Difference between revisions of "FlexChem"

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On this page we provide information about the FlexChem chemical solver, which was introduced in [[GEOS-Chem v11-01#v11-01g|GEOS-Chem v11-01g]].
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This content has been migrated to:
  
== Overview ==
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* [https://kpp.readthedocs.io <tt>kpp.readthedocs.io</tt>]: User manual for The Kinetic Preprocessor (KPP)
 
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* [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)&mdash;known as '''FlexChem'''&mdash;is nearing full integration into GEOS-Chem. Most of the remaining FlexChem development work will focus on replacing legacy infrastructure&mdash;which prevents GEOS-Chem from operating efficiently in high-performance computing (HPC) environments&mdash;with newer, more efficient algorithms.
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Check back soon for the latest information!
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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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|-valign="top" bgcolor="#CCCCCC"
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!width="600px"|Task
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!width="150px"|Developer
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!width="250px"|Status
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|-valign="top"
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|Add FlexChem into v11-01c
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|Mike Long
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|Completed 14 Dec 2015
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|-valign="top"
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|Enable the “tropchem” mechanism
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|Mike Long
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|Completed 14 Dec 2015
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|-valign="top"
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|Restore the OH and HO2 diagnostics (ND43)
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|Melissa Sulprizio
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|Completed 18 Dec 2015
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|-valign="top"
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|Remove CSPEC array and replaced with State_Chm%Species
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|Melissa Sulprizio
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|Completed 22 Dec 2015
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|-valign="top"
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|Enable a temporary workaround for family tracers (ISOPN, MMN)
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|Mike Long
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|Completed 25 Jan 2016
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|-valign="top"
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|Enable FAST-JX photochemistry
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|Mike Long
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|Completed 25 Jan 2016
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|-valign="top"
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|Enable the "benchmark" chemistry mechanism
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|Melissa Sulprizio
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|Completed 29 Jan 2016
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|-valign="top"
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|Fix HBr and HOBr hetchem rates for the "tropchem" mechanism
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|Melissa Sulprizio
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|Completed 04 Feb 2016
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|-valign="top"
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|Fix unit conversions for heterogeneous chemistry
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|Mike Long
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|Completed 18 Feb 2016
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|-valign="top"
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|Restore the broken J-value diagnostic (ND22)
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|Melissa Sulprizio
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|Completed 15 Mar 2016
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|-valign="top"
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|Parallelize the main KPP driver loop; fixed other minor issues
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|Bob Yantosca
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|Completed 30 Mar 2016
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|-valign="top"
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|Enable the SOA and SOA-SVPOA mechanisms
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|Lizzie Lundgren
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|Completed 01 Apr 2016
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|-valign="top"
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|Add more parallelization fixes
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|Bob Yantosca
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|Completed 18 Apr 2016
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|-valign="top"
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|Merge 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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|Add KPP repository to Bitbucket (https://bitbucket.org/gcst/kpp)
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|Mike Long
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|Completed 19 Apr 2016
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|-valign="top"
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|Create new gckpp* files from the updated KPP solver package
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|Melissa Sulprizio
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|Completed 22 Apr 2016
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|-valign="top"
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|Enable the UCX mechanism
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|Melissa Sulprizio
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|Completed 26 Apr 2016
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|-valign="top"
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|Introduce a new prod/loss diagnostic into the KPP solver package
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|Mike Long
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|Completed 29 Apr 2016
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|-valign="top"
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|Fix various other bugs and cleaned up some leftover things
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|Melissa Sulprizio
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|Completed 04 May 2016
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|-valign="top"
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|Complete unit tests and 1-month benchmarks for the tropchem, benchmark, UCX, SOA, and SOA-SVPOA simulations
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|Melissa Sulprizio<br>Lizzie Lundgren
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|Completed 05 May 2016
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|-valign="top"
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|Remove tracer indices of Rn, Pb, Be, Hg, and POPs simulations from <code>tracerid_mod.F</code>. (This paves the way for us to retire <code>tracerid_mod.F</code>.)
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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 advected tracers with the list of KPP chemical species and remove duplicate entries).
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|Bob Yantosca
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|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.
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|Bob Yantosca
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|Completed 09 May 2016
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|-valign="top"
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|Merge FlexChem with other v11-01g updates
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|Bob Yantosca
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|Completed 17 May 2016
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|-valign="top"
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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>.  These were only used by SMVGEAR and are now obsolete.
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|Bob Yantosca
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|Completed 18 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
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|Bob Yantosca
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|Completed 19 May 2016
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|-valign="top"
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|Remove all 1-D loop indexing variables (<code>JLOOP, KLOOP, KTLOOP, JLOP, IXSAVE, IYSAVE, IZSAVE</code>) that were used by SMVGEAR
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|Melissa Sulprizio
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|Completed 19 May 2016
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|-valign="top"
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|Remove SMVGEAR input files (<code>globchem.dat, mglob.dat</code>) and associated subroutines (<code>readchem.F, reader.F</code>)
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|Melissa Sulprizio
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|Completed 30 Jun 2016
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|-valign="top"
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|Remove <code>tracerid_mod.F</code> and related tracer ID flags (<code>IDTxxxx</code>, <code>IDxxxx</code>) from GEOS-Chem.
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|GCST
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|
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*Completed 24 Jun 2016
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*Validated 27 Jun 2016
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|-valign="top"
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|Use the GEOS-Chem species database to retrieve species index from species name
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|GCST
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*Completed 24 Jun 2016
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*Validated 27 Jun 2016
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|-valign="top"
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|Remove tracers from restart files and read/write restart file species only
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|Lizzie Lundgren
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*Completed 12 Jul 2016
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|-valign="top"
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|Create unit conversion routines for species that mimic existing routines for tracers or convert to/from molecules/cm3
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|Lizzie Lundgren
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*Completed 25 Jul 2016
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|-valign="top"
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|Add State_Chm variable to track species units throughout GEOS-Chem (State_Chm%Spc_Units)
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|Lizzie Lundgren
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*Completed 25 Jul 2016
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|-valign="top"
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|Remove the remaining family tracers (ISOPN, MMN, CFCX, HCFCX). Henceforth,  FlexChem will only work with individual species.
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|Melissa Sulprizio
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*Completed 28 Jul 2016
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*Validated 01 Aug 2016
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|-valign="top"
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|Move the non-advected species initial unit conversion of background values from init_flexchem (called during chemistry) to read_gc_restart (called during restart file read)
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|Lizzie Lundgren
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*Completed 4 Aug 2016
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|-valign="top"
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|Store species background concentrations values previously stored in globchem.dat in the species database
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|Lizzie Lundgren
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*Completed 11 Aug 2016
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|-valign="top"
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|Attach the new KPP prod/loss output to the GEOS-Chem prod/loss diagnostic
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|Melissa Sulprizio
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*Completed 11 Aug 2016
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*Validated 11 Aug 2016
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|-valign="top"
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|Remove <code>State_Chm%Tracers</code> and use species concentrations in <code>State_Chm%Species</code> instead
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|GCST
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|In progress
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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.
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|GCST
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|TBD
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|-valign="top"
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|Validate FlexChem with additional debugging, unit testing, and benchmarking
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|GCST
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|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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|GCST
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|TBD
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|}
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--[[User:Lizzie Lundgren|Lizzie Lundgren]] ([[User talk:Lizzie Lundgren|talk]]) 21:41, 11 August 2016 (UTC)
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== Adding chemical mechanisms in FlexChem ==
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=== KPP source code ===
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The KPP source code for FlexChem is currently available as a Git repository on Bitbucket. It can be obtained using:
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git clone https://bitbucket.org/gcst/kpp
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Once you have KPP on your system, you will need to build it:
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cd kpp/kpp-2.2.3_01
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make clean
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make
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If the build completed successfully, you should see the executable <tt>kpp</tt> in the <tt>kpp/kpp-2.2.3_01/bin/</tt> directory. Next, add KPP to your PATH. For bash users, add the following lines the <tt>~/.bashrc</tt> file:
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export PATH=$PATH:/PATH_TO_KPP/KPP/kpp-2.2.3_01/bin/
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export KPP_HOME=/PATH_TO_KPP/KPP/kpp-2.2.3_01
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--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:18, 10 August 2016 (UTC)
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=== Building a custom chemical mechanism ===
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[[GEOS-Chem v11-01#v11-01g|GEOS-Chem v11-01g]] has five pre-built chemical mechanisms: standard, tropchem, SOA, SOA-SVPOA, and UCX. These mechanisms are described on our [[GEOS-Chem_chemistry_mechanisms#Mechanisms_in_GEOS-Chem_v10-01_and_later_versions|''GEOS-Chem chemistry mechanisms'' wiki page]].
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GEOS-Chem will eventually include the option to create a custom chemistry mechanism and automatically build that mechanism with KPP when GEOS-Chem is compiled. For now, users still need to build custom chemistry mechanisms manually. The [[#KPP source code|KPP Git repository]] includes the following files:
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  geos2kpp_parser.pl
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  gckpp.kpp
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  rename_f90.sh
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  copy_gckpp.sh
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These files can be used to build a custom chemistry mechanisms with KPP. Follow these steps:
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#The <tt>geos2kpp_parser.pl</tt> script can be used to create <tt>globchem.eqn</tt>, <tt>globchem.spc</tt>, and <tt>globchem.def</tt> files from a <tt>globchem.dat</tt> file. You may also choose to start from the preexisting <tt>globchem.eqn</tt>, <tt>globchem.spc</tt>, and <tt>globchem.def</tt> files found in the <tt>KPP</tt> subdirectories of the GEOS-Chem source code (e.g. <tt>Code.v11-01/KPP/Standard/</tt>).
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#If needed, edit <tt>globchem.eqn</tt> to add/modify reactions for your mechanism and edit <tt>globchem.spc</tt> to add/modify species to your mechanism. Put the final <tt>globchem.*</tt> files in the same directory as the <tt>gckpp.kpp</tt> file.
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#Execute KPP using <code>kpp gckpp.kpp</code>. This will create the necessary <tt>gckpp_*.f90</tt> files.
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#Run <code>rename_f90.sh</code> to rename <tt>gckpp_*.f90</tt> to <tt>gckpp_*.F90</tt>.
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#Open <tt>copy_gckpp.sh</tt> and modify the lines for <tt>codedir</tt>. Save and run <code>copy_gckpp.sh</code>. This will copy the <tt>gckpp_*.F90</tt> files to <tt>codedir/Custom</tt>.
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#Compile GEOS-Chem for the new mechanism by including <tt>CHEM=Custom</tt> in your make command.
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--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:18, 10 August 2016 (UTC)
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=== Production & loss diagnostic ===
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Mike Long implemented prod/loss structure parsing in the KPP source code. This option can be turned on by adding the line <tt>#FLUX on</tt> to the <tt>gckpp.kpp</tt> file. For example:
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  #INTEGRATOR rosenbrock
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  #LANGUAGE Fortran90
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  #DRIVER none
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  #HESSIAN off
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  #MEX off
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  #STOICMAT off
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  <span style="color:red">#FLUX on</span>
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  #INCLUDE globchem.spc
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  #INCLUDE globchem.eqn
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For the FLUX option to work properly, MEX and HESSIAN must be turned off as shown above.
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When changing any of the settings in <tt>gckpp.kpp</tt>, the chemistry mechanism will need to be rebuilt with KPP as [[#Building the chemical mechanism|described above]].
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The pre-built chemistry mechanisms (Standard, Tropchem, SOA, SOA-SVPOA, and UCX) were built with the FLUX option turned on. The prod/loss rates from KPP can be saved out in GEOS-Chem via the [http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#PLMenu ND65 diagnostic].
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--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:18, 10 August 2016 (UTC)
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==== Inefficiencies in prod/loss code ====
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The current implementation of the prod/loss diagnostic output in KPP is somewhat inefficient. The code is set up so that KPP calculates the prod/loss of ALL species, even though a user may only want prod/loss rates for a few species. This likely adds considerable memory overhead because KPP has <tt>NREAC</tt> additional species to track. Making this code more efficient is a task for future development.
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--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:18, 10 August 2016 (UTC)
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==== Comparing KPP and SMVGEAR prod/loss output ====
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During the implementation of FlexChem in [[GEOS-Chem v11-01#v11-01g|GEOS-Chem v11-01g]], KPP's new prod/loss diagnostics were validated against SMVGEAR's prod/loss diagnostics. We list the prod/loss rates [molec/cm3/s] for several families after a 20-minute run below:
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{| border=1 cellspacing=0 cellpadding=5
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|-bgcolor="#CCCCCC"
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!width="100px"|Family Name
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!width="100px"|v11-01f<br>(SMVGEAR)
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!width="100px"|v11-01g<br>(KPP)
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|-
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|POX
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|666.15
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|194722.60
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|-
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|LOX
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|15410.74
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|208939.00
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|-
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|PCO
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|5623.75
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|5610.81
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|-
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|LCO
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|9129.74
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|8771.62
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|-
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|PBrOx
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|5703.22
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|58242.10
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|-
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|PBry
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|2.04
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|74904.60
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|-
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|LBry
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|1.96E-04
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|74902.59
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|}
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The differences in the prod/loss rates returned by SMVGEAR versus KPP are large for most of the families. Examination of the prod/loss code revealed that SMVGEAR is missing many of the reactions that KPP is flagging for inclusion in the prod/loss rate calculations. For example, the reactions that KPP uses for calculating PBrOx in the [[NOx-Ox-HC-Aer-Br_chemistry_mechanism|tropchem mechanism]] are listed below:
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* HBr + OH --> RR240 + Br + H2O
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  2 BrO --> RR241 + 2 Br + O2
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  BrO + NO --> RR243 + Br + NO2
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* Br2 + OH --> RR245 + HOBr + Br
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  BrO + OH --> RR246 + Br + HO2
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* CHBr3 + OH --> RR255 + 3 Br
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* CH2Br2 + OH --> RR256 + 2 Br
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* CH3Br + OH --> RR257 + Br
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* Br2 --> RR382 + 2 Br
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  BrO --> RR383 + Br + O3
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* HOBr --> RR384 + Br + OH
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* BrNO3 --> RR385 + Br + NO3
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* BrNO2 --> RR387 + Br + NO2
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* CHBr3 --> RR388 + 3 Br
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  Br + O3 --> RR237 + BrO + O2
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  Br + NO3 --> RR247 + BrO + NO2
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* BrNO3 --> RR386 + BrO + NO2
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The starred reactions indicate reactions that SMVGEAR uses to compute PBrOx. KPP uses 17 total reactions for PBrOx, while SMVGEAR only uses 11 reactions. The number of reactions used in the prod/loss rate calculations for SMVGEAR and KPP (for the [[NOx-Ox-HC-Aer-Br_chemistry_mechanism|tropchem mechanism]]) are summarized below:
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{| border=1 cellspacing=0 cellpadding=5
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|-bgcolor="#CCCCCC"
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!width="100px"|Family Name
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!width="100px"|v11-01f<br>(SMVGEAR)
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!width="100px"|v11-01g<br>(KPP)
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|-
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|POX
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|92
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|163
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|-
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|LOX
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|45
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|100
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|-
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|PCO
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|57
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|57
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|-
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|LCO
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|7
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|7
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|-
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|PBrOx
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|11
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|17
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|-
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|PBry
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|4
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|34
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|-
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|LBry
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|0
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|30
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|}
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The KPP generally use many more reactions in the prod/loss calculations than SMVGEAR. This may explain the large differences in the prod/loss rates returned by KPP as compared to SMVGEAR.
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Note that SMVGEAR and KPP use the same number of reactions for calculating PCO and LCO (in fact, the reactions used are identical). The PCO and LCO rate values listed in the first table are also fairly similar between the SMVGEAR and KPP runs. This indicates that we can reasonably reproduce the old prod/loss rates from SMVGEAR when KPP uses the same reactions.
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--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:00, 11 August 2016 (UTC)
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== Validation ==
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TBD
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== Known issues ==
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TBD
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Latest revision as of 20:24, 4 August 2022

This content has been migrated to: