GEOS-Chem v10-01 benchmark history

On this page we have posted complete information about all benchmark simulations (both 1-month and 1-year) for GEOS-Chem v10-01.

1-yr benchmarks

v10-01c-Run1

This 1-year benchmark simulation was approved by the GEOS-Chem Steering Committee on 26 Jun 2014.

Three GEOS-Chem model versions were compared to each other:

Color	Quantity Plotted	Met Type	Year	Chemistry mechanism	Photolysis	Linoz	Annual Mean OH [105 molec/cm3]
Red	v9-02r-geosfp-Run1	GEOS-FP, 47L, 4x5	2013	Same as v9-02r-geos5-Run0	Same as v9-02r-geos5-Run0	ON	12.689
Green	v10-01c-Run0	GEOS-FP, 47L, 4x5	2013	" "	FAST-JX v7.0 photolysis mechanism, with the following fixes included: Reactivation of Br species photolysis for tropospheric simulation Bug fix in reducing wavelength bins for tropospheric simulation Updates to VOC photolysis in Fast-JX v7.0 Final recommendation for J(HAC) and J(PAN) in FAST-JX v7.0	ON	12.550
Blue	v10-01c-Run1	GEOS-FP, 72L, 4x5	2013	UCX chemistry mechanism, includes: Stratospheric chemistry Stratospheric aerosols	" "	ON	11.885
Black	Observations

The output plots for Run1 (both PostScript and PDF format) may be downloaded from:

ftp ftp.as.harvard.edu
cd gcgrid/geos-chem/1yr_benchmarks/v10-01/v10-01c/Run1/output/ps
mget *
cd gcgrid/geos-chem/1yr_benchmarks/v10-01/v10-01c/Run1/output/pdf
mget *

You may also view the PDF files online by pointing your browser to

http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v10-01/v10-01c/Run1/output/pdf/

--Melissa Sulprizio 16:54, 23 June 2014 (EDT)

v10-01c-Run0

This 1-year benchmark simulation was approved by the GEOS-Chem Steering Committee on 26 Jun 2014.

Three GEOS-Chem model versions were compared to each other:

Color	Quantity Plotted	Met Type	Year	Emissions	Photolysis	Linoz	Annual Mean OH [105 molec/cm3]
Red	v9-02r-geosfp-Run0	GEOS-FP, 47L, 4x5	2013	Same as v9-02r-geos5-Run0 (scaled all emissions to 2005)	Same as v9-02r-geos5-Run0	ON	12.389
Green	v9-02r-geosfp-Run1	GEOS-FP, 47L, 4x5	2013	Anthropogenic emissions scaled to 2010 (latest available) + 2011 GFED3 emissions (latest available) + Olson 2001 land map	" "	ON	12.689
Blue	v10-01c-Run0	GEOS-FP, 47L, 4x5	2013	" "	FAST-JX v7.0 photolysis mechanism, with the following fixes included: Reactivation of Br species photolysis for tropospheric simulation Bug fix in reducing wavelength bins for tropospheric simulation Updates to VOC photolysis in Fast-JX v7.0 Final recommendation for J(HAC) and J(PAN) in FAST-JX v7.0	ON	12.550
Black	Observations

The output plots for Run0 (both PostScript and PDF format) may be downloaded from:

ftp ftp.as.harvard.edu
cd gcgrid/geos-chem/1yr_benchmarks/v10-01/v10-01c/Run0/output/ps
mget *
cd gcgrid/geos-chem/1yr_benchmarks/v10-01/v10-01c/Run0/output/pdf
mget *

You may also view the PDF files online by pointing your browser to

http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v10-01/v10-01c/Run0/output/pdf/

--Melissa Sulprizio 14:56, 10 June 2014 (EDT)

1-month benchmarks

v10-01e

We performed two 1-month benchmark simulations for v10-01e:

1. v10-01e_trop: 1-month benchmark with tropopsheric chemistry
2. v10-01e_UCX: 1-month benchmark with UCX strat-trop chemistry (72 vertical levels)

1-month benchmark v10-01e with UCX chemistry

Here is the assessment form for 1-month benchmark simulation v10-01e with UCX chemistry (aka v10-01e_UCX).

Description
New features added into GEOS-Chem:	Features affecting the full-chemistry simulation in this benchmark: HEMCO emissions component Features not affecting the full-chemistry simulation in this benchmark: Removing references to modules made obsolete by GIGC and HEMCO Reactivating dust tracers in TOMAS simulations Fix for ND61 diagnostic in TOMAS simulations
Developer name(s) and institution(s):	HEMCO: Christoph Keller (Harvard), GEOS-Chem Support Team, GMAO Removal of obsolete modules: GEOS-Chem Support Team TOMAS dust fixes: Jeff Pierce (CSU), David Ridley (MIT) TOMAS diagnostic fix: Betty Croft (Dalhousie)
Version, resolution, met fields used:	v10-01, GEOS-FP (72L), 4x5, July 2013
1-month benchmark finished on:	Wed Oct 22 21:57:13 EDT 2014
Performance statistics:	Ran on 8 CPUs of bench@titan-10.as.harvard.edu (2.659 GHz x 8 CPU) Wall time: 5:48 Scalability: 6.9905
Compared to previous benchmark:	v10-01d_UCX
This update will impact: (select all that apply with boldface)	Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify):
Unit test results may be viewed at:	TBD
Plots may be viewed at:	ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v10-01e_UCX/
Metrics
Global mean OH (from log file):	12.9863212020235 x 105 molec/cm3
Methyl chloroform lifetime:	4.7844 years
Did either of these change by more than 5%?	No. The mean OH differs by -0.73%, and the MCF lifetime differs by 0.47%.
At the SURFACE, list all species that changed by 10% or more:	NO, PAN, ALK4, ISOP, HNO3, H2O2, ACET, MEK, ALD2, RCHO, MVK, MACR, PMN, PPN, R4N2, PRPE, C3H8, CH2O, C2H6, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, OCPI, OCPO, DST4, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPN, MOBA, PROPNN, HAC, GLYC, MMN, RIP, IEPOX, MAP, NO2, NO3, HNO2, BrCl, Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl2O2, OH, HO2
Comments on SURFACE differences:	NO concentrations at the surface may be higher due to the fact that the EPA/NEI2005 emissions have now been lumped into a single level in the HEMCO data file. In v10-01d and prior versions, the emissions data came at 5 vertical levels. This may account for the similar differences observed in O3 and other relevant species. The difference in ISOP and related biogenic species can be attributed to the fact that the MEGAN biogenic emissions in HEMCO were modified to only use the current day's leaf area index (LAI). In v10-01d and prior versions, the LAI was interpolated from the previous and current months. Many of the differences are evident in the boreal forests, and in the Amazon, where a small change in LAI could result in a big increase in ISOP. ISOP increases by about ~5ppb in these regions. Differences in ACET, and DMS may be attributed to the fact that HEMCO uses a new updated air-sea exchange module. The air-sea exchange module centralizes this computation. (In v10-01d and prior versions, this computation was repeated in several locations in the code.) The new air-sea exchange module seems to give lower concentrations than the prior code. Differences in HNO3 seem to be related to NO. Differences in C2H6 over China/SE Asia may be attributed to the fact that we are overwriting Yaping Xiao's C2H6 inventory w a different inventory (still checking)
At 500 hPa, list all species that changed by 10% or more:	NO, PAN, ALK4, ISOP, HNO3, H2O2, MEK, ALD2, RCHO, MVK, MACR, PMN, R4N2, PRPE, C2H6, N2O5, HNO4, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, OCPI, OCPO, DST4, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, ISOPN, MOBA, PROPNN, HAC, GLYC, MMN, RIP, IEPOX, MAP, NO2, NO3, HNO2, BrCl, Cl, ClNO2, OClO, Cl2, Cl2O2
Comments on 500 hPa differences:
In the ZONAL MEAN differences, list all species that changed by 10% or more:	NO, PAN, ALK4, ISOP, HNO3, MEK, ALD2, RCHO, MVK, MACR, PMN, PPN, PRPE, C3H8, C2H6, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, OCPI, BCPO, OCPO, DST1, DST2, DST3, SALC, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, ISOPN, MOBA, PROPNN, HAC, GLYC, MMN, RIP, IEPOX, MAP, NO2, NO3, HNO2, OCS, BrCl, CCl4, CH3CCl3, CFC11, H1211, H1301, H2402, Cl, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl2O2, OH
Comments on ZONAL MEAN differences:
In the EMISSION RATIO maps, list all species that changed by 10% or more:	Anthropogenic emissions: ACET, ALD2, ALK4, C2H6, C3H8, CH2O, CO, MEK, NH3, NO, PRPE, SO2, SO4 Biomass emissions: ACET, ALD2, ALK4, C2H6, C3H8, CH2O, CO, MEK, OC, PRPE, SO2 Biogenic emissions: ACET, DMS, ISOP, PRPE OTHER: ACET from MONOT emissions, ACET from MBO emissions, ACET direct emissions, ACET from ocean source emissions CO from MONOT emissions NO aircraft emissions, NO fertilizer emissions, NO soil emissions, NO lightning emissions SO2 aircraft emissions, SO2 ship emissions
Comments on EMISSION RATIO differences:	HEMCO does not separate anthropogenic and biofuel emissions HEMCO now passes ACET ocean sink to dry deposition, and doesn't explicitly write it out as a diagnostic HEMCO now lumps eruptive and non-eruptive volcano emissions into one diagnostic (SO2-EV-$)
Additional or summary comments:
Approval
Requires further investigation:	TBD
Approved by:	TBD
Date of approval:	TBD

--Melissa Sulprizio 10:16, 2 October 2014 (EDT)

1-month benchmark v10-01e with tropospheric chemistry

Here is the assessment form for 1-month benchmark simulation v10-01e with tropospheric chemistry (aka v10-01e_trop).

Description
New features added into GEOS-Chem:	Features affecting the full-chemistry simulation in this benchmark: HEMCO emissions component Features not affecting the full-chemistry simulation in this benchmark: Removing references to modules made obsolete by GIGC and HEMCO Reactivating dust tracers in TOMAS simulations Fix for ND61 diagnostic in TOMAS simulations
Developer name(s) and institution(s):	HEMCO: Christoph Keller (Harvard), GEOS-Chem Support Team, GMAO Removal of obsolete modules: GEOS-Chem Support Team TOMAS dust fixes: Jeff Pierce (CSU), David Ridley (MIT) TOMAS diagnostic fix: Betty Croft (Dalhousie)
Version, resolution, met fields used:	v10-01, GEOS-FP (47L), 4x5, July 2013
1-month benchmark finished on:	Tue Oct 21 17:05:20 EDT 2014
Performance statistics:	Ran on 8 CPUs of bench@titan-10.as.harvard.edu (2.659 GHz x 8 CPU) Wall time: 2:41 Scalability: 7.1470
Compared to previous benchmark:	v10-01d_trop
This update will impact: (select all that apply with boldface)	Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify):
Unit test results may be viewed at:	TBD
Plots may be viewed at:	ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v10-01e_trop/
Metrics
Global mean OH (from log file):	13.5056204186113 x 105 molec/cm3
Methyl chloroform lifetime:	4.7611 years
Did either of these change by more than 5%?	No. The mean OH differs by -0.61%, and the MCF lifetime differs by 0.20%.
At the SURFACE, list all species that changed by 10% or more:	NO, PAN, ALK4, ISOP, HNO3, H2O2, ACET, MEK, ALD2, RCHO, MVK, MACR, PMN, PPN, R4N2, PRPE, C3H8, CH2O, C2H6, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, OCPI, OCPO, DST4, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPN, MOBA, PROPNN, HAC, GLYC, MMN, RIP, IEPOX, MAP, NO2, NO3, HNO2, OH, HO2
Comments on SURFACE differences:	NO concentrations at the surface may be higher due to the fact that the EPA/NEI2005 emissions have now been lumped into a single level in the HEMCO data file. In v10-01d and prior versions, the emissions data came at 5 vertical levels. This may account for the similar differences observed in O3 and other relevant species. The difference in ISOP and related biogenic species can be attributed to the fact that the MEGAN biogenic emissions in HEMCO were modified to only use the current day's leaf area index (LAI). In v10-01d and prior versions, the LAI was interpolated from the previous and current months. Many of the differences are evident in the boreal forests, and in the Amazon, where a small change in LAI could result in a big increase in ISOP. ISOP increases by about ~5ppb in these regions. Differences in ACET, and DMS may be attributed to the fact that HEMCO uses a new updated air-sea exchange module. The air-sea exchange module centralizes this computation. (In v10-01d and prior versions, this computation was repeated in several locations in the code.) The new air-sea exchange module seems to give lower concentrations than the prior code.
At 500 hPa, list all species that changed by 10% or more:	NO, PAN, ALK4, ISOP, HNO3, H2O2, MEK, ALD2, RCHO, MVK, MACR, PMN, R4N2, PRPE, C2H6, N2O5, HNO4, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, OCPI, OCPO, DST4, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, ISOPN, MOBA, PROPNN, HAC, GLYC, MMN, RIP, IEPOX, MAP, NO2, NO3, HNO2
Comments on 500 hPa differences:	Mostly the same the COMMENTS ON SURFACE DIFFERENCES
In the ZONAL MEAN differences, list all species that changed by 10% or more:	NO, PAN, ALK4, ISOP, HNO3, MEK, ALD2, RCHO, MVK, MACR, PMN, PPN, PRPE, C3H8, CH2O, C2H6, N2O5, HNO4, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, OCPI, BCPO, OCPO, DST3, SALC, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPN, MOBA, PROPNN, HAC, GLYC, MMN, RIP, IEPOX, MAP, NO2, NO3, HNO2, OH
Comments on ZONAL MEAN differences:	Most zonal diffs are small in absolute value but may be large in % value. This may reflect small-number statistics. Differences in DMS and ACET may be attributed to the new air-sea exchange module used by HEMCO. Differences in C2H6 may be related to how aircraft emissions are vertically regridded by HEMCO. Differences in OCPI may be due to many inventories carrying either BC or OC but not separating them into hydrophobic/hydrophilic parts. This may be a diagnostic issue. Differences of ISOP and other related biogenic species over the Northern boreal latitudes may be attributed to the change that was made in MEGAN. MEGAN now uses the current day's LAI instead of interpolating it from the previous & current months. Changes in H2O2 may be related to wet deposition. Differences in OCPI and OCPO may be due to the fact that HEMCO carries OC as a species but does not separate them into OCPI and OCPO. The separation is done outside of HEMCO.
In the EMISSION RATIO maps, list all species that changed by 10% or more:	Anthropogenic emissions: ACET, ALD2, ALK4, C2H6, C3H8, CH2O, CO, MEK, NH3, NO, PRPE, SO2, SO4 Biomass emissions: ACET, ALD2, ALK4, C2H6, C3H8, CH2O, CO, MEK, OC, PRPE, SO2 Biogenic emissions: ACET, DMS, ISOP, PRPE OTHER: ACET from MONOT emissions, ACET from MBO emissions, ACET direct emissions, ACET from ocean source emissions CO from MONOT emissions NO aircraft emissions, NO fertilizer emissions, NO soil emissions, NO lightning emissions SO2 aircraft emissions, SO2 ship emissions
Comments on EMISSION RATIO differences:	HEMCO does not separate anthropogenic and biofuel emissions. Some differences in the plots are caused by biofuel emissions being lumped together with the anthropogenic emissions. HEMCO now passes ACET ocean sink to dry deposition, and doesn't explicitly write it out as a diagnostic HEMCO now lumps eruptive and non-eruptive volcano emissions into one diagnostic (SO2-EV-$) HEMCO introduces a centralized module for computing Henry's law coefficients and air-sea exchange. These were done in many separate locations in v10-01d and prior versions. This affects ACET and DMS. HEMCO now regrids certain emissions (aircraft, volcanoes) in the vertical (with code from MESSy) instead of reading from separate, grid-dependent files. HEMCO often uses finer-resolution mask files for regional emissions than in v10-01d and prior versions. The HEMCO MEGAN extension now only uses the current day's LAI (instead of interpolating it from the previous & current months). This attributes for the increase in ISOP, especially in boreal regions. Ditto for similar biogenic species. The decrease in NH3 over SE Asia may be related to the Streets NH3 inventory.
Additional or summary comments:	GEOS-Chem v10-01d and prior versions use a klunky emissions interface. There was a significant amount of hardwiring, especially in the application of scale factors and masks. In v10-01e, HEMCO has completely replaced this legacy emissions interface. We have tried to replicate the emissions output r of v10-01d to the greatest extent possible. But in v10-01e+HEMCO, we have also brought in a couple of newer inventories (volcanoes, etc.) while also introducing a new vertical regridding scheme. So we will not be able to replicate the v10-01d emissions to 100% accuracy. As of this benchmark, the following simulations are not yet fully compatible with HEMCO. Tagged CO simulation Mercury TOMAS aerosol microphysics The APM aerosol microphysics will have to be completely re-integrated once v10-01 ships.
Approval
Requires further investigation:	No
Approved by:	Bob Y.
Date of approval:	22 Oct 2014

--Bob Y. 14:54, 22 October 2014 (EDT)

v10-01d

We performed two 1-month benchmark simulations for v10-01d:

1. v10-01d_trop: 1-month benchmark with tropopsheric chemistry
2. v10-01d_UCX: 1-month benchmark with UCX strat-trop chemistry (72 vertical levels)

1-month benchmark v10-01d with UCX chemistry

Here is the assessment form for 1-month benchmark simulation v10-01d with UCX chemistry (aka v10-01d_UCX).

Description
New features added into GEOS-Chem:	Features affecting the full-chemistry simulation in this benchmark: Fix error in ISOPO2 isomerization reaction in globchem.dat Implement final recommendation for J(HAC) and J(PAN) in FAST-JX v7.0 Features not affecting the full-chemistry simulation in this benchmark: Modify NcdfUtil code to allow re-opening of netCDF "define mode" Fix parallelization error in nested grid simulations Fixed bug in ND44 drydep diagnostic for sea salt aerosols
Developer name(s) and institution(s):	ISOPO2 isomerization reaction fix: Ploy Achakulwisut (Harvard) FAST-JX v7.0 update: Sebastian Eastham (MIT), Jingqiu Mao (Princeton) NetCDF define mode: GEOS-Chem Support Team Nested grid parallelization fix: Jintai Lin (Peking U.) ND44 fix for sea salt: Kateryna Lapina (CU Boulder)
Version, resolution, met fields used:	v10-01, GEOS-FP (72L), 4x5, July 2013
1-month benchmark finished on:	Mon Jun 2 20:00:41 EDT 2014
Performance statistics:	Ran on 8 CPUs of bench@titan-08.as.harvard.edu (2.659 GHz x 8 CPU) Wall time: 5:52 Scalability: 6.8095
Compared to previous benchmark:	v10-01c with UCX chemistry
This update will impact: (select all that apply with boldface)	Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify):
Unit test results may be viewed at:	ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v10-01/v10-01d/v10-01d.results.html
Plots may be viewed at:	ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v10-01/v10-01d/
Metrics
Global mean OH (from log file):	13.0813437885412 x 105 molec/cm3
Methyl chloroform lifetime:	4.7621 years
Did either of these change by more than 5%?	No. The mean OH differs by -0.25%, and the MCF lifetime differs by 0.34%.
At the SURFACE, list all species that changed by 10% or more:	NO, PAN, ISOP, H2O2, MVK, MACR, PMN, PRPE, CH2O, N2O5, HNO4, MP, DMS, NIT, DST4, Br, ISOPN, MOBA, HAC, GLYC, MMN, RIP, IEPOX, MAP, Cl, OClO, Cl2O2, HO2
Comments on SURFACE differences:	HAC shows large increases at the surface. We attribute this to the fix for J(HAC) added to this version. The other species listed here (particularly ISOP and its oxidation products) show large percent differences. But these occur in places where the concentrations of these species are already very low. We may attribute these differences to small-number statistics.
At 500 hPa, list all species that changed by 10% or more:	NO, ISOP, MVK, MACR, PMN, PRPE, CH2O, N2O5, DMS, NH3, NIT, DST4, BrNO2, ISOPN, MOBA, HAC, GLYC, MMN, RIP, IEPOX, MAP, Cl, OClO, Cl2O2
Comments on 500 hPa differences:	HAC shows large increases at 500 hPa. We attribute this to the fix for J(HAC) added to this version. The other species listed here (particularly ISOP and its oxidation products) show large percent differences. But these occur in places where the concentrations of these species are already very low. We may attribute these differences to small-number statistics.
In the ZONAL MEAN differences, list all species that changed by 10% or more:	PAN, ALK4, ISOP, MVK, MACR, PMN, PRPE, C3H8, N2O5, SO4s, NH3, NIT, NITs, DST2, DST3, SALC, Br, BrNO3, ISOPN, MOBA, HAC, MMN, RIP, IEPOX, MAP, OCS, CCl4, CH3CCl3, CFC11, H1211, H1301, H2402, Cl, ClNO2, Cl2O2
Comments on ZONAL MEAN differences:	HAC shows large zonal mean differences. We attribute this to the fix for J(HAC) added to this version. Several species (particularly ISOP and its oxidation products) show large percent differences but small (~0.1 ppbv) absolute differences. The "numerical noise" patterns in the NH3 and NIT percent differences may be attributed to ISORROPIA II.
In the EMISSION RATIO maps, list all species that changed by 10% or more:	None
Comments on EMISSION RATIO differences:	None needed.
Additional or summary comments:	This benchmark was done to test a few last minute-fixes into the code before integrating HEMCO into GEOS-Chem. HEMCO will be tested with benchmark simulation v10-01e. The fix for the ND44 drydep diagnostic described above only affects simulations done where the non-local PBL mixing is turned OFF. In this benchmark (and all GEOS-Chem benchmarks), we use the non-local PBL mixing scheme.
Approval
Requires further investigation:	NO
Approved by:	Melissa Sulprizio and Bob Yantosca
Date of approval:	03 Jun 2014

--Melissa Sulprizio 14:47, 2 June 2014 (EDT)
--Bob Y. 11:39, 3 June 2014 (EDT)

1-month benchmark v10-01d with tropospheric chemistry

Here is the assessment form for 1-month benchmark simulation v10-01d with tropospheric chemistry (aka v10-01d_trop).

Description
New features added into GEOS-Chem:	Features affecting the full-chemistry simulation in this benchmark: Fix error in ISOPO2 isomerization reaction in globchem.dat Implement final recommendation for J(HAC) and J(PAN) in FAST-JX v7.0 Features not affecting the full-chemistry simulation in this benchmark: Modify NcdfUtil code to allow re-opening of netCDF "define mode" Fix parallelization error in nested grid simulations Fixed bug in ND44 drydep diagnostic for sea salt aerosols
Developer name(s) and institution(s):	ISOPO2 isomerization reaction fix: Ploy Achakulwisut (Harvard) FAST-JX v7.0 update: Sebastian Eastham (MIT), Jingqiu Mao (Princeton) NetCDF define mode: GEOS-Chem Support Team Nested grid parallelization fix: Jintai Lin (Peking U.) ND44 fix for sea salt: Kateryna Lapina (CU Boulder)
Version, resolution, met fields used:	v10-01, GEOS-FP (47L), 4x5, July 2013
1-month benchmark finished on:	Mon Jun 16 13:24:57 EDT 2014
Performance statistics:	Ran on 8 CPUs of bench@titan-08.as.harvard.edu (2.659 GHz x 8 CPU) Wall time: 2:47 Scalability: 6.8980
Compared to previous benchmark:	v10-01c with tropospheric chemistry
This update will impact: (select all that apply with boldface)	Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify):
Unit test results may be viewed at:	ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v10-01/v10-01d/v10-01d.results.html
Plots may be viewed at:	ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v10-01/v10-01d_trop/
Metrics
Global mean OH (from log file):	13.5883620833673 x 105 molec/cm3
Methyl chloroform lifetime:	4.7516 years
Did either of these change by more than 5%?	No. The mean OH differs by -0.29%, and the MCF lifetime differs by 0.35%.
At the SURFACE, list all species that changed by 10% or more:	NO, PAN, ISOP, H2O2, MVK, MACR, PMN, PRPE, CH2O, N2O5, HNO4, MP, DMS, NIT, DST4, Br, BrO, ISOPN, MOBA, HAC, GLYC, MMN, RIP, IEPOX, MAP
Comments on SURFACE differences:	HAC shows large increases at the surface. We attribute this to the fix for J(HAC) added to this version. The other species listed here (particularly ISOP and its oxidation products) show large percent differences. But these occur in places where the concentrations of these species are already very low. We may attribute these differences to small-number statistics.
At 500 hPa, list all species that changed by 10% or more:	NO, ISOP, MVK, MACR, PMN, PRPE, CH2O, N2O5, DMS, NH3, NIT, DST4, BrNO2, BrNO3, ISOPN, MOBA, HAC, GLYC, MMN, RIP, IEPOX, MAP
Comments on 500 hPa differences:	HAC shows large increases at 500 hPa. We attribute this to the fix for J(HAC) added to this version. The other species listed here (particularly ISOP and its oxidation products) show large percent differences. But these occur in places where the concentrations of these species are already very low. We may attribute these differences to small-number statistics.
In the ZONAL MEAN differences, list all species that changed by 10% or more:	NO, ALK4, ISOP, MVK, MACR, PMN, PRPE, C3H8, N2O5, SO4s, NH3, NIT, NITs, ISOPN, MOBA, HAC, GLYC, MMN, RIP, IEPOX, MAP
Comments on ZONAL MEAN differences:	HAC shows large zonal mean differences. We attribute this to the fix for J(HAC) added to this version. Several species (particularly ISOP and its oxidation products) show large percent differences but small (~0.1 ppbv) absolute differences. The "numerical noise" patterns in the NH3 and NIT percent differences may be attributed to ISORROPIA II.
In the EMISSION RATIO maps, list all species that changed by 10% or more:	None
Comments on EMISSION RATIO differences:	None needed.
Additional or summary comments:	This benchmark was done to test a few last minute-fixes into the code before integrating HEMCO into GEOS-Chem. HEMCO will be tested with benchmark simulation v10-01e. The fix for the ND44 drydep diagnostic described above only affects simulations done where the non-local PBL mixing is turned OFF. In this benchmark (and all GEOS-Chem benchmarks), we use the non-local PBL mixing scheme.
Approval
Requires further investigation:	NO
Approved by:	Melissa Sulprizio and Bob Yantosca
Date of approval:	03 Jun 2014

--Melissa Sulprizio 14:47, 2 June 2014 (EDT)
--Bob Y. 11:39, 3 June 2014 (EDT)

v10-01c

Because GEOS-Chem v10-01c was the version where we introduced the UCX chemistry mechanism, we performed two 1-month benchmark simulations:

1. v10-01c_trop: 1-month benchmark with tropopsheric chemistry
2. v10-01c_UCX: 1-month benchmark with UCX strat-trop chemistry (72 vertical levels)

--Bob Y. 13:15, 30 May 2014 (EDT)

Final recommendation for J-values

We were not able to include this final recommendation for J(HAC) and J(PAN) into the v10-01c_trop and v10-01c_UCX 1-month benchmarks. We will include these in the 1-year benchmarks for v10-01c.

--Bob Y. 17:16, 30 May 2014 (EDT)

1-month benchmark v10-01c with UCX chemistry

Here is the assessment form for 1-month benchmark simulation v10-01c with UCX chemistry (aka v10-01c_UCX).

Description
New features added into GEOS-Chem:	Features affecting the chemistry in this benchmark: UCX strat chem mechanism, includes: Stratospheric chemistry Stratospheric aerosols Fast-JX v7.0 photolysis mechanism, with the following fixes included: Reactivation of Br species photolysis for tropospheric simulation Bug fix in reducing wavelength bins for tropospheric simulation Updates to VOC photolysis in Fast-JX 7.0 Features not affecting the chemistry in this benchmark: Bug fix for determining when to use TOMS O3 columns Add support for TAU performance profiler Fixes for timeseries diagnostics to allow for more transported tracers Fixes for the stratospheric chemistry module Various updates for GEOS-Chem specialty simulations Updates to speed up GEOS-Chem execution
Developer name(s) and institution(s):	UCX: Sebastian Eastham (MIT) Fast-JX: Sebastian Eastham (MIT), Jingqiu Mao (Princeton) TOMS O3 fix: Jintai Lin (Peking U.) TAU profiler: John Linford (ParaTools,Inc), GEOS-Chem Support Team Timeseries diagnostic fixes: GEOS-Chem Support Team Strat chem module fixes: GEOS-Chem Support Team Specialty simualton fixes: Jeffrey Pierce (CSU), Kevin Wecht (Harvard), Matthew Johnson (NASA), GEOS-Chem Support Team Speed-up of GEOS-Chem: GEOS-Chem Support Team
Version, resolution, met fields used:	v10-01, GEOS-FP (72L), 4x5, July 2013
1-month benchmark finished on:	Thu May 29 00:01:33 2014
Performance statistics:	Ran on 8 CPUs of bench@titan-09.as.harvard.edu (2.659 GHz x 8 CPU) Wall time: 5:51 Scalability: 6.7089
Compared to previous benchmark:	v10-01c with tropospheric chemistry
This update will impact: (select all that apply with boldface)	Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify):
Unit test results may be viewed at:	ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v10-01/v10-01c/v10-01c_UCX/v10-01c_Final.results.html
Plots may be viewed at:	ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v10-01/v10-01c/v10-01c_UCX/
Metrics
Global mean OH (from log file):	13.1136815995777 x 105 molec/cm3
Methyl chloroform lifetime:	4.7459 years
Did either of these change by more than 5%?	No. The mean OH differs by -3.77%, and the MCF lifetimes differ by 0.23%.
At the SURFACE, list all species that changed by 10% or more:	NO, PAN, ALK4, ISOP, HNO3, H2O2, MEK, RCHO, MVK, MACR, PMN, PPN, PRPE, N2O5, HNO4, MP, DMS, SO4s, NH3, NIT, NITs, DST4, Br2, Br, BrO, HBr, BrNO2, BrNO3, MPN, ISOPN, MOBA, HAC, GLYC, MMN, RIP, IEPOX, NO2, NO3, HNO2, OH, HO2
Comments on SURFACE differences:	Differences in the ratio plots of ISOP and its oxidation products over the oceans probably reflect small number differences.
At 500 hPa, list all species that changed by 10% or more:	NO, ALK4, ISOP, HNO3, MEK, RCHO, MVK, MACR, PMN, PRPE, C3H8, N2O5, HNO4, MP, DMS, SO2, NH3, NIT, NITs, DST4, Br2, Br, BrO, HBr, BrNO2, BrNO3, MPN, ISOPN, MOBA, HAC, GLYC, MMN, RIP, IEPOX, NO2, NO3, HNO2, OH, HO2
Comments on 500 hPa differences:	The "noise" pattern in the NIT and NH3 plots reflect the numerical drift caused by ISORROPIA II
In the ZONAL MEAN differences, list all species that changed by 10% or more:	All species, except for MSA and OCPI, changed by 10% or more.
Comments on ZONAL MEAN differences:	It is understandable that we would see differences of this magnitude in these species given that we have activated stratospheric chemistry. We are also using the full 72-layer grid as opposed to the 47-layer grid in the tropopause-only simulation. The following species show small absolute differences but large percent differences: ALK4, ISOP, MEK, ALD2, RCHO, MVK, MACR, PMN, R4N2, PRPE, C3H8, CH2O, C2H6, SO2, SO4s, MSA, NH3, NH4, NITs, BCPO, OCPO, DST1, DST2, DST3, DST4, SALA, SALC, BrNO2, CHBr3, CH2Br2, ISOPN, HAC, GLYC, MMN, HNO2
In the EMISSION RATIO maps, list all species that changed by 10% or more:	None
Comments on EMISSION RATIO differences:	NOx sources (anthropogenic, aircraft, lightning, soils) changed very slightly in this run. This may be an artifact of comparing the data on the full 72-layer grid to the 47-layer grid of the previous benchmark. The acetone ocean sink also decreased slightly (-0.000638 Tg C). This may also be an artifact of comparing the 72-level grid to the 47-level grid.
Additional or summary comments:	This simulation uses the KPP chemistry solver, while all past benchmarks have used SMVGEAR. UCX simulations are extremely slow when SMVGEAR is used, so KPP is the recommended solver. Many of the structural updates (i.e. to speed up GEOS-Chem, to reduce the memory footprint, to fix issues in the specialty simulations) do not impact the full-chemistry simulation. This was validated with unit tests and difference tests. IMPORTANT: We were unable to add the Final recommendation for J-values into this 1-month benchmark. We will add this into the 1-year benchmarks for v10-01c.
Approval
Requires further investigation:	NO
Approved by:	Daniel Jacob, Jingqiu Mao, Sebastian Eastham
Date of approval:	29 May 2014

--Bob Y. 13:11, 30 May 2014 (EDT)

1-month benchmark v10-01c with tropospheric chemistry

Here is the assessment form for 1-month benchmark simulation v10-01c with tropospheric chemistry (i.e. UCX off, aka v10-01c_trop).

Description
New features added into GEOS-Chem:	Features affecting the chemistry in this benchmark: Fast-JX v7.0 photolysis mechanism, with the following fixes included: Reactivation of bromine species photolysis for tropospheric simulation Bug fix in reducing wavelength bins for tropospheric simulation Updates to VOC photolysis in Fast-JX 7.0 Features not affecting the chemistry in this benchmark: Bug fix for determining when to use TOMS O3 columns Add support for TAU performance profiler Fixes for timeseries diagnostics to allow for more transported tracers Fixes for the stratospheric chemistry module Various updates for GEOS-Chem specialty simulations Updates to speed up GEOS-Chem execution
Developer name(s) and institution(s):	Fast-JX: Sebastian Eastham (MIT), Jingqiu Mao (Princeton) TOMS O3 fix: Jintai Lin (Peking U.) TAU profiler: John Linford (ParaTools,Inc), GEOS-Chem Support Team Timeseries diagnostic fixes: GEOS-Chem Support Team Strat chem module fixes: GEOS-Chem Support Team Specialty simualton fixes: Jeffrey Pierce (CSU), Kevin Wecht (Harvard), Matthew Johnson (NASA), GEOS-Chem Support Team Speed-up of GEOS-Chem: GEOS-Chem Support Team
Version, resolution, met fields used:	v10-01, GEOS-FP (47L), 4x5, July 2013
1-month benchmark finished on:	Wed May 28 17:57:45 2014
Performance statistics:	Ran on 8 CPUs of bench@titan-09.as.harvard.edu (2.659 GHz x 8 CPU) Wall time: 2:49 Scalability: 6.7835
Compared to previous benchmark:	v10-01b
This update will impact: (select all that apply with boldface)	Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify):
Unit test results may be viewed at:	ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v10-01/v10-01c/v10-01c_trop/v10-01c_Final.results.html
Plots may be viewed at:	ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v10-01/v10-01c/v10-01c_trop
Metrics
Global mean OH (from log file):	13.6273583437531 x 105 molec/cm3
Methyl chloroform lifetime:	4.7349 years
Did either of these change by more than 5%?	No. The mean OH differs by -0.77%, and the MCF lifetimes differ by 1.37%.
At the SURFACE, list all species that changed by 10% or more:	NO, PAN, ALK4, ISOP, H2O2, MEK, RCHO, MVK, MACR, PMN, PPN, PRPE, CH2O, N2O5, HNO4, MP, DMS, NIT, DST4, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPN, MOBA, PROPNN, HAC, GLYC, MMN, RIP, IEPOX, MAP, NO3, HNO2, OH, HO2
Comments on surface differences:	Most of the differences in ISOP and its products are over the oceans. This could be due to small number differences, since there is not a lot of ISOP in these locations. We believe that the following differences are due to photolysis (FAST-JX in v10-01c_trop vs. FAST-J in v10-01b): Differences in NO at the south pole Differences in bromine species, particularly at the poles Differences observed in DST4
At 500 hPa, list all species that changed by 10% or more:	NO, PAN, ALK4, ISOP, H2O2, ACET, MEK, MVK, MACR, PMN, PRPE, CH2O, N2O5, HNO4, MP, DMS, SO2, NH3, NIT, DST4, Br2, Br, BrO, BrNO2, BrNO3, ISOPN, MOBA, PROPNN, HAC, GLYC, MMN, RIP, IEPOX, MAP, NO2, NO3, HNO2
Comments on 500 hPa differences:	Most of the differences in ISOP and its products are over the oceans. This could be due to small number differences, since there is not a lot of ISOP in these locations. We believe that the following differences are due to photolysis (FAST-JX in v10-01c_trop vs. FAST-J in v10-01b): Differences in NO at the south pole Differences in bromine species, particularly at the poles Differences observed in DST4
In the ZONAL MEAN differences, list all species that changed by 10% or more:	NO, PAN, ALK4, ISOP, H2O2, ACET, MEK, MVK, MACR, PMN, PRPE, C3H8, CH2O, N2O5, MP, DMS, SO4s, NH3, NIT, NITs, Br2, Br, BrO, HOBr, BrNO2, BrNO3, MPN, ISOPN, MOBA, HAC, GLYC, MMN, RIP, IEPOX, MAP, NO3, HNO2, OH, HO2
Comments on ZONAL MEAN differences:	The following species show large percent differences but small absolute differences: NO, PAN, ALK4, ISOP, MEK, MVK, MACR, PMN, R4N2, PRPE, CH2O, C3H8 (at top of atmosphere), N2O5, DMS, SO4s (at top of atmosphere), NITs (at top of atmosphere), DST4, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, CHBr3, ISOPN, MOBA, NO2, NO3, HNO2, Differences in ACET are probably caused by v10-01c having the correct pressure dependency for J(ACET) but v10-01b not having this fix applied. Differences in NH3 and NIT are due to the numerical instability in ISORROPIA II. Differences in HAC and GLYC are due to photolysis (FAST-JX vs. FAST-J).
In the EMISSION RATIO maps, list all species that changed by 10% or more:	None
Comments on EMISSION RATIO differences:	The NO anthropogenic emissions only very slightly higher in v10-01c_trop (by 0.000343 Tg N). This is most likely due to the fix for FAST-JX wavelength bins propagating through to the PARANOX ship emissions plume model. The ACET ocean sink is only slightly smaller (-0.106) in v10-01c_trop.
Additional or summary comments:	Many of the structural updates (i.e. to speed up GEOS-Chem, to reduce the memory footprint, to fix issues in the specialty simulations) do not impact the full-chemistry simulation. This was validated with unit tests and difference tests. IMPORTANT: We were unable to add the Final recommendation for J-values into this 1-month benchmark. We will add this into the 1-year benchmarks for v10-01c.
Approval
Requires further investigation:	NO
Approved by:	Daniel Jacob, Jingqiu Mao, Sebastian Eastham
Date of approval:	29 May 2014

--Bob Y. 14:20, 30 May 2014 (EDT)

v10-01b

Here is the assessment form for 1-month benchmark simulation v10-01b.

Description
New features added into GEOS-Chem:	Correct molecular weight for the PROPNN tracer in input.geos Use MAP_A2A to regrid 1x1 TOMS O3 to model resolution
Developer name(s) and institution(s):	PROPNN molecular weight: Jenny Fisher (U. Wollongong) TOMS O3 regridding: Jintai Lin (Peking U.)
Version, resolution, met fields used:	v10-01, GEOS-FP (47L), 4x5, July 2013
1-month benchmark finished on:	Wed Mar 5 15:06:00 EST 2014
Performance statistics:	Ran on 8 CPUs of bench@titan-11.as.harvard.edu (2.659 GHz x 8 CPU) Wall time: 2:55 Scalability: 6.7949
Compared to previous benchmark:	v10-01a
This update will impact: (select all that apply with boldface)	Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify):
Plots may be viewed at:	ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v10-01/v10-01b/
Metrics
Global mean OH (from log file):	13.7339945052522 x 105 molec/cm3
Methyl chloroform lifetime:	4.6706 years
Did either of these change by more than 5%?	No. Both the mean OH and MCF lifetimes differ by < 0.01%.
At the SURFACE, list all species that changed by 10% or more:	NO, ISOP, MVK, MACR, PMN, NIT, DST4, ISOPN, MOBA, RIP
Comments on SURFACE differences:	Differences in most species are due to small number differences over the oceans or poles, where concentrations are small. Differences in NIT can be attributed to numerical noise from ISORROPIA.
At 500 hPa, list all species that changed by 10% or more:	NO, ISOP, NH3, NIT, DST4, ISOPN, MOBA, RIP
Comments on 500 hPa differences:	Differences in most species are due to small number differences over the oceans or poles, where concentrations are small. Differences in NIT can be attributed to numerical noise from ISORROPIA.
In the ZONAL MEAN differences, list all species that changed by 10% or more:	ALK4, ISOP, C3H8, SO4s, NH3, NIT, GLYC
Comments on ZONAL MEAN differences:	Differences in most species are due to small number differences above ~200 hPa, where concentrations are small. Differences in NIT can be attributed to numerical noise from ISORROPIA.
In the EMISSION RATIO maps, list all species that changed by 10% or more:	None
Comments on EMISSION RATIO differences:
Additional or summary comments:	Differences caused by the TOMS O3 update are not seen in the benchmark output. The benchmark simulation uses O3 columns from the GEOS-FP met fields, so TOMS O3 columns are not used.
Approval
Requires further investigation:	No
Approved by:	Jenny Fisher, Fabien Paulot
Date of approval:	06 Mar 2014

--Melissa Sulprizio 11:34, 6 March 2014 (EST)

v10-01a

Here is the assessment form for 1-month benchmark simulation v10-01a.

Description
New features added into GEOS-Chem:	Updates to dry deposition when using the Olson 2001 land map
Developer name(s) and institution(s):	Patrick Kim (Harvard)
Version, resolution, met fields used:	v10-01, GEOS-FP (47L), 4x5, July 2013
1-month benchmark finished on:	Mon Feb 3 15:05:32 EST 2014
Performance statistics:	Ran on 8 CPUs of bench@titan-09.as.harvard.edu (2.659 GHz x 8 CPU) Wall time: 2:48 Scalability: 6.8703
Compared to previous benchmark:	v9-02r w/ GEOS-FP meteorology
This update will impact: (select all that apply with boldface)	Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify):
Plots may be viewed at:	ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v10-01/v10-01a/
Metrics
Global mean OH (from log file):	13.7338316128900 x 105 molec/cm3
Methyl chloroform lifetime:	4.6707 years
Did either of these change by more than 5%?	No. The mean OH differs by -0.02%, and the MCF lifetimes differ by 0.07%.
At the SURFACE, list all species that changed by 10% or more:	NO, O3, PAN, ISOP, HNO3, H2O2, MEK, ALD2, RCHO, MVK, MACR, PMN, PPN, R4N2, PRPE, N2O5, DMS, NH3, NH4, NIT, OCPI, DST4, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPN, MOBA, PROPNN, HAC, GLYC, MMN, RIP, IEPOX, MAP, NO3, OH
Comments on SURFACE differences:	Differences in isoprene related tracers can be attributed to changing biogenic emissions because we now force the MODIS LAI year to 2008. Differences in NO, DST4, and the bromine species are due to small number differences where concentrations are low. Differences in NH4 and NIT can be attributed to numerical noise from ISORROPIA.
At 500 hPa, list all species that changed by 10% or more:	NO, ISOP, MVK, MACR, PMN, PRPE, N2O5, DMS, NH3, NIT, DST4, Br2, ISOPN, MOBA, HAC, GLYC, MMN, RIP, IEPOX, NO3
Comments on 500 hPa differences:	Differences in NO, DST4, and Br2 are due to small number differences where concentrations are low. Differences in NH3 and NIT can be attributed to numerical noise from ISORROPIA.
In the ZONAL MEAN differences, list all species that changed by 10% or more:	NO, ALK4, ISOP, MVK, MACR, PMN, PRPE, C3H8, N2O5, NH3, NIT, NITs, DST4, Br2, ISOPN, MOBA, HAC, GLYC, MMN, RIP, IEPOX
Comments on ZONAL MEAN differences:	Differences in isoprene related tracers can be attributed to changing biogenic emissions because we now force the MODIS LAI year to 2008. Differences in NO, ALK4, C3H8, N2O5, NITs, DST4, Br2, are due to small number differences where concentrations are low. Differences in NH3 and NIT can be attributed to numerical noise from ISORROPIA.
In the EMISSION RATIO maps, list all species that changed by 10% or more:	ISOP, ACET, OC, PRPE, CO from monoterpenes
Comments on EMISSION RATIO differences:	Biogenic emissions differ because we now force the use of MODIS LAI for 2008 if the simulation year is beyond 2008. MODIS LAI for 2009 was used in the benchmark v9-02r w/ GEOS-FP met, but there are large differences in the 2009 file that still need to be investigated.
Additional or summary comments:	We still need to determine what caused the changes in the MODIS LAI input files. As per our earlier discussion, we have put in an error trap in drydep_mod to make sure that the changes are only made for simulations using GEOS-FP and the Olson 2001 land map.
Approval
Requires further investigation:	No
Approved by:	Patrick Kim
Date of approval:	5 Feb 2014

--Melissa Sulprizio 12:16, 3 February 2014 (EST)