Development of Fast-JX in GEOS-Chem

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This page describes the implementation of Fast-JX in GEOS-Chem.

A few things about Fast-JX

I implemented Fast-JX (v6.2) into GEOS-Chem v8-01-02. This version of Fast-JX includes 18 bins of wavelengths. A few good things for this new version:

  • This version can be used for stratospheric chemistry with 11 wavelength bins in UV.
  • This version of Fast-JX handles thick clouds much better, because it uses a log-spacing to add sub-layers for thick clouds or aerosol layers. We had some problems in the standard version when cloud or aerosols are too thick (the old Fast-J uses linear spacing to ad sub-layers). See Too many levels in photolysis_code.
  • This version of Fast-JX is supposed to do a better job over polar region,where solar zenith angle gets close to 90.
  • I combined most files into one module: fast_jx_mod.f. This will provide a much better platform to get updates from newer version of Fast-JX for future development.
  • Fast-JX takes into account the photolysis of O2, which will make a little bit more ozone in upper troposphere.

If you need the source code, please contact Jingqiu Mao on this.

How does the new Fast-JX work?

Fast-JX calculates scattering at five wavelength 200nm, 300nm, 400nm, 600nm and 999nm. Fast-J calculates at four wavelength 300nm, 400nm, 600nm and 999nm (without 200nm).

  1. In chemdr.f, Fast-JX is initialized (call INPHOT(LLTROP, NPHOT)).
  2. In chemdr.f, Fast-JX is calculated by calling FAST_J( SUNCOS, OPTD, UVALBEDO).
  3. In fast_j.f, it was first determined which cloud overlap scheme (linear, random,or maximum) to be used. Then send single column properties to PHOTOJ for calculation, including:
    1. pressure profile
    2. temperature profile
    3. surface albedo
    4. Aerosol OD profile
    5. Mineral dust OD profile
    6. Cloud OD profile
  4. In calcrate.f, send J-values to smvgear by calling fjfunc.f.

Modules in fast_jx_mod.f

  • INPHOT
    • Read in labels of photolysis (call RD_JS)
    • Match Fast-JX species with Harvard species (call JV_INDEX)
    • Read in Fast-JX X-sections (spectral data) (call RD_XXX)
    • Read in T & O3 climatology (call RD_PROF)
    • Select aerosol/cloud types to be used (call SET_AER)
  • PHOTOJ
    • Set up Air, O3, BC profiles on GEOS-Chem vertical levels (call set_prof.f), this is the same as the old fast-j.
    • calculate air mass factors by calling sphere2. This is different from the old fast-j: the new AMF2 does each of the half-layers of the CTM separately, whereas the original, based on the pratmo code did the whole layers and thus calculated the ray-path to the CTM layer edges, NOT the middle.
    • add sub-layers (JXTRA) to thick cloud/aerosol layers by calling EXTRAL. This version sets up log-spaced sub-layers of increasing thickness ATAU. Given the aerosol+cloud OD/layer in visible (600 nm) calculate how to add additonal levels at top of clouds (now uses log spacing). This was linear spacing in Fast-J, so caused lots of problems for thick clouds.
    • For each wavelength bin, call OPMIE to calculate the mean actinic flux in each layer (AVGF), then save the flux into FFF (1:LPAR).
    • call JRATET to convert FFF to J-values for all species.

How does the current Fast-J work in GEOS-Chem?

Step 1: inphot.f

Require input files (cmn_fj.h, jv_cmn.h, ratj.d, jv_spec.dat, jv_atms.dat)

  1. Error check # of layers (call ERROR_STOP)
  2. Read in labels of photolysis rates required (call RD_JS.f)
  3. translate between GEOS-Chem species nomenclature and Fast-J species nomenclature(call JV_INDEX.f)
  4. Read in JPL spectral data set (e.g. X-sections, quantum yields) (call RD_TJPL.f)
  5. Read in T & O3 climatology (cf. Nagatani/92 and McPeters/91) (call RD_PROF.f)
  6. Select Aerosol/Cloud types to be used (call SET_AER.f)

Step 2: fast_j.f

For each (NLON,NLAT) location, call subroutine PHOTOJ (in a parallel loop to compute J-values for the entire column. J-values will be stored in the common-block variable ZPJ, and will be later accessed via function FJFUNC).

  1. Read TOMS O3 columns if it's a new month(call READ_TOMSO3 from "toms_mod.f“).
  2. Cloud overlap options
  • Linear Approximation (used up to v7-04-12)->call photoj.f
  • Approximate Random Overlap (default)->call photoj.f
  • Maximum Random Overlap (MRAN, computation intensive)->call photoj.f+mmran_16.f

Step 3: photoj.f

  • Set up Air, O3, BC profiles on GEOS-Chem vertical levels (call set_prof.f)
  • Set up cloud and surface properties (Call CLDSRF.f).
  • Set up pressure levels for O3/T climatology.
  • Select appropriate monthly and latitudinal profiles
  • Apportion O3 and T on supplied climatology z* levels onto CTM levels with mass (pressure) weighting, assuming constant mixing ratio and temperature half a layer on either side of the point supplied.
  • Calculate effective altitudes using scale height at each level
  • Add aerosol column - include aerosol types here. Currently use soot water and ice; assume black carbon x-section of 10 m2/g, independent of wavelength; assume limiting temperature for ice of -40 deg C.
  • Calculate column quantities for FAST-J: monthly mean air column and monthly mean O3 column.
  • Weight the O3 column by the observed monthly mean TOMS data.
  • Interpolate O3 column to current day (TOMS data is half month time resolution). Scale monthly O3 profile to the daily O3 profile.
  • Compute actinic flux at each GEOS-CHEM vertical level (call JVALUE.f). In which, calculate air mass factors for each layer (call sphere.f). Loop over all wavelength bins to call OPMIE.f:
  • Pick nearest Mie wavelength, no interpolation.
  • For Mie code scale extinction at 1000 nm to wavelength WAVEL (QXMIE)
  • Set up total optical depth over each CTM level, DTAUX
  • Fractional extinction for Rayleigh scattering and each aerosol type
  • Define the scattering phase fn. with mix of Rayleigh(1) & Mie(MIEDX), No. of quadrature pts fixed at 4 (M__), expansion of phase fn @ 8
  • Calculate attenuated incident beam EXP(-TTAU/U0) and flux on surface
  • Take optical properties on CTM layers and convert to a photolysis level grid corresponding to layer centres and boundaries
  • Calculate cumulative total and define levels we want J-values at. Sum upwards for levels, and then downwards for Mie code readjustments.
  • SET UP FOR MIE CODE. Transpose the ascending TTAU grid to a descending ZTAU grid. This is required so that J-values can be calculated for the centre of CTM layers; the index of these layers is kept in the jndlev array.
  • Insert new levels, working downwards from the top of the atmosphere to the surface (down in 'j', up in 'k').
  • call MIESCT.f
(1) fix scattering to 4 Gauss pts = 8-stream(CALL GAUSSP.f)
(2) solve eqn of R.T. only for first-order M=1(call LEGND0.f)
(3) call BLKSLV.f to solve the block tri-diagonal system.
(4) call GEN.f and MATIN4.f.
  • Calculate J-values for all species(call JRATET.f)
  • Scale actinic flux (FFF) by Solar distance factor (SOLF)
  • With model temperature, call XSECO2.f(FLINT.f); call XSECO3.f(FLINT.f); call XSEC1D.f(FLINT.f)
  • Calculate Jvalues for O2,O3,O1D
  • Calculate remaining J-values with T-dep X-sections

Step 4: fjfunc.f

supplies J-values to SMVGEAR solver

Implementation of Fast-JX

New input files

  1. spec2008.dat: fast-J X-sections (spectral data)
  2. atmos_std.dat: T & O3 climatology data
  3. chemJ2008.d: this is a tranfer map from the J's automatically calculated in fast-JX onto the names and order in the users chemistry code.

Major changes

  • Aerosol_mod.f
old new
# include "cmn_fj.h" # include "jv_cmn.h" # include "fj2008.h"
RW(R) = RAA(4,IND(N)+R-1) RW(R) = RAA(5,IND(N)+R-1)
QW(R) = QAA(4,IND(N)+R-1)*FWET + QAA(4,IND(N))*(1.d0-FWET) QW(R) = QAA(5,IND(N)+R-1)*FWET + QAA(5,IND(N))*(1.d0-FWET)
WAERSL(I,J,L,N) * QAA(4,IND(N)) WAERSL(I,J,L,N) * QAA(5,IND(N))
DAERSL(I,J,L,N-1) * QAA(4,IND(N)) DAERSL(I,J,L,N-1) * QAA(5,IND(N))
REFF = 1.0D-4 * RAA(4,IND(N)) REFF = 1.0D-4 * RAA(5,IND(N))
QAA(2,IND(N)+R-1) / QAA(4,IND(N)+R-1) QAA(3,IND(N)+R-1) / QAA(5,IND(N)+R-1)

All these are because there is one more wavelength bin for mie scattering(200nm), so RAA (effective radius) and QAA(aerosol extinction coefficient) all need to be changed accordingly.

  • dust_mod.f
old new
# include "cmn_fj.h" # include "jv_cmn.h" # include "fj2008.h"
DUST(I,J,L,N) * QAA(4,14+N)/ ( MSDENS(N) * RAA(4,14+N) * 1.0D-6 ) DUST(I,J,L,N) * QAA(5,14+N)/ ( MSDENS(N) * RAA(5,14+N) * 1.0D-6 )
ERADIUS(JLOOP,N) = RAA(4,14+N) * 1.0D-4 ERADIUS(JLOOP,N) = RAA(5,14+N) * 1.0D-4
( ODMDUST(I,J,L,N) * QAA(2,14+N) / QAA(4,14+N) ) ( ODMDUST(I,J,L,N) * QAA(3,14+N) / QAA(5,14+N) )
DUST(I,J,L,N) * QAA(4,14+N) / ( MSDENS(N) * RAA(4,14+N) * 1.0D-6 ) DUST(I,J,L,N) * QAA(5,14+N)/ ( MSDENS(N) * RAA(5,14+N) * 1.0D-6 )
ERADIUS(JLOOP,N) = RAA(4,14+N) * 1.0D-4 ERADIUS(JLOOP,N) = RAA(5,14+N) * 1.0D-4
( ODMDUST(I,J,L,N) * QAA(2,14+N) / QAA(4,14+N) ) ( ODMDUST(I,J,L,N) * QAA(3,14+N) / QAA(5,14+N) )
  • fast_j.f, fjfunc.f, fjfunc.f
USE FAST_JX_MOD, ONLY : PHOTOJ
# include "cmn_fj.h" # include "jv_cmn.h" # include "fj2008.h"


  • fast_jx_mod.f- this is a new file and it is the main file for Fast-J.


  • planeflight_mod.f
old new
# include "cmn_fj.h" # include "jv_cmn.h" # include "fj2008.h"
S400nm = QAA(2,IND(N)+RH-1) / & QAA(4,IND(N)+RH-1) S400nm = QAA(3,IND(N)+RH-1) / & QAA(5,IND(N)+RH-1)
S400nm = QAA(2,IND(N)+RH-1) / & QAA(4,IND(N)+RH-1) S400nm = QAA(3,IND(N)+RH-1) / & QAA(5,IND(N)+RH-1)

Other related changes

  • ch3i_mod.f

add this line at the beginning; “USE FAST_JX_MOD” Because ch3i_mod.f needs fast_j to calculate something for ch3i simulations.

  • Chemdr.f

Add this line: “USE FAST_JX_MOD, ONLY : INPHOT” Because inphot.f is now merged into fast_jx_mod.f

  • chemistry_mod.f

Add this line: USE FAST_JX_MOD

  • diag48_mod.f, diag49_mod.f, diag50_mod.f, diag51_mod.f
old new
USE FAST_JX_MOD, ONLY : PHOTOJ
# include "cmn_fj.h" # include "jv_cmn.h" # include "fj2008.h"

Files removed from v8-01-02

Filename Notes
BLKSLV.f Merged into “fastjx_mod.f”
CLDSRF.f Merged into “fastjx_mod.f”
cmn_fj.h Input files, now merged into “fj2008.h”.
EFOLD.f Removed, not even used in fast-j
FLINT.f Merged into “fastjx_mod.f” (Three-point linear interpolation function)
GAUSSP.f Merged into “fastjx_mod.f”
GEN.f Merged into “fastjx_mod.f”
inphot.f Merged into “fastjx_mod.f”
JRATET.f Merged into “fastjx_mod.f”
JVALUE.f Merged into PHOTOJ in “fastjx_mod.f”
jv_cmn.h Input files, now merged into “fj2008.h”.
jv_index.f Merged into “fastjx_mod.f”
jv_mie.h Input files, now merged into “fj2008.h”.
LEGND0.f Merged into “fastjx_mod.f”
MATIN4.f Merged into “fastjx_mod.f”
MIESCT.f Merged into “fastjx_mod.f”
NOABS.f Removed, not even used in fast-j
OPMIE.f Merged into “fastjx_mod.f”
photoj.f Merged into “fastjx_mod.f”
rd_js.f Merged into “fastjx_mod.f”
rd_prof.f Merged into “fastjx_mod.f”
RD_TJPL.f This is changed to “RD_XXX” in “fastjx_mod.f”.
set_aer.f Merged into “fastjx_mod.f”
set_prof.f Merged into “fastjx_mod.f”
SPHERE.f Merged into “fastjx_mod.f”, now changed to sphere2 function.
XSEC1D.f Merged into PHOTOJ in “fastjx_mod.f”
XSECO2.f Merged into PHOTOJ in “fastjx_mod.f”
XSECO3.f Merged into PHOTOJ in “fastjx_mod.f”
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