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The Maxima source code can be compiled on many systems, includingWindows, Linux, and MacOS X. The source code for all systems andprecompiled binaries for Windows and Linux are available atthe SourceForge file manager.
The Maxima branch of Macsyma was maintainedby WilliamSchelter from 1982 until he passed away in 2001. In 1998 heobtained permission to release the sourcecode under the GNU General Public License (GPL). It was hisefforts and skill which have made the survival of Maxima possible, andwe are very grateful to him for volunteering his time and expertknowledge to keep the original DOE Macsyma code alive and well. Sincehis death, a group of users and developers has formed to bring Maximato a wider audience.
Maxima is updated very frequently, to fix bugs and improve the codeand the documentation. We welcome suggestions and contributions fromthe community of Maxima users. Most discussion is conducted onthe Maxima mailing list.
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The size an intermediate file is dictated by constants in the Squirrel code, and the maximum size of an intermediate file and the creation of new intermediate files (when the last file gets too big) are all handled internally within the Squirrel infrastructure. The user should never have to worry about modifying the code or worry about any maintenance of file size. Intermediate files should generally be no bigger than ~ 370 MB. This maximum limit is to allow easier transfer of intermediate files between computers. The items that take the most space are the raw spectra (for both the DAQ and the intermediate files). The _m DAQ files have the MSOpen and the MSClosed data sets. The intermediate files have these raw spectra data sets: MSOpen_p, MSClosed_p, MSDiff_p, and the baseline subtracted versions: MSOpenLessBaseL_p, MSClosedLessBaseL_p, MSDiffnLessBaseL_p. A good rule of thumb is that the sum total of the intermediate files when doing pika should be about 3 x size of the DAQ files.
The custom wave has to be a start-stop type of wave. The code needs to know the beginning and ending points of each new time period so it knows how to do a weighted average of the time intervals of the AMS data. The code assumes that the time wave you selected has consecutive times indicating the beginning and ending points. So the AMS time series wave that is created will be 1 points less than the custom wave. So if your custom time wave has data points:12:00:00, 12:05:00, 12:10:00, etc. the code would look for any AMS run that has data between 12:00 and 12:4:59, etc. If it does have data within that time interval it would generate a weighted average for that time point. So if your AMS Org data is (recall AMS time is the END of the measurement)12:00:00 1012:02:00 2012:04:00 3012:06:00 40it would do an average like this(2*20 + 2*30 + 1*40)/5 = 28 for the first data point (between 12:00 and 12:05:00).
Yes, squirrel was designed to allow experiments to grow, as would be the case where one is acquiring ambient data for several days. At the Get Index step the folder and all subsequent folders are searched for DAQ hdfs; the search is recursive. If one adds new/more DAQ hdfs to the selected folder and subsequently presses the Get index button, the code will find these new files. When one is copying newly acquired DAQ hdf files from the AMS's computer, one should not copy the very last hdf. This is because (1) the DAQ may need access to that file to write more data and one doesn't want to possibly supersede DAQ commands and (2) Squirrel may get confused about runs in the file if more runs or more data from a run is added.
When one retrieves a raw spectra (or an average from a todo wave via the MS tab, Average Mass Spectrum Raw vs iTOF or raw vs m/z, a correction is applied to conserve area under the curves. This correction is the first derivative, dt/dmz, and this does have a power term so it behaves very similarly to the duty cycle correction. Within the code this term is defined as dtdmz_tmp=mzpower[p1]*(mzslope[p1]^(1/mzpower[p1]))*((p-mzint[p1])^(1-(1/mzpower[p1]))) where p1 is the row number of the run in question. (You can search for this line in the code yourself if you like.) The reason for this term is to allow users to do integrations 'properly' on the raw spectra and to allow for a more intuitive unit of Hz/samplingtime. When squirrel recalculates sticks it does not use the results of the average raw spectra as generated from the MS tab; the order of operations in which the m/z duty cycle is accounted for is different.
The table under the autoset checkbox serves as either an output, in the case where the Auto-set checkbox is checked, or an input, in the case where the Auto-set checkbox is not checked. If you wish to use values not automatically calculated, you need to manually enter values in the table, you need to have the Auto-set checkbox unchecked, and then press the Do Corrections button. The pressing of the Do Corrections button trigger the code to accept and incorporate the values in the table (they become inputs).
This correction is necessary because we know that the MCP degrades over time. We attempt to quantify this degradation by the assumption that the amount of N2 present in all samples is constant. The idea is to select a period (AB reference period) of ambient measurement close to a calibration where all values are known. The idea is then to use the ratio of the /z 28 signal of the reference period to all other periods as our correction factor. After the ratio has been calculated, we presume all fluctuations in N2, regardless of their origin, have been quantified. So to correctly apply this factor, one should hold the ionization efficiency value to be constant. Thus the AB correction code creates the wave root:diagnostics:ioneff and inserts a constant value (the ion eff during the reference period) for ALL runs. This ioneff wave (not ioneff_,logged) is subsequently used in all conversions to ug/m3, regardless of whether the 'Use MS AB correction' checkbox is checked. So to be consistent, one should always use the AB correction once it has been found.
This is an additive offset to the flowrate called airbeam_ref_flowOffset_sv in the code. In theory when the flow rate would extrapolate to zero when the airbeam values are zero, but often times it is not. If you plot flow rate vs airbeam you would get a slope and the intercept (Y axis is flow rate) would be this flowrate offset.
Use the button in the MS tab labelled 'Calc UMR 2d matrix (not plotted, no RIE)'.It is important to know that the RIE and CE are *NOT* applied to the Org and Org error matrix if you choose unit so ug/m3. The general convention is that whenever Squirrel or Pika outputs anything with an m/z dimension the units are NO3-equivalent. The thinking behind this convention is that whenever we have an m/z dimension, such as with an average mass spectra, we want to be able to sum the unit resolution sticks to get back to the unspeciated signal an any nominal mass. The code will also generate a minimum error time series wave typically needed for input into PMF.
We also don't filter for a minimum number of runs per hour bin. You could have 100 measurements in the 7-8am bin and 2 measurements in the 8-9am bin and the code wouldn't necessarily alert you to the lopsided number of points in each bin. The number of points in each bin can be found in the wave root:panel:diurnals:DiurnalCounter
One declares open or closed m/z parameters in the mz calibration panel. Select to fit the open (or closed) spectra in step 1, fit in step 3 and declare in step 6. In Pika Step 4 and 5 one can elect to use these separate parameters or not via checkbox checkbox 4iii. When not checked, the code will use the last calculated m/z calibration values. To determine if separate open/closed mz cal parameters are needed one should examine isolated ions in the Pika graph window and see a characteristic sharp up-down or down-up pattern in the raw spectra (black dots) across several mzs, when checkbox 4iii is unchecked.
ePToF data, or 'efficient' or 'encoded' PToF data, is acquired with a chopper that has multiple slits in the wheel, corresponding to approximately half open, half closed. ePToF acquisition has been available since approximately 2013. Previous AMS Users Meetings have included talks describing it's acquisition and sample data, including 2013: John Jayne, 2015:Pedro Campuzano-Jost, Leah Williams, and Peter DeCarlo, 2016: Joel Kimmel, Leah Williams.
PAHs are poly aromatic hydrocarbons, a subset of the organic species in squirrel. For most ambient measurements these values are too low to be interesting. However, for very polluted regions there may be interest in quantifying PAHs. In squirrel there are two frag waves that deal with PAHs: frag_PAH and frag_OrgLessPAH. These frag waves were generated from work done by Dzepina et al, International Journal of Mass Spectrometry, 263(2-3), 152-170, 2007. Beginning at m/z 198, estimates of PAH are indicated in frag_PAH and subtracted in frag_OrgLessPAH. If users are interested in examining the PAH organic component, then one must manually enter and execute this one lines of code:
If the user chooses to correct for relative humidity, it is imperative that the RH values reflect the at the AMS sampling inlet AFTER the dryer and at the temperature of the aerodynamic lens, *not the ambient relative humidity outside* or some other value. The code will not execute if the user requests to use a relative humidity wave that has nans in it. It is left to the user to interpolate the relative humidity wave as appropriate; recall that any relative humidity value less than 80 (or the user defined inflection point) will have not effect on the CDCE. 2b1af7f3a8