66-
Note: This code is copied from the CCPP Framework.
6766
>>> standard_name_to_long_name({'standard_name':'cloud_optical_depth_layers_from_0p55mu_to_0p99mu'})
6867
'Cloud optical depth layers from 0.55mu to 0.99mu'
6968
>>> standard_name_to_long_name({'local_name':'foo'}) #doctest: +IGNORE_EXCEPTION_DETAIL
7069
Traceback (most recent call last):
71-
CCPPError: No standard name to convert foo to long name
70+
KeyError: No standard name to convert foo to long name
7271
>>> standard_name_to_long_name({}) #doctest: +IGNORE_EXCEPTION_DETAIL
7372
Traceback (most recent call last):
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CCPPError: No standard name to convert to long name
73+
KeyError: No standard name to convert to long name
7574
>>> standard_name_to_long_name({'local_name':'foo'}, context=ParseContext(linenum=3, filename='foo.F90')) #doctest: +IGNORE_EXCEPTION_DETAIL
7675
Traceback (most recent call last):
77-
CCPPError: No standard name to convert foo to long name at foo.F90:3
76+
KeyError: No standard name to convert foo to long name at foo.F90:3
7877
>>> standard_name_to_long_name({}, context=ParseContext(linenum=3, filename='foo.F90')) #doctest: +IGNORE_EXCEPTION_DETAIL
7978
Traceback (most recent call last):
80-
CCPPError: No standard name to convert to long name at foo.F90:3
79+
KeyError: No standard name to convert to long name at foo.F90:3
8180
"""
8281
# We assume that standar_name has been checked for validity
8382
# Make the first char uppercase and replace each underscore with a space
@@ -104,7 +103,7 @@ def standard_name_to_long_name(prop_dict, context=None):
104103
# end if
105104
ctxt = context_string(context)
106105
emsg = 'No standard name to convert{} to long name{}'
107-
raise CCPPError(emsg.format(lname, ctxt))
106+
raise KeyError(emsg.format(lname, ctxt))
108107
# end if
109108
return long_name
110109

@@ -129,7 +128,7 @@ def parse_command_line(args, description):
129128
def convert_xml_to_markdown(root, library_name, snl):
130129
###############################################################################
131130
snl.write('# {}\n'.format(library_name))
132-
# Write a table of contents
131+
# Write a table of contents for top-level sections
133132
snl.write('#### Table of Contents\n')
134133
for section in root:
135134
sec_name = section.get('name')
@@ -138,15 +137,19 @@ def convert_xml_to_markdown(root, library_name, snl):
138137
# end for
139138
snl.write('\n')
140139
for section in root:
140+
parse_section(snl, section)
141+
142+
###############################################################################
143+
def parse_section(snl, sec, level='##'):
144+
###############################################################################
141145
# Step through the sections
142-
sec_name = section.get('name')
143-
sec_comment = section.get('comment')
144-
snl.write('## {}\n'.format(sec_name))
146+
sec_name = sec.get('name')
147+
sec_comment = sec.get('comment')
148+
snl.write(f'{level} {sec_name}\n')
145149
if sec_comment is not None:
146150
# First, squeeze out the spacing
147151
while sec_comment.find(' ') >= 0:
148152
sec_comment = sec_comment.replace(' ', ' ')
149-
# end while
150153
while sec_comment:
151154
sec_comment = sec_comment.lstrip()
152155
cind = sec_comment.find('\\n')
@@ -159,7 +162,10 @@ def convert_xml_to_markdown(root, library_name, snl):
159162
# end if
160163
# end while
161164
# end if
162-
for std_name in section:
165+
for std_name in sec:
166+
if std_name.tag == 'section':
167+
parse_section(snl, std_name, level + '#')
168+
continue
163169
stdn_name = std_name.get('name')
164170
stdn_longname = std_name.get('long_name')
165171
if stdn_longname is None:

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