Chemical solver design¶
This document concern the steady-state gas- and solid-phase chemistry solver in ProDiMo. The chemical equilibrium solver is not discussed here. A couple of papers described the philosophy behind the chemical networks used in modelling the chemistry in protoplanetary disks. Here we focus on the technical aspects such that maintenance, modifications, and additions can be performed on the code.
Chemical type acronyms¶
Internally, each type of chemical reaction is assigned a 2 letters (in capital) keys. The reactions are sorted by rate_coeffs.f where the actual rates are computed on-the-spot or via another routine for the complex treatments. Warning: the internal keys are either inferred by ProDoMo during the
initialization phase (read_***_reactions ***.f) or read explicitly from the database.
Default gas-phase reactions¶
This types of reactions follow the Arrhenius law
where and .
Types included
| Key | Description |
|---|---|
| NN | neutral-neutral |
| IN | ion-neutral : no barrier (c=0) |
| CE | charge exchange |
| II | ion-ion neutralisation |
| DR | dissociative recombination |
| RR | radiative recombination (+Xrays for high Temp) |
| AD | associative detachment |
| RA | radiative association |
| CL | collider (mostly three-body) |
| CD | collisional dissociation |
| CI | chemi-ionisation/collisional ionization |
| CE | charge exchange |
| IM | ion-molecule neutralisation |
| MN | IM in UMIST 2012 |
| K3 | KIDA type 3 formula |
| K4 | KIDA ionpol1 formula |
| K5 | KIDA ionpol2 formula |
Cosmic-ray/particle collision induced reactions¶
| Key | Description |
|---|---|
| XP | Xray primary ionization leading to 2 Auger el |
| XX | Xray primary ionization leading to 1 Auger el |
| XS | Xray secondary ionisation by fast electrons (for hydrogen and the heavy elements) |
| XI | Xray secondary ionisation by fast electrons (H2) |
| XG | Xray secondary ionisation by fast electrons (He) |
| XU | Xray photo-induced reactions (similar to CP) |
| RD | Xray radiative and dielectronic recombination |
| XA | Xray charge exchange with double ionised species (reaction partner H or H2 only) |
| XB | Collisional ionization of H2exc by electrons |
| XC | Collisional de-excitation of H2exc by He-coll |
| XD | Collisions with H2 giving (de-) excitation of H2 |
| SX | special charge exchange reactions (source ?) |
| IH | collisional ionization using the Verner routine multiply the rates with electron by 1.7e-4 see Hollenbach & McKee 1979 |
| RI | ionization due to radioactive decay see Umebayashi & Nakano (2009) |
| CP | cosmic-ray particle |
| CR | gas-phase cosmic-ray induced photo reaction |
| PH | gas-phaseUV-photon induced photodissociation |
| P3 | gas-phase photo-reactions requiring 3 parameters (a,b, and c) |
Grain surface/cores reactions¶
| Key | Description |
|---|---|
| GG | A# + B -> AB# (product stay on ice surface). =S1 which does not exist. Only one ice species involved. |
| S2 | gas-grain reaction A#+B -> AB. It is previously GG reactions (product is in the gas-phase). Only one ice species is involved. |
| H1 | gas-grain formation of H2 (if H2 formation is explicitly simulated) H + H# -> H2# and H + H# -> H2 |
| H2 | grain-grain formation of H2 (if H2 formation is explicitly simulated) H# + H# -> H2 and H# + H# -> H2# |
| S3 | A# + B# -> AB#. Two ice species are involved in this reaction. |
| S4 | A# + B# -> AB. Two ice species involved. The product is ejected to the gas-phase: chemidesorption. |
| S5 | ice surface cosmic-ray induced photoreaction. Only 1 species involved. |
| S6 | ice surface UV-photon induced photodissociation. Use the mostly gas-phase rates. Only one ice specie is involved. The number of layers involved is set by the NlayS6 switch default to 200 (2/8/2018) |
| S7 | AB# + C# -> AC + B#. Two ice species involved. |
Special reactions¶
| Key | Description |
|---|---|
| HG | grain surface formation. Several treatments with different levels of sophistication are possible see H2_formation |
| OS | OSU special reaction type Harada, Herbst, and Wakelam (2010) in Sect. 2.2 |
| IH | collisional ionization with H if gas phase reaction = false |
| DE | collisional de-excitation of H2exc by H2-collisions |
| KE | collisional/kinetic excitation of H2/HD by H/H2 to H2exc/HDexc |
| SP | spontaneous de-excitation of excited H2 |
| PU | FUV pumping of H2 to H2exc |
Grain charging¶
| Key | Description |
|---|---|
| ZR | ion recombination on negatively charged grains see Draine & Suttin 1987 (DS) |
| ZC | grain charge CR photodetachment/photoionization |
| EA | Z+ + e- -> Z recombination/attachment |
| PE | Z- + PE -> Z + e- Photoelectric/Photodetachment |
| ET | Z- + THERM -> Z + e- thermionic |
| ZZ | Z- + Z+ -> Z + Z grain-grain neutralization |
Ice reactions¶
| Key | Description |
|---|---|
| IC | ice formation on grains. i Reactions.in : H2O FORM H2O# 0.0 0.0 5400 c=5400 is the adsorption energy on Kelvin |
| DT / ST | thermal desorption of an ice (physisorbed) species |
| DC | cosmic-ray induced desorption of ice |
| DP | photo-desorption of ice |
PAH chemistry¶
| Key | Description |
|---|---|
| HP | simple chemistry concerning hydrogenated PAHs |
| PC | PAH chemistry |