Difference between revisions of "GEOS-Chem 12"
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The following known issues are slated to be fixed in GEOS-Chem 12: | The following known issues are slated to be fixed in GEOS-Chem 12: | ||
+ | |||
+ | === Bug fix for HEMCO soil NOx error with ifort 17 === | ||
+ | |||
+ | <span style="color:darkorange">'''''This fix will be included in [[GEOS-Chem 12#12.0.0|GEOS-Chem 12.0.0]].'''''</span> | ||
+ | |||
+ | '''''[[User:Jaf|Jenny Fisher]] wrote:''''' | ||
+ | |||
+ | <blockqquote> | ||
+ | I am having a really bizarre HEMCO error running [[GEOS-Chem v11-02#v11-02f|GEOS-Chem v11-02f]] (with modifications to use the Australian nested grid, but nothing that would affect HEMCO), tropchem. | ||
+ | |||
+ | The following is appearing in my <tt>HEMCO.log</tt> file:</blockquote> | ||
+ | |||
+ | Use soil NOx emissions (extension module) | ||
+ | |||
+ | - NOx species : | ?(v;+^@^@^B^@^@^@^G^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@ -1 | ||
+ | - NOx scale factor : 1.000000 | ||
+ | - NOx scale field : none | ||
+ | - Use fertilizer NOx : T | ||
+ | - Fertilizer scale factor: 6.800000090152025E-003 | ||
+ | |||
+ | <blockquote>So soil NOx is not being defined properly. I traced this through the HEMCO code and discovered that the issue is arising in <tt>HCO_GetExtHcoID</tt> in <tt>HEMCO/Core/hco_state_mod.F90</tt>. I’ve printed virtually everything here, and all looks good until this loop:</blockquote> | ||
+ | |||
+ | ! Extract species information | ||
+ | DO I = 1, nSpc | ||
+ | SpcNames(I) = TRIM(SUBSTR(I)) | ||
+ | HcoIDs(I) = HCO_GetHcoID( TRIM(SpcNames(I)), HcoState ) | ||
+ | ENDDO | ||
+ | |||
+ | <blockquote>If I print <tt>SUBSTR(I)</tt> in that loop, all looks good – it prints NO as expected. However, if I print <tt>SpcNames(I)</tt> it comes up blank. I even tried as a test manually assigning <tt>SpcNames(1)</tt> to be NO by adding the following before the HcoIDs line:</tt></blockquote> | ||
+ | |||
+ | IF (ExtNr == 104) print*,'soil nox' | ||
+ | IF (ExtNr == 104) SpcNames(1) = 'NO' | ||
+ | print*,trim(spcnames(I)) | ||
+ | call flush(6) | ||
+ | |||
+ | <blockquote>My "soil nox" message gets printed, but <tt>SpcNames(I)</tt> still prints an empty string.</blockquote> | ||
+ | |||
+ | Note that none of the other species being read by HEMCO have any problem. I am compiling with <tt>DEBUG=yes BOUNDS=yes TRACEBACK=yes</tt>, and have tried two different versions of the ifort compiler (17.0.1 and 17.0.4) – all to no avail. | ||
+ | |||
+ | Do you have any idea what is going on here or how to fix it?? For now I am putting in a kludge to manually set <tt>Inst%IDTNO = 1</tt> in <tt>hcox_soilnox_mod.F90</tt> – but this is clearly not an appropriate solution.</blockquote> | ||
+ | |||
+ | --[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:04, 26 June 2018 (UTC) | ||
=== FlexChem bug fix: do not zero ACTA, EOH, HCOOH === | === FlexChem bug fix: do not zero ACTA, EOH, HCOOH === | ||
− | <span style="color:darkorange">'''''This fix will be included in GEOS-Chem 12.'''''</span> | + | <span style="color:darkorange">'''''This fix will be included in [[GEOS-Chem 12#12.0.0|GEOS-Chem 12.0.0]].'''''</span> |
'''''[[User:Katherine Travis|Katie Travis]] wrote:''''' | '''''[[User:Katherine Travis|Katie Travis]] wrote:''''' |
Revision as of 15:04, 26 June 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
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.
12.3.0
The items listed below are slated to be included in GEOS-Chem 12.3.0. This is a feature release which will be validated with a 1-month benchmark simulation.
Feature | Submitted by | Type | Status |
---|---|---|---|
Features affecting the full-chemistry simulation: | |||
Update ISORROPIA from v2.0 to v2.2, in order to remove persistent noise in output | Seb Eastham (Harvard) | Science |
|
Update MODIS LAI fields for 2005-2016 using Yuan et al. (2011) | Jenny Fisher (Wollongong) Barron Henderson (US EPA) |
Science |
|
Extend UCX into the mesosphere | Sebastian Eastham (MIT) | Science | |
OMI-based Volcanic emissions 2005-2012 | Cui Ge (U. Iowa) Jun Wang (U. Iowa) |
Science |
|
12.2.0
The items listed below are slated to be included in GEOS-Chem 12.2.0. This is a feature release which will be benchmarked with a 1-month benchmark simulation and a 1-year Rn-Pb-Be benchmark simulation.
Feature | Submitted by | Type | Status |
---|---|---|---|
Features NOT affecting the full-chemistry simulation: | |||
Common set of tracers in GEOS-Chem and GEOS | Transport WG GCST |
Benchmarking |
|
12.1.0
The items listed below are slated to be included in GEOS-Chem 12.1.0. This is a feature release which will be validated with a 1-month benchmark simulation.
Feature | Submitted by | Type | Status |
---|---|---|---|
Features affecting the full-chemistry simulation: | |||
FlexGrid: Use HEMCO to read met fields and enable nested simulations over any custom domains | Jiawei Zhuang (Harvard) Jintai Lin (PKU) |
Structural |
|
Anthropogenic PM2.5 dust source | Sajeev Philip (Dalhousie) | Science |
|
NetCDF Output Phase 3b: Updates to eliminate differences between single and multi-segmented GEOS-Chem runs | GCST Christoph Keller |
Bug Fix & Structural |
|
Features NOT affecting the full-chemistry simulation: | |||
Updated flux diagnostics | Chris Holmes (Florida State) GCST |
Structural/ Benchmarking |
12.0.0
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.
The following updates and fixes are slated to be added to GEOS-Chem 12.0.0 (aka v11-02-final). Many of these updates fix issues that were identified during the GEOS-Chem v11-02 "release candidate" testing period.
Feature | Submitted by | Type | Status |
---|---|---|---|
Features affecting the full-chemistry simulation: | |||
Grid offset bug fix in high-resolution MEGAN files at southern mid-latitudes | Jenny Fisher (Wollongong) Dylan Millet (UMN) |
Bug fix | New files received Run directory updates not yet applied |
Bug fix in FlexChem: do not zero out ACTA, EOH, HCOOH concentrations | Katie Holmes | Bug Fix | In progress |
Features NOT affecting the full-chemistry simulation: | |||
Bug fixes for v11-02 simulations using the RRTMG radiative transfer model | Chris Holmes (U. Florida) | Bug Fix | Implemented 26 Jun 2018 |
Now always declare the netCDF time variable with an unlimited dimension | Chris Holmes (U. Florida) | Structural | Implemented 26 Jun 2018 |
Bug fix for HEMCO soil NOx error with ifort 17 | Jenny Fisher (U. Wollongong) | Structural | In progress |
Make two-way nesting option compatible with GEOS-Chem v11-02 code | Yingying Yan (PKU) Jintai Lin (PKU) |
Bug Fix | Awaiting code from developer |
Bug fix for ARCTAS_SHIP in HEMCO_Config.rc file | Barron Henderson (EPA) | Bug Fix | A minor edit to HEMCO_Config.rc is necessary. This will likely change the benchmark results, so validation will be necessary. |
--Bob Yantosca (talk) 14:31, 21 June 2018 (UTC)
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 |
---|---|---|---|
TBD |
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 v11-03.
Outstanding issues not yet resolved in GEOS-Chem 12
The following known issues are slated to be fixed 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.
Jenny Fisher wrote:
<blockqquote> I am having a really bizarre HEMCO error running GEOS-Chem v11-02f (with modifications to use the Australian nested grid, but nothing that would affect HEMCO), tropchem.
The following is appearing in my HEMCO.log file:</blockquote>
Use soil NOx emissions (extension module)
- NOx species : | ?(v;+^@^@^B^@^@^@^G^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@ -1 - NOx scale factor : 1.000000 - NOx scale field : none - Use fertilizer NOx : T - Fertilizer scale factor: 6.800000090152025E-003
So soil NOx is not being defined properly. I traced this through the HEMCO code and discovered that the issue is arising in HCO_GetExtHcoID in HEMCO/Core/hco_state_mod.F90. I’ve printed virtually everything here, and all looks good until this loop:
! Extract species information DO I = 1, nSpc SpcNames(I) = TRIM(SUBSTR(I)) HcoIDs(I) = HCO_GetHcoID( TRIM(SpcNames(I)), HcoState ) ENDDO
If I print SUBSTR(I) in that loop, all looks good – it prints NO as expected. However, if I print SpcNames(I) it comes up blank. I even tried as a test manually assigning SpcNames(1) to be NO by adding the following before the HcoIDs line:</tt>
IF (ExtNr == 104) print*,'soil nox' IF (ExtNr == 104) SpcNames(1) = 'NO' print*,trim(spcnames(I)) call flush(6)
My "soil nox" message gets printed, but SpcNames(I) still prints an empty string.
Note that none of the other species being read by HEMCO have any problem. I am compiling with DEBUG=yes BOUNDS=yes TRACEBACK=yes, and have tried two different versions of the ifort compiler (17.0.1 and 17.0.4) – all to no avail.
Do you have any idea what is going on here or how to fix it?? For now I am putting in a kludge to manually set Inst%IDTNO = 1 in hcox_soilnox_mod.F90 – but this is clearly not an appropriate solution.</blockquote>
--Bob Yantosca (talk) 15:04, 26 June 2018 (UTC)
FlexChem bug fix: do not zero ACTA, EOH, HCOOH
This fix will be included in GEOS-Chem 12.0.0.
Katie Travis wrote:
I am working on a VOC simulation, and noticed that in my copy of v11-02f, the following species are set to zero in two places:
! Zero certain species C(ind_ACTA) = 0.e0_dp C(ind_EOH) = 0.e0_dp C(ind_HCOOH) = 0.e0_dp
And
C(ind_ACTA) = 0.0_dp C(ind_HCOOH) = 0.0_dp
Since none of these species are fixed in Tropchem.eqn, shouldn’t they NOT be set to zero?
Mike Long wrote:'
I think the code should be removed. This must have been a patch added to maintain parity with SMVGEAR w/o anticipating that the species would become active.
--Bob Yantosca (talk) 16:19, 17 May 2018 (UTC)
Avoid double counting CEDS and GEIA NH3 biofuel emissions
This fix will be included GEOS-Chem 12.
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.
--Bob Yantosca (talk) 16:33, 17 May 2018 (UTC)