def obyo(y, tag, nusdx, nus, mdbCO, mdbH2O, cdbH2H2, cdbH2He):
#CO
SijM_CO, ngammaLM_CO, nsigmaDl_CO = exomol(mdbCO, Tarr, Parr, R_CO,
molmassCO)
xsm_CO = xsmatrix(cnu_CO, indexnu_CO, R_CO, pmarray_CO, nsigmaDl_CO,
ngammaLM_CO, SijM_CO, nus, dgm_ngammaL_CO)
dtaumCO = dtauM(dParr, jnp.abs(xsm_CO), MMR_CO * ONEARR, molmassCO, g)
#H2O
SijM_H2O, ngammaLM_H2O, nsigmaDl_H2O = exomol(mdbH2O, Tarr, Parr,
R_H2O, molmassH2O)
xsm_H2O = xsmatrix(cnu_H2O, indexnu_H2O, R_H2O, pmarray_H2O,
nsigmaDl_H2O, ngammaLM_H2O, SijM_H2O, nus,
dgm_ngammaL_H2O)
dtaumH2O = dtauM(dParr, jnp.abs(xsm_H2O), MMR_H2O * ONEARR, molmassH2O,
g)
#CIA
dtaucH2H2=dtauCIA(nus,Tarr,Parr,dParr,vmrH2,vmrH2,\
mmw,g,cdbH2H2.nucia,cdbH2H2.tcia,cdbH2H2.logac)
dtaucH2He=dtauCIA(nus,Tarr,Parr,dParr,vmrH2,vmrHe,\
mmw,g,cdbH2He.nucia,cdbH2He.tcia,cdbH2He.logac)
dtau = dtaumCO + dtaumH2O + dtaucH2H2 + dtaucH2He
sourcef = planck.piBarr(Tarr, nus)
Ftoa = Fref / Rp**2
F0 = rtrun(dtau, sourcef) / baseline / Ftoa
Frot = response.rigidrot(nus, F0, vsini, u1, u2)
mu = response.ipgauss_sampling(nusdx, nus, Frot, beta, RV)
errall = jnp.sqrt(e1**2 + sigma**2)
numpyro.sample(tag, dist.Normal(mu, errall), obs=y)
def model_c(nu1, y1, e1):
Rp = sample('Rp', dist.Uniform(0.5, 1.5))
Mp = sample('Mp', dist.Normal(33.5, 0.3))
RV = sample('RV', dist.Uniform(26.0, 30.0))
MMR_CO = sample('MMR_CO', dist.Uniform(0.0, maxMMR_CO))
MMR_H2O = sample('MMR_H2O', dist.Uniform(0.0, maxMMR_H2O))
T0 = sample('T0', dist.Uniform(1000.0, 1700.0))
alpha = sample('alpha', dist.Uniform(0.05, 0.15))
vsini = sample('vsini', dist.Uniform(10.0, 20.0))
# Kipping Limb Darkening Prior
q1 = sample('q1', dist.Uniform(0.0, 1.0))
q2 = sample('q2', dist.Uniform(0.0, 1.0))
u1, u2 = ld_kipping(q1, q2)
#GP
logtau = sample('logtau', dist.Uniform(-1.5, 0.5)) #tau=1 <=> 5A
tau = 10**(logtau)
loga = sample('loga', dist.Uniform(-4.0, -2.0))
a = 10**(loga)
#gravity
g = getjov_gravity(Rp, Mp)
#T-P model//
Tarr = T0 * (Parr / Pref)**alpha
#CO
SijM_CO, gammaLM_CO, sigmaDM_CO = exomol(mdbCO, Tarr, Parr, molmassCO)
xsm_CO = xsmatrix(numatrix_CO, sigmaDM_CO, gammaLM_CO, SijM_CO)
dtaumCO = dtauM(dParr, xsm_CO, MMR_CO * ONEARR, molmassCO, g)
#H2O
SijM_H2O, gammaLM_H2O, sigmaDM_H2O = exomol(mdbH2O, Tarr, Parr, molmassH2O)
xsm_H2O = xsmatrix(numatrix_H2O, sigmaDM_H2O, gammaLM_H2O, SijM_H2O)
dtaumH2O = dtauM(dParr, xsm_H2O, MMR_H2O * ONEARR, molmassH2O, g)
#CIA
dtaucH2H2=dtauCIA(nus,Tarr,Parr,dParr,vmrH2,vmrH2,\
mmw,g,cdbH2H2.nucia,cdbH2H2.tcia,cdbH2H2.logac)
dtaucH2He=dtauCIA(nus,Tarr,Parr,dParr,vmrH2,vmrHe,\
mmw,g,cdbH2He.nucia,cdbH2He.tcia,cdbH2He.logac)
dtau = dtaumCO + dtaumH2O + dtaucH2H2 + dtaucH2He
sourcef = planck.piBarr(Tarr, nus)
Ftoa = Fref / Rp**2
F0 = rtrun(dtau, sourcef) / baseline / Ftoa
Frot = response.rigidrot(nus, F0, vsini, u1, u2)
mu = response.ipgauss_sampling(nu1, nus, Frot, beta, RV)
cov = gpkernel_RBF(nu1, tau, a, e1)
sample("y1",
dist.MultivariateNormal(loc=mu, covariance_matrix=cov),
obs=y1)
def obyo(y, tag, nusd, nus, numatrix_CO, numatrix_H2O, mdbCO, mdbH2O,
cdbH2H2, cdbH2He):
#CO
SijM_CO=jit(vmap(SijT,(0,None,None,None,0)))\
(Tarr,mdbCO.logsij0,mdbCO.dev_nu_lines,mdbCO.elower,qt_CO)
gammaLMP_CO = jit(vmap(gamma_hitran,(0,0,0,None,None,None)))\
(Parr*0.99,Tarr,Parr*0.01,mdbCO.n_air,mdbCO.gamma_air,mdbCO.gamma_self)
gammaLMN_CO = gamma_natural(mdbCO.A)
gammaLM_CO = gammaLMP_CO + gammaLMN_CO[None, :]
sigmaDM_CO=jit(vmap(doppler_sigma,(None,0,None)))\
(mdbCO.dev_nu_lines,Tarr,molmassCO)
xsm_CO = xsmatrix(numatrix_CO, sigmaDM_CO, gammaLM_CO, SijM_CO)
dtaumCO = dtauM(dParr, xsm_CO, MMR_CO * ONEARR, molmassCO, g)
#H2O
SijM_H2O=jit(vmap(SijT,(0,None,None,None,0)))\
(Tarr,mdbH2O.logsij0,mdbH2O.dev_nu_lines,mdbH2O.elower,qt_H2O)
gammaLMP_H2O = jit(vmap(gamma_exomol,(0,0,None,None)))\
(Parr,Tarr,mdbH2O.n_Texp,mdbH2O.alpha_ref)
gammaLMN_H2O = gamma_natural(mdbH2O.A)
gammaLM_H2O = gammaLMP_H2O + gammaLMN_H2O[None, :]
sigmaDM_H2O=jit(vmap(doppler_sigma,(None,0,None)))\
(mdbH2O.dev_nu_lines,Tarr,molmassH2O)
xsm_H2O = xsmatrix(numatrix_H2O, sigmaDM_H2O, gammaLM_H2O, SijM_H2O)
dtaumH2O = dtauM(dParr, xsm_H2O, MMR_H2O * ONEARR, molmassH2O, g)
#CIA
dtaucH2H2=dtauCIA(nus,Tarr,Parr,dParr,vmrH2,vmrH2,\
mmw,g,cdbH2H2.nucia,cdbH2H2.tcia,cdbH2H2.logac)
dtaucH2He=dtauCIA(nus,Tarr,Parr,dParr,vmrH2,vmrHe,\
mmw,g,cdbH2He.nucia,cdbH2He.tcia,cdbH2He.logac)
dtau = dtaumCO + dtaumH2O + dtaucH2H2 + dtaucH2He
sourcef = planck.piBarr(Tarr, nus)
Ftoa = Fref / (Rp**2)
F0 = rtrun(dtau, sourcef) / baseline / Ftoa
Frot = response.rigidrot(nus, F0, vsini, u1, u2)
mu = response.ipgauss_sampling(nusd, nus, Frot, beta, RV)
#errall=jnp.sqrt(e1**2+sigma**2)
errall = e1
cov = modelcov(nusd, tau, a, errall)
#cov = modelcov(nusd,tau,a,e1)
#numpyro.sample(tag, dist.Normal(mu, e1), obs=y)
numpyro.sample(tag,
dist.MultivariateNormal(loc=mu, covariance_matrix=cov),
obs=y)
def obyo(y, tag, nusd, nus, numatrix_CO, mdbCO, cdbH2H2):
# CO
SijM_CO = jit(vmap(SijT,
(0, None, None, None, 0)))(Tarr, mdbCO.logsij0,
mdbCO.dev_nu_lines,
mdbCO.elower, qt_CO)
gammaLMP_CO = jit(vmap(gamma_exomol,
(0, 0, None, None)))(Parr, Tarr, mdbCO.n_Texp,
mdbCO.alpha_ref)
gammaLMN_CO = gamma_natural(mdbCO.A)
gammaLM_CO = gammaLMP_CO + gammaLMN_CO[None, :]
sigmaDM_CO = jit(vmap(doppler_sigma,
(None, 0, None)))(mdbCO.dev_nu_lines, Tarr,
molmassCO)
xsm_CO = xsmatrix(numatrix_CO, sigmaDM_CO, gammaLM_CO, SijM_CO)
dtaumCO = dtauM(dParr, xsm_CO, MMR_CO * ONEARR, molmassCO, g)
# CIA
dtaucH2H2 = dtauCIA(nus, Tarr, Parr, dParr, vmrH2, vmrH2, mmw, g,
cdbH2H2.nucia, cdbH2H2.tcia, cdbH2H2.logac)
dtau = dtaumCO + dtaucH2H2
sourcef = planck.piBarr(Tarr, nus)
F0 = rtrun(dtau, sourcef) / norm
Frot = response.rigidrot(nus, F0, vsini, u1, u2)
mu = response.ipgauss_sampling(nusd, nus, Frot, beta, RV)
numpyro.sample(tag, dist.Normal(mu, sigmain), obs=y)
def obyo(y, tag, nusd, nus, numatrix_CO, numatrix_H2O, mdbCO, mdbH2O,
cdbH2H2, cdbH2He):
#CO
SijM_CO=jit(vmap(SijT,(0,None,None,None,0)))\
(Tarr,mdbCO.logsij0,mdbCO.dev_nu_lines,mdbCO.elower,qt_CO)
gammaLMP_CO = jit(vmap(gamma_exomol,(0,0,None,None)))\
(Parr,Tarr,mdbCO.n_Texp,mdbCO.alpha_ref)
gammaLMN_CO = gamma_natural(mdbCO.A)
gammaLM_CO = gammaLMP_CO + gammaLMN_CO[None, :]
sigmaDM_CO=jit(vmap(doppler_sigma,(None,0,None)))\
(mdbCO.dev_nu_lines,Tarr,molmassCO)
xsm_CO = xsmatrix(numatrix_CO, sigmaDM_CO, gammaLM_CO, SijM_CO)
dtaumCO = dtauM(dParr, xsm_CO, MMR_CO * ONEARR, molmassCO, g)
#H2O
SijM_H2O=jit(vmap(SijT,(0,None,None,None,0)))\
(Tarr,mdbH2O.logsij0,mdbH2O.dev_nu_lines,mdbH2O.elower,qt_H2O)
gammaLMP_H2O = jit(vmap(gamma_exomol,(0,0,None,None)))\
(Parr,Tarr,mdbH2O.n_Texp,mdbH2O.alpha_ref)
gammaLMN_H2O = gamma_natural(mdbH2O.A)
gammaLM_H2O = gammaLMP_H2O + gammaLMN_H2O[None, :]
sigmaDM_H2O=jit(vmap(doppler_sigma,(None,0,None)))\
(mdbH2O.dev_nu_lines,Tarr,molmassH2O)
xsm_H2O = xsmatrix(numatrix_H2O, sigmaDM_H2O, gammaLM_H2O, SijM_H2O)
dtaumH2O = dtauM(dParr, xsm_H2O, MMR_H2O * ONEARR, molmassH2O, g)
#CIA
dtaucH2H2=dtauCIA(nus,Tarr,Parr,dParr,vmrH2,vmrH2,\
mmw,g,cdbH2H2.nucia,cdbH2H2.tcia,cdbH2H2.logac)
dtaucH2He=dtauCIA(nus,Tarr,Parr,dParr,vmrH2,vmrHe,\
mmw,g,cdbH2He.nucia,cdbH2He.tcia,cdbH2He.logac)
dtau = dtaumCO + dtaumH2O + dtaucH2H2 + dtaucH2He
sourcef = planck.piBarr(Tarr, nus)
Ftoa = Fref / Rp**2
F0 = rtrun(dtau, sourcef) / baseline / Ftoa
Frot = response.rigidrot(nus, F0, vsini, u1, u2)
mu = response.ipgauss_sampling(nusd, nus, Frot, beta, RV)
np.savez("dtau_lpf.npz", [nus, dtaumCO, dtaumH2O])
return mu
def obyo(y, tag, nusdx, nus, mdbCO, mdbH2O, cdbH2H2, cdbH2He):
#CO
SijM_CO, ngammaLM_CO, nsigmaDl_CO = exomol(mdbCO, Tarr, Parr, R_CO,
molmassCO)
xsm_CO = xsmatrix(cnu_CO, indexnu_CO, R_CO, pmarray_CO, nsigmaDl_CO,
ngammaLM_CO, SijM_CO, nus, dgm_ngammaL_CO)
dtaumCO = dtauM(dParr, jnp.abs(xsm_CO), MMR_CO * ONEARR, molmassCO, g)
#H2O
SijM_H2O, ngammaLM_H2O, nsigmaDl_H2O = exomol(mdbH2O, Tarr, Parr,
R_H2O, molmassH2O)
xsm_H2O = xsmatrix(cnu_H2O, indexnu_H2O, R_H2O, pmarray_H2O,
nsigmaDl_H2O, ngammaLM_H2O, SijM_H2O, nus,
dgm_ngammaL_H2O)
dtaumH2O = dtauM(dParr, jnp.abs(xsm_H2O), MMR_H2O * ONEARR, molmassH2O,
g)
#CIA
dtaucH2H2=dtauCIA(nus,Tarr,Parr,dParr,vmrH2,vmrH2,\
mmw,g,cdbH2H2.nucia,cdbH2H2.tcia,cdbH2H2.logac)
dtaucH2He=dtauCIA(nus,Tarr,Parr,dParr,vmrH2,vmrHe,\
mmw,g,cdbH2He.nucia,cdbH2He.tcia,cdbH2He.logac)
dtau = dtaumCO + dtaumH2O + dtaucH2H2 + dtaucH2He
sourcef = planck.piBarr(Tarr, nus)
Ftoa = Fref / Rp**2
F0 = rtrun(dtau, sourcef) / baseline / Ftoa
Frot = response.rigidrot(nus, F0, vsini, u1, u2)
mu = response.ipgauss_sampling(nusdx, nus, Frot, beta, RV)
if FP64 == True:
np.savez("dtau_modit" + str(N) + "_64.npz",
[nus, dtaumCO, dtaumH2O])
else:
np.savez("dtau_modit" + str(N) + ".npz", [nus, dtaumCO, dtaumH2O])
return mu
def xsmatrix(self, Tarr, Parr):
"""cross section matrix.
Args:
Tarr: temperature layer (K)
Parr: pressure layer (bar)
Returns:
cross section (cm2)
"""
mdb = self.mdb
if self.database == 'ExoMol':
qt = vmap(mdb.qr_interp)(Tarr)
gammaLMP = jit(vmap(gamma_exomol,
(0, 0, None, None)))(Parr, Tarr, mdb.n_Texp,
mdb.alpha_ref)
gammaLMN = gamma_natural(mdb.A)
gammaLM = gammaLMP + gammaLMN[None, :]
self.molmass = mdb.molmass
SijM = jit(vmap(SijT, (0, None, None, None, 0)))(Tarr, mdb.logsij0,
mdb.nu_lines,
mdb.elower, qt)
elif self.database == 'HITRAN' or self.database == 'HITEMP':
qt = mdb.Qr_layer(Tarr)
gammaLM = jit(vmap(gamma_hitran, (0, 0, 0, None, None, None)))(Parr, Tarr, Parr, mdb.n_air, mdb.gamma_air, mdb.gamma_self)\
+ gamma_natural(mdb.A)
self.molmass = molinfo.molmass(self.molecules)
SijM = jit(vmap(SijT, (0, None, None, None, 0)))(Tarr, mdb.logsij0,
mdb.nu_lines,
mdb.elower, qt)
print('# of lines', len(mdb.nu_lines))
memory_size = 15.0
d = int(memory_size / (len(mdb.nu_lines) * 4 / 1024. / 1024.)) + 1
d2 = 100
Nlayer, Nline = np.shape(SijM)
if self.xsmode == 'auto':
xsmode = self.select_xsmode(Nline)
else:
xsmode = self.xsmode
print('xsmode=', xsmode)
if xsmode == 'lpf' or xsmode == 'LPF':
sigmaDM = jit(vmap(doppler_sigma,
(None, 0, None)))(mdb.nu_lines, Tarr,
self.molmass)
Nj = int(Nline / d2)
xsm = []
for i in tqdm.tqdm(range(0, int(len(self.nus) / d) + 1)):
s = int(i * d)
e = int((i + 1) * d)
e = min(e, len(self.nus))
xsmtmp = np.zeros((Nlayer, e - s))
for j in range(0, Nj + 1):
s2 = int(j * d2)
e2 = int((j + 1) * d2)
e2 = min(e2, Nline)
numatrix = make_numatrix0(self.nus[s:e],
mdb.nu_lines[s2:e2])
xsmtmp = xsmtmp +\
lpf.xsmatrix(
numatrix, sigmaDM[:, s2:e2], gammaLM[:, s2:e2], SijM[:, s2:e2])
if i == 0:
xsm = np.copy(xsmtmp.T)
else:
xsm = np.concatenate([xsm, xsmtmp.T])
xsm = xsm.T
elif xsmode == 'modit' or xsmode == 'MODIT':
cnu, indexnu, R_mol, pmarray = initspec.init_modit(
mdb.nu_lines, self.nus)
nsigmaDl = normalized_doppler_sigma(Tarr, self.molmass,
R_mol)[:, np.newaxis]
ngammaLM = gammaLM / (mdb.nu_lines / R_mol)
dgm_ngammaL = modit.dgmatrix(ngammaLM, 0.1)
xsm = modit.xsmatrix(cnu, indexnu, R_mol, pmarray, nsigmaDl,
ngammaLM, SijM, self.nus, dgm_ngammaL)
xsm = self.nonnegative_xsm(xsm)
elif xsmode == 'dit' or xsmode == 'DIT':
cnu, indexnu, pmarray = initspec.init_dit(mdb.nu_lines, self.nus)
sigmaDM = jit(vmap(doppler_sigma,
(None, 0, None)))(mdb.nu_lines, Tarr,
self.molmass)
dgm_sigmaD = dit.dgmatrix(sigmaDM, 0.1)
dgm_gammaL = dit.dgmatrix(gammaLM, 0.2)
xsm = dit.xsmatrix(cnu, indexnu, pmarray, sigmaDM, gammaLM, SijM,
self.nus, dgm_sigmaD, dgm_gammaL)
xsm = self.nonnegative_xsm(xsm)
else:
print('No such xsmode=', xsmode)
xsm = None
return xsm