Ocotillo

Multi-wavelength post-processing radiative transfer code.

setup instructions

Fork the repository to your account using the "Fork" button at the top of the webpage: https://github.com/cookhe/ocotillo

Clone the repository to your local machine with either of the following methods

SSH is the preferred method. (see github's guide to setting up ssh keys)

git clone git@github.com:cookhe/ocotillo.git

or HTTPS:

git clone https://github.com/cookhe/ocotillo.git

Add the code's directory to your PATH variable in your .bashrc file (or equivalent: e.g. .bash_profile, .profile, etc.) by adding the following lines:

# ocotillo code
export OCO_HOME="$HOME/<path-to-code>/ocotillo"
export PATH="$OCO_HOME/bin:$PATH"

where <path-to-code> is where you've cloned the code in the previous step. Don't forget to source the file so these changes take effect!

source ~/.bashrc

test ocotillo

Try running the autotest.

rt_autotest

If you've set things up correctly, this can be run from anywhere. Doing so executes the file bin/rt_autotest that runs a few tests in samples/ to verify the code is functional.

Each successful autotest will print out some information about the runtime.

 processor column time =    1.4114999999999999E-002  seconds.
 Execution time =  0.14414828431372551       micro-seconds per wavelength point per mesh point.
 
 Wall time =    3.2466000000000002E-002  seconds.
 Execution time =  0.16577818627450980       micro-seconds per wavelength point per mesh point.

If the test fails, you will see additional output with the difference between the diagnostic file just produced samples/<sample name>/output/diagnostics.txt and a reference file samples/<sample name>/reference.out.

1,10c1,10
<      1    0.15145E+12    0.10205E+13    0.35091E-26    0.35128E-26
<      2    0.15145E+12    0.10205E+13    0.35091E-26    0.35128E-26
<      3    0.15145E+12    0.10205E+13    0.35091E-26    0.35128E-26
<      4    0.15145E+12    0.10205E+13    0.35091E-26    0.35128E-26
<      5    0.94922E+14    0.22690E+15    0.11264E-11    0.39839E-12
<      6    0.94922E+14    0.22690E+15    0.11264E-11    0.39839E-12
<      7    0.15145E+12    0.10205E+13    0.35091E-26    0.35128E-26
<      8    0.15145E+12    0.10205E+13    0.35091E-26    0.35128E-26
<      9    0.15145E+12    0.10205E+13    0.35091E-26    0.35128E-26
<     10    0.15145E+12    0.10205E+13    0.35091E-26    0.35128E-26
---
>      1    0.32026E+13    0.13668E+14    0.35091E-26    0.35128E-26
>      2    0.32026E+13    0.13668E+14    0.35091E-26    0.35128E-26
>      3    0.32026E+13    0.13668E+14    0.35091E-26    0.35128E-26
>      4    0.32026E+13    0.13668E+14    0.35091E-26    0.35128E-26
>      5    0.94812E+14    0.22106E+15    0.51488E-13    0.27311E-13
>      6    0.94812E+14    0.22106E+15    0.51488E-13    0.27311E-13
>      7    0.32026E+13    0.13668E+14    0.35091E-26    0.35128E-26
>      8    0.32026E+13    0.13668E+14    0.35091E-26    0.35128E-26
>      9    0.32026E+13    0.13668E+14    0.35091E-26    0.35128E-26
>     10    0.32026E+13    0.13668E+14    0.35091E-26    0.35128E-26

run on your data

Create a working directory (this can be anywhere) and link the source files.

mkdir rt-nest && cd rt-nest
rt_setup

Next, you'll need to provide information about your data set in two files input.in and resolution.in

Contents of input.in:

!  -*-f90-*-  (for Emacs)    vim:set filetype=fortran:  (for vim)
&input
  z0 = -5d15
  z1 =  5d15
  sigma_grey=0.4
  lgrey=T
  lread_athena=F
/
&temperature_input
  isoTemp = 1. !64857.04298198191
  sigma = 1e30 !2.54d14
  midTemp = 1. !61341
  floorTemp = 2000.
/
&density_input
  rho0=1d-9
  rho_floor=1d-24
  H=1.496d14
/
&gas_state_input
  fully_ionized_T = 2.d4
/

Contents of resolution.in:

!  -*-f90-*-  (for Emacs)    vim:set filetype=fortran:  (for vim)
integer, parameter :: nw=1   ! Number of wavelengths
integer, parameter :: nx=1,ny=1,nz=10  ! Number of grid points in computational domain
integer, parameter :: nprocx=1,nprocy=1,nprocz=1
!
integer, parameter :: nyloc=ny/nprocy,nxloc=nx/nprocx  ! Number of grid points in computational domain   

opacity calculations with python

A simple python version of the opacities is included in tools/ocotillo-py/.

See the INSTRUCTIONS.md file located in that directory for guidance on usage and expected output.