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[TEP007] Isotope uniform config option #762

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merged 8 commits into from
Jul 14, 2017
Merged

[TEP007] Isotope uniform config option #762

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96a42c5
Add option to read uniform isotope_abundance in Model
vg3095 Jul 7, 2017
aaa218d
Normalize isotope abundances
vg3095 Jul 7, 2017
0297ba7
Seperate type of abundances under Model from_config
vg3095 Jul 7, 2017
4886a7d
Use pyne to parse isotopes
vg3095 Jul 7, 2017
721bc69
Fix import and a typo
vg3095 Jul 7, 2017
9992da2
Move isotope_abundance up in initialization list
vg3095 Jul 10, 2017
495b874
Move uniform abundance code block to separate func
vg3095 Jul 11, 2017
2171cc3
Use pyne to parse uniform normal abundances
vg3095 Jul 13, 2017
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39 changes: 28 additions & 11 deletions tardis/model/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,9 +2,10 @@
import logging
import numpy as np
import pandas as pd
from pyne import nucname
from astropy import constants, units as u

from tardis.util import quantity_linspace, element_symbol2atomic_number
from tardis.util import quantity_linspace, element_symbol2atomic_number, MalformedElementSymbolError
from tardis.io.model_reader import read_density_file, read_abundances_file
from tardis.io.util import HDFWriterMixin
from density import HomologousDensity
Expand Down Expand Up @@ -59,11 +60,10 @@ class Radial1DModel(HDFWriterMixin):
"""
hdf_properties = ['t_inner', 'w', 't_radiative', 'v_inner', 'v_outer', 'homologous_density']
hdf_name = 'model'

def __init__(self, velocity, homologous_density, abundance, time_explosion,
t_inner, luminosity_requested=None, t_radiative=None,
dilution_factor=None, v_boundary_inner=None,
v_boundary_outer=None):

def __init__(self, velocity, homologous_density, abundance, isotope_abundance,
time_explosion, t_inner, luminosity_requested=None, t_radiative=None,
dilution_factor=None, v_boundary_inner=None, v_boundary_outer=None):
self._v_boundary_inner = None
self._v_boundary_outer = None
self._velocity = None
Expand All @@ -73,6 +73,10 @@ def __init__(self, velocity, homologous_density, abundance, time_explosion,
self.homologous_density = homologous_density
self._abundance = abundance
self.time_explosion = time_explosion

self.raw_abundance = self._abundance
self.raw_isotope_abundance = isotope_abundance

if t_inner is None:
if luminosity_requested is not None:
self.t_inner = ((luminosity_requested /
Expand Down Expand Up @@ -317,17 +321,29 @@ def from_config(cls, config):
t_inner = config.plasma.initial_t_inner

abundances_section = config.model.abundances
isotope_index = pd.MultiIndex(
[[]] * 2, [[]] * 2, names=['atomic_number', 'mass_number'])
isotope_abundance = pd.DataFrame(columns=np.arange(no_of_shells),
index=isotope_index,
dtype=np.float64)

if abundances_section.type == 'uniform':
abundance = pd.DataFrame(columns=np.arange(no_of_shells),
index=pd.Index(np.arange(1, 120),
name='atomic_number'),
dtype=np.float64)

for element_symbol_string in abundances_section:
if element_symbol_string == 'type':
continue
z = element_symbol2atomic_number(element_symbol_string)
abundance.ix[z] = float(abundances_section[element_symbol_string])
try:
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maybe this splitting - might be better performed earlier in the process and not in the init of the model (generally keeping logic out of inits is good practice).

z = element_symbol2atomic_number(element_symbol_string)
abundance.ix[z] = float(
abundances_section[element_symbol_string])
except MalformedElementSymbolError:
mass_no = nucname.anum(element_symbol_string)
z = nucname.znum(element_symbol_string)
isotope_abundance.loc[(z, mass_no), :] = float(
abundances_section[element_symbol_string])

elif abundances_section.type == 'file':
if os.path.isabs(abundances_section.filename):
Expand All @@ -342,17 +358,18 @@ def from_config(cls, config):
abundance = abundance.replace(np.nan, 0.0)
abundance = abundance[abundance.sum(axis=1) > 0]

norm_factor = abundance.sum(axis=0)
norm_factor = abundance.sum(axis=0) + isotope_abundance.sum(axis=0)

if np.any(np.abs(norm_factor - 1) > 1e-12):
logger.warning("Abundances have not been normalized to 1."
" - normalizing")
abundance /= norm_factor

isotope_abundance /= norm_factor

return cls(velocity=velocity,
homologous_density=homologous_density,
abundance=abundance,
isotope_abundance=isotope_abundance,
time_explosion=time_explosion,
t_radiative=t_radiative,
t_inner=t_inner,
Expand Down