VPFIT: SETUP FILE
12 April 2005

The file associated with the environment variable VPFSETUP can contain a selection from this list (which is almost certainly incomplete):

lastchtied v           w,x,y,z are special flags for b and logN       [default is z]
bvalmax 50000.0        Maximum b value                                [5000 5000]
bvalmin 0.10 5.0       Minimum b-value (should be << that expected)   [0.05 0.05]
bltdrop 0.101          drop system if b value less than this AND ..   [0.05]
clogltdrop 14.3        if log column density less than this.          [14.0]
bgtdrop 50001.         Drop any system with b .gt. this (> bvalmax, so none). [4999]
cvalmax 25.0           Maximum allowed column density                 [30]
fcollallzn 4.162e22    Minimum Fik*col for inclusion everywhere.      [4.162E18]
cvaldrop 8.0           column density below which a system is dropped [8.0]
llscollim 15.0         Include Lyman limit absorption for log HI above this value.        [15.0]    
llsbmult 3.0           Interpolation parameter highest order Lyman line and Lyman limit.  [3.0]  
! housekeeping
date                   datestamp the '26' summary output
dots 1000              Suppress the dots on screen print.             [30]
gcursor                Use cursor input for guesses (is the default anyway)
keyboard               Use keyboard input for initial interactive guesses (and not the cursor).
sigscalemult 1.00      global sigma scale factor (-> chi^2/sigsc**2)
! auto line finder parameters
abmins  3              minimum smoothing (in channels) for line finder
abmnhb  25.0           min Doppler parameter for weak HI
abbsep  20.0           minimum Doppler parameter for which a line may be split
absigl  5.0            significance level for a line detection
absigp  4.5            significance level for peak in component relative to zero level
absigx  5.0            significance level for component separation
guessl HI 1215         if no lines in list, assume lines found are (ion, wavelength) [HI 1215.67]
xlist HI 0.0 CIV -3.0  if either CIV or HI added, add the other with logN(CIV)-logN(HI)=-3.0 [none]
nofix                  remove orphan fix flags left over if reference line is removed [leave them]
! line splitting in add line mode
adsplit 2.5            split line if upward deviation > adsplit*downward  [1.75]
maxadrem 25            give up after maxadrem add/remove line cycles [25]
adcontf 2.2 10 5.0 12.5  add continuum adjustment when norm chi^2 < 2.2   [1.8 10 5.0 12.5]
! output
nopchan                control running output: 0:minimal; 1:screen; 2: screen+file [2]
wr13s f13.w            end summary root filename (fort.13 format). [if absent, omitted]
wr26s f26.w            fort.26 summary root filename. [If absent, goes to fort.26]
wr25                   Write final Hessian matrix to fort.25
wrcitn                 Write (and update) current iteration to junk.dat, and remove at successful completion
! miscellaneous
enotify                execute vpgti.done (if it exists) when finished [do nothing]
pcvals                 prompt for controls (il, stepsize etc) [no such prompting]
interactive            prompts rather than ends if it hits a problem [terminates]
verbose                print out lots of obscure variables

Defaults are shown in square brackets, or are the values shown. The ones with descriptions in dark red are generally used for tests and program diagnostics,  and should not usually be needed. Those shown in light grey are recent additions [in version 8, which is still being tested and is not yet available]

Comment lines are those which start with ! followed by a space .. the rest of the line is then ignored.

There are a few debug options, of the form debug #, which are not listed here. They control test printout, and the actual implementation depends on what is being tested at the time.



For those where the comments above are a bit obscure:

bvalmin and bvalmax may have two parameters associated with them. Where two are given the first applies to all lines except those of hydrogen, and the second to hydrogen only. Where the second is omitted the first is used for hydrogen as well, i.e. the same value is adopted for all atomic species.

lastchtied v - last character for used as tied or fixed parameters rather than some supposed enhancement. Later letters applied to column densities give total properties for a complex, and if used for Doppler parameters an attempt is made to decompose the velocities into temperatures and turbulent components using the atomic masses.

enotify execute ./vpgti.done when finished (which might contain 'mail -s vpfit <your ID> < message' if you want mail notification). May be useful if you are running it as background.

dots 10 Minimum number of systems for which dots printed to reassure you that the program is actually doing something. This can be comforting if you are running a large set on a slow machine, but has no further use. To suppress the dots use 'dots 1000' or any other ridiculously large number.

llscollim 15.0 Include Lyman limit absorption in regions where appropriate if log HI column density exceeds value.

llsbmult 3.0 Used for interpolation of transmitted flux between highest order Lyman line and Lyman limit. It actually interpolates from limit to (minimum Lyman line wavelength in table)*(1.0+llsbmult*bvalue/c).

sigscalemult 1.0 Multiply (data-fit) by this number to account for data smoothing e.g. from rebinning. So the chi**2 values are multiplied by no.**2. This single scalefactor is applied to the whole spectrum, and its use is not recommended. If you are going to do this you should set up a wavelength dependent scale factors file.

wr13sum f13.w Write restart values at end to f13.wnnnn, where nnnn is the integer part of the central wavelength of the first region in the list of fitting regions.

wr26sum f26.w m  If m=0, or is absent, write the summary of results to f26.wnnnn instead of fort.26, where nnnn is the central wavelength of the first region in the list of fitting regions. If m=1, then the form of the file is f26.wnnnn.n, and m=2 or more uses the central wavelength to two decimal places.

adsplit #1     Parameter for auto line fitting  It is the significance ratio an emission peak has to have over the biggest residual absorption before an attempt is made to split a line. This bias is built in for speed -- guesses for line splitting are less easy to get right, so it takes longer to iterate when lines are split, and often adding needed components to shoulders of lines drives the result the same way.

adcontf #1 #2 #3 #4   Used in auto continuum fitting

 
 

To determine sigscalemult is appropriate for your data, display the data with IRAF splot, choose a flat lineless bit of spectrum, and mark the limits of this using 'm' (at left) and 'm' (at right) in the IRAF splot cursor. It then tells you the mean, rms, S/N. Note down the rms, then overplot ('o') the sigma array and 'm' out the same region. the mean of the sigma array divided by the rms of the data is the number which should be entered. Alternatively, plot the data in cursor mode in RDGEN, and then use 'm' and 'm' and the command window will give the wavelength and sigscalemult as the first two listed values.