Known Problems and Limitations
Please check the website, http://pgopher.chm.bris.ac.uk/
and the beta version page http://pgopher.chm.bris.ac.uk/~ctcmw/pgopher
The following are not implemented in the current version of PGOPHER, but may be in a future version:
- Spherical Tops
- Nuclear spin effects in symmetric tops are limited to nuclei on
the symmetry axis only.
- Electron Spin effects in Symmetric Tops.
- Magnetic dipole transitions in Symmetric Tops
- Internal rotation effects
- Vibrational dependence of rotational constants. (The current
design requires the constants for each vibronic state to be entered
- The Help menu only works on Microsoft Windows (but the
documentation can be read using any web browser).
- The Linux and Mac versions are less polished than the windows
version. Any problems are, however, likely to affect the user interface
only, rather than the calculations. (A comprehensive test suite for the
calculations passes on all systems.)
- External molecules can be created, but are not yet useful as
loading is not implemented.
Upgrading from previous
Newer versions of PGOPHER
can always read files from older versions, though design changes
may mean some changes must be made on loading, as noted below. Older
versions can normally read files from newer versions, though use of new
feature can trigger a warning about unread items. If an error prevents
the file from loading at all in an older version, an ordinary text
editor can be used to remove the problem item if use of an older
version is essential.
- After 6.0.188 the ContourFile setting has been moved to the
Overlays object. This
setting change cannot be made automatically, as it will be in a
different file, but a notification is displayed.
- After 6.0.199 the JAdjustSym setting
be a per Molecule, rather then a per Mixture setting.
files will be updated automatically on
- After 6.0.224 the Correlations object
.pgo file if ShowEstUnc is set,
which will cause an error in previous
versions. Turn off ShowEstUnc if
compatibility is required with previous versions.
- After 6.0.228 IntensityUnits = EinsteinASum is required to
achieve the old IntensityUnits = EinsteinA behavior, with EinsteinA now giving a
radiative rate. EinsteinA
is converted to EinsteinASum on
Formulae for a description of the settings.
- After 7.0.105 the interpretation of
the Strength parameter of
the electronic transition moment in multidimensional
Condon factors in the vibration only calculation mode
changed to be consistent with transition dipoles used for rotational
structure calculations. Values from older files are multiplied by
Sqrt(3) on loading. Note also that linear molecule Franck-Condon factor
calculations for states with non zero vibronic angular momentum had
incorrect intensities, as the degeneracies were not properly accounted
New Features and Fixed problems
- New Features in 7.1.108
- The Level Window now does not
update the plot automatically
if AutoReplot is off for the Mixture; a plot button has been added to
update the plot in these circumstances.
- Compiler used for Windows version updated to Delphi 2007.
- The IncludeSPFIT
directive can now handle the case where unused quantum
numbers are zero, rather than blank.
- Fixed Problems in 7.1.108
- In the vibrational only mode, linear molecule Franck-Condon
factor calculations for states with non
zero vibronic angular momentum had incorrect intensities, as the
degeneracies were not properly accounted for. In fixing this, the
interpretation of the Strength
parameter of the electronic transition moment in multidimensional Franck Condon factors
was changed to be consistent with transition dipoles used for
rotational structure calculations.
- Bitmap overlays display code
tweaked to avoid crashes at large magnifications.
- BlockMatrix = true caused crash for
some combinations of
molecule type and LimitSearch.
- StdDev column output for least squares fit will use
scientific format if appropriate. (Zero could be displayed for combined
microwave/visible fits if cm-1units were used.)
- Operation menu items for TElectronicState
should only show if nNuclei > 0.
- "Set Zero from Visible" menu item should only be visible when
there is an overlay.
- New Features in 7.0.101
- Interactive adjustment of
parameters with the mouse.
- Simplified line list format for fitting introduced as an
alternative to the standard format, designed particularly for use with
line lists from external sources.
- IntensityUnits = EinsteinA now
behavior). Detailed documentation of all the IntensityUnits settings
is now provided under Intensity
- Transitions Window now
offers option to display Hönl-London factors instead
of the S pol related
- "Weight" is now referred to as "Standard Deviation" or "Std
Dev" throughout, including fit outputs and the line
. This makes clearer that theweights required are the
(relative) standard deviations, rather than their reciprocal which
might be implied by the name.
- Estimated uncertainties in calculated line positions are now
calculated in line listings, and displayed in the line list window if ShowEstUnc is set at
the top level. To implement this,
standard deviations of parameters, and the correlations between them,
are now displayed in the constants window (note the Correlations object) and are now saved
in .pgo files if ShowEstUnc is
- Correlations between observations can now be set in line
lists for least squares fitting using the correlationdirective.
- Default for SVDThresh changed to
1e-15, and least squares fit adjusted to provide
more information when combinations of parameters are not changed.
- Binary format for line list
output, controlled by additional PrintLevel settings.
setting, to check Hamiltonian matrix for
factorization into blocks before diagonalisation. If blocks are found,
these are diagonalized separately, ensuring states that have no
connecting matrix elements are not accidentallymixed if the eigenvalues
happen to be very close. Defaults to on.
- Initial implementation of C 4h
, C 5h , C 6h , S 4 , S 6 , S 8 , S 10 , S 12 . (Not fully
- Initial hyperfine implementation for symmetric tops -
currently on-axis quadrupole and nuclear spin-rotation only.
- Compress of experimental
overlays can now specify new x axis interval instead of number of
points to average.
- Use LAPACK singular value decomposition routine in least
- Calibration fits now use standard deviation of a parameter
from the last cycle as increment for numerical derivatives in the next
- Toggle between arbitrary and normalized vertical scale for
- Print and export to file available by right clicking any
- .pgo files and .ovr files can also be read if they are
renamed to have an extension of .xml, which simplifies handling of
- Fits to combination differences.
- Prompt on import item on Overlays menu to force prompting for
layout of data on import.
- Adjust automatic naming of plots within overlays.
double peak line shape, as in Fourier transform
- Add upper and lower state energy and intensity to line list
- Overlay units default to the current plot units, rather than
- Read normal modes from Gaussian output files where
(recommended) option freq=hpmode
- NoLineList setting in Mixture to
allow larger calculations.
- Tspin parameter in simulations
to allow for non-equilibrated
nuclear spin states.
- Parameter context menu in constants window has entry to show
full parameter name for setting constraints.
- Fixed problems in 7.0.101
or NormPopDist intensity
values did not display correctly in the line
- Franck-Condon factors for linear molecules with vibrational
or electronic angular momentum were calculated incorrectly in some
- "Square" checkbox on Transition Selection was ignored.
- Updates to import of SPCAT/SPFIT input files, mainly for
- Quote "<" and ">" in attribute values, so XML produced
- (Global)MoveUp/MoveDown for vibrational not working reliably.
- State/Manifold not displayed for vibrational wavefunctions.
- Vibrational mode names beginning with numbers produced
unreadable .pgo files.
- Fit can fail if more than one species present
- Join of experimental plots was discarding offset and scale.
- Export of plot as text file could loose traces.
- Wrong symbolic matrix element for spin-spin constant in
vibrational structure mode.
- Allow all symmetry names in custom populations.
- Etalon actual positions set wrongly if actual position
specified for one or both starting peaks.
- Molecule names can now have spaces in them, though this is
- Log window could be invisible if main window fills screen.
- Detection of line list in imported text files broken.
- Discard lines with negative width, and display warning
- Name change of vibrational mode not propagated properly.
- Intensity fits not always converting units correctly.
- Convoluting an overlay with a line width incompletely
- Import of JPL .cat files as overlay was broken.
- Eigenvalue selection problems in transition selection window.
- QuantumNumberFormat J+1/2 directive not recognized in input
- Fixed crash on empty mixture.
- Fixed possible crash when adding to overlay when overlays
- 64 bit compilation fixes.
- Fixed problems in 6.0.111
Log of older changes
- New Features in 6.0.110 (Note that not all changes have been
listed for this major revision)
- Wavefunctions can now be complex if
this is disabled by default.
- State dependent widths implemented for symmetric tops.
- Variable character size on printer, clipboard and exported
plots can now be disabled.
- Convolute option
experimental plots to allow them to be
convoluted with the simulation linewidth(s).
- "Add all levels" to prepare custom populations can now be
applied to a state as well as a manifold.
- Add InterpolatedPartitionFunction
objects to allow partition functions to be generated from
external tables as afunction of temperature, such as those available
- Partial implementation of C 3h symmetry.
- Add (partial) import of OceanOptics .ProcSpec files.
- Symmetry directive in
observations file to select symmetry to use on
BranchFormat input for cases such as symmetric tops where two
otherwiseidentical transitionsare found.
- Add centrifugal distortion of qplus term for symmetric tops.
- Implement 'auto' component for transition moments in
- Add symmetric top to the choice available in File, New.
- Pick destination form switched to using radio buttons to
select destination channels and add "None" button.
- Spin terms added as perturbation types for asymmetric tops,
allowing higher centrifugal distortion terms in spin-rotation coupling
to be added.
- Add "ScalePrev "
perturbation types to allow fixed
combinations of operators to be expressed, such as that required for Bbar
in asymmetric tops.
- "Split ", "As Linelist" , "Hide Out of
Range" operations added to overlay menu on plot.
- "Copy Branch Table"
added to "More" menuon
line list form
- "Spline" option
and dialog box in calibration form.
- Log output control ("PrintLevel"
) added to log window
- Detailed printout of parameters and matrix elements to log if PrintLevel set
- Initial External Molecule implementation.
- State eigenvector can now be limited to displaying the n largest contributors to any
state, rather than all
- Fixed problems in 6.0
- kl label not
generated from the correct state for
symmetric top transitions involving degenerate states.
- Intensities of transitions arising from a rotational
moment in a linear molecule were a factor of 3 too large. The default
units have also been switched to nuclear magnetons, μN ,
from Bohr magnetons, μB .
- Plots exported as SVG can now be read directly by Firefox.
- For transitions with contributions from multiple ranks
rank 0 and rank 2 together) some low J transitions could be excluded
- Jmax for upper manifold was being taken from lower manifold
- Multiphoton transitions in symmetric tops had been broken
- HITRAN line list input can now cope with states with
vibrational angular momentum.
- Accept .5 as well as 0.5 for quantum number input.
- Allow "$$" at start of line for comment in .jdx files.
- Allow "," at end of free format numbers in .jdx files.
- Adding new transition moment for symmetric top molecules
failed in tree view.
- Adjust branch format (such as pQ(10)) to make use on input
- Bitmap overlays would not save after being compacted
fix to pngimage library).
- Edit, Copy Picture and File, Export, Plot menu items split
into separate items for Fortrat and main plot window. Also fix right
click on plots to copy correct plot.
- Etalon peak finding mode works with partially calibrated
plot; speed up.
- ComboBox form settings were not restored correctly from a
.pgo file if previous value was not the default.
- Speed up selecting states by index number; this was very
if no J selection.
- Add choice of methods for timing; note that no method is
guaranteed to give sensible values, particularly on multiple CPU
- Empty line list not always saved as empty.
- JCAMP-DX files with units of "MICROMETERS" not loaded
- Transitions with Colour = clHide now not used for contour
- Some default values written to .pgo files.
- Use "FrequencyScale"
not shift in frequency.