Difference between revisions of "GEOS-Chem directory structure"

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(Code directory structure)
(GEOS-Chem Code structure (13.0.0 and later versions))
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{| border=1 cellspacing=0 cellpadding=5  
 
{| border=1 cellspacing=0 cellpadding=5  
 
|- bgcolor="#CCCCCC"
 
|- bgcolor="#CCCCCC"
!width="280px"|Code folder or routine
+
!width="375px"|Code folder or routine
!width="400px"|Description
+
!width="375px"|Description
 
!width="225px"|Location in prior versions
 
!width="225px"|Location in prior versions
 
!width="225px"|Notes
 
!width="225px"|Notes
  
 
|-valign="top"
 
|-valign="top"
|<tt>src/GEOS-Chem</tt>
+
|<tt>GCClassic/src/GEOS-Chem</tt>
|Main-level directory for GEOS-Chem  
+
|Main-level directory for the GEOS-Chem "science codebase".
 
|<tt>GEOS-Chem</tt>
 
|<tt>GEOS-Chem</tt>
 
|
 
|
  
 
|-valign="top"
 
|-valign="top"
|<tt>src/GEOS-Chem/GTMM</tt>
+
|<tt>GCClassic/src/GEOS-Chem/GTMM</tt>
 
|Directory containing source code files for the [[Global_Terrestrial_Mercury_Model|Global Terrestrial Mercury Model (GTMM)]] simulation
 
|Directory containing source code files for the [[Global_Terrestrial_Mercury_Model|Global Terrestrial Mercury Model (GTMM)]] simulation
 
|<tt>GEOS-Chem/GTMM</tt>
 
|<tt>GEOS-Chem/GTMM</tt>
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|-valign="top"
 
|-valign="top"
|<tt>src/GEOS-Chem/GeosCore</tt>
+
|<tt>GCClassic/src/GEOS-Chem/GeosCore</tt>
 
|Directory containing most GEOS-Chem modules and routines
 
|Directory containing most GEOS-Chem modules and routines
 
|<tt>GEOS-Chem/GeosCore</tt>
 
|<tt>GEOS-Chem/GeosCore</tt>
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|-valign="top"
 
|-valign="top"
|<tt>src/GEOS-Chem/GeosRad</tt>
+
|<tt>GCClassic/src/GEOS-Chem/GeosRad</tt>
 
|Directory containing source code files for the [[Coupling_GEOS-Chem_with_RRTMG|RRTMG radiative transfer model]]
 
|Directory containing source code files for the [[Coupling_GEOS-Chem_with_RRTMG|RRTMG radiative transfer model]]
 
|<tt>GEOS-Chem/GeosRad</tt>
 
|<tt>GEOS-Chem/GeosRad</tt>
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|-valign="top"
 
|-valign="top"
|<tt>src/GEOS-Chem/GeosUtil</tt>
+
|<tt>GCClassicsrc/GEOS-Chem/GeosUtil</tt>
 
|Directory containing GEOS-Chem utility modules
 
|Directory containing GEOS-Chem utility modules
 
|<tt>GEOS-Chem/GeosUtil</tt>
 
|<tt>GEOS-Chem/GeosUtil</tt>
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|-valign="top"
 
|-valign="top"
|<tt>src/GEOS-Chem/Headers</tt>
+
|<tt>GCClassic/src/GEOS-Chem/Headers</tt>
 
|Directory containing module files with fixed parameters and derived-type definitions
 
|Directory containing module files with fixed parameters and derived-type definitions
 
|<tt>GEOS-Chem/Headers</tt>
 
|<tt>GEOS-Chem/Headers</tt>
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|-valign="top"
 
|-valign="top"
|<tt>src/GEOS-Chem/History</tt>
+
|<tt>GCClassic/src/GEOS-Chem/History</tt>
 
|Directory containing module files to archive diagnostics from GEOS-Chem "Classic" simulations to netCDF file format
 
|Directory containing module files to archive diagnostics from GEOS-Chem "Classic" simulations to netCDF file format
 
|<tt>GEOS-Chem/History</tt>
 
|<tt>GEOS-Chem/History</tt>
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|-valign="top"
 
|-valign="top"
|<tt>src/GEOS-Chem/ISORROPIA</tt>
+
|<tt>GCClasic/src/GEOS-Chem/ISORROPIA</tt>
 
|Directory containing the [[ISORROPIA_II|ISORROPIA II]] source code files  
 
|Directory containing the [[ISORROPIA_II|ISORROPIA II]] source code files  
 
|<tt>GEOS-Chem/ISORROPIA</tt>
 
|<tt>GEOS-Chem/ISORROPIA</tt>
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|-valign="top"
 
|-valign="top"
|<tt>src/GEOS-Chem/KPP</tt>
+
|<tt>GCClassic/src/GEOS-Chem/KPP</tt>
 
|Main-level directory for the [[KPP_solvers_FAQ|KPP chemical solver]]
 
|Main-level directory for the [[KPP_solvers_FAQ|KPP chemical solver]]
 
|<tt>GEOS-Chem/KPP</tt>
 
|<tt>GEOS-Chem/KPP</tt>
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|-valign="top"
 
|-valign="top"
|<tt>src/GEOS-Chem/KPP/fullchem</tt>
+
|<tt>GCClassic/src/GEOS-Chem/KPP/fullchem</tt>
 
|Directory containing KPP source code files for the GEOS-Chem "full-chemistry" mechanism
 
|Directory containing KPP source code files for the GEOS-Chem "full-chemistry" mechanism
 
|
 
|
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|-valign="top"
 
|-valign="top"
|<tt>src/GEOS-Chem/KPP/custom</tt>
+
|<tt>GCClassic/src/GEOS-Chem/KPP/custom</tt>
 
|Directory containing KPP source code files for creating custom mechanisms
 
|Directory containing KPP source code files for creating custom mechanisms
 
|<tt>GEOS-Chem/KPP/SOA_SVPOA</tt>
 
|<tt>GEOS-Chem/KPP/SOA_SVPOA</tt>
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|-valign="top"
 
|-valign="top"
|<tt>src/GEOS-Chem/KPP/int</tt>
+
|<tt>GCClassic/src/GEOS-Chem/KPP/int</tt>
 
|Directory containing the integrators (rosenbrock, runge-kutta, lsodes, etc.) for KPP
 
|Directory containing the integrators (rosenbrock, runge-kutta, lsodes, etc.) for KPP
 
|<tt>GEOS-Chem/KPP/int</tt>
 
|<tt>GEOS-Chem/KPP/int</tt>
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|-valign="top"
 
|-valign="top"
|<tt>src/GEOS-Chem/NcdfUtil</tt>
+
|<tt>GCClassic/src/GEOS-Chem/NcdfUtil</tt>
 
|Directory containing source code files for netCDF I/O. This code is from Bob Yantosca's NcdfUtilities package
 
|Directory containing source code files for netCDF I/O. This code is from Bob Yantosca's NcdfUtilities package
 
|<tt>GEOS-Chem/NcdfUtil</tt>
 
|<tt>GEOS-Chem/NcdfUtil</tt>
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|-valign="top"
 
|-valign="top"
|<tt>src/GEOS-Chem/NcdfUtil/perl</tt>
+
|<tt>GCClassic/src/GEOS-Chem/NcdfUtil/perl</tt>
 
|Directory containing perl scripts from the NcdfUtilities package that can be used to generate Fortran code for defining, writing, and reading a netCDF file
 
|Directory containing perl scripts from the NcdfUtilities package that can be used to generate Fortran code for defining, writing, and reading a netCDF file
 
|<tt>GEOS-Chem/NcdfUtil/perl</tt>
 
|<tt>GEOS-Chem/NcdfUtil/perl</tt>
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|-valign="top"
 
|-valign="top"
|<tt>src/GEOS-Chem/ObsPack</tt>
+
|<tt>GCClassic/src/GEOS-Chem/ObsPack</tt>
 
|Directory containing the [[ObsPack diagnostic]] code.
 
|Directory containing the [[ObsPack diagnostic]] code.
 
|<tt>GEOS-Chem/ObsPack</tt>
 
|<tt>GEOS-Chem/ObsPack</tt>
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|-valign="top"
 
|-valign="top"
|<tt>src/GEOS-Chem/PKUCPL</tt>
+
|<tt>GCClassic/src/GEOS-Chem/PKUCPL</tt>
 
|Directory containing the PKU 2-way coupler code.
 
|Directory containing the PKU 2-way coupler code.
 
|<tt>GEOS-Chem/PKUCPL</tt>
 
|<tt>GEOS-Chem/PKUCPL</tt>
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|-valign="top"
 
|-valign="top"
|<tt>src/GEOS-Chem/Interfaces/main.F90</tt>
+
|<tt>GCClassic/src/GEOS-Chem/Interfaces/main.F90</tt>
 
|Main driver program for GEOS-Chem "Classic".
 
|Main driver program for GEOS-Chem "Classic".
 
|<tt>GEOS-Chem/GeosCore/main.F90</tt>
 
|<tt>GEOS-Chem/GeosCore/main.F90</tt>

Revision as of 14:33, 8 December 2020

Previous | Next | Getting Started with GEOS-Chem

  1. Minimum system requirements
  2. Installing required software
  3. Configuring your computational environment
  4. Downloading source code
  5. Downloading data directories
  6. Creating run directories
  7. Configuring runs
  8. Compiling
  9. Running
  10. Output files
  11. Visualizing and processing output
  12. Coding and debugging
  13. Further reading


Code directory structure

The tables below list the folders in which various components of GEOS-Chem and HEMCO reside.

GEOS-Chem Code structure (13.0.0 and later versions)

The table below lists the directory structure in GEOS-Chem 12 along with descriptions of each subdirectory and its Makefile (if one is present).

Code folder or routine Description Location in prior versions Notes
GCClassic/src/GEOS-Chem Main-level directory for the GEOS-Chem "science codebase". GEOS-Chem
GCClassic/src/GEOS-Chem/GTMM Directory containing source code files for the Global Terrestrial Mercury Model (GTMM) simulation GEOS-Chem/GTMM
  • GTMM simulation is currently broken in GEOS-Chem 13.0.0
GCClassic/src/GEOS-Chem/GeosCore Directory containing most GEOS-Chem modules and routines GEOS-Chem/GeosCore
GCClassic/src/GEOS-Chem/GeosRad Directory containing source code files for the RRTMG radiative transfer model GEOS-Chem/GeosRad
GCClassicsrc/GEOS-Chem/GeosUtil Directory containing GEOS-Chem utility modules GEOS-Chem/GeosUtil
GCClassic/src/GEOS-Chem/Headers Directory containing module files with fixed parameters and derived-type definitions GEOS-Chem/Headers
GCClassic/src/GEOS-Chem/History Directory containing module files to archive diagnostics from GEOS-Chem "Classic" simulations to netCDF file format GEOS-Chem/History
GCClasic/src/GEOS-Chem/ISORROPIA Directory containing the ISORROPIA II source code files GEOS-Chem/ISORROPIA
GCClassic/src/GEOS-Chem/KPP Main-level directory for the KPP chemical solver GEOS-Chem/KPP
GCClassic/src/GEOS-Chem/KPP/fullchem Directory containing KPP source code files for the GEOS-Chem "full-chemistry" mechanism Prior versions used these code folders:
  • GEOS-Chem/KPP/Standard
  • GEOS-Chem/KPP/Tropchem
  • GEOS-Chem/KPP/SOA_SVPOA
GCClassic/src/GEOS-Chem/KPP/custom Directory containing KPP source code files for creating custom mechanisms GEOS-Chem/KPP/SOA_SVPOA
GCClassic/src/GEOS-Chem/KPP/int Directory containing the integrators (rosenbrock, runge-kutta, lsodes, etc.) for KPP GEOS-Chem/KPP/int
GCClassic/src/GEOS-Chem/NcdfUtil Directory containing source code files for netCDF I/O. This code is from Bob Yantosca's NcdfUtilities package GEOS-Chem/NcdfUtil
GCClassic/src/GEOS-Chem/NcdfUtil/perl Directory containing perl scripts from the NcdfUtilities package that can be used to generate Fortran code for defining, writing, and reading a netCDF file GEOS-Chem/NcdfUtil/perl
GCClassic/src/GEOS-Chem/ObsPack Directory containing the ObsPack diagnostic code. GEOS-Chem/ObsPack
GCClassic/src/GEOS-Chem/PKUCPL Directory containing the PKU 2-way coupler code. GEOS-Chem/PKUCPL
GCClassic/src/GEOS-Chem/Interfaces/main.F90 Main driver program for GEOS-Chem "Classic". GEOS-Chem/GeosCore/main.F90

HEMCO code structrure (version 3.0.0 and later)

Code folder or routine Description Location in prior versions Notes
src/HEMCO Main-level directory for HEMCO GEOS-Chem/HEMCO
src/HEMCO/src/Core Directory containing HEMCO modules and routines for reading, storing, and updating data used for calculating emissions GEOS-Chem/HEMCO/Core
src/HEMCO/src/Extensions Directory containing HEMCO modules and routines for calculating emissions that depend on meteorological input variables and/or non-linear parameterizations GEOS-Chem/HEMCO/Extensions
src/HEMCO/src/Interfaces Directory containing HEMCO modules and routines that provide the link between HEMCO and the model environment GEOS-Chem/HEMCO/Interfaces
src/HEMCO/src/Shared Directory containing HEMCO modules and routines that provide the link between HEMCO and the model environment - Not present in earlier versions



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