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== feel free to experiment here ==
=== Species added ===


{|border="1" width="1000px" bordercolor="#000000" cellspacing="0" cellpadding="5" align="center"
Species added between versions 14.5.0-alpha.5 and 14.5.0-alpha.9:


|-valign="middle" height="80" bgcolor="#0099FF" align="center"
{| border=1 cellspacing=0 cellpadding=5
|<p><font color="#FFFFFF" size="+3">'''GEOS&#150;Chem Wiki'''</font></p>
!width='100px' bgcolor='#CCCCCC'|Name
!width='100px' bgcolor='#CCCCCC'|Formula
!width='200px' bgcolor='#CCCCCC'|Fullname
!width='30px' bgcolor='#CCCCCC'|Advected
!width='30px' bgcolor='#CCCCCC'|Dry deposited
!width='30px' bgcolor='#CCCCCC'|Gas
!width='30px' bgcolor='#CCCCCC'|Photolyzed
!width='30px' bgcolor='#CCCCCC'|Wet deposited


|}
|-valign='top'
 
|ACO3
{|border="0" width="1000px" bordercolor="#FFFFFF" cellspacing="0" cellpadding="5" align="center"
|C3H3O3
 
|Peroxyacetyl radical for APAN
|-valign="top"
|
|
|X
|
|
|-valign='top'
|ACR
|C3H4O
|Acrolein
|X
|X
|X
|X
|
|-valign='top'
|ACRO2
|C3H5O4
|Peroxy radical from ACR
|
|
|X
|
|
|-valign='top'
|ALK7
|C7H16
|Lumped >= C6 Alkanes
|X
|
|X
|
|
|-valign='top'
|APAN
|C3H3NO5
|Peroxyacryloyl nitrate
|X
|X
|X
|X
|X
|-valign='top'
|APINN
|C10H17NO4
|1st gen organic nitrate from APIN
|X
|X
|X
|X
|X
|-valign='top'
|APINO2
|C10H17O3
|Peroxy radical from APIN
|
|
|X
|
|
|-valign='top'
|APINP
|C10H18O3
|Hydroperoxide from APIN
|X
|X
|X
|
|X
|-valign='top'
|AROMCHO
|C5H6O4
|ACCOMECHO from MCM
|X
|X
|X
|
|X
|-valign='top'
|AROMCO3
|C5H5O6
|Lumped aromatic peroxyacetyl radical
|
|
|X
|
|
|-valign='top'
|AROMPN
|C5H5NO8
|Lumped PN from aromatics
|X
|X
|X
|X
|X
|-valign='top'
|BPINN
|C10H17NO4
|Saturated 1st gen BPIN organic nitrate
|X
|X
|X
|X
|X
|-valign='top'
|BPINO
|C9H14O
|Ketone from BPIN
|X
|X
|X
|
|X
|-valign='top'
|BPINO2
|C10H17O3
|Peroxy radical from BPIN
|
|
|X
|
|
|-valign='top'
|BPINON
|C9H13NO4
|Saturated 2nd gen BPIN organic nitrate
|X
|X
|X
|X
|X
|-valign='top'
|BPINOO2
|C10H17O3
|2nd-gen peroxy radical from BPIN
|
|
|X
|
|
|-valign='top'
|BPINOOH
|C9H14O3
|2nd-gen peroxide from BPIN
|X
|X
|X
|
|X
|-valign='top'
|BPINP
|C10H18O3
|Peroxide from BPIN
|X
|X
|X
|
|X
|-valign='top'
|BUTN
|C4H7NO4
|C4H6 alkyl nitrate
|X
|X
|X
|
|X
|-valign='top'
|BUTO2
|C4H7O3
|peroxy radical from C4H6
|
|
|X
|
|
|-valign='top'
|C4H6
|C4H6
|1,3-butadiene
|X
|
|X
|
|
|-valign='top'
|C96N
|C9H15NO4
|Saturated 2nd gen monoterpene organic nitrate
|X
|X
|X
|X
|X
|-valign='top'
|C96O2
|C10H17O3
|2nd-gen peroxy radical from APIN
|
|
|X
|
|
|-valign='top'
|C96O2H
|C9H16O3
|Peroxide from APIN 2nd gen
|X
|X
|X
|
|X
|-valign='top'
|EBZ
|C8H10
|Ethylbenzene
|X
|
|X
|
|
|-valign='top'
|GCO3
|HOCH2CO3
|Peroxyacetyl radical for PHAN
|
|
|X
|
|
|-valign='top'
|HACTA
|HOCH2CO2H
|Hydroxyacetic/glycolic acid
|X
|X
|X
|
|X
|-valign='top'
|LIMAL
|C10H16O2
|Aldehyde from limonene
|X
|X
|X
|
|X
|-valign='top'
|LIMKB
|C10H16O3
|2nd gen ketone from limonene
|X
|X
|X
|
|X
|-valign='top'
|LIMKET
|C10H16O2
|Ketone from limonene
|X
|X
|X
|
|X
|-valign='top'
|LIMKO2
|C10H17O3
|2nd-gen peroxy radical from LIMO
|
|
|X
|
|
|-valign='top'
|LIMN
|C10H17NO4
|Saturated 1st gen limonene organic nitrate
|X
|X
|X
|X
|X
|-valign='top'
|LIMNB
|C10H15NO4
|Saturated 1st gen LIMO organic nitrate
|X
|X
|X
|X
|X
|-valign='top'
|LIMO2H
|C10H18O3
|Acid from LIMO
|X
|X
|X
|
|X
|-valign='top'
|LIMO3
|C10H17O3
|Acylperoxy radical from LIMO
|
|
|X
|
|
|-valign='top'
|LIMO3H
|C10H18O4
|Peracid from LIMO
|X
|X
|X
|
|X
|-valign='top'
|LIMPAN
|C10H17NO4
|PAN from LIMO
|X
|X
|X
|X
|X
|-valign='top'
|MEKCO3
|C3H5O4
|False
|
|
|X
|
|
|-valign='top'
|MEKPN
|C3H5NO6
|MEK peroxyacetyl nitrate
|X
|X
|X
|X
|X
|-valign='top'
|MYRCO
|C10H18O3
|Aldehyde or ketone from myrcene
|X
|X
|X
|
|X
|-valign='top'
|PHAN
|C2H3NO6
|Peroxyhydroxyacetic nitric anhydride
|X
|X
|X
|X
|X
|-valign='top'
|PIN
|C10H17NO4
|Saturated 1st gen monoterpene organic nitrate
|X
|X
|X
|X
|X
|-valign='top'
|PINAL
|C10H16O2
|Pinonaldehyde
|X
|X
|X
|
|X
|-valign='top'
|PINO3
|C10H17O3
|Acylperoxy radical from APIN
|
|
|X
|
|
|-valign='top'
|PINO3H
|C10H18O4
|Pinonic peracid
|X
|X
|X
|
|X
|-valign='top'
|PINONIC
|C10H18O3
|Pinonic acid
|X
|X
|X
|
|X
|-valign='top'
|PINPAN
|C10H17NO4
|PAN from pinonaldehyde
|X
|X
|X
|X
|X
|-valign='top'
|R7N1
|C7H15NO5
|Peroxy radical from R7N2
|
|
|X
|
|
|-valign='top'
|R7N2
|RO2NO
|C7 Lumped alkyl nitrate
|X
|X
|X
|X
|X
|-valign='top'
|R7O2
|C7H15O2
|Peroxy radical from ALK7
|
|
|X
|
|
|-valign='top'
|R7P
|C7H16O2
|Peroxide from R7O2
|X
|X
|X
|X
|X
|-valign='top'
|RNO3
|RO2NO
|Lumped aromatic nitrate
|X
|X
|X
|X
|X
|-valign='top'
|STYR
|C8H8
|Styrene
|X
|
|X
|
|
|-valign='top'
|TLFUO2
|C5H7O5
|False
|
|
|X
|
|
|-valign='top'
|TLFUONE
|C5H6O2
|Aromatic furanones
|X
|X
|X
|
|
The [http://acmg.seas.harvard.edu/geos/ GEOS–Chem model] is a global 3-D model of atmospheric composition driven by assimilated meteorological observations from the Goddard Earth Observing System (GEOS) of the [http://gmao.gsfc.nasa.gov/ NASA Global Modeling and Assimilation Office]. It is applied by [http://acmg.seas.harvard.edu/geos/geos_people.html research groups around the world] to a wide range of atmospheric composition problems, Central management and support of the model is provided by the [http://acmg.seas.harvard.edu/index.html Atmospheric Chemistry Modeling Group at Harvard University.]
|X
 
This wiki is meant to facilitate communication between GEOS-Chem users and developers. If this is '''your first time here''', check out [[Features of the GEOS-Chem public wiki|the features page]]. If you would like to contribute to the wiki, please register as a user by clicking ''create account'' at the top right corner of this page.
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New information is continually being added to the wiki, so please check back here often, or even better, [[Features_of_the_GEOS-Chem_public_wiki#Let_the_GEOS-Chem_wiki_inform_you_of_recent_changes.21|subscribe to the recent changes' RSS feed]]: you will not miss a discussion!
|C8H10
 
|Trimethylbenzenes
|}
 
{|border="1" width="1000px" bordercolor="#000000" cellspacing="0" cellpadding="5" align="center"
 
|-valign="top" align="center"
|width="334px"|'''Getting started w/ GEOS-Chem:'''
|width="333px"|'''[[GEOS-Chem welcome letter for new users|Welcome letter for new users]]'''
|width="333px"|'''[[GEOS-Chem basics]]'''
 
|-valign="top" bgcolor="#CCFFFF" align="center"
|'''Current public release:'''
|'''[[GEOS-Chem v10-01]]'''
|'''[[GEOS-Chem v10-01 benchmark history|v10-01 benchmark history]]'''
 
|-valign="top" align="center"
|'''Version in development:'''
|'''[[GEOS-Chem v11-01]]'''
|'''[[GEOS-Chem v11-01 benchmark history|v11-01 benchmark history]]'''
 
|-valign="top" align="center"
|'''Version for high-performance<br>computing (HPC) environments:'''
|'''[[GEOS-Chem HP]]'''
|'''[[GEOS-Chem HP Dev Kit]]'''
 
|-valign="top" align="center"
|'''List of publications:'''
|'''[http://acmg.seas.harvard.edu/geos/geos_pub.html Refer to this page]'''
|
 
|}
 
<br>
 
{|border="1" width="1000px" bordercolor="#000000" cellspacing="0" cellpadding="5" align="center"
 
|-height="50" bgcolor="#00AAAA" align="center"
|colspan="2"|<p><font color="#FFFFFF" size="+2">'''General information about GEOS-Chem'''</font></p>
 
|-valign="top" bgcolor="#CCCCCC"
!width="500px"|<big>Introduction and overview</big>
!width="500px"|<big>Steering Committee and working groups</big>
 
|-valign="top"
| <!-- Intro and overview -->
* [[GEOS-Chem welcome letter for new users]]
* [[GEOS-Chem basics]]
* [[Features of the GEOS-Chem public wiki]]
* [[Customizing your GEOS-Chem Wiki Settings]]
* [http://acmg.seas.harvard.edu/geos/geos_overview.html GEOS-Chem Overview]
* [http://acmg.seas.harvard.edu/geos/geos_people.html GEOS-Chem People & Projects]
* [http://acmg.seas.harvard.edu/geos/word_pdf_docs/resources_guidelines_tips.pdf User Resources, Code Development Guidelines, and Debugging Tips]
* [[GEOS-Chem Support Team]]
* [[GEOS-Chem newsletters]]
* [http://acmg.seas.harvard.edu/geos/geos_search.html GEOS-Chem Search Engines]
* [http://acmg.seas.harvard.edu/geos/geos_new_developments.html Recommendations for offering co-authorships to GEOS-Chem developers]
* [http://acmg.seas.harvard.edu/geos/geos_dev_history.html GEOS-Chem code development history]
| <!-- Steering committee etc -->
* [http://acmg.seas.harvard.edu/geos/geos_steering_cmte.html GEOS-Chem Steering Committee]
** [[GEOS-Chem model development priorities]]
* [http://acmg.seas.harvard.edu/geos/geos_working_groups.html GEOS-Chem Working Groups]
** [[GEOS-Chem Adjoint|Adjoint Model and Data Assimilation Working Group]]
** [[Aerosols Working Group]]
** [[Carbon Cycle Working Group]]
** [[Chemistry-Climate Working Group]]
** [[GEOS-Chem High Performance Working Group]]
** [[Hg and POPs Working Group]]
** [[Organics Working Group]]
** [[Chemistry Issues|Oxidants and Chemistry Working Group]]
** [[Nested Model Working Group]]
** [[Sources and Sinks Working Group|Sources and Surface Uptake Working Group]]
** [[Transport Working Group]]
 
|-valign="top" bgcolor="#CCCCCC"
!width="500px"|<big>Getting started with GEOS-Chem</big>
!width="500px"|<big>General technical information</big>
 
|-valign="top"
|
|
* [[Frequently asked questions about GEOS-Chem]]
* [[Minimum system requirements for GEOS-Chem]]
* [[GEOS-Chem supported platforms and compilers]]
* [[Downloading GEOS-Chem source code and data]]
* [[Creating GEOS-Chem run directories]]
* [[GEOS-Chem programming resources]] (e.g. tutorials, user guides, etc.)
* [http://acmg.seas.harvard.edu/geos/doc/man/appendix_7.html GEOS-Chem Programming Style Guide]
|
|
* [[Initial conditions for GEOS-Chem]]
|X
* [[Centralized chemistry time step]]
* [[GEOS-Chem coding and debugging#GEOS-Chem debugging tips|Tips on how to debug GEOS-Chem effectively]]
* [[Reporting GEOS-Chem bugs]]
* [[Debugging with the GEOS-Chem unit tester]]
* [[Parallelizing GEOS-Chem]] with the OpenMP directives
* [[Common GEOS-Chem error messages]]
* [[Adding tracers to GEOS-Chem|Adding advected tracers and chemical species to GEOS-Chem]]
* [[Adding Passive Tracers|Adding passive (CO-like) tracers to GEOS-Chem]]
|}
 
<br>
 
{|border="1" width="1000px" bordercolor="#000000" cellspacing="0" cellpadding="5" align="center"
 
|-height="50" bgcolor="#00AAAA" align="center"
|colspan="2"|<p><font color="#FFFFFF" size="+2">'''GEOS-Chem Code Developers' Forums'''</font></p>
 
|-valign="top" bgcolor="#CCCCCC"
!width="500px"|<big>Coding</big>
!width="500px"|<big>Diagnostics</big>
 
|-valign="top"
| <!-- Coding -->
* [[GEOS-Chem versions under development]]
* [[Bugs and fixes|List of GEOS-Chem bugs and in which version they were resolved]]
* [[Currently unresolved issues in GEOS-Chem]]
* [[Common GEOS-Chem error messages]]
* [[Known issues caused by compiler bugs|Known GEOS-Chem issues caused by compiler bugs]]
* [[GEOS-Chem performance]]
* [[Machine issues and portability]]
* [[Passing array arguments efficiently in GEOS-Chem]]
* [[Floating point math issues]]
* [[Version control with Git]]
| <!-- Diagnostics -->
* [http://acmg.seas.harvard.edu/geos/doc/man/appendix_5.html Overview of diagnostics characteristics]
* [[Diagnostic time step]]
* [[Mass Flux (ND24/25/26)]]
* [[Additional diagnostics]]
 
|-valign="top" bgcolor="#CCCCCC"
!width="500px"|<big>Emissions</big>
!width="500px"|<big><Chemistry/big>
 
|-valign="top"
|<!-- Emissions -->
* [[HEMCO|HEMCO emissions component]]
* [[HEMCO data directories]]
* [[Aerosol emissions]]
* [[Aircraft emissions]]
* [[Anthropogenic emissions]]
* [[Scale factors for anthropogenic emissions]]
* [[Biofuel emissions]]
* [[Biogenic emissions]]
* [[Biomass burning emissions]]
* [[Lightning NOx emissions]]
* [[Ship emissions]]
* [[Soil NOx emissions]]
* [[Volcanic SO2 emissions from Aerocom|Volcanic emissions]]
* [[Historical and Future Emissions|Historical and future emissions]]
|<!-- Chemistry -->
* [[GEOS-Chem chemistry mechanisms]]
* [[GEOS-Chem chemistry mechanisms#Stratospheric chemistry|Stratopsheric chemistry options]]
* [[GEOS-Chem chemistry mechanisms#Specialty simulations|Specialty simulations (aka "offline simulations")]]
* Other resources
** [[Chemistry Issues]]
** [[Process Analysis Diagnostics]]
** [[Photolysis mechanism|Photolysis mechanisms used in GEOS-Chem]]
** [[DSMACC chemical box model]]
** [[Isoprene|List of recent papers about isoprene]]
** [[Linking GEOS-Chem to CMAQ]]
** [[Coupling GEOS-Chem with RRTMG]]
*[[GEOS-Chem species database]] <span style="color:red">'''(NEW in [[GEOS-Chem v11-01|v11-01]]!)'''</span>
*[[Physical properties of GEOS-Chem species]] <span style="color:red">'''(NEW in [[GEOS-Chem v11-01|v11-01]]!)'''</span>
*[[Species_indexing_in_GEOS-Chem|Species and tracer indexing in GEOS-Chem]] <span style="color:red">'''(NEW in [[GEOS-Chem v11-01|v11-01]]!)'''</span>
 
|-valign="top" bgcolor="#CCCCCC"
!width="500px"|<big></big>
!width="500px"|<big></big>
 
|-valign="top"
| <!-- Intro and overview -->
 
| <!-- Steering committee etc -->
 
 
|-valign="top" bgcolor="#CCCCCC"
!width="500px"|<big></big>
!width="500px"|<big></big>
 
|-valign="top"
|
|
|
|
 
|-valign="top" bgcolor="#CCCCCC"
|-valign='top'
!width="500px"|<big></big>
|ZRO2
!width="500px"|<big></big>
|C7H9O5
 
|RO2 for making lumped aromatic nitrate
|-valign="top"
| <!-- Intro and overview -->
 
| <!-- Steering committee etc -->
 
 
|-valign="top" bgcolor="#CCCCCC"
!width="500px"|<big></big>
!width="500px"|<big></big>
 
|-valign="top"
|
|
|
|
 
|X
 
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|}


|-valign="top" bgcolor="#CCCCCC"
!width="500px"|<big></big>
=== Species removed===
!width="500px"|<big></big>
 
|-valign="top"
| <!-- Intro and overview -->
 
| <!-- Steering committee etc -->
 
|-valign="top" bgcolor="#CCCCCC"
!width="500px"|<big></big>
!width="500px"|<big></big>


Species removed between versions 14.5.0-alpha.5 and 14.5.0-alpha.9:


{| border=1 cellspacing=0 cellpadding=5
!width='100px' bgcolor='#CCCCCC'|Name
!width='100px' bgcolor='#CCCCCC'|Formula
!width='200px' bgcolor='#CCCCCC'|Fullname
!width='30px' bgcolor='#CCCCCC'|Advected
!width='30px' bgcolor='#CCCCCC'|Dry deposited
!width='30px' bgcolor='#CCCCCC'|Gas
!width='30px' bgcolor='#CCCCCC'|Photolyzed
!width='30px' bgcolor='#CCCCCC'|Wet deposited


|}
|}
<!-- ======================================================== -->
<!-- ===== CODE DEVELOPER'S FORUMS: TITLE              ===== -->
<!-- ======================================================== -->
<p>&nbsp;</p>
<table width="100%" border="1" bordercolor="#000000" cellspacing="0" cellpadding="5" align="center">
</tr>
<!-- ======================================================== -->
<!-- ===== CODE DEVELOPER'S FORUMS : SECOND ROW        ===== -->
<!-- ======================================================== -->
<!-- Header title -->
<tr bgcolor="#cccccc">
<th width="50%"scope="col"><big>Emissions</big></th>
<th width="50%"scope="col"><big>Chemistry</big></th>
</tr>
<tr>
<!-- Emissions: Links -->
<td width="50%" valign="top">
</td>
<!-- Chemistry Links -->
<td width="50%" valign="top">
</tr>
<!-- ======================================================== -->
<!-- ===== CODE DEVELOPER'S FORUMS : THIRD ROW        ===== -->
<!-- ======================================================== -->
<!-- Header title -->
<tr bgcolor="#cccccc">
<th width="50%"scope="col"><big>Dynamics</big></th>
<th width="50%"scope="col"><big>Deposition</big></th>
</tr>
<tr>
<!-- Dynamics: Links -->
<td width="50%" valign="top">
* [[Advection scheme TPCORE]]
* [[Boundary layer mixing]]
* [[Cloud convection]]
* [[Dynamic tropopause]]
</td>
<!-- Deposition: Links -->
<td width="50%" valign="top">
* [[Dry deposition]]
**[[Leaf area indices in GEOS-Chem]]
* [[Wet deposition]]
</td>
</tr>
<!-- ======================================================== -->
<!-- ===== CODE DEVELOPER'S FORUMS : FOURTH ROW        ===== -->
<!-- ======================================================== -->
<!-- Header title -->
<tr bgcolor="#cccccc">
<th width="50%"scope="col"><big>Aerosols</big></th>
<th width="50%"scope="col"><big>Met Fields</big></th>
</tr>
<tr>
<!-- Aerosols: Links -->
<td width="50%" valign="top">
* [[Aerosols overview: projects and developments|Aerosols working group]]
* [[Aerosol-only simulation]]
* [[Aerosol optical properties]]
* [[Aerosol thermodynamical equilibrium]]
* [[Carbonaceous aerosols]]
* [[Mineral dust aerosols]]
* [[Secondary organic aerosols]]
* [[Sea salt aerosols]]
* [[Sulfate aerosols]]
* Aerosol Microphysics
** [[APM aerosol microphysics|APM]]
** [[TOMAS aerosol microphysics|TOMAS]]
</td>
<!-- Met Fields: Links -->
<td width="50%" valign="top">
* [[GCAP]]
** [[List of GCAP met fields|List of GCAP met fields used by GEOS-Chem]]
* [[Overview of GMAO met data products]]
* [[Version history of GMAO met data products]]
* [[GMAO GEOS-4]]
** [[List of GEOS-4 met fields|List of GEOS-4 met fields used by GEOS-Chem]]
* [[GEOS-5|GMAO GEOS-5.2.0]]
** [[List of GEOS-5 met fields|List of GEOS-5.2.0 met fields used by GEOS-Chem]]
** [[GEOS-5 issues|Issues with GEOS-5.2.0 met data]]
* [[MERRA|GMAO MERRA "reanalysis"]]
** [[List of MERRA met fields|List of MERRA met fields used by GEOS-Chem]]
** [[MERRA implementation details|Implementing MERRA into GEOS-Chem]]
* [[GEOS-FP|GMAO GEOS-FP]]
** [[List of GEOS-FP met fields|List of GEOS-FP met fields used by GEOS-Chem]]
** [[GEOS-FP implementation details|Implementing GEOS-FP into GEOS-Chem]]
* [[MERRA-2|GMAO MERRA-2]]
** [[List of MERRA-2 met fields|List of MERRA-2 met fields used by GEOS-Chem]]
** [[MERRA-2 implementation details|Implementing MERRA-2 into GEOS-Chem]]
* [[Notes regarding GEOS vertical grids]]
* [[Available met data for nested grid simulations]]
* [[List of reprocessed met fields]]
</td>
</tr>
<!-- ======================================================== -->
<!-- ===== CODE DEVELOPER'S FORUMS : FIFTH ROW          ===== -->
<!-- ======================================================== -->
<tr bgcolor="#cccccc">
<th width="50%"scope="col"><big>Nested Grid Simulations</big></th>
<th width="50%"scope="col"><big>Earth System Model Framework</big></th>
</tr>
<tr>
<!-- Nested Grid Simulations: Links -->
<td width="50%" valign="top">
* [[GEOS-Chem nested grid simulations]]
* [[Setting up GEOS-Chem nested grid simulations]]
* [[Available met data for nested grid simulations]]
* [http://acmg.seas.harvard.edu/geos/wiki_docs/nested_grids/geos_data_downloads.pdf Protocol for nested-grid data downloads]
* [[Steps to setup new nested domains]]
* [[GEOS-Chem nested model publications]]
</td>
<!-- Libraries -->
<td width="50%" valign="top">
* [[Installing ESMF and other required libraries]]
* [[Code development with the Earth System Model Framework]]
* [[Automatic documentation with protex|Generating automatic LaTeX documentation with protex]]
** [http://frodo.elon.edu/tutorial/tutorial/tutorial.html Web-based LaTeX tutorial]
</td>
</tr>
<!-- ======================================================== -->
<!-- ===== CODE DEVELOPER'S FORUMS : SIXTH ROW          ===== -->
<!-- ======================================================== -->
<tr bgcolor="#cccccc">
<th width="50%"scope="col"><big>Benchmarking and Evaluation</big></th>
<th width="50%"scope="col"><big>Related Projects</big></th>
</tr>
<tr>
<!-- Diagnostics: Links -->
<td width="50%" valign="top">
* [http://acmg.seas.harvard.edu/geos/geos_benchmark.html General info about GEOS-Chem benchmark simulations]
* [http://acmg.seas.harvard.edu/geos/geos_1yr_plots.html List of GEOS-Chem 1-year benchmark simulations]
* [[Mean OH lifetime in GEOS-Chem]]
* [ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/ FTP site with output from 1-year GEOS-Chem benchmark simulations]
* [[GEOS-Chem participation in community intercomparisons]]
* [[Satellite_Specifications_Table|Satellite Instrument Specifications Table]]
</td>
<!-- Related Projects: Links -->
<td width="50%" valign="top">
* [[Grid-independent GEOS-Chem]]
* [[GEOS-Chem Adjoint]]
* [[GEOS-Chem Near-Real-Time Simulations]]
* [[FlexAOD]]
</td>
</tr>
</table>
<!-- ======================================================== -->
<!-- ===== REFERENCE: TITLE                            ===== -->
<!-- ======================================================== -->
<p>&nbsp;</p>
<table width="100%" border="1" bordercolor="#000000" cellspacing="0" cellpadding="5" align="center">
<tr bgcolor="#00AAAA">
<th colspan="2" height="50" valign="middle"><p><font color="#FFFFFF" size="+2">Reference Section</font></p></th>
</tr>
<!-- ======================================================== -->
<!-- ===== REFERENCE: FIRST ROW                        ===== -->
<!-- ======================================================== -->
<tr bgcolor="#cccccc">
<th width="50%"scope="col"><big>IDL</big></th>
<th width="50%"scope="col"><big>GAMAP</big></th>
</tr>
<tr>
<!-- IDL: Links -->
<td width="50%" valign="top">
* [http://www.exelisvis.com/ Exelis Visual Information Solutions (vendor)]
* [http://www.exelisvis.com/docs/routines-1.html Online IDL Reference Manual @ Exelis website]
* [http://idlastro.gsfc.nasa.gov/idl_html_help/Structures.html Structures in IDL]
* [http://idlastro.gsfc.nasa.gov/idl_html_help/Pointers.html Pointers in IDL]
* [http://idlastro.gsfc.nasa.gov/idl_html_help/Overview_of_Mathematics_in_IDL.html Overview of Mathematics in IDL]
* [http://www.dfanning.com/ Coyote's Guide to IDL Programming (David Fanning's Web Site)] - Lots of tips on how to accomplish programming tasks
* [http://www.mpimet.mpg.de/en/misc/software/idl IDL Page at Max Planck Institute for Meteorology]
* [http://www.mpimet.mpg.de/en/misc/software/idl/doc/mgs_script.pdf Martin Schultz's IDL Tutorial (PDF Format)]
* [http://idlastro.gsfc.nasa.gov/homepage.html IDL Astronomy User's Library]
* [http://fermi.jhuapl.edu/s1r/idl/idl.html JHU/APL/S1R IDL routines page]
* [http://cow.physics.wisc.edu/~craigm/idl/idl.html Craig Markwardt's IDL library]
* [http://cimss.ssec.wisc.edu/~gumley/doc/idltips.pdf The Underground Guide to IDL by Liam Gumley (PDF)]
* [[Reading binary files in IDL]]
</td>
<!-- Diagnostics: Links -->
<td width="50%" valign="top">
* [http://acmg.seas.harvard.edu/gamap/ GAMAP web page]
* [http://acmg.seas.harvard.edu/gamap/doc/ GAMAP on-line users' guide]
* [[GAMAP bugs and fixes]]
* [[GAMAP tips and tricks]]
**[[General GAMAP usage]]
**[[TVMAP cheat sheet]]
**[[File I/O with GAMAP]]
***[http://acmg.seas.harvard.edu/gamap/doc/timeseries_brief_tutorial.pdf Working with timeseries output in GAMAP]
**[[Color and graphics with GAMAP]]
*** [http://acmg.seas.harvard.edu/geos/wiki_docs/gamap/gamap_color_table_file.pdf Loading Color Tables in GAMAP v2.12]
*** [http://acmg.seas.harvard.edu/forum_files/cdh_ColorInIDL.pdf Working with color in IDL by Chris Holmes]
**[[Regridding with GAMAP]]
**[[Date and time computations with GAMAP]]
**[[Text manipulation with GAMAP]]
</td>
</tr>
<!-- ======================================================== -->
<!-- ===== REFERENCE: SECOND ROW                        ===== -->
<!-- ======================================================== -->
<!-- Header title -->
<tr bgcolor="#cccccc">
<th width="50%"scope="col"><big>Fortran</big></th>
<th width="50%"scope="col"><big>Perl</big></th>
</tr>
<tr>
<!-- Fortran: Links -->
<td width="50%" valign="top">
* [[Intel Fortran Compiler]]
** [http://acmg.seas.harvard.edu/geos/wiki_docs/compilers/main_for_lin_v11.pdf Version 11.1]
** [http://acmg.seas.harvard.edu/geos/wiki_docs/compilers/main_for_lin_v12.pdf Version 12.1]
** [https://nf.nci.org.au/facilities/software/intel-ct/13.2.146/Documentation/en_US/compiler_f/main_for/index.htm#GUID-81DC012F-20D6-46B1-A524-BFAC4B6F7747.htm#GUID-81DC012F-20D6-46B1-A524-BFAC4B6F7747 Version XE 13.1]
** [https://software.intel.com/en-us/compiler_15.0_ug_f Version 15.0]
* [[PGI Fortran compiler]]
**[http://acmg.seas.harvard.edu/geos/wiki_docs/compilers/pgiug.pdf User Guide]
**[http://acmg.seas.harvard.edu/geos/wiki_docs/compilers/pgifortref.pdf Reference Guide]
* [[GNU Fortran compiler]]
* [http://www-01.ibm.com/software/awdtools/fortran/xlfortran/ IBM XL Fortran]
* [http://docs.sun.com/app/docs/doc/819-3686 Sun Studio 11 Fortran Compiler]
* [http://www.liv.ac.uk/HPC/HTMLF90Course/HTMLF90CourseSlides.html Modular Programming w/ Fortran 90 (U. Liverpool)]
* [http://www.liv.ac.uk/HPC/F90page.html Other University of Liverpool F90 tutorials and courses]
* [http://sunsite.unc.edu/pub/languages/fortran/index.html User Notes on FORTRAN Programming]
* [http://www.nsc.liu.se/~boein/f77to90/f77to90.html Fortran 90 for the FORTRAN 77 Programmer]
* [http://www.kcl.ac.uk/kis/support/cc/fortran/f90home.html#1.0 Fortran 90 Home Page at King's College, London]
* [http://www.cs.rpi.edu/~szymansk/oof90.html Object Oriented Fortran 90 Programming]
</td>
<!-- Perl: Links  -->
<td width="50%" valign="top">
* [http://www.perl.com Perl.com]
* [http://www.perl.org/books/beginning-perl/ ''Beginning Perl'' by Simon Cozens (free online book)]
* [http://backpan.perl.org/authors/id/Q/QU/QUONG/perlin20.html Perl in 20 pages]
* [http://www.enginsite.com/Library-Robert%27s-Perl-Tutorial.htm MediaWiki User's Guide]
* [http://www.cpan.org/ Comprehensive Perl Archive Network (CPAN.org)]
</td>
</tr>
<!-- Header title -->
<tr bgcolor="#cccccc">
<th width="50%"scope="col"><big>R</big></th>
<th width="50%"scope="col"><big>Python</big></th>
</tr>
<tr>
<!-- R: links -->
<td width="50%" valign="top">
*[http://www.r-project.org/ The R project for statistical computing]
*[http://journal.r-project.org/ The R journal]
*[http://www.mayin.org/ajayshah/KB/R/index.html R by example]
*[[Using R to analyze GEOS-Chem data]]
</td>
<!-- Python: links -->
<td width="50%" valign="top">
*[[Python code for GEOS-Chem]]
*[http://www.python.org Python.org]: Main site for all things Python
*[http://docs.python.org/2/tutorial/ Python.org Tutorial]
*[http://wiki.python.org/moin/BeginnersGuide/Programmers PythonWiki.org: List of tutorials and resources]
*[https://developers.google.com/edu/python/ Google's Python tutorial]
</td>
</tr>
<!-- Header title -->
<tr bgcolor="#cccccc">
<th width="50%"scope="col"><big>NCAR Command Language (NCL)</big></th>
<th width="50%"scope="col"><big>Wiki Documentation</big></th>
</tr>
<tr>
<!-- Wiki Documentation: Links -->
<td width="50%" valign="top">
* [http://www.ncl.ucar.edu/ NCL main page]
* [http://www.ncl.ucar.edu/Applications/ NCL applications]
* [http://www.ncl.ucar.edu/Document/ NCL documentation]
* [http://www.ncl.ucar.edu/Support/email_lists.shtml Sign up for NCL-Talk email list]
* [[NCL_tools_for_GEOS-Chem|NCL4GC: NCL tools for GEOS-Chem]]
</td>
<td width="50%" valign="top">
* [[Sandbox]]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [http://meta.wikimedia.org/wiki/Help:Contents MediaWiki User's Guide]
* [http://meta.wikimedia.org/wiki/Help:Wikitext Examples of Wiki markup text]
* [http://meta.wikimedia.org/wiki/Help:Reference_card One-page editing reference card]
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration Settings list]
* [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
</td>
</tr>
</table>

Latest revision as of 19:10, 3 October 2024

Species added

Species added between versions 14.5.0-alpha.5 and 14.5.0-alpha.9:

Name Formula Fullname Advected Dry deposited Gas Photolyzed Wet deposited
ACO3 C3H3O3 Peroxyacetyl radical for APAN X
ACR C3H4O Acrolein X X X X
ACRO2 C3H5O4 Peroxy radical from ACR X
ALK7 C7H16 Lumped >= C6 Alkanes X X
APAN C3H3NO5 Peroxyacryloyl nitrate X X X X X
APINN C10H17NO4 1st gen organic nitrate from APIN X X X X X
APINO2 C10H17O3 Peroxy radical from APIN X
APINP C10H18O3 Hydroperoxide from APIN X X X X
AROMCHO C5H6O4 ACCOMECHO from MCM X X X X
AROMCO3 C5H5O6 Lumped aromatic peroxyacetyl radical X
AROMPN C5H5NO8 Lumped PN from aromatics X X X X X
BPINN C10H17NO4 Saturated 1st gen BPIN organic nitrate X X X X X
BPINO C9H14O Ketone from BPIN X X X X
BPINO2 C10H17O3 Peroxy radical from BPIN X
BPINON C9H13NO4 Saturated 2nd gen BPIN organic nitrate X X X X X
BPINOO2 C10H17O3 2nd-gen peroxy radical from BPIN X
BPINOOH C9H14O3 2nd-gen peroxide from BPIN X X X X
BPINP C10H18O3 Peroxide from BPIN X X X X
BUTN C4H7NO4 C4H6 alkyl nitrate X X X X
BUTO2 C4H7O3 peroxy radical from C4H6 X
C4H6 C4H6 1,3-butadiene X X
C96N C9H15NO4 Saturated 2nd gen monoterpene organic nitrate X X X X X
C96O2 C10H17O3 2nd-gen peroxy radical from APIN X
C96O2H C9H16O3 Peroxide from APIN 2nd gen X X X X
EBZ C8H10 Ethylbenzene X X
GCO3 HOCH2CO3 Peroxyacetyl radical for PHAN X
HACTA HOCH2CO2H Hydroxyacetic/glycolic acid X X X X
LIMAL C10H16O2 Aldehyde from limonene X X X X
LIMKB C10H16O3 2nd gen ketone from limonene X X X X
LIMKET C10H16O2 Ketone from limonene X X X X
LIMKO2 C10H17O3 2nd-gen peroxy radical from LIMO X
LIMN C10H17NO4 Saturated 1st gen limonene organic nitrate X X X X X
LIMNB C10H15NO4 Saturated 1st gen LIMO organic nitrate X X X X X
LIMO2H C10H18O3 Acid from LIMO X X X X
LIMO3 C10H17O3 Acylperoxy radical from LIMO X
LIMO3H C10H18O4 Peracid from LIMO X X X X
LIMPAN C10H17NO4 PAN from LIMO X X X X X
MEKCO3 C3H5O4 False X
MEKPN C3H5NO6 MEK peroxyacetyl nitrate X X X X X
MYRCO C10H18O3 Aldehyde or ketone from myrcene X X X X
PHAN C2H3NO6 Peroxyhydroxyacetic nitric anhydride X X X X X
PIN C10H17NO4 Saturated 1st gen monoterpene organic nitrate X X X X X
PINAL C10H16O2 Pinonaldehyde X X X X
PINO3 C10H17O3 Acylperoxy radical from APIN X
PINO3H C10H18O4 Pinonic peracid X X X X
PINONIC C10H18O3 Pinonic acid X X X X
PINPAN C10H17NO4 PAN from pinonaldehyde X X X X X
R7N1 C7H15NO5 Peroxy radical from R7N2 X
R7N2 RO2NO C7 Lumped alkyl nitrate X X X X X
R7O2 C7H15O2 Peroxy radical from ALK7 X
R7P C7H16O2 Peroxide from R7O2 X X X X X
RNO3 RO2NO Lumped aromatic nitrate X X X X X
STYR C8H8 Styrene X X
TLFUO2 C5H7O5 False X
TLFUONE C5H6O2 Aromatic furanones X X X X
TMB C8H10 Trimethylbenzenes X
ZRO2 C7H9O5 RO2 for making lumped aromatic nitrate X


Species removed

Species removed between versions 14.5.0-alpha.5 and 14.5.0-alpha.9:

Name Formula Fullname Advected Dry deposited Gas Photolyzed Wet deposited
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