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Cloudy cooling tools

Hello! This code is very old. It mostly still works, but is poorly organized and documented. Contributions very welcome and appreciated. Contact Britton Smith at [email protected] with any questions.

What is this?

This repository contains a code called CIAOLoop, which is capable of running and colating grids of Cloudy models in parallel. It has multiple running modes for creating:

  • cooling tables for Grackle
  • ionization balance tables for trident
  • xray emissivity tables for yt
  • line emissivity tables like those used in the FOGGIE II paper
  • any dimensional grids of Cloudy runs to fill your heart with joy

In addition, there are also:

  • cloudy_grids - Python routines for converting ascii tables to hdf5
  • scripts - helpful Perl scripts for making cooling tables
  • examples - example parameter files for making various types of data
  • parallel_tools - some tools for running in parallel

Executables:

  • CIAOLoop - the main cooling map generation code (a.k.a. ROCO in Smith, Sigurdsson, & Abel 2008) Type ./CIAOLoop -h for options.

Scripts:

  • combine_runfile_parts.pl - combines partial run files made when using the -mp option with CIAOLoop. Type ./combine_runfile_parts.pl with no argument for usage.
  • find_map_zeros.pl - Looks for gaps in the cooling data and fills with zeroes.
  • subtract_cooling.pl - used to make metals only cooling data. Subtracts metal-only cooling data from data with all elements to make metal-only data. USE THE OTHER ONE. Type ./subtract_cooling.pl with no argument for usage.
  • subtract_cooling_lite.pl - same as subtract_cooling.pl, except uses less ram and may be slightly slower. USE THIS ONE.

Examples:

  • grackle - directory of parameter files for making grackle tables
  • sample_cooling.par - sample cooling map parameter file.
  • sample_cooling_metal_free.par - sample parameter file for metal-free cooling.
  • metal_free.dat - additional Cloudy commands for disabling metals with metals-free cooling data.
  • xray_emissivity.par - sample parameter file for making x-ray emissivity maps.

Running CIAOLoop:

See sample_cooling.par for a sample parameter file.

CIAOLoop: Usage: ./CIAOLoop [flags] -h: print this help text. -m : supply machine file for running on multiple machines. -mp : break run into parts to be run separately. -np : run on multiple cores on a single machine. -r: restart run from last file finished. -x: reprocess existing output data instead of running Cloudy.

For restarts, the code will go through the previously made run file, and restart the last map on the list.

Parallelism

To run on more than one node, you need to specify a machine file. Example machine file:

machine1:1
machine1:1
machine2:1
machine2:1

See the note below for running batch jobs on distributed memory systems.

Changing the precision of the cooling maps.

Change the values of the variables:

$temperaturePrecision (Line 189)
$heatingPrecision (Line 192)
$coolingPrecision (Line 195)
$mmwPrecision (Line 198)

Note on Cloudy versions.

The file format for the cooling output was changed between Cloudy versions 06 and 07. If you are using versions 06 or earlier, uncomment line 2017 and comment out line 2006. If you are using version 07 or later, comment out line 2020, and uncomment line 2006. ROCO is currently set to work with versions 07 and later.

Running on distributed systems

Note, this is very old and probably doesn't work well anymore.

To run this in parallel on a distributed memory system, you will just need to supply a machine file at run time that has the full list of available nodes. The parallel tools directory contains some crude scripts to help out with that.

  • make_machine_list.pl - this will read in the id of the job from a file called "job.dat" and will parse "qstat -f" to get the allocated nodes. It will then write a machine file called "machines.dat" that can be used with CIAOLoop.
  • submit_job.pl - this is a simple wrapper around the qsub command that will write the job id to a file called "job.dat" that can be used with the above script. Give the name of the batch script file on the command line.

An example of using these to run a parallel CIAOLoop job on a supercomputing system with a queue.

In the batch script:

./make_machine_list.pl

./CIAOLoop -m machines.dat <parameter_file>

To submit the job:

./submit_job.pl <batch script>

Converting Ascii tables to HDF5

The cloudy_grids directory has Python tools for converting cooling, ionization balance, x-ray emission, and line emissivity tables to hdf5. To use it, do:

cd cloudy_grids
pip install -e .

For documentation on running the various functions do (in Python):

>>> from cloudy_grids import *
>>> # see what functions exist
>>> dir()
>>> # use help to get documentation
>>> help(convert_cooling_tables)

The cloudy_grids/scripts file contains a script used to convert hdf5 files into Grackle-readable format. It may need a little TLC.