Package: popmodel
# popmodel[![Build Status](https://travis-ci.org/awbirdsall/popmodel.svg?branch=master)](https://travis-ci.org/awbirdsall/popmodel)Python package to calculate the population of molecules in particular quantum states using a master equation approach. Designed for (and currently only usable) for excitation of the hydroxyl radical (OH) to one excited vibrational state and one excited electronic state, with two different lasers, and up to four vibronic states being tracked.This represents a slow accumulation of calculations I’ve needed to do for a research project, and would need some work to become more generalized.## CapabilitiesExtract absorption feature information (upper/lower states, energy gap, degeneracies, Einstein coefficients, …) from a HITRAN-type file usingloadhitran. (Vibrational lines of OH only, with limited parsing of H2O.)Calculate shape of absorption feature from Doppler and pressure broadening (absprofile.AbsProfileobject).Automatically define fast modulation of narrow laser linewidth over broadened absorption feature (sweep.Sweepobject).Solve system of ODEs to calculate population in each state over time. Processes included in the ODEs are stimulated absorption/emission, spontaneous emission, and lambda doublet/rotational/vibrational/electronic relaxation (main.KineticsRunobject).Creatematplotlibfigures of populations or laser frequency over time; create figure of infrared absorption feature (main.KineticsRun.[…]figure()functions).convenience unit conversion functions related to atmospheric science (atmcalcs)constants and functions related to OH spectroscopy (ohcalcs)The core ofpopmodelis theKineticsRunobject. EachKineticsRuninstance requires dictionaries of parameters describing rates of spectroscopic transitions, lasers, detection cell, transition lines, and ODE integration.  The expected dictionary format is designed for extraction from a YAML file and compatible with command line use.## Required input files### Hitran fileInfrared line parameters are extracted from the 140-character-format HITRAN 2012 file for OH (default filename13_hit12.par), which can be accessed athttps://www.cfa.harvard.edu/HITRAN/. Some low-level functions withinloadhitranmodule can also read other molecules’ HITRAN files, but trying to go through the full workflow called byloadhitran.processhitran()used in setting up aKineticsRunwill not work due to the need to parse strings describing molecule-specific term descriptions. See the HITRAN website for more documentation related to the record format.An 200-line excerpt from the OH HITRAN file is included atsrc/popmodel/data/hitran_sample.parfor use by the test module. To extract the path tohitran_sample.par:~~~
from pkg_resources import resource_filename
hpath = resource_filename(‘popmodel’,’data/hitran_sample.par’)
~~~### YAML parameter fileParameters for setting up aKineticsRuninstance are organized in dictionaries corresponding to a YAML parameter file. A template for the format that the YAML file must follow can be found atsrc/popmodel/data/parameters_template.yaml.To extract the path toparameters_template.yamlwithinpopmodel:~~~
from pkg_resources import resource_filename
yamlpath = resource_filename(‘popmodel’,’data/parameters_template.yaml’)
~~~## Example usage### Command lineInstallation usingpipcreates command-line commandpopmodel. Format of command line arguments:HITFILE PARAMETERS [-l] LOGFILE [-c] CSVOUTPUT [-i] IMAGE [-v]For example:~~~
popmodel 13_hit12.par parameters.yaml -l output.log -c output.csv -i output.png
~~~### Python sessionBasic usage:~~~
import popmodel as pm
pm.add_streamhandler() # optional, print logging.INFO to screen
pm.add_filehandler(“path/to.log”) # optional, write logging.INFO to file
par = pm.importyaml(“path_to/yaml/parameters.yaml”)
hpar = pm.loadhitran.processhitran(“path_to/13_hit12.par”)
k = pm.KineticsRun(hpar,**par)
k.solveode()
k.popsfigure()
~~~## Installationpip install popmodelinstall from PyPIpip install git+https://github.com/awbirdsall/popmodelinstalls most recent commit on github## DependenciesTested for Python 2.7 and 3.5.Requiresnumpy,scipy,pandas,pyyamlandmatplotlib>=1.5(automatically handled if usingpipto install).Tests written usingpytestusing the [pytest-mplplugin](https://github.com/astrofrog/pytest-mpl).Developed in a Windows environment.