SpecView - the most powerful package
for simulation and analysis of molecular spectra, by Vadim Stakhursky. My Photo Gallery
Snapshot of the month. To enlarge click on the picture
-!-!-!- License renewed! Fourier Transform & Genetic Algorithm for profile fitting!!! Sophisticated data processing. Calculation of the partition function and spectra normalization - SpecView Version 2008-!-!-!- SpecView2008 download page
New model for vibrational analysis - Dunham expressions (up to 6 modes)
--To use upgrades from this page you have to have the original package SpecVi38a.exe installed for proper files configuration.--
SpecView
Today:
Intuitive interface
Simulates
spectra of ALL molecular systems (a variety of models is included in SpecView Library)
Handles
electronic, vibrational and microwave transitions
Displays
simulated spectral lines, or convoluted simulated spectra
--Dynamic Constants--
Allows for
the user to increment molecular constants with a mouse wheel and to see changes immediately
Lorentzian,
Doppler or Voigt line profiles is a standard
Uploads
experimental spectra
Offers
on-screen comparison of simulated and experimental spectra and tools to
manipulate them
Able
to output critical spectral information – lines’ quantum number assignments,
frequencies, intensities,
and internal information like state
wavefunctions
Builds
energy level diagrams along with all spectroscopic information about states
Provides
easy visual tools for experimental spectral lines assignment
Fits
line by line assigned spectra with various options, all the lines are tracked
by wavefunctions (other options available)
Fits
broad features to generate best set of molecular constants without line by line
assignment – Profile Fit (using variety of converging algorithms including GENETIC ALGORITHM)
Fourier transform for
data analysis, experimental spectra manipulation and fourier images fit gives you the best in
conjunction with GENETIC ALGORITHM profile fit!
Exports
simulations – stick plots, energy levels, convoluted spectra, assignments
Saves
all the simulations and assignments into binary *.svw file ready to be open the
next time you work on analysis
Reads
and writes assignments into ascii files
Prints
simulations
Links to the original package Manual (HTML) or PDF formatted Manual
--To use upgrades from this page you have to have the original package SpecVi38a.exe installed for proper files configuration.--
That is first bug-free version of SpecView available online.
Currently we are working on a couple of new models –
- Liner singlets model for homonuclear linear molecules (C3 , joint project with Laszlo Nemes)
- Model to describe rovibronic states of asymmetrically deuterated methoxy ( and wide group of other molecules spectra of which could not be approximated by inclusion simply spin-rotation terms due to limitations of perturbation theory).
New models are available upon request.
SpecView NEWS
- New bug free version is available from the following link. It includes a couple of new features, mostly developed for Profile Fit and Genetic Algorithm. The constants' variation during the fit is now can be customized individually. SpecView55FFT download page 01/05/2005
- Also another version - SpecView45secure.exe - is replaced by SpecView55FFT download page, it includes
Doppler-Lorentz convolution improvement,
Data file sharing violation is fixed,
Reading experimental data is getting smarter, the ascii file will be understood even if frequency numbers are in reversed order
If you work with wavenumbers, and your experimental data file is in units of nm, you can convert automatically and reorder the data file by using File->Import data file -> Convert nm to cm-1 applications main Menu option
- Some work has been done on profile fitting – the capability to fit the Hamiltonian constants without line by line assignment. Two programs were created based on SpecView engine. The first one builds a lattice and finds combination of constants to reproduce experimental spectra to the best. The algorithm is straightforward and tries all the possible combinations of the “adjustable” constants. Though quite slow, the computation time is still affordable for simultaneous optimization of 6 to 7 constants. The second program utilizes Levenberg – Marquett non-linear least square algorithm to fit simulated profile to experimental data. While extremely inexpensive in terms of computation time, you never know if global minimum is found. On the other side the last one is perfect for automatic temperature detection.
- What is also available??? Someone might think the SpecView application is limited to the simulation of the spectra set by real Hamiltonian matrix. While most of the models indeed could be created without imaginary terms in the Hamiltonian (which is always, of course, Hermitian), for some cases we had to diagonalize non-real matrix. That was the case for spin-rotation part of the Hamiltonian in case of C1 symmetry of the molecule. The architecture of the program slightly differs from standard SpecView, and DLL model file has an extra function – that describes the imaginary part of the Hamiltonian. The SpecViewComplex.exe engine as well as DLL model describing asymmetric rotor with Spin-Rotation for the case of C1 symmetry molecule is available upon request.
Standard Hamiltonian models are available:
1. Asymmetric top (Watson Hamiltonian).
2. Vibronic manifold, asymmetric top (Watson Hamiltonian).
3. Symmetric top with degenerate electronic state and Jahn-Teller (doublet S = 1/2) (methoxy).
4. Asymmetric top with degenerate electronic state and Jahn-Teller (doublet S = 1/2) (deuterated methoxy).
5. Asymmetric top with spin-rotation Cs symmetry (alkoxies).
6. Asymmetric top with spin-rotation C1 symmetry (alkoxies).
7. Asymmetric top with spin-rotation C1 symmetry (alkoxies).
8. Diatomic dublets, S = 1/2 (CN, CF, NO, OH).
9. Diatomic dublets, with nuclei spin coupling, S = 1/2, I=1/2.
10. Diatomic triplets sigma states, S = 1, Lambda = 0.
11. Diatomic singlets.
12. Linear singlets, bosons, rovibronic simulations (C3).
13. Vibronic bands.
And many more...
Simulations of absorption, emission, LIF, SEP spectra are easy and straightforward!
Some
models that did not make it to the original package
Here is the model used for rotational analysis of various methoxy bands published in J. Chem. Phys. 106 (17), D. Powers, M. Pushlarsky, T. Miller “Rovibronic analysis of the laser induced fluorescence excitation spectrum of the jet-cooled methoxy radical” It’s a C3v symmetry symmetric top with spin-orbit coupling, centrifugal distortion, Coriolis coupling and JT correction terms of Endo’s Hamiltonian.
Since a considerable work in our lab was done on open shell molecules where spin-rotation effects could not be neglected, we own an extensive library of models describing such systems. It includes: Cs symmetry molecules - Case a (strong spin coupling), Case b(weak spin coupling), C1 (no symmetry) - Case b basis set
Diatomic molecules:
At the moment we have 4 models describing linear systems:
1. Open shell heteronuclear diatomic (for example, CF, CN, CH, OH, NO), with spin-orbit coupling, spin-rotation and other... (S = 1/2)
2. It's next level from the model described above - coupling with the nuclear spin is included (I = 1/2)
3. Closed shell homonuclear linear Hamiltonian, Singlet (S = 0), bosons (for example, C3), with that model you can simulate ro-vibronic manifold of the system (up to 50 vibronic bands at the moment) Single band simulations for Linear Singlets could be found here
4. Triplet Sigma - Triplet Sigma Heteronuclear diatomics (for example, SO), with spin-spin and spin-rotation interaction terms (S=3, Lambda = 0)
Here you can find some examples of important diatomics
Developing new models:
It is clear that SpecView package allows to simulate vast variety of molecular systems with the already developed library of molecular Hamiltonians. At the same time, the original architecture was planned to allow for the user to alter easily the Hamiltonian model introducing new perturbations or modifications. It is not difficult to start writing the model from scratch, and even easier to make corrections to models included in the library. Remember, we will be glad to share our code upon request. The sample project described in the Manual can be found here - Asymmetric rotor project.
Future plans:
1.As part of standard SpecView package we plan to include the simulation *.svw files for "important" molecules. such as OH, NO, CH3O, H2O. That will give quick estimate for positions of the lines and temperature dependence of the spectra.
2.Another innovation coming is the ability to upload assignment from simple ascii file. This version exists, but still at the stage of debugging. Click on the link to get beta version of SpecView45_seleg.exe. To use the new feature go to File -> Legacy -> Save/Open assignment file.
Little tips
Once you start using SpecView it will become part of you spectroscopic life. Here we offer little models that help you to analyze spectra qualitatively and get best fit constants. We do use them everyday, though because of their petrifying simplicity they were not included in the standard model library:
1. If you are IR spectroscopist, this one could be useful - "Vibrations" - simple generation of up to 3 vib modes spectra, with overtones, fundamentals and intensities for those set approximately by FC parameters. As I said, the model is cruel, but it uses w1, w2, w3 frequencies and unharmonicity coefficients d1..2..3. Cross terms can be added. If you do not know how to add the model to the library - read the manual, what you have to know - the name of the model - "Vibrations" and the DLL file itself - vibrationsFC.dll
Other soft for spectroscopy: Franck-Condon factors and Rotational constants
1.This is a small application that allows you to calculate rotational constants for the molecule if you have a Cartesian matrix input (conveniently in a free format) for atoms positions. Helps a lot for the determination of the orientation of principal axes. A, B, C rotational constants and inertial Iab matrix.
2.This is a small tool written in VC++ with a simple GUI for the determination of the Franck-Condon factors in one dimensional case (primarily used for diatomics). The program uses unperturbed Hermite polynomials as a basis set and considers up to 8 vibrational overtones in each electronic state. There is not much special about this applet, just could not find anything from the Google, and had to spend an hour to write my own. Franck-Condon intensities.
How to cite SpecView
If you used SpecView for the analysis of your spectral data you should cite it properly when you publish a paper. At the time one should use the following:
SpecView: Simulation and Fitting Of Rotational Structure Of Electronic And Vibronic Bands. V.L. Stakhursky, T.A. Miller, 56th Molecular Spectroscopy Symposium.
http://www.chemistry.ohio-state.edu/~vstakhur
Please send all the correspondence to
T.A.Miller Lab
Department of Chemistry
Ohio State University
100 W 18th Ave.,
Columbus, OH, 43210
1-614-292-4387
I would appreciate if you share Hamiltonian models developed in your lab for the analysis of new molecular systems.
For all the inquiries e-mail me specview@yahoo.com
You are very welcome to leave comments or express feelings you experienced using SpecView. Your feedback is important for development of the best spectrum analysis tools.
Last revised on December 31, 1969, 7:00 pm