Project 2

This is the second project for the TALENT course: nuclear theory for astrophysics (2014).

Table of contents

• Roles
• Topic
• Building and running
• Input format
• Scripts for analysis

Roles

• Analysis: Fei Yuan
• Code: Amber Lauer
• Parameter: Tsunghan Yeh

Topic

Modelling X-ray burst nucleosynthesis with the XNet reaction network solver, following the model of Fisker et al (2007): the premade model for a CNO X-ray burst.

Building and running

Firstly, be sure to run the following script to generate Makefile using Makefile.in as input:

./configure

The makefile can do several things:

• download and unpack ReduceReaclib and XNet if necessary

• compile ReduceReaclib and XNet

• run XNet and ReduceReaclib with the parameters in:

  • th: thermodynamic trajectory
  • ab: initial abundance
  • control: control file
  • sunet: nuclide list

Note: XNet is run inside a subdirectory under runs.

Commonly used targets in the makefile are:

• all: compile both reducereaclib and xnet

• reducereaclib: compile ReduceReaclib

• xnet: compile XNet

• clean: delete the entire dist directory

• run: equivalent to run-xnet

• run-xnet: run XNet

• run-reducereaclib: run ReduceReaclib

When compiling, the code for XNet and ReduceReaclib are automatically downloaded to the dist directory.

For example, to run XNet in runs/my_run:

make RUN_DIR=my_run run

Input format

Here are the input formats inferred from the Fortran code as well as the sample input files. The formats here are shown using an EBNF-like notation.

The ... indicates that Fortran will ignore all trailing garbage on that line so feel free to put whatever in there.

Control file (control)

<control> ::=
    "## Problem Description"                                    "\n"
    <str:description1>                                          "\n"
    <str:description2>                                          "\n"
    <str:description3>                                          "\n"
    "## Job Controls"                                           "\n"
    <int:initial_zone>                                      ... "\n"
    <int:num_of_zones>                                      ... "\n"
    <int:include_weak_reactions>                            ... "\n"
    <int:include_screening>                                 ... "\n"
    <int:process_nuclear_data_at_runtime>                   ... "\n"
    "## Integration Controls"                                   "\n"
    <int:choice_of_integration_scheme>                      ... "\n"
    <int:max_num_of_timesteps_before_quit>                  ... "\n"
    <int:max_iterations_per_step>                           ... "\n"
    <int:convergence_condition>                             ... "\n"
    <float:max_abundance_change_per_timestep>               ... "\n"
    <float:smallest_abundance_used_in_timestep_calculation> ... "\n"
    <float:mass_conservation_limit>                         ... "\n"
    <float:convergence_criterion>                           ... "\n"
    <float:lower_abundance_limit>                           ... "\n"
    <float:max_factor_to_change_dt_in_a_time_step>          ... "\n"
    "## Output Controls"                                        "\n"
    <int:diagnostic_output_level>                           ... "\n"
    <int:per_timestep_output_level>                         ... "\n"
                                                            ... "\n"
    <str:ascii_output_filename_root>                            "\n"
                                                            ... "\n"
    <str:binary_output_filename_root>                           "\n"
                                                            ... "\n"
    <str:nuclide>{repeat 14 times}                              "\n"
    "## Input Controls"                                         "\n"
                                                            ... "\n"
    <str:data_dir>                                              "\n"
                                                            ... "\n"
    (<str:ab_filename> "\n"
     <str:th_filename> "\n){repeat as many times as num_of_zones}

Initial abundance (ab)

<ab>    ::= <str:description>            "\n"
            (<item> <item> <item> <item> "\n")*
<item>  ::= <str:nuclide> <float:abundance>

Thermodynamic trajectory (th)

<th>    ::= <str:description>        "\n"
            <float:start_time>   ... "\n"
            <float:stop_time>    ... "\n"
            <float:dt_initial>   ... "\n"
            <row>*
<row>   ::= <float:time> <float:temperature> <float:density> ... "\n"

Nuclide list (sunet)

<sunet> ::= (<str:nuclide> "\n")*

Note that <str:nuclide> must be right-aligned and occupy exactly 5 characters.

Scripts for analysis

Note: most of the Python codes require Numpy, and some will also require Matplotlib for visualization.

tso_reader.py

Python module that reads the binary output files ("tso" files) from XNet.

This is based on a script originally written by Kevin Siegl.

dump-tso

Reads a tso file and writes the abundances (as well as time) in an ASCII format. Nuclides that don't participate at all are excluded (i.e. sum of abundances less than a certain threshold).

Dependencies:

• tso_reader.py
• elements.py

plot-tso

Reads a tso file and plots the abundances against time.

Dependencies:

• tso_reader.py
• elements.py

plot-chart

Reads a tso file and plots the abundances on the nuclear chart as an animation.

Dependencies:

• chart-all
• chart-stable
• tso_reader.py

Note: requires ffmpeg to be installed, though you can also change the encoder used by Matplotlib by modifying the script.

This is based on a script originally written by Kaitlin J. Cook. Nuclear data was provided by Kaitlin J. Cook (chart-stable) and Alison Dreyfuss (chart-all).