PGOPHER

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Release Notes

• Spherical Tops
• Nuclear spin effects in symmetric tops are limited to nuclei on the symmetry axis only.
  
• Electron Spin effects in Symmetric Tops are partly implemented.
• Magnetic dipole transitions in Symmetric Tops
• Internal rotation and other large amplitude motion effects can only currently be dealt with if the effects are small, and can be accounted for by adding one or two terms to the Hamiltonian - see the discussion around the data file nd3x0one.pgo in The pure rotational spectrum of the ground state of NH₃ for an example involving the inversion doubling in ammonia.
  

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.)

Upgrading from previous versions

• 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.
• After 7.1.137 the handling of imaginary operators for asymmetric tops is improved so that a well defined phase is used for such operators. This mainly affects perturbations, and perturbations involving odd powers of J_y or S_y will have their sign changed on loading if required to give results consistent with earlier versions. The treatment of some electron spin-rotation and nuclear hyperfine terms is also affected. See AllowComplex and PhaseAdjust for options in handling imaginary operators.
• After 7.1.142 the simulation of hyperfine structure for pairs of equivalent nuclei requires different settings for the statistical weights for both linear molecules and asymmetric tops. For a single pair of equivalent nuclei (such as in I₂) the statistical weights should  be SymWt=1, AsymWt = 0, rather than both 1. This change is made automatically on loading an older version. The change is made so that multiple pairs of equivalent nuclei are now simulated correctly; the older versions were incorrect if hyperfine structure was simulated for some or all of the equivalent nuclei. For asymmetric tops with two equivalent nuclei two of the weights will be 1, and the other two 0. See Hyperfine structure in the B-X transition in I₂ and the Stark effect in (NO)₂ for examples.
• After 7.1.315 the  C and D parameters of Transition Moment objects have been removed in favour of the more general Custom Transition Moment Function for modelling  J dependence of the transition moment. Data files containing non-zero C or D values are converted to use this automatically on loading.
• After 7.1.323 the definition of the spin-spin parameters alpha and beta for Symmetric and Asymmetric tops has been changed to be consistent with the literature. Values in older files are converted on loading by multiplying alpha by sqrt(5) and beta by sqrt(6).
• After 7.1.370 the import of the l matrix from Molden or Molpro files assumes average mass for nuclei, rather than the exact mass for the most abundant isotope. In addition a different set of atomic co-ordinates is taken from Molpro xml files, as the one originally chosen did not use a consistent axis system.
• After 7.1.515 contour fitting residuals are expressed in simulation intensity units, rather than the vertical scale of the experimental spectrum.
  

New Features and Fixed problems

• New Features in 8.0.100
  
• Tweaks for Mac usage, including more (Mac) standard shortcut keys and dropping of files onto main window.
  
• Much increased flexibility in the use of HITRAN files.
• ExoMol files can be used in a variety of ways by PGOPHER.
  
• Added η and γ_S terms to the linear molecule Hamiltonian. These are required for some states with S > 1.
  
• Custom Transition Moment Function provides a more general way of modeling any J dependence of the transition moment, replacing the  C and D parameters of Transition Moment objects. Data files containing non-zero C or D values are converted to use this automatically on loading.
  
• Axis Switching effects can now be simulated.
  
• More symbolic matrix elements - selected transition moments, ...
  
• half spin Vib
  
• Open shell symmetric tops.
• Documented lambda doubling for delta and higher states.
  
• scalestddev directive in fit files to allow relative standard deviations to be set as a fraction of the observed value - mainly intended for fitting intensities.
  
• removespins directive in fit files now works for intensity fits, as well as line position fits.
  
• Linelist window has many more options - fit as branch format, save as branch format.
• A Variables object can be used to add dummy parameters for constrained fits.
  
• Constrained parameters are forced to be not floated as part of the fit setup process.
  
• Level Window now has option to use J(J+1) for the x axis, rather than just J.
  
• Rename of Molecule or Manifold will offer the option of making the required name change in the linelist window.
  
• Simplified line list format extended to be more flexible for linear molecules, and to allow fitting to levels as well as transitions.
  
• Right click on Molecule or Manifold now offers "Energy Level List" option, sorted by symmetry or energy, and "Partition Function Table" which prints out a table of partition functions for the selected node as a function of temperature. It will also display the fraction of partition function due to levels up to the level set in "Level List by energy".
• The numerical data from many files produced by Origin (.OPJ files) can now be read.
  
• Print out of Stark or Zeeman shifts now estimates linear, quadratic field shifts and fits to an intermediate two level model.
• When plotting parts of an overall spectrum, the different coloured spectra are always plotted in a consistent order.
  
• Images from many PDF files can now be read as a bitmap overlay.
  
• UsePopParams as an alternative, per manifold, way of setting the use of numerical populations.
  
• The vertical range of both overlays and simulations can now optionally be set, rather than always auto scaling. This is controlled by the AutoMin and AutoMax settings in overlays and simulations. The toolbar on the main window has been updated to provide some control over these.
  
• Consistent handling of imaginary operators for asymmetric tops.
  
• LAPACK upgraded to 3.4.2
  
• Symbolic matrix elements and convert to perturbation now implemented for symmetric tops.
  
• Initial implementation of custom population functions.
  
• Initial implementation of D₃, D₄ ... D₈ point groups for symmetric tops.
  
• Compact of a bitmap now prompts for a threshold.
• When simulating spectra in the presence of a static electric or magnetic field, the partition function is now calculated with static fields on, rather than at zero field.
• 64 bit version (using unicode internally) now part of the standard release.
  
• Fixed Problems in in 8.0.100
• When importing l matrices from Gaussian output, read both the "Input orientation" and "Standard orientation" atomic co-ordinates and use the most recent set when reading vibrations to allow files produced with the "nosymm" flag to be read.
  
• Very low temperatures (~0.01 K or less) could cause some transitions to be missed if Tspin is not the default. An error message is now printed in these circumstances.
  
• Spin forbidden transition moments in linear molecules were incorrectly giving zero intensity for q = 0 components in certain circumstances. The definition of the Strength parameter has been adjusted to fix this.
  
• Added progress indicator to constructing large vibrational bases to allow abort on large problems.
  
• The import of the l matrix from Molden or Molpro files now assumes average mass for nuclei, rather than the exact mass for the most abundant isotope. In addition a different set of atomic co-ordinates is taken from Molpro xml files, as the one originally chosen did not use a consistent axis system. For all l matrix imports an orthogonality check is done and a message displayed if the result is too large.
  
• Default vMax for a Vibrational Mode is now zero, unless there are 3 or less modes, in which case it is 3. This prevents triggering a very large calculation by accident; the default was 5 for all modes.
  
• Line list output - column headed S is actually S_pol - change header appropriately.
  
• Linear Perturbations with Scomp <> 0 were not displayed correctly in the object treeview.
  
• Contour fits now permit undefined values for the observed intensity.
  
• Fix crash of following use of recently opened files on Mac by replacing TdfsMRUFileList component with simplified equivalent.
  
• Switching units scales Displacement in VibrationModeChange does not change spectrum. (Effective units are 1/Sqrt(Energy)).
  
• Move Up/Move Down of plots in overlays window was ignored until overlay file saved and reloaded.
  
• Level Window gave corrupt plots if a very small vertical range was selected.
  
• Transitions Window was not showing matrices for selected transitions in the vibration only mode.
  
• Selected transitions omitted for the unusual point groups C_3h...C_6h (involving states with E symmetry) and S₄...S₁₂ (for non totally symmetric states) point groups.
  
• Force use of "." for decimal point, even if changed for system while program running. (This is required so that data files are not language dependent.)
  
• Fix blank edit boxes on main window toolbar if system font set to large on Windows.
  
• Matrix printout in log window for high print levels could crash.
  
• Equivalent nuclei case handled incorrectly in presence of static field.
  
• Degeneracies printed incorrectly in level lists in presence of static electric or magnetic field.
• Einstein A coefficient printed incorrectly in line lists if the plot units were different to the calculation units.
  
• Covert units button on constants form failed when AsNext set for equivalent nuclei.
• Statistical weights calculated incorrectly for the case of more than one pair of equivalent nuclei when hyperfine structure was included.
  
• Hyperfine structure with more than one set of equivalent nuclei, or different nuclei using an equivalent coupling scheme like I₁₂ = I₁ + I₂; F₂ = J + I₁₂; I₃₄ = I₃ + I₄; F = F₂ + I₃₄ was not calculated correctly.
  
• Potentially complex fine and hyperfine terms in asymmetric tops were not necessarily handled correctly. This affects "off-diagonal" terms such as eabbar, Tab and CHIab. This is fixed by the introduction of consistent handling of imaginary operators for asymmetric tops.
• Fixes for symbolic matrix elements for asymmetric tops (Origin and BBar).
  
• State dependent widths (wK, wJ) for symmetric tops were ignored.
  
• "Another" button on level plot was broken.
  
• Energy level fit to lower level failed if no default manifold.
  

• 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^-1 units 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 correlation directive.
• 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 accidentally mixed if the eigenvalues happen to be very close. Defaults to on.
• Initial implementation of C_4h , C_5h , C_6h , S₄ , S₆ , S₈ , S₁₀ , S₁₂ . (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.