Understanding the outputs

Output files are written to the sims/ directory (unless specified otherwise) after the code has fully converged. The code generates multiple output files with different suffixes:

• .pdr.fin: Species abundances

• .line.fin: Line emission data

• .cool.fin: Cooling functions

• .heat.fin: Heating functions

• .COOL.spop.fin: Level populations for each coolant (where COOL is the coolant name)

• .species: Species index/name key used to interpret the abundance columns of .pdr.fin

• .params: Global model parameters (radiation field, cosmic-ray rate, metallicity, turbulent velocity, grid size)

• .RTspop.fin: Per-cell level populations for every coolant in a single file, used as input to The RT-tool Algorithm

Note

Outputs are in ASCII format and can be plotted using standard tools like GNUPLOT or PYTHON.

One-dimensional Outputs

OUTPUT.pdr.fin

Column	Value	Comments
1	ID	Cell identity (integer)
2	x	Position (pc)
3	Av	Visual extinction (mag)
4	Tgas	Gas temperature (K)
5	Tdust	Dust temperature (K)
6	etype	Type of cell (integer)
7	nH	Number density (cm⁻³)
8	UV	FUV intensity (Draine units)
9+	…	Species abundances

Species abundances follow the sequence in species_NETWORK.d.

OUTPUT.cool.fin

Column	Value	Comments
1	ID	Cell identity (integer)
2	x	Position (pc)
3	Av	Visual extinction (mag)
4	CO	CO cooling function
5	C+	C+ cooling function
6	C	C cooling function
7	O	O cooling function
8+	…	Additional coolant cooling
Last	Total	Total cooling (sum of all)

Coolant sequence matches the order in params.dat. Without additional coolants, total cooling is column 8.

OUTPUT.heat.fin

Column	Value	Comments
1	ID	Cell identity (integer)
2	x	Position (pc)
3	Av	Visual extinction (mag)
4	HR01	Not contributing
5	HR02	Photoelectric heating
6	HR03	Not contributing
7	HR04	Carbon ionization heating
8	HR05	H₂ formation heating
9	HR06	H₂ photodissociation heating
10	HR07	FUV pumping heating
11	HR08	Cosmic-ray heating
12	HR09	Turbulent heating
13	HR10	Chemical heating
14	HR11	Gas-grain heating
15	HR12	Total heating (sum of all)

Three-dimensional Outputs

3D-OUTPUT.pdr.fin

Column	Value	Comments
1	ID	Cell identity (integer)
2	x	x position (pc)
3	y	y position (pc)
4	z	z position (pc)
5	Tgas	Gas temperature (K)
6	Tdust	Dust temperature (K)
7	etype	Type of cell (integer)
8	nH	Number density (cm⁻³)
9	UV	FUV intensity (Draine units)
10-10+species	…	Species abundances
11+species-…	Av	Visual extinction per HEALPix ray

Additional Outputs (1D and 3D)

The three files below are written for every model, regardless of DIMENSIONS.

OUTPUT.species

A plain index/name key for the chemical network used, one species per line:

1 Mg
2 He+
3 HNCO
...

The line number (first column) matches the species ordering in species_NETWORK.d (see The species_[network].d), which is the same order the abundance columns appear in OUTPUT.pdr.fin (column 9 onward for 1D, column 10 onward for 3D). Use this file to map an abundance column back to its species name without having to count columns manually.

OUTPUT.params

A compact record of the global parameters the model was run with, written as three lines:

Line	Contents
1	FUV field, CR ionization rate (or the CR attenuation model choice if CRATTENUATION=1), metallicity, turbulent velocity
2	Grid dimensions nxc nyc nzc (number of cells along x, y, z)
3	Physical box size xlx yly zlz (pc)

Note

The exact contents of line 1 depend on the CRATTENUATION flag (see The makefile):

• CRATTENUATION = 0: FUV field, \(\zeta\) (CR ionization rate), metallicity, turbulent velocity.

• CRATTENUATION = 1: FUV field, the CR attenuation model choice (L/H/U), metallicity, turbulent velocity.

This file is primarily consumed by downstream analysis and plotting tools (including PDR-studio, see PDR-studio) that need the model’s global setup without re-parsing params.dat.

OUTPUT.RTspop.fin

A single file collecting the level populations of every coolant for every grid cell, intended as the direct input to The RT-tool Algorithm for computing synthetic radiation/excitation temperatures. Its structure is:

NETWORK
LMAX=N
coolant_file_1.dat
coolant_file_2.dat
...
ENDCOOLFILES
<level populations for cell 1, all coolants concatenated>
<level populations for cell 2, all coolants concatenated>
...

• Line 1: the compiled chemical network name (REDUCED, MEDIUM, or FULL).

• Line 2: LMAX=N, the value of lmax_levels used at runtime — 0 if the The LEVMAX flag cap was not applied (all levels from each LAMDA file were used), or the -lmax=N value otherwise.

• Coolant file list: one line per coolant, terminated by the ENDCOOLFILES marker.

• Data rows: one row per grid cell; for each coolant, the populations of its levels (1 to cnlev, capped by LMAX if active) are written consecutively on that row, in the same coolant order as the file list above.

Important

Because the number of levels per coolant can be truncated by LMAX, downstream tools must read the LMAX=N line (and the coolant list) to know how many columns to expect for each coolant — the row width is not fixed across differently-configured runs.