Chemical Reaction Rate Databases

TODO: Merge those two, the Chemical rates one is more up-to-date it seems The information can also be found now at Chemical rates

ProDiMo has the option to use different well know chemical reaction rate databases (mostly gas phase). Please note that there are significant differences for a few species when using the different databases. It is up to the user to choose his/her favourite database and rates. For a comparison of different chemical, networks see Kamp et al. (2017).

In addition to those chemical databases also an additional Rection input file is required. For further details see below.

Please always cite the chemical databases correctly in your ProDiMo paper. Details for the proper citation are given below.

UMIST gas phase network

By default, ProDiMo uses the UMIST 2006 database Woodall et al. (2007). The database file is included in the ProDiMo data directory (file UMIST2006.dat)

However, we recommend using the more recent version from 2012 McElroy et al. (2013) (see also [https://umistdatabase.uk/]). This can simply be done by setting the switch:

.true.  ! UMIST2012

The database file can be found here UMIST2012.dat. Additionally one can also provide an alternative database (has to be in UMIST format) by using

yourdatabase.dat ! UMISTDB

Then the rates are read from the file yourdatabase.dat which has to be in the ProDiMo_datapath or better in your local model directory (see Adapt chemical data files). In case one uses a custom database please check the reaction types available in ProDiMo (see chemistry_solver_design).

The default UMIST2012.dat database file also includes the collider reactions (i.e. is not identical to the version from the UMIST webpage). If you want to use the file without collider reactions you can use UMIST2012_NOCL.dat.

For other changes/fixes to the original UMIST database file, please check the git history.

Citation

PLEASE cite the above-mentioned papers if you use one of the UMIST databases.

KIDA gas phase network

The KIDA rate database for astrochemical modelling has been compiled by Valentine Wakelam and co-workers (See [http://kida.obs.u-bordeaux1.fr]).

The switch:

.true.  ! KIDA_rates

will make ProDiMo to use the high-temperature KIDA network (file KIDA_ProDiMo_2011.dat) instead of the UMIST 2006/2012 database. The additional rates in Reactions.in will be treated the same way as before according to the switches.

To use the more recent 2014 version of KIDA (file KIDA_ProDiMo_2014.dat) you have to additionally set

KIDA_ProDiMo_2014.dat  ! KIDADB

One can also use a different file as long as it is in the KIDA format and does not include any Reaction types that are unknown by ProDiMo (see chemistry_solver_design).

Citation

  • KIDA 2011 release: Wakelam+ (2012)

  • KIDA 2014 release: Wakelam+ (2015)

  • On the KIDA website, it is written:

    If you are using KIDA for your research or to make your data available, we would appreciate it if you could mention it in your publications. Typical sentences in this regard are given below.

    The data published in this paper have been added to the online database KIDA (Wakelam et al. 2012, http://kida.obs.u-bordeaux1.fr).

    The (some) kinetic data we used have been downloaded from the online database KIDA (Wakelam et al. 2012, http://kida.obs.u-bordeaux1.fr).

OSU (Ohio State University)

The OSU rate database for astrochemical modelling has been compiled by Eric Herbst and co-workers (See [http://www.physics.ohio-state.edu/~eric/research.html], the page doesn't seem to exist anymore).

The switch:

.true.  ! OSU_rates

will make ProDiMo use the high-temperature OSU network (files osu_09_2012_ht_ProDiMo.dat and osu_pol_data.dat) instead of the UMIST 2006 database. The additional rates in Reactions.in will be treated the same way as before according to the switches.

Citation

A New Network for Higher-temperature Gas-phase Chemistry. I. A Preliminary Study of Accretion Disks in Active Galactic Nuclei, Harada, Nanase; Herbst, Eric; Wakelam, Valentine, 2010, ApJ. 721, 1570H and the Erratum

OSU/AlCHEMIC

Dimitry Semenov added surface reactions based on the Hasegawa & Herbst network to the standard OSU gas-phase network. The main purpose of the Alchemic network is to enable a comparison between parts of the ProDiMo surface chemistry implementations (see /examples/Benchmarks/Benchmark_SURFACE_CHEMISTRY). Not all the surface chemistry physics that are in ProDiMo is tested by the benchmark.

.true.      ! OSU_Alchemic       : use the network of the benchmark
.false.     ! other_reactions
.true.      ! surface_chemistry

If you set the

.true.      ! other_reactions

then reactions in the Reactions.in file are considered as well according to the switch used (only_add, replace)

Citation

Chemistry in disks. IV. Benchmarking gas-grain chemical models with surface reactions, Semenov et al. A&A, Volume 522, id.A42, 12 pp. 2010

STAND2020

we can also import reactions from the STAND 2020 network designed for planetary atomsphere, including lots of three-body reactions, see STAND2020 network for details.

own file Reactions.in/ReactionsDEV.in/Reactions.csv

In addition to these databases, ProDiMo allows providing 'own' reactions via a separate file. This file can be either formatted (Reactions.in/ReactionsDEV.in) or in csv format. The file Reactions.in.csv resides in the /data/ChemicalNetwork/ directory and is the one that is checked/updated centrally. It comprises our entire collection of reactions including deuterium chemistry, and surface chemistry.

If you want to read the file in csv format, you need to use

.true.      ! read_reactions_in_csv

in which case Reactions.in.csv is read from the directory /data/ChemicalNetwork/. You can also provide your own filename using

yourreactions.incsv   ! CSVDB

The Reactions.in.csv file follows the formatting of the UMIST2012 database. As such, reaction types, gas-phase T/F flags are now explicitly included as well as temperature ranges for the rates (T_min, T_max, for now set to dummy values). This means that the user has to ensure that these reaction types, flags are correctly set.