Difference between revisions of "Benchmark/GEOS-Chem 12.5.0"

Latest revision as of 16:19, 26 August 2020

This page includes information about all benchmark simulations for GEOS-Chem 12.5.0 (DOI: 10.5281/zenodo.3403111).

GEOS-Chem Classic 1-month benchmark

Benchmark plots

Enable PDF bookmarks¹ in the files linked below to navigate between species. See the Species in GEOS-Chem wiki page for species definitions and details.

Species Category²	Plots					Additional Information
	Level Map		Zonal Mean		Emissions
Oxidants O3, CO, OH, NOx	sfc	500hPa	full column	stratosphere	sfc
Aerosols NH4, NIT, SO4, DST1, DST2, DST3, DST4, BC, OC, AERI, BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s, SOA_Simple, SOA_Complex	sfc	500hPa	full column	stratosphere	sfc	AOD
Bromine Bry, BrOx, Br, Br2, BrCl, BrNO2, BrNO3, BrO, CH4Br, CH2Br2, CH2Br2, CH3Br3, HOBr, HBr	sfc	500hPa	full column	stratosphere	sfc
Chlorine Cly, ClOx, Cl, ClO, Cl2, Cl2O2, ClOO, ClNO2, ClNO3, CCl4, CFCs, CH3Cl, CH2Cl2, CH4CCl3, HOCl, HCl, Halons, HCFCs, OClO	sfc	500hPa	full column	stratosphere	--
Iodine Iy, IxOy, I, I2, IBr, ICl, IO, INO2, IONO2, CH3I, CH2I2, CH2ICl, CH2IBr, HI, HOI, OIO	sfc	500hPa	full column	stratosphere	sfc
Nitrogen NOy, NOx, HNO2, HNO3, HNO4, IMPN, NIT, NO, NO2, NO3, N2O5, MPN, PAN, PPN, N2O, NHx, NH3, NH4	sfc	500hPa	full column	stratosphere	sfc
Primary Organics ALK4, BENZ, CH4, C2H6, C2H4, C3H8, PRPE, TOLU, XYLE, ISOP, MTPA, MTPO, LIMO, GLYX, HCOOH, MAP, MBO, MOH, RCHO	sfc	500hPa	full column	stratosphere	sfc
Secondary Organics ACET, MEK, MVK, ALD2, CH2O, HPALD, MP, ISOPN, IEPOX, ACTA, EOH, MOH	sfc	500hPa	full column	stratosphere	sfc
Secondary Organic Aerosols SOAP, SOAS, TSOA0, TSOA1, TSOA2, TSOA3, ISOA1, ISOA2, ISOA3, ASOA1, ASOA2, ASOA3, ASOAN, TSOG0, TSOG1, TSOG2, TSOG3, ISOG1, ISOG2, ISOG3, ASOG1, ASOG2, ASOG3, INDIOL, ISN1OA, LVOCOA, SOAIE, SOAGX, SOAME, SOAMG	sfc	500hPa	full column	stratosphere	sfc
Sulfur SOx, DMS, OCS, SO2, SO4	sfc	500hPa	full column	stratosphere	sfc
ROy H2O2, H, H2, H2O, HO2, O1D, OH, RO2	sfc	500hPa	full column	stratosphere	--
J-values	sfc	500hPa	full column	stratosphere	--	--

Emissions by HEMCO category	Total, Aircraft, Anthropogenic, Biomass Burning, Biogenic, Lightning, Natural, Ocean, Seabirds, Decaying Plants, Ship, Soil, Degassing Volcanoes, Erupting Volcanoes
Emission totals	Tables by species, Tables by inventory
Global mass	Entire atmosphere, Troposphere only
Budget	Ox and CO budgets

¹All plots created with GCPy have PDF bookmarks. If you do not see them in your browser try using a different browser (not Safari) or installing an Adobe Acrobat plug-in.

²Species category and lumped species definitions are simple to adjust. Updating them requires only editing the json files.

Benchmark assessment form

Description

New features added into GEOS-Chem

Feature	Submitted by
Updates that will affect full-chemistry simulations
Retire obsolete emission inventories	Eloise Marais (Leicester) Emissions and Deposition Working Group
Updated offline biogenic emissions generated with GEOS-Chem 12.3.0 Includes fixes for biogenic SOAP, SOAS, and CO emissions	Hongjian Weng (PKU)
Updated volcano emissions to include eruptive emissions through April 2018	Christoph Keller (NASA/GMAO)
Remove CO from MEGAN HEMCO extension to avoid double counting	Jenny Fisher (Wollongong)
Fixes for GFED4 emissions, including: Change the HEMCO cycling flag so that the model crashes if it doesn't find the right GFED year Remove the 27% scaling of POG to POA and emit 1:1 instead	Sidhant Pai (MIT)
Scale DICE-Africa emissions to address errors in inventory	Eloise Marais (Leicester)
Bug fix for C3H8 anthropogenic emissions	Melissa Sulprizio (GCST)
Separate anthropogenic PM2.5 dust source from the DustDead extension	Melissa Sulprizio (GCST)
Corrections for CFCs in the chemistry mechanism	Xuan Wang (Harvard)
Fix typo in CLD_PARAMS routine in gckpp_HetRates.F90	Stephen Steenrod (NASA GMAO)
Bug fix: make sure stratospheric BrY concentrations are read properly each month	Lyatt Jaeglé (U. Washington)
Updates that will NOT affect full-chemistry simulations
Enable accurate cloud pH diagnostic calculation via post-processing	Jonathan Moch (Harvard)
Bug fix for proposed Henry's law constants	Jenny Fisher (Wollongong)
Updates that will only affect GCHP
Update GCHP to use MAPL v1.0.0 and ESMF v8.0.0 beta snapshot 28	Lizzie Lundgren (GCST)
Replace 4x5 input files with higher resolution equivalents to avoid ESMF domain decomposition issue at high core counts	Lizzie Lundgren (GCST)

Version, resolution, met fields used:

GEOS-FP (72L), 4x5, July 2016

1-month benchmark finished on:

Wed Aug 28 03:28:34 EDT 2019

Performance statistics:

Compiled with ifort 17.0.4
Ran on 24 CPUs of holyjacob01.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2680 v3 "Haswell" @ 2.50 GHz)
Wall time: 07:28:13
CPU time / wall time: 21.1711
% of ideal performance: 88.21%
Memory: 13.8379 GB

Compared to previous benchmark:

12.4.0

This update will impact:
(select all that apply with boldface)

Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Emissions, Photolysis, Chemistry, Other (please specify): Diagnostics

Unit test results may be viewed at:

http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/GC_12.5.0_Aug08.results.html

Metrics

Global mean OH from log file (% change):

12.3915975939893 x 10⁵ molec/cm³ (-0.65%)

Methyl chloroform lifetime (% change):

4.9487 (1.06%)

Methane lifetime (% change):

8.3312 years (1.10%)

List all SURFACE species, J-Values, and COLUMN AOD values that changed by 10% or more:

Oxidants: O3 CO OH NOx
Aerosols: NH4 NIT SO4 DST1 AERI BrSALA BrSALC ISALA ISALC NITs SO4s SOA_Complex SOA_Simple
Nitrogen: NOy NOx HNO2 HNO3 HNO4 IPMN NIT NO NO2 NO3 N2O5 MPN PAN PPN NHx NH3 NH4
ROy: H2O2 H HO2 O1D OH RO2
Sulfur: SOx DMS SO2 SO4
Iodine: Iy IxOy I I2 IBr ICl IO INO2 IONO2 HI HOI OIO
Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl HCFCs OClO
Primary_Organics: ALK4 BENZ C2H6 C3H8 PRPE TOLU XYLE ISOP MTPA MTPO LIMO GLYX HCOOH MAP RCHO
Secondary_Organics: ACET MEK MVK ALD2 CH2O HPALD MP ISOPN IEPOX ACTA EOH SOAIE LVOCOA
J-Values: CCl4 CFC11 CFC113 CFC114 CFC115 CFC12 CH2Cl2 CH3CCl3 CH3Cl HCFC123 HCFC141b HCFC142b N2O O2
Column AOD: Dust OCPI SO4 SOA_from_Aqueous_ISOP Total

List all 500 hPa species and J-Values that changed by 10% or more :

Oxidants: OH NOx
Aerosols: NH4 NIT SO4 DST1 AERI BrSALA BrSALC ISALC NITs SO4s SOA_Complex SOA_Simple
Nitrogen: NOx HNO2 HNO4 IPMN NIT NO NO2 NO3 N2O5 MPN PAN PPN NHx NH3 NH4
ROy: OH
Sulfur: SOx DMS SO2 SO4
Iodine: I2 ICl INO2 IONO2 CH2I2 HI OIO
Bromine: BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
Chlorine: ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl OClO
Primary_Organics: ALK4 BENZ C2H6 C3H8 PRPE TOLU XYLE ISOP MTPA MTPO LIMO GLYX HCOOH MAP RCHO
Secondary_Organics: ACET MEK MVK ALD2 HPALD MP ISOPN IEPOX ACTA EOH SOAIE LVOCOA
J-Values: None

List all ZONAL MEAN species and J-Values that changed by 10% or more:

Oxidants: OH NOx
Aerosols: NH4 NIT SO4 DST1 BrSALA BrSALC NITs SO4s SOA_Complex SOA_Simple
Nitrogen: NOy NOx HNO2 HNO3 IPMN NIT NO2 NO3 N2O5 MPN PAN PPN NH3 NH4
ROy: OH RO2
Sulfur: SOx SO2 SO4
Iodine: I2 IBr ICl INO2 IONO2 CH2I2 HI OIO
Bromine: BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl OClO
Primary_Organics: ALK4 C2H6 C3H8 PRPE TOLU XYLE ISOP MTPA MTPO LIMO GLYX HCOOH MAP RCHO
Secondary_Organics: ACET MEK MVK ALD2 CH2O HPALD ISOPN IEPOX ACTA EOH SOAIE LVOCOA
J-Values: None

List all EMISSIONS that changed by 10% or more:

Anthro: ALD2 ALK4 BCPI BCPO C2H6 C3H8 CO HAC MEK NH3 NO pFe PRPE SO2 SO4 SOAP
Biogenic: ACET ALD2 EOH ISOP LIMO PRPE SOAP SOAS
Ship: CO HNO3 NO2 NO O3 SO2 SOAP
Total: ACET ALD2 ALK4 BCPI BCPO C2H6 C3H8 CO EOH GLYX ISOP MEK MGLY MTPA NH3 NO pFe PRPE SO2 SO4 SOAP
VolcDegas: SO2
VolcErupt: SO2

Comments on observed differences:

Below we summarize the notable changes caused by specific updates.

Retire obsolete emission inventories

Retiring the EMEP, Bond, RETRO, and Yevich & Logan biofuel inventories results in large fractional differences in anthropogenic emissions and species concentrations over Europe, South America, Central America, Russia, and Australia, where the global anthropogenic, biofuel, and ship emissions from the CEDS inventory are now used. The impact on emission totals are included below.

  ###############################################################################
  ### Emissions totals                                                        ###
  ### Ref = GC_12.4.0; Dev = GC_12.5.0                                        ###
  ###############################################################################
                                   Ref            Dev            Dev - Ref
  ACET Anthro               :      0.171664       0.069874      -0.101790 Tg C
  ALD2 Anthro               :      0.042310       0.042140      -0.000169 Tg C
  ALK4 Anthro               :      2.407840       2.572299       0.164460 Tg C
  BCPI Anthro               :      0.106725       0.106747       0.000021 Tg
  BCPO Anthro               :      0.426900       0.426986       0.000086 Tg
  C2H6 Anthro               :      0.473419       0.664990       0.191571 Tg C
  C3H8 Anthro               :      0.399813       0.595361       0.195548 Tg C
  CH2O Anthro               :      0.263482       0.235037      -0.028445 Tg
  CO Anthro                 :     42.984464      40.778317      -2.206146 Tg
  HAC Anthro                :      0.212160       0.042432      -0.169728 Tg
  HCOOH Anthro              :      0.577087       0.571744      -0.005343 Tg
  MEK Anthro                :      0.043368       0.064733       0.021364 Tg C
  NH3 Anthro                :      4.430414       4.592343       0.161929 Tg
  NO Anthro                 :      5.543591       5.293092      -0.250499 Tg
  OCPI Anthro               :      0.628814       0.610537      -0.018278 Tg
  OCPO Anthro               :      0.628815       0.610537      -0.018278 Tg
  pFe Anthro                :      0.006943       0.006628      -0.000315 Tg
  PRPE Anthro               :      0.490600       0.448865      -0.041735 Tg C
  SO2 Anthro                :      6.974655       7.092453       0.117797 Tg
  SO4 Anthro                :      0.218581       0.210372      -0.008208 Tg
  SOAP Anthro               :      2.978745       2.826521      -0.152224 Tg
  TOLU Anthro               :      0.584716       0.553756      -0.030960 Tg C
  CO Ship                   :      0.079328       0.059695      -0.019634 Tg
  HNO3 Ship                 :      1.484222       1.449563      -0.034659 Tg
  NO Ship                   :      0.081681       0.082875       0.001195 Tg
  NO2 Ship                  :      0.771094       0.738918      -0.032176 Tg
  SO2 Ship                  :      0.805693       0.773045      -0.032648 Tg
  SOAP Ship                 :      0.005474       0.004119      -0.001355 Tg

Updated offline biogenic emissions generated with GEOS-Chem 12.3.0

The offline biogenic emissions were updated to include recent fixes to the MEGAN extension. With this update, emissions for MTPA and MTPO are now included, as opposed to the individual components (APIN, BPIN, BCAR, etc.) included in the previous version. CO from monoterpenes has been removed to avoid double-counting that source. In addition, the SOAP and SOAS emissions from the offline biogenic VOC files are ignored, and SOAP and SOAS emissions are instead computed by scaling isoprene and monoterpene emissions. The impact on biogenic emission totals are included below.

  ###############################################################################
  ### Inventory totals for OFFLINEBIOVOC                                      ###
  ### Ref = GC_12.4.0; Dev = GC_12.5.0                                        ###
  ###############################################################################
                                   Ref            Dev            Dev - Ref
  OFFLINEBIOVOC ACET        :      2.677313       2.982478       0.305164 Tg C
  OFFLINEBIOVOC ALD2        :      1.032241       1.037183       0.004942 Tg C
  OFFLINEBIOVOC CO          :      5.504973            nan            nan Tg C
  OFFLINEBIOVOC EOH         :      0.987091       0.991817       0.004726 Tg C
  OFFLINEBIOVOC ISOP        :     35.759849      33.723910      -2.035939 Tg C
  OFFLINEBIOVOC LIMO        :      1.022397       0.976173      -0.046225 Tg C
  OFFLINEBIOVOC MTPA        :           nan       8.644930            nan Tg C
  OFFLINEBIOVOC MTPO        :           nan       4.000710            nan Tg C
  OFFLINEBIOVOC PRPE        :      2.126864       2.030293      -0.096571 Tg C
  OFFLINEBIOVOC SOAP        :      0.621433       1.467334       0.845901 Tg C
  OFFLINEBIOVOC SOAS        :      0.621433       1.467334       0.845901 Tg C

While it appears that SOAP and SOAS emissions have a large increase from 12.4.0, these emission totals are now more in-line with 12.3.0 emission totals using online emissions from the MEGAN extension. In 12.3.0, emission totals of SOAP and SOAS were each 1.294232 Tg C.

Jeff Pierce pointed out that we see a much larger increase in the complex SOA concentrations as compared to the simple SOA concentrations (see the last two pages of this file). However, when we do the comparison of 12.5.0 vs 12.3.0, the differences are much lower altogether and have varying signs, consistent with the retirement of several emission inventories (see the last two pages of this file). The 12.5.0 vs 12.3.0 are the comparisons to focus on because the 12.4.0 biogenic emissions were generated with and older version of MEGAN from GEOS-Chem v11-02. An outcome of the 12.4.0 benchmarking was that we should apply scaling of isoprene emissions to match the 12.3.0 annual totals. That scaling would impact the complex SOA species but not the simple SOA species which were read directly from the offline biogenic VOC files. In 12.5.0, the Aerosol WG decided not to read the simple SOA species directly from the offline biogenic VOC files after finding that the emissions in those files were too low compared to 12.3.0. Instead we now compute the SOAP and SOAS emissions by scaling the isoprene and monoterpene emissions from the offline biogenic VOC files. For the complete set of plots comparing 12.5.0 to 12.3.0, please visit http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots_vs_12.3.0/.

In this benchmark, we also introduced the Secondary Organic Aerosols benchmark category and global mass tables to assist with evaluating this update. These plots will be included in future benchmarks.

Updated volcano emissions to include eruptive emissions through April 2018

This update increased both eruptive and degassing volcanic emissions, as summarized below. As a result, localized increases in SO2 and SO4 can be seen in the species concentration plots.

  ###############################################################################
  ### Inventory totals for VOLCANO                                            ###
  ### Ref = GC_12.4.0; Dev = GC_12.5.0                                        ###
  ###############################################################################
                                   Ref            Dev            Dev - Ref
  VOLCANOerupt SO2          :      0.000000       0.035000       0.035000 Tg
  VOLCANOdegas SO2          :      1.509524       1.951957       0.442434 Tg

Scale DICE-Africa emissions to address errors in inventory

This update contributes to changes in BC and OC concentrations over and just downwind of Africa. Slight differences can also be seen over Africa in the emission maps. The impact on the inventory emission totals are included below.

  ###############################################################################
  ### Inventory totals for DICEAfrica                                         ###
  ### Ref = GC_12.4.0; Dev = GC_12.5.0                                        ###
  ###############################################################################
                                   Ref            Dev            Dev - Ref
  DICEAfrica BCPI           :      0.004131       0.004153       0.000022 Tg
  DICEAfrica BCPO           :      0.016526       0.016612       0.000086 Tg
  DICEAfrica CH2O           :      0.044793       0.016348      -0.028445 Tg
  DICEAfrica CO             :      5.651943       3.648702      -2.003242 Tg
  DICEAfrica HAC            :      0.212160       0.042432      -0.169728 Tg
  DICEAfrica HCOOH          :      0.006679       0.001336      -0.005343 Tg
  DICEAfrica NH3            :      0.294221       0.284477      -0.009744 Tg
  DICEAfrica NO             :      0.153533       0.151820      -0.001713 Tg
  DICEAfrica OCPI           :      0.035185       0.016907      -0.018278 Tg
  DICEAfrica OCPO           :      0.035185       0.016907      -0.018278 Tg
  DICEAfrica PRPE           :      0.057572       0.019730      -0.037842 Tg
  DICEAfrica SOAP           :      0.389982       0.251758      -0.138224 Tg
  DICEAfrica TOLU           :      0.054817       0.020857      -0.033960 Tg

Bug fix for C3H8 anthropogenic emissions

C3H8 anthropogenic emissions increase with the implementation of this fix, addressing low C3H8 totals in the CEDS inventory:

  ###############################################################################
  ### Emissions totals for species C3H8                                       ###
  ### Ref = GC_12.4.0; Dev = GC_12.5.0                                        ###
  ###############################################################################
                                   Ref            Dev            Dev - Ref
  C3H8 Anthro               :      0.399813       0.595361       0.195548 Tg C

Separate anthropogenic PM2.5 dust source from the DustDead extension

This update reintroduces the anthropogenic PM2.5 fine dust source and increases concentrations of DST1. The impact on DST1 emission totals are included below.

  ###############################################################################
  ### Inventory totals for AFCID                                              ###
  ### Ref = GC_12.5.0; Dev = GC_12.5.0                                        ###
  ###############################################################################
                                   Ref            Dev            Dev - Ref
  AFCID DST1                :           nan       1.087876            nan Tg

The following updates produced small changes, primarily over the southern hemisphere oceans and at high altitudes:

Comments on additional differences in GCHP:

GCHP 12.5.0 uses MAPL version tag "gchp/v1.0.0" released in early 2019. The MAPL library, which is developed by NASA, is a wrapper for the Earth System Modeling Framework (ESMF), and handles not only I/O but also passing of data between components. With this version update GCHP input speed executes roughly 3-4 times faster than previous versions! This speed-up is due to parallelization within input read across one node, and the MAPL updates in this version are just the beginning of improvements to GCHP I/O bottlenecks.

While we are encouraged by the improvements to GCHP in 12.5.0, a few issues remain open until the next MAPL update later this year.

GCHP 12.5.0 currently has a slow memory leak due to updates to MAPL ExtData. NASA is aware of the issue and will be developing a fix soon. The memory leak is more pronounced for long simulations and can result in a simulation crashing due to exceeding memory available. Breaking up long runs into smaller consecutive runs avoids the issue but we find that doing so changes the output. Lizzie Lundgren (GCST) is investigating differences in GCHP output that happen when restarting a simulation, which may or may not be a problem with GEOS-Chem Classic as well. We are documenting all single versus multi-run differences at http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/multi_vs_single_run/. Look there to assess if the scale of the differences would be a problem for you.
GCHP 12.5.0 uses online ESMF regridding weights rather than external tile files for regridding. Due to ESMF domain decomposition rules this can result in a MAPL error if an input grid is too coarse for a run’s configured core count. We have seen this problem for 4°x5° input files when using >600 cores. GMAO has fixed this problem in a more recent version of MAPL. All 4°x5° input files are replaced with higher resolution files for GCHP 12.5.0 to avoid this issue. However, users may still run into problems if running with thousands of cores.
There is a positive bias in surface ozone over the Southern Ocean in GCHP. It shows in comparisons with both GCC 12.5.0 and GCHP 12.4.0. The issue is resolution-dependent and occurs in FV3. An issue has been created on GEOS github for this: https://github.com/GEOS-ESM/GEOSgcm_GridComp/issues/48. To evaluate this bias at different resolutions, we also ran and GCHP 12.5.0 benchmark at c24. Results from that simulation may be viewed at this link.

Approval

Requires further investigation:

No

Approved by:

Jeff Pierce, Daniel Jacob

Date of approval:

06 Sep 2019

GCHP 1-month benchmark

The following sections contain validation plots for GCHP 12.5.0.

Comparison of GCHP versions

This table contains plots comparing GCHP 12.4.0 (Ref) and GCHP 12.5.0 (Dev) for a 1-month simulation.

Category	Plots					Additional Information
	Level Map		Zonal Mean		Emissions
Oxidants	sfc	500hPa	full column	stratosphere	full column
Aerosols	sfc	500hPa	full column	stratosphere	full column	Column AOD
Bromine	sfc	500hPa	full column	stratosphere	full column
Chlorine	sfc	500hPa	full column	stratosphere	--
Iodine	sfc	500hPa	full column	stratosphere	full column
Nitrogen	sfc	500hPa	full column	stratosphere	full column
Primary Organics	sfc	500hPa	full column	stratosphere	full column
Secondary Organics	sfc	500hPa	full column	stratosphere	full column
Sulfur	sfc	500hPa	full column	stratosphere	full column
Emissions by HEMCO category	Aircraft, Anthro, Bioburn, Biogenic, Lightning, Monoterp, Natural, Ocean, Seabirds, DecayingPlants, Ship, Soil, Total, VolcDegas, VolcErupt,					Emission totals

Comparison of GCHP and GEOS-Chem Classic

This table contains plots comparing GEOS-Chem Classic 12.5.0 (Ref) against GCHP 12.5.0 (Dev) for a 1-month simulation.

Category	Plots					Additional Information
	Level Map		Zonal Mean		Emissions
Oxidants	sfc	500hPa	full column	stratosphere	full column
Aerosols	sfc	500hPa	full column	stratosphere	full column	Column AOD
Bromine	sfc	500hPa	full column	stratosphere	full column
Chlorine	sfc	500hPa	full column	stratosphere	--
Iodine	sfc	500hPa	full column	stratosphere	full column
Nitrogen	sfc	500hPa	full column	stratosphere	full column
Primary Organics	sfc	500hPa	full column	stratosphere	full column
Secondary Organics	sfc	500hPa	full column	stratosphere	full column
Sulfur	sfc	500hPa	full column	stratosphere	full column
Emissions by HEMCO category	Aircraft, Anthro, Bioburn, Biogenic, Lightning, Monoterp, Natural, Ocean, Seabirds, DecayingPlants, Ship, Soil, Total, VolcDegas, VolcErupt,					Emission totals

GCHP and GEOS-Chem Classic difference of differences

This table contains plots comparing the difference [GCHP 12.5.0 - GCHP 12.4.0] against the difference [GC Classic 12.5.0 - GC Classic 12.4.0], taken from 1-month benchmark simulations.

Category	Plots
	Level Map		Zonal Mean
Oxidants	sfc	500hPa	full column	stratosphere
Aerosols	sfc	500hPa	full column	stratosphere
Bromine	sfc	500hPa	full column	stratosphere
Chlorine	sfc	500hPa	full column	stratosphere
Iodine	sfc	500hPa	full column	stratosphere
Nitrogen	sfc	500hPa	full column	stratosphere
Primary Organics	sfc	500hPa	full column	stratosphere
Secondary Organics	sfc	500hPa	full column	stratosphere
Sulfur	sfc	500hPa	full column	stratosphere

NOTE: At present, we have only created the diff-of-diffs plots for species concentration. This can be extended to other categories in the future.

Validation of netCDF diagnostics

In this version, we did a complete comparison of the BPCH diagnostics to the netCDF diagnostics in preparation for retiring the old BPCH diagnostics. Comparison plots can be accessed via the links below. A summary of the results may be found on this Google spreadsheet.

NetCDF collection	BPCH equivalent(s)	Plots
		Level Map	Zonal Mean
AdvFluxMerid	ND25	sfc	full column
AdvFluxVert	ND26	sfc	full column
AdvFluxZonal	ND24	sfc	full column
AerosolMass	ND42	sfc	full column
Aerosols	ND21	sfc	full column
CloudConvFlux	ND14	500hPa	full column
ConcAfterChem	ND43	sfc	full column
DryDep	ND44	sfc
Emissions (i.e. HEMCO diagnostics)	ND06, ND07, ND08, ND11, ND13, ND28, ND29, ND32, ND34, ND36, ND46	sfc PlantDecay
JValues (24-hr avg)	ND22	sfc	full column
JValuesLocalNoon	ND22	sfc	full column
LevelEdgeDiags	ND31, ND66	850hPa	full column
ProdLoss	ND05, ND07, ND65	sfc	full column
SpeciesConc	ND45	sfc	full column
StateChm	ND73	sfc	full column
StateMet	ND57 ND31, ND55, ND66, ND67, ND68, ND69	sfc sfc	full column full column
WetLossConv	ND38, ND37	850hPa	full column
WetLossLS	ND39	850hPa	full column

Difference between revisions of "Benchmark/GEOS-Chem 12.5.0"

Latest revision as of 16:19, 26 August 2020

Contents

GEOS-Chem Classic 1-month benchmark

Benchmark plots

Benchmark assessment form

GCHP 1-month benchmark

Comparison of GCHP versions

Comparison of GCHP and GEOS-Chem Classic

GCHP and GEOS-Chem Classic difference of differences

Validation of netCDF diagnostics

Navigation menu

Personal tools

Namespaces

Variants

Views

More

Search

Navigation

Tools

@@ Line 1: / Line 1: @@
 __FORCETOC__
-[[Image:Page is under construction.jpg]]
-<span style="color:red">'''''NOTE: This page contains prelimary plots used to identify problems -- it does not contain the official benchmark results yet!'''''</span>
+This page includes information about all benchmark simulations for [[GEOS-Chem 12#12.5.0|GEOS-Chem 12.5.0]] ([https://doi.org/10.5281/zenodo.3403111 DOI: 10.5281/zenodo.3403111]).
-This page includes information about all benchmark simulations for [[GEOS-Chem 12#12.5.0|GEOS-Chem 12.5.0]].
 == GEOS-Chem Classic 1-month benchmark ==
@@ Line 10: / Line 7: @@
 === Benchmark plots ===
-These benchmarks were primarily made with [https://github.com/geoschem/gcpy GCPy]. Some benchmark plots created by GAMAP still remain because they have not been recreated in GCPy yet.
+Enable PDF bookmarks<sup>1</sup> in the files linked below to navigate between species. See the [[Species in GEOS-Chem]] wiki page for species definitions and details.
 {| border=1 cellspacing=0 cellpadding=5
 |-
-!colspan="1" bgcolor="#CCFFFF"|Category<sup>1</sup>
+!colspan="1" bgcolor="#CCFFFF" width="325px"|Species Category<sup>2</sup>
 !colspan="5" bgcolor="#CCFFFF"|Plots
 !colspan="1" bgcolor="#CCFFFF"|Additional Information
@@ Line 27: / Line 24: @@
 |-valign="top"
-|Primary
+|'''Oxidants'''
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Primary/Primary_Surface.pdf sfc]
+O3, CO, OH, NOx
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Primary/Primary_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Oxidants/Oxidants_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Primary/Primary_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Oxidants/Oxidants_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Primary/Primary_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Oxidants/Oxidants_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Primary/Primary_Emissions.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Oxidants/Oxidants_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Oxidants/Oxidants_Emissions.pdf sfc]
 |
 |-valign="top"
-|Aerosols
+|'''Aerosols'''
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Aerosols/Aerosols_Surface.pdf sfc]
+NH4, NIT, SO4, DST1, DST2, DST3, DST4, BC, OC, AERI, BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s, SOA_Simple, SOA_Complex
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Aerosols/Aerosols_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Aerosols/Aerosols_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Aerosols/Aerosols_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Aerosols/Aerosols_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Aerosols/Aerosols_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Aerosols/Aerosols_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Aerosols/Aerosols_Emissions.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Aerosols/Aerosols_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Aerosols/Aerosols_ColumnOptDepth.pdf AOD]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Aerosols/Aerosols_Emissions.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Aerosols/Aerosols_ColumnOptDepth.pdf AOD]
 |-valign="top"
-|Bromine
+|'''Bromine'''
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Bromine/Bromine_Surface.pdf sfc]
+Bry, BrOx, Br, Br2, BrCl, BrNO2, BrNO3, BrO, CH4Br, CH2Br2, CH2Br2, CH3Br3, HOBr, HBr
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Bromine/Bromine_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Bromine/Bromine_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Bromine/Bromine_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Bromine/Bromine_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Bromine/Bromine_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Bromine/Bromine_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Bromine/Bromine_Emissions.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Bromine/Bromine_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Bromine/Bromine_Emissions.pdf sfc]
 |
 |-valign="top"
-|Chlorine
+|'''Chlorine'''
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Chlorine/Chlorine_Surface.pdf sfc]
+Cly, ClOx, Cl, ClO, Cl2, Cl2O2, ClOO, ClNO2, ClNO3, CCl4, CFCs, CH3Cl, CH2Cl2, CH4CCl3, HOCl, HCl, Halons, HCFCs, OClO
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Chlorine/Chlorine_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Chlorine/Chlorine_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Chlorine/Chlorine_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Chlorine/Chlorine_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Chlorine/Chlorine_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Chlorine/Chlorine_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Chlorine/Chlorine_Strat_ZonalMean.pdf stratosphere]
 | --
 |
 |-valign="top"
-|Iodine
+|'''Iodine'''
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Iodine/Iodine_Surface.pdf sfc]
+Iy, IxOy, I, I2, IBr, ICl, IO, INO2, IONO2, CH3I, CH2I2, CH2ICl, CH2IBr, HI, HOI, OIO
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Iodine/Iodine_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Iodine/Iodine_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Iodine/Iodine_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Iodine/Iodine_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Iodine/Iodine_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Iodine/Iodine_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Iodine/Iodine_Emissions.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Iodine/Iodine_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Iodine/Iodine_Emissions.pdf sfc]
 |
 |-valign="top"
-|Nitrogen
+|'''Nitrogen'''
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Nitrogen/Nitrogen_Surface.pdf sfc]
+NOy, NOx, HNO2, HNO3, HNO4, IMPN, NIT, NO, NO2, NO3, N2O5, MPN, PAN, PPN, N2O, NHx, NH3, NH4
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Nitrogen/Nitrogen_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Nitrogen/Nitrogen_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Nitrogen/Nitrogen_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Nitrogen/Nitrogen_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Nitrogen/Nitrogen_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Nitrogen/Nitrogen_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Nitrogen/Nitrogen_Emissions.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Nitrogen/Nitrogen_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Nitrogen/Nitrogen_Emissions.pdf sfc]
 |
 |-valign="top"
-|Primary Organics
+|'''Primary Organics'''
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Primary_Organics/Primary_Organics_Surface.pdf sfc]
+ALK4, BENZ, CH4, C2H6, C2H4, C3H8, PRPE, TOLU, XYLE, ISOP, MTPA, MTPO, LIMO, GLYX, HCOOH, MAP, MBO, MOH, RCHO
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Primary_Organics/Primary_Organics_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Primary_Organics/Primary_Organics_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Primary_FullColumn_Organics/Primary_Organics_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Primary_Organics/Primary_Organics_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Primary_Strat_Organics/Primary_Organics_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Primary_Organics/Primary_Organics_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Primary_Organics/Primary_Organics_Emissions.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Primary_Organics/Primary_Organics_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Primary_Organics/Primary_Organics_Emissions.pdf sfc]
 |
 |-valign="top"
-|Secondary Organics
+|'''Secondary Organics'''
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Secondary_Organics/Secondary_Organics_Surface.pdf sfc]
+ACET, MEK, MVK, ALD2, CH2O, HPALD, MP, ISOPN, IEPOX, ACTA, EOH, MOH
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Secondary_Organics/Secondary_Organics_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Secondary_Organics/Secondary_Organics_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Secondary_FullColumn_Organics/Secondary_Organics_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Secondary_Organics/Secondary_Organics_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Secondary_Strat_Organics/Secondary_Organics_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Secondary_Organics/Secondary_Organics_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Secondary_Organics/Secondary_Organics_Emissions.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Secondary_Organics/Secondary_Organics_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Secondary_Organics/Secondary_Organics_Emissions.pdf sfc]
 |
 |-valign="top"
-|ROy
+|'''Secondary Organic Aerosols'''
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/ROy/ROy_Surface.pdf sfc]
+SOAP, SOAS, TSOA0, TSOA1, TSOA2, TSOA3, ISOA1, ISOA2, ISOA3, ASOA1, ASOA2, ASOA3, ASOAN, TSOG0, TSOG1, TSOG2, TSOG3, ISOG1, ISOG2, ISOG3, ASOG1, ASOG2, ASOG3, INDIOL, ISN1OA, LVOCOA, SOAIE, SOAGX, SOAME, SOAMG
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/ROy/ROy_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Secondary_Organic_Aerosols/Secondary_Organic_Aerosols_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/ROy/ROy_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Secondary_Organic_Aerosols/Secondary_Organic_Aerosols_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/ROy/ROy_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Secondary_Organic_Aerosols/Secondary_Organic_Aerosols_FullColumn_ZonalMean.pdf full column]
-| --
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Secondary_Organic_Aerosols/Secondary_Organic_Aerosols_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Secondary_Organic_Aerosols/Secondary_Organic_Aerosols_Emissions.pdf sfc]
 |
 |-valign="top"
-|Sulfur
+|'''Sulfur'''
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Sulfur/Sulfur_Surface.pdf sfc]
+SOx, DMS, OCS, SO2, SO4
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Sulfur/Sulfur_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Sulfur/Sulfur_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Sulfur/Sulfur_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Sulfur/Sulfur_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Sulfur/Sulfur_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Sulfur/Sulfur_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Sulfur/Sulfur_Emissions.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Sulfur/Sulfur_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Sulfur/Sulfur_Emissions.pdf sfc]
 |
 |-valign="top"
-|Emissions by HEMCO category
+|'''ROy'''
-!colspan="5"|
+H2O2, H, H2, H2O, HO2, O1D, OH, RO2
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Emissions/Total_Emissions.pdf Total],
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/ROy/ROy_Surface.pdf sfc]
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Emissions/Aircraft_Emissions.pdf Aircraft],
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/ROy/ROy_500hPa.pdf 500hPa]
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Emissions/Anthro_Emissions.pdf Anthro],
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/ROy/ROy_FullColumn_ZonalMean.pdf full column]
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Emissions/Bioburn_Emissions.pdf Bioburn],
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/ROy/ROy_Strat_ZonalMean.pdf stratosphere]
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Emissions/Biofuel_Emissions.pdf Biofuel],
+| --
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Emissions/Biogenic_Emissions.pdf Biogenic],<br>
+|
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Emissions/Lightning_Emissions.pdf Lightning],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Emissions/Monoterp_Emissions.pdf Monoterp],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Emissions/Natural_Emissions.pdf Natural],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Emissions/Ocean_Emissions.pdf Ocean],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Emissions/Seabirds_Emissions.pdf Seabirds],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Emissions/Senesc_Emissions.pdf SenescingPlants],<br>
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Emissions/Ship_Emissions.pdf Ship],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Emissions/Soil_Emissions.pdf Soil],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Emissions/VolcDegas_Emissions.pdf VolcDegas],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Emissions/VolcErupt_Emissions.pdf VolcErupt],
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/Emissions/Emission_totals.txt Emissions tables]
 |-valign="top"
 |J-values
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/JValues/JVal_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/JValues/Jval_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/JValues/JVal_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/JValues/Jval_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/JValues/JVal_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/JValues/Jval_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/JValues/JVal_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/JValues/Jval_Strat_ZonalMean.pdf stratosphere]
 | --
 | --
 |-valign="top"
-!colspan="7" bgcolor="#CCCCCC"|Plots still created by GAMAP
+!colspan="7" bgcolor="#CCCCCC"|&nbsp;
+|-valign="top"
+|Emissions by HEMCO category
+|colspan="6"|
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Emissions/Total_Emissions.pdf Total],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Emissions/Aircraft_Emissions.pdf Aircraft],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Emissions/Anthro_Emissions.pdf Anthropogenic],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Emissions/BioBurn_Emissions.pdf Biomass Burning],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Emissions/Biogenic_Emissions.pdf Biogenic],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Emissions/Lightning_Emissions.pdf Lightning],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Emissions/Natural_Emissions.pdf Natural],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Emissions/Ocean_Emissions.pdf Ocean],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Emissions/Seabirds_Emissions.pdf Seabirds],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Emissions/PlantDecay_Emissions.pdf Decaying Plants],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Emissions/Ship_Emissions.pdf Ship],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Emissions/Soil_Emissions.pdf Soil],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Emissions/VolcDegas_Emissions.pdf Degassing Volcanoes],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Emissions/VolcErupt_Emissions.pdf Erupting Volcanoes]
+|-valign="top"
+|Emission totals
+|colspan="6"|
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Emissions/Emission_totals.txt Tables by species],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Emissions/Inventory_totals.txt Tables by inventory]
+|-valign="top"
+|Global mass
+|colspan="6"|
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/GC_12.5.0_GlobalMass_TropStrat.txt Entire atmosphere],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/GC_12.5.0_GlobalMass_Trop.txt Troposphere only]
 |-valign="top"
 |Budget
-| --
+|colspan="6"|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/GC_12.5.0.budget.txt Ox and CO budgets]
-| --
-| --
-| --
-| --
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/GC_12.5.0.budget.txt Ox and CO budgets]
 |}
-<sup>1</sup>'''Benchmark category definitions:''' [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/benchmark_categories.json benchmark_categories.json]<br>
+<sup>1</sup>All plots created with GCPy have PDF bookmarks. If you do not see them in your browser try using a different browser (not Safari) or installing an Adobe Acrobat plug-in.
-<sup>2</sup>'''Lumped species definitions:''' [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/lumped_species.json lumped_species.json]<br>
-'''NOTES:'''
+<sup>2</sup>[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/benchmark_categories.json Species category] and [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/lumped_species.json lumped species] definitions are simple to adjust. Updating them requires only editing the json files.
-#[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/benchmark_categories.json Category] and [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Official/lumped_species.json lumped species] definitions are simple to adjust. Updating them requires only editing the json files.
-#All plots created with GCPy have PDF bookmarks. If you do not see them in your browser try using a different browser (not Safari) or installing an Adobe Acrobat plug-in.
 === Benchmark assessment form ===
@@ Line 187: / Line 203: @@
 |-valign="top"
-|[[Stratospheric_chemistry#Bug_fix:_make_sure_stratospheric_BrY_concentrations_are_read_properly_each_month|Bug fix: make sure stratospheric BrY concentrations are read properly each month]]
+|[[Issues_now_resolved_in_GEOS-Chem_12#Retire_obsolete_emission_inventories|Retire obsolete emission inventories]]
-|Lyatt Jaegl&eacute; (U. Washington)
+|Eloise Marais (Leicester)<br>[[Emissions and Deposition Working Group]]
 |-valign="top"
-|[[GEOS-Chem_12#Retire_obsolete_emission_inventories|Retire obsolete emission inventories]]
+|[[Grid-independent_emissions#Biogenic_VOC_emissions|Updated offline biogenic emissions generated with GEOS-Chem 12.3.0]]
-|Eloise Marais (Leicester)<br>[[Emissions and Deposition Working Group]]
+*Includes [[Grid-independent_emissions#Fixes_for_biogenic_SOAP.2C_SOAS.2C_and_CO_emissions|fixes for biogenic SOAP, SOAS, and CO emissions]]
+|Hongjian Weng (PKU)
+|-valign="top"
+|[[Volcanic_SO2_emissions|Updated volcano emissions to include eruptive emissions through April 2018]]
+|Christoph Keller (NASA/GMAO)
+|-valign="top"
+|[[MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions#Remove_biogenic_CO_emissions_to_avoid_double_counting|Remove CO from MEGAN HEMCO extension to avoid double counting]]
+|Jenny Fisher (Wollongong)
 |-valign="top"
@@ Line 201: / Line 226: @@
 |-valign="top"
-|[[GEOS-Chem_12#Corrections_for_CFCs_in_the_chemistry_mechanism|Corrections for CFCs in the chemistry mechanism]]
+|[[DICE-Africa_anthropogenic_emissions_inventory#Scale_DICE-Africa_emissions_to_address_errors_in_inventory|Scale DICE-Africa emissions to address errors in inventory]]
+|Eloise Marais (Leicester)
+|-valign="top"
+|[[Issues_now_resolved_in_GEOS-Chem_12#Bug_fix_for_C3H8_anthropogenic_emissions|Bug fix for C3H8 anthropogenic emissions]]
+|Melissa Sulprizio ([[GCST]])
+|-valign="top"
+|[[Mineral_dust_aerosols#Separate_AFCID_from_DustDead_extension|Separate anthropogenic PM2.5 dust source from the DustDead extension]]
+|Melissa Sulprizio ([[GCST]])
+|-valign="top"
+|[[Issues_now_resolved_in_GEOS-Chem_12#Corrections_for_CFCs_in_the_chemistry_mechanism|Corrections for CFCs in the chemistry mechanism]]
 |Xuan Wang (Harvard)
 |-valign="top"
-|[[GEOS-Chem_12#Fix_typo_in_CLD_PARAMS_routine_in_gckpp_HetRates.F90|Fix typo in CLD_PARAMS routine in gckpp_HetRates.F90]]
+|[[Issues_now_resolved_in_GEOS-Chem_12#Fix_typo_in_CLD_PARAMS_routine_in_gckpp_HetRates.F90|Fix typo in CLD_PARAMS routine in gckpp_HetRates.F90]]
 |Stephen Steenrod (NASA GMAO)
 |-valign="top"
-!colspan="2" bgcolor="#CCFFFF"|Updates that will NOT affect full-chemistry simulations
+|[[Stratospheric_chemistry#Bug_fix:_make_sure_stratospheric_BrY_concentrations_are_read_properly_each_month|Bug fix: make sure stratospheric BrY concentrations are read properly each month]]
+|Lyatt Jaegl&eacute; (U. Washington)
 |-valign="top"
-|[[List_of_diagnostics_archived_to_netCDF_format#Sample_HISTORY.rc_diagnostic_input_file|Enable GEOS-Chem "Classic" netCDF (History) diagnostics to be subsetted vertically and horizontally]]
+!colspan="2" bgcolor="#CCFFFF"|Updates that will NOT affect full-chemistry simulations
-|Bob Yantosca (GCST)
 |-valign="top"
-|[[GEOS-Chem_12#Enable_accurate_cloud_pH_diagnostic_calculation|Enable accurate cloud pH diagnostic calculation via post-processing]]
+|[[Issues_now_resolved_in_GEOS-Chem_12#Enable_accurate_cloud_pH_diagnostic_calculation|Enable accurate cloud pH diagnostic calculation via post-processing]]
 |Jonathan Moch (Harvard)
+|-valign="top"
+|[[Physical_properties_of_GEOS-Chem_species#Proposed_list_of_Henry.27s_law_constants_from_the_literature|Bug fix for proposed Henry's law constants]]
+|Jenny Fisher (Wollongong)
 |-valign="top"
@@ Line 223: / Line 264: @@
 |-valign="top"
-|Update GCHP to use MAPL v1.0.0 and ESMF v8.0.0 beta snapshot 28
+|[[Getting_Started_with_GCHP#New_in_12.5.0|Update GCHP to use MAPL v1.0.0 and ESMF v8.0.0 beta snapshot 28]]
 |Lizzie Lundgren (GCST)
+|-valign="top"
+|[[Getting_Started_with_GCHP#New_in_12.5.0|Replace 4x5 input files with higher resolution equivalents to avoid ESMF domain decomposition issue at high core counts]]
+|Lizzie Lundgren (GCST)
 |}
@@ Line 233: / Line 279: @@
 |-valign="top"
 |1-month benchmark finished on:
-|Fri May 24 06:51:03 EDT 2019
+|Wed Aug 28 03:28:34 EDT 2019
 |-valign="top"
@@ Line 240: / Line 286: @@
 *Compiled with ifort 17.0.4
 *Ran on 24 CPUs of holyjacob01.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2680 v3 "Haswell" @ 2.50 GHz)
-*Wall time: TBD
+*Wall time: 07:28:13
-*[[Scalability|CPU time / wall time]]: TBD
+*[[Scalability|CPU time / wall time]]: 21.1711
-*% of ideal performance: TBD
+*% of ideal performance: 88.21%
-*Memory: TBD
+*Memory: 13.8379 GB
 |-valign="top"
@@ Line 255: / Line 301: @@
 |-valign="top"
 |[[GEOS-Chem Unit Tester|Unit test]] results may be viewed at:
-|TBD
+|http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/GC_12.5.0_Aug08.results.html
 |-valign="top" bgcolor="#cccccc"
@@ Line 263: / Line 309: @@
 |-valign="top"
 |Global mean OH from log file (% change):
-|12.6185673606414 x 10<sup>5</sup> molec/cm<sup>3</sup> (TBD)
+|12.3915975939893 x 10<sup>5</sup> molec/cm<sup>3</sup> (-0.65%)
 |-valign="top"
 |Methyl chloroform lifetime (% change):
-|TBD (TBD)
+|4.9487 (1.06%)
 |-valign="top"
 |Methane lifetime (% change):
-|TBD years (TBD
+|8.3312 years (1.10%)
 |-valign="top"
-|List all SURFACE SPECIES, SURFACE J-VALUES<br>AND COLUMN AOD SPECIES for which<br><tt>ABS(MAX(frac. diff))) > 0.1</tt>:
+|List all SURFACE species, J-Values, and COLUMN AOD values that changed by 10% or more:
 |
-* Primary: O3 CO OH NOx
+* Oxidants: O3 CO OH NOx
-* Aerosols: NH4 NIT SO4 AERI BrSALA BrSALC ISALA ISALC NITs SO4s SOA_Simple
+* Aerosols: NH4 NIT SO4 DST1 AERI BrSALA BrSALC ISALA ISALC NITs SO4s SOA_Complex SOA_Simple
 * Nitrogen: NOy NOx HNO2 HNO3 HNO4 IPMN NIT NO NO2 NO3 N2O5 MPN PAN PPN NHx NH3 NH4
 * ROy: H2O2 H HO2 O1D OH RO2
@@ Line 283: / Line 329: @@
 * Iodine: Iy IxOy I I2 IBr ICl IO INO2 IONO2 HI HOI OIO
 * Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
-* Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl OClO
+* Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl HCFCs OClO
-* Primary_Organics: ALK4 BENZ C2H6 C3H8 PRPE TOLU XYLE ISOP MTPA MTPO LIMO GLYX MAP RCHO
+* Primary_Organics: ALK4 BENZ C2H6 C3H8 PRPE TOLU XYLE ISOP MTPA MTPO LIMO GLYX HCOOH MAP RCHO
-* Secondary_Organics: ACET MEK MVK ALD2 CH2O HPALD MP ISOPN IEPOX ACTA EOH
+* Secondary_Organics: ACET MEK MVK ALD2 CH2O HPALD MP ISOPN IEPOX ACTA EOH SOAIE LVOCOA
-* J-Values: CCl4 CFC11 CFC113 CFC114 CFC115 CH2Cl2 CH3CCl3 HCFC123 HCFC141b N2O O2
+* J-Values: CCl4 CFC11 CFC113 CFC114 CFC115 CFC12 CH2Cl2 CH3CCl3 CH3Cl HCFC123 HCFC141b HCFC142b N2O O2
-* Column AOD: SO4 SOA_from_Aqueous_ISOP Total
+* Column AOD: Dust OCPI SO4 SOA_from_Aqueous_ISOP Total
 |-valign="top"
-|Comments on SURFACE differences:
+|List all 500 hPa species and J-Values that changed by 10% or more :
-|TBD
-|-valign="top"
-|List all 500 hPa SPECIES and<br>500 hPA J-VALUES for which<br><tt>ABS(MAX(frac. diff.) > 0.1</tt>:
 |
-* Aerosols: NH4 NIT BrSALA BrSALC SO4s
+* Oxidants: OH NOx
-* Nitrogen: IPMN NIT PPN NHx NH3 NH4
+* Aerosols: NH4 NIT SO4 DST1 AERI BrSALA BrSALC ISALC NITs SO4s SOA_Complex SOA_Simple
-* Sulfur: DMS SO2
+* Nitrogen: NOx HNO2 HNO4 IPMN NIT NO NO2 NO3 N2O5 MPN PAN PPN NHx NH3 NH4
-* Iodine: I2 INO2 CH2I2
+* ROy: OH
-* Bromine: BrOx Br Br2 BrO HOBr HBr
+* Sulfur: SOx DMS SO2 SO4
-* Chlorine: Cl2O2 ClNO2 HCl OClO
+* Iodine: I2 ICl INO2 IONO2 CH2I2 HI OIO
-* Primary_Organics: ALK4 C2H6 C3H8 PRPE TOLU XYLE ISOP MTPA LIMO GLYX MAP RCHO
+* Bromine: BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
-* Secondary_Organics: ACET MEK MVK ALD2 HPALD ISOPN IEPOX EOH
+* Chlorine: ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl OClO
+* Primary_Organics: ALK4 BENZ C2H6 C3H8 PRPE TOLU XYLE ISOP MTPA MTPO LIMO GLYX HCOOH MAP RCHO
+* Secondary_Organics: ACET MEK MVK ALD2 HPALD MP ISOPN IEPOX ACTA EOH SOAIE LVOCOA
+* J-Values: None
 |-valign="top"
-|Comments on 500 hPa differences:
+|List all ZONAL MEAN species and J-Values that changed by 10% or more:
-|TBD
-|-valign="top"
-|List all ZONAL MEAN SPECIES<br>and ZONAL MEAN J-VALUES for which<br><tt>ABS(MAX(frac. diff))) > 0.1</tt>:
 |
-* Aerosols: NIT BrSALA BrSALC NITs SO4s
+* Oxidants: OH NOx
-* Nitrogen: NOy HNO3 IPMN NIT NO3 N2O5 MPN PPN NH3
+* Aerosols: NH4 NIT SO4 DST1 BrSALA BrSALC NITs SO4s SOA_Complex SOA_Simple
-* Sulfur: SOx SO2
+* Nitrogen: NOy NOx HNO2 HNO3 IPMN NIT NO2 NO3 N2O5 MPN PAN PPN NH3 NH4
-* Iodine: I2 IBr ICl INO2 IONO2 CH2I2 OIO
+* ROy: OH RO2
+* Sulfur: SOx SO2 SO4
+* Iodine: I2 IBr ICl INO2 IONO2 CH2I2 HI OIO
 * Bromine: BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
-* Chlorine: Cly ClOx Cl Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl OClO
+* Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl OClO
-* Primary_Organics: ALK4 C2H6 C3H8 PRPE ISOP MTPA LIMO GLYX RCHO
+* Primary_Organics: ALK4 C2H6 C3H8 PRPE TOLU XYLE ISOP MTPA MTPO LIMO GLYX HCOOH MAP RCHO
-* Secondary_Organics: MEK MVK HPALD ISOPN IEPOX
+* Secondary_Organics: ACET MEK MVK ALD2 CH2O HPALD ISOPN IEPOX ACTA EOH SOAIE LVOCOA
+* J-Values: None
 |-valign="top"
-|Comments on ZONAL MEAN differences:
+|List all EMISSIONS that changed by 10% or more:
-|TBD
-|-valign="top"
-|List all EMISSIONS for which<br><tt>ABS(MAX(frac. diff))) > 0.1</tt>:
 |
-* Anthro: ALD2 ALK4 C2H6 C3H8 CO MEK NH3 NO pFe PRPE SO2 SO4 SOAP
+* Anthro: ALD2 ALK4 BCPI BCPO C2H6 C3H8 CO HAC MEK NH3 NO pFe PRPE SO2 SO4 SOAP
+* Biogenic: ACET ALD2 EOH ISOP LIMO PRPE SOAP SOAS
 * Ship: CO HNO3 NO2 NO O3 SO2 SOAP
-* Total: ALD2 ALK4 C2H6 C3H8 CO GLYX MEK MGLY NH3 NO pFe PRPE SO2 SO4 SOAP
+* Total: ACET ALD2 ALK4 BCPI BCPO C2H6 C3H8 CO EOH GLYX ISOP MEK MGLY MTPA NH3 NO pFe PRPE SO2 SO4 SOAP
+* VolcDegas: SO2
+* VolcErupt: SO2
 |-valign="top"
-|Comments on EMISSIONS differences:
+|Comments on observed differences:
-|TBD
+|'''''Below we summarize the notable changes caused by specific updates.'''''
+'''[[GEOS-Chem_12#Retire_obsolete_emission_inventories|Retire obsolete emission inventories]]'''
+:Retiring the EMEP, Bond, RETRO, and Yevich & Logan biofuel inventories results in large fractional differences in anthropogenic emissions and species concentrations over Europe, South America, Central America, Russia, and Australia, where the global anthropogenic, biofuel, and ship emissions from the CEDS inventory are now used. The impact on emission totals are included below.
+   ###############################################################################
+   ### Emissions totals                                                        ###
+   ### Ref = GC_12.4.0; Dev = GC_12.5.0                                        ###
+   ###############################################################################
+                                    Ref            Dev            Dev - Ref
+   ACET Anthro               :      0.171664       0.069874      -0.101790 Tg C
+   ALD2 Anthro               :      0.042310       0.042140      -0.000169 Tg C
+   ALK4 Anthro               :      2.407840       2.572299       0.164460 Tg C
+   BCPI Anthro               :      0.106725       0.106747       0.000021 Tg
+   BCPO Anthro               :      0.426900       0.426986       0.000086 Tg
+   C2H6 Anthro               :      0.473419       0.664990       0.191571 Tg C
+   C3H8 Anthro               :      0.399813       0.595361       0.195548 Tg C
+   CH2O Anthro               :      0.263482       0.235037      -0.028445 Tg
+   CO Anthro                 :     42.984464      40.778317      -2.206146 Tg
+   HAC Anthro                :      0.212160       0.042432      -0.169728 Tg
+   HCOOH Anthro              :      0.577087       0.571744      -0.005343 Tg
+   MEK Anthro                :      0.043368       0.064733       0.021364 Tg C
+   NH3 Anthro                :      4.430414       4.592343       0.161929 Tg
+   NO Anthro                 :      5.543591       5.293092      -0.250499 Tg
+   OCPI Anthro               :      0.628814       0.610537      -0.018278 Tg
+   OCPO Anthro               :      0.628815       0.610537      -0.018278 Tg
+   pFe Anthro                :      0.006943       0.006628      -0.000315 Tg
+   PRPE Anthro               :      0.490600       0.448865      -0.041735 Tg C
+   SO2 Anthro                :      6.974655       7.092453       0.117797 Tg
+   SO4 Anthro                :      0.218581       0.210372      -0.008208 Tg
+   SOAP Anthro               :      2.978745       2.826521      -0.152224 Tg
+   TOLU Anthro               :      0.584716       0.553756      -0.030960 Tg C
+   CO Ship                   :      0.079328       0.059695      -0.019634 Tg
+   HNO3 Ship                 :      1.484222       1.449563      -0.034659 Tg
+   NO Ship                   :      0.081681       0.082875       0.001195 Tg
+   NO2 Ship                  :      0.771094       0.738918      -0.032176 Tg
+   SO2 Ship                  :      0.805693       0.773045      -0.032648 Tg
+   SOAP Ship                 :      0.005474       0.004119      -0.001355 Tg
+'''[[Grid-independent_emissions#Biogenic_VOC_emissions|Updated offline biogenic emissions generated with GEOS-Chem 12.3.0]]'''
+:The offline biogenic emissions were updated to include recent fixes to the MEGAN extension. With this update, emissions for MTPA and MTPO are now included, as opposed to the individual components (APIN, BPIN, BCAR, etc.) included in the previous version. [[MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions#Remove_biogenic_CO_emissions_to_avoid_double_counting|CO from monoterpenes has been removed]] to avoid double-counting that source. In addition, the SOAP and SOAS emissions from the offline biogenic VOC files are ignored, and [[Grid-independent_emissions#Fixes_for_biogenic_SOAP.2C_SOAS.2C_and_CO_emissions|SOAP and SOAS emissions are instead computed by scaling isoprene and monoterpene emissions]]. The impact on biogenic emission totals are included below.
+   ###############################################################################
+   ### Inventory totals for OFFLINEBIOVOC                                      ###
+   ### Ref = GC_12.4.0; Dev = GC_12.5.0                                        ###
+   ###############################################################################
+                                    Ref            Dev            Dev - Ref
+   OFFLINEBIOVOC ACET        :      2.677313       2.982478       0.305164 Tg C
+   OFFLINEBIOVOC ALD2        :      1.032241       1.037183       0.004942 Tg C
+   OFFLINEBIOVOC CO          :      5.504973            nan            nan Tg C
+   OFFLINEBIOVOC EOH         :      0.987091       0.991817       0.004726 Tg C
+   OFFLINEBIOVOC ISOP        :     35.759849      33.723910      -2.035939 Tg C
+   OFFLINEBIOVOC LIMO        :      1.022397       0.976173      -0.046225 Tg C
+   OFFLINEBIOVOC MTPA        :           nan       8.644930            nan Tg C
+   OFFLINEBIOVOC MTPO        :           nan       4.000710            nan Tg C
+   OFFLINEBIOVOC PRPE        :      2.126864       2.030293      -0.096571 Tg C
+   OFFLINEBIOVOC SOAP        :      0.621433       1.467334       0.845901 Tg C
+   OFFLINEBIOVOC SOAS        :      0.621433       1.467334       0.845901 Tg C
+:While it appears that SOAP and SOAS emissions have a large increase from 12.4.0, these emission totals are now more in-line with 12.3.0 emission totals using online emissions from the MEGAN extension. In 12.3.0, emission totals of SOAP and SOAS were each 1.294232 Tg C.
+:Jeff Pierce pointed out that we see a much larger increase in the complex SOA concentrations as compared to the simple SOA concentrations (see the last two pages of [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Aerosols/Aerosols_Surface.pdf this file]). However, when we do the comparison of 12.5.0 vs 12.3.0, the differences are much lower altogether and have varying signs, consistent with the retirement of several emission inventories (see the last two pages of [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots_vs_12.3.0/Aerosols/Aerosols_Surface.pdf this file]). The 12.5.0 vs 12.3.0 are the comparisons to focus on because the 12.4.0 biogenic emissions were generated with and older version of MEGAN from GEOS-Chem v11-02. An outcome of the 12.4.0 benchmarking was that we should apply scaling of isoprene emissions to match the 12.3.0 annual totals. That scaling would impact the complex SOA species but not the simple SOA species which were read directly from the offline biogenic VOC files. In 12.5.0, the Aerosol WG decided not to read the simple SOA species directly from the offline biogenic VOC files after finding that the emissions in those files were too low compared to 12.3.0. Instead we now compute the SOAP and SOAS emissions by scaling the isoprene and monoterpene emissions from the offline biogenic VOC files. For the complete set of plots comparing 12.5.0 to 12.3.0, please visit http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots_vs_12.3.0/.
+:In this benchmark, we also introduced the [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/Secondary_Organic_Aerosols/ Secondary Organic Aerosols] benchmark category and [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Plots/GC_12.5.0_GlobalMass_TropStrat.txt global mass tables] to assist with evaluating this update. These plots will be included in future benchmarks.
+'''[[Volcanic_SO2_emissions|Updated volcano emissions to include eruptive emissions through April 2018]]'''
+:This update increased both eruptive and degassing volcanic emissions, as summarized below. As a result, localized increases in SO2 and SO4 can be seen in the species concentration plots.
+   ###############################################################################
+   ### Inventory totals for VOLCANO                                            ###
+   ### Ref = GC_12.4.0; Dev = GC_12.5.0                                        ###
+   ###############################################################################
+                                    Ref            Dev            Dev - Ref
+   VOLCANOerupt SO2          :      0.000000       0.035000       0.035000 Tg
+   VOLCANOdegas SO2          :      1.509524       1.951957       0.442434 Tg
+'''[[DICE-Africa_anthropogenic_emissions_inventory#Scale_DICE-Africa_emissions_to_address_errors_in_inventory|Scale DICE-Africa emissions to address errors in inventory]]'''
+:This update contributes to changes in BC and OC concentrations over and just downwind of Africa. Slight differences can also be seen over Africa in the emission maps. The impact on the inventory emission totals are included below.
+   ###############################################################################
+   ### Inventory totals for DICEAfrica                                         ###
+   ### Ref = GC_12.4.0; Dev = GC_12.5.0                                        ###
+   ###############################################################################
+                                    Ref            Dev            Dev - Ref
+   DICEAfrica BCPI           :      0.004131       0.004153       0.000022 Tg
+   DICEAfrica BCPO           :      0.016526       0.016612       0.000086 Tg
+   DICEAfrica CH2O           :      0.044793       0.016348      -0.028445 Tg
+   DICEAfrica CO             :      5.651943       3.648702      -2.003242 Tg
+   DICEAfrica HAC            :      0.212160       0.042432      -0.169728 Tg
+   DICEAfrica HCOOH          :      0.006679       0.001336      -0.005343 Tg
+   DICEAfrica NH3            :      0.294221       0.284477      -0.009744 Tg
+   DICEAfrica NO             :      0.153533       0.151820      -0.001713 Tg
+   DICEAfrica OCPI           :      0.035185       0.016907      -0.018278 Tg
+   DICEAfrica OCPO           :      0.035185       0.016907      -0.018278 Tg
+   DICEAfrica PRPE           :      0.057572       0.019730      -0.037842 Tg
+   DICEAfrica SOAP           :      0.389982       0.251758      -0.138224 Tg
+   DICEAfrica TOLU           :      0.054817       0.020857      -0.033960 Tg
+'''[[Issues_now_resolved_in_GEOS-Chem_12#Bug_fix_for_C3H8_anthropogenic_emissions|Bug fix for C3H8 anthropogenic emissions]]'''
+:C3H8 anthropogenic emissions increase with the implementation of this fix, addressing low C3H8 totals in the CEDS inventory:
+   ###############################################################################
+   ### Emissions totals for species C3H8                                       ###
+   ### Ref = GC_12.4.0; Dev = GC_12.5.0                                        ###
+   ###############################################################################
+                                    Ref            Dev            Dev - Ref
+   C3H8 Anthro               :      0.399813       0.595361       0.195548 Tg C
+'''[[Mineral_dust_aerosols#Separate_AFCID_from_DustDead_extension|Separate anthropogenic PM2.5 dust source from the DustDead extension]]'''
+:This update reintroduces the anthropogenic PM2.5 fine dust source and increases concentrations of DST1. The impact on DST1 emission totals are included below.
+   ###############################################################################
+   ### Inventory totals for AFCID                                              ###
+   ### Ref = GC_12.5.0; Dev = GC_12.5.0                                        ###
+   ###############################################################################
+                                    Ref            Dev            Dev - Ref
+   AFCID DST1                :           nan       1.087876            nan Tg
+'''The following updates produced small changes, primarily over the southern hemisphere oceans and at high altitudes:'''
+*[[GEOS-Chem_12#Corrections_for_CFCs_in_the_chemistry_mechanism|Corrections for CFCs in the chemistry mechanism]]
+*[[GEOS-Chem_12#Fix_typo_in_CLD_PARAMS_routine_in_gckpp_HetRates.F90|Fix typo in CLD_PARAMS routine in gckpp_HetRates.F90]]
+*[[Stratospheric_chemistry#Bug_fix:_make_sure_stratospheric_BrY_concentrations_are_read_properly_each_month|Bug fix: make sure stratospheric BrY concentrations are read properly each month]]
 |-valign="top"
-|Additional or summary comments:
+|Comments on additional [[Benchmark/GEOS-Chem_12.5.0#GCHP_1-month_benchmark|differences in GCHP]]:
-|TBD
+|
+GCHP 12.5.0 uses MAPL version tag "gchp/v1.0.0" released in early 2019. The MAPL library, which is developed by NASA, is a wrapper for the Earth System Modeling Framework (ESMF), and handles not only I/O but also passing of data between components. With this version update GCHP input speed executes roughly 3-4 times faster than previous versions! This speed-up is due to parallelization within input read across one node, and the MAPL updates in this version are just the beginning of improvements to GCHP I/O bottlenecks.
+While we are encouraged by the improvements to GCHP in 12.5.0, a few issues remain open until the next MAPL update later this year.
+*GCHP 12.5.0 currently has a slow memory leak due to updates to MAPL ExtData. NASA is aware of the issue and will be developing a fix soon. The memory leak is more pronounced for long simulations and can result in a simulation crashing due to exceeding memory available. Breaking up long runs into smaller consecutive runs avoids the issue but we find that doing so changes the output. Lizzie Lundgren (GCST) is investigating differences in GCHP output that happen when restarting a simulation, which may or may not be a problem with GEOS-Chem Classic as well. We are documenting all single versus multi-run differences at [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/multi_vs_single_run/ http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/multi_vs_single_run/]. Look there to assess if the scale of the differences would be a problem for you.
+*GCHP 12.5.0 uses online ESMF regridding weights rather than external tile files for regridding. Due to ESMF domain decomposition rules this can result in a MAPL error if an input grid is too coarse for a run’s configured core count. We have seen this problem for 4°x5° input files when using >600 cores. GMAO has fixed this problem in a more recent version of MAPL. All 4°x5° input files are replaced with higher resolution files for GCHP 12.5.0 to avoid this issue. However, users may still run into problems if running with thousands of cores.
+*There is a positive bias in surface ozone over the Southern Ocean in GCHP. It shows in comparisons with both GCC 12.5.0 and GCHP 12.4.0. The issue is resolution-dependent and occurs in FV3. An issue has been created on GEOS github for this: https://github.com/GEOS-ESM/GEOSgcm_GridComp/issues/48. To evaluate this bias at different resolutions, we also ran and GCHP 12.5.0 benchmark at c24. Results from that simulation may be viewed at [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP_c24/plots/ this link].
 |-bgcolor="#cccccc"
 !Approval
@@ Line 346: / Line 527: @@
 |-valign="top"
 |Requires further investigation:
-|TBD
+|No
 |-valign="top"
 |Approved by:
-|
+|Jeff Pierce, Daniel Jacob
 |-valign="top"
 |Date of approval:
-|
+|06 Sep 2019
 |}
 == GCHP 1-month benchmark ==
-[[Image:Page is under construction.jpg]]
-<span style="color:red">'''''NOTE: The GCHP benchmark has not been completed yet.  The links below will not work.'''''</span>
 The following sections contain validation plots for GCHP 12.5.0.
@@ Line 366: / Line 544: @@
 === Comparison of GCHP versions ===
-This table contains plots comparing GCHP 12.3.2 (Ref) and GCHP 12.5.0 (Dev) for a 1-month simulation.
+This table contains plots comparing GCHP 12.4.0 (Ref) and GCHP 12.5.0 (Dev) for a 1-month simulation.
 {| border=1 cellspacing=0 cellpadding=5
 |-valign="top"
-!width="225px" bgcolor="#CCFFFF"|Category<sup>1</sup>
+!width="225px" bgcolor="#CCFFFF"|Category
-!colspan="5" bgcolor="#CCFFFF"|Plots<sup>2</sup>
+!colspan="5" bgcolor="#CCFFFF"|Plots
 !bgcolor="#CCFFFF"|Additional Information
@@ Line 383: / Line 561: @@
 |-valign="top"
-|Primary
+|Oxidants
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Primary/Primary_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Oxidants/Oxidants_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Primary/Primary_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Oxidants/Oxidants_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Primary/Primary_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Oxidants/Oxidants_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Primary/Primary_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Oxidants/Oxidants_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Primary/Primary_Emissions.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Oxidants/Oxidants_Emissions.pdf full column]
 |
 |-valign="top"
 |Aerosols
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Aerosols/Aerosols_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Aerosols/Aerosols_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Aerosols/Aerosols_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Aerosols/Aerosols_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Aerosols/Aerosols_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Aerosols/Aerosols_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Aerosols/Aerosols_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Aerosols/Aerosols_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Aerosols/Aerosols_Emissions.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Aerosols/Aerosols_Emissions.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Aerosols/Aerosols_ColumnOptDepth.pdf Column AOD]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Aerosols/Aerosols_ColumnOptDepth.pdf Column AOD]
 |-valign="top"
 |Bromine
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Bromine/Bromine_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Bromine/Bromine_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Bromine/Bromine_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Bromine/Bromine_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Bromine/Bromine_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Bromine/Bromine_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Bromine/Bromine_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Bromine/Bromine_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Bromine/Bromine_Emissions.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Bromine/Bromine_Emissions.pdf full column]
 |
 |-valign="top"
 |Chlorine
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Chlorine/Chlorine_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Chlorine/Chlorine_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Chlorine/Chlorine_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Chlorine/Chlorine_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Chlorine/Chlorine_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Chlorine/Chlorine_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Chlorine/Chlorine_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Chlorine/Chlorine_Strat_ZonalMean.pdf stratosphere]
 | --
 |
@@ Line 420: / Line 598: @@
 |-valign="top"
 |Iodine
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Iodine/Iodine_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Iodine/Iodine_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Iodine/Iodine_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Iodine/Iodine_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Iodine/Iodine_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Iodine/Iodine_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Iodine/Iodine_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Iodine/Iodine_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Iodine/Iodine_Emissions.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Iodine/Iodine_Emissions.pdf full column]
 |
 |-valign="top"
 |Nitrogen
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Nitrogen/Nitrogen_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Nitrogen/Nitrogen_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Nitrogen/Nitrogen_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Nitrogen/Nitrogen_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Nitrogen/Nitrogen_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Nitrogen/Nitrogen_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Nitrogen/Nitrogen_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Nitrogen/Nitrogen_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Nitrogen/Nitrogen_Emissions.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Nitrogen/Nitrogen_Emissions.pdf full column]
 |
 |-valign="top"
 |Primary Organics
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Primary_Organics/Primary_Organics_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Primary_Organics/Primary_Organics_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Primary_Organics/Primary_Organics_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Primary_Organics/Primary_Organics_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Primary_FullColumn_Organics/Primary_Organics_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Primary_FullColumn_Organics/Primary_Organics_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Primary_Strat_Organics/Primary_Organics_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Primary_Strat_Organics/Primary_Organics_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Primary_Organics/Primary_Organics_Emissions.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Primary_Organics/Primary_Organics_Emissions.pdf full column]
 |
 |-valign="top"
 |Secondary Organics
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Secondary_Organics/Secondary_Organics_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Secondary_Organics/Secondary_Organics_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Secondary_Organics/Secondary_Organics_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Secondary_Organics/Secondary_Organics_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Secondary_FullColumn_Organics/Secondary_Organics_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Secondary_FullColumn_Organics/Secondary_Organics_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Secondary_Strat_Organics/Secondary_Organics_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Secondary_Strat_Organics/Secondary_Organics_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Secondary_Organics/Secondary_Organics_Emissions.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Secondary_Organics/Secondary_Organics_Emissions.pdf full column]
 |
 |-valign="top"
 |Sulfur
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Sulfur/Sulfur_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Sulfur/Sulfur_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Sulfur/Sulfur_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Sulfur/Sulfur_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Sulfur/Sulfur_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Sulfur/Sulfur_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Sulfur/Sulfur_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Sulfur/Sulfur_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Sulfur/Sulfur_Emissions.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Sulfur/Sulfur_Emissions.pdf full column]
 |
@@ Line 466: / Line 644: @@
 |Emissions by HEMCO category
 !colspan="5"|
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Emissions/Aircraft_Emissions.pdf Aircraft],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Emissions/Aircraft_Emissions.pdf Aircraft],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Emissions/Anthro_Emissions.pdf Anthro],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Emissions/Anthro_Emissions.pdf Anthro],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Emissions/Bioburn_Emissions.pdf Bioburn],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Emissions/Bioburn_Emissions.pdf Bioburn],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Emissions/Biofuel_Emissions.pdf Biofuel],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Emissions/Biogenic_Emissions.pdf Biogenic],<br>
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Emissions/Biogenic_Emissions.pdf Biogenic],<br>
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Emissions/Lightning_Emissions.pdf Lightning],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Emissions/Lightning_Emissions.pdf Lightning],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Emissions/Monoterp_Emissions.pdf Monoterp],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Emissions/Monoterp_Emissions.pdf Monoterp],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Emissions/Natural_Emissions.pdf Natural],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Emissions/Natural_Emissions.pdf Natural],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Emissions/Ocean_Emissions.pdf Ocean],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Emissions/Ocean_Emissions.pdf Ocean],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Emissions/Seabirds_Emissions.pdf Seabirds],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Emissions/Seabirds_Emissions.pdf Seabirds],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Emissions/PlantDecay_Emissions.pdf DecayingPlants],<br>
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Emissions/Senesc_Emissions.pdf SenescingPlants],<br>
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Emissions/Ship_Emissions.pdf Ship],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Emissions/Ship_Emissions.pdf Ship],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Emissions/Soil_Emissions.pdf Soil],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Emissions/Soil_Emissions.pdf Soil],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Emissions/Total_Emissions.pdf Total],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Emissions/Total_Emissions.pdf Total],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Emissions/VolcDegas_Emissions.pdf VolcDegas],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Emissions/VolcDegas_Emissions.pdf VolcDegas],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Emissions/VolcErupt_Emissions.pdf VolcErupt],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Emissions/VolcErupt_Emissions.pdf VolcErupt],
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_version_comparison/Emissions/Emission_totals.txt Emission totals]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/Emissions/Emission_totals.txt Emission totals]
 |}
-<sup>1</sup>'''Benchmark category definitions:''' [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/benchmark_categories.json benchmark_categories.json]<br>
-<sup>2</sup>'''Lumped species definitions:''' [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_version_comparison/lumped_species.json lumped_species.json]<br>
 === Comparison of GCHP and GEOS-Chem Classic ===
@@ Line 496: / Line 670: @@
 |-valign="top"
-!width="225px" bgcolor="#CCFFFF"|Category<sup>1</sup>
+!width="225px" bgcolor="#CCFFFF"|Category
-!colspan="5" bgcolor="#CCFFFF"|Plots<sup>2</sup>
+!colspan="5" bgcolor="#CCFFFF"|Plots
 !bgcolor="#CCFFFF"|Additional Information
@@ Line 508: / Line 682: @@
 |-valign="top"
-|Primary
+|Oxidants
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Primary/Primary_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Oxidants/Oxidants_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Primary/Primary_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Oxidants/Oxidants_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Primary/Primary_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Oxidants/Oxidants_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Primary/Primary_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Oxidants/Oxidants_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Primary/Primary_Emissions.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Oxidants/Oxidants_Emissions.pdf full column]
 |
 |-valign="top"
 |Aerosols
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Aerosols/Aerosols_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Aerosols/Aerosols_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Aerosols/Aerosols_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Aerosols/Aerosols_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Aerosols/Aerosols_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Aerosols/Aerosols_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Aerosols/Aerosols_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Aerosols/Aerosols_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Aerosols/Aerosols_Emissions.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Aerosols/Aerosols_Emissions.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Aerosols/Aerosols_ColumnOptDepth.pdf Column AOD]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Aerosols/Aerosols_ColumnOptDepth.pdf Column AOD]
 |-valign="top"
 |Bromine
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Bromine/Bromine_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Bromine/Bromine_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Bromine/Bromine_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Bromine/Bromine_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Bromine/Bromine_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Bromine/Bromine_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Bromine/Bromine_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Bromine/Bromine_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Bromine/Bromine_Emissions.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Bromine/Bromine_Emissions.pdf full column]
 |
 |-valign="top"
 |Chlorine
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Chlorine/Chlorine_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Chlorine/Chlorine_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Chlorine/Chlorine_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Chlorine/Chlorine_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Chlorine/Chlorine_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Chlorine/Chlorine_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Chlorine/Chlorine_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Chlorine/Chlorine_Strat_ZonalMean.pdf stratosphere]
 | --
 |
@@ Line 545: / Line 719: @@
 |-valign="top"
 |Iodine
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Iodine/Iodine_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Iodine/Iodine_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Iodine/Iodine_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Iodine/Iodine_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Iodine/Iodine_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Iodine/Iodine_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Iodine/Iodine_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Iodine/Iodine_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Iodine/Iodine_Emissions.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Iodine/Iodine_Emissions.pdf full column]
 |
 |-valign="top"
 |Nitrogen
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Nitrogen/Nitrogen_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Nitrogen/Nitrogen_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Nitrogen/Nitrogen_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Nitrogen/Nitrogen_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Nitrogen/Nitrogen_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Nitrogen/Nitrogen_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Nitrogen/Nitrogen_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Nitrogen/Nitrogen_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Nitrogen/Nitrogen_Emissions.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Nitrogen/Nitrogen_Emissions.pdf full column]
 |
 |-valign="top"
 |Primary Organics
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Primary_Organics/Primary_Organics_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Primary_Organics/Primary_Organics_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Primary_Organics/Primary_Organics_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Primary_Organics/Primary_Organics_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Primary_FullColumn_Organics/Primary_Organics_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Primary_FullColumn_Organics/Primary_Organics_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Primary_Strat_Organics/Primary_Organics_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Primary_Strat_Organics/Primary_Organics_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Primary_Organics/Primary_Organics_Emissions.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Primary_Organics/Primary_Organics_Emissions.pdf full column]
 |
 |-valign="top"
 |Secondary Organics
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Secondary_Organics/Secondary_Organics_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Secondary_Organics/Secondary_Organics_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Secondary_Organics/Secondary_Organics_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Secondary_Organics/Secondary_Organics_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Secondary_FullColumn_Organics/Secondary_Organics_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Secondary_FullColumn_Organics/Secondary_Organics_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Secondary_Strat_Organics/Secondary_Organics_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Secondary_Strat_Organics/Secondary_Organics_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Secondary_Organics/Secondary_Organics_Emissions.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Secondary_Organics/Secondary_Organics_Emissions.pdf full column]
 |
 |-valign="top"
 |Sulfur
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Sulfur/Sulfur_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Sulfur/Sulfur_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Sulfur/Sulfur_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Sulfur/Sulfur_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Sulfur/Sulfur_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Sulfur/Sulfur_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Sulfur/Sulfur_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Sulfur/Sulfur_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Sulfur/Sulfur_Emissions.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Sulfur/Sulfur_Emissions.pdf full column]
 |
@@ Line 591: / Line 765: @@
 |Emissions by HEMCO category
 !colspan="5"|
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Emissions/Aircraft_Emissions.pdf Aircraft],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Emissions/Aircraft_Emissions.pdf Aircraft],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Emissions/Anthro_Emissions.pdf Anthro],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Emissions/Anthro_Emissions.pdf Anthro],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Emissions/Bioburn_Emissions.pdf Bioburn],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Emissions/Bioburn_Emissions.pdf Bioburn],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Emissions/Biofuel_Emissions.pdf Biofuel],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Emissions/Biogenic_Emissions.pdf Biogenic],<br>
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Emissions/Biogenic_Emissions.pdf Biogenic],<br>
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Emissions/Lightning_Emissions.pdf Lightning],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Emissions/Lightning_Emissions.pdf Lightning],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Emissions/Monoterp_Emissions.pdf Monoterp],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Emissions/Monoterp_Emissions.pdf Monoterp],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Emissions/Natural_Emissions.pdf Natural],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Emissions/Natural_Emissions.pdf Natural],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Emissions/Ocean_Emissions.pdf Ocean],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Emissions/Ocean_Emissions.pdf Ocean],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Emissions/Seabirds_Emissions.pdf Seabirds],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Emissions/Seabirds_Emissions.pdf Seabirds],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Emissions/PlantDecay_Emissions.pdf DecayingPlants],<br>
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Emissions/Senesc_Emissions.pdf SenescingPlants],<br>
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Emissions/Ship_Emissions.pdf Ship],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Emissions/Ship_Emissions.pdf Ship],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Emissions/Soil_Emissions.pdf Soil],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Emissions/Soil_Emissions.pdf Soil],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Emissions/Total_Emissions.pdf Total],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Emissions/Total_Emissions.pdf Total],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Emissions/VolcDegas_Emissions.pdf VolcDegas],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Emissions/VolcDegas_Emissions.pdf VolcDegas],
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Emissions/VolcErupt_Emissions.pdf VolcErupt],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Emissions/VolcErupt_Emissions.pdf VolcErupt],
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_comparison/Emissions/Emission_totals.txt Emission totals]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/Emissions/Emission_totals.txt Emission totals]
 |}
-<sup>1</sup>'''Benchmark category definitions:''' [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/output/benchmark_categories.json benchmark_categories.json]<br>
-<sup>2</sup>'''Lumped species definitions:''' [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_comparison/output/lumped_species.json lumped_species.json]<br>
 === GCHP and GEOS-Chem Classic difference of differences ===
-This table contains plots comparing the difference [GCHP 12.5.0 - GCHP 12.3.2] against the difference [GC Classic 12.5.0 - GC Classic 12.3.0], taken from 1-month benchmark simulations.
+This table contains plots comparing the difference [GCHP 12.5.0 - GCHP 12.4.0] against the difference [GC Classic 12.5.0 - GC Classic 12.4.0], taken from 1-month benchmark simulations.
 {| border=1 cellspacing=0 cellpadding=5
 |-valign="top"
-!width="225px" bgcolor="#CCFFFF"|Category<sup>1</sup>
+!width="225px" bgcolor="#CCFFFF"|Category
-!colspan="4" bgcolor="#CCFFFF"|Plots<sup>2</sup>
+!colspan="4" bgcolor="#CCFFFF"|Plots
 |-valign="top"
@@ Line 631: / Line 800: @@
 |-valign="top"
-|Primary
+|Oxidants
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Primary/Primary_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Oxidants/Oxidants_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Primary/Primary_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Oxidants/Oxidants_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Primary/Primary_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Oxidants/Oxidants_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Primary/Primary_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Oxidants/Oxidants_Strat_ZonalMean.pdf stratosphere]
 |-valign="top"
 |Aerosols
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Aerosols/Aerosols_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Aerosols/Aerosols_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Aerosols/Aerosols_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Aerosols/Aerosols_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Aerosols/Aerosols_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Aerosols/Aerosols_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Aerosols/Aerosols_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Aerosols/Aerosols_Strat_ZonalMean.pdf stratosphere]
 |-valign="top"
 |Bromine
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Bromine/Bromine_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Bromine/Bromine_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Bromine/Bromine_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Bromine/Bromine_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Bromine/Bromine_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Bromine/Bromine_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Bromine/Bromine_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Bromine/Bromine_Strat_ZonalMean.pdf stratosphere]
 |-valign="top"
 |Chlorine
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Chlorine/Chlorine_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Chlorine/Chlorine_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Chlorine/Chlorine_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Chlorine/Chlorine_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Chlorine/Chlorine_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Chlorine/Chlorine_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Chlorine/Chlorine_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Chlorine/Chlorine_Strat_ZonalMean.pdf stratosphere]
 |-valign="top"
 |Iodine
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Iodine/Iodine_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Iodine/Iodine_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Iodine/Iodine_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Iodine/Iodine_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Iodine/Iodine_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Iodine/Iodine_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Iodine/Iodine_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Iodine/Iodine_Strat_ZonalMean.pdf stratosphere]
 |-valign="top"
 |Nitrogen
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Nitrogen/Nitrogen_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Nitrogen/Nitrogen_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Nitrogen/Nitrogen_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Nitrogen/Nitrogen_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Nitrogen/Nitrogen_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Nitrogen/Nitrogen_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Nitrogen/Nitrogen_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Nitrogen/Nitrogen_Strat_ZonalMean.pdf stratosphere]
 |-valign="top"
 |Primary Organics
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Primary_Organics/Primary_Organics_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Primary_Organics/Primary_Organics_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Primary_Organics/Primary_Organics_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Primary_Organics/Primary_Organics_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Primary_FullColumn_Organics/Primary_Organics_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Primary_Organics/Primary_Organics_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Primary_Strat_Organics/Primary_Organics_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Primary_Organics/Primary_Organics_Strat_ZonalMean.pdf stratosphere]
 |-valign="top"
 |Secondary Organics
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Secondary_Organics/Secondary_Organics_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Secondary_Organics/Secondary_Organics_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Secondary_Organics/Secondary_Organics_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Secondary_Organics/Secondary_Organics_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Secondary_FullColumn_Organics/Secondary_Organics_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Secondary_Organics/Secondary_Organics_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Secondary_Strat_Organics/Secondary_Organics_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Secondary_Organics/Secondary_Organics_Strat_ZonalMean.pdf stratosphere]
 |-valign="top"
 |Sulfur
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Sulfur/Sulfur_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Sulfur/Sulfur_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Sulfur/Sulfur_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Sulfur/Sulfur_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Sulfur/Sulfur_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Sulfur/Sulfur_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/Sulfur/Sulfur_Strat_ZonalMean.pdf stratosphere]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/plots/GCHP_GCC_diff_of_diffs/Sulfur/Sulfur_Strat_ZonalMean.pdf stratosphere]
 |}
-<sup>1</sup>'''Benchmark category definitions:''' [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/output/benchmark_categories.json benchmark_categories.json]<br>
+NOTE: At present, we have only created the diff-of-diffs plots for species concentration.  This can be extended to other categories in the future.
-<sup>2</sup>'''Lumped species definitions:''' [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCHP/GCHP_GCC_diff_of_diffs/output/lumped_species.json lumped_species.json]<br>
-'''NOTES:'''
+== Validation of netCDF diagnostics ==
-#At present, we have only created the diff-of-diffs plots for species concentration.  This can be extended to other categories in the future.
-== Special benchmarks ==
+In this version, we did a complete comparison of the [[List_of_diagnostics_archived_to_bpch_format|BPCH diagnostics]] to the [[Guide_to_GEOS-Chem_History_diagnostics|netCDF diagnostics]] in preparation for retiring the old BPCH diagnostics. Comparison plots can be accessed via the links below.  A summary of the results may be found [https://docs.google.com/spreadsheets/d/1sIZwKmxSN_sey1CWsJcGp01ZVyARZHmD4r-DTVw5Vmc/ on this Google spreadsheet].
-In this section we list information about special (i.e. non-official) benchmark simulations that were performed.  These are often necessary to validate certain model features.
-=== GEOS-Chem Classic 12.5.0 BPCH only ===
-These benchmarks were primarily made with [https://github.com/geoschem/gcpy GCPy]. Some benchmark plots created by GAMAP still remain because they have not been recreated in GCPy yet.
 {| border=1 cellspacing=0 cellpadding=5
-|-
-!colspan="1" bgcolor="#CCFFFF"|Category<sup>1</sup>
-!colspan="5" bgcolor="#CCFFFF"|Plots
-!colspan="1" bgcolor="#CCFFFF"|Additional Information
-|-
-!colspan="1"|
-!colspan="2"|Level Map
-!colspan="2"|Zonal Mean
-!colspan="1"|Emissions
-!colspan="1"|
 |-valign="top"
-|Primary
+!width="160px" bgcolor="#CCFFFF"|NetCDF collection
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Primary/Primary_Surface.pdf sfc]
+!width="200px" bgcolor="#CCFFFF"|BPCH equivalent(s)
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12,5.0/GCC/Bpch_Only/output/Primary/Primary_500hPa.pdf 500hPa]
+!colspan="2" bgcolor="#CCFFFF"|Plots
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12,5.0/GCC/Bpch_Only/output/Primary/Primary_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12,5.0/GCC/Bpch_Only/output/Primary/Primary_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Primary/Primary_Emissions.pdf sfc]
-|
 |-valign="top"
-|Aerosols
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Aerosols/Aerosols_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Aerosols/Aerosols_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Aerosols/Aerosols_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Aerosols/Aerosols_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Aerosols/Aerosols_Emissions.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Aerosols/Aerosols_ColumnOptDepth.pdf AOD]
-|-valign="top"
-|Bromine
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Bromine/Bromine_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Bromine/Bromine_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Bromine/Bromine_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Bromine/Bromine_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Bromine/Bromine_Emissions.pdf sfc]
-|
-|-valign="top"
-|Chlorine
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Chlorine/Chlorine_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Chlorine/Chlorine_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Chlorine/Chlorine_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Chlorine/Chlorine_Strat_ZonalMean.pdf stratosphere]
-| --
-|
-|-valign="top"
-|Iodine
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Iodine/Iodine_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Iodine/Iodine_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Iodine/Iodine_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Iodine/Iodine_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Iodine/Iodine_Emissions.pdf sfc]
-|
-|-valign="top"
-|Nitrogen
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Nitrogen/Nitrogen_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Nitrogen/Nitrogen_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Nitrogen/Nitrogen_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Nitrogen/Nitrogen_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Nitrogen/Nitrogen_Emissions.pdf sfc]
-|
-|-valign="top"
-|Primary Organics
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Primary_Organics/Primary_Organics_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Primary_Organics/Primary_Organics_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Primary_FullColumn_Organics/Primary_Organics_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Primary_Strat_Organics/Primary_Organics_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Primary_Organics/Primary_Organics_Emissions.pdf sfc]
-|
-|-valign="top"
-|Secondary Organics
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Secondary_Organics/Secondary_Organics_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Secondary_Organics/Secondary_Organics_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Secondary_FullColumn_Organics/Secondary_Organics_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Secondary_Strat_Organics/Secondary_Organics_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Secondary_Organics/Secondary_Organics_Emissions.pdf sfc]
-|
-|-valign="top"
-|ROy
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/ROy/ROy_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/ROy/ROy_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/ROy/ROy_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/ROy/ROy_Strat_ZonalMean.pdf stratosphere]
-| --
-|
-|-valign="top"
-|Sulfur
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Sulfur/Sulfur_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Sulfur/Sulfur_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Sulfur/Sulfur_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Sulfur/Sulfur_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Sulfur/Sulfur_Emissions.pdf sfc]
-|
-|-valign="top"
-|Emissions by HEMCO category
-!colspan="5"|
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Emissions/Total_Emissions.pdf Total],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Emissions/Aircraft_Emissions.pdf Aircraft],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Emissions/Anthro_Emissions.pdf Anthro],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Emissions/Bioburn_Emissions.pdf Bioburn],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Emissions/Biofuel_Emissions.pdf Biofuel],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Emissions/Biogenic_Emissions.pdf Biogenic],<br>
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Emissions/Lightning_Emissions.pdf Lightning],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Emissions/Monoterp_Emissions.pdf Monoterp],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Emissions/Natural_Emissions.pdf Natural],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Emissions/Ocean_Emissions.pdf Ocean],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Emissions/Seabirds_Emissions.pdf Seabirds],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Emissions/Senesc_Emissions.pdf SenescingPlants],<br>
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Emissions/Ship_Emissions.pdf Ship],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Emissions/Soil_Emissions.pdf Soil],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Emissions/VolcDegas_Emissions.pdf VolcDegas],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Emissions/VolcErupt_Emissions.pdf VolcErupt],
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/Emissions/Emission_totals.txt Emissions tables]
-|-valign="top"
-|J-values
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/JValues/JVal_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/JValues/JVal_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/JValues/JVal_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/JValues/JVal_Strat_ZonalMean.pdf stratosphere]
-| --
-| --
-|-valign="top"
-!colspan="7" bgcolor="#CCCCCC"|Plots still created by GAMAP
-|-valign="top"
-|Budget
-| --
-| --
-| --
-| --
-| --
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/GC_12.5.0.budget.txt Ox and CO budgets]
-|}
-<sup>1</sup>'''Benchmark category definitions:''' [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/benchmark_categories.json benchmark_categories.json]<br>
-<sup>2</sup>'''Lumped species definitions:''' [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/lumped_species.json lumped_species.json]<br>
-'''NOTES:'''
-#[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/benchmark_categories.json Category] and [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/Bpch_Only/output/lumped_species.json lumped species] definitions are simple to adjust. Updating them requires only editing the json files.
-#All plots created with GCPy have PDF bookmarks. If you do not see them in your browser try using a different browser (not Safari) or installing an Adobe Acrobat plug-in.
-==== Benchmark assessment form for GEOS-Chem 12.5.0 BPCH only ====
-{| border=1 cellspacing=0 cellpadding=5
-|-bgcolor="#CCCCCC"
-!width="325px"|Description
-!
-|-valign="top"
-|New features added into GEOS-Chem
-|[[#Benchmark assessment form|Same as listed above]]
-|-valign="top"
-|Version, resolution, met fields used:
-|GEOS-FP (72L), 4x5, July 2016
-|-valign="top"
-|1-month benchmark finished on:
-|TBD
-|-valign="top"
-|Performance statistics:
-|
-*Compiled with ifort 17.0.4
-*Ran on 24 CPUs of holyjacob01.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2680 v3 "Haswell" @ 2.50 GHz)
-*Wall time: TBD
-*[[Scalability|CPU time / wall time]]: TBD
-*% of ideal performance: TBD
-*Memory: TBD
-|-valign="top"
-|Compared to previous benchmark:
-|[[GEOS-Chem_12#12.4.0|12.4.0]]
-|-valign="top"
-|This update will impact:<br>(select all that apply with '''boldface''')
-|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Emissions, Photolysis, Chemistry, Other (please specify): '''Diagnostics'''
-|-valign="top"
-|[[GEOS-Chem Unit Tester|Unit test]] results may be viewed at:
-|TBD
-|-valign="top" bgcolor="#cccccc"
-!Metrics
-!
-|-valign="top"
-|Global mean OH from log file (% change):
-|12.6185908670819 x 10<sup>5</sup> molec/cm<sup>3</sup> (TBD)
-|-valign="top"
-|Methyl chloroform lifetime (% change):
-|TBD (TBD)
-|-valign="top"
-|Methane lifetime (% change):
-|TBD years (TBD
-|-valign="top"
-|List all SURFACE SPECIES, SURFACE J-VALUES<br>AND COLUMN AOD SPECIES for which<br><tt>ABS(MAX(frac. diff))) > 0.1</tt>:
-|
-|-valign="top"
-|Comments on SURFACE differences:
-|TBD
-|-valign="top"
-|List all 500 hPa SPECIES and<br>500 hPA J-VALUES for which<br><tt>ABS(MAX(frac. diff.) > 0.1</tt>:
-|
-|-valign="top"
-|Comments on 500 hPa differences:
-|TBD
-|-valign="top"
-|List all ZONAL MEAN SPECIES<br>and ZONAL MEAN J-VALUES for which<br><tt>ABS(MAX(frac. diff))) > 0.1</tt>:
-|
-|-valign="top"
-|Comments on ZONAL MEAN differences:
-|TBD
-|-valign="top"
-|List all EMISSIONS for which<br><tt>ABS(MAX(frac. diff))) > 0.1</tt>:
-|
-|-valign="top"
-|Comments on EMISSIONS differences:
-|TBD
-|-valign="top"
-|Additional or summary comments:
-|TBD
-|-bgcolor="#cccccc"
-!Approval
 !
+!
+!width="100px"|Level Map
+!width="100px"|Zonal Mean
 |-valign="top"
-|Requires further investigation:
+|AdvFluxMerid
-|TBD
+|[[List_of_diagnostics_archived_to_bpch_format#ND24_-_ND26:_Mass_transport_flux|ND25]]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/AdvFluxMerid_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/AdvFluxMerid_FullColumn_ZonalMean.pdf full column]
 |-valign="top"
-|Approved by:
+|AdvFluxVert
-|
+|[[List_of_diagnostics_archived_to_bpch_format#ND24_-_ND26:_Mass_transport_flux|ND26]]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/AdvFluxVert_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/AdvFluxVert_FullColumn_ZonalMean.pdf full column]
 |-valign="top"
-|Date of approval:
+|AdvFluxZonal
-|
+|[[List_of_diagnostics_archived_to_bpch_format#ND24_-_ND26:_Mass_transport_flux|ND24]]
-|}
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/AdvFluxZonal_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/AdvFluxZonal_FullColumn_ZonalMean.pdf full column]
-=== GEOS-Chem Classic 12.5.0 netCDF only ===
-These benchmarks were primarily made with [https://github.com/geoschem/gcpy GCPy]. Some benchmark plots created by GAMAP still remain because they have not been recreated in GCPy yet.
-{| border=1 cellspacing=0 cellpadding=5
-|-
-!colspan="1" bgcolor="#CCFFFF"|Category<sup>1</sup>
-!colspan="5" bgcolor="#CCFFFF"|Plots
-!colspan="1" bgcolor="#CCFFFF"|Additional Information
-|-
-!colspan="1"|
-!colspan="2"|Level Map
-!colspan="2"|Zonal Mean
-!colspan="1"|Emissions
-!colspan="1"|
 |-valign="top"
-|Primary
+|[[History_collections_for_aerosols#The_AerosolMass_collection|AerosolMass]]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Primary/Primary_Surface.pdf sfc]
+|[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42]]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12,5.0/GCC/NetCDF_Only/output/Primary/Primary_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/AerosolMass_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12,5.0/GCC/NetCDF_Only/output/Primary/Primary_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/AerosolMass_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12,5.0/GCC/NetCDF_Only/output/Primary/Primary_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Primary/Primary_Emissions.pdf sfc]
-|
 |-valign="top"
-|Aerosols
+|[[History_collections_for_aerosols#The_Aerosols_collection|Aerosols]]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Aerosols/Aerosols_Surface.pdf sfc]
+|[[List_of_diagnostics_archived_to_bpch_format#ND21:_Cloud_diagnostics|ND21]]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Aerosols/Aerosols_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/Aerosols_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Aerosols/Aerosols_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/Aerosols_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Aerosols/Aerosols_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Aerosols/Aerosols_Emissions.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Aerosols/Aerosols_ColumnOptDepth.pdf AOD]
 |-valign="top"
-|Bromine
+|[[History_collections_for_convection_and_wet_deposition#The_CloudConvFlux_collection|CloudConvFlux]]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Bromine/Bromine_Surface.pdf sfc]
+|[[List_of_diagnostics_archived_to_bpch_format|ND14]]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Bromine/Bromine_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/CloudConvFlux_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Bromine/Bromine_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/CloudConvFlux_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Bromine/Bromine_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Bromine/Bromine_Emissions.pdf sfc]
-|
 |-valign="top"
-|Chlorine
+|[[History_collections_for_chemistry_and_photolysis#The_ConcAfterChem_collection|ConcAfterChem]]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Chlorine/Chlorine_Surface.pdf sfc]
+|[[List_of_diagnostics_archived_to_bpch_format|ND43]]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Chlorine/Chlorine_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/ConcAfterChem_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Chlorine/Chlorine_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/ConcAfterChem_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Chlorine/Chlorine_Strat_ZonalMean.pdf stratosphere]
-| --
-|
 |-valign="top"
-|Iodine
+|[[History_collections_for_dry_deposition#The_DryDep_collection|DryDep]]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Iodine/Iodine_Surface.pdf sfc]
+|[[List_of_diagnostics_archived_to_bpch_format#ND44:_Dry_deposition_diagnostics|ND44]]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Iodine/Iodine_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/DryDep_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Iodine/Iodine_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Iodine/Iodine_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Iodine/Iodine_Emissions.pdf sfc]
 |
 |-valign="top"
-|Nitrogen
+|[[Guide_to_HEMCO_emissions_diagnostics|Emissions]]<br>(i.e. HEMCO diagnostics)
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Nitrogen/Nitrogen_Surface.pdf sfc]
+|[[List_of_diagnostics_archived_to_bpch_format#ND06:_Dust_emissions|ND06]], [[List_of_diagnostics_archived_to_bpch_format#ND07:_BC_and_OC_sources|ND07]], [[List_of_diagnostics_archived_to_bpch_format#ND08:_Sea_salt_emissions|ND08]], [[List_of_diagnostics_archived_to_bpch_format#ND11:_Acetone_sources_and_sinks|ND11]],<br>[[List_of_diagnostics_archived_to_bpch_format#ND13:_Sulfur_emissions|ND13]], [[List_of_diagnostics_archived_to_bpch_format#ND28:_Biomass_burning_emissions|ND28]], [[List_of_diagnostics_archived_to_bpch_format#ND29:_CO_sources|ND29]], [[List_of_diagnostics_archived_to_bpch_format#ND32:_NO_emissions|ND32]],<br>[[List_of_diagnostics_archived_to_bpch_format#ND34:_Biofuel_emissions|ND34]], [[List_of_diagnostics_archived_to_bpch_format#ND36:_Anthropogenic_emissions|ND36]], [[List_of_diagnostics_archived_to_bpch_format#ND46:_Biogenic_emissions|ND46]]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Nitrogen/Nitrogen_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/Emis_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Nitrogen/Nitrogen_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Nitrogen/Nitrogen_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Nitrogen/Nitrogen_Emissions.pdf sfc]
-|
-|-valign="top"
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/Emis_PlantDecay_Surface.pdf PlantDecay]
-|Primary Organics
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Primary_Organics/Primary_Organics_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Primary_Organics/Primary_Organics_500hPa.pdf 500hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Primary_FullColumn_Organics/Primary_Organics_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Primary_Strat_Organics/Primary_Organics_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Primary_Organics/Primary_Organics_Emissions.pdf sfc]
 |
 |-valign="top"
-|Secondary Organics
+|[[History_collections_for_chemistry_and_photolysis#The_JValues_collection|JValues (24-hr avg)]]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Secondary_Organics/Secondary_Organics_Surface.pdf sfc]
+|[[List_of_diagnostics_archived_to_bpch_format#ND22:_Photolysis_diagnostics|ND22]]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Secondary_Organics/Secondary_Organics_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/JValues_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Secondary_FullColumn_Organics/Secondary_Organics_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/JValues_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Secondary_Strat_Organics/Secondary_Organics_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Secondary_Organics/Secondary_Organics_Emissions.pdf sfc]
-|
 |-valign="top"
-|ROy
+|[[History_collections_for_chemistry_and_photolysis#The_JValues_collection|JValuesLocalNoon]]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/ROy/ROy_Surface.pdf sfc]
+|[[List_of_diagnostics_archived_to_bpch_format#ND22:_Photolysis_diagnostics|ND22]]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/ROy/ROy_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/JValuesLocalNoon_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/ROy/ROy_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/JValuesLocalNoon_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/ROy/ROy_Strat_ZonalMean.pdf stratosphere]
-| --
-|
 |-valign="top"
-|Sulfur
+|[[History_collections_for_chemistry_and_photolysis#The_LevelEdgeDiags_collection|LevelEdgeDiags]]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Sulfur/Sulfur_Surface.pdf sfc]
+|[[List_of_diagnostics_archived_to_bpch_format#ND31:_Pressure_at_model_edges|ND31]], [[List_of_diagnostics_archived_to_bpch_format#ND66:_GMAO_3-D_met_fields|ND66]]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Sulfur/Sulfur_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/LevelEdgeDiags_850hPa.pdf 850hPa]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Sulfur/Sulfur_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/LevelEdgeDiags_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Sulfur/Sulfur_Strat_ZonalMean.pdf stratosphere]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Sulfur/Sulfur_Emissions.pdf sfc]
-|
 |-valign="top"
-|Emissions by HEMCO category
+|[[History_collections_for_chemistry_and_photolysis#The_ProdLoss_Collection|ProdLoss]]
-!colspan="5"|
+|[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05]], [[List_of_diagnostics_archived_to_bpch_format#ND07:_BC_and_OC_sources|ND07]], [[List_of_diagnostics_archived_to_bpch_format#ND65:_Chemical_production_and_loss_diagnostics|ND65]]
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Emissions/Total_Emissions.pdf Total],
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/ProdLoss_Surface.pdf sfc]
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Emissions/Aircraft_Emissions.pdf Aircraft],
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/ProdLoss_FullColumn_ZonalMean.pdf full column]
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Emissions/Anthro_Emissions.pdf Anthro],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Emissions/Bioburn_Emissions.pdf Bioburn],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Emissions/Biofuel_Emissions.pdf Biofuel],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Emissions/Biogenic_Emissions.pdf Biogenic],<br>
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Emissions/Lightning_Emissions.pdf Lightning],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Emissions/Monoterp_Emissions.pdf Monoterp],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Emissions/Natural_Emissions.pdf Natural],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Emissions/Ocean_Emissions.pdf Ocean],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Emissions/Seabirds_Emissions.pdf Seabirds],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Emissions/Senesc_Emissions.pdf SenescingPlants],<br>
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Emissions/Ship_Emissions.pdf Ship],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Emissions/Soil_Emissions.pdf Soil],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Emissions/VolcDegas_Emissions.pdf VolcDegas],
-[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Emissions/VolcErupt_Emissions.pdf VolcErupt],
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/Emissions/Emission_totals.txt Emissions tables]
 |-valign="top"
-|J-values
+|[[History_collections_for_species_concentrations#The_SpeciesConc_collection|SpeciesConc]]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/JValues/JVal_Surface.pdf sfc]
+|[[List_of_diagnostics_archived_to_bpch_format#ND45:_Species_concentrations|ND45]]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/JValues/JVal_500hPa.pdf 500hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/SpeciesConc_Surface.pdf sfc]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/JValues/JVal_FullColumn_ZonalMean.pdf full column]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/SpeciesConc_FullColumn_ZonalMean.pdf full column]
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/JValues/JVal_Strat_ZonalMean.pdf stratosphere]
-| --
-| --
 |-valign="top"
-!colspan="7" bgcolor="#CCCCCC"|Plots still created by GAMAP
+|[[History_collections_for_species_concentrations#The_StateChm_collection|StateChm]]
+|[[List_of_diagnostics_archived_to_bpch_format#ND73: ISORROPIA diagnostics|ND73]]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/StateChm_Surface.pdf sfc]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/StateChm_FullColumn_ZonalMean.pdf full column]
 |-valign="top"
-|Budget
+|[[History_collections_for_met_fields_and_related_quantities#The_StateMet_collection|StateMet]]
-| --
+|[[List_of_diagnostics_archived_to_bpch_format#ND57:_Potential_temperature|ND57]]
-| --
-| --
-| --
-| --
-|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/GC_12.5.0.budget.txt Ox and CO budgets]
-|}
+[[List_of_diagnostics_archived_to_bpch_format#ND31:_Pressure_at_model_edges|ND31]], [[List_of_diagnostics_archived_to_bpch_format#ND55:_Tropopause_diagnostics|ND55]], [[List_of_diagnostics_archived_to_bpch_format#ND66:_GMAO_3-D_met_fields|ND66]], [[List_of_diagnostics_archived_to_bpch_format#ND67:_GMAO_2-D_met_fields|ND67]], [[List_of_diagnostics_archived_to_bpch_format#ND68:_Air_mass_and_related_quantities|ND68]], [[List_of_diagnostics_archived_to_bpch_format#ND68:_Air_mass_and_related_quantities|ND69]]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/MetTheta_Surface.pdf sfc]
-<sup>1</sup>'''Benchmark category definitions:''' [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/benchmark_categories.json benchmark_categories.json]<br>
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/StateMet_Surface.pdf sfc]
-<sup>2</sup>'''Lumped species definitions:''' [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/lumped_species.json lumped_species.json]<br>
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/MetTheta_FullColumn_ZonalMean.pdf full column]
-'''NOTES:'''
+[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/StateMet_FullColumn_ZonalMean.pdf full column]
-#[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/benchmark_categories.json Category] and [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.5.0/GCC/NetCDF_Only/output/lumped_species.json lumped species] definitions are simple to adjust. Updating them requires only editing the json files.
-#All plots created with GCPy have PDF bookmarks. If you do not see them in your browser try using a different browser (not Safari) or installing an Adobe Acrobat plug-in.
-==== Benchmark assessment form for GEOS-Chem 12.5.0 netCDF only ====
-{| border=1 cellspacing=0 cellpadding=5
-|-bgcolor="#CCCCCC"
-!width="325px"|Description
-!
 |-valign="top"
-|New features added into GEOS-Chem
+|[[History_collections_for_convection_and_wet_deposition#The_WetLossConv_collection|WetLossConv]]
-|[[#Benchmark assessment form|Same as listed above]]
+|[[List_of_diagnostics_archived_to_bpch_format#ND38:_Loss_of_species_by_convection|ND38]], [[List_of_diagnostics_archived_to_bpch_format#ND37:_Fraction_of_species_scavenged_in_updrafts|ND37]]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/WetLossConv_850hPa.pdf 850hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/WetLossConv_FullColumn_ZonalMean.pdf full column]
 |-valign="top"
-|Version, resolution, met fields used:
+|[[History_collections_for_convection_and_wet_deposition#The_WetLossLS_collection|WetLossLS]]
-|GEOS-FP (72L), 4x5, July 2016
+|[[List_of_diagnostics_archived_to_bpch_format#ND39:_Loss_of_species_by_rainout_and_washout|ND39]]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/WetLossLS_850hPa.pdf 850hPa]
+|[http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/GC_12.5.0_bpch_vs_nc/WetLossLS_FullColumn_ZonalMean.pdf full column]
-|-valign="top"
-|1-month benchmark finished on:
-|TBD
-|-valign="top"
-|Performance statistics:
-|
-*Compiled with ifort 17.0.4
-*Ran on 24 CPUs of holyjacob01.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2680 v3 "Haswell" @ 2.50 GHz)
-*Wall time: TBD
-*[[Scalability|CPU time / wall time]]: TBD
-*% of ideal performance: TBD
-*Memory: TBD
-|-valign="top"
-|Compared to previous benchmark:
-|[[GEOS-Chem_12#12.4.0|12.4.0]]
-|-valign="top"
-|This update will impact:<br>(select all that apply with '''boldface''')
-|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Emissions, Photolysis, Chemistry, Other (please specify): '''Diagnostics'''
-|-valign="top"
-|[[GEOS-Chem Unit Tester|Unit test]] results may be viewed at:
-|TBD
-|-valign="top" bgcolor="#cccccc"
-!Metrics
-!
-|-valign="top"
-|Global mean OH from log file (% change):
-|12.6185890695857 x 10<sup>5</sup> molec/cm<sup>3</sup> (TBD)
-|-valign="top"
-|Methyl chloroform lifetime (% change):
-|TBD (TBD)
-|-valign="top"
-|Methane lifetime (% change):
-|TBD years (TBD
-|-valign="top"
-|List all SURFACE SPECIES, SURFACE J-VALUES<br>AND COLUMN AOD SPECIES for which<br><tt>ABS(MAX(frac. diff))) > 0.1</tt>:
-|
-|-valign="top"
-|Comments on SURFACE differences:
-|TBD
-|-valign="top"
-|List all 500 hPa SPECIES and<br>500 hPA J-VALUES for which<br><tt>ABS(MAX(frac. diff.) > 0.1</tt>:
-|
-|-valign="top"
-|Comments on 500 hPa differences:
-|TBD
-|-valign="top"
-|List all ZONAL MEAN SPECIES<br>and ZONAL MEAN J-VALUES for which<br><tt>ABS(MAX(frac. diff))) > 0.1</tt>:
-|
-|-valign="top"
-|Comments on ZONAL MEAN differences:
-|TBD
-|-valign="top"
-|List all EMISSIONS for which<br><tt>ABS(MAX(frac. diff))) > 0.1</tt>:
-|
-|-valign="top"
-|Comments on EMISSIONS differences:
-|TBD
-|-valign="top"
-|Additional or summary comments:
-|TBD
-|-bgcolor="#cccccc"
-!Approval
-!
-|-valign="top"
-|Requires further investigation:
-|TBD
-|-valign="top"
-|Approved by:
-|
-|-valign="top"
-|Date of approval:
-|
 |}