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
def ap(fobs, nusd, ws, we, Nx): mask = (ws < wavd[::-1]) * (wavd[::-1] < we) #additional mask to remove a strong telluric mask = mask * ((22898.5 > wavd[::-1]) + (wavd[::-1] > 22899.5)) fobsx = fobs[mask] nusdx = nusd[mask] wavdx = 1.e8 / nusdx[::-1] errx = err[mask] nus, wav, res = nugrid(ws - 5.0, we + 5.0, Nx, unit="AA") #loading molecular database mdbCO = moldb.MdbExomol('.database/CO/12C-16O/Li2015', nus) mdbH2O = moldb.MdbExomol('.database/H2O/1H2-16O/POKAZATEL', nus, crit=1.e-46) #LOADING CIA cdbH2H2 = contdb.CdbCIA('.database/H2-H2_2011.cia', nus) cdbH2He = contdb.CdbCIA('.database/H2-He_2011.cia', nus) #REDUCING UNNECESSARY LINES #1. CO Tarr = T0c * np.ones_like(Parr) qt = vmap(mdbCO.qr_interp)(Tarr) gammaLMP = jit(vmap(gamma_exomol,(0,0,None,None)))\ (Parr,Tarr,mdbCO.n_Texp,mdbCO.alpha_ref) gammaLMN = gamma_natural(mdbCO.A) gammaLM = gammaLMP + gammaLMN[None, :] SijM=jit(vmap(SijT,(0,None,None,None,0)))\ (Tarr,mdbCO.logsij0,mdbCO.nu_lines,mdbCO.elower,qt) sigmaDM=jit(vmap(doppler_sigma,(None,0,None)))\ (mdbCO.nu_lines,Tarr,molmassCO) mask_CO, maxcf, maxcia = mask_weakline(mdbCO, Parr, dParr, Tarr, SijM, gammaLM, sigmaDM, maxMMR_CO * ONEARR, molmassCO, mmw, g, vmrH2, cdbH2H2, margin=2) mdbCO.masking(mask_CO) #plot_maxpoint(mask_CO,Parr,maxcf,maxcia,mol="CO") #plt.savefig("maxpoint_CO.pdf", bbox_inches="tight", pad_inches=0.0) #2. H2O T0xarr = list(range(500, 1800, 100)) for k, T0x in enumerate(T0xarr): Tarr = T0x * np.ones_like(Parr) qt = vmap(mdbH2O.qr_interp)(Tarr) gammaLMP = jit(vmap(gamma_exomol,(0,0,None,None)))\ (Parr,Tarr,mdbH2O.n_Texp,mdbH2O.alpha_ref) gammaLMN = gamma_natural(mdbH2O.A) gammaLM = gammaLMP + gammaLMN[None, :] SijM=jit(vmap(SijT,(0,None,None,None,0)))\ (Tarr,mdbH2O.logsij0,mdbH2O.nu_lines,mdbH2O.elower,qt) sigmaDM=jit(vmap(doppler_sigma,(None,0,None)))\ (mdbH2O.nu_lines,Tarr,molmassH2O) mask_H2O_tmp, maxcf, maxcia = mask_weakline(mdbH2O, Parr, dParr, Tarr, SijM, gammaLM, sigmaDM, maxMMR_H2O * ONEARR, molmassH2O, mmw, g, vmrH2, cdbH2H2, margin=2) if k == 0: mask_H2O = np.copy(mask_H2O_tmp) else: mask_H2O = mask_H2O + mask_H2O_tmp if k == len(T0xarr) - 1: print("H2O ") plot_maxpoint(mask_H2O_tmp, Parr, maxcf, maxcia, mol="H2O") plt.savefig("maxpoint_H2O.pdf", bbox_inches="tight", pad_inches=0.0) print("H2O saved") mdbH2O.masking(mask_H2O) print("Final:", len(mask_H2O), "->", np.sum(mask_H2O)) #nu matrix numatrix_CO = make_numatrix0(nus, mdbCO.nu_lines) numatrix_H2O = make_numatrix0(nus, mdbH2O.nu_lines) return fobsx, nusdx, wavdx, errx, nus, wav, res, mdbCO, mdbH2O, numatrix_CO, numatrix_H2O, cdbH2H2, cdbH2He
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))
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 Pref = 1.0 # bar ONEARR = np.ones_like(Parr) ONEWAV = jnp.ones_like(nflux) # cnu_H2O, indexnu_H2O, R_H2O, pmarray_H2O = initspec.init_modit( mdbH2O.nu_lines, nus) cnu_CO, indexnu_CO, R_CO, pmarray_CO = initspec.init_modit(mdbCO.nu_lines, nus) R = R_CO # Precomputing gdm_ngammaL
def ap(fobs, nusd, ws, we, Nx): mask = (ws < wavd[::-1]) * (wavd[::-1] < we) #additional mask mask = mask * ((22898.5 > wavd[::-1]) + (wavd[::-1] > 22899.5)) fobsx = fobs[mask] nusdx = nusd[mask] wavdx = 1.e8 / nusdx[::-1] errx = err[mask] nus, wav, res = nugrid(ws - 5.0, we + 5.0, Nx, unit="AA") #loading molecular database #mdbCO=moldb.MdbExomol('.database/CO/12C-16O/Li2015',nus) mdbCO = moldb.MdbHit('05_HITEMP2019.par.bz2', nus) mdbCO.ExomolQT('.database/CO/12C-16O/Li2015') ##use HITEMP later mdbH2O = moldb.MdbExomol('H2O/1H2-16O/POKAZATEL', nus, crit=1.e-45) # mdbH2O=moldb.MdbExomol('.database/H2O/1H2-16O/POKAZATEL',nus) print("resolution=", res) #LOADING CIA cdbH2H2 = contdb.CdbCIA('H2-H2_2011.cia', nus) cdbH2He = contdb.CdbCIA('H2-He_2011.cia', nus) ### REDUCING UNNECESSARY LINES ####################################################### #1. CO Tarr = T0c * np.ones_like(Parr) qt = vmap(mdbCO.qr_interp)(Tarr) # gammaL = gamma_hitran(Pfix,Tfix, Ppart, mdbCO.n_air, \ # mdbCO.gamma_air, mdbCO.gamma_self) \ gammaLMP = 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 = gamma_natural(mdbCO.A) #(Nlayer, Nlines)+(None, Nlines)=(Nlayers, Nlines) gammaLM = gammaLMP + gammaLMN[None, :] SijM=jit(vmap(SijT,(0,None,None,None,0)))\ (Tarr,mdbCO.logsij0,mdbCO.nu_lines,mdbCO.elower,qt) sigmaDM=jit(vmap(doppler_sigma,(None,0,None)))\ (mdbCO.nu_lines,Tarr,molmassCO) mask_CO, maxcf, maxcia = mask_weakline(mdbCO, Parr, dParr, Tarr, SijM, gammaLM, sigmaDM, maxMMR_CO * ONEARR, molmassCO, mmw, g, vmrH2, cdbH2H2) mdbCO.masking(mask_CO) plot_maxpoint(mask_CO, Parr, maxcf, maxcia, mol="CO") plt.savefig("npz/maxpoint_CO.pdf", bbox_inches="tight", pad_inches=0.0) #2. H2O T0xarr = list(range(500, 1800, 100)) for k, T0x in enumerate(T0xarr): Tarr = T0x * np.ones_like(Parr) qt = vmap(mdbH2O.qr_interp)(Tarr) gammaLMP = jit(vmap(gamma_exomol,(0,0,None,None)))\ (Parr,Tarr,mdbH2O.n_Texp,mdbH2O.alpha_ref) gammaLMN = gamma_natural(mdbH2O.A) gammaLM = gammaLMP + gammaLMN[None, :] SijM=jit(vmap(SijT,(0,None,None,None,0)))\ (Tarr,mdbH2O.logsij0,mdbH2O.nu_lines,mdbH2O.elower,qt) sigmaDM=jit(vmap(doppler_sigma,(None,0,None)))\ (mdbH2O.nu_lines,Tarr,molmassH2O) mask_H2O_tmp, maxcf, maxcia = mask_weakline(mdbH2O, Parr, dParr, Tarr, SijM, gammaLM, sigmaDM, maxMMR_H2O * ONEARR, molmassH2O, mmw, g, vmrH2, cdbH2H2) if k == 0: mask_H2O = np.copy(mask_H2O_tmp) else: mask_H2O = mask_H2O + mask_H2O_tmp if T0x == 1700.0: plot_maxpoint(mask_H2O_tmp, Parr, maxcf, maxcia, mol="H2O") plt.savefig("maxpoint_H2O.pdf", bbox_inches="tight", pad_inches=0.0) mdbH2O.masking(mask_H2O) print("Final:", len(mask_H2O), "->", np.sum(mask_H2O)) #nu matrix numatrix_CO = make_numatrix0(nus, mdbCO.nu_lines) numatrix_H2O = make_numatrix0(nus, mdbH2O.nu_lines) cdbH2H2 = contdb.CdbCIA('.database/H2-H2_2011.cia', nus) cdbH2He = contdb.CdbCIA('.database/H2-He_2011.cia', nus) return fobsx, nusdx, wavdx, errx, nus, wav, res, mdbCO, mdbH2O, numatrix_CO, numatrix_H2O, cdbH2H2, cdbH2He