Welcome to pyTOPSScrape’s documentation!

pyTOPSScrape

A package which aims to make the programmatic retrieval and use of high temperature radiative opacity tables from LANL somewhat simple

pyTOPSScrape provides both a command line and a Python interface. The command line interface runs through the generateTOPStables script (which will have been installed to your path when you installed this package)

The Python interface can mimic the full command line interface (including error checking and rate limiting) using the full_run function. If however, you wish to dig down to a more granular level the api module includes both query and convert sub modules which may be composed as needed.

Installation

PyPi

>>> pip install pyTOPSScrape

GitHub

>>> git clone https://github.com/tboudreaux/pytopsscrape.git
>>> cd pytopsscrape
>>> python setup.py install

Simple Examples

Assuming you have the files GS98.abun and rescalings.dat in your current working directory

Command Line

>>> generateTOPStables GS98.abun rescalings.dat -d ./rawOutput -o GS98.opac -j 20

This will save intermediate results to the folder rawOutput (which must not exist before running this script). Moreover, this will use 20 concurrent processes to query. This helps speed up the script as it is network and not CPU limited.

Python Interface

You can replicate the behavior of the command line using the full_run() function.

>>> from pyTOPSScrape import full_run
>>> kwargs = kwargs = {
>>>        "abunTable": "./GS98.abun",
>>>        "abunMap": "./exampleAbunMap.dat",
>>>        "force": False,
>>>        "outputDirectory": "./rawOutput",
>>>        "noopal" : False,
>>>        "nofetch" : False,
>>>        "output" : "./GS98TestResult.opac",
>>>        "hardforce" : True,
>>>        "jobs" : 20,
>>>        "rect" : False
>>>        }
>>> full_run(kwargs)

Alternatively, you can call pyTOPSScrape in a more granular manner. For example, if you just wish to query the tables from the TOPS web form but not perform any conversion on them one could use the following Python code.

>>> from pyTOPSScrape.api import call
>>> import os
>>> if not os.path.exists("./rawOutput"):
>>>     os.mkdir("./rawOutput")
>>> call("./rescalings.dat", "./GS98.dat", "./rawOutput", 20)

Additional Examples

Examples of both the command line interface and the Python interface (notebook) are included in the pyTOPSScrape repository.

Command Line Arguments

usage

generateTOPStables [-h] [-f] [-d OUTPUTDIRECTORY] [–noopal] [–nofetch] [-o OUTPUT] [–hardforce] [-j JOBS] [–rect] abunTable abunMap

Positional Arguments

abunTable

Table to pull abundances from. If set numFracProgram must point to executable expecting table input

abunMap

Map of which classical compositions to query the TOPS web form for. Each classical composition will be achieved by rescaling the base composition described in the abunTable

Optional Arguments

-h, --help

show this help message and exit

-f, --force

force the generation of new abunance tables

-d OUTPUTDIRECTORY, --outputDirectory OUTPUTDIRECTORY

directory to save abundance files to

--noopal

Run the code to convert TOPS table toOPAL compatible tables

--nofetch

do not fetch opacity tables from TOPS

-o OUTPUT, --output OUTPUT

file to write OPAL formated table to

--hardforce

Override all already extant directories

-j JOBS, --jobs JOBS

Number of processes to query the TOPS web form on

--rect

if True store OPAL tables rectangurally. This is not how DSEP uses tables; however, by way of wider applicability –rect may be used

Input File Formats

pyTOPSScrape requires two input files to run. One (the first positional argument and hereafter the ‘composition file’) describes the base composition. The second positional argument (hereafter the ‘map file’) describes the set of classical compositions which will be queried from the TOPS web form. Each of these compositions will be a rescaling of the base composition (therefore the metal mass fractions wrt. Z will be maintained)

Composition file

The composition file should be in the following form

#STD [Fe/H] [alpha/Fe] [C/Fe] [N/Fe] [O/Fe] [r/Fe] [s/Fe] C/O X Y,Z
F -1.13 0.32 -0.43 -0.28 0.31 -1.13 -1.13 0.10 0.7584 0.2400,1.599E-03
#H He Li Be B C N O F Ne
12.00 10.898 -0.08 0.25 1.57 6.87 6.42 7.87 3.43 7.12
#Na Mg Al Si P S Cl Ar K Ca
5.11 6.86 5.21 6.65 4.28 6.31 -1.13 5.59 3.90 5.21
#Sc Ti V Cr Mn Fe Co Ni Cu Zn
2.02 3.82 2.80 4.51 4.30 6.37 3.86 5.09 3.06 2.30
#Ga Ge As Se Br Kr Rb Sr Y Zr
0.78 1.39 0.04 1.08 0.28 0.99 0.26 0.61 1.08 1.45
#Nb Mo Tc Ru Rh Pd Ag Cd In Sn
-0.80 -0.38 -99.00 -0.51 -1.35 -0.69 -1.32 -0.55 -1.46 -0.22
#Sb Te I Xe Cs Ba La Ce Pr Nd
-1.25 -0.08 -0.71 -0.02 -1.18 1.05 -0.03 0.45 -1.54 0.29
#Pm Sm Eu Gd Tb Dy Ho Er Tm Yb
-99.00 -1.30 -0.61 -1.19 -1.96 -1.16 -1.78 -1.34 -2.16 -1.42
#Lu Hf Ta W Re Os Ir Pt Au Hg
-2.16 -1.41 -2.38 -1.41 -2.00 -0.86 -0.88 -0.64 -1.34 -1.09
#Tl Pb Bi Po At Rn Fr Ra Ac Th
-1.36 -0.51 -1.61 -99.00 -99.00 -99.00 -99.00 -99.00 -99.00 -2.20
#Pa U
-99.00 -2.80

Map file

The map file should be in the following form

0.75,0.24,0.01
0.75,0.23,0.02

Where each row is X,Y,Z. The number of rows in this file will correspond to the number of queries issued against the TOPS web form (i.e. if you have a Map file with three rows then the TOPS webform will be queried three times. For DSEP we use a file of 126 rows so for a single DSEP formatted OPAL table we merge the contents of 126 queries against the TOPS webform)

Testing

pyTOPSScrape ships with a number of tests which should be run to make sure that it installed correctly on your system. Additionally, as it is reliant on an external server it is a certainty that one day it will break. To run the tests a script has been included. From the pyTOPSScrape root directory

>>> cd tests
>>> ./runTests.sh

Etiquette & Cacheing

pyTOPSScrape makes use web servers hosted at Los Alamos National Labs (LANL). Before releasing this software I spoke with the T-1 group at LANL and received their assent. However, try to limit requests made against their web servers as much as possible. Obviously, if you are querying a few hundred tables because your stellar evolution code needs a few hundred opacity tables there is little to be done; however, do try and make sure that you have sorted out any and all bugs or typos in your input files before you query so that you won’t have to go back and query multiple times. We want to be respectful of of the generosity of LANL here!

Additionally, pyTOPSScrape caches the raw query results to whatever directory is specified by the -d or –outputDirectory flag. This is so that if you want to implement your own converter you can do so without constantly re running the query functions. These results are cached in whatever directory is set in the –outputDirectory (or -d) command line option. To call the command line interface with cache usage enabled use the –nofetch flag. If you want to fetch tables and don’t want to run the conversion set use the –noopal flag.

As an example, if you have already queried the TOPS web form using the command

>>> generateTOPStables GS98.abun rescalings.dat -d ./rawOutput -o GS98.opac -j 20 --noopal

This will save all the raw output to the directory ./rawOutput (if you run the first example from this docs page this will also cache the results). You can then convert these to DSEP’s OPAL format using the command

>>> generateTOPStables GS98.abun rescalings.dat -d ./rawOutput -o GS98.opac -j 20 --nofetch

Notes & References

Website

https://aphysics2.lanl.gov/apps/

Paper Describing Opacity Tables

Colgan, James, et al. “A new generation of Los Alamos opacity tables.” The Astrophysical Journal 817.2 (2016): 116.

• Home
  • Subpackages
    • pyTOPSScrape.api package
      • Submodules
      • pyTOPSScrape.api.api module
      • pyTOPSScrape.api.convert module
      • pyTOPSScrape.api.utils module
      • Module contents
    • pyTOPSScrape.err package
      • Submodules
      • pyTOPSScrape.err.err module
      • Module contents
    • pyTOPSScrape.misc package
      • Subpackages
        • pyTOPSScrape.misc.dataFiles package
          • Module contents
      • Submodules
      • pyTOPSScrape.misc.utils module
      • Module contents
    • pyTOPSScrape.parse package
      • Submodules
      • pyTOPSScrape.parse.abundance module
      • pyTOPSScrape.parse.opal module
      • pyTOPSScrape.parse.tops module
      • Module contents
    • pyTOPSScrape.scripts package
      • Submodules
      • pyTOPSScrape.scripts.main module
      • Module contents
  • Module contents
    • pyTOPSScrape
    • Installation
      • PyPi
      • GitHub
    • Simple Examples
      • Command Line
      • Python Interface
      • Additional Examples
    • Command Line Arguments
      • Positional Arguments
      • Optional Arguments
    • Input File Formats
      • Composition file
      • Map file
    • Testing
    • Etiquette & Cacheing
    • Notes & References
• API
  • Submodules
  • pyTOPSScrape.api.api module
  • pyTOPSScrape.api.convert module
  • pyTOPSScrape.api.utils module
  • Module contents
• Errors
  • Submodules
  • pyTOPSScrape.err.err module
  • Module contents
• Parsing
  • Submodules
  • pyTOPSScrape.parse.abundance module
  • pyTOPSScrape.parse.opal module
  • pyTOPSScrape.parse.tops module
  • Module contents
• Scripts
  • Submodules
  • pyTOPSScrape.scripts.main module
  • Module contents
• Misc
  • Subpackages
    • pyTOPSScrape.misc.dataFiles package
      • Module contents
  • Submodules
  • pyTOPSScrape.misc.utils module
  • Module contents