Update 5.2Beta with recent changes from EPA CMAQ Team #5
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-removed the M3EXIT call when the modeled ozone column exceeds 10% of observed
total column
-set the stratospheric ozone column to allow minimum fraction
times observed observed column when the modeled ozone column exceeds the minimum fraction
-revised the log messages stating that problem has occurred, what are possible
causes, and what PHOTDIAG file output help to describe the problem.
-added a logical flag called ADJUST_OZONE that is set to false. If it is set to TRUE,
the code reduces the simulated ozone optical depth based on the extended of the exceedance.
The value of false was selected so the above actions cause less than or equal to 1.0E-4 ppm
differences in ozone predictions over test simulations for January, April and July 2011
periods. The first two period showed the largest differences when exceedance occur. No
exceeds for the July period.
new file: phot/inline/SEAS_STRAT_O3_MIN.F
-module contains data and routine for determine minimum fraction
of ozone column in stratosphere. The module's routine interpolates
over to find the stratospheric fraction of total ozone column at 18
latitude point. It then returns the minimum value of these fractions.
The data interpolated comes from a seasonal climatology for the meridian
cross-section of ozone concentrations. McPeters and Labow (2012)
assembled the climatology based on Aura Microwave Limb Soundings
(2004-2010) and balloon sondes (1988-2010). Their data was lasted accessed
July 11, 2016 under the URL, ftp://toms.gsfc.nasa.gov/pub/ML_climatology/
References:
McPeters, R. D., and G. J. Labow (2012), Climatology 2011: An MLS and sonde
derived ozone climatology for satellite retrieval algorithms, J. Geophys. Res.,
117, D10303, doi:10.1029/2011JD017006.
modified: phot/inline/opphot.F
-added two variables to the PHOTDIAG1 files.
1) TROPO_O3_EXCEED -mean exceedance of modeled ozone column from expected fraction
of total column based on the minimum allowed stratospheric fraction. The mean is over
the output time step.
2) N_EXCEED_TROPO3 -number of exceedances to tropospheric ozone column over the
output time step
modified: phot/inline/phot.F
-added a time dependent value for minimum fraction of ozone column in
based on the PTOP of the model domain. The value is determine by
calling SEASONAL_STRAT_O3 in the SEAS_STRAT_O3_MIN module.
-added lines and variables from the new diagnostic file output based on
changes to opphot.F
-added lines writing to the log file summarizing exceedances of the modeled
ozone column from expected fraction of total column based on the minimum
allowed stratospheric fraction. Lines are written only if exceedances
occur.
-corrected unintilialized variable
modified: phot/inline/opphot.F
modified: phot/inline/phot.F
-further changed to diagnostic messages and output files
-further tuning for diagnostic TROPO_O3_EXCEED
modified: phot/inline/phot.F
-changed TROPO_O3_EXCEED from instataneous values to average over
output time step
…S_STRAT_O3_MIN.F
-changed error message to prevent segmentation fault
the surrogate is used. Updated by David Wong. modified: CCTM/src/hadv/yamo/advbc_map.F On branch davidPR
Constructed water soluble and insoluble list dynamically
based on a given chemical mechanism and AE scheme
Cosmetic changes (removed commented out lines)
-moved setting stratospheric ozone column to minimum values above
the IF( OBEY_STRATO3_MINS ) block so it is execute when SUCCESS is
FALSE
-added line to reset the TROPO_O3_TOGGLE to one if ADJUST_OZONE
is FALSE
-changed LOG messages to state that the error in ozone column accumulates
downward from the specified layer and define diagnose output
-removed comment line stating 100mb or 50mb as strat column application limit
modified: CCTM/src/phot/inline/SEAS_STRAT_O3_MIN.F
-modified the calculation of YEAR to prevent type casing or
math error between real and integer variables
modified: CCTM/src/phot/inline/phot.F
-added IF block to calculate MIN_STRATO3_FRAC and MAX_TROPOO3_FRAC when
JDATE does not equal JD_STRAT_O3MIN. JD_STRAT_O3MIN is initialized to zero
but reset to JDATE when IF condition is TRUE
modified: CCTM/src/phot/inline/PHOT_MOD.F
modified: CCTM/src/phot/inline/SEAS_STRAT_O3_MIN.F
modified: CCTM/src/phot/inline/phot.F
…s if necessary On branch BC_Check modified: CCTM/src/aero/aero6/AERO_DATA.F modified: CCTM/src/hadv/yamo/rdbcon.F
The code now checks before it goes out of bounds and will
exit with a warning. This situation tends to happen when additional
aerosol species are added to the model and they all use the same
deposition surrogates. The number of species that can use a surrogate
is indicated by mxsrg. The check is only performed at FIRSTTIME,
but will be checked on each processor. The warning will look like:
*** ERROR ABORT in subroutine AQ_DATA on PE 017
lsrg will index out of bounds. Increase mxsrg in AQ_DATA.F
PM3EXIT: date&time specified as 0
Date&time specified as 0
On branch aq.data.msg
Changes to be committed:
modified: src/cloud/acm_ae6/AQ_DATA.F
modified: src/cloud/acm_ae6_mp/AQ_DATA.F
modified: src/cloud/acm_ae6i_kmti/AQ_DATA.F
On branch specdef Changes to be committed: modified: MECHS/saprc07tic_ae6i_aq/SpecDef_Dep_saprc07tic_ae6i_aq.txt modified: MECHS/saprc07tic_ae6invPOA_aq/SpecDef_Dep_saprc07tic_ae6invPOA_aq2.txt
On branch specdef Changes to be committed: new file: MECHS/saprc07tb_ae6_aq/SpecDef_Dep_saprc07tb_ae6_aq.txt typechange: MECHS/saprc07tc_ae6_aq/SpecDef_Dep_saprc07tc_ae6_aq.txt typechange: MECHS/saprc07tc_ae6nvPOA_aq/SpecDef_Dep_saprc07tc_ae6nvPOA_aq.txt Changed but not updated: deleted: MECHS/saprc07tb_ae6_aq/SpecDef_Dep_saprc07tb_ae6i_aq.txt
On branch specdef Changes to be committed: deleted: SpecDef_Dep_saprc07tb_ae6i_aq.txt
On branch specdef Changes to be committed: renamed: SpecDef_Dep_saprc07tic_ae6invPOA_aq2.txt -> SpecDef_Dep_saprc07tic_ae6invPOA_aq.txt
Add EPA Disclaimer and Creative Commons License to README
Fixed the include path of mpif.h
Added AQ_DATA check to prevent array out of bounds.
On branch BC_Check modified: src/aero/aero6/AERO_DATA.F modified: src/hadv/yamo/rdbcon.F
Adds routines and calls for checking size dist from BCs.
Specdef deposition files updated for s07t mechanisms
Fix typo in name of SOA surrogates for the oxidized organic vapors
Skip precursor mapping algorithm if it has been executed already. @sergeynk has checked this implementation before the pull request was issued and it works. No change in model output. Some reduction in mapping execution time.
Remove trims
Fixes warning in AQ_DATA and adds comments to explain logic
On branch BCfix modified: hadv/yamo/hadvyppm.F
…l layers On branch BCfix modified: hadv/yamo/hadvyppm.F modified: hadv/yamo/rdbcon.F
On branch BCfix modified: hadv/yamo/hadvyppm.F
This is merged without review because the scope of the changes are small and the code has been tested. The code also needs to get to CMAS today and it will be advantageous to have the BC error printed consistent with the changes made in this commit.
Reduces number of redundant MPI operations. David has tested this code.
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Mar 7, 2019
Revise negative emissions error check to only check for
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-remove transport requirement for tracked ISAM species
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Update master species tables for nonvolatile POA
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(cherry picked from commit 4f46963)
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Oct 12, 2020
Updated issue #5 with R. Mathur's and D. Wong's suggested comments.
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Jul 8, 2022
Update documentation output from routines in WIKI_TABLE.F
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Update speciation profiles in CMAQ_Control namelists for the 2D-VBS m…
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Add -std=legancy flag to allow GNU versions 10+ to compile.
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The updates to the 5.2Beta will appear temporarily on a separate branch called 5.2Gamma so that the changes can be kept separate from the Beta version released to the public in October. These updates will be incorporated in the testing performed by CMAS and eventually merged into the v5.2 release.