Generating Parameter Line lists¶
Parameter Line list Overview¶
- The MATS program uses a spectroscopic line list that varies from the traditional HITRAN and HAPI formats to accomodate the full HTP parameterization including temperature dependencies for all parameters (other than the correlation parameter and first order line-mixing). The spectroscopic line list format has rows that correspond to each molecular transition and columns that correspond to the various HTP parameters. The necessary column headers are below, where there needs to be a column for each parameter for each diluent (ie. air, self) in the dataset. Additionally, there needs to be a line-mixing term for each nominal temperature in the dataset, where the nominal temperature is the included as the suffix of the column header.
molec_id: HITRAN molecule id number
local_iso_id: HITRAN local isotope id number
nu: line center (\(cm^{-1}\))
sw : spectral line intensity (\(\frac{cm^{-1}}{molecule \cdot cm^{-2}}\)) at Tref=296K
elower: The lower-state energy of the transition (\(cm^{-1}\))
gamma0_diluent: collisional half-width (\(\frac{cm^{-1}}{atm}\)) at Tref=296K and reference pressure pref=1atm for a given diluent
n_gamma0_diluent: coefficient of the temperature dependence of the collisional half-width
delta0_diluent: pressure shift (\(\frac{cm^{-1}}{atm}\)) at Tref=296K and pref=1atm of the line position with respect to line center
n_delta0_diluent: the coefficient of the temperature dependence of the pressure shift
SD_gamma_diluent: the ratio of the speed dependent width to the collisional half-width at reference temperature and pressure
n_gamma2_diluent: the coefficient of the temperature dependence of the speed-dependent width NOTE: This is the temperature dependence of the speed-dependent width not the temperature dependence of the ratio of the speed-dependent width to the collisional half-width
SD_delta_diluent: the ratio of the speed-dependent shift to the collisional shift at reference temperature and pressure
n_delta2_diluent: the coefficient of the temperature dependence of the speed-dependent shift NOTE: This is the temperature dependence of the speed-dependent shift not the temperature dependence of the ratio of the speed-dependent shift to the pressure shift
nuVC_diluent: Dicke narrowing term (\(\frac{cm^{-1}}{atm}\)) at reference temperature and pressure
n__nuVC_diluent: coefficient of the temperature dependence of the Dicke narrowing term
eta_diluent: correlation parameter
y_diluent_nominaltemp: line mixing term (\(\frac{cm^{-1}}{atm}\)) NOTE: As currently written , this doesn’t have a temperature dependence, so there is a different column for each nominal temperature.
Generating Parameter Line list from HITRAN¶
The parameter line list .csv file can be generated manually, but this notebook generates a parameter list using the HITRAN Application Programming Interface (HAPI). The overview below walks through this notebook.
Imports¶
Import the numpy, pandas, os, and sys packages. Set pandas dataframe to show all of the rows.
import numpy as np
import pandas as pd
pd.set_option("display.max_rows", 101)
import os, sys
Optional imports include matplotlib and seaborn for plotting.
import matplotlib.pyplot as plt
import seaborn as sns
sns.set_style("whitegrid")
sns.set_style("ticks")
sns.set_context("poster")
Molecule and Isotope Information¶
HAPI provides a dictionary called ISO_ID, where the global isotope id acts as the key, with a sub-dictionary containing the molecule id, local isotope id, isotope name, relative abundance, mass, and molecule name. The following command will generate the dictionary as the output. This provides the necessary global isotope id information for interfacing with HAPI to access HITRAN infomation.
print_iso_id()
The dictionary "ISO_ID" contains information on "global" IDs of isotopologues in HITRAN
id M I iso_name abundance mass mol_name
1 : 1 1 H2(16O) 0.9973170000 18.010565 H2O
2 : 1 2 H2(18O) 0.0019998300 20.014811 H2O
3 : 1 3 H2(17O) 0.0003720000 19.014780 H2O
4 : 1 4 HD(16O) 0.0003106900 19.016740 H2O
5 : 1 5 HD(18O) 0.0000006230 21.020985 H2O
6 : 1 6 HD(17O) 0.0000001160 20.020956 H2O
129 : 1 7 D2(16O) 0.0000000242 20.022915 H2O
7 : 2 1 (12C)(16O)2 0.9842040000 43.989830 CO2
8 : 2 2 (13C)(16O)2 0.0110570000 44.993185 CO2
9 : 2 3 (16O)(12C)(18O) 0.0039471000 45.994076 CO2
10 : 2 4 (16O)(12C)(17O) 0.0007340000 44.994045 CO2
11 : 2 5 (16O)(13C)(18O) 0.0000443400 46.997431 CO2
12 : 2 6 (16O)(13C)(17O) 0.0000082500 45.997400 CO2
13 : 2 7 (12C)(18O)2 0.0000039573 47.998322 CO2
14 : 2 8 (17O)(12C)(18O) 0.0000014700 46.998291 CO2
121 : 2 9 (12C)(17O)2 0.0000001368 45.998262 CO2
15 : 2 10 (13C)(18O)2 0.0000000450 49.001675 CO2
120 : 2 11 (18O)(13C)(17O) 0.0000000165 48.001650 CO2
122 : 2 12 (13C)(17O)2 0.0000000015 47.001618 CO2
16 : 3 1 (16O)3 0.9929010000 47.984745 O3
17 : 3 2 (16O)(16O)(18O) 0.0039819400 49.988991 O3
18 : 3 3 (16O)(18O)(16O) 0.0019909700 49.988991 O3
19 : 3 4 (16O)(16O)(17O) 0.0007400000 48.988960 O3
20 : 3 5 (16O)(17O)(16O) 0.0003700000 48.988960 O3
21 : 4 1 (14N)2(16O) 0.9903330000 44.001062 N2O
22 : 4 2 (14N)(15N)(16O) 0.0036409000 44.998096 N2O
23 : 4 3 (15N)(14N)(16O) 0.0036409000 44.998096 N2O
24 : 4 4 (14N)2(18O) 0.0019858200 46.005308 N2O
25 : 4 5 (14N)2(17O) 0.0003690000 45.005278 N2O
26 : 5 1 (12C)(16O) 0.9865400000 27.994915 CO
27 : 5 2 (13C)(16O) 0.0110800000 28.998270 CO
28 : 5 3 (12C)(18O) 0.0019782000 29.999161 CO
29 : 5 4 (12C)(17O) 0.0003680000 28.999130 CO
30 : 5 5 (13C)(18O) 0.0000222200 31.002516 CO
31 : 5 6 (13C)(17O) 0.0000041300 30.002485 CO
32 : 6 1 (12C)H4 0.9882700000 16.031300 CH4
33 : 6 2 (13C)H4 0.0111000000 17.034655 CH4
34 : 6 3 (12C)H3D 0.0006157500 17.037475 CH4
35 : 6 4 (13C)H3D 0.0000049203 18.040830 CH4
36 : 7 1 (16O)2 0.9952620000 31.989830 O2
37 : 7 2 (16O)(18O) 0.0039914100 33.994076 O2
38 : 7 3 (16O)(17O) 0.0007420000 32.994045 O2
39 : 8 1 (14N)(16O) 0.9939740000 29.997989 NO
40 : 8 2 (15N)(16O) 0.0036543000 30.995023 NO
41 : 8 3 (14N)(18O) 0.0019931200 32.002234 NO
42 : 9 1 (32S)(16O)2 0.9456800000 63.961901 SO2
43 : 9 2 (34S)(16O)2 0.0419500000 65.957695 SO2
44 : 10 1 (14N)(16O)2 0.9916160000 45.992904 NO2
45 : 11 1 (14N)H3 0.9958715000 17.026549 NH3
46 : 11 2 (15N)H3 0.0036613000 18.023583 NH3
47 : 12 1 H(14N)(16O)3 0.9891100000 62.995644 HNO3
117 : 12 2 H(15N)(16O)3 0.0036360000 63.992680 HNO3
48 : 13 1 (16O)H 0.9974730000 17.002740 OH
49 : 13 2 (18O)H 0.0020001400 19.006986 OH
50 : 13 3 (16O)D 0.0001553700 18.008915 OH
51 : 14 1 H(19F) 0.9998442500 20.006229 HF
110 : 14 2 D(19F) 0.0001150000 21.012505 HF
52 : 15 1 H(35Cl) 0.7575870000 35.976678 HCl
53 : 15 2 H(37Cl) 0.2422570000 37.973729 HCl
107 : 15 3 D(35Cl) 0.0001180050 36.982954 HCl
108 : 15 4 D(37Cl) 0.0000377350 38.980004 HCl
54 : 16 1 H(79Br) 0.5067800000 79.926160 HBr
55 : 16 2 H(81Br) 0.4930600000 81.924115 HBr
111 : 16 3 D(79Br) 0.0000582935 80.932439 HBr
112 : 16 4 D(81Br) 0.0000567065 82.930392 HBr
56 : 17 1 H(127I) 0.9998442500 127.912297 HI
113 : 17 2 D(127I) 0.0001150000 128.918575 HI
57 : 18 1 (35Cl)(16O) 0.7559100000 50.963768 ClO
58 : 18 2 (37Cl)(16O) 0.2417200000 52.960819 ClO
59 : 19 1 (16O)(12C)(32S) 0.9373900000 59.966986 OCS
60 : 19 2 (16O)(12C)(34S) 0.0415800000 61.962780 OCS
61 : 19 3 (16O)(13C)(32S) 0.0105300000 60.970341 OCS
62 : 19 4 (16O)(12C)(33S) 0.0105300000 60.966371 OCS
63 : 19 5 (18O)(12C)(32S) 0.0018800000 61.971231 OCS
64 : 20 1 H2(12C)(16O) 0.9862400000 30.010565 H2CO
65 : 20 2 H2(13C)(16O) 0.0110800000 31.013920 H2CO
66 : 20 3 H2(12C)(18O) 0.0019776000 32.014811 H2CO
67 : 21 1 H(16O)(35Cl) 0.7557900000 51.971593 HOCl
68 : 21 2 H(16O)(37Cl) 0.2416800000 53.968644 HOCl
69 : 22 1 (14N)2 0.9926874000 28.006147 N2
118 : 22 2 (14N)(15N) 0.0072535000 29.997989 N2
70 : 23 1 H(12C)(14N) 0.9851100000 27.010899 HCN
71 : 23 2 H(13C)(14N) 0.0110700000 28.014254 HCN
72 : 23 3 H(12C)(15N) 0.0036217000 28.007933 HCN
73 : 24 1 (12C)H3(35Cl) 0.7489400000 49.992328 CH3Cl
74 : 24 2 (12C)H3(37Cl) 0.2394900000 51.989379 CH3Cl
75 : 25 1 H2(16O)2 0.9949520000 34.005480 H2O2
76 : 26 1 (12C)2H2 0.9776000000 26.015650 C2H2
77 : 26 2 (12C)(13C)H2 0.0219700000 27.019005 C2H2
105 : 26 3 (12C)2HD 0.0003045500 27.021825 C2H2
78 : 27 1 (12C)2H6 0.9769900000 30.046950 C2H6
106 : 27 2 (12C)H3(13C)H3 0.0219526110 31.050305 C2H6
79 : 28 1 (31P)H3 0.9995328300 33.997238 PH3
80 : 29 1 (12C)(16O)(19F)2 0.9865400000 65.991722 COF2
119 : 29 2 (13C)(16O)(19F)2 0.0110834000 66.995083 COF2
126 : 30 1 (32S)(19F)6 0.9501800000 145.962492 SF6
81 : 31 1 H2(32S) 0.9498800000 33.987721 H2S
82 : 31 2 H2(34S) 0.0421400000 35.983515 H2S
83 : 31 3 H2(33S) 0.0074980000 34.987105 H2S
84 : 32 1 H(12C)(16O)(16O)H 0.9838980000 46.005480 HCOOH
85 : 33 1 H(16O)2 0.9951070000 32.997655 HO2
86 : 34 1 (16O) 0.9976280000 15.994915 O
87 : 36 1 (14N)(16O)+ 0.9939740000 29.997989 NOp
88 : 37 1 H(16O)(79Br) 0.5056000000 95.921076 HOBr
89 : 37 2 H(16O)(81Br) 0.4919000000 97.919027 HOBr
90 : 38 1 (12C)2H4 0.9773000000 28.031300 C2H4
91 : 38 2 (12C)H2(13C)H2 0.0219600000 29.034655 C2H4
92 : 39 1 (12C)H3(16O)H 0.9859300000 32.026215 CH3OH
93 : 40 1 (12C)H3(79Br) 0.5013000000 93.941811 CH3Br
94 : 40 2 (12C)H3(81Br) 0.4876600000 95.939764 CH3Br
95 : 41 1 (12C)H3(12C)(14N) 0.9748200000 41.026549 CH3CN
96 : 42 1 (12C)(19F)4 0.9893000000 87.993616 CF4
116 : 43 1 (12C)4H2 0.9559980000 50.015650 C4H2
109 : 44 1 H(12C)3(14N) 0.9646069000 51.010899 HC3N
103 : 45 1 H2 0.9996880000 2.015650 H2
115 : 45 2 HD 0.0003114320 3.021825 H2
97 : 46 1 (12C)(32S) 0.9396240000 43.971036 CS
98 : 46 2 (12C)(34S) 0.0416817000 45.966787 CS
99 : 46 3 (13C)(32S) 0.0105565000 44.974368 CS
100 : 46 4 (12C)(33S) 0.0074166800 44.970399 CS
114 : 47 1 (32S)(16O)3 0.9423964000 79.956820 SO3
123 : 48 1 (12C)2(14N)2 0.9707524330 52.006148 C2N2
124 : 49 1 (12C)(16O)(35Cl)2 0.5663917610 97.932620 COCl2
125 : 49 2 (12C)(16O)(35Cl)(37Cl) 0.3622352780 99.929670 COCl2
Generate HITRAN and Initial Guess Line lists from HAPI Call¶
The next section of the example contains a function and function call where the output is a MATS compatible line list. The HITRANlinelist_to_csv takes a list of global isotope numbers and minimum and maximum wavenumbers as variables with a tablename, filename, temperature, and option to calculate the speed-dependent broadening as optional parameters. The spectroscopic data for the isotopes in the global isotope list over the specified wavenumber range will be retrieved from HITRANOnline. HITRAN breaks-up the HTP line parameters into temperature regimes, so the temperature specied selects for the most relevant parameters. The tablename parameter sets the ame of the table generated by the HAPI call, where the filename parameter sets the base for the resulting .csv files. The HITRANlinelist_to_csv function generates two outputs, the first is a HITRAN line list with all data available in HITRAN for the isotopes and spectral range (based on the parsed parameters in the HITRAN_parameter_list). The second file generates the highest order line shape list using the HITRAN values and formats for MATS. This line list also will fill in temperature dependences and missing broadener information and if calculate_aw is True calculate the speed dependence based on theory.
def HITRANlinelist_to_csv(isotopes, minimum_wavenumber, maximum_wavenumber, tablename = 'tmp', temperature = 296, calculate_aw = False):
"""Generates two .csv files generated information available from HTIRAN. The first line list matches the information available from HITRAN (_HITRAN.csv) and the second supplements the HITRAN information with theoretical values and translates into MATS input format (_initguess.csv)
Outline
1. Gets a line list from HITRAN and saves all available parameters to filename_HITRAN.csv
2. Goes through the data provided from HITRAN and collects the highest order line shape information.
3. Where there is missing information for the complete HTP linelist set to 0 or make the following substitutions
- for missing diluent information fill values with air
- set missing shift temperature dependences equal to 0 (linear temperature dependence)
- calculate the SD_gamma based on theory (if calculate aw = True)
- set the gamma_2 temperature exponent equal to the gamma0 temperature exponent
- set the delta_2 temperature exponent equal to the delta0 temperature exponent
- set the dicke narrowing temperature exponent to 1
4. Save the supplemented and MATS formatted HITRAN information as filename_initguess.csv
Parameters
----------
isotopes : list
list of the HITRAN global isotope numbers to include in the HAPI call
minimum_wavenumber : float
minimum line center (cm-1) to include in the HAPI call.
maximum_wavenumber : float
maximum line center (cm-1) to include in the HAPI call.
tablename : str, optional
desired name for table generated from HAPI call. The default is 'tmp'.
temperature : float, optional
Nominal temperature of interest. HITRAN breaks-up the HTP line parameters into temperature regimes. This allows for selection of the most approriate parameter information. The default is 296.
calculate_aw : float, optional
Boolean flag to present option to calculate speed-dependent shift based on theoretical approximation based on temperature exponent, mass of the absorber, and mass of the perturber
Returns
-------
linelist_select : dataframe
pandas dataframe corresponding to the HITRAN information supplemented by theoretical values/assumptions.
tablename_HITRAN.csv : .csv file
file corresponding to available HITRAN information
tablename_initguess.csv : .csv file
file corresponding to available HITRAN information supplemented by theory and assumptions in MATS format
"""
Use Example for HITRANlinelist_to_csv¶
To select the relevant information from HITRAN you will need to provide:
table name (str)
an array containing the global isotope numbers of the molecules/isotopes of interest
the minimum and maximum wavenumbers
the minimum line intensity of interest
The example below would generate a HITRAN table named ‘CO’ that contains all \(CO\) isotopes (global isotopes 26 - 31) and the most abundant \(CO_{2}\) isotope (global isotope 7) in the spectral region between 6200 and 6500 \(cm^{-1}\) that have line intensities greater than 1e-30 \(\frac{cm^{-1}}{molecule \cdot cm^{-2}}\). Additionally, it calculates the theoretical aw value and assumes that measurements are at 296 (temperature = 296 is default).
tablename = 'CO'
global_isotopes = [26, 27, 28, 29, 30,31,7]
wave_min = 6200
wave_max = 6500
intensity_cutoff = 1e-30
linelist_select = (HITRANlinelist_to_csv(global_isotopes, wave_min, wave_max, tablename = tablename, calculate_aw = True))