Gas-cell Simulator User Guide
Blackbody Calculator Background Information
Solar Calculator Background Information
Frequently Asked Questions
Glossary
Terms of Use
Frequently Asked Questions
- What does the Gas-cell Simulator do?
- How do I operate the Gas-cell Simulator?
- How does the Gas-cell Simulator model the spectra?
- What does the Line List Browser do?
- Why do I only have to specify the length of the gas cell, not its volume?
- What line shape is used in the computation?
- How is the spectral resolution determined?
- Do you include effects from absorption lines outside my spectral bandpass?
- How can I compare the Gas-cell Simulator results to a spectrum measured in air?
- How can I import my own line list?
- What are the benefits of subscribing?
- What can I do for free?
- How big of a waveband can I simulate?
- The Gas-cell Simulator says "No absorption lines found." What did I do wrong?
- What is the relative abundance of a particular isotopologue?
- Can I simulate different abundances of isotopologues?
- What is "line intensity"?
- I just need coarse spectra. How do I get this?
- What is an "Instrument Function"?
- How can I subscribe?
- Is there a publication describing the calculation?
- I can't use PayPal. How can I subscribe?
- How do I manage a group subscription?
- How do I join a group?
- How can I import my own spectra?
- How are vertical path spectra calculated?
- Are effects other than molecular line absorption/emission included?
- How are continua modeled?
- What are cross section spectra used for?
What does the Gas-cell Simulator do?
The Gas-cell Simulator models gas spectra. With just a few clicks you can accurately simulate the spectra of most of the important trace gas species in the Earth's atmosphere, such as water vapor, carbon dioxide, ozone, methane and dozens more. Spectra are calculated in the user-specified waveband with full resolution, fine enough to accurately capture the shape of even the narrowest molecular absorption line. The underlying software is scientifically rigorous and has been used in support of a number of NASA research projects.
The basic setup models the transmittance through a "gas cell" -- an imaginary sealed container with transparent walls. The transmittance is simply the fraction of radiation that makes it through the gas cell. This is illustrated below.
The transmittance, τ, is the ratio of the intensity of the transmitted radiation, I, to the incident, I0. You control the pressure, P, temperature, T and length, L, of the gas cell, the concentration of the absorbing gas inside, g, and the range of wavenumbers over which to compute the spectrum. The Gas-cell Simulator then accurately calculates the full-resolution transmittance spectrum.
Subscribers have access to some advanced features. They can simulate mixtures of several gases and can "stack" up to six gas cells end-to-end, controlling the conditions of each. They can choose to compute emission spectra rather than transmittance spectra, and add an optional blackbody source behind the gas cells. Instrument lineshape functions that "apodize" or smooth the spectra can also be included. These features are illustrated below.
Click here for a comprehensive list of features available to subscribers.
How do I operate the Gas-cell Simulator?
Choose your waveband, set up your gas cells, and press Calculate! Many variations are possible, so we've divided the inputs into functional "tabs" to make things more manageable.
- Observer Tab - choose the waveband and any other instrument parameters
- Gas Cells Tab - specify the gases to simulate and gas cell conditions
- Source Tab (optional) - include a blackbody background
- Plot Options Tab (optional) - control plot features like log or linear scaling
- My Settings Tab (optional) - save and retrieve simulation setups
How does the Gas-cell Simulator model the spectra?
The Gas-cell Simulator uses a line-by-line model called LinePakTM to accurately model the spectra of molecular absorption lines. The shape, position and depth of each line are described by parameters in a line list such as HITRAN, and adjusted for the user-specified pressure, temperature, and gas concentration. We maintain an up-to-date copy of the HITRAN line parameters, and allow alternate line lists to be used as well. Details of the calculation are given here.
What does the Line List Browser do?
The Line List browser lets you quickly and easily see where gases have absorption lines, and how strongly they absorb, without the time and effort of performing a detailed simulation. This tool displays the contents of HITRAN, GEISA and other line list databases. You can also download the line list data here, selecting the complete datasets or just the molecules and wavebands you want.
Why do I only have to specify the length of the gas cell, not its volume?
The length of the gas cell is the only dimension that matters because the simulation is of a single beam through the gas cell. Only molecules along the line-of-sight will affect this radiation.
What line shape is used in the computation?
At all but very low wavenumbers, the LinePakTM software uses the Voigt profile. The Voigt profile combines the pressure-induced line broadening effects of molecular collisions, and the thermal-induced Doppler effect resulting from their randomly oriented motions. At very low wavenumbers (below 200 cm-1) the Van Vleck Weisskopf line shape is used.
LinePakTM can easily accommodate more complex line shapes, such as the Galatry or speed-dependent profiles, but the spectroscopic parameters needed for these are currently available only for a small number of absorption lines. Note that these provide only a very small improvement, and in most situations, the Voigt profile adds no significant error.
How is the spectral resolution determined?
The spectral resolution is chosen to be fine enough to fully capture the line shape of the thinnest absorption line in the spectrum. The Gas-cell Simulator software first surveys all absorption lines needed for the calculation, including lines centered outside the spectral bandpass whose wings may contribute to the measured spectral range. The algorithm then determines the smallest width of all the absorbing lines, adjusted for pressure and temperature. The spectral resolution is set to 1/20th of this smallest halfwidth.
Do you include effects from absorption lines outside my spectral bandpass?
Yes. In many situations, the spectrum in a specified bandpass will have significant contributions from absorption lines centered outside the bandpass. To ensure that this is modeled correctly, the Gas-cell Simulator software calculates the spectra over a larger waveband, extended by 120 cm-1 on either side of the specified range.
How can I compare the Gas-cell Simulator results to a spectrum measured in air?
The Gas-cell Simulator reports spectra as would be measured in vacuum. (Outside the gas cell a vacuum is assumed). In some applications, spectra are measured in air. Because the speed of light is slower in air than in vacuum, the observed wavenumber (1/c in cm-1) is slightly larger than it would have been if it had been observed in vacuum. To compare Gas-cell Simulator results to spectra measured in air (or some other media), this shift must be accounted for.
How can I import my own line list?
Subscribers can import their own spectral line lists using the My Line Lists tab on the Linelist Browser tool. The line list must be a text file in HITRAN format. Up to 100,000 lines are allowed. The list can include only molecules/isotopologues that are already in the public HITRAN distribution. (If you have line parameters for molecules/isotopologues not in HITRAN, please contact us and we will help get your data uploaded.) It can take several minutes for the conversion, validation and upload process. Once your data is uploaded, your line list will be visible under My Line Lists and available for browsing or spectral calculations. Other subscribers will not be able to access your line lists.
What are the benefits of subscribing?
There are many benefits of becoming a subscriber. Some of the more popular features include the ability to simulate large wavebands, multiple gases and multiple gas cells. Subscribers have access to publication quality graphics and can download the raw data in text format. They can store their simulation setups for recall in later sessions. Subscribers can also upload their own custom line lists for testing and validation. Emission spectra can be computed with an optional blackbody source function, and instrument lineshape functions can be customized and applied to the spectra. Click here for a comparison of the features available with and without a subscription.
What can I do for free?
The basic functionality of all the tools at SpectralCalc.com is freely available without subscribing. You can simulate transmittance spectra of gases with the same fast, accurate software used by many NASA remote sensing missions, and visually browse the HITRAN and other line list databases. The Blackbody Calculator, Atmosphere Browser and Solar Calculator are all freely available. Click here for a description of the many additional features available with a subscription.
How big of a waveband can I simulate?
The number of calculations needed for a simulation depends on the number of absorption lines in the region and the spectral resolution needed to resolve the narrowest significant line. To ensure fast and accurate performance, we therefore limit the size of the waveband as follows:
| No. of gases | Min. cell pressure | Waveband lower limit | Max. waveband size |
|---|---|---|---|
| 1 | ≥ 100 mbar | ≥ 500 cm-1 | 5000 cm-1 |
| 1 | ≥ 100 mbar | < 500 cm-1 | 2000 cm-1 |
| 1 | < 100 mbar | ≥ 500 cm-1 | 1000 cm-1 |
| 1 | < 100 mbar | < 500 cm-1 | 500 cm-1 |
| > 1 | ≥ 100 mbar | ≥ 500 cm-1 | 1000 cm-1 |
| > 1 | ≥ 100 mbar | < 500 cm-1 | 500 cm-1 |
| > 1 | < 100 mbar | ≥ 500 cm-1 | 250 cm-1 |
| > 1 | < 100 mbar | < 500 cm-1 | 100 cm-1 |
If using microns, the waveband is converted to wavenumbers and then checked against these limits. Note that "gases" includes all gases from all cells, hence 1 gas in each of two cells counts as 2 gases.
The Gas-cell Simulator says "No absorption lines found." What did I do wrong?
Maybe nothing. This simply means there are no absorption lines for the selected gas in the specified waveband. You may wish to visit the Line List Browser to identify spectral regions in which each gas does have absorption lines, and adjust your waveband and/or gas accordingly.
What is the relative abundance of a particular isotopologue?
The Gas-cell Simulator assumes the same natural abundances of the various isotopologues as HITRAN. Click here to view the list of assumed abundances.
Can I simulate different abundances of isotopologues?
Yes. On the Gas Cells Tab, simply select the isotopologue to be simulated and specify the desired abundance. Subscribers can simulate mixtures of different isotopologues, and can control the concentration of each. Note: the concentration of individual isotopologues is automatically scaled by their natural abundance, so you will need to take this into account to achieve a particular vmr.
What is "line intensity"?
Line intensity is the strength of a molecular absorption/emission line. In most catalogs, including HITRAN, line intensities are given in units of cm-1 / (molecule cm-2) at 296 K.
I just need coarse spectra. How do I get this?
Subscribers can select an instrument function (Observers Tab) to model spectra as would be obtained from a coarser resolution instrument. Adjusting the width of the instrument function will control the resolution of the resulting spectrum.
What is an "Instrument Function"?
The Gas-cell Simulator models transmittance and emission with very fine spectral resolution – fine enough to capture every spectral feature. Real instruments, however, have some inherent spectral resolution, and smooth or "apodize" the spectrum by convolving it with an instrumental line shape function. Subscribers can select a particular instrument function from the Observers Tab. This allows you to model spectra as would be obtained from a coarser resolution instrument. Adjusting the width of the instrument function will control the resolution of the resulting spectrum. The various instrument functions are shown below.
Click on the image to see a larger version
How can I subscribe?
Subscribing is quick and easy. Follow this link and fill out the "New Users" information with your own username and password. Press "Submit", and select your desired subscription plan from the menu. (Take advantage of our discounted rates on longer subscriptions.) Finally, press the "Buy Now" button and proceed with check-out at the PayPal website. You do not need a PayPal account to complete this, only a valid credit card. Your subscription will be active immediately after completion of the payment.
Is there a publication describing the calculation?
Yes. The underlying algorithm was first described in the following paper: Gordley et al., LINEPAK: Algorithm for Modeling Spectral Transmittance and Radiance, J. Quant. Spectrosc. Radiat. Transfer Vol. 52, No. 5, pp.563-580, 1994
I can't use PayPal. How can I subscribe?
We can also accept checks and money orders. Please contact us, and we will arrange for a convenient payment solution.
How do I manage a group subscription?
Administrators can manage the group account from "My Account". Here you will see a list of all users currently in the group. You can add or delete users, and can designate an additional administrator if desired. Users can also join the group by logging in and entering the group code in "My Account".
Notes:
Users must be registered.
Group accounts can have up to 12 users, including the administrator(s).
Administrator(s) will receive email confirmation when a user joins the group.
A group account can have a maximum of 2 administrators.
Group codes are chosen by the administrator at time of purchase.
Group accounts can have up to 12 users, including the administrator(s).
Administrator(s) will receive email confirmation when a user joins the group.
A group account can have a maximum of 2 administrators.
Group codes are chosen by the administrator at time of purchase.
How do I join a group?
To join a group account, go to "My Account" and click on "Join Group". Here you will be prompted to enter the group code. Contact the group administrator for this code.
Notes:
Users must be registered.
Group accounts can have up to 12 users, including the administrator(s).
Administrator(s) will receive email confirmation when a user joins the group.
Group codes are chosen by the administrator at time of purchase.
Group accounts can have up to 12 users, including the administrator(s).
Administrator(s) will receive email confirmation when a user joins the group.
Group codes are chosen by the administrator at time of purchase.
How can I import my own spectra?
Subscribers can import their transmittance or radiance spectra by using the Upload tab on the My Spectra tool. Enter the full name (including directory path) of the file to upload, or use the Browse button to locate the file on your computer. Choose a short descriptive name to identify the spectrum, and select Transmittance or Radiance for the spectrum type. A description of the file can be typed into the text box provided. Once uploaded, the spectrum will be available on the My Spectra tab, where it can be viewed, downloaded, deleted, etc. (Other users do not have access to your stored spectra.)
File requirements: The uploaded spectrum file must be in plain text format with two columns, the first column containing the wavenumber (cm-1) values, and the second containing the transmittance or radiance values (W/m2/sr/cm-1). Files must be no bigger than 20 MB, and contain no more than 400,000 spectral points. Header lines (lines that begin with something other than a space, a digit or a decimal point) are allowed at the beginning of the file, but are ignored. The columns can be space-, tab- or comma-delimited. Any text following the second column is ignored. Wavenumbers are assumed to be equally spaced and increasing. Wavenumber spacing must be in the range 1e-8 to 100 cm-1. (Only the first and last wavenumber are actually stored. The grid is reconstructed each time the data are retrieved from our database.) Transmittance values must be between -1 and 2, and radiance values must be between 0 and 1000 W/m2/sr/cm-1.
How are vertical path spectra calculated?
Transmittance and radiance spectra for vertical paths can be simulated with the Atmospheric Path tool. The atmosphere is modeled as a series of uniform layers. The conditions in each layer are determined from our atmospheric profile database (see the Atmosphere Browser), selecting values for each layer from the requested atmosphere type.
The number of layers used to simulate a given path depends on the total path length. A maximum of fifteen layers are used. This is typically sufficient for accurate results. If needed, higher accuracy can be achieved by breaking the total path into segments, and simulating the transmittance of each segment separately. Simply save each spectrum and compute their product using the My Spectra tool.
For each layer, the pressure, temperature and mixing ratio are chosen to best approximate the varying atmosphere in the layer. Details are given here.
Note that radiance spectra for up-looking and downlooking spectra are different, whereas transmittance spectra are the same for both directions.
Are effects other than molecular line absorption/emission included?
Yes, continuum absorption/emission for N2, O2 and H2O are included. These effects are automatically included as needed for simulations involving these molecules. Other effects, such as Rayleigh (molecular) and Mie (particulate) scattering, are not yet included.
How are continua modeled?
Continuum absorption/emission effects for N2, O2 and H2O are modeled using the approaches described by Clough, et al. [1] and Lafferty et al. [2]. These continuum models augment the standard "line-by-line" calculation, more accurately accounting for far-wing effects at high pressures.
For O2 and N2, the spectral ranges affected are 1345-1820 cm-1 and 2105-2620 cm-1 respectively. The H2O continuum is significat at wavenumbers below 600 cm-1 and between 1200 and 2000 cm-1.
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Any simulation of N2, O2 and H2O spectra in any of the above wavebands will automatically include the appropriate continuum model(s). No action is needed from the user.
For all three gases, the effect is proportional to pressure, and is negligible at pressures less than ~10mbar. Temperature dependence of the continua is included in the model, derived from laboratory measurements between 70 and 350 K. Continuum absorption for spectra at higher temperatures is based on extrapolation of these data, and therefore may contain some inaccuracies. Note, however that the continuum effects are inversely proportional to temperature, so the overall magnitude become negligible for high temperatures.
[1] Clough, S. A., F. X. Kneizys, and R. W. Davies, "Lineshape and the water vapor continuum," Atmos. Res. 23, 229-241 (1989)
[2] Lafferty, W. J., A. M. Solodov, A. Weber, W. B. Olson, and J. Hartmann, "Infrared collision-induced absorption by N2 near 4.3 µm for atmospheric applications: measurements and empirical modeling," Appl. Opt. 35, 5911-5917 (1996)
What are cross section spectra used for?
Cross sections are normalized molecular absorption spectra. These are often used to simulate broad absorption features that are not well modeled using line-by-line techniques, or for which adequate line parameters are not available. Cross section spectra are typically given in units of cm2 per molecule at each wavenumber.
Infrared spectra of polyatomic "heavy" molecules such as CFCs, and UV absorption features of several important atmospheric species, most notably ozone, are better simulated using cross sections than line-by-line models. Cross section spectra for these molecules can be accessed in the Line List Browser, by selecting Plot Type-->Cross Sections.
We're working on integrating the capability of simulating spectra using cross sections to our online tools, but have not yet validated and tested a general-purpose interface for this.
GLOSSARY
absorption--fractional amount of incident radiation absorbed by a gas. Absorption = 1 – transmittance. In general, absorption varies with the frequency of the radiation.
absorption line-- The decrease in a transmittance spectrum corresponding to the radiation absorbed by a particular transition between quantum states of a molecule. Early spectra were recorded on strips of film, where molecular absorption features appeared as dark lines across the continuous spectrum, hence the name "absorption line".
abundance--The relative amount, or concentration, of a gas in a volume. This is typically specified by the gas' volume mixing ratio.
blackbody--a hypothetical object that absorbs all incident radiation while maintaining thermal equilibrium. No light is reflected from or passes through a blackbody, but radiation is emitted, and is called blackbody radiation. The prefix "black" is used because at room temperature such an object would emit almost no visible light, appearing black to an observer. No physical object exactly fits this definition, but most behave at least in part as blackbodies. Planck's law gives the spectral distribution of radiation emitted by a blackbody.
cross sections--normalized molecular absorption spectra, given in units of cm2 per molecule at each wavenumber. These are used to model spectra where line parameters are insufficient or unavailable.
Doppler effect--the change in frequency of observed radiation resulting from motion of the source relative to the observer.
emissivity--a unitless spectral quantity equal to the ratio of energy emitted by an object to that emitted by a blackbody at the same temperature.
emission (see radiance)
GEISA--a compilation of spectroscopic line parameters, similar to HITRAN (GEISA = Gestion et Etude des Informations Spectroscopiques Atmosphériques.)
HITEMP--the high-temperature analogue of HITRAN. The current compilation contains parameters for water vapor, carbon dioxide and carbon monoxide.
HITRAN--High-resolution transmission molecular absorption database. HITRAN is a compilation of spectroscopic parameters widely used for simulating the transmission and emission of radiation of gases in the atmosphere. See www.hitran.com for more details.
The HITRAN data can be downloaded to your computer (go to Line List Browser, Extract Data Tab). Subscribers can also upload their own line list files. The required format is the HITRAN format -- a fixed-field text file with the following fields
| Field width | FORTRAN format | |
| molecule number | 2 | I2 |
| isotopologue number | 1 | I1 |
| transition frequency (cm-1) | 12 | F12.6 |
| line Intensity | 10 | 1PE10.3 |
| Einstein A-coefficient | 10 | E10.3 |
| air-broadened width | 5 | 0PF5.4 |
| self-broadened width | 5 | F5.4 |
| lower-state energy | 10 | 1PF10.4 |
| temperature dependence (of air width) | 4 | 0PF4.2 |
| pressure shift | 8 | F8.6 |
| upper vibrational quanta | 15 | A15 |
| lower vibrational quanta | 15 | A15 |
| upper local quanta | 15 | A15 |
| lower local quanta | 15 | A15 |
| error codes | 6 | 6I1 |
| reference codes | 12 | 6I2 |
| flag for line-mixing | 1 | A1 |
| upper statistical weight | 7 | F7.1 |
| lower statistical weight | 7 | F7.1 |
Isotopologue--A molecule with a specific atomic weight of each constituent elements. For example, the 6 most common naturally occurring CO2 isotopes are: (16)O(12)C(16)O, (16)O(13)C(16)O, (16)O(12)C(18)O, (16)O(12)C(17)O, (16)O(13)C(18)O, (16)O(13)C(17)O. The isotopic abundances used in the Gas-cell Simulator are listed here:Abundances
LinePakTM--The GATS library of radiative transfer software used by SpectralCalc. LinePak performs detailed "line-by-line" modeling of molecular absorption and emission. Efficient and flexible, LinePakTM is at the heart of analysis systems for many major atmospheric remote sensing missions including HALOE, LIMS, SABER, CRISTA, CLAES and SOFIE. More details.
Line List--A list of parameters used in modeling molecular absorption spectra. Each molecular absorption line is described by a set of parameters including its center frequency, halfwidth, and intensity. These parameters allow the radiative transfer code (LINEPAK) to accurately model the absorption line shape at any temperature, pressure and gas concentration. See HITRAN for a more complete description of the parameters in a line list.
micron--10-6 meters. microns are a common unit for the wavelength of infrared radiation.
millibar (mbar)--a unit of pressure equal to 100 Pascals. Other common conversions are: 1 atmosphere = 1013.25 mbar, 1 lb/in2 = 68.9476 mbar
radiance--emitted power per unit surface area per solid angle per spectral interval. Common units are (W m-2 sr-1 cm-1) or (photons s-1 m-2 sr-1 m-1). Also referred to as emission.
Torr-- A unit of pressure equal to 1/760 atmosphere, or 101325/760 Pa.
transmittance--ratio of the intensity of radiation exiting a medium to the incident intensity. In general, transmittance varies with the frequency of radiation. Absorption = 1 – transmittance.
volume mixing ratio (vmr)--the fractional number of molecules of a species in a mixture. vmr = M/N where M is the number of molecules of the species in a volume and N is the total number of molecules. For trace gases, vmr is often given in parts per million or parts per billion.
wavenumber--the number of cycles of electromagnetic radiation per cm. The wavenumber, in cm-1, is equal to 10000 / (wavelength in microns).