Release notes and log of changes to older versions (8.0 and earlier)

Upgrading from previous versions

The default for display of quantum numbers from 5.2.343 is now to display, and accept as input, true values throughout, so a quantum number of 1/2 is now displayed as 0.5 rather than 1. Associated with this the variable setting the display style has changed from DoubleQnos to QuantumNumberFormat at the Mixture level. To revert to the previous style of working set this to 2J rather than the default of J. Some care needs to be taken with data files when moving between versions; while the .pgo files always have quantum numbers written as doubled values line list files used for fitting may well use the wrong format when reading as they will default to the format determined by QuantumNumberFormat (or DoubleQnos). This can be adjusted as required by adding one of the following directives to the line list file:
```
QuantumNumberFormat 2J
QuantumNumberFormat J
```
The window positions and other settings can now be written to the .pgo file. If this is done the files can't be read by versions of PGOPHER before 5.2.343 - an error message along the lines of "Can't find FormSettings" will be displayed. Saving this additional information can be disabled by turning off the "Save" settings under File, File Options. Alternatively, these are separate objects in the .pgo file and can be removed with a text editor if necessary.
In version 5.2 of PGOPHER a different numbering scheme is introduced to label the rovibronic symmetry for asymmetric tops. This has a more straightforward relationship with the various ways of denoting symmetry, and the schemes are as described in Axis systems and symmetries for asymmetric tops. This only affects molecules with C_2v, D₂and D_2h symmetry, but does imply that for these the input and display of symmetry for transitions has necessarily changed. This is perhaps most obvious for line list files for fits; files produced for the old version can only be read by the new version if the following directive is added at the top of the line list file:

pgopherversion 5.1

In the course of full implementation of the PseudoC2v setting in version 5.2 the numbering scheme for some of the symmetries has changed; see the documentation for the new numbering scheme. Some input line list files may require manual editing to work with the new version as as a result.
For asymmetric top molecules the default value of LimitSearch in manifold is now true rather than false. Old files loaded into the new version will normally use the new setting rather than the old, which may affect the values displayed for the Ka and Kc quantum numbers in some circumstances. It does not affect the energy levels or intensities calculated, merely the algorithm used to generate quantum numbers for display. See Manifold for a discussion of this.
The default IntensityUnits in Simulation are now (after 5.1.44) Normalized, rather than Arbitrary. As default values for settings are not written to .pgo files, files saved by older versions of the program with IntensityUnits=Arbitrary will now load with it set as IntensityUnits=Normalized. This change was made as a setting of IntensityUnits=Arbitrary gives misleading relative intensities for isotopologues or isotopomers with different symmetry or statistical weights, such as ³⁵Cl₂ and ³⁵Cl³⁷Cl. (The calculation is "correct", in that the partition function is excluded by design when IntensityUnits=Arbitrary but it means this setting makes a poor default.) No action is required by this change unless abundances or transition moments have been set to work around this issue.
Statistical weights were treated incorrectly for D_2d, D_4d,D_6d,D_8d symmetric tops in versions before 5.2.513. Files prepared with older versions using these point groups may give a warning on loading, and the statistical weights will typically need correcting.
After version 5.3.137 a "Parameter" directive is normally required at the start of a line in an observation file adding a parameter as an input value for fit. (Without this directive otherwise valid input files could be misread.)
In versions before 5.3.330 the relative intensity of magnetic dipole transitions was not always correct with respect to electric dipole transitions. For the units used for the Strength of transition moments (Debye for electric dipole, Bohr Magneton for magnetic dipole) the intensities of magnetic dipole transitions need to be scaled by 10⁴²μ_B² = 8.6007252×10^-5 to give the correct relative intensity. This factor was included when the simulation had units (IntensityUnits = EinsteinA, nm2MHzperMolecule, cm2WavenumberperMolecule or HzperMolecule) but not otherwise. The appearance of simulations with no units will not change unless both electric and magnetic dipole transitions are present in the same simulation. To obtain the same absolute intensities scale the magnetic dipole moments by 10^-21/μ_B.
In versions before 5.3.335 intensities of transitions arising from a rotational magnetic moment in a linear molecule were a factor of 3 too large. The units for rotational magnetic moments have also been switched to nuclear magnetons, μ_N, from Bohr magnetons, μ_B so the Strength will need scaling by m_e/m_p.
The Rank property was removed from some TransitionMoment objects in version 5.3.335, as it was superfluous.
The branch label format for symmetric tops has changed in versions after 5.3.335. All spaces have been removed, and the kl labels now show as '+', '-' or nothing, rather than '+1', '-1' and space. In addition a problem with degenerate states in symmetric tops has been fixed; the kl label was sometimes taken from the upper, rather than the lower state in the transition.
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 behaviour, with EinsteinA now giving a radiative rate. EinsteinA is converted to EinsteinASumon 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.
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.
After 8.0.101 calculated angles for an electronic state are shown in degrees, rather than radians.
After 8.0.186, files with Polarization objects set to something other than the default of 1 will give an error message on loading. This can be ignored, though earlier calculation with such a setting are likely to have been wrong. The rank is now taken from the transition moment.
To allow all nuclear spin states to be included in calculating partition functions, the SymWt setting in linear molecules is now (from 8.0.217) included in intensity calculations even for molecules without a centre of symmetry. (This is not normally required, but can be important in, for example, calculations of thermodynamic properties.) To avoid inconsistencies loading data files prepared with older versions of the program will force SymWt to 1 for linear molecules without a centre of symmetry.
Versions before 8.0.258 swapped the +l and -l labels 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). The calculated energy levels and intensities are not affected, just the labels of the states. Input files for fitting produced by or for older versions may require adjustment for degenerate vibronic states in the affected point groups (D_4d and other groups with 5 fold or higher rotation axes).
The J adjusted symmetry handling and associated JAdjustSym setting and A+/A- B+/B- symmetry notation was only fully implemented in version 8.0.285. Linelists used for fitting by earlier versions may require adjustment if J adjusted symmetry is used in specifying states. (Some of development versions had + and - swapped.)
The method used for determining the assumed origin for Boltzmann calculations changed in 8.0.333. The AssumedOrigin parameter was introduced allowing this to be explicitly set if required. In addition the logic for linear molecules was slightly adjusted for some cases, which may mean that different results are now obtained if the IntensityUnits are set to Arbitrary. The difference will only be a constant scale factor (exp(-ΔE/kT) where ΔE is the difference between the old and new origins.
Parameters are scaled by default during fitting in versions after 8.0.389, as controlled by ScaledParameters.This changes the useful values for SVDThresh, so the default for SVDThresh has changed from 10^-15 to 10^-6. The previous behaviour is obtained by setting ScaledParameters to false, and this is forced on loading old .pgo files if SVDThresh is set in the file.

Fixed problems and new features

Fixed Problems in 8.0.102

Calculated angles for a state more than 138.5 degrees shown as 180-angle. In fixing this, the angle display has been changed to degrees, rather than radians.
Level and states window crash on Mac (only), and fixed some layout issues.
Inconsistent results depending on whether the Internal Coordinates and related windows displayed or not.
Fixed inconsistent use of Principal axis system in selected vibrational calculations.
Molden import of l matrix files now normalizes all the normal co-ordinates.

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 Vibrational calculation.
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 = EinsteinAnow 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 _polrelated 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=hpmodeis 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 C₃_h 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_barin 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.

New Features in 5.2.524

Import of selected .svw files from Ohio SpecView program.
Right click in Fortrat plot only shows lines close to selected J. (Previously only the horizontal position of the mouse was used to select lines.)
Speed up of importing spectrum data files.
Paste of file from Windows Explorer implemented.
Initial implementation of spline fitting for calibration.
Option to print constants used in I₂ calibration simulation.
Implemented equivalent nuclei in linear molecules, and initial implementation for asymmetric tops (C_2v, pairs only).
General constraints on parameter values in fits.

Fixed problems in 5.2.524

Right click in Fortrat diagram was not always giving lines under mouse.
Read of linear molecule JPL .cat files when J not specified in quantum numbers in .cat file was failing.
Drag and drop of .pgo file on to plot window discarded limits.
Save Overlay and Save Overlay As menu items in main window failed if Overlays window was not open.
Display of partition function sum was not using QuantumNumberFormat.
Calculate Boltzmann factor for cm^-1 and eV by conversion so that identical populations are obtained when compared with energy levels calculated using MHz. Previously a value tabulated to the (relatively low) precision of k was used, giving slightly different populations with notionally identical constants
Unit conversion incorrectly treated C and D in a transition.moment as having units.
Intensity incorrectly scaled for some IntensityUnits when the PlotUnits were different to the calculations Units.
Crash on hitting F1 for help in main window.
Adjust height of individual items in the constants window to make it less likely to show scroll bars when not really needed, and make sure selected item in tree is always visible.
In line list displays, make column heading "Position" rather than "Frequency" (as line position is often not in frequency units).
Fix column header alignment in line list export.
Line list for IntensityUnits = PopDist was blank, and fix related problems when right clicking on a population distribution plot.
Optimize logic for not saving default form settings.
Force legal symmetries following point group changes.
Possible I/O error 105 in Slave Editor.
Width conversion to/from velocity scale wrong.
Default Kmin and Kmax display as "all" for asymmetric tops.
Foffset on simulation incorrectly taken into account when peak measuring on a simulation in calibration mode.
Adding a new linear state to a manifold in the tree view defaults to the same g/u value as the other states in the manifold.
Close and re-open transition selection window does not loose manifold/state selection.
"Auto" checkbox in linelist dialog was always treated as checked.
Measure using mouse of peak position on simulated spectrum does not result in automatic assignment in line list window.
Right click in vertical axis region of simulation should not find lines.
TransitionMoments with more than 2 components and at least 2 different ranks may not simulate correctly.
TransitionMoment selection with the transition selection window not working.
Various fixes to calibration methods.
Potential crash when form closed when editing a value in a grid.
Statistical weights wrong for D_2d, D_4d,D_6d,D_8d. As a consequence old data files with these point groups will give a warning on loading.
Symbolic matrix element output now honours QuantumNumberFormat.
Transition strength calculation fixes for symmetric tops.

New Features in 5.2.343

Slave Editor added to distribution.
"Hide others/Show All" menu items in overlay context menu on main and overlay forms.
Colour = clHide lines now excluded from consideration in more contexts, including line count, scaling and right click on plot.
Choose random overlay colour (rather than black) if no unused colours available.
Upgrade to Eigenvalue routines from version 3.1 of LAPACK.
Implement Branch style input in .lin files for symmetric tops.
Add velocity (in units of cm^-1/2) as a horizontal scale in spectrum plots.
Hyperfine quantum number display for basis states has been adjusted - now always shows J.
Read .sp files from (at least some) Perkin-Elmer spectrometers.
Prompt when clearing line list window when there are some assigned lines.
Swap frequency and intensity, discard intensity operations added to experimental plots.
Mouse over on observed-calculated line on main plot shows linelist number on both ends.
Small adjustments for Microsoft Windows Vista.
Temperature in I₂ calibration spectrum independent of overall simulation temperature.
Simulation parameters (such as linewidth and temperature) are now recorded in a separate Simulation object rather than the base Mixture object. This allows for multiple Simulation objects corresponding to multiple simulation windows. For back compatibility if there is only one Simulation object its values and settings are written to (and read from) the base Mixture object. .pgo files written with more than one simulation object can't be read by previous versions.
Optionally save and restore more settings, including parameters for energy level and transition windows, and form positions.
Constants and overlay windows will rearrange their contents depending on their aspect ratio.
Replace DoubleQnos with QuantumNumberFormat, Mixture, and set the default to undoubled quantum number display.
Symmetry selection in the transition (and other) windows now uses symmetry names, rather than numbers.
Write version to .pgo files. (It is ignored on input for the time being.)
SMargin now implemented in simulation, which defines how many additional points to calculate off either end of a spectrum.

Fixed problems in in 5.2.343

Do not permit JAdjustedSym when hyperfine structure present in asymmetric tops.
Allow .pgo files that trigger errors to load so they can be fixed.
Hyperfine quantum numbers not displayed for asymmetric tops.
Compilation fixes for 64 bit and Mac/Intel.
Fix crash on pasting too many items into parameters in constants form; allow copy/paste in settings grid.
Load of some overlay files could fail for a if the frequency was not sufficiently varying.
Cancel on "File Changed - discard?" prompt not always effective.
Fix error handling for failures in calculating eigenvalues.
Data file name shown in task bar.
Detect spurious xml entries in .pgo file, rather than silently ignoring them.
Wrong sign in documentation for spherical transition moments.

New features in 5.2.149

Experimental support for multiple CPU cores is now available for selected calculations; this is most useful for fitting. It is disabled by default, as it is only helpful for larger problems and can reveal obscure bugs. To try this, select the number of threads using the View, Threads menu item - twice the actual number of processors is a good starting point.
PseudoC2v is now implemented for all appropriate point groups and full documentation prepared. The numbering scheme for some of the symmetries has changed so some line list input files may need manual adjustment.
Change in numbering scheme for labellings rovibronic symmetry for asymmetric tops - now directly related to standard symmetry labels as described in Axis systems and symmetries for asymmetric tops
Adjust overlay scaling algorithm - for IntensityUnits = Normalized now uses current Baseline and Scale.
The least squares fit routine now displays Watson's sensitivity parameter (J. K. G. Watson, J. Mol. Spectrosc. 66, 500 (1977)) for each floated variable, and uses this to determine the number of figures to display in the estimated error for each parameter.
The least squares fit routine will display the results of a singular value decomposition if Mixture.FitDetails is set to True. Singular value decomposition eigenvalues less than Mixture.SVDThresh will be discarded. This is normally 0, but small values can be used to limit changes to combinations of parameters that are poorly or completely undetermined.
Parameters can now be used as "observed" values in fits as a method of applying constraints.
Overall rovibronic symmetry selection has now been generalized so it applies to all types of states and perturbations.
The number of lines displayed in the Line List window on right clicking on a simulation can now be adjusted (click on More, Options in the line list window.) The default is now to display the 10 strongest lines with intensity more than 5% of the strongest, and to assign lines that are more that 25% of the intensity of the strongest.
Level plot can now select by other quantum numbers, including K_a and K_c (Asymmetric tops) and Ω for Linear molecules.
Better handling of overflow in Boltzmann case - see J Range and Partition Functions.
Several processing commands for numerical (as opposed to bitmap) overlays, including smoothing and joining spectra together.
Selected calibration spectra are now built into PGOPHER (I₂, Ne, Fe) for use with the new calibration system.
A full calibration process is now available for overlaid spectra.
IntensityUnits in overlays now implemented
IntensityUnits = PopDist, NormPopDist for simulating time of flight spectra or similar cases where energy levels are seen, rather than transitions.
Fitting and associated plots now work for fitting to energy levels, as well as transitions. (Use blank upper manifold name and J = '-' in fit files to indicate this).
Colour coded names in constants and overlay tree view.
Several improvements to the linelist window, and fix some bugs causing range check errors.
Symbolic Matrix elements now available for Linear Molecules and Asymmetric tops
Plate tracing has been updated to allow accurate determination of the plate angle, and selection of the area to trace.
Float setting for parameters can now be toggled by single (rather than double) mouse click or space bar.
Ctrl + Left mouse now also offsets spectra as well as Alt + Left mouse, to allow for Linux window managers that use Alt+Left to drag windows.
Updates to non-Boltzmann populations.
Add K selection to asymmetric top perturbations.

Fixed problems in 5.2.149

Asymmetric tops with C_i symmetry have approximately 1/4 of the rotational states missing.
Transitions with exactly zero frequency within a Manifold are now discarded; previously these could appear twice in a line list (with zero intensity).
Plot of overlay with negative intensity scale could have scale problems.
Peak find on a line list including more than one peak took the first line in the range, rather than an average when all the peaks in the range had the same intensity.
Asymmetric tops with C_2h symmetry have half the rotational states missing for states with A_u or B_u vibronic symmetry.
Auto detection of frequency channel of overlay can fail if intensity channel is flat.
Parameters with an absolute value less than about 10^-18 are not saved in the pgo file.
Minor adjustment to phase choice for linear molecule LS perturbation matrix element for the case that Λ' = Λ. Now chooses parameter to be matrix element such that largest S is on the left.
Right click on first spectrum from File, New, Linear Molecule did not show assignments.
Some asymmetric top perturbation matrix elements not calculated correctly for operators containing J_xⁿJ_y^m with m ≠ n and m ≠ 0 and n ≠ 0.
Fixed problem with Normalized intensities introduced in earlier development version
Quantum number label is always shown as J in Fortrat plots, even if not appropriate.
Mouse over on Level plot could indicate wrong line in observations file on status bar.

New features in 5.1.222

Convert for compilation with Delphi2006.
JPL line lists (.cat) as overlay.
K selection in symmetric tops.
Cartesian transition moments now accepted for symmetric tops.
Perturbations in symmetric tops now implemented.

Fixed problems in 5.1.222

ζ constant in symmetric tops was incorrectly converted when switching units.
Copy with linked items, then paste fails when there is more than one transition moments object.
Linux/Mac version: Linelist export no longer crashes
Mac version: fixed problems due to compiler.
State assignment in Cs or lower symmetry asymmetric tops.
Count in exported linelists wrong.
Intensity fits of transitions within a manifold could be to wrong state.

New features in 5.1.164

Line fits can now be to intensities as well as positions.
Non-Boltzmann population distributions can now be entered and fit
Residuals from fit can now be plotted in a variety of ways in the Log window.
Multiple views of the same spectrum now available from View, Another. The plot range is independently selectable, and the frequency offset, temperature and linewidths can be synchronized or independent.
Saturation parameter.
Add Quadrupole and Nuclear Spin - Rotation matrix elements to asymmetric tops.
Options to exclude some or all spins when line fitting to some or all lines.
More options for energy level plots.
More options for Fortrat plots.
Linear molecule states can now be restricted by Ω and parity (This is particularly designed for Hund's case (c) or other cases where there are many perturbations.)
Linear molecule perturbations can now be symmetry and omega selective
Least squares fit to line positions now gives file and line number in the output log.
HITRAN format line lists (.par files) can now be used as overlay files or as line position or intensity input to least squares fits.

Fixed problems in 5.1.164:

Preliminary fix for C_3v perpendicular band intensities.
Change to default method for displaying quantum numbers for asymmetric top molecules (see discussion above).
Drag and drop of multiple files of the same type forces merge mode
Improve prompt when loading files with two or more spectra in the same file.
Mis-pelt colour names in observation file now gives error message, rather than prompting for colour.
Fixed problem where save (rather than save as) of overlay file sometimes goes to wrong directory.
Intensities more consistent when switching from spectra with width to "stick" spectra where width does not show.
Fix problem with vertical axes on multiple plots.
Fix incorrect printing of weighted overall residual after fit.
Negative and zero fit increments not displayed in constants window
Allow units in observed line file to differ from units in constants window.
Export of individual overlay of multiple fixed
File including itself gives error message rather than crashing
Adjust partition function convergence algorithm and add AutoQConverge setting.
Copy and paste of linked items in constants window now renames transition moments
Decimal separator now forced to be "." regardless of system setting.
Default IntensityUnits now Normalized (See comment about upgrading above)
Switch Delphi version to use FastMM memory manager
mkpgopher.bat build script fixed
Exclude *.cfg files from source distribution
Minor change to number output style

In 5.1.44

Cancel in rename of new matrix element deletes new object
Remove possibly confusing test for ungerade states in symmetric linear molecules
Add Suncouple as perturbation type for linear molecules
Allow state number selection in transition dialog
Correct error in formula given in the documentation for linear molecule statistical weights

In 5.1.42

In level plots:

Fix observed level plot problem with emission spectra
Simple symmetry selection
Observed level plot can now be both upper and lower states simultaneously
Fix observed level plot problem where transition is within a single manifold

.pgo files (these changes are backward compatible)

"Name" of matrix element style items no longer written to file ("Bra" and "Ket" are sufficient).
Display name in tree of Mixture is just filename part of full path

Sample data files:

Add ¹⁸O¹⁶O to show different isotopes and symmetry
Add ¹⁷O¹⁶O to show nuclear hyperfine structure

Clear observed line marks menu item
Colour of sum spectrum is now always black
Fix plotting glitch with multiple spectra
Add "Hide" colour; "None" will show as black.
Documentation: Add "forbidden transitions in linear molecules" section
Fix display glitch in bitmap overlays
Fix state assignment problem when EigenSearch = True and LimitSearch = False

In 5.1.34

CFBr sample data file corrupt
Octic centrifugal distortion in symmetric tops
States form display fix

In 5.1.34

C_3v symmetric tops now working
Fixed crash when deleting overlays with overlays property window open

In 5.1.32

File, Print and Edit, Styles now working
Version numbers now consistent