Changelog for ProDiMo

There was no proper release management in the past for ProDiMo. From now we plan to produce stable releases more often and recommend using one of those tagged releases.

ProDiMo master (possibly unstable)

If you are using the latest version of the ProDiMo code from the master branch, please also check if the Automatic Tests Results are okay.

  • 2025-12-19 MR 155
    Changes default parameter settings and checks for X-rays/EUV and Hatom.
    • noEUV=.true. is still the default (i.e, not using any EUV cross-sections from Leiden)
    • if noEUV=.true. and EUV is not included in the X-ray range; ensure that there is indeed no radiation in the stellar spectrum (for clarity).
    • There are no checks for noEUV at the moment, so one can experiment with it.
  • 2025-12-16 MR 157 Some (small) bugfixes for the dust_charge chemistry/heating implementation.
  • 2025-12-10 MR 154 Use JNU_FROM_RT_SHIELDED in rate_coffs for the dust_charge_chemistry.
  • 2025-12-06 MR 153
    Added checks and improvements for SEDs with a large number of wavelength points.
    • new parameter write_image_out, if false, image.out is not written
    • check if NLamSED > 75000 (SPECMAX), which is the current limit
    • Multiple inclinations are now also possible for pixel images (e.g., image_i002.fits)*
  • 2025-12-02 MR 152 First step of code refactoring to reduce dependencies on Nlmax and NLAMmax
  • 2025-11-21 MR 151
    Cleaning and documentation of the 2D interface implementation, enabling the passing of Tgas and Tdust.
    • Documentation: (https://prodimowiki.readthedocs.io/en/latest/userguide/interface2D.html)
    • Also, the 2D interface tools in prodimopy have been updated: (https://prodimopy.readthedocs.io/en/latest/interface2D/interface2D.html)
  • 2025-11-18 [MR 150](https://gitlab.astro.rug.nl/prodimo/prodimo/-/merge_requests/150 Disable use_chemsol if freeze_chemistry or freeze_Tgas is true.
  • 2025-11-12 MR 149 nonLTE CO2 and HCN
  • 2025-11-11 MR 148 Bugfix: For 2-zone models with a2min < amin and no dust_settling (code stopped during init).
  • 2025-10-17 MR 146
    Removed handle_UMIST and num_noerase from essential Parameters list, and some new defaults:
    • Jback_from_RT=.true. by default, as required by new_escape which is true by default
    • parallel_chem=.true. if compiled with OMP
    • set conserve_pressure=.false. if solve_disktruc=.false. or solve_diskstruc=true and MCMAX_LIKE=.true.
    • new Model setup: examples/Technical/DefaultModel , has only required parameters.
  • 2025-10-16 MR 145
    Properly initialise e- abundance/density if el_is_sp=true.
    • also made NewChemScan=.true. the default
  • 2025-10-08 MR 134 Option to use a big Hydrogen model atom (n=200), via a newly generated Lamda file.
  • 2025-10-02 MR 144 Removed some unused parameters (SED_no_scattering,metals_bf_heating,restart_from_age,CO_Nelec,line_vkeppgrad)
  • 2025-10-01 MR 143
    Some parameter checks for
    • chemanalysis_fits (don't try to write it if stop_afer_init/RT, don't allow in MC mode)
    • STAND with el_is_sp not possible, added a check
    • self_shielding with Rphoto_bandint not allowed (check already in read_parameter)
  • 2025-09-13 MR 142 dust heating by gas lines consistent with new escape probability method & two new heating/cooling compensations
  • 2025-09-05 MR 141 Fix problems with running a restart model that has el_is_sp=true, but the "old" model had el_is_sp=false.
  • 2025-09-04 MR 140 Better handling of errors when reading the Reactions.in fails or if it does not exist.
  • 2025-08-04 MR 139 Use single precision to write population levels to ProDiMoForFlits.fits
  • 2025-07-24 MR 137 BUGFIX: PAH_in_RT without PAHs as species with newUVphoto is now working.
  • 2025-07-14 MR 136 Use fits a file to write out the data required for chemanalysis (new parameter chemanalysis_fits).
  • 2025-07-03 MR 135 Make the use of memLimitGB more user friendly and also added a wiki documentation.
  • 2025-06-26 MR 133 call write_sysinfo at the beginning of read_parameter.
  • 2025-06-26 MR 132 Improvements for conda makefiles and special FirstModel for the wiki documentation.
  • 2025-06-25 MR 131 bug-fix double accounting of H2 fluorescent excitation for heating when using UV_H2
  • 2025-05-14 MR 130 DECO branch
  • 2025-05-07 MR 129 Set default values for ABS_CRI=3 (i.e. Padovani 2009/2023)
  • 2025-05-06 MR 128
    On-the-fly allocation for most of the line (SYS) data (i.e. get rid of Ndims). Also
    • some code cleaning
    • nicer log output for init_heatcool and init of SYS
    • write Parameter.out also in slab_escape mode.
  • 2025-04-01 MR 127 new H2O non-LTE expansion, OH and H2O chemical pumping, and split viscous heat
  • 2025-03-31 MR 126 Technical: New run of Umist2012 benchmark
  • 2025-03-31 MR 122 Refactoring of water line data
  • 2025-03-25 MR 125 Rename AdsorptionEnergies.dat to AdsorptionEnergies.in in data directory (e.g. will be chosen as default).
  • 2025-03-24 MR 124 Technical: Uses ifx in example makefiles and documentation
  • 2025-03-14 MR 123 merge heatcool_shielded with master
  • 2025-02-11 MR 121 Change numericalJacobian to numerical_jacobian in various example input files.
  • 2025-01-30 MR 119 Technical: Use consistently SPlen+4 for the length of line/molname.
  • 2025-01-28 MR 120 CR induced UV
  • 2025-01-21 MR 118 Technical: Refactoring memory allocation for line transfer (LINE_PRECALC).
  • 2025-01-20 MR 117 avoid element carriers when evaluating balance in solve_chemistry to switch on...
  • 2025-01-14 MR 116 Implementation of Minissale's adsorption energies and vibration frequencies
  • 2024-08-13 MR 115 Exomol nirspec
  • 2024-08-05 MR 112 Option to include custom hitran lines in the heating/cooling balance as coolants.
  • 2024-08-05 MR 113 Add OH+ Exomol data as a custom HITRAN molecule.
  • 2024-07-30 MR 103 Added CH3+ photodissociation cross-sections
  • 2024-07-29 MR 111 Technical: Custom hitran indexing
  • 2024-07-28 MR 105 Added SiO, CH+, CH, and H3+ HITRAN data; converted from ExoMol in the MIRI range
  • 2024-07-27 MR 110 Implementation of KIDA 2024 chemical network
  • 2024-07-26 MR 109 Update to selection rules for Hitran lines
  • 2024-07-22 MR 106 Updated thermo data
  • 2024-07-21 MR 102 Added CH3+ to mid-IR lines
  • 2024-07-12 MR 94 Simple C13\mathrm{C^{13}} fractionation
  • 2024-07-11 MR 100 Added CI to work with immediate lines
  • 2024-07-01 MR 101 Technical: Speed-up by having different SOLVE_CHEM variants (quadp,num.Jac) and remembering the last successful solution method
  • 2024-06-21 MR 53 Technical: Removing NR routines
  • 2024-04-12 MR 98 No automatic CO self-shielding from RT
  • 2024-04-10 MR 96 Remove c13 c12
  • 2024-04-06 MR 92 Implementation of Osu high t chemical network
  • 2024-04-05 MR 91 Bugfix: init reactions checks
  • 2024-04-04 MR 89 MR 97 Implementation of gas phase KIDA 2022 chemical network
  • 2024-04-02 MR 90 Update examples/Processes/SurfaceChemistry/Parameter.in
  • 2024-03-28 MR 71 Technical: refactoring of init_heatcool (and related stuff) to make adding a new coolant/line easier
  • 2024-03-25 MR 83 MR 84 MR 85 Updated examples in examples/MolecularCloud (e.g. UMIST2022)
  • 2024-03-28 MR 77 MR 78 MR 79 MR 80 MR 81 MR 86 Implementation of UMIST2022 chemical network

Version v3.0.0 (stable)

new code features

  • new escape probability [new_escape=T, new_escape_lineflux=T] (doc): takes into account continuum emission/absorption effects in the line emission regions, leading to both increased escape and pumping probabilities. As a consequence, gas and dust are now energetically more tightly coupled by the exchange of line photons in the midplane, which turns out to be more efficient than thermal accommodation. The new escape probabilities are now also applied to the line-flux estimations and determinations of the line emitting regions, details in Woitke+2023 (ADS)

  • new setup for UV photorates and molecular shielding [new_shielding=T, self_shielding=T, C_shielding=T, H2_shielding=T, HD_shielding=T, gas_shielded_photodesorption=T] (doc): introducing a better way to deal with the 2D geometry of direct and scattered UV irradiation for the computation of photorates and molecular shielding factors. A number of improvements have been made, including the activation or several mutual and self-shielding factors from the literature, details in Woitke+2023(ADS)

  • improved reaction network [UMISTDB="UMIST2012_Meisner.dat", read_reactions_in_csv=T]: The default reaction network is now read from data/ChemicalNetwork/UMIST2012_Meisner.dat and data/ChemicalNetwork/Reactions.in.csv. UMIST2012_Meisner.dat includes low-T rates with tunneling for a few important reactions (ADS) and the Collider reactions that were present in the UMIST network version of 2016. Reactions.in.csv includes additional rates from KIDA for larger hydrocarbon molecules (ADS). A number of additional fixes and additions have been made.

  • updated H2-formation rate on grain surfaces [H2_Cazaux2010=T, H2_Cazaux2017=T]: now by default latest edition Cazaux+2010 (ADS)

  • HITRAN 2020 [hitran2020=T]: now by default selected as the source for the line lists of the LTE-molecules like CO2, HCN, and C2H2. Improved default line selection criteria implemented to extend the line lists down to 4.5 micron.

  • large CO ro-vibronic model molecule [custom_COrovib=T, COX_Nrot=60, COX_Nvib=4, COA_Nvib=0] (doc): from Thi+2013 (ADS) now activated by default

  • new non-LTE ro-vibrational OH model molecule [OH_ExoMol=T] (doc)

  • new photo-dissociation heating rate [Heat_per_PhotoDiss=2.0]: explained in Woitke+2023 (ADS)

  • improved code speed and stability [el_is_sp=T, chem_scale=T, quadp_solver=T]: ProDiMo now uses by default the option to have electrons as additional species, use the quadruple precision chemistry solver if necessary, and a better scaling of the chemical rate equations.

new optional features

  • new options for consistent molecular shielding [newUVphoto=0 by default (3 is recommended), UVphoto_highres=F (F is recommended)] (doc): Users can now use the tabulated Leiden molecular shielding factors (link) and/or can use the high-resolution Leiden photo-cross-sections from the Leiden photodissociation and photoionisation database to calculate these shielding factors themselves on the fly, including all combinations of mutual and self-shielding effects. Yet unpublished.

  • new options for having an increasing surface density at the inner rim [reduc, reduc, deduc, daduc] and subsequent disk zones: explained in Woitke+ (2023).

bugfixes

  • OI heating/cooling bug fixed. Code was unintentionally using the old 3-level atom for atomic oxygen, whereas, with UVpumping=T, it should use the Oatom_Lambda_extra_NIST model atom with 91 levels and more collisional partners.

Version v2.0.0 14.04.2022 (stable)

Version v2.0.0 is a special release as it is the first official one. In the following, we list some main features that were developed in the last couple of years

new default features

New features and improvements that are activated by default and hence might change results for older models. Those are switched on by default as it is an improvement. For backward compatibility, they can also be switched off again (see the links to the documentation).

  • diffusion approximation for dust radiative transfer (doc): improves the radiative transfer and dust temperature determination in the optically thick midplane of the disk by using the diffusion approximation.

  • new photo cross-sections for the chemistry (doc): using new photo cross-sections for photoreactions in the chemistry. However, only small differences are expected compared to the previously used cross-sections.

  • N2 self-shielding activated by default (doc): Self-shielding of N2. Significantly affects species such as N2H+, including the line flux.

  • Fixed some UMIST2012 reactions (history) Fixed reaction 5990: the products should be N+ and H, not N and H+. Fixed the CRPHOT reactions for He and N (Reactions: 928,932). Those fixes affect the chemical abundances, but our tests indicate that the changes are not significant.

new features (optional)

  • 1D input interface (doc): option to provide input for the gas and dust structure as a function of radius.

  • self-consistent model with ice-opacities (doc): include ice-opacities in the radiative transfer. This is done consistently with the chemistry. Also allows to produce synthetic observables for ice features.

  • images and spectral line cubes in fits format (doc): use fits format for observables such as continuum images or spectral line cubes. Can be easily used in e.g. CASA

  • Improvements for the chemical solver: More stability and better performance for more complex chemical networks Possible options: use quadrupole precision, treat electrons as species ...

TODO: is there already a wiki page for that

  • grain surface chemistry doc): option to include dust surface chemistry; requires also special chemical networks). This is still an experimental feature.

TODO: is the documentation up-to-date

  • chemical equilibrium computation: GGchem (used in phyllosilicate paper)

TODO: some description, is there documentation?

  • new cooling lines: CF+, H13CO+

TODO: do we know which ones are new

  • PAH/dust charge chemistry

TODO: Reference to the paper TODO: is there a species wiki page

  • simple grain charging and MRI viscous heating

TODO: is there a wiki page TODO: link to the paper ?