def addcia(self, interaction, mmr1, mmr2): """ Args: interaction: e.g. H2-H2, H2-He mmr1: mass mixing ratio for molecule 1 mmr2: mass mixing ratio for molecule 2 """ mol1, mol2 = defcia.interaction2mols(interaction) molmass1 = molinfo.molmass(mol1) molmass2 = molinfo.molmass(mol2) vmr1 = (mmr1 * self.mmw / molmass1) vmr2 = (mmr2 * self.mmw / molmass2) ciapath = pathlib.Path(self.databasedir) / \ pathlib.Path(defcia.ciafile(interaction)) cdb = contdb.CdbCIA(str(ciapath), [self.nus[0], self.nus[-1]]) dtauc = dtauCIA(self.nus, self.Tarr, self.Parr, self.dParr, vmr1, vmr2, self.mmw, self.gravity, cdb.nucia, cdb.tcia, cdb.logac) self.dtau = self.dtau + dtauc
from exojax.spec.rtransfer import nugrid from exojax.spec import moldb, molinfo from exojax.spec.exomol import gamma_exomol from exojax.spec import SijT, doppler_sigma, gamma_natural from exojax.spec import planck import jax.numpy as jnp from jax import vmap, jit N = 1500 nus, wav, res = nugrid(22900, 22960, N, unit='AA') # mdbM=moldb.MdbExomol('.database/CO/12C-16O/Li2015',nus) # loading molecular database # molmass=molinfo.molmass("CO") #molecular mass (CO) mdbM = moldb.MdbExomol('.database/H2O/1H2-16O/POKAZATEL', nus, crit=1.e-45) # loading molecular dat molmassM = molinfo.molmass('H2O') # molecular mass (H2O) q = mdbM.qr_interp(1500.0) S = SijT(1500.0, mdbM.logsij0, mdbM.nu_lines, mdbM.elower, q) mask = S > 1.e-25 mdbM.masking(mask) Tarr = jnp.logspace(jnp.log10(800), jnp.log10(1600), 100) qt = vmap(mdbM.qr_interp)(Tarr) SijM = jit(vmap(SijT, (0, None, None, None, 0)))(Tarr, mdbM.logsij0, mdbM.nu_lines, mdbM.elower, qt) imax = jnp.argmax(SijM, axis=0) Tmax = Tarr[imax] print(jnp.min(Tmax))
#loading spectrum dat = pd.read_csv("../data/luhman16a_spectra_detector1.csv", delimiter=",") wavd = (dat["wavelength_micron"].values) * 1.e4 #AA nusd = 1.e8 / wavd[::-1] fobs = (dat["normalized_flux"].values)[::-1] err = (dat["err_normalized_flux"].values)[::-1] #ATMOSPHERE NP = 100 Parr, dParr, k = rt.pressure_layer(NP=NP) mmw = 2.33 #mean molecular weight R = 100000. beta = c / (2.0 * np.sqrt(2.0 * np.log(2.0)) * R) #IP sigma need check ONEARR = np.ones_like(Parr) #ones_array for MMR molmassCO = molinfo.molmass("CO") #molecular mass (CO) molmassH2O = molinfo.molmass("H2O") #molecular mass (H2O) #LOADING CIA mmrH2 = 0.74 mmrHe = 0.25 molmassH2 = molinfo.molmass("H2") molmassHe = molinfo.molmass("He") vmrH2 = (mmrH2 * mmw / molmassH2) vmrHe = (mmrHe * mmw / molmassHe) #LINES g = 10**(5.0) T0c = 1700.0 Tarr = T0c * np.ones_like(Parr) maxMMR_CO = 0.01
def test_VALD_MODIT(): #wavelength range wls, wll = 10395, 10405 #Set a model atmospheric layers, wavenumber range for the model, an instrument NP = 100 Parr, dParr, k = pressure_layer(NP=NP) Pref = 1.0 #bar ONEARR = np.ones_like(Parr) Nx = 2000 nus, wav, res = nugrid(wls - 5.0, wll + 5.0, Nx, unit="AA", xsmode="modit") Rinst = 100000. #instrumental spectral resolution beta_inst = R2STD( Rinst) #equivalent to beta=c/(2.0*np.sqrt(2.0*np.log(2.0))*R) #atoms and ions from VALD adbV = moldb.AdbVald( path_ValdLineList, nus, crit=1e-100 ) #The crit is defined just in case some weak lines may cause an error that results in a gamma of 0... (220219) asdb = moldb.AdbSepVald(adbV) #molecules from exomol mdbH2O = moldb.MdbExomol('.database/H2O/1H2-16O/POKAZATEL', nus, crit=1e-50) #,crit = 1e-40) mdbTiO = moldb.MdbExomol('.database/TiO/48Ti-16O/Toto', nus, crit=1e-50) #,crit = 1e-50) mdbOH = moldb.MdbExomol('.database/OH/16O-1H/MoLLIST', nus) mdbFeH = moldb.MdbExomol('.database/FeH/56Fe-1H/MoLLIST', nus) #CIA cdbH2H2 = contdb.CdbCIA('.database/H2-H2_2011.cia', nus) #molecular mass molmassH2O = molinfo.molmass("H2O") molmassTiO = molinfo.molmass("TiO") molmassOH = molinfo.molmass("OH") molmassFeH = molinfo.molmass("FeH") molmassH = molinfo.molmass("H") molmassH2 = molinfo.molmass("H2") #Initialization of MODIT (for separate VALD species, and exomol molecules(e.g., FeH)) cnuS, indexnuS, R, pmarray = initspec.init_modit_vald( asdb.nu_lines, nus, asdb.N_usp) cnu_FeH, indexnu_FeH, R, pmarray = initspec.init_modit( mdbFeH.nu_lines, nus) cnu_H2O, indexnu_H2O, R, pmarray = initspec.init_modit( mdbH2O.nu_lines, nus) cnu_OH, indexnu_OH, R, pmarray = initspec.init_modit(mdbOH.nu_lines, nus) cnu_TiO, indexnu_TiO, R, pmarray = initspec.init_modit( mdbTiO.nu_lines, nus) #sampling the max/min of temperature profiles fT = lambda T0, alpha: T0[:, None] * (Parr[None, :] / Pref)**alpha[:, None] T0_test = np.array([1500.0, 4000.0, 1500.0, 4000.0]) alpha_test = np.array([0.2, 0.2, 0.05, 0.05]) res = 0.2 #Assume typical atmosphere H_He_HH_VMR_ref = [0.1, 0.15, 0.75] PH_ref = Parr * H_He_HH_VMR_ref[0] PHe_ref = Parr * H_He_HH_VMR_ref[1] PHH_ref = Parr * H_He_HH_VMR_ref[2] #Precomputing dgm_ngammaL dgm_ngammaL_VALD = setdgm_vald_all(asdb, PH_ref, PHe_ref, PHH_ref, R, fT, res, T0_test, alpha_test) dgm_ngammaL_FeH = setdgm_exomol(mdbFeH, fT, Parr, R, molmassFeH, res, T0_test, alpha_test) dgm_ngammaL_H2O = setdgm_exomol(mdbH2O, fT, Parr, R, molmassH2O, res, T0_test, alpha_test) dgm_ngammaL_OH = setdgm_exomol(mdbOH, fT, Parr, R, molmassOH, res, T0_test, alpha_test) dgm_ngammaL_TiO = setdgm_exomol(mdbTiO, fT, Parr, R, molmassTiO, res, T0_test, alpha_test) T0 = 3000. alpha = 0.07 Mp = 0.155 * 1.99e33 / 1.90e30 Rp = 0.186 * 6.96e10 / 6.99e9 u1 = 0.0 u2 = 0.0 RV = 0.00 vsini = 2.0 mmw = 2.33 * ONEARR #mean molecular weight log_e_H = -4.2 VMR_H = 0.09 VMR_H2 = 0.77 VMR_FeH = 10**-8 VMR_H2O = 10**-4 VMR_OH = 10**-4 VMR_TiO = 10**-8 A_Fe = 1.5 A_Ti = 1.2 adjust_continuum = 0.99 ga = 2478.57730044555 * Mp / Rp**2 Tarr = T0 * (Parr / Pref)**alpha PH = Parr * VMR_H PHe = Parr * (1 - VMR_H - VMR_H2) PHH = Parr * VMR_H2 VMR_e = VMR_H * 10**log_e_H #VMR of atoms and ions (+Abundance modification) mods_ID = jnp.array([[26, 1], [22, 1]]) mods = jnp.array([A_Fe, A_Ti]) VMR_uspecies = atomll.get_VMR_uspecies(asdb.uspecies, mods_ID, mods) VMR_uspecies = VMR_uspecies[:, None] * ONEARR #Compute delta tau #Atom & ions (VALD) SijMS, ngammaLMS, nsigmaDlS = vald_all(asdb, Tarr, PH, PHe, PHH, R) xsmS = xsmatrix_vald(cnuS, indexnuS, R, pmarray, nsigmaDlS, ngammaLMS, SijMS, nus, dgm_ngammaL_VALD) dtauatom = dtauVALD(dParr, xsmS, VMR_uspecies, mmw, ga) #FeH SijM_FeH, ngammaLM_FeH, nsigmaDl_FeH = exomol(mdbFeH, Tarr, Parr, R, molmassFeH) xsm_FeH = xsmatrix(cnu_FeH, indexnu_FeH, R, pmarray, nsigmaDl_FeH, ngammaLM_FeH, SijM_FeH, nus, dgm_ngammaL_FeH) dtaum_FeH = dtauM_mmwl(dParr, jnp.abs(xsm_FeH), VMR_FeH * ONEARR, mmw, ga) #H2O SijM_H2O, ngammaLM_H2O, nsigmaDl_H2O = exomol(mdbH2O, Tarr, Parr, R, molmassH2O) xsm_H2O = xsmatrix(cnu_H2O, indexnu_H2O, R, pmarray, nsigmaDl_H2O, ngammaLM_H2O, SijM_H2O, nus, dgm_ngammaL_H2O) dtaum_H2O = dtauM_mmwl(dParr, jnp.abs(xsm_H2O), VMR_H2O * ONEARR, mmw, ga) #OH SijM_OH, ngammaLM_OH, nsigmaDl_OH = exomol(mdbOH, Tarr, Parr, R, molmassOH) xsm_OH = xsmatrix(cnu_OH, indexnu_OH, R, pmarray, nsigmaDl_OH, ngammaLM_OH, SijM_OH, nus, dgm_ngammaL_OH) dtaum_OH = dtauM_mmwl(dParr, jnp.abs(xsm_OH), VMR_OH * ONEARR, mmw, ga) #TiO SijM_TiO, ngammaLM_TiO, nsigmaDl_TiO = exomol(mdbTiO, Tarr, Parr, R, molmassTiO) xsm_TiO = xsmatrix(cnu_TiO, indexnu_TiO, R, pmarray, nsigmaDl_TiO, ngammaLM_TiO, SijM_TiO, nus, dgm_ngammaL_TiO) dtaum_TiO = dtauM_mmwl(dParr, jnp.abs(xsm_TiO), VMR_TiO * ONEARR, mmw, ga) #Hminus dtau_Hm = dtauHminus_mmwl(nus, Tarr, Parr, dParr, VMR_e * ONEARR, VMR_H * ONEARR, mmw, ga) #CIA dtauc_H2H2 = dtauCIA_mmwl(nus, Tarr, Parr, dParr, VMR_H2 * ONEARR, VMR_H2 * ONEARR, mmw, ga, cdbH2H2.nucia, cdbH2H2.tcia, cdbH2H2.logac) #Summations dtau = dtauatom + dtaum_FeH + dtaum_H2O + dtaum_OH + dtaum_TiO + dtau_Hm + dtauc_H2H2 sourcef = planck.piBarr(Tarr, nus) F0 = rtrun(dtau, sourcef) Frot = response.rigidrot(nus, F0, vsini, u1, u2) wavd = jnp.linspace(wls, wll, 500) nusd = jnp.array(1.e8 / wavd[::-1]) mu = response.ipgauss_sampling(nusd, nus, Frot, beta_inst, RV) mu = mu / jnp.nanmax(mu) * adjust_continuum assert (np.all(~np.isnan(mu)) * \ np.all(mu != 0) * \ np.all(abs(mu) != np.inf))
nflux = flux[::-1] / np.median(flux) nusd = jnp.array(1.e8 / wavd[::-1]) NP = 100 Parr, dParr, k = rt.pressure_layer(NP=NP) Nx = 5000 nus, wav, res = nugrid(np.min(wavd) - 10.0, np.max(wavd) + 10.0, Nx, unit='AA', xsmode='modit') Rinst = 100000. beta_inst = R2STD(Rinst) molmassH2O = molinfo.molmass('H2O') molmassCO = molinfo.molmass('CO') mmw = 2.33 # mean molecular weight mmrH2 = 0.74 molmassH2 = molinfo.molmass('H2') vmrH2 = (mmrH2 * mmw / molmassH2) # VMR # Mp = 33.2 mdbH2O = moldb.MdbExomol('.database/H2O/1H2-16O/POKAZATEL/', nus, crit=1.e-50) mdbCO = moldb.MdbExomol('.database/CO/12C-16O/Li2015/', nus) cdbH2H2 = contdb.CdbCIA('.database/H2-H2_2011.cia', nus) print('N=', len(mdbH2O.nu_lines)) # Reference pressure for a T-P model
sigmain = 0.05 norm = 20000 nflux = flux / norm + np.random.normal(0, sigmain, len(wavd)) NP = 100 Parr, dParr, k = rt.pressure_layer(NP=NP) Nx = 5000 nus, wav, res = nugrid(np.min(wavd) - 5.0, np.max(wavd) + 5.0, Nx, unit='AA', xsmode='modit') Rinst = 100000. beta_inst = R2STD(Rinst) molmassCH4 = molinfo.molmass('CH4') mmw = 2.33 # mean molecular weight mmrH2 = 0.74 molmassH2 = molinfo.molmass('H2') vmrH2 = (mmrH2 * mmw / molmassH2) # VMR # Mp = 33.2 mdbCH4 = moldb.MdbExomol('.database/CH4/12C-1H4/YT10to10/', nus, crit=1.e-30) cdbH2H2 = contdb.CdbCIA('.database/H2-H2_2011.cia', nus) print('N=', len(mdbCH4.nu_lines)) # Reference pressure for a T-P model Pref = 1.0 # bar ONEARR = np.ones_like(Parr) ONEWAV = jnp.ones_like(nflux)
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
def xsection(self, T, P): """cross section. Args: T: temperature (K) P: pressure (bar) Returns: cross section (cm2) """ mdb = self.mdb if self.database == 'ExoMol': gammaL = gamma_exomol(P, T, mdb.n_Texp, mdb.alpha_ref) + gamma_natural(mdb.A) molmass = mdb.molmass elif self.database == 'HITRAN' or self.database == 'HITEMP': gammaL = gamma_hitran(P, T, P, mdb.n_air, mdb.gamma_air, mdb.gamma_self) + gamma_natural(mdb.A) molmass = molinfo.molmass(self.molecules) Sij = self.linest(T) if self.xsmode == 'auto': xsmode = self.select_xsmode(len(mdb.nu_lines)) else: xsmode = self.xsmode if xsmode == 'lpf' or xsmode == 'LPF': sigmaD = doppler_sigma(mdb.nu_lines, T, molmass) xsv = xsection(self.nus, mdb.nu_lines, sigmaD, gammaL, Sij, memory_size=self.memory_size) elif xsmode == 'modit' or xsmode == 'MODIT': checknus = check_scale_nugrid(self.nus, gridmode='ESLOG') nus = self.autonus(checknus, 'ESLOG') cnu, indexnu, R_mol, pmarray = initspec.init_modit( mdb.nu_lines, nus) nsigmaD = normalized_doppler_sigma(T, molmass, R_mol) ngammaL = gammaL / (mdb.nu_lines / R_mol) ngammaL_grid = modit.ditgrid(ngammaL, res=0.1) xsv = modit.xsvector(cnu, indexnu, R_mol, pmarray, nsigmaD, ngammaL, Sij, nus, ngammaL_grid) if ~checknus and self.autogridconv: xsv = jnp.interp(self.nus, nus, xsv) elif xsmode == 'dit' or xsmode == 'DIT': sigmaD = doppler_sigma(mdb.nu_lines, T, molmass) checknus = check_scale_nugrid(self.nus, gridmode='ESLIN') nus = self.autonus(checknus, 'ESLIN') sigmaD_grid = dit.ditgrid(sigmaD, res=0.1) gammaL_grid = dit.ditgrid(gammaL, res=0.1) cnu, indexnu, pmarray = initspec.init_dit(mdb.nu_lines, nus) xsv = dit.xsvector(cnu, indexnu, pmarray, sigmaD, gammaL, Sij, nus, sigmaD_grid, gammaL_grid) if ~checknus and self.autogridconv: xsv = jnp.interp(self.nus, nus, xsv) else: print('Error:', xsmode, ' is unavailable (auto/LPF/DIT).') xsv = None return xsv
def Rpg(Mp, logg): #R from logg and M in MJ, RJ return np.sqrt(2478.58 * Mp / 10**logg) def est(val, N=3): per = np.percentile(val, [5, 95]) med = np.round(np.median(val), N) per0 = np.round(per[0] - med, N) per1 = np.round(per[1] - med, N) print(str(med) + '_{' + str(per0) + '}^{' + str(per1) + '}') p = np.load("npz/savepos.npz", allow_pickle=True)["arr_0"][0] mCO = molinfo.molmass("CO") #molecular mass (CO) mH2O = molinfo.molmass("H2O") #molecular mass (CO) T0 = p["T0"] mmrCO = p["MMR_CO"] mmrH2O = p["MMR_H2O"] corat = (1.0 + (mCO * mmrH2O) / (mH2O * mmrCO))**-1 est(T0) est(corat) est(mmrCO, 4) est(mmrH2O, 4) #plt.hist(corat,bins=100) #plt.savefig("coratio.pdf", bbox_inches="tight", pad_inches=0.0) #plt.show()