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| − | == Overview ==
| + | * [https://kpp.readthedocs.io <tt>kpp.readthedocs.io</tt>]: User manual for The Kinetic Preprocessor (KPP) |
| − | | + | * [https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/using-kpp-with-gc.html '''Update chemical mechanisms with KPP''' at <tt>geos-chem.readthedocs.io</tt>] |
| − | The clean and flexible reimplementation of the Kinetic PreProcessor package (aka KPP)—known as '''FlexChem'''—is nearing full integration into GEOS-Chem. Most of the remaining FlexChem development work will focus on replacing legacy infrastructure—which prevents GEOS-Chem from operating efficiently in high-performance computing (HPC) environments—with newer, more efficient algorithms.
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| − | More information will be posted here soon!
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| − | --[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:58, 19 May 2016 (UTC)
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| − | == Milestones ==
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| − | The following table shows several milestones that were achieved in the FlexChem implementation, development, as well as ongoing development tasks.
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| − | {| border=1 cellspacing=0 cellpadding=5
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| − | !width="600px"|Task
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| − | !width="150px"|Developer
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| − | !width="200px"|Status
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| − | |Added FlexChem into v11-01c.
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| − | |Mike Long
| + | |
| − | |Completed 14 Dec 2015
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| − | |-valign="top"
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| − | |Enabled the “tropchem” mechanism.
| + | |
| − | |Mike Long
| + | |
| − | |Completed 14 Dec 2015
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| − | |-valign="top"
| + | |
| − | |Restored the OH and HO2 diagnostics (ND43) \
| + | |
| − | |Melissa Sulprizio
| + | |
| − | |Completed 18 Dec 2015
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| − | |-valign="top"
| + | |
| − | |Removed CSPEC array and replaced with State_Chm%Species
| + | |
| − | |Melissa Sulprizio
| + | |
| − | |Completed 22 Dec 2015
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| − | |-valign="top"
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| − | |Enabled a temporary workaround for family tracers (ISOPN, MMN)
| + | |
| − | |Mike Long
| + | |
| − | |Completed 25 Jan 2016
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| − | |Enabled FAST-JX photochemistry
| + | |
| − | |Mike Long
| + | |
| − | |Completed 25 Jan 2016
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| − | |-valign="top"
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| − | |Enabled the "benchmark" chemistry mechanism
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| − | |Melissa Sulprizio
| + | |
| − | |Completed 29 Jan 2016
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| − | |-valign="top"
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| − | |Fixed HBr and HOBr hetchem rates for the "tropchem" mechanism
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| − | |Melissa Sulprizio
| + | |
| − | |Completed 04 Feb 2016
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| − | |Fixed unit conversions for heterogeneous chemistry
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| − | |Mike Long
| + | |
| − | |Completed 18 Feb 2016
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| − | |Restored the broken J-value diagnostic (ND22)
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| − | |Melissa Sulprizio
| + | |
| − | |Completed 15 Mar 2016
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| − | |Parallelized the main KPP driver loop; fixed other minor issues
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| − | |Bob Yantosca
| + | |
| − | |Completed 30 Mar 2016
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| − | |Enabled the SOA and SOA-SVPOA mechanisms
| + | |
| − | |Lizzie Lundgren
| + | |
| − | |Completed 01 Apr 2016
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| − | |-valign="top"
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| − | |Added more parallelization fixes
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| − | |Bob Yantosca
| + | |
| − | |Completed 18 Apr 2016
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| − | |-valign="top"
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| − | |Merged FlexChem with v11-01f
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| − | |Melissa Sulprizio
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| − | |Completed 20 Apr 2016
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| − | |-valign="top"
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| − | |Added KPP repository to Bitbucket (https://bitbucket.org/gcst/kpp)
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| − | |Mike Long
| + | |
| − | |Completed 19 Apr 2016
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| − | |Created new gckpp* files from the updated KPP solver package
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| − | |Melissa Sulprizio
| + | |
| − | |Completed 22 Apr 2016
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| − | |-valign="top"
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| − | |Enabled the UCX mechanism
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| − | |Melissa Sulprizio
| + | |
| − | |Completed 26 Apr 2016
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| − | |Introduced a prod/loss diagnostic into the KPP solver package
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| − | |Mike Long
| + | |
| − | |Completed 29 Apr 2016
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| − | | + | |
| − | |-valign="top"
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| − | |Fixed various other bugs and cleaned up some leftover things
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| − | |Melissa Sulprizio
| + | |
| − | |Completed 04 May 2016
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| − | | + | |
| − | |-valign="top"
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| − | |Completed unit tests and 1-month benchmarks for the tropchem, benchmark, UCX, SOA, and SOA-SVPOA simulations
| + | |
| − | |Melissa Sulprizio<br>Lizzie Lundgren
| + | |
| − | |Completed 05 May 2016
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| − | |Remove tracer indices of Rn, Pb, Be, Hg, and POPs simulations from tracerid_mod.F. (This paves the way for us to retire tracerid_mod.F.)
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| − | |Bob Yantosca
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| − | |Completed 02 May 2016
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| − | |-valign="top"
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| − | |Add a fast species name lookup algorithm
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| − | |Bob Yantosca
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| − | |Code is in place as of 04 May 2016, but has not been implemented throughout GEOS-Chem yet.
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| − | |-valign="top"
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| − | |Store the unique list of GEOS-Chem species in the GEOS-Chem species database object. (In other words, we combine the list of
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| − | advected tracers with the list of KPP chemical species and remove duplicate entries).
| + | |
| − | |Bob Yantosca
| + | |
| − | |Completed 09 May 2016
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| − | |-valign="top"
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| − | |Store the indices of each species in the KPP chemical reaction matrix in the GEOS-Chem species database object.
| + | |
| − | |Bob Yantosca
| + | |
| − | |Completed 09 May 2016
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| − | |Remove family tracer fields of the <code>Input_Opt</code> object, namely : <code>TRACER_N_CONST, TRACER_CONST, TRACER_COEFF, ID_EMITTED</code>
| + | |
| − | |Bob Yantoscao
| + | |
| − | |Completed 19 May 2016
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| − | |-valign="top"
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| − | |Create mapping vectors in the <code>State_Chm</code> object to store the ID numbers of species that are advected, dry-deposited, wet-deposited, and/or included in the KPP chemical mechanism
| + | |
| − | |Bob Yantosca
| + | |
| − | |Completed 19 May 2016
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| − | | + | |
| − | |-valign="top"
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| − | |Remove all 1-D loop indexing variables (JLOOP, KLOOP, KTLOOP, JLOP, IXSAVE, IYSAVE, IZSAVE) that were used by SMVGEAR
| + | |
| − | |Melissa Sulprizio
| + | |
| − | |Completed 19 May 2016
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| − | | + | |
| − | |-valign="top"
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| − | |Removal of SMVGEAR input files (globchem.dat, mglob.dat) and associated subroutines (readchem.F, reader.F)
| + | |
| − | |Melissa Sulprizio
| + | |
| − | |In progress
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| − | | + | |
| − | |-valign="top"
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| − | |Removal of <code>Input_Opt%TCVV</code> and <code>Input_Opt%XNUMOL</code> fields
| + | |
| − | |Lizzie Lundgren
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| − | |In progress
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| − | | + | |
| − | |-valign="top"
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| − | |Store all species concentrations in State_Chm%Species (thus making State_Chm%Tracers redundant)
| + | |
| − | |GCST
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| − | |In progress
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| − | | + | |
| − | |-valign="top"
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| − | |Remove tracerid_mod.F and related tracer ID flags (<code>IDTxxxx</code>, <code>IDxxxx</code>) from GEOS-Chem.
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| − | |GCST
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| − | |To be done at the Code-a-Thon
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| − | | + | |
| − | |-valign="top"
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| − | |Rely totally on the GEOS-Chem species database for looking up a species index from its name.
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| − | |GCST
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| − | |Imminent
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| − | | + | |
| − | |-valign="top"
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| − | |Update the GEOS-Chem Makefiles so that a fresh version of KPP will be built (using a custom chemical mechanism that you specify) each time GEOS-Chem is compiled.
| + | |
| − | |GCST
| + | |
| − | |TBD
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| − | | + | |
| − | |-valign="top"
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| − | |Attach the new KPP prod/loss diagnostics to GEOS-Chem Chem’s netCDF diagnostic output capability.
| + | |
| − | |GCST
| + | |
| − | |TBD
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| − | | + | |
| − | |-valign="top"
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| − | |Remove the remaining family tracers (ISOPN, MMN). Henceforth, FlexChem will only work with individual species.
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| − | |GCST
| + | |
| − | |TBD
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| − | | + | |
| − | |-valign="top"
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| − | |Validate FlexChem with additional debugging, unit testing, and benchmarking
| + | |
| − | |TBD
| + | |
| − | |TBD
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| − | | + | |
| − | |-valign="top"
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| − | |Update GEOS-Chem documentation and user manual for v11-01
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| − | |TBD
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| − | |TBD
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| − | | + | |
| − | |}
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| − | | + | |
| − | --[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:17, 19 May 2016 (UTC)
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