def wrapVector(rho, var, xmass, species):
"""
Wrapper for J.Schwab's Helmholtz python module, which is
itself also one for Timmes' Helmholtz EoS.
Checks rho for length and comparison so that it can be
used for single points.
Args:
rho(float): query density.
var(float): auxilliary thermodynamic variable (T, P, S or E(int)).
xmass(float): query mass fractions.
species(str): query nuclide list.
Returns:
(trojan): [[rho/s], [var/s], [abar/s], [zbar/s]]
"""
try:
pnts = len(rho)
except TypeError:
_, abar, zbar = convXmass2Abun(species, xmass)
return [[rho], [var], [abar], [zbar]]
allp = []
for p in range(pnts):
_, abar, zbar = convXmass2Abun(species, xmass[p])
allp.append((rho[p], var[p], abar, zbar))
vr, vv, va, vz = zip(*allp)
return [vr, vv, va, vz]
def buildHelmTrojan(fname, offset=1, geom='spherical'):
"""Frankensteinian bridge between flash checkpoints and
J.Schwab's Helmholtz python module.
Joined inward/outward and spewing cj data to avoid
calling yt more than once.
Args:
fname(str): filename.
offset(int): zone offset from shock.
"""
props = ['dens', 'temp', 'pres', 'eint']
nprops = len(props)
data, species = hdf5yt.getLineout(fname,
fields=props,
species=True,
geom=geom)
nspecs = len(species)
xin, xout, cjin, cjout, time, xmatch = getRayleighVelocities(fname)
# get fuel and ash for outward shock
# xin/xout == ray @ len([x for x in ray['r'][rsort] if x<xout])
inw = len([x for x in data[0] if x < xout]) + offset
ouw = inw - 2 * offset
inv, ouv = [], []
for i in range(1, nprops + 1):
inv.append(data[i][inw])
ouv.append(data[i][ouw])
xmin, xmou = [], []
for i in range(nprops + 1, nprops + 1 + nspecs):
xmin.append(data[i][inw])
xmou.append(data[i][ouw])
_, abar, zbar = convXmass2Abun(species, xmin)
# [pressure, eint], [rho], [temp], [abar], [zbar]]
fuelo = [[inv[-2], inv[-1]], [inv[0]], [inv[1]], [abar], [zbar]]
_, abar, zbar = convXmass2Abun(species, xmou)
asho = [[ouv[-2], ouv[-1]], [ouv[0]], [ouv[1]], [abar], [zbar]]
# get fuel and ash for inward shock
inw = len([x for x in data[0] if x < xin]) - offset
ouw = inw + 2 * offset
inv, ouv = [], []
for i in range(1, nprops + 1):
inv.append(data[i][inw])
ouv.append(data[i][ouw])
xmin, xmou = [], []
for i in range(nprops + 1, nprops + 1 + nspecs):
xmin.append(data[i][inw])
xmou.append(data[i][ouw])
_, abar, zbar = convXmass2Abun(species, xmin)
fueli = [[inv[-2], inv[-1]], [inv[0]], [inv[1]], [abar], [zbar]]
_, abar, zbar = convXmass2Abun(species, xmou)
ashi = [[ouv[-2], ouv[-1]], [ouv[0]], [ouv[1]], [abar], [zbar]]
return fueli, ashi, fuelo, asho, [xin, xout, cjin, cjout, time, xmatch]
def getMassEnergy(prof, trueA=False):
"""calculate total binding energy per cell
for a dmat(lineout) in erg/g.
"""
# molar in mol/g
factors = nuc.getBinding(prof.species, trueA=trueA)
binding = []
sumy = []
for cell in range(len(prof.density)):
# for each cell get all the mass fractions and convert to molar
xis = prof.data[cell, len(prof.bulkprops)-1:]
molar, abar, zbar = nuc.convXmass2Abun(prof.species, xis)
sumy.append(np.sum(molar))
binding.append(np.dot(factors, molar)*nuc.Avogadro)
return sumy, binding # binding in erg/g