Difference between revisions of "GEOS-Chem 12"
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[[GEOS-Chem model development priorities#12.0.0|GEOS-Chem 12.0.0]] is currently under development. It will be released in early August 2018, pending validation. | [[GEOS-Chem model development priorities#12.0.0|GEOS-Chem 12.0.0]] is currently under development. It will be released in early August 2018, pending validation. | ||
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== Current stable version == | == Current stable version == | ||
Revision as of 21:10, 2 August 2018
GEOS-Chem v11-02-final will also carry the designation GEOS-Chem 12.0.0. We are migrating to a purely numeric versioning system in order to adhere more closely to software development best practices. For a complete description of the new versioning system, please see our GEOS-Chem version numbering system wiki page.
Contents
- 1 Version history
- 2 Version in development
- 3 Current stable version
- 4 New data directories
- 5 Validation
- 6 Previous issues now resolved in GEOS-Chem 12
- 6.1 Bug fix for HEMCO soil NOx error with ifort 17
- 6.2 FlexChem bug fix: do not zero ACTA, EOH, HCOOH
- 6.3 Avoid double counting CEDS and GEIA NH3 biofuel emissions
- 6.4 Fix bug in ARCTAS_SHIP_SO2 scale factors
- 6.5 Fix issues in complexSOA and complexSOA_SVPOA restart files
- 6.6 Bug fix for reference time in netCDF diagnostic files
- 6.7 Bug fix for CH4 boundary conditions
- 6.8 Fixed typo in call to GAMMA_HOBr_AER
- 6.9 Bug fix for liquid water content in gckpp_HetRates.F90
- 6.10 Add PH2O2 to the default list of prod/loss families in the KPP mechanisms
- 6.11 Fixed typo that prevented PM2.5 from being archived to netCDF output
- 6.12 Add entries to HEMCO_Config.rc for SOAP and pFe in CEDS inventory
- 6.13 Remove duplicate C3HI spectrum in FJX_spec.dat and FJX_j2j.dat
- 7 Outstanding issues not yet resolved in GEOS-Chem 12
Version history
The table below shows the previous, current, and successive major GEOS-Chem versions:
| Previous major release | Current release candidate | Pending major release | Next stable version | Successive major release |
|---|---|---|---|---|
| GEOS-Chem v11-01-public | v11-02-release-candidate (aka v11-02-rc) |
GEOS-Chem 12.0.0 aka v11-02-final in the old version number system |
GEOS-Chem 12.1.0 | GEOS-Chem 13.0.0 |
| RELEASED 01 Feb 2017 | RELEASED 22 Jun 2018 | RELEASE TBD | RELEASE TBD | RELEASE TBD 2019 |
| GC v11-01 online manual | GC v11-02 benchmark history | GC 12 online manual | GC 12 benchmark history |
The sections below describe each GEOS-Chem feature version and GEOS-Chem patch version belonging to the GEOS-Chem 12 series. Each feature version carries the tag 12.Y.0, which indicates that the version will be (or has been) validated with a 1-month benchmark simulation (and one or more 1-year benchmark simulations if necessary). Each patch version carries the tag 12.Y.Z, which denotes that the version preserves backwards-compatibility with the prior feature version 12.Y.0. For more information, please see our GEOS-Chem version numbering system wiki page.
In the pipeline
Several GEOS-Chem updates have been proposed by the relevant Working Groups, but have not yet been assigned to a specific GEOS-Chem version. For a complete list of these updates, please visit our GEOS-Chem model development priorities wiki page.
Version in development
12.0.0
GEOS-Chem 12.0.0 is currently under development. It will be released in early August 2018, pending validation.
Current stable version
New data directories
The following HEMCO data directories have been added or updated for GEOS-Chem 12. You will have to download the directories relevant to your simulation.
| Inventory | What was added? | When added? | Directory |
|---|---|---|---|
| GFED4 biomass inventory | GFED4.1 data files for 2015 and 2016 have been added | 12.0.0 | HEMCO/GFED4/v2015-10/2015 HEMCO/GFED4/v2015-10/2016 |
--Bob Yantosca (talk) 20:02, 29 June 2018 (UTC)
Validation
In this section we provide information about the benchmarks and tests that we have done to validate GEOS-Chem v11-03.
1-month and 1-year benchmarks
For complete information about the benchmark simulations used to validate GEOS-Chem v11-03, please see our GEOS-Chem 12 benchmark history wiki page.
Unit tests for GEOS-Chem 12
We perform a full set of unit tests on GEOS-Chem on an almost daily basis. These tests ensure that each new feature being added does not break any existing functionality.
Here are the unit tests that we ran before submitting 1-month benchmark simulation for v11-03. Click on the links below to see the results from each set of unit tests:
| Unit test | Date |
|---|---|
| TBD |
Previous issues now resolved in GEOS-Chem 12
The following bugs and/or technical issues have been resolved in GEOS-Chem 12.
Bug fix for HEMCO soil NOx error with ifort 17
This fix will be included in GEOS-Chem 12.0.0.
For complete information about this issue and how it was resolved, please see this post on our Implementation of HEMCO in GEOS-Chem wiki page..
--Bob Yantosca (talk) 13:54, 27 June 2018 (UTC)
FlexChem bug fix: do not zero ACTA, EOH, HCOOH
This fix will be included in GEOS-Chem 12.0.0.
For complete information about this bug and how it was fixed, please see this post on our FlexChem wiki page.
--Bob Yantosca (talk) 14:42, 27 June 2018 (UTC)
Avoid double counting CEDS and GEIA NH3 biofuel emissions
This fix will be included GEOS-Chem 12.0.0.
Eloise Marais wrote:
If CEDS includes NH3 emissions, then this will be double counting. I recommend using CEDS, as GEIA is very out of date (1998 according to the HEMCO configuration file I have).
Daniel Jacob replied:
We should use the GEIA NH3 natural emission inventory (1° x 1° file from Eleanor Morris) but not the GEIA NH3 biofuel inventory.
UPDATE 29 Jun 2018:
We discovered that HEMCO's default behavior is to ignore the GEIA NH3 anthro and biofuel emissions if CEDS is turned on. This is shown in the HEMCO.log file when VERBOSE = 3:
Register_Base: Checking GEIA_NH3_ANTH HEMCO: Entering Get_targetID (hco_config_mod.F90) ( 4) Skip container GEIA_NH3_ANTH because of CEDS_NH3_WST . . . Register_Base: Checking GEIA_NH3_BIOF HEMCO: Entering Get_targetID (hco_config_mod.F90) ( 4) Skip container GEIA_NH3_BIOF because of CEDS_NH3_WST_Cat00002
But for the sake of clarity, we will modify the HEMCO_Config.rc files to explicitly request this behavior:
(((.not.CEDS.or.EDGARv43 # GEIA NH3 anthro (skip if CEDS or EDGARv43 is on) 0 GEIA_NH3_ANTH $ROOT/NH3/v2014-07/NH3_geos.4x5.nc NH3_ANTH 1990/1-12/1/0 C xy kg/m2/s NH3 - 1 1 # GEIA NH3 biofuel (skip if CEDS or EDGARv43 is on) (((BIOFUEL 0 GEIA_NH3_BIOF $ROOT/NH3/v2014-07/NH3_biofuel.geos.1x1.nc NH3_BIOFUEL 1998/1-12/1/0 C xy kg/m2/s NH3 - 2 1 )))BIOFUEL ))).not.CEDS.or.EDGARv43
--Bob Yantosca (talk) 21:02, 29 June 2018 (UTC)
Fix bug in ARCTAS_SHIP_SO2 scale factors
This fix will be included GEOS-Chem 12.0.0.
For a complete description of this issue and how it was resolved, please see this post on our Ship Emissions wiki page.
--Bob Yantosca (talk) 15:54, 3 July 2018 (UTC)
Fix issues in complexSOA and complexSOA_SVPOA restart files
This fix will be included GEOS-Chem 12.0.0.
Eloise Marais wrote:
I just wanted to draw your attention to a few issues with the restart files provided on the ftp site (http://ftp.as.harvard.edu/gcgrid/data/ExtData/SPC_RESTARTS/). The complexSOA and complexSOA_SVPOA restart files (4° x 5° and 2° x 2.5°) both have a species entry for IEPOX and also IEPOXD, IEPOXB, and IEPOXA, but should only have the latter 3. This is the same for RIP. The number of species in the 4° x 5° and 2° x 2.5° files for complexSOA is also different.
To fix these issues, we have generated new restart files for the complexSOA and complexSOA_SVPOA simulations. You can download these to your SPC_RESTARTS folder with the following commands:
wget "ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/SPC_RESTARTS/initial_GEOSChem_rst.2x25_complexSOA.nc" wget "ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/SPC_RESTARTS/initial_GEOSChem_rst.2x25_complexSOA_SVPOA.nc" wget "ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/SPC_RESTARTS/initial_GEOSChem_rst.4x5_complexSOA.nc" wget "ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/SPC_RESTARTS/initial_GEOSChem_rst.4x5_complexSOA_SVPOA.nc"
--Bob Yantosca (talk) 18:01, 5 July 2018 (UTC)
Bug fix for reference time in netCDF diagnostic files
This fix will be included GEOS-Chem 12.0.0.
Maria Zatko wrote:
For the sake of run time, we would like to run GEOS-Chem with the old (15/30 minute timesteps) instead of the recommended timesteps (10/20 minutes). I noticed that the output netcdf files have different timestamps depending on the timestep (e.g., 10/20 minutes, 15/30 minutes) used. For example, when 10/20 minute timesteps are used, the time units in the following netcdf output files range from 0 to 23 UTC:
GEOSChem3hrInst.SpeciesConcWithMet.20150701_0000z.nc4 (file size: 4.6 GB)
GEOSChem3hrInst.SpeciesConcWithMet.20150702_0000z.nc4 (file size: 5.3 GB)
time:units = "minutes since 2015-07-01 00:00:00 UTC"
When 15/30 minute timesteps are used, the time units in the following output files include hour 24:
GEOSChem3hrInst.SpeciesConcWithMet.20150701_0000z.nc4 (file size: 4.6 GB)
GEOSChem3hrInst.SpeciesConcWithMet.20150701_2400z.nc4 (file size: 5.3 GB)
GEOSChem3hrInst.SpeciesConcWithMet.20150702_2400z.nc4 (file size: 5.3 GB)
time:units = "minutes since 2015-07-01 24:00:00 UTC"
I wanted to check in to see if others have run into this issue as well.
Bob Yantosca replied:
This issue is caused by floating-point roundoff error in converting from the Julian date to the calendar date. I have created a more robust fix for this issue, which now computes the correct netCDF file reference time independent of the model "heartbeat" timestep.To apply the fix:
The fix will be standardized in the GEOS-Chem 12.0.0 release.
- Copy the patch file ftp://ftp.as.harvard.edu/pub/exchange/bmy/nc_ref_time_fix.txt to your computational server.
- Change to your GEOS-Chem v11-02 release candidate code directory and check out the "master" branch.
- Type: git am < nc_ref_time_fix.txt
--Bob Yantosca (talk) 15:10, 12 July 2018 (UTC)
Bug fix for CH4 boundary conditions
This fix will be included GEOS-Chem 12.0.0.
Lee Murray wrote:
I’ve been testing the release candidate, and believe that we need to change the default input.geos options for the Standard and Benchmark simulations in the unit tester to :
%%% EMISSIONS MENU %%% :
Turn on emissions? : T
HEMCO Input file : HEMCO_Config.rc
=> 1ppt MBL BRO Sim.? : F
Switches for UCX :---
=> Use CH4 emissions? : F
=> Turn on surface BCs :---
=> CH4? : F
=> OCS? : T
=> CFCs? : T
=> Cl species? : T
=> Br species? : F
=> N2O? : T
=> Set initial glob MRs:---
=> strat. H2O? : T
=> CFC emission year : 0
By default in the unit tester, => CH4 is still enabled. This appears to set up conflict between the older UCX surface layer and the newer HEMCO methane PBL boundary conditions, causing air to be a mix of preindustrial and present-day values (see below for Jul 1, 2013 surface methane in a benchmark run). Setting it to F and/or removing LCH4SBC causes the methane to behave as expected, i.e., being set by HEMCO in all simulations, with the expected spatial pattern. Also, we can slate Online CH4 chemistry? : T in the Chemistry Menu and Input_Opt%LCH4CHEM for future removal, as it no longer does anything.
--Melissa Sulprizio (talk) 18:16, 16 July 2018 (UTC)
Fixed typo in call to GAMMA_HOBr_AER
This fix will be included GEOS-Chem 12.0.0.
Xuan Wang wrote:
When looking back at the standard GC codes of v11-02d, I found a bug in the function HETHOBr_SS_JS (in module KPP/Standard/gckpp_HetRates.F90). When calling the gamma calculation, in v11-02d, around line 3514, we have:
CALL Gamma_HOBr_AER(rAer, denAir, 2, TK, clConc, brConc, &
hConc, GAM_HOBr, r_gp)
This will cause both HOBr+Cl- (X=1) and HOBr+Br- (X=2) on sea salt use the gamma of HOBr + Br- (X=2). It should be:
CALL Gamma_HOBr_AER(rAer, denAir, X, TK, clConc, brConc, &
hConc, GAM_HOBr, r_gp)
It looks like a typo which could lead to quite different result for halogen chemistry.
--Bob Yantosca (talk) 20:26, 17 July 2018 (UTC)
Bug fix for liquid water content in gckpp_HetRates.F90
This fix will be included GEOS-Chem 12.0.0.
Jiayue Huang wrote:
Qianjie Chen and I think that there is potential a bug in KPP/Standard/gckpp_HetRates.F90 for halogen chemistry in the model v11-02d/e/f.In the original code, we were using the grid-box average liquid water content, which likely underestimates the in-cloud Br- and Cl- concentration. So we think that we should change it to in-cloud liquid water content by dividing the cloud fraction. This results in increases the S(IV)+Br reaction in cloud, and thus reduces the BrO abundance, mainly in the 30-90N region.
This bug fix is to use cloud fraction when calculating liquid water content [cm3 H2O/cm3 air] in routine GET_HALIDE_CLDConc, which is used to calculate the in-cloud concentrations of Br- and Cl-.
--Bob Yantosca (talk) 15:48, 20 July 2018 (UTC)
Add PH2O2 to the default list of prod/loss families in the KPP mechanisms
This fix will be included GEOS-Chem 12.0.0.
The P(H2O2) field is required as input in the aerosol-only simulations. To simplify saving out new oxidant fields, we now include P(H2O2) by default in the prod/loss families so that it is saved out when users turn on the prod/loss diagnostic in either bpch or netCDF format.
--Bob Yantosca (talk) 16:16, 20 July 2018 (UTC)
Fixed typo that prevented PM2.5 from being archived to netCDF output
This fix will be included GEOS-Chem 12.0.0.
In routine Set_AerMass_Diagnostic of module GeosCore/diagnostics_mod.F90, there was a typo in the IF block where the PM2.5 diagnostic values get copied into State_Diag%PM25. The code in RED below:
IF ( Archive_BetaNO ) THEN
State_Diag%PM25(I,J,L) = ...etc...
needs to be replaced by the code in GREEN:
IF ( Archive_PM25 ) THEN
State_Diag%PM25(I,J,L) = ...etc...
--Bob Yantosca (talk) 20:33, 24 July 2018 (UTC)
Add entries to HEMCO_Config.rc for SOAP and pFe in CEDS inventory
This fix will be included GEOS-Chem 12.0.0.
The CEDS emissions entries in HEMCO_Config.rc were missing for species SOAP and pFe. To fix this, add the following lines in GREEN:
0 CEDS_CO_AGR $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc CO_agr 1950-2014/1-12/1/0 C xy kg/m2/s CO 26 1/2/12 5 0 CEDS_SOAP_AGR - - - - - - SOAP 26/280 1/2/12 5 0 CEDS_CO_ENE $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc CO_ene 1950-2014/1-12/1/0 C xy kg/m2/s CO 26 1/2/12 5 0 CEDS_SOAP_ENE - - - - - - SOAP 26/280 1/2/12 5 0 CEDS_CO_IND $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc CO_ind 1950-2014/1-12/1/0 C xy kg/m2/s CO 26 1/2/12 5 0 CEDS_SOAP_IND - - - - - - SOAP 26/280 1/2/12 5 0 CEDS_CO_TRA $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc CO_tra 1950-2014/1-12/1/0 C xy kg/m2/s CO 26 1/2/12 5 0 CEDS_SOAP_TRA - - - - - - SOAP 26/280 1/2/12 5 0 CEDS_CO_SLV $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc CO_slv 1950-2014/1-12/1/0 C xy kg/m2/s CO 26 1/2/12 5 0 CEDS_SOAP_SLV - - - - - - SOAP 26/280 1/2/12 5 0 CEDS_CO_WST $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc CO_wst 1950-2014/1-12/1/0 C xy kg/m2/s CO 26 1/2/12 5 0 CEDS_SOAP_WST - - - - - - SOAP 26/280 1/2/12 5 0 CEDS_SO2_AGR $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc SO2_agr 1950-2014/1-12/1/0 C xy kg/m2/s SO2 - 1/2/12 5 0 CEDS_SO4_AGR - - - - - - SO4 63 1/2/12 5 0 CEDS_pFe_AGR - - - - - - pFe 66 1/2/12 5 0 CEDS_SO2_ENE $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc SO2_ene 1950-2014/1-12/1/0 C xy kg/m2/s SO2 - 1/2/12 5 0 CEDS_SO4_ENE - - - - - - SO4 63 1/2/12 5 0 CEDS_pFe_ENE - - - - - - pFe 66 1/2/12 5 0 CEDS_SO2_IND $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc SO2_ind 1950-2014/1-12/1/0 C xy kg/m2/s SO2 - 1/2/12 5 0 CEDS_SO4_IND - - - - - - SO4 63 1/2/12 5 0 CEDS_pFe_IND - - - - - - pFe 66 1/2/12 5 0 CEDS_SO2_TRA $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc SO2_tra 1950-2014/1-12/1/0 C xy kg/m2/s SO2 - 1/2/12 5 0 CEDS_SO4_TRA - - - - - - SO4 63 1/2/12 5 0 CEDS_pFe_TRA - - - - - - pFe 66 1/2/12 5 0 CEDS_SO2_SLV $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc SO2_slv 1950-2014/1-12/1/0 C xy kg/m2/s SO2 - 1/2/12 5 0 CEDS_SO4_SLV - - - - - - SO4 63 1/2/12 5 0 CEDS_pFe_SLV - - - - - - pFe 66 1/2/12 5 0 CEDS_SO2_WST $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc SO2_wst 1950-2014/1-12/1/0 C xy kg/m2/s SO2 - 1/2/12 5 0 CEDS_SO4_WST - - - - - - SO4 63 1/2/12 5 0 CEDS_pFe_WST - - - - - - pFe 66 1/2/12 5
--Melissa Sulprizio (talk) 16:07, 27 July 2018 (UTC)
Remove duplicate C3HI spectrum in FJX_spec.dat and FJX_j2j.dat
This fix will be included GEOS-Chem 12.0.0.
Tomas Sherwen wrote:
- I've just found that both FJX_spec.dat the redundant CH3I spectrum and the new spectrum are both present in FJX_spec.dat and FJX_j2j.dat (in v12.0.0). This will have been due to the spectrum in my branch being under the species alias of "CH3IT" to preserve (and ignore) the use of "CH3I" in the namespace of the code for the existing methyl iodide simulation when the iodine simulation was developed. The "CH3IT" variables were replaced "CH3I" in the v11-1-Patches branches with halogen chemistry provided to GCST, but the existing methyl iodide simulation variable was not removed. There are no double ups in the KPP mechanism itself.
- Please remove lines 276-281 in FJX_spec.dat (copied below).
"
CH3I 243 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 J10
3.958E-20 4.769E-20 8.257E-19 2.154E-19 7.349E-20 3.351E-20
1.034E-20 4.435E-21 2.272E-21 4.393E-22 4.052E-24 0.000E+00
CH3I 300 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 J10
3.958E-20 4.769E-20 8.376E-19 2.438E-19 9.355E-20 4.680E-20
1.529E-20 6.532E-21 3.328E-21 6.783E-22 1.038E-23 0.000E+00
"
- Please also remove the line 124 in FJX_j2j.dat (copied below).
"
123 CH3I PHOTON I PRODUCTS 1.000 /CH3I /
"
--Melissa Sulprizio (talk) 17:44, 27 July 2018 (UTC)
Outstanding issues not yet resolved in GEOS-Chem 12
The following known issues are slated to be fixed in GEOS-Chem 12.
