.. _code_directory_structure: ############################# GEOS-Chem Classic folder tree ############################# The tables below list the folders in which various components of GEOS-Chem Classic reside. .. code-block:: bash GCClassic | +---CMakeScripts # Utility functions for CMake | +---docs # Root directory for ReadTheDocs documentation | | | +---source # Subdivides documentation into subdirectories | | | +---gcclassic-user-guide # Markup files (ReST format) for ReadTheDocs | | | +---geos-chem-shared-docs # Submodule containing shared documentation files | | # (such as common supplemental guides) | | | +---getting-started # Markup files (reST format) for ReadTheDocs | | | +---help-and-reference # Markup files (reST format) for ReadTheDocs | | | +---_static # Static content (e.g. images) for ReadTheDocs | | | +---supplemental-guides # Markup files (reST format) for ReadTheDocs | # (Content specific to GEOS-Chem Classic) | +---run # Link to src/GEOS-Chem/run/GCClassic | +---src # Contains submodules used by GEOS-Chem Classic | | | +---Cloud-J # Cloud-J submodule source code | | | | | +---CMakeScripts # Utility functions for CMake | | | | | +---docs # Cloud-J documentation files | | | | | +---src # Cloud-J source code | | | | | +---tables # Input lookup tables for Cloud-J | | | | | +---tools # Tools for Cloud-J | | | | | +---AddXs # Source code to add new cross-sections | | | +---GEOS_Chem # GEOS-Chem submodule, contains | | | | | +---APM # Source code for APM microphysics module | | | | | +---CMakeScripts # Utility functions for CMake | | | | | +---GeosCore # Source code for most GEOS-Chem science routines | | | | | +---GeosRad # RRTMG radiative transfer model source code | | | | | +---GeosUtil # Source code for various utility routines | | | | | +---GTMM # Global Terrestrial Mercury Model source code | | | # (NOTE: This feature has fallen into disuse) | | | | | +---Headers # Source code for defining the GEOS-Chem state objects | | | | | +---History # Source code for History diagnostics | | | | | +---Interfaces # Driver code for various implementations of GEOS-Chem | | | | | | | +---CESM # Source code to connect GEOS-Chem to CESM | | | | | | | +---GCClassic # "Main program" source code for GEOS-Chem Classic | | | | | | | +---GCHP # "Main program" source code for GCHP | | | | | | | +---GEOS # Source code to connect GEOS-Chem in the NASA GEOS ESM | | | | | +---KPP # Root folder KPP-generated solver code | | | | | | | +---carbon # KPP-generated code for the carbon mechanism | | | | | | | +---custom # "Sandbox" for generating custom mechanisms | | | | | | | +---fullchem # KPP-generated code for the full-chemistry mechanism | | | | | | | +---Hg # KPP-generated code for the mercury (Hg) mechanism | | | | | +---NcdfUtil # Source code for netCDF file I/O | | | | | +---ObsPack # Source code for the ObsPack diagnostic | | | | | +---PKUCPL # Source code for PKU two way coupler | | | # (NOTE: This feature has fallen into disuse) | | | | | +---run # Root folder for run directory creation scripts | | | | | | | +---CESM # Rundir creation scripts/files for CESM | | | | | | | +---GCClassic # Rundir creation scripts/files for GEOS-CHem Classic | | | | | | | +---GCHP # Rundir creation scripts/files for GCHP | | | | | | | +---GEOS # Rundir creation scripts/files for NASA GEOS ESM | | | | | | | +---shared # Common scripts and configuration file snippets | | | | | | | +---WRF # Rundir creation scripts/files for WRF-GC | | | | | +---test # Root folder for integration test scripts | | | | | +---difference # Scripts to compare the results of two integrationtests | | | | | +---integration # Top-level integration test folder | | | | | | | +---GCClassic # Scripts to run integration tests for GEOS-Chem Classic | | | | | | | +---GCHP # Scripts to run integration tests for GCHP | | | | | +---parallel # Top-level parallelization test folder | | | | | | | +---GCClassic # Scripts to run parallel tests for GEOS-Chem Classic | | | | | +---shared # Common scripts for integration & parallel tests | | | +---HEMCO # Harmonized Emissions Component (HEMCO) submodule | | | | | +---CMakeScripts # Utility functions for CMake | | | | | +---docs # Root directory for ReadTheDocs documentation | | | | | | | +---source # Subdivides documentation into subdirectories | | | | | | | +---coupling # Markup files (ReST format) for ReadTheDocs | | | | | | | +---geos-chem-shared-docs # Submodule containing shared documentation files | | | | # (such as common supplemental guides) | | | | | | | +---hco-ref-guide # Markup files (reST format) for ReadTheDocs | | | | | | | +---hco-sa-guide # Markup files (reST format) for ReadTheDocs | | | | | | | +---reference # Markup files (reST format) for ReadTheDocs | | | | | | | +---_static # Static content (e.g. images) for ReadTheDocs | | | | | +---run # Rundir creation scripts/files for HEMCO standalone | | | | | +---src # Top-level source code folder | | | | | +---Core # Source code for core HEMCO routines | | | | | +---Extensions # Source code for HEMCO extensions | | | | | | | +---PreProcess # Scripts for creating the FINN or GFED include file | | | | | +---Interfaces # Driver programs for the various HEMCO implementations | | | | | | | +--GEOS # Source code to connect HEMCO to the NASA GEOS ESM | | | | | | | +--MAPL_ESMF # Source code to run HEMCO in the ESMF/MAPL environment | | | | | | | +--Shared # Common files for run directory creation | | | | | | | +--Standalone # "Main Program" for the HEMCO standalone model | | | | | +---Shared # Top-level folder for shared code | | | | | +---GeosUtil # Local copies of source code in GEOS-Chem/GeosUtil | | | | | +---Headers # Local copies of source code in GEOS-Chem/Headers | | | | | +---NcdfUtil # Local copies of source code in GEOS-Chem/NcdfUtil | | | +---HETP # ISORROPIA/HETP submodule source code | | | +---CMakeScripts # Utility functions for CMake | | | +---Core # Source code for HETP | | | +---Test # "Main program" for testing HETP in standalone mode | | +---spack # Link to docs/source/geos-chem-shared-docs/spack | +---test # Link to src/GEOS-Chem/test