*JAC Section

1. Jacobians for can be either
   • Scalar: e.g. surface parameters, homogeneous gas paths (HOM flag) or whole column atmospheric perturbations, in which case SPECIES is the only field within each record; or
   • Vector: where the perturbation is confined to a specific layer in the atmosphere, in which case subsequent fields ALT, FILALT or 'TAN' are used to define the layer(s)
2. Jacobian output files are created for each species at each perturbation altitude, and represent the difference (perturbed−unperturbed). The filenames are those of the normal output spectra but with an additional string inserted after the [s][t] component representing the perturbed parameter and, if applicable, perturbed altitude. e.g. if the normal (unperturbed) radiance spectrum is file rad_a08000.asc there will be additional Jacobian spectra such as rad_a08000_h2o11000.asc (for h2o perturbed at 11 km), repeated for each species and each altitude

   Specifying Altitudes

3. Jacobians are always specified by altitude. If the RFM internal grid is specified in pressure coordinates (first profile in the *ATM section) it is necessary to include an altitude profile if layer Jacobians are required. However, the actual altitudes have no significance except to identify the profile levels, so you could just assign numbers: 1, 2, 3 km etc.
4. Layer perturbations are 'triangular', defined by an altitude for the maximum perturbation (in % or K, of amplitude as listed in the above table) and altitudes for which the perturbation decreases (linearly) to zero. If these altitudes are not already in the user-defined profile (*ATM section) then extra levels are automatically inserted.
5. For a single layer perturbation, three ALT values are required specifying the lower bound, the perturbation maximum and the upper bound (ALT values must always increase monotonically). For multiple layer perturbations the adacent values are used to specify the bounds. For example a set of ALT values of 3, 6, 9 and 12 will generate Jacobian spectra at 6 km (corresponding to a perturbed atmosphere between 3 and 9 km) and at 9 km (perturbation from 6 to 12 km). Therefore, N ALT values will produced Jacobian spectra for N-2 perturbation altitudes.
6. The first ALT value may be below the lowest altitude of the atmospheric profile, which has the special interpretation of a partial column perturbation for the first Jacobian. E.g. ALT values of -1, 6 and 9, for an atmospheric profile starting at 0 km, will have the unit perturbation applied over the whole range 0–6 km, and then decreasing linearly from 6–9 km. Similarly if the last value in the ALT section is above the top of the atmospheric profile this applies a uniform perturbation for the whole atmosphere above the penultimate ALT value used to define the highest Jacobian.
7. Since all the ALT values have to be contained within a single record, it may be more convenient to list these in a generic data input file, identified using FILALT. Note that the RFM effectively expands the contents of FILALT within the record, so that a mixture of explicit ALT values and FILALT file(s) can be used, as long as they obey the requirement of monotonically increasing values.
8. The 3-character string 'TAN' (upper or lower case) may also be used as a shorthand for the set of tangent altitudes specified in the *TAN section (limb-viewing mode only), but again with the requirement that these are monotonically increasing. You will probably also want to add altitudes before and after 'TAN' to generate Jacobian spectra for the lowest and highest tangent point values. If using the JTP flag, using 'TAN' is mandatory.

   Species

9. TEM and PRE Jacobians are strictly local, independent perturbations in these quantities without any regard to re-establishing hydrostatic equilibrium through the rest of the profile. However, local air density, and therefore absorber concentrations expressed in VMR, are modified. Although density changes also modify refraction, any change in ray paths is assumed to be of second order and is ignored.
10. [gas] can be any absorber listed in the *GAS section, also allowing for alternative names or HITRAN indices that the RFM can identify as belonging to the same molecule.
11. [gas(i)] For Jacobians of specific isotopes, add the HITRAN isotope index in brackets, e.g. H2O(1) for the most abundant water vapour isotope.
    • RFM Handling of Isotopologues.
12. [gas(i)(v)] For Jacobians of Vibrational Temperatures it is necessary to specify both an isotope and a 'Global Quantum Number' identifying the vibrational level (see RFM Vibrational Level Assignments), and a matching VT profile has to be loaded via the *ATM or *NTE sections.
13. Pointing (line-of-sight) Jacobians can also be generated, but this is via the LOS Flag.

*JAC              
     O3 5 8 11 14 ! Perturb O3 levels @ 8,11 km in 3km layers
    TEM 5 8 11 14 ! Perturb Temp levels @ 8, 11 km in 3km layers
    PRE           ! Perturb pressure for whole profile
    sfctem        ! Surface temperature Jacobian
     H2O(1)       ! Perturb H2O main isotope column
     H2O(2)       ! Perturb H2O second isotope column
     H2O          ! Perturb remaining H2O isotopes (#3,#4 etc) column