chimes_main_data

The chimes_main_data.hdf5 file encodes all of the chemical reactions that go into the network, and tabulates the reaction rate coefficients. The reactions are organised into different groups according to how their rate coefficients are calculated (for example, whether they are constant, depend on temperature etc). The idea is that, in a given sub-step of the chemistry solver, the rate coefficients of all reactions in a given group are updated in the same way, which involves a single loop over all reactions in that group.

The various reaction groups are described in more detail below. For each group, we also describe the various data arrays that are included in chimes_main_data.hdf5.

constant

Reactions for which the rate coefficients are just constants. They do not need to be updated every sub-step in the chemistry solver, they can just be taken directly from the data tables.

Data Array Description
N_reactions
A 1-dimensional array of length 2 containing the number of reactions in
this group. The first number gives the number of reactions that do not
involve molecules, while the second number gives the total number of
reactions, including molecules.
reactants
A 2-dimensional array of size (N_reactions x 2) that gives the
species indices of each reactant in each reaction. All reactions in this
group have exactly 2 reactants. Note that these indices correspond to the
position of the species in the full CHIMES network. When CHIMES is used
with a reduced network (i.e. if some metal elements have been switched
off), then CHIMES will internally re-map these indices to the
corresponding positions in the reduced network.
products
A 2-dimensional array of size (N_reactions x 3) that gives the
species indices of each product in each reaction. If a reaction has fewer
than 3 product, the remaining indices are set to -1. No reactions
have more than 3 products. Note that these indices correspond to the
position of the species in the full CHIMES network. When CHIMES is used
with a reduced network (i.e. if some metal elements have been switched
off), then CHIMES will internally re-map these indices to the
corresponding positions in the reduced network.
rates
A 1-dimensional array of length N_reactions that gives the constant
rate coefficients in cgs units (as linear, not log) for each reaction.
element_incl
A 2-dimensional array of size (N_reactions x 9) that encodes which
elements are involved in each reaction. For each reaction we have an array
of 9 integers that can be 0 or 1, indicating that the corresponding
element either is not or is involved in the given reaction, respectively.
The elements are encoded in the order C, N, O, Ne, Mg, Si, S, Ca, Fe. Then
if one or more of the elements needed for a given reaction has been
switched off, that reaction will be skipped and will not be included in
the reduced network. Note that hydrogen and helium cannot be switched off,
so we do not include flags for these.
molecular_flag
A 1-dimensional array of integers of length N_reactions that can take
the value 0 (if no molecules are involved in the given reaction) or
1 (if molecules are involved). CHIMES constructs two networks, one
including the molecular chemistry and one without it, and switches between
them based on the temperature. This allows us to switch off molecules at
high temperatures. We can then use the molecular_flag from the tables
to determine which reactions can be included in the non-molecular network.
Note that the reactions in each group are organised such that those that
include molecules are at the end of the group.
H2_form_heating_
reaction_index
Index giving the position of the H2 gas-phase formation reaction in this
group. This is needed by the cooling routines, as this reaction
contributes to the heating rate, so we will need to access the
corresponding reaction rate.

T_dependent

Reactions for which the rate coefficients are functions of temperature only. If thermal evolution is switched on, they will need to be updated every sub-step of the integration. The rates are tabulated as a function of temperature, so to update the rate coefficients requires a 1-dimensional interpolation for each reaction.

Data Array Description
N_reactions
A 1-dimensional array of length 2 containing the number of reactions in
this group. See the description under the constant group for details.
reactants
A 2-dimensional array of size (N_reactions x 3) that gives the
species indices of each reactant in each reaction. If a reaction has fewer
than 3 reactants, the remaining indices are set to -1. No reactions
have more than 3 reactants. See the description under the constant
group for further details.
products
A 2-dimensional array of size (N_reactions x 3) that gives the
species indices of each product in each reaction. If a reaction has fewer
than 3 product, the remaining indices are set to -1. No reactions
have more than 3 products. See the description under the constant
group for further details.
rates
A 2-dimensional array of size (N_reactions x N_Temperatures) that
tabulates the rate coefficients of each reaction as a function of
temperature. These are given as log10(rate) in cgs units.
element_incl
A 2-dimensional array of size (N_reactions x 9) that encodes which
elements are involved in each reaction. See the description under the
constant group for details.
molecular_flag
A 1-dimensional array of integers of length N_reactions that can take
the value 0 (if no molecules are involved in the given reaction) or
1 (if molecules are involved). See the description under the
constant group for details.
H2_collis_dissoc_
heating_reaction_
index
Index giving the position of the H2 collisional dissociation reaction in
this group. This is needed by the cooling routines, as this reaction
contributes to the heating rate, so we will need to access the
corresponding reaction rate.
H2_form_heating_
reaction_index
Index giving the position of the H2 gas-phase formation reaction in this
group. This is needed by the cooling routines, as this reaction
contributes to the heating rate, so we will need to access the
corresponding reaction rate.

recombination_AB

For the recombination of singly ionised hydrogen and helium, CHIMES switches between case A and case B recombination based on whether the gas is optically thin to the corresponding recombination radiation (as determined by the column densities of HI and HeI, respectively). In this reaction group, we have therefore tabulated the corresponding temperature-dependent case A and case B rate coefficients separately. The CHIMES solver will then select which one to use accordingly.

Data Array Description
N_reactions
A 1-dimensional array of length 2 containing the number of reactions in
this group. See the description under the constant group for details.
reactants
A 2-dimensional array of size (N_reactions x 2) that gives the
species indices of each reactant in each reaction. All reactions in this
group have exactly 2 reactants. See the description under the constant
group for further details.
products
A 1-dimensional array of length N_reactions that gives the species
indices of the product in each reaction. All reactions in this group have
only 1 product, which is why we only use a 1-dimensional array here. See
the description under the constant group for further details.
rates_caseA
A 2-dimensional array of size (N_reactions x N_Temperatures) that
tabulates the rate coefficients of the case A recombination reactions as a
function of temperature. These are given as log10(rate) in cgs units.
rates_caseB
A 2-dimensional array of size (N_reactions x N_Temperatures) that
tabulates the rate coefficients of the case B recombination reactions as a
function of temperature. These are given as log10(rate) in cgs units.
element_incl
A 2-dimensional array of size (N_reactions x 9) that encodes which
elements are involved in each reaction. See the description under the
constant group for details.
molecular_flag
A 1-dimensional array of integers of length N_reactions that can take
the value 0 (if no molecules are involved in the given reaction) or
1 (if molecules are involved). See the description under the
constant group for details.

grain_recombination

Recombination of ions with electrons on the surface of dust grains. The rate coefficients depend on temperature and on the parameter Psi = G0 exp(-2.77 Av) T^0.5 / ne, where G0 is the strength of the radiation field in the 6-13.6 eV band in Habing units, Av is the dust extinction, T is the gas temperature, and ne is the electron density in cgs units.

Data Array Description
N_reactions
A 1-dimensional array of length 2 containing the number of reactions in
this group. See the description under the constant group for details.
reactants
A 2-dimensional array of size (N_reactions x 2) that gives the
species indices of each reactant in each reaction. All reactions in this
group have exactly 2 reactants. See the description under the constant
group for further details.
products
A 1-dimensional array of length N_reactions that gives the species
indices of the product in each reaction. All reactions in this group have
only 1 product, which is why we only use a 1-dimensional array here. See
the description under the constant group for further details.
rates
A 3-dimensional array of size (N_reactions x N_Temperatures x
N_Psi) that tabulates the rate coefficients of each reaction as a
function of temperature and Psi. These are given as log10(rate) in cgs
units.
element_incl
A 2-dimensional array of size (N_reactions x 9) that encodes which
elements are involved in each reaction. See the description under the
constant group for details.
molecular_flag
A 1-dimensional array of integers of length N_reactions that can take
the value 0 (if no molecules are involved in the given reaction) or
1 (if molecules are involved). See the description under the
constant group for details.

H2_dust_formation

Formation of H2 on the surface of dust grains. The rate coefficient dependends on gas temperature and dust temperature. There is only one reaction in this group.

Data Array Description
N_reactions
A 1-dimensional array of length 2 containing the number of reactions in
this group. See the description under the constant group for details.
reactants
A 1-dimensional array of length 3 that gives the species indices of each
reactant in this reaction. Since there is only one reaction in this group,
this array is only 1-dimensional. Also, this reaction only has 2
reactants, so the third index is -1 and is ignored by the code. See the
description under the constant group for further details.
products
A 1-dimensional array of length 3 that gives the species indices of the
product in this reaction. Since there is only one reaction in this group,
this array is only 1-dimensional. Also, this reaction only has 1 product,
so the second and third indices are -1 and are ignored by the code. See
the description under the constant group for further details.
rates
A 2-dimensional array of size (N_Temperatures x
N_Dust_Temperatures) that tabulates the rate coefficient of this
reaction as a function of gas temperature and dust temperature. These are
given as log10(rate) in cgs units. Note that, to get the reaction rate per
unit volume, we need to multiply this rate coefficient by
nHI * nHtot * dust_ratio, and not by nHI^2, where nHI and
nHtot are the HI and total hydrogen densities, respectively, and
dust_ratio is the dust-to-gas ratio relative to the Milky Way value.
element_incl
A 1-dimensional array of length 9 that encodes which elements are involved
in this reaction. See the description under the constant group for
details.
molecular_flag
A single integer that can take the value of 0 (if no molecules are
involved in this reaction) or 1 (if molecules are involved). See the
description under the constant group for details.

H2_collis_dissoc

Dissociation of H2 via collisions with electrons, HI and HeI. As well as temperature, the rate coefficients for these reactions also depend on the densities of HI, H2 and HeI, which determine whether the rate coefficient is in the low-density regime or LTE.

Data Array Description
N_reactions
A 1-dimensional array of length 2 containing the number of reactions in
this group. See the description under the constant group for details.
reactants
A 2-dimensional array of size (N_reactions x 2) that gives the
species indices of each reactant in each reaction. All reactions in this
group have exactly 2 reactants. See the description under the constant
group for further details.
products
A 2-dimensional array of size (N_reactions x 3) that gives the
species indices of each product in each reaction. All reactions in this
group have exactly 3 products. See the description under the constant
group for further details.
critical_density_H
A 1-dimensional array of length N_Temperatures that tabulates the
critical density of H2 due to collisions with HI as a function of
temperature. These are given as log10(critical density) in cgs units.
critical_density_H2
A 1-dimensional array of length N_Temperatures that tabulates the
critical density of H2 due to collisions with H2 as a function of
temperature. These are given as log10(critical density) in cgs units.
critical_density_He
A 1-dimensional array of length N_Temperatures that tabulates the
critical density of H2 due to collisions with HI as a function of
temperature. These are given as log10(critical density) in cgs units.
k0 and kLTE
Two 2-dimensional arrays, each of size (N_reactions x
N_Temperatures), that tabulate the low-density (k0) and LTE
(kLTE) rate coefficients for each reaction as a function of
temperature. These are given as log10(rate coefficient) in cgs units. The
overall rate coefficient for each reaction is then calculated as follows:
log10(rate coefficient) =
(n_over_cr / (1 + n_over_cr)) * log10(kLTE) +
(1 / (1 + n_over_cr)) * log10(k0),
where:
n_over_cr = (nHI / critical_density_H) +
(2 * nH2 / critical_density_H2) + (nHeI / critical_density_He)
element_incl
A 2-dimensional array of size (N_reactions x 9) that encodes which
elements are involved in each reaction. See the description under the
constant group for details.
molecular_flag
A 1-dimensional array of integers of length N_reactions that can take
the value 0 (if no molecules are involved in the given reaction) or
1 (if molecules are involved). See the description under the
constant group for details.

cosmic_ray

Ionisation and dissociation by cosmic rays. All rates are normalised relative to the cosmic ray ionisation rate of HI, which is given as a parameter in the gasVariables structure.

Data Array Description
N_reactions
A 1-dimensional array of length 2 containing the number of reactions in
this group. See the description under the constant group for details.
reactants
A 1-dimensional array of length N_reactions that gives the species
indices of each reactant in each reaction. All reactions in this group
have only 1 reactant. See the description under the constant group for
further details.
products
A 2-dimensional array of size (N_reactions x 3) that gives the
species indices of each product in each reaction. If a reaction has fewer
than 3 product, the remaining indices are set to -1. No reactions
have more than 3 products. See the description under the constant
group for further details.
rates
A 1-dimensional array of length N_reactions that gives the rates of
each reaction relative to the HI cosmic ray ionisation rate. These are
stored as the linear, not the log, of this ratio. The rate of each
reaction in units of s^-1 is then given by:
rates * gasVariables.cr_rate.
secondary_ratio
A 2-dimensional array of size (2 x N_secondary_cosmic_ray_xHII). This
gives the ratio of secondary to primary cosmic ray ionisation rate for HI
and HeI, tabulated as a function of the HII fraction, xHII. The
corresponding cosmic ray ionisation rates are then multiplied by
(1 + secondary_ratio).
secondary_base_reaction
A 1-dimensional array of length 2 that gives the positions of the HI and
HeI cosmic ray ionisation reactions in the cosmic_ray group. This
allows us to find those reactions so that we can update their rates to
include secondary ionisations, using the secondary_ratio array given
above.
element_incl
A 2-dimensional array of size (N_reactions x 9) that encodes which
elements are involved in each reaction. See the description under the
constant group for details.
molecular_flag
A 1-dimensional array of integers of length N_reactions that can take
the value 0 (if no molecules are involved in the given reaction) or
1 (if molecules are involved). See the description under the
constant group for details.

CO_cosmic_ray

Dissociation of CO by cosmic rays. This reaction has additional dependencies on the gas temperature and the H2 and CO abundances, and so is grouped separately from the rest of the cosmic ray reactions.

Data Array Description
N_reactions
A 1-dimensional array of length 2 containing the number of reactions in
this group. In practice, there is only 1 reaction in this group.
reactants
A 1-dimensional array of length N_reactions that gives the species
indices of each reactant. The only reaction in this group has 1 reactant.
See the description under the constant group for further details.
products
A 2-dimensional array of size (N_reactions x 2) that gives the species
indices of each product. The only reaction in this group has 2 products.
See the description under the constant group for further details.
rates
A 2-dimensional array of size (N_reactions x N_Temperatures) that
gives the rate relative to the HI cosmic ray ionisation rate as a function
of gas temperature, stored as log10(rate). Note that there are also extra
dependencies on the CO and H2 abundances (xCO and xH2,
respectively). The final rate per CO molecule, in units of s^-1, is
then given by:
rate * gasVariables.cr_rate * xH2 / sqrt(xCO).
element_incl
A 2-dimensional array of size (N_reactions x 9) that encodes which
elements are involved in each reaction. See the description under the
constant group for details.
molecular_flag
A 1-dimensional array of integers of length N_reactions that can take
the value 0 (if no molecules are involved in the given reaction) or
1 (if molecules are involved). See the description under the
constant group for details.

photodissoc_group1

Photodissociation of molecules (and also the negative ions C- and O-) for which the rate is attenuated by dust extinction, Av, simply as exp(-gamma * Av), where gamma is a parameter that we tabulate for each reaction.

Data Array Description
N_reactions
A 1-dimensional array of length 2 containing the number of reactions in
this group. See the description under the constant group for details.
reactants
A 1-dimensional array of length N_reactions that gives the species
indices of each reactant in each reaction. All reactions in this group
have only 1 reactant. See the description under the constant group for
further details.
products
A 2-dimensional array of size (N_reactions x 2) that gives the species
indices of each product in each reaction. All reactions in this group have
exactly 2 products. See the description under the constant group for
further details.
gamma
A 1-dimensional array of length N_reactions that contains the gamma
parameter for each reaction, which is used for the dust attenuation (see
below).
rates
A 1-dimensional array of length N_reactions that contains the
optically thin dissociation rates for each reaction, in units s^-1.
These are stored as the linear rate, and NOT as the log. The reaction
rates then scale linearly with the strength of the radiation field in the
6-13.6 eV band in Habing units, i.e. the G0 parameter, and are
attenuated by dust extinction, Av. The full rate is then given by:
rate * G0 * exp(-gamma Av).
element_incl
A 2-dimensional array of size (N_reactions x 9) that encodes which
elements are involved in each reaction. See the description under the
constant group for details.
molecular_flag
A 1-dimensional array of integers of length N_reactions that can take
the value 0 (if no molecules are involved in the given reaction) or
1 (if molecules are involved). See the description under the
constant group for details.

photodissoc_group2

Photodissociation of molecules for which the rate is attenuated by dust extinction, Av, with a more complex functional form as exp(-gamma_coeff[0] * Av) if Av > 15 and exp(-gamma_coeff[1] * Av + gamma_coeff[2] * Av * Av) otherwise, where the gamma_coeff coefficients are the same for all reactions in this group (see below).

Data Array Description
N_reactions
A 1-dimensional array of length 2 containing the number of reactions in
this group. See the description under the constant group for details.
reactants
A 1-dimensional array of length N_reactions that gives the species
indices of each reactant in each reaction. All reactions in this group
have only 1 reactant. See the description under the constant group for
further details.
products
A 2-dimensional array of size (N_reactions x 2) that gives the species
indices of each product in each reaction. All reactions in this group have
exactly 2 products. See the description under the constant group for
further details.
gamma_coeff
A 1-dimensional array of length 3 that contains the gamma coefficients
that are used to calculate the dust attenuation (see above). These are the
same for all reactions in this group.
rates
A 1-dimensional array of length N_reactions that contains the
optically thin dissociation rates for each reaction, in units s^-1.
These are stored as the linear rate, and NOT as the log. The reaction
rates then scale linearly with the strength of the radiation field in the
6-13.6 eV band in Habing units, i.e. the G0 parameter, and are
attenuated by dust extinction, Av. The full rate, R, is then given
by:
if (Av > 15)
R = rate * G0 * exp(-gamma_coeff[0] * Av)
else
R = rate * G0 * exp(-gamma_coeff[1] * Av + gamma_coeff[2] * Av * Av)
element_incl
A 2-dimensional array of size (N_reactions x 9) that encodes which
elements are involved in each reaction. See the description under the
constant group for details.
molecular_flag
A 1-dimensional array of integers of length N_reactions that can take
the value 0 (if no molecules are involved in the given reaction) or
1 (if molecules are involved). See the description under the
constant group for details.

H2_photodissoc

Photodissociation of H2. Includes attenutation using the H2 self-shielding function of Richings et al. (2014b) and dust attenuation.

Data Array Description
N_reactions
A 1-dimensional array of length 2 containing the number of reactions in
this group. In practice, there is only 1 reaction in this group.
reactants
A 1-dimensional array of length N_reactions that gives the species
indices of each reactant. The only reaction in this group has 1 reactant.
See the description under the constant group for further details.
products
A 2-dimensional array of size (N_reactions x 2) that gives the species
indices of each product. The only reaction in this group has 2 products.
See the description under the constant group for further details.
gamma
A 1-dimensional array of length N_reactions that contains the gamma
parameter, which is used for the dust attenuation (see below).
self_shielding
A 4-dimensional array of size (N_reactions x N_Temperatures x
N_H2self_column_densities x N_b_turbulence), which tabulates the H2
self-shielding function with respect to gas temperature, H2 column density
and turbulent broadening parameter (see Richings et al. 2014b).
rates
A 1-dimensional array of length N_reactions that contains the
optically thin dissociation rate for this reaction, in units s^-1.
This is stored as the linear rate, and NOT as the log. The reaction rate
then scales linearly with the strength of the radiation field in the
12.24-13.51 eV band as parameterised by the H2_dissocJ parameter, and
is attenuated by dust extinction, Av, and H2 self-shielding. The full
rate is then given by:
rate * H2_dissocJ * isotropic_photon_density * speed_of_light
* exp(-gamma Av) * S_H2
where S_H2 is calculated from the self_shielding array given above
as a function of temperature, H2 column density and turbulent Doppler
broadening.
element_incl
A 2-dimensional array of size (N_reactions x 9) that encodes which
elements are involved in this reaction. See the description under the
constant group for details.
molecular_flag
A 1-dimensional array of integers of length N_reactions that can take
the value 0 (if no molecules are involved in the given reaction) or
1 (if molecules are involved). See the description under the
constant group for details.

CO_photodissoc

Photodissociation of CO. Includes attenutation CO self-shielding, H2 cross-shielding, and dust shielding.

Data Array Description
N_reactions
A 1-dimensional array of length 2 containing the number of reactions in
this group. In practice, there is only 1 reaction in this group.
reactants
A 1-dimensional array of length N_reactions that gives the species
indices of each reactant. The only reaction in this group has 1 reactant.
See the description under the constant group for further details.
products
A 2-dimensional array of size (N_reactions x 2) that gives the species
indices of each product. The only reaction in this group has 2 products.
See the description under the constant group for further details.
gamma
A 1-dimensional array of length N_reactions that contains the gamma
parameter, which is used for the dust attenuation (see below).
self_shielding
A 2-dimensional array of size (N_reactions x N_COself_column_densities
x N_H2CO_column_densities, which tabulates the shielding of CO by
itself and by H2 as a function of the CO and H2 column densities (see
Richings et al. 2014b for details).
rates
A 1-dimensional array of length N_reactions that contains the
optically thin dissociation rate for this reaction, in units s^-1.
This is stored as the linear rate, and NOT as the log. The reaction rate
then scales linearly with the strength of the radiation field in the
6-13.6 eV band in Habing units, i.e. the G0 parameter, and is
attenuated by dust, CO and H2. The full rate is then given by:
rate * G0 * exp(-gamma Av) * S_CO
where S_CO is calculated from the self_shielding array given above
as a function of the CO and H2 column densities.
element_incl
A 2-dimensional array of size (N_reactions x 9) that encodes which
elements are involved in this reaction. See the description under the
constant group for details.
molecular_flag
A 1-dimensional array of integers of length N_reactions that can take
the value 0 (if no molecules are involved in the given reaction) or
1 (if molecules are involved). See the description under the
constant group for details.

photoion_fuv

Photoionisation of species with an ionisation energy <13.6 eV. Additional information from the cross-sections tables for each UV spectrum will be needed to compute the rates of each reaction in this group; see the cross_sections section of this User Guide for details.

Data Array Description
N_reactions
A 1-dimensional array of length 2 containing the number of reactions in
this group. See the description under the constant group for details.
reactants
A 1-dimensional array of length N_reactions that gives the species
indices of each reactant in each reaction. All reactions in this group
have only 1 reactant. See the description under the constant group for
further details.
products
A 2-dimensional array of size (N_reactions x 2) that gives the species
indices of each product in each reaction. All reactions in this group have
exactly 2 products. See the description under the constant group for
further details.
gamma
A 1-dimensional array of length N_reactions that contains the gamma
parameter for each reaction. The attenuation of the photoionisation rate
due to dust extinction Av is then given as exp(-gamma * Av).
E_thresh
A 1-dimensional array of length N_reactions that contains the
ionisation energy of each reaction. Photons above this energy threshold
contribute to the given photoionisation reaction.
element_incl
A 2-dimensional array of size (N_reactions x 9) that encodes which
elements are involved in each reaction. See the description under the
constant group for details.
molecular_flag
A 1-dimensional array of integers of length N_reactions that can take
the value 0 (if no molecules are involved in the given reaction) or
1 (if molecules are involved). See the description under the
constant group for details.

photoion_euv

Photoionisation of species with an ionisation energy >13.6 eV. Additional information from the cross-sections tables for each UV spectrum will be needed to compute the rates of each reaction in this group; see the cross_sections section of this User Guide for details.

Data Array Description
N_reactions
A 1-dimensional array of length 2 containing the number of reactions in
this group. See the description under the constant group for details.
reactants
A 1-dimensional array of length N_reactions that gives the species
indices of each reactant in each reaction. All reactions in this group
have only 1 reactant. See the description under the constant group for
further details.
products
A 2-dimensional array of size (N_reactions x 2) that gives the species
indices of each product in each reaction. All reactions in this group have
exactly 2 products. See the description under the constant group for
further details.
E_thresh
A 1-dimensional array of length N_reactions that contains the
ionisation energy of each reaction. Photons above this energy threshold
contribute to the given photoionisation reaction.
element_incl
A 2-dimensional array of size (N_reactions x 9) that encodes which
elements are involved in each reaction. See the description under the
constant group for details.
molecular_flag
A 1-dimensional array of integers of length N_reactions that can take
the value 0 (if no molecules are involved in the given reaction) or
1 (if molecules are involved). See the description under the
constant group for details.

photoion_auger_fuv

Auger photoionisation of species with an ionisation energy <13.6 eV, where a single photon is absorbed by an inner shell electron with enough energy to remove further electrons from the outer shells. Additional information from the cross-sections tables for each UV spectrum will be needed to compute the rates of each reaction in this group; see the cross_sections section of this User Guide for details.

Data Array Description
N_reactions
A 1-dimensional array of length 2 containing the number of reactions in
this group. See the description under the constant group for details.
reactants
A 1-dimensional array of length N_reactions that gives the species
indices of each reactant in each reaction. All reactions in this group
have only 1 reactant. See the description under the constant group for
further details.
products
A 2-dimensional array of size (N_reactions x 2) that gives the species
indices of each product in each reaction. This array gives the products as
the final ion and an electron. However, in practice multiple electrons are
produced. The number of electrons from each reaction is calculated from
the difference between the initial and final ionisation states.
base_reaction
A 1-dimensional array of length N_reactions that contains the position
of the base reaction (i.e. the photoionisation of the same reactant that
releases a single electron) in the photoion_fuv group.
element_incl
A 2-dimensional array of size (N_reactions x 9) that encodes which
elements are involved in each reaction. See the description under the
constant group for details.
molecular_flag
A 1-dimensional array of integers of length N_reactions that can take
the value 0 (if no molecules are involved in the given reaction) or
1 (if molecules are involved). See the description under the
constant group for details.

photoion_auger_euv

Auger photoionisation of species with an ionisation energy >13.6 eV, where a single photon is absorbed by an inner shell electron with enough energy to remove further electrons from the outer shells. Additional information from the cross-sections tables for each UV spectrum will be needed to compute the rates of each reaction in this group; see the cross_sections section of this User Guide for details.

Data Array Description
N_reactions
A 1-dimensional array of length 2 containing the number of reactions in
this group. See the description under the constant group for details.
reactants
A 1-dimensional array of length N_reactions that gives the species
indices of each reactant in each reaction. All reactions in this group
have only 1 reactant. See the description under the constant group for
further details.
products
A 2-dimensional array of size (N_reactions x 2) that gives the species
indices of each product in each reaction. This array gives the products as
the final ion and an electron. However, in practice multiple electrons are
produced. The number of electrons from each reaction is calculated from
the difference between the initial and final ionisation states.
base_reaction
A 1-dimensional array of length N_reactions that contains the position
of the base reaction (i.e. the photoionisation of the same reactant that
releases a single electron) in the photoion_euv group.
element_incl
A 2-dimensional array of size (N_reactions x 9) that encodes which
elements are involved in each reaction. See the description under the
constant group for details.
molecular_flag
A 1-dimensional array of integers of length N_reactions that can take
the value 0 (if no molecules are involved in the given reaction) or
1 (if molecules are involved). See the description under the
constant group for details.

cooling

The cooling group in chimes_main_data.hdf5 contains the per-ion cooling and heating rates. These data arrays are described in detail below.

Data Array Description
N_coolants
The number of species for which the cooling rate per ion is simply a
function of temperature.
coolants
A 1-dimensional array of length N_coolants containing the species
indices for these coolants.
rates
A 2-dimensional array of size (N_coolants x N_Temperatures)
containing the temperature-dependent cooling rates per ion for each
coolant. Stored as log10(rate) in cgs units.
N_coolants_2d
The number of species for which the cooling rate per ion is a function of
temperature and electron density at low temperatures. For these coolants,
the cooling rate does not simply scale linearly with the electron density,
so we cannot simply multiply by the electron density as we do for the
standard coolants. At high temperatures, we switch to purely temperature-
dependent rates.
coolants_2d
A 1-dimensional array of length N_coolants_2d containing the species
indices for these coolants.
rates_2d
A 3-dimensional array of size (N_coolants_2d x
N_cool_2d_Temperatures x N_cool_2d_ElectronDensities) containing
the cooling rates per ion for these coolants as a function of temperature
and electron density. Stored as log10(rate) in cgs units. These are used
at low temperatures.
rates_hiT_2d
A 2-dimensional array of size (N_coolants_2d x
N_cool_2d_hiT_Temperatures) containing the cooling rates per ion for
these coolants as a function of temperature only. Stored as log10(rate) in
cgs units. These are used at high temperatures.
N_coolants_4d
The number of species for which the cooling rate per ion is a function of
temperature, HI density, electron density and HII density at low
temperatures. At high temperatures, we switch to purely temperature-
dependent rates.
coolants_4d
A 1-dimensional array of length N_coolants_4d containing the species
indices for these coolants.
rates_4d
A 5-dimensional array of size (N_coolants_4d x
N_cool_4d_Temperatures x N_cool_4d_HIDensities x
N_cool_4d_ElectronDensities x N_cool_4d_HIIDensities) containing
the cooling rates per ion for these coolants as a function of temperature
and the densities of HI, electrons and HII. Stored as log10(rate) in cgs
units. These are used at low temperatures.
rates_hiT_4d
A 2-dimensional array of size (N_coolants_4d x
N_cool_4d_hiT_Temperatures) containing the cooling rates per ion for
these coolants as a function of temperature only. Stored as log10(rate) in
cgs units. These are used at high temperatures.
H2_cool_LTE
A 1-dimensional array of length N_mol_cool_Temperatures containing the
temperature-dependent H2 cooling rate in the LTE limit, used in the H2
cooling function in CHIMES (see Glover & Abel 2008; Richings et al 2014a).
Stored as log10(rate) in cgs units.
H2_cool_lowDens_H2
A 1-dimensional array of length N_mol_cool_Temperatures containing the
temperature-dependent H2 cooling rate in the low-density limit from
collisions with H2. Used in the H2 cooling function in CHIMES (see Glover
& Abel 2008; Richings et al 2014a). Stored as log10(rate) in cgs units.
H2_cool_lowDens_HI
A 1-dimensional array of length N_mol_cool_Temperatures containing the
temperature-dependent H2 cooling rate in the low-density limit from
collisions with HI. Used in the H2 cooling function in CHIMES (see Glover
& Abel 2008; Richings et al 2014a). Stored as log10(rate) in cgs units.
H2_cool_lowDens_HII
A 1-dimensional array of length N_mol_cool_Temperatures containing the
temperature-dependent H2 cooling rate in the low-density limit from
collisions with HII. Used in the H2 cooling function in CHIMES (see Glover
& Abel 2008; Richings et al 2014a). Stored as log10(rate) in cgs units.
H2_cool_lowDens_HeI
A 1-dimensional array of length N_mol_cool_Temperatures containing the
temperature-dependent H2 cooling rate in the low-density limit from
collisions with HeI. Used in the H2 cooling function in CHIMES (see Glover
& Abel 2008; Richings et al 2014a). Stored as log10(rate) in cgs units.
H2_cool_lowDens_elec
A 1-dimensional array of length N_mol_cool_Temperatures containing the
temperature-dependent H2 cooling rate in the low-density limit from
collisions with electrons. Used in the H2 cooling function in CHIMES (see
Glover & Abel 2008; Richings et al 2014a). Stored as log10(rate) in cgs
units.
CO_cool_rot_L0
A 1-dimensional array of length N_mol_cool_Temperatures containing the
temperature-dependent CO cooling rate from rotational transitions in the
low-density limit. Used in the CO cooling function in CHIMES (see Neufeld
& Kaufman 1993; Neufeld et al. 1995; Glover et al. 2010; Richings et al.
2014a). Stored as log10(rate) in cgs units.
CO_cool_rot_Llte
A 2-dimensional array of size (N_mol_cool_Temperatures x
N_CO_cool_rot_ColumnDensities) containing the CO cooling rate from
rotational transitions in the LTE limit as a function of temperature and
effective CO column density. Used in the CO cooling function in CHIMES
(see Neufeld & Kaufman 1993; Neufeld et al. 1995; Glover et al. 2010;
Richings et al. 2014a). Stored as log10(rate) in cgs units.
CO_cool_rot_a
A 2-dimensional array of size (N_mol_cool_Temperatures x
N_CO_cool_rot_ColumnDensities) containing the alpha parameter as a
function of temperature and effective CO column density. Used in the CO
cooling function in CHIMES (see Neufeld & Kaufman 1993; Neufeld et al.
1995; Glover et al. 2010; Richings et al. 2014a). Stored as log10(rate) in
cgs units.
CO_cool_rot_nhalf
A 2-dimensional array of size (N_mol_cool_Temperatures x
N_CO_cool_rot_ColumnDensities) containing the nhalf parameter as a
function of temperature and effective CO column density. Used in the CO
cooling function in CHIMES (see Neufeld & Kaufman 1993; Neufeld et al.
1995; Glover et al. 2010; Richings et al. 2014a). Stored as log10(rate) in
cgs units.
CO_cool_vib_L0
A 1-dimensional array of length N_mol_cool_Temperatures containing the
temperature-dependent CO cooling rate from vibrational transitions in the
low-density limit. Used in the CO cooling function in CHIMES (see Neufeld
& Kaufman 1993; Neufeld et al. 1995; Glover et al. 2010; Richings et al.
2014a). Stored as log10(rate) in cgs units.
CO_cool_vib_Llte
A 2-dimensional array of size (N_mol_cool_Temperatures x
N_CO_cool_vib_ColumnDensities) containing the CO cooling rate from
vibrational transitions in the LTE limit as a function of temperature and
effective CO column density. Used in the CO cooling function in CHIMES
(see Neufeld & Kaufman 1993; Neufeld et al. 1995; Glover et al. 2010;
Richings et al. 2014a). Stored as log10(rate) in cgs units.
H2O_cool_rot_
hiT_L0
A 1-dimensional array of length N_H2O_cool_hiT_Temperatures containing
the temperature-dependent H2O cooling rate from rotational transitions in
the low-density limit, at high temperatures. Used in the H2O cooling
function in CHIMES (see Neufeld & Kaufman 1993; Neufeld et al. 1995;
Glover et al. 2010; Richings et al. 2014a). Stored as log10(rate) in cgs
units.
H2O_cool_rot_
hiT_Llte
A 2-dimensional array of size (N_H2O_cool_hiT_Temperatures x
N_H2O_cool_rot_ColumnDensities) containing the H2O cooling rate from
rotational transitions in the LTE limit as a function of temperature and
effective H2O column density, at high temperatures. Used in the H2O
cooling function in CHIMES (see Neufeld & Kaufman 1993; Neufeld et al.
1995; Glover et al. 2010; Richings et al. 2014a). Stored as log10(rate) in
cgs units.
H2O_cool_rot_
hiT_a
A 2-dimensional array of size (N_H2O_cool_hiT_Temperatures x
N_H2O_cool_rot_ColumnDensities) containing the alpha parameter as a
function of temperature and effective H2O column density, at high
temperatures. Used in the H2O cooling function in CHIMES (see Neufeld &
Kaufman 1993; Neufeld et al. 1995; Glover et al. 2010; Richings et al.
2014a). Stored as log10(rate) in cgs units.
H2O_cool_rot_
hiT_nhalf
A 2-dimensional array of size (N_H2O_cool_hiT_Temperatures x
N_H2O_cool_rot_ColumnDensities) containing the nhalf parameter as a
function of temperature and effective H2O column density, at high
temperatures. Used in the H2O cooling function in CHIMES (see Neufeld &
Kaufman 1993; Neufeld et al. 1995; Glover et al. 2010; Richings et al.
2014a). Stored as log10(rate) in cgs units.
H2Oortho_cool_
rot_lowT_L0
A 1-dimensional array of length N_H2O_cool_lowT_Temperatures
containing the temperature-dependent ortho-H2O cooling rate from
rotational transitions in the low-density limit, at low temperatures.
Used in the H2O cooling function in CHIMES (see Neufeld & Kaufman
1993; Neufeld et al. 1995; Glover et al. 2010; Richings et al. 2014a).
Stored as log10(rate) in cgs units.
H2Oortho_cool_
rot_lowT_Llte
A 2-dimensional array of size (N_H2O_cool_lowT_Temperatures x
N_H2O_cool_rot_ColumnDensities) containing the ortho-H2O cooling
rate from rotational transitions in the LTE limit as a function of
temperature and effective H2O column density, at low temperatures.
Used in the H2O cooling function in CHIMES (see Neufeld & Kaufman
1993; Neufeld et al. 1995; Glover et al. 2010; Richings et al. 2014a).
Stored as log10(rate) in cgs units.
H2Oortho_cool_
rot_lowT_a
A 2-dimensional array of size (N_H2O_cool_lowT_Temperatures x
N_H2O_cool_rot_ColumnDensities) containing the alpha parameter as a
function of temperature and effective H2O column density, at low
temperatures. Used in the H2O cooling function in CHIMES (see
Neufeld & Kaufman 1993; Neufeld et al. 1995; Glover et al. 2010;
Richings et al. 2014a). Stored as log10(rate) in cgs units.
H2Oortho_cool_
rot_lowT_nhalf
A 2-dimensional array of size (N_H2O_cool_lowT_Temperatures x
N_H2O_cool_rot_ColumnDensities) containing the nhalf parameter as a
function of temperature and effective H2O column density, at low
temperatures. Used in the H2O cooling function in CHIMES (see
Neufeld & Kaufman 1993; Neufeld et al. 1995; Glover et al. 2010;
Richings et al. 2014a). Stored as log10(rate) in cgs units.
H2Opara_cool_
rot_lowT_L0
A 1-dimensional array of length N_H2O_cool_lowT_Temperatures
containing the temperature-dependent para-H2O cooling rate from
rotational transitions in the low-density limit, at low temperatures.
Used in the H2O cooling function in CHIMES (see Neufeld &
Kaufman 1993; Neufeld et al. 1995; Glover et al. 2010; Richings et
al. 2014a). Stored as log10(rate) in cgs units.
H2Opara_cool_
rot_lowT_Llte
A 2-dimensional array of size (N_H2O_cool_lowT_Temperatures x
N_H2O_cool_rot_ColumnDensities) containing the para-H2O cooling
rate from rotational transitions in the LTE limit as a function of
temperature and effective H2O column density, at low temperatures.
Used in the H2O cooling function in CHIMES (see Neufeld & Kaufman
1993; Neufeld et al. 1995; Glover et al. 2010; Richings et al. 2014a).
Stored as log10(rate) in cgs units.
H2Opara_cool_
rot_lowT_a
A 2-dimensional array of size (N_H2O_cool_lowT_Temperatures x
N_H2O_cool_rot_ColumnDensities) containing the alpha parameter as a
function of temperature and effective H2O column density, at low
temperatures. Used in the H2O cooling function in CHIMES (see Neufeld &
Kaufman 1993; Neufeld et al. 1995; Glover et al. 2010; Richings et al.
2014a). Stored as log10(rate) in cgs units.
H2Opara_cool_
rot_lowT_nhalf
A 2-dimensional array of size (N_H2O_cool_lowT_Temperatures x
N_H2O_cool_rot_ColumnDensities) containing the nhalf parameter as a
function of temperature and effective H2O column density, at low
temperatures. Used in the H2O cooling function in CHIMES (see Neufeld &
Kaufman 1993; Neufeld et al. 1995; Glover et al. 2010; Richings et al.
2014a). Stored as log10(rate) in cgs units.
gas_grain_transfer
A 1-dimensional array of length N_Temperatures containing the cooling
rate due to energy exchange between the gas and the dust, as a function
of gas temperature, T_gas. Stored as log10(rate) in cgs units. To get
the overall cooling rate, we also need the dust-to-gas ratio relative to
the local ISM (dust_ratio) and the temperature difference between
T_gas and the dust temperature T_dust. The final rate (in units
of erg cm^3 s^-1) is then:
rate * dust_ratio * (T_gas - T_dust).
See Richings et al. (2014a) for details.
grain_recombination
A 2-dimensional array of size (N_Temperatures x N_Psi) containing
the grain recombination cooling rates as a function of gas temperature
T and the parameter Psi = G0 exp(-2.77 Av) T^0.5 / ne, where
G0 is the strength of the radiation field in the 6-13.6 eV band in
Habing units, Av is the dust extinction and ne is the electron
density. Stored as log10(rate) in cgs units. To get the overall cooling
rate, we also need the dust-to-gas ratio relative to the local ISM
(dust_ratio). The final rate (in units of erg cm^3 s^-1) is then:
rate * dust_ratio * ne / nHtot.
(See Glover & Jappsen 2007; Richings et al. 2014a).
photoelectric_heating
A 2-dimensional array of size (N_Temperatures x N_Psi) containing
the photoelectric heating rates as a function of gas temperature T
and the parameter Psi = G0 exp(-2.77 Av) T^0.5 / ne, where G0 is
the strength of the radiation field in the 6-13.6 eV band in Habing units,
Av is the dust extinction and ne is the electron density. Stored
as log10(rate) in cgs units. To get the overall heating rate, we also need
the dust-to-gas ratio relative to the local ISM (dust_ratio). The
final rate (in units of erg cm^3 s^-1) is then:
rate * dust_ratio * G0 * exp(-2.77 Av) / nHtot.
(See Bakes & Tielens 1994; Wolfire et al. 2003; Richings et al. 2014a).

TableBins

The TableBins group in chimes_main_data.hdf5 contains all of the table bins that are used to tabulate and interpolate the various data arrays described above.