PGOPHER
Colin
Western (help-pgopher@bristol.ac.uk)
School of Chemistry, University of Bristol, UK
See Getting Started for pointers
to key pages in the documentation.
3 Dec 2018: Paper describing updated
automatic fitting and Nearest Lines
Plots available on-line: “Automatic and semi-automatic
assignment and fitting of spectra with PGOPHER”,
Colin M Western and Brant E Billinghurst, Physical Chemistry
Chemical Physics, 2019, doi:10.1039/c8cp06493h;
the accepted manuscript is
available here.
Version 10.1.180 (30 Nov 2018): Formal
release of version 10.1. This includes a significant update to the
automatic fitting, particularly the addition of Nearest Lines Plots; see Automatic fitting of the nu5 band of cis
1,2-Dichloroethene, Automatic fitting
of an N2O IR spectrum and Automatic
fitting of an N2O IR spectrum with additional diagnostic tools
for detailed instructions. For a more formal description see 3 Dec
2018 entry above. A variety of other improvements have been made,
including improvements in line intensity fitting and better
handling of larger problems. See the release
notes for a more detailed list of changes and bugs fixed.
Upgrading is recommended for all users to make use of speed ups
and bug fixes; the user interface has not changed significantly,
apart from some changes to the automatic fitting process, and the
.pgo files from older versions will work in the new
version except for unusual cases, which will generate a message on
loading.
4 Apr 2017: Paper describing Automatic Fitting as implemented in
version 10.0 now available on line: "Automatic Assignment and
Fitting of Spectra with PGOPHER". C. M. Western and B.
E. Billinghurst, Physical Chemistry Chemical Physics,
2017, doi:10.1039/c7cp00266a.
The accepted manuscript is also
available.
Version 10.0.505 (14 Feb 2017): Formal
release of version 10. The major new feature is Automatic Fitting as described in
"Automatic assignment and fitting of spectra with PGOPHER",
but there are many other improvements and fixes, including faster
handling of large problems and faster importing of large files
with spectra. See the release notes for a
more detailed list of changes. As ever, .pgo files from
older versions will work without modification in the new version,
except in a few unusual cases, which will give a warning message
on loading. The .pgo files remain essentially compatible
with older versions, though expect warning messages if newer
features are used.
3 Nov 2016: Final version of the paper
giving a formal description of the program works now available on
line: "PGOPHER, A Program for Simulating Rotational,
Vibrational and Electronic Spectra", C. M. Western, Journal of
Quantitative Spectroscopy and Radiative Transfer, 186
221-242 (2016) doi:10.1016/j.jqsrt.2016.04.010.
The accepted manuscript is also
available.
Version 9.1.100 (8 Jan 2016):
Formal release of version 9. In addition to the new features
listed below, a comprehensive tutorial
Walkthrough
of Simulating and Fitting a Simple Spectrum has been added
to the documentation, including an N
2O sample spectrum
to work with, and other new features include
Custom Width Functions to
provide a simple empirical way of specifying quantum number
dependent line widths and intensities and a significant rework of
the
Transitions Window to allow
selection by more quantum numbers and other options. See the
release notes for a more detailed list. As
ever,
.pgo files from older versions will work without
modification in the new version, except in a few unusual cases,
which will give a warning message on loading. The .
.pgo
files remain essentially compatible with older versions, though
expect warning messages if newer features are used.
Version 9.0.101 (5 July 2015): Update of Mac version only,
to avoid hard crash on some error messages. Mac users should
update. Minor updates to documentation also.
Version 9.0.100 (11 June 2015): A draft release of version
9. New features include faster calculations for larger problems,
Loomis-Wood plots, a wider selection
of units for calculated quantities (for example Angstroms
and Oscillator Strength), a
Vibrational Partition
Function for calculating complete partition functions, a
Check Derivatives
command to assess the accuracy of numerical derivatives, other
tools to assist in fitting and many other smaller improvements and
bug fixes.
Version 8.0.102 (11 December 2013): Minor update to fix
crashes in energy level plots in the Mac version, and some issues
with vibrational calculations.
Version 8.0 (2 December 2013): A significant new
release of
PGOPHER, with the major new feature being the
addition of the calculations involved in a
Force Field Analysis to
PGOPHER.
This allows vibrational frequencies and many other related
quantities including Franck-Condon factors and centrifugal
distortion distortion constants to be calculated from a force
field expressed in terms of bond bending and stretching
coordinates or symmetry coordinates. Fitting the force field to
any reasonable combination of observations is also possible, and
this has been set up so that scaling or otherwise adapting
ab
initio force fields is straightforward. Other significant
new features include:
See the
release notes for a detailed list
of changes, including notes on
upgrading
from previous versions.
Version 7.1 (13 September 2010): Bug fix release - 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. A few other
minor issues
have also been fixed.
Version 7.0 (15 June 2010): Apart from many
minor improvements and bug fixes, several features have been added
at the request of users:
- Interactive adjustment
of
parameters with the mouse.
- Fits to combination differences.
- Uncertainties in calculated line positions can now be
estimated from the results of least squares fitting. This is
enabled by the ShowEstUnc
setting at the top level.
- A separate nuclear spin temperature can be set, Tspin, to model the non
equilibration of nuclear spin states on cooling, such as the
ortho and para states in H2.
- Alternative, simplified line
list format.
- A command line version of PGOPHER is also now
available, with text or Binary
format output. This is particularly suitable for using PGOPHER with other
programs.
- Doppler double peak line shape, as
often found in Fourier transform microwave spectroscopy which
can be used in addition to the standard Gaussian, Lorentzian
and Voigt line shapes.
Version (6.0):
- A mode for simulating vibrational
structure, including anharmonic and Renner-Teller
effects, starting from a harmonic model. The intensity
calculation includes full multidimensional Franck-Condon
factors taking account of both mode displacements and mixing
between modes (The Dushinsky effect).
- Spectra in the presence of static
external electric and/or magnetic fields can now be
simulated, including plots of energy levels against electric
field suitable for predicting Stark deceleration, focusing and
trapping of molecules.
Introduction
PGOPHER is a
general purpose program for simulating and fitting rotational,
vibrational and electronic spectra. It represents a distillation
of several programs written and used over the past decade or so
within the Bristol
laser group and elsewhere, but is a re-write from scratch
to produce a general purpose and flexible program. PGOPHER will handle
linear molecules and symmetric and asymmetric tops, including
effects due to unpaired electrons and nuclear spin, with a
separate mode for vibrational structure. The program can handle
many sorts of transitions, including Raman, multiphoton and
forbidden transitions. It can simulate multiple species and
states simultaneously, including special effects such as
perturbations and state dependent predissociation. Fitting can
be to line positions, intensities or band contours.
PGOPHER is
designed to be easy to use; it uses a standard graphical user
interface and the program is currently in use for undergraduate
practicals and workshops as well as research work. It has
features to make comparison with, and fitting to, spectra from
various sources easy. In addition to overlaying numerical
spectra it is also possible to overlay pictures from pdf files
and even plate spectra to assist in checking that published
constants are being used correctly.
The program is freely downloadable from a supporting web site at
Bristol (http://pgopher.chm.bris.ac.uk),
for Microsoft Windows, Apple Mac and Linux, with a beta version
available for the . The data files are the same, regardless of the
platform. The program is released as open source, and can be
compiled with open source tools.
Graphical User Interface Features
- Simple enough to use for undergraduate practicals, but
flexible enough to use for multiple interacting states.
- Multiple simulations coloured by species, isotope, state or
transition type.
- Interactively changing spectrum range, temperature,
linewidth, display style.
- Displaying Fortrat diagrams and energy level plots
- Select transitions by lower
or upper state J, symmetry or ΔJ.
- Right clicking on peaks to see assignment.
- Overlaying experimental spectra
from file(s) or the clipboard (frequency, intensity format).
- Overlay pictures from pdf
files or other sources.
- Alt+left mouse dragging experimental spectra to adjust
offset between simulation and overlay.
- Built in Calibration (I2,
Ne, Fe) for experimental spectra.
- Energy Level plots.
Calculation Features
- Size of calculation (number of states, species, interactions
and maximum J) limited by available memory only.
- Linear molecules in Hund's
case (a) or (b). (Other cases can be handled with some
restrictions.)
- Symmetric top molecules
- Asymmetric top molecules
- A separate mode for simulating Vibrational structure
only, based on a harmonic model, but anharmonic and
Renner-Teller effects can be added. The intensity calculation
includes full multidimensional Franck-Condon factors including
both mode displacements and mixing between modes (The
Dushinsky effect).
- Spectra in the presence of static
external electric and/or magnetic fields can be
simulated, including plots of energy level against electric
field suitable for predicting Stark deceleration, focusing and
trapping of molecules
- Open and closed shell systems (symmetric tops are currently
closed shell only)
- Simulates microwave, infra-red and electronic absorption and
emission spectra.
- Multiphoton and Raman transitions,
with any combination of transition moments including
interfering transition moments.
- Handling an arbitrary number of states and perturbations
between them.
- Fitting to line positions,
band contours or line intensities.
- Flexible input formats,
including HITRAN (http://www.hitran.com)
.par files and JPL (http://spec.jpl.nasa.gov/)
.cat files.
- Many molecular parameter (.par) data files for Herb
Pickett's CALPGM spectroscopy program suite (http://spec.jpl.nasa.gov/)
can be imported as
PGOPHER input
files.
- Handling arbitrary combinations of isotopes and molecules
with spectra coloured for easy identification.
- Simulate effects of quantum number dependent predissociation
on line width and intensity.
- Hyperfine structure (not currently for symmetric tops).
- Symbolic matrix elements available for linear molecules and
asymmetric tops. (Right click on a state or constant and
select Matrix Elements)
- For larger calculations, parallel
calculations can be done on systems with multiple CPU's.
Supported Platforms
System Requirements
Most calculations will run on any machine;
larger calculations involving multiple states can benefit from
more memory or processors. Some features, particularly Interactive
fits, are much easier with a two or three button mouse rather than
a trackpad or touch screen.