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Fix to support WRF Pnetcdf + quilting configuration when coupled to ROMS #217

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Fix to support WRF Pnetcdf + quilting configuration when coupled to ROMS #217

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46d8d81
Fix the MPI job hanging after completion, if WRF is configured with p…
SeregaOsipov Jan 16, 2024
13543fa
1. AQABA version of the Air Quality
SeregaOsipov Jan 17, 2024
df24a47
Merge remote-tracking branch 'origin/main'
SeregaOsipov Jan 17, 2024
9f56f1a
office progress sync before vacation
SeregaOsipov May 15, 2024
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9 changes: 9 additions & 0 deletions Master/mct_driver.h
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Original file line number Diff line number Diff line change
Expand Up @@ -590,6 +590,8 @@
END IF
# endif
# ifdef WRF_COUPLING
WRITE (stdout,84) MyRank
84 FORMAT (/,' osipov mct_coupler - Rank before finalize_ocn2atm_coupling ' ,i5.5)
IF (roms_exit.eq.NoError) THEN
CALL finalize_ocn2atm_coupling
ELSE
Expand All @@ -604,8 +606,15 @@
! Terminates all the mpi-processing and coupling.
!-----------------------------------------------------------------------
!

WRITE (stdout,85) MyRank
85 FORMAT (/,' osipov mct_coupler - Rank before mpi_barrier ' ,i5.5)
CALL mpi_barrier (MPI_COMM_WORLD, MyError)
WRITE (stdout,86) MyRank
86 FORMAT (/,' osipov mct_coupler - Rank before MCTWorld_clean ' ,i5.5)
CALL MCTWorld_clean ()
WRITE (stdout,87) MyRank
87 FORMAT (/,' osipov mct_coupler - Rank before mpi_finalize ' ,i5.5)
CALL mpi_finalize (MyError)

STOP
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20 changes: 17 additions & 3 deletions WRF/Registry/registry.chem
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Expand Up @@ -699,9 +699,11 @@ state real erup_beg ij misc 1 - i{13} "ERUP_
state real erup_end ij misc 1 - i{13} "ERUP_END" "END TIME OF ERUPTION" "?"
#
# following used for output to look at all kinds of stuff
state real dep_vel_o3 ij misc 1 - - "DEP_VEL" "deposition velocities for o3" "?"
# TODO: osipov nc name for dep_vel_o3 conflicts with dep_vel (general array)
state real dep_vel_o3 ij misc 1 - - "DEP_VEL_O3" "deposition velocities for o3" "?"
state real cu_co_ten ikj misc 1 - - "CU_CO_TEN" "CONV. TRANSPORT FOR CO" "?"


# Tendency diagnostics for chemistry (chemdiag)
#
# Currently index references to chem array is done within the code and requires
Expand Down Expand Up @@ -1130,6 +1132,13 @@ state real uvrad ij misc 1 - - "uv_
state real tcosz ij misc 1 - - "TCOSZ " "daily average cossza" "?"
state real ttday ij misc 1 - - "TTDAY " "" "?"

# osipov aerosol ph, can't use the name pH because it is taken by the "pertubation height"
# instead of ph I used the full name denoting the "potential of hydrogen"
state real pot_hyd_ph ikj misc 1 - rh "potential_of_hydrogen_pH" "aerosol potential of hydrogen (pH)" ""
# osipov flag to activate the effect of the dust crustal material on thermodynamics
rconfig logical do_crustal namelist,chem 1 .false. rh "activates the effects of crustal material" "true activates cations from dust" ""
rconfig real crustal_mobility namelist,chem max_domains 0.05 rh "mobility of the dust cations" "" ""

#soa diagnostic
state real tsoa ikj misc 1 - r "TSOA" "soa dry mass" "ug m^-3"
state real bsoa ikj misc 1 - r "BSOA" "bsoa dry mass" "ug m^-3"
Expand Down Expand Up @@ -3887,6 +3896,11 @@ rconfig real emiss_ash_hgt namelist,chem 1 0.

# additional namelist variables to control deposition of the organic condensable vapors
rconfig real depo_fact namelist,chem max_domains 0.25 rh "deposition factor for SOA vapors" "" ""
# osipov parametrize fine and coarse dust fraction in the emitted size distribution (for GOCART). NOTE: that coarse mode is derived as 1 - dust_i_fraction
rconfig real dust_i_fraction namelist,chem max_domains 0.001 rh "fraction of the emitted dust allocated to the accumulation mode" "" ""
# osipov multiplicative parameter to tune dust emissions (dust emissions *= dust_emis_sensitivity)
rconfig real dust_emis_sensitivity namelist,chem max_domains 1.0 rh "multiplicative parameter to tune overall dust emissions" "" ""


# track input
rconfig integer track_chem_num namelist,chem 1 0 - "number of track chem requested" "" ""
Expand All @@ -3904,8 +3918,8 @@ rconfig integer mosaic_aerchem_optaa namelist,chem 1
rconfig real af_lambda_start namelist,chem max_domains 200. rh "start wavelength for AF output" "nm" ""
rconfig real af_lambda_end namelist,chem max_domains 340. rh "end wavelength for AF output" "nm" ""
# Control for ISORROPIA in MADE/SORGAM schemes
rconfig logical do_isorropia namelist,chem 1 .false. rh "flag to use ISORROPIA"
rconfig logical do_n2o5het namelsit,chem 1 .false. rh "flag to do n2o5 heterogenous chemistry via chlorine pathway"
rconfig logical do_isorropia namelist,chem 1 .false. rh "flag to use ISORROPIA" "" ""
rconfig logical do_n2o5het namelist,chem 1 .false. rh "flag to do n2o5 heterogenous chemistry via chlorine pathway" "" ""

# CHEMISTRY PACKAGE DEFINITIONS
#
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2 changes: 1 addition & 1 deletion WRF/arch/postamble
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Expand Up @@ -84,7 +84,7 @@ io_only: esmf_time CONFIGURE_WRFIO_NF CONFIGURE_WRFIO_NFPAR CONFIGURE_WRFIO_PNF

## jcw
CPP = /usr/bin/cpp -P -traditional
CFLAGS_LOCAL += -DNCEP_DEBUG_GLOBALSTDOUT -DNCEP_DEBUG_MULTIDIR
# CFLAGS_LOCAL += -DNCEP_DEBUG_GLOBALSTDOUT -DNCEP_DEBUG_MULTIDIR # osipov disable to split the rsls into individual files



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14 changes: 14 additions & 0 deletions WRF/chem/KPP/mechanisms/racm_soa_vbs_het/racm_soa_vbs_het.tuv.jmap
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@@ -0,0 +1,14 @@
o31d : j_o1d
o33p : j_o3p
no2 : j_no2
n2o5 : j_n2o5_b
hno3 : j_hno3
no3o : j_no3_a
hno4 : j_hno4
ch3o2h : j_ch3ooh
ch2or : j_ch2o_r
ch2om : j_ch2o_m
h2o2 : j_h2o2
ch3cho : j_ch3cho_a + j_ch3cho_b + j_ch3cho_c
ch3cocho : j_mgly
pan : j_pan_a + j_pan_b
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