Important new structural developments in GEOS-Chem v11

Transcription

1 Important new structural developments in GEOS-Chem v11 Bob Yantosca Senior Software Engineer GEOS-Chem Support Team Jacob Group Meeting 10 Aug 2016 with: Melissa, Matt, Lizzie, Mike

2 Table of Contents Motivation for structural updates Addition of GEOS-Chem Species Database Removal of tracerid_mod.f Removal of STT and State_Chm%TRACERS Removal of family tracers New P/L diagnostics Mike, Melissa

3 Motivation for structural updates FlexChem will allow us to define any chemical mechanism with whatever species you want cf. Mike Long's last group meeting Uses KPP instead of SMVGEAR Much easier to add new species, etc. But: to be 100% flexible, we can no longer assume that any mechanism will have a particular species

4 Motivation for structural updates Before FlexChem could be fully integrated, we had to remove/replace several areas of legacy code In short, wherever species information was hardwired tracerid_mod.f wetscav_mod.f drydep_mod.f Etc.

5 Motivation for structural updates Physical constants had multiple definitions in different locations throughout GC p was defined with different #'s of decimal places Lizzie fixed these! Now stored Headers/physconstants.F Formerly known as CMN_GCTM_mod.F

6 Physical parameter updates by Lizzie Lundgren

7 Motivation for structural updates There were also duplicate definitions of species properties in multiple locations Molecular weights are read from input.geos These were also hardcoded in drydep_mod.f Bob fixed these! Now incorporated into the GC species database

8 Resolving duplicate molecular weight definitions by Bob Yantosca

9 GEOS-Chem Species Database Was introduced into v11-01e Is a one-stop shop for important physical parameters and other relevant species info To remove duplication of parameters Has allowed us to simplify code structure and remove hardwiring

10 GEOS-Chem Species Database Is a vector of derived-type objects, wholly contained in the State_Chm object Each element of the species database: Is itself an object of type SPECIES Which contains many sub-fields relevant to a particular GC species, including Indices and inquiry variables (i.e. is it advected?) Molecular weights and Henry's law constants Wetdep, drydep, aerosol, and other relevant parameters

11 A DERIVED TYPE is like the blueprint for a house or building. Each room in the blueprint specifies a different type of variable (e.g. either scalars or arrays of integer, floating-point, characters, etc.) An OBJECT is a variable that is built to the specifications of a DERIVED TYPE. It is like a house that is built according to a specific blueprint. A VECTOR OF OBJECTS is like a row of identical houses, all built from the same blueprint. The GEOS-Chem Species Database is this type of data structure.

12 GEOS-Chem Species Database

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14 Indices Names Inquiry

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20 Adding new species To add a new species, add the relevant information into GEOS-Chem module Headers/species_database_mod.F90

21 Adding new species There are several options you can specify when you add a new species: Gas or aerosol? Is it advected? Is it dry-deposited? Is it wet-deposited? Is it carried in moles of carbon?

22 Using mapping arrays to find species

23 Using mapping arrays to find species

24 Using mapping arrays to find species Replaces the following variables: DEPNAME NDVZIND NTRAIND Input_Opt%DEPNAME Input_Opt%NDVZIND Input_Opt%NTRAIND

25 Using mapping arrays to find species Replaces the following functions: GET_WETDEP_IDWETD GET_WETDEP_NSOL GET_ISOL

26 Using mapping arrays to find species

27 Reduction of infrastructure The GEOS-Chem Species Database has allowed us to remove species-specific hardwiring in several different modules Example: Wet deposition module Subroutine: COMPUTE_F Returns the fraction of soluble species scavenged out of the column in convective uprafts

28 An entry in the large IF block located in GC v10 routine COMPUTE_F (in module wetscav_mod.f)

29 Another entry in the large IF block in v10 COMPUTE_F

30 Yet another entry in the large IF block in v10 COMPUTE_F

31 Even yet another entry in the large IF block in v10 COMPUTE_F. All of these lines of code for just 4 species!!!

32 Reduction of infrastructure What did we notice? Computations for a given species were handled in hardwired species-specific IF blocks Using the IDTxxxx tracer flags from tracerid_mod.f Similar blocks of code were repeated several times The only differences were the hardwired number values used for each species Can we do better?

33 With the species database we can reduce all of those of the entries in the IF statement to a single entry. The same computations are done in the Compute_Ki function, which is called for all gas-phase soluble species.

34 Within the routine Compute_Ki, all species-specific values are obtained for the species database. This eliminates us having to add species-specific hardwiring deep into the wetdeposition code.

35 Reduction of infrastructure Before species database: (v10-01) wetscav_mod.f: 9236 LOC (lines of code) drydep_mod.f: 5925 LOC After species database (v11-01e) wetscav_mod.f: 6193 LOC drydep_mod.f: 4370 LOC

36 Removal of tracerid_mod.f Prior to GC v11-01, tracer ID flags were hardwired in tracerid_mod.f A separate set of chemical species flags were also hardwired in tracerid_mod.f These bore no relation to the indexing used by the GC Species Database and by FlexChem/KPP So they had to go!

37 In routine INIT_TRACERID (located in tracerid_mod.f ): There was a big CASE statement where each of the tracer ID flags (IDTNO, IDTO3, IDTCO,..) were defined. Over the years, this code structure became big and unwieldy. We focused on removing this during the recent Code-A-Thon.

38 Also in INIT_TRACERID: Chemical species ID's (corresponding to the ordering used in the SMVGEAR arrays) were defined separately from the tracer ID flags. We focused on removing these during the recent Code-A-Thon.

39 New method: function Ind_() This function returns the species index that is consistent with the ordering in the GEOS-Chem species database. This is also consistent with the chemical species ordering for FlexChem.

40 NOTE: In v11-01, you will be able to use the 'A' option to return the advected species id, namely: AdvectId = Ind_( 'HNO3', 'A' )

41 The id_*variables are now locally defined in the various modules where they are used. For efficiency, we initialize the id_* flags during GEOS-Chem initialization.

42 Removal of State_Chm%TRACERS The State_Chm object has two big 4-D arrays. TRACERS holds the advected tracers in units of v/v. SPECIES holds the concentrations of chemical species in molec/cm3. This is duplicate storage!!

43 Removal of State_Chm%TRACERS SMVGEAR used to require a separate array for chemical species, called CSPEC CSPEC had dimensions IIPAR*JJPAR*LLPAR Vector ordering, no longer efficient Data was copied: State_Chm%Species <=> CSPEC With SMVGEAR gone, there is no reason to keep TRACERS and SPECIES as separate fields We are keeping SPECIES, removing TRACERS Unit conversions can be applied to SPECIES as needed

44 Removal of State_Chm%TRACERS We are replacing all instances of State_Chm%Tracers(I,J,L,N) With: State_Chm%Species(I,J,L,N)

45 Removal of State_Chm%TRACERS We are replacing all instances of STT => State_Chm%Tracers STT(I,J,L,N) =... With: Spc => State_Chm%Species Spc(I,J,L,N) =...

46 Removal of State_Chm%TRACERS This has been a slow process We added temporary arrays to copy data from State_Chm%TRACERS to State_Chm%SPECIES in several routines in an incremental fashion Then we removed references to State_Chm%TRACERS in these routines Validated with difference tests and unit tests

47 Removal of family tracers NOx and Ox were removed in v9-02 But Fabien's isoprene mechanism added families: ISOPN = ISOPND + ISOPNB MVKN = MACRN + MVKN Also the UCX mechanism added families: CFCX = CFC113 + CFC114 + CFC115 HCFCX = HCFC22 + HCFC141b + HCFC142b

48 Removal of family tracers FlexChem/KPP cannot handle family tracers It is set up to solve for single species You can combine species together in post-processing Melissa has removed these final family tracers from GEOS-Chem v11-01g. This has also removed many kludges from dry deposition, diagnostics, restart file I/O, etc.

49 New P/L diagnostic No P/L diagnostic in the current KPP in GC This is a serious setback Mike has modified the internals of the KPP code to add this P/L capability back in Melissa is connecting this to the GC diagnostic output stream: bpch (for now) and netcdf

50 New P/L diagnostic For now, the new P/L diagnostic, it will compute P/L for all species in the KPP mechanism This adds some computational overhead We will work on a more flexible interface later Goal: for users to select which P/L quantities they need This may have to wait until v12

51 Thank you!