PGOPHER

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Known Problems and Limitations

• 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 separately.)
  

Known problems

• 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 versions

• 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 has been moved to be a per Molecule, rather then a per Mixture setting. Old data files will be updated automatically on loading.
• After 6.0.224 the Correlations object is written to the .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 reading old data files. See Intensity Formulae for a description of the settings.
• After 7.0.105 the interpretation of the Strength parameter of the electronic transition moment in multidimensional Franck 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 for.
  

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 comes in two varieties,  EinsteinA and EinsteinASum (the old behavior). Detailed documentation of all the IntensityUnits settings is now provided under Intensity Formulae .
• Transitions Window now offers option to display Hönl-London factors instead of the S _pol related matrix elements currently displayed.
• "Weight" is now referred to as "Standard Deviation" or "Std Dev" throughout, including fit outputs and the line list window . 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 set.
• 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.
• BlockMatrix 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 tested.)
• 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 squares fitting.
• Calibration fits now use standard deviation of a parameter from the last cycle as increment for numerical derivatives in the next cycle.
• Toggle between arbitrary and normalized vertical scale for overlays.
• Print and export to file available by right clicking any plot.
• .pgo files and .ovr files can also be read if they are renamed to have an extension of .xml, which simplifies handling of these files.
• 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.
• Doppler double peak line shape, as in Fourier transform microwave spectroscopy.
• Add upper and lower state energy and intensity to line list input selection.
• Overlay units default to the current plot units, rather than cm^-1 .
• Read normal modes from Gaussian output files where (recommended) option freq=hpmode is used.
• 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
• IntensityUnits = PopDist or NormPopDist intensity values did not display correctly in the line list window.
• Franck-Condon factors for linear molecules with vibrational or electronic angular momentum were calculated incorrectly in some cases.
• "Square" checkbox on Transition Selection was ignored.
• Updates to import of SPCAT/SPFIT input files, mainly for symmetric tops.
• Quote "<" and ">" in attribute values, so XML produced is valid.
• (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 not recommended.
• 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 message.
• Name change of vibrational mode not propagated properly.
• Intensity fits not always converting units correctly.
• Convoluting an overlay with a line width incompletely implemented.
• 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 file.
• Fixed crash on empty mixture.
• Fixed possible crash when adding to overlay when overlays window open.
• 64 bit compilation fixes.

• Fixed problems in 6.0.111
• Changing the rank of a spherical transition moment did not take effect until saved and loaded from a .pgo file.

• New Features in 6.0.110 (Note that not all changes have been listed for this major revision)
• New vibrational structure mode.
• Effects of static external electric and/or magnetic fields can now be simulated.
• Wavefunctions can now be complex if necessary, though 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 added to 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 from HITRAN.
• 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 symmetric tops.
• 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 " setting to perturbation types to allow fixed combinations of operators to be expressed, such as that required for B_bar 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 appropriately.
  
• Initial External Molecule implementation.
• State eigenvector can now be limited to displaying the n largest contributors to any state, rather than all basis states.
  
• Fixed problems in 6.0
• kl label not always generated from the correct state for symmetric top transitions involving degenerate states.
• Intensities of transitions arising from a rotational magnetic moment in a linear molecule were a factor of 3 too large. The default units have also been switched to nuclear magnetons, μ_N , from Bohr magnetons, μ_B .
• Plots exported as SVG can now be read directly by Firefox.
• For transitions with contributions from multiple ranks (e.g. 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 by previous change.
• 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 easier.
• Bitmap overlays would not save after being compacted (needed 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 slow if no J selection.
• Add choice of methods for timing; note that no method is guaranteed to give sensible values, particularly on multiple CPU systems.
• Empty line list not always saved as empty.
• JCAMP-DX files with units of "MICROMETERS" not loaded correctly.
• Transitions with Colour = clHide now not used for contour fitting.
• Some default values written to .pgo files.
• Use "FrequencyScale" on plots adjusted so that centre point of plot does not shift in frequency.