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 are partly implemented
  
• 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 Mac version is 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

• In version 10.0.21 the method of calculation for two photon (and higher rank) transitions in the presence of external fields was changed, and earlier versions will have given wrong results for perpendicular polarization. See Polarization objects for more information.
• In version 10.0 an adjustment has been made to the phase of some transition moments; see the discussion at the end of Transition Moments and Line Strengths for more details. For the most correct calculations FixTransitionPhase should be set to true, and this is likely to become the default. In practice this will not affect most calculations, but may change calculations involving multiple interfering transition moments, particularly if they are of different types.
• In version 10.0.502 the default order of J and F within a given basis set changed from decreasing to increasing. This can provide better quantum number assignments under some circumstances, though in most cases will have no effect. To force compatibility by reverting to the older order set OldHyperfineOrder to True.
• In versions after 10.1.108, inverting an Experimental Plot simply multiplies it by -1. Previous versions used the transformation I_inverted =  I_max + I_min - I.
• The Lorentzian and Gaussian variable names in a LineShape object changed in 10.1.145 to avoid confusion with the function names. Old files will normally be converted automatically.
• The hyperfine parameter, dJ was implemented fully in 10.1.151, and the results from the initial implementation in earlier versions will only be approximately consistent.
• For versions before 10.1.160, if specifying populations of individual levels (see Non-Boltzmann Populations) in the presence of a field, reading back saved populations from a .pgo file could fail for linear molecules. This is now fixed, but the format has changed slightly. Old files will normally be read correctly, but the new files can't be read by older versions.
• Plots in version 10.1 now always plot the same quantity for intensity by default, regardless of the frequency or wavelength scale chosen. This removes some confusion when comparing or fitting to experimental spectra, though the implied peak area then depends on the plot units chosen. Setting PreserveArea true restores the old behaviour, and this may need to be done when loading older files to match earlier simulations. See the documentation on this parameter for more details.
  

New Features and Fixed problems

• Fixed Problems in 10.1.183 (Change to source only)
• PgopherU.manifest missing from source zip file.

• Fixed Problems in 10.1.182
• Fix for crash following creation of a Variables object in the Overlays Window.
• Fix for Unicode enabled windows versions only to handle display scaling.

• New Features in 10.1.180
• Significant updates to the automatic fitting process, particularly the introduction of the Nearest Lines Window. Two detailed walk-throughs, Automatic Fitting of the nu5 band of cis 1,2-Dichloroethene and  N2O IR spectrum with additional diagnostic tools show how to use this. In addition the user interface to the automatic fitting algorithm has changed slightly, with the fit and check lines indicated on the spectrum and the new MinCheck setting; see Automatic fitting of an N2O IR spectrum for the updated process.
  
• Weighted Contour Fitting is now possible; weights can be taken from an extra channel on import, or calculated from the intensity and/or frequency - see Calculated Intensity Weight.
  
• More options for exporting plots to files (and via clipboard) described in Exporting Plots, including:
• PowerPoint (.pptx) format
• Windows metafiles (WMF) or enhanced metafiles (EMF files).
• Right clicking on a line in a simulated spectrum now does not add a line to the Line List Window if it is already present, but simply highlights the first line if no lines are added. To always add lines, turn off "Discard Duplicates" in the Line Selection Options Window or use Shift+Right Click. The options window also allows the sort order on adding lines to be chosen.
  
• Assignment of lines underneath the mouse cursor is now shown in the status bar of the main window.
  
• A series of features has been added to assist in handling larger problems, particularly where many states are involved. See Combined and Multi-State Fits and Constructing Large (Multi-State) Files for an overview; new features include:
• Constants Plot Window
• File, Export, Constants To...
• Detail/Linelist output now has much less repetitive output of matrix elements.
• Export as Matrix...
• Include statements in line list files can now include .pgo files
• Make Lower/Make Higher in constants window.
• "Edit observation" in a residuals window can now open .pgo files in a second copy of PGOPHER, as well as text files.
  
• Line intensity measurements can now be made at the same time as line position measurements, and they can be used as a check on peak assignments, or in their own right for determining temperature. See automatic fitting of the N₂O IR spectrum for a walk-through of the new features, which include:
• Intensity can be set and fitted in the line list window at the same time as a peak position.
• Line lists in general can can contain both frequency and intensity; the ValuesPresent directive indicates what is present.
  
• Intensity residuals window, including a Boltzmann plot. The main residuals window has also been enhanced, with a greater selection of plot options.
  
• Fractional Intensity fits, where the default estimated error is taken as a fraction of the value
  
• MergeBlends mode for fitting blended lines as a single observation.
  
• Additional linear molecule parameters - TSpinParity (parity dependent anisotropic g factor), the nuclear hyperfine interactions dJ and cIp and higher orders for the centrifugal distortion of A, A_H, A_L, A_M.
  
• Several enhancements to the way fluorescence spectra are calculated, overcoming previous limitations and giving more flexible output. This includes the Fluorescence simulation setting, the AbsoluteE molecule setting and the WperMolecule intensity units. See Emission Spectra for how these are used.
• Text Size option on the view menu - particularly helpful if demonstrating the program on a computer projector.
  
• Enhancements for Fortrat plots, including showing assignment on mouse hover.
  
• The restriction of only having a single TransitionMoments object for any given pair of manifolds has been relaxed. This allows colour coding according to individual transition types, such as a and b type transitions in asymmetric tops, as colours can be associated with TransitionMoments objects, but not individual transition moments. Note that separating transition moments in this way will ignore interference between the separated transition moment objects, which can lead to significant errors. However for the common use case of straightforward asymmetric top spectra no error is introduced.
• FrequencyOffset and FrequencyScale directives can take a variable name, rather than a constant value, and the variable can be used in fitting.
• Select in line lists can be on a wider range of quantum numbers.
• SingleSubBasis setting to adjust the algorithm used to assign K_a and K_c quantum numbers.
• LAPACK upgraded to 3.8.0
• Fixed Problems in 10.1.180
• The algorithm used to determine colours for transitions was inconsistent with the documentation in Determining Colours and J ranges. The results now agree with the  documentation, though the older behaviour can be invoked with the OldColourOrder setting.
  
• If EigenSearch was False, then under certain circumstances (typically simulating after a fit) spurious eigenvectors could be used for subsequent calculations, which manifested itself as incorrect intensities.
  
• MinI of zero in Fortrat plots was plotting no transitions (rather than all).
  
• Calibrating spectra was broken from version 9.
  
• Loading .pgo files from older versions will set the eigenvalue number columns (labelled #) in the line list window to a negative number if they were saved as blank.
• Table updates via the GUI required a Clear Cache (or save/load) to take effect.
• If specifying populations of individual levels (see Non-Boltzmann Populations) in the presence of a field, reading back saved populations from a .pgo file could fail for linear molecules.
• Some energy level plots against hyperfine quantum numbers other than F failed.
• Some unrecognised parameters on the command line were simply ignored, rather than triggering an error message.
  
• Plots now always plot the same quantity for intensity by default, regardless of the frequency or wavelength scale chosen. Set the PreserveArea setting true to restore the older behaviour; see the documentation on this parameter for more details.

• New Features in 10.0.505
  
• Automatic Fitting as described in "Automatic assignment and fitting of spectra with PGOPHER". There are knock on changes in the Residuals Window, Transitions Window and Line List Window.
• Automatic baseline and peak finding; see under Automatic Fitting for worked examples.
• More general lineshape functions - see Lineshape Function and Custom Lineshape Function.
• Forbidden Transition Moment to allow a wider range of forbidden transitions to be simulated.
  
• Bulk Import From Table for states, transitions and perturbations.
  
• Import of Excel (.XLS, .XLSX) files and selected other spreadsheet formats, depending on the platform.
• The full set of Unicode characters are now handled in many contexts, though it is recommended that object names are restricted to the standard ASCII set to avoid problems with earlier versions of the program. PGOPHER assumes UTF8 encoding in text files in the absence of any other information.
  
• The default value of MinI is now 0.01, which typically gives more useful Fortrat plots as many weak transitions are excluded.
  
• Initial implementation of import of Bruker Opus files (typically *.0).
  
• Initial implementation of handling of spectra in FITS format, common for astronomical data.
  
• Text file overlay import faster and more robust, and will also import comment lines from the start of the file.
  
• In the overlay menu, "Deglitch" is now "Delete point", and "Delete Points" command has been added.
• On-line help is now connected on Linux and Mac.
  
• Enhancements to SPFIT/SPCAT file handling - see the qfmt and MapState directives.
  
• Significant speed-ups for selected operations, particularly handling large line lists and experimental data files.
• LAPACK upgraded to 3.6.1
• "Offset By..." menu item on manifolds to shift all state origins by a constant amount.
• Stack traces on non-windows systems now show in the log window, rather than the console.
• More consistent keyboard shortcuts in Mac version.
• Overlay linelists can include estimated error values; these are not plotted, but if the peak finder finds a single peak the value will be copied to the "Std Dev" column in the linelist window.
  
• Fixed Problems in 10.0.505
  
• An adjustment has been made to the phase of some transition moments; see the discussion at the end of Transition Moments and Line Strengths for more details. For the most correct calculations FixTransitionPhase should be set to true
• M dependent line strengths for perpendicular multiphoton transitions. See Polarization objects for more information.
• Change in definition of spin forbidden gS; now discards quantum number dependence
• Changing units changes increment as well as value and standard deviation
• On non-windows machines, save and restore of a setup with multiple plot windows open gave a (harmless) error message.
• Colours lost in line list window.
  

• New Features in 9.1.100
  
• Comprehensive tutorial Walkthrough of Simulating and Fitting a Simple Spectrum added to the documentation, including an N₂O sample spectrum to work with.
  
• Custom Width Functions provide an alternative simple empirical way of specifying quantum number dependent line widths and intensities.
• Significant rework of the Transitions Window to allow selection by more quantum numbers and other options.
• BranchExpr format added as an option to the linelist window.
• Remove forced sorting of transition moments by rank.
  
• Settings set to Auto have the actual value displayed in the hint in the constants window and in detailed line listings.
• Rename parameter command added to the Variables object, and others to which parameters can be added.
• makesvn script to give a starting point for compiling PGOPHER if the available binaries are not suitable.
• Updated fundamental constants to the CODATA 2014 set from http://physics.nist.gov. The largest effect of this is a to scale effective absolute temperatures by 1.000000274, the amount by which k/h has changed.
• Atomic masses taken from v4.1 of the NIST "Atomic Weights and Isotopic Compositions" at http://physics.nist.gov/PhysRefData/Compositions
• LAPACK upgraded to 3.6.0
• MaxDJ setting for Linear,  Symmetric, Asymmetric Top nuclei to limit the maximum  ΔJ to consider in evaluating hyperfine matrix elements.
• Fixed Problems in 9.1.100
• Disable global menu on Ubuntu Unity for PGOPHER, as it interacts badly with the multiple windows used.
  
• Speed up rejection of vibrational states above Emax.
  
• All Button on plot now resets vertical scale as well as the horizontal scale.
  
• If Signed of a Custom Transition Function was True the function was called twice, both with and without the signed quantum numbers. The is only an issue if the Value variable was used.
  
• Copy Branch Table/Copy Simple Format and corresponding fits in the linelist window fixed for linear case for several combinations of ShowOmega, ShowFNumber and Showef.
• Transitions window would show 4th power of transformed transition matrix elements if transition moments with multiple ranks contributed to it, rather than the square as labelled.
• In Transitions window update symmetry names if molecule JAdjustSym setting is changed.

• Fixed Problems in 9.0.101
  
• Better handling of multiple spin 0 nuclei on .par/.var import.
• Some error messages in Mac version resulted in crash.
  

• New Features in 9.0.100
  
• Vibrational Partition Function for calculating complete partition functions.
  
• Command line export of Hamiltonian and transition matrices.
  
• Scale relative magnitudes of parameters when fitting, based on the derivatives. This is controlled by the ScaledParameters setting.
  
• Switch memory manager to FastMM, which is significantly faster on some workloads. In addition changes have been made to the code that gives significant speed-ups for large problems on multi-core machines.
  
• Export to CSV file added as option in right clicking an object in the constants window.
  
• AssumedOrigin parameter to override automatic estimate of this.
  
• OmegaOrder setting to override automatic mechanism for assigning Ω, N and F number in linear molecules.
  
• l-matrix and other vibrational calculation windows have an option to rotate the plot plane about the axis plotted horizontally. (A full 3D plot option is planned for the next version.)
  
• More plot options in the Residuals window, including ratios and logarithmic scales most useful when fitting intensities, and the population option now works.
  
• zMatrix has a show calculated parameters menu command.
  
• A+ and A- (and B+/B-) notation for symmetry alternating with J in Symmetric Tops.
  
• IntensityUnits directive in observation files to specify the units of intensity observations.
  
• Default Symmetry in observations files can be specified as either  J adjusted or non J adjusted.
  
• Branches in linelists for fitting can be expressed in a more general way using the BranchExpr directive, to allow easy adjustment to assignments.
  
• Custom Population functions now have EB and Origin variables, to allow a closer match to the PGOPHER calculation.
  
• Simple calculator for testing expressions.
  
• Table object for use with expressions.
  
• Objects having an expression, such as Custom Population Functions or Custom Transition Functions now display with an enlarged (and correctly labelled) window in the Constants Window.
  
• OscillatorStrength is now an intensity option.
  
• Sub-basis numbers can be included in the quantum number display.
  
• The SymWt setting in linear molecules is now included in intensity calculations even for molecules without a centre of symmetry to allow all nuclear spins to be included in partition function calculations.
  
• The size of matrix that the 64 bit version can handle is now limited by available memory, rather than 16384×16384.
• Check Derivatives option to fitting to assess the accuracy of numerical derivatives, and other tools to assist in fitting.
  
• Branch format allows specification of symmetry for symmetric tops.
  
• Setting SVDThresh negative switches the least squares process to a QR factorisation method.
  
• Simple line list format extended for symmetric tops, and other fixes to K quantum number handling, including branch format input. See the SymmetryLabels and CompactKLabels flags. As part of this fix Copy simple format from the linelist window now works for symmetric tops.
  
• Detailed output now includes simulation parameters, and fundamental constants used.
  
• Custom populations can now specify an M dependence in the presence of external field, either in a custom population function, or as numerical populations specfied in a manifold.
  
• Force constants in internal coordinates can now specify the electronic states they operate on, allowing for Jahn-Teller or similar terms that act between electronic states to be handled.
  
• Added zero point rotational constants Bx0, By0 and Bz0 to calculated parameters for an electronic state. These and the inertial defect are calculated to avoid problems with resonances for zero point level, as in A. L. L. East, C. S. Johnson and W. D. Allen, J. Chem. Phys. 98, 1299 (1993).
  
• Switched fundamental constants to CODATA 2010 set (was 2006 set). This has a small effect, most significantly on intensities. (A temperature of 300.000375 K is required to reproduce earlier spectra at 300 K).
  
• Threshold for zero frequency vibrational modes and other small values now adjustable via SmallCoefficient.
• Loomis-Wood plots.
  
• Debug setting added to Custom Population functions and Custom Transition Moment functions.
• Angstroms (or Å) now a valid unit.
  
• LAPACK upgraded to 3.5.0
• Correlations object now always written to .pgo file if present. (It was not in version 8 to avoid compatibility problems with earlier versions.)
  
• Fixed Problems in 9.0.100
  
• Adjusted treatment of exclude perturbations flag when plotting observed energy levels.
• Negative Error Multiplier in energy level plots scales errors by the estimated error of the observation.
  
• Inconsistent observation colours in level and residual plots.
  
• Improve F1/F2/F3 numbering and N assignment if OmegaSelect is used for linear molecules. Note that unexpected results are still possible - see the documentation for OmegaSelect.
• If Symmetry Coordinates are used the largest coefficient in the L matrix for a given mode is forced positive by multiplying the mode by -1. This helps to give consistent signs for Coriolis coupling constants and some other values.
  
• Equivalent nuclei with spin 0 that have been explicitly included in the calculation now have the correct statistical weight applied. As part of this fix, the irrelevant Spin and AsNext settings were removed from nuclei for vibrational calculations.
  
• The I₂ built in calibration overlay was broken.
  
• Hönl-London checkbox disabled in Transitions Window if external fields present, as it does not do a relevant calculation.
• Documentation for Scomp values for linear perturbations was wrong - values in text were doubled.
  
• Width setting in vibrational simulations was treated incorrectly.
  
• +l and -l labels were swapped in symmetric tops for levels of E₂ and E₅ vibronic symmetry (not rovibronic symmetry) as compared to the definition given by Hoy and Mills J. Molec Spectrosc. 46, 333 (1973).
• Specifying individual level populations failed when overall J was half integral.
  
• l matrix import from molpro was not handling dummy atoms.
  
• Complex transition moment matrices were not displayed correctly in the transition moments window.
  
• The RemoveSpins directive was not correctly removing all terms involving electron spin.
  
• Display of symmetric top perturbations in constants tree inverted if lChange not zero.
  
• Convert to Perturbations for symmetric tops corrupted zeta.
  
• Branch format linelists failed for linear molecules with hyperfine structure.
  
• HITRAN files for O₂, NO and OH would not import; ignore lines not beginning with a number.
  
• Spectra in the presence of external fields involving symmetric tops with degenerate vibronic states included spurious extra transitions.
  
• M dependence of multiphoton transitions always used 1 as the transition rank, giving incorrect intensities in the presence of an external field. As part of the fix for this Rank has been removed as a setting in Polarization objects; the rank is now taken from the transition moment. In addition spectra with random polarisation in the presence of an external field had the wrong relative intensity between ΔM = 0 and ΔM ≠ 0 for all ranks.
  
• Energy level lists of a single state in a manifold only show levels assigned to that state.
  
• Display of vibrations fails in the presence of dummy atoms.
  
• Force failure when redundant coordinates used and UU^T = 1 test fails.
  
• Do not decompose Dushinsky Matrix into equivalent rotations if determinant negative.
  
• G^-1 matrix printed out incorrectly
  
• Force field analysis printout used two different meanings for the A matrix.
  
• Documentation wrong for FixCentre.
  
• Allow FrequencyOffset and FrequencyScale to be set in a .ovr file at the same time as a calibration function.
  
• Remove order dependence of node fixup.
  
• Fixed crash on level printout if widths present.
  
• Peak finding reported positions to insufficient precision for spectra with a very non-uniform frequency scale, such as spectra arising from combining non-adjacent individual spectra.
  
• Custom Population functions and Custom Transition Moment functions used ½ the required values for the Fn variable.
  
• Precision lost in Voigt profile on some platforms
  
• Units directive more flexible: accepts cm1, nmVac, nmAir, angVac, angAir, Angstroms. (Previous versions had no way of specifying air wavelengths.)
• Fixes for compilation using the free Pascal compiler under windows.