PGOPHER is also available in a command line version, pgo[.exe] without the graphical user interface but with otherwise identical code. This is most useful when the output is to be used with other programs. Typical usage is:
which will output a linelist as a text file using the parameters in the .pgo file. Common alternatives include:
pgo Mixture.PrintLevel=CSV file.pgo >file.csv
pgo Mixture.PrintLevel=Binary Mixture.OThreshold=0 file.pgo >file.bin
Here Mixture.OThreshold=0 is being used to set a value in the Mixture object, in this case the cut off in line intensity; setting it to 0 ensures all lines are output. Any other parameter in any object can be set in this way; right click on the parameter in the constants view to show the name.Some of the intermediate objects can be omitted if their is no ambiguity; for example in the linear molecule example Mixture.Species.LinearMolecule.Excited.v=1.B can be abbreviated to Mixture.v=1.B.
To fit use:
pgo --fit file.pgo line.lin
The second file contains the observations. Alternative options
||Normal line list fit
||Observations are intensity,
not line positions
||Fit to lower state energies
||Fit to upper state energies
||Contour fit; second file
should normally be an overlay file in this case.
||Fit to lower state common
||Fit to upper state common differences|
To produce a plot use:
pgo --plot file.pgo plot.txt
This produces a simple text file with the plot
data as lists of x,y values; other available formats are .svg and
.xfig. Use --eplot
to generate a plot as a function of electric or magnetic field.
Other command line options are shown below.
||Use n threads when calculating.
||When fitting, write out a new .pgo file with the new parameters on
top of the old one.
|--newpgo||When fitting write out a new .pgo file with the new parameters to a
file with name file1.pgo.
(The number is chosen so as not to overwrite any existing
||Show time and memory usage at
end of run
||Show selected processing
times at end of run.
||Divert output to given file, rather than
The full graphical user interface version will
load all the files given on the command line, and will also
respond to most of the commands given above.
Hamiltonian matrices (as shown by the State
Details Window) can be exported in numerical format using
For example, using the data file described in How PGOPHER works:
pgo --H(X,4.5,f) OHAX00eg.pgo
as shown on that page.H(OHAX00eg.pgo.Species.LinearMolecule.X,4.5,-) X v=0 4.5 - 1.5 X v=0 4.5 - 0.5
X v=0 4.5 - 1.5 375.595 -90.3971942125418
X v=0 4.5 - 0.5 -90.3971942125418 552.297
Transition matrices (as shown by the Transition Selection and Details
Window) can be exported using the option:
For example, using the same data file as before:
yields the matrix shown on in How PGOPHER works:--T(X,4.5,f,A,4.5,e)
Note that these matrices are in the original basis, i.e. not transformed using the eigenvectors from the diagonalisation of the Hamiltonian.T(OHAX00eg.pgo.Species.LinearMolecule.X,4.5,-),OHAX00eg.pgo.Species.LinearMolecule.A,4.5,+)) A v=0 4.5 + 0.5
X v=0 4.5 - 1.5 1.27128345232746
X v=0 4.5 - 0.5 1.2974982402692
pgo nd3_b0x0.pgo "Mixture.<X|mu|B>.<0+|T(2,1)|0>.Strength:=0"To include a double quote in a parameter, precede it by \ :
pgo nd3_b0x0.pgo "Mixture.ND3.wt(A1',A1\"):=5"What requires quoting depends slightly on the platform; on Windows only " is used for quoting; on other platforms the standard UNIX quoting rules are used.