This chapter describes how to install and run GaussSum on computers running Windows or Linux. Note that there are two choices for installing in Windows. One is to install an all-in-one bundle of Python/Numpy/Matplotlib/cclib/GaussSum (the easier method), the other is to install the GaussSum sources and the required libraries separately.
Installing an all-in-one bundle on Windows
Download the quite large all-in-one bundle from here. Doubleclick on the .msi file to install it into something like C:\Program Files\GaussSum. A shortcut will be added to the Start Menu.
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Installing the GaussSum scripts on Windows
GaussSum requires Python, which is a programming language commonly used for scripting.
Go to the Python install page. Download and run the Windows installer for a recent version of Python 3 (e.g. Python 3.6).
Install Numpy
GaussSum requires Numpy, which is a Python extension that allows efficient matrix algebra. You can install this with pip at the command-line: py -m pip install numpy
Install Matplotlib
In order to draw the graphs, GaussSum requires the Python package Matplotlib. You can install this with pip at the command-line: py -m pip install matplotlib
Install cclib
In order to extract information from comp chem log files, the Python package cclib is need. You can install this with pip at the command-line: py -m pip install cclib
Install the GaussSum Python scripts
The scripts can be found here. Extract the zip file into something like C:\Program Files\GaussSum.
Create a shortcut on your desktop to GaussSum.py (to do this, right-click on an empty part of the desktop, choose New -> Shortcut, browse to the folder where you installed GaussSum and choose GaussSum.py). To change the icon, right-click on the icon, choose Properties -> General -> Change Icon -> Browse. Find the folder where you installed GaussSum and choose GaussSum.ico. In addition, change the program used to open GaussSum by following these instructions: right-click on the icon, choose Properties -> General -> Opens with -> Change -> PythonW. If you want to set a startup folder, right-click on the icon, choose Properties -> Shortcut -> Start in:, and type the name of the startup folder.
If you have any questions or requests, or if you wish to be added to the mailing list for information on new versions and bug fixes, please send an email to gausssum-help@lists.sourceforge.net.
Start GaussSum
Just double-click the shortcut to GaussSum.py to start GaussSum.
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Installing on Linux
Check to see if you already have Gnuplot, by typing 'which gnuplot' in a shell window. If Gnuplot is installed, you need to make sure that it is version 4.0 or newer ('gnuplot --version').
If you need to install Gnuplot, rpms are available from rpmfind.net and gzipped tar files from SourceForge. If you are using Debian Linux, Gnuplot will be downloaded and installed if you issue the following command as root: 'apt-get install gnuplot'.
Install Python
Check to see if you already have Python, by typing 'which python3' in a shell window.
If you have Python, type 'python3'. The version number should be displayed. If this is less than 3.1, the scripts may not work with your currently installed Python version. (Press 'CTRL+D, ENTER' to exit.)
If you need to install Python, follow the appropriate instructions for your system at www.python.org. You should install the latest version of Python 3.3 (although Python 3.1 and 3.2 also work fine with GaussSum). If you are using Debian Linux, Python will be downloaded and installed if you issue the following command as root: 'apt-get install python3 python3-tk'.
Install Numpy
Numpy is an extension to Python that allows efficient matrix manipulation. You should try to find a binary package for your system rather than compiling it yourself (check your package management system). If you are using Debian Linux, Numpy will be downloaded and installed if you issue the following command as root: 'apt-get install python3-numpy'.
Install Matplotlib
Matplotlib is a Python package for drawing graphs. It should be available through your package manager. You should install the version for Python3. If it is not available, you should download and build it from source. Instructions are available from the Matplotlib website.
Install cclib
cclib is a Python package for extracting information from comp chem output files. You should install the latest version. This is most easily done with pip. You should use the Python3 version of pip which may be available through your package manager. Once installed, it can be used as follows: pip install cclib --upgrade
Download GaussSum
Download a gzipped tar of GaussSumhere. This should be untarred into a folder in the usual way, using 'tar zxvf GaussSum-3.0.2.tar.gz'.
If you wish to be added to the mailing list for information on new versions and bug fixes, please send an email to gausssum-help@lists.sourceforge.net.
Start GaussSum
To run GaussSum, change directory to the GaussSum directory and type 'python GaussSum.py'. You can also pass a filename as an argument: for example, 'python GaussSum.py myoutputfile.out'.
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Chapter 2. How do I find all lines with a certain phrase?
Chapter 2. How do I find all lines with a certain phrase?
Chapter 2. How do I find all lines with a certain phrase?
Open the file you wish to search and choose Find from the list of operations on the left.
Either choose one of the default search terms or choose Custom. If you choose Custom, enter a search term into the box. Note: you can change the default search terms using the Settings dialog box.
Click on the GaussSum logo to start the script.
If you wish to find all lines containing either TERM_A or TERM_B, then use the following notation, TERM_A%TERM_B, for the search term. Any number of terms may be combined in this way.
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Chapter 3. How do I follow the progress of an SCF convergence?
Chapter 3. How do I follow the progress of an SCF convergence?
Chapter 3. How do I follow the progress of an SCF convergence?
For Gaussian to print SCF convergence information, it is necessary to specify additional print, by using #P in the route section.
Using GaussSum, open the file you want to examine. Usually this will be the output file of a job which is currently running.
Choose Monitor SCF and click on the GaussSum logo to run the script. A graph will be plotted of the progress of the SCF convergence versus step number. Details of the SCF cycles are written to the screen. Where there is information on several SCF convergence cycles in a log file (e.g. in the case of a geometry optimisation), GaussSum plots the one closest to the end of the file.
The progress of the SCF convergence is calculated by considering the convergence criteria. For example, for Gaussian, these criteria are the RMS density, MAX density and change in energy. Each of the current values is divided by the target values. The log is taken of any results greater than 1. The 'progress value' is then calculated by summing the logs. Note that convergence is achieved when the progress value equals 0.
You may wish to leave out the initial points, so as to focus on the last few points. You can do this by entering a non-zero value into the box labeled "Leave out the first n points", and re-running the script.
Note that, at the moment, this procedure does not work for SCF=QC (Gaussian).
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Chapter 4. How do I follow the progress of a geometry optimisation?
Chapter 4. How do I follow the progress of a geometry optimisation?
Chapter 4. How do I follow the progress of a geometry optimisation?
Using GaussSum open the file you want to examine. Usually this will be the output file of a job which is currently running.
Choose Monitor GeoOpt and click on the GaussSum logo to run the script.
Two graphs will be plotted. The first is of energy vs optimisation step. The second is the deviation from the targets vs optimisation step.
The deviation is found by considering the convergence criteria. Each of the current values is divided by the target values. The log is taken of any results greater than 1. The deviation is then calculated by summing the logs. Note that convergence is achieved when the progress value equals 0.
You may wish to leave out the initial points, so as to focus on the last few points. You can do this by entering a non-zero value into the box labeled "Leave out the first n points", and re-running the script.
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Chapter 5. How do I get the IR or Raman spectrum of a molecule?
Chapter 5. How do I get the IR or Raman spectrum of a molecule?
Chapter 5. How do I get the IR or Raman spectrum of a molecule?
(Gaussian,GAMESS)
Next, open a log file containing the results of a freq calculation. It isn't necessary to specify whether you wish to calculate the IR or the Raman spectrum - the IR spectrum will always be calculated, and if you ran a freq=raman job, then the Raman activity and Raman intensity spectra will be calculated.
Choose Frequencies from the list of operations on the left.
Parameters for Frequencies
Start, End
The spectra will be calculated for wavelengths between Start and End. The units of Start and End are cm-1.
Num pts
This parameter determines the number of points in the calculated spectra.
FWHM
The Full Width at Half Maximum of each peak.
Scaling factor
You can choose either a general or individual scaling factor (see below).The calculated frequencies are multiplied by the scaling factor. The scaled frequencies are then used to generate the spectra.
Exc. wavelength (nm)
(Only available for Raman) The value of the excitation wavelength is used to calculate the Raman intensities from the Raman activity (see below) using the equation described by Krishnakumar et al. (J. Mol. Struct., 2004, 702, 9) and Keresztury et al. (Spectrochimica Acta, 1993, 49A, 2007).
Temp. (K)
(Only available for Raman) This value determines the temperature used in the Raman intensity equation (see above).
Click on the GaussSum icon to run the script.
The spectra are convoluted with Lorentzian curves and then plotted with Gnuplot.
Information on the each spectrum and on the normal modes are written to gausssum3.0/IRSpectrum.txt and gausssum3.0/RamanSpectrum.txt.
The first few lines of an example IRSpectrum.txt are shown below. Tabs are used to separate each column of information. This allows easy import into spreadsheet software (e.g. Excel), just by right-clicking on the file and choosing "Open with".
Spectrum Normal Modes
Freq (cm-1) IR act Mode Label Freq (cm-1) IR act Scaling factors Unscaled freq
8 0.000612391353264 1 A 466.3941 0.0 1.0 466.3941
16 0.000624493504806 2 A 466.3945 0.0 1.0 466.3945
24 0.000636968752613 3 A 698.2427 0.0 1.0 698.2427
32 0.000649832766662 4 A 698.2429 0.0 1.0 698.2429
If you want to use individual scaling factors, you should open a previously created IRSpectrum.txt or RamanSpectrum.txt and edit the column titled 'Scaling Factors'. You can do this in (for example) Excel, and then save as 'Tab Delimited'. Run the Frequencies option again but choose individual scaling factors this time. The new IRSpectrum.txt or RamanSpectrum.txt will contain the scaled frequencies.
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Chapter 6. How do I extract molecular orbital information?
Chapter 6. How do I extract molecular orbital information?
This chapter has been divided into three sections. The first section describes how to extract information on the eigenvalues and symmetries of the molecular orbitals. The second section describes how to extract information on the contributions of groups of atoms to each of the molecular orbitals. The third section describes how to extract information on the nature of the overlap between different groups of atoms.
How to extract basic information (DOS)
Open the log file containing the relevant information and choose Orbitals from the list of operations on the left. Pick the DOS option.
The boxes labeled "Start" and "End" are the start and end points (in eV) of the density of states spectrum. The box labeled "FWHM" is the full width at half-maximum (in eV) of the gaussian curves used to convolute the DOS and COOP spectra.
Click on the GaussSum logo to start the script. The molecular orbital information is written to gausssum3.0/orbital_data.txt.
The density of states (DOS) spectrum is convoluted using Gaussian curves of unit height and the specified full width at half-maximum. Gnuplot is then used to plot the spectrum. The details are written to gausssum3.0/DOS_spectrum.txt.
If you tick the box labelled "Create originorbs.txt?", a file gausssum3.0/orginorbs.txt will be created which can be used to plot the orbital energies as a series of bars, one above the other, using a program such as Origin (Windows) or Grace (Linux). See the worked example on the GaussSum web site for more information.
Unrestricted calculations are supported for Gaussian. The same files are created but with the data broken down into sections for alpha and beta electrons. The DOS spectrum plotted is also different, containing an alpha DOS, a beta DOS and a (scaled) total DOS. If you ticked the box to create originorbs.txt, the beta eigenvalues are listed after all of the alpha eigenvalues.
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How to find the % contribution of a group to each molecular orbital (PDOS)
How to find the % contribution of a group to each molecular orbital (PDOS)
The first line needs to be either "atoms", "orbitals", "allatoms" or "allorbitals". If it is "allatoms" or "allorbitals", then no further input is required and a separate group will be made for each atom or each orbital. Otherwise, as in the example above, you need to describe which atoms or which orbitals are in each group. The numbers correspond to the order of the atoms/orbitals in the output file. An easy way to obtain these for Gaussian calculations is to open the output file in GaussView and turn on the labels. Groups.txt needs to obey the following rules:
Every atom in the molecule must be listed
No atom may be listed more than once
A single point calculation should be done with the following keywords: (Gaussian) pop=full iop(3/33=1,3/36=-1), (GAMESS) NPRINT=3. This creates a large log file containing information on the overlap matrix among other things. (Note: the 3/36=-1 option for Gaussian prevents the calculation and printing of the multipole matrices; this is purely to keep the output file size as small as possible. In some cases, for example SCRF calculations, the multipole matrices must be calculated - if so, leave out the 3/36=-1. It will not affect the calculation of the PDOS.)
Using GaussSum open the log file and choose Orbitals. Pick the DOS option. See the previous section for information on the options.
Click on the GaussSum logo. GaussSum calculates the percent contributions of each of the groups to each of the molecular orbitals. This may take a few minutes.
Afterwards, the partial density of states spectra (PDOS) are plotted. Note that each one is stacked on top of the previous one, which means that the line at the greatest height is equal to the sum of all of the partial density of states, and hence equal to the total density of states spectrum. The stacking order is undefined. Information on the spectra is written to gausssum3.0/DOS_spectrum.txt which can be used to plot your own graphs.
Information on the molecular orbitals and the percent contributions of the groups is written to gausssum3.0/orbital_data.txt. The last few columns of orbital_data.txt contain more accurate values for the percent contributions and are used by the Electronic transitions operation. You should not edit this file if you wish to use the information in it to calculate the changes in charge density associated with electronic transitions, as described in Chapter 7, How do I get the UV-Vis or circular dichroism spectrum of a molecule?.
Note that the percent contributions are calculated based on Mulliken Population Analysis (MPA). MPA has some well-known deficiencies which can lead to unphysical values such as negative percentage contributions. If this happens for an orbital in which you are interested, remember that the exact figures are less important than the trend across a group of compounds.
Creation of PDOS spectra is also supported for unrestricted calculations with Gaussian. The spectrum plotted is of the total DOS broken down by the contribution of each of the groups. orbital_data.txt contains information on the breakdown of the alpha and beta electrons by group.
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How to find the nature of the overlap between different groups of atoms (COOP)
How to find the nature of the overlap between different groups of atoms (COOP)
How to find the nature of the overlap between different groups of atoms (COOP)
Crystal Orbital Overlap Population (COOP) diagrams were first developed by Huckel. They are especially used in the area of extended solids. They are equivalent to a multiplication of the DOS spectrum and the overlap population (positive or negative) between two groups. In this way, the bond between two groups can be described as bonding or antibonding with respect to each of the molecular orbitals.
Exactly the same information as for creating a PDOS diagram is needed for creating a COOP diagram. That is, you need a log file which is the result of a single-point calculation containing the same keywords as described in "How to find the % contribution of a group to each molecular orbital". You also need a file Groups.txt describing the groups of interest in the molecule (see "How to find the % contribution of a group to each molecular orbital"). The rules for Groups.txt are not as strict in this case: no atom can be listed twice, but not every atom needs to be listed.
Choose COOP after picking Orbitals. The options for creating a COOP diagram are the same as for creating a DOS or PDOS diagram.
Click on the GaussSum logo to calculate the COOP. Information on the overlap is written to gausssum3.0/COOP_data.txt and gausssum3.0/COOP_spectrum.txt.
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Chapter 7. How do I get the UV-Vis or circular dichroism spectrum of a molecule?
Chapter 7. How do I get the UV-Vis or circular dichroism spectrum of a molecule?
Open a log file that is the result of a TD-DFT calculation. For best results, a Gaussian TD-DFT calculation should include the following keyword "IOP(9/40=2)".
Choose the Electronic transitions from the list of operations on the left.
Choose the start and end (in nm) of the convoluted spectrum, as well as the number of points you wish to have in the calculated spectrum. FWHM refers to the full width at half-maximum of the gaussian curves used to convolute the spectrum. FWHM should be entered in cm-1.
After you have set the various parameters, click on the GaussSum logo to run convolute the spectrum.
The details are written to gausssum3.0/UVSpectrum.txt and gausssum3.0/UVData.txt. The file UVData.txt contains information on the contribution of singly-excited configurations to each electronic transition.
If there is a file in the gausssum3.0 directory called orbital_data.txt containing information on the percent contributions of various groups (e.g. ligands and metal centers) to the various molecular orbitals, GaussSum will use that data. It will calculate, for each transition, the change in charge density on each group. This information will be added to gausssum3.0/UVData.txt. (For more information, please see "How to find the % contribution of a group to each molecular orbital".)
For information on the formula used to convolute the UV-Vis spectrum, please see this pdf.
Open a log file that is the result of a TD-DFT calculation. For best results, a Gaussian TD-DFT calculation should include the following keyword "IOP(9/40=2)".
From the list of operations on the left, choose Electronic transitions.
Choose the start and end (in nm) of the convoluted spectrum, as well as the number of points you wish to have in the calculated spectrum. Sigma refers to the width of the band at 1/e height for the gaussian curves used to convolute the spectrum. The units for sigma are eV. (The equation used is Equation 8 from Stephens and Harada, Chirality, 2010, 22, 229-233. Delta in that equation is Sigma/2.)
After you have set the various parameters, click on the GaussSum logo to convolute the spectrum. The details are written to gausssum3.0/CDSpectrum.txt.
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The electron density difference map (EDDM) [Gaussian only]
The electron density difference map (EDDM) [Gaussian only]
The electron density difference map (EDDM) [Gaussian only]
An EDDM is a representation of the changes in electron density that occur for a given electronic transition. It is calculated using the information on the single-excited configurations
that contribute to each transition. The relative contribution is based on the square of the configuration's coefficient. Note that for some programs (e.g. Gaussian) these squares are not guaranteed to sum to 1.0 and so should not be regarded as scientifically accurate. However, they should be sufficient for the purposes of generating a diagram.
After you have plotted the UV-Vis or circular dichroism spectrum, copy a checkpoint file (or formatted checkpoint file) into the gausssum3.0 directory. Then select "Electronic transitions" and choose the "Create EDDM script?" option. Click on the GaussSum logo to convolute the spectrum and generate gausssum3.0/eddm.bat (gausssum3.0/eddm.sh on Linux).
Next you need to set the environment variable G03DIR to the directory containing the Gaussian binaries. To generate the EDDM, at a command prompt run "eddm.bat N", where N is the transition number (starting from 1 for the lowest energy transition).
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Chapter 8. How can I automate spectra generation for multiple files? [Advanced]
Chapter 8. How can I automate spectra generation for multiple files? [Advanced]
If you have a large number of log files, you may find it slow to use GaussSum to generate spectra for each file one-by-one. In order to speed things up, it is possible to write a Python script to automate this process. The following sections give example Python scripts that you could use. You should try to understand these before adapting them for your own purposes.
Generate UV-Vis spectra for multiple files
This example script generates a UV-Vis spectrum for each ".out" file in the current directory. Before running, you should set the PYTHONPATH to the directory containing GaussSum.py and make sure that there is no existing GaussSum output folder present.
import os
import sys
import glob
import logging
from gausssum.electrontrans import ET
from gausssum.cclib.parser import ccopen
ver = "3.0"
def gaussdir(filename):
return os.path.join(os.path.dirname(filename), "gausssum%s" % ver)
if __name__ == "__main__":
start, end = 200, 500
numpts, fwhm = 500, 3000
filenames = glob.glob("*.out")
for filename in filenames:
log = ccopen(filename)
log.logger.setLevel(logging.ERROR)
data = log.parse(filename)
ET(None, sys.stdout, data, filename, start, end, numpts, fwhm, True,
False)
os.rename(gaussdir(filename), filename.split(".")[0] +"_gs")
GaussSum parses the output files of ADF, Dalton, Firefly, GAMESS, GAMESS-UK, Gaussian, Jaguar, Molpro, NWChem, ORCA, Psi and QChem calculations to extract useful information.
It is written by Noel O'Boyle and is available for free under the GNU Public License. For up-to-date information, please see http://gausssum.sf.net.
GaussSum version 3.0 can do the following:
display all lines containing a certain phrase
follow the progress of the SCF convergence
follow the progress of a geometry optimisation
extract molecular orbital information, including contributions of groups of atoms to the molecular orbitals
plot the density of states spectrum (and the partial density of states, in the case of groups of atoms)
plot the crystal orbital overlap population (COOP) spectrum, which gives information on the bonding/anti-bonding nature of an overlap between atoms/groups
extract information on the UV-Vis transitions, including the change in the charge density of groups of atoms
plot the UV-Vis spectrum and the circular dichroism spectrum
extract information on IR and Raman vibrations
plot the IR and Raman spectra, which may be scaled using general or individual scaling factors
Handle compressed log files (.zip, .gz, .bz2) as easily as regular log files.
Release Notes for Version 3.0.2:
Update in parsing library (to cclib 1.5)
No longer include cclib as part of the GaussSum source distribution
Create a DOS spectrum even where one or more eigen values are "nan" (e.g. asterisks in a Gaussian output file). Such values are simply ignored.
Correct the size of the About box (Daniel Liedert)
Release Notes for Version 3.0.1:
Update in parsing library (to cclib 1.3.1+) adding support for several additional computational chemistry packages
Avoid use of deprecated "oldnumeric" numpy module (Clyde Fare, Erlendur Jónsson)
Correct name of output folder to gausssum3 (Angelo Rossi)
Correct the size of the About box (Daniel Liedert)
Release Notes for Version 3.0:
This is the first version of GaussSum that uses Python 3 instead of Python 2
Use Matplotlib instead of Gnuplot
Update in parsing library (to cclib r1064)
Release Notes for Version 2.2.6.1: Bugfix for 2.2.6. Gnuplot location undefined for new users of GaussSum (Guillaume Lamoureux).
Release Notes for Version 2.2.6: A patch from Thomas Pijper was integrated to enable calculation of Raman intensities (from Raman activity). Support has been added for calculating charge density changes for unrestricted calculations (requested by Phil Schauer). Blank lines in Groups.txt are now ignored.
Release Notes for Version 2.2.5: Parser updated to cclib r923 (Ben Stein, Marius Retegan). Removed minus signs in output for TD-DFT (previously these indicated the sign of the contribution). Corrected equation used for circular dichroism to match that from Stephens and Harada (see circular dichroism docs for ref). Thanks to Li-She Gan for identifying this problem and pointing me to this paper.
Release Notes for Version 2.2.4: Parser updated to cclib r912 (Tiago Silva).
Release Notes for Version 2.2.3: Fix serious bug with EDDM (Carlo Nervi, Carlos Silva Lopez). Parser updated to cclib r884 (Mahesh Kumar, Dan Matusek).
Release Notes for Version 2.2.2: Fix problems with Linux version (Daniel Liedert). Minor doc fixes (Irena Efremenko).
Release Notes for Version 2.2.1: Fix bug in importing cclib (Daniel Liedert). Parser updated to handle Gaussian09 CD output (Rino Pescitelli).
Release Notes for Version 2.2.0:
Update in parsing library (to cclib r877)
Added support for creating EDDM maps with Gaussian
Release Notes for Version 2.1.6: Can now handle unrestricted TD-DFT calculations correctly (previously there were errors in the contribution descriptions in UVData.txt).
Release Notes for Version 2.1.5: Updated cclib to cclib 0.9+ (r840). Fixed problem reparsing GeoOpts. Fixed problem with exe on Windows with default Gnuplot and Docs locations.
Release Notes for Version 2.1.4: Bugfixes for UVData.txt which had incorrect % contributions of singly-excited configurations and incorrect changes in electron density of groups.
Release Notes for Version 2.1.3: Bugfixes for incorrect data for energies in CDSpectrum.txt and incorrect units in heading in UVData.txt. Updated cclib to cclib 0.8 beta
Release Notes for Version 2.1.2: Bugfix for off-by-one error in orbital names in major and minor contributions in UVData.txt.
Release Notes for Version 2.1.1: Updated the code to save results to gausssum2.1 subfolder, along with some minor documentation fixes
Release Notes for Version 2.1.0:
Major update in parsing library (upgraded from cclib 0.6.1 to cclib 0.8dev)
Jaguar log files now supported
Compressed log files (.zip, .gz., .bz2) supported
Underlying code now uses Numpy for numerical calculation, rather than the deprecated Numeric
Fixed error in the output of DOS_spectrum.txt where the 'Total' column was equal to the values for the first group
Fixed problem plotting the COOP
Release Notes for Version 2.0.6: Plotting the PDOS was failing due to 'type' issues with Numeric arrays (due to changes in cclib 0.6.1).
Release Notes for Version 2.0.5: Parsing was failing for Gaussian files with "pop=regular".
Release Notes for Version 2.0.4: Plotting vibrational frequencies now works for GAMESS calculations that have imaginary frequencies (bug fix in cclib).
Release Notes for Version 2.0.3: Plotting vibrational frequencies now works for frequencies that don't have symmetry labels.
Release Notes for Version 2.0.2: COOP now works for unrestricted calculations.
Release Notes for Version 2.0: main differences compared to GaussSum 1.0
This is the first release of GaussSum that uses cclib to parse output files.
Calculation of the DOS and COOP uses matrix algebra now, and is almost instant.
Images can now be saved as .png files.
Groups can be described in terms of atomic orbitals now (and not just atoms).
If you use GaussSum to obtain results for publication, please cite it as follows:
N. M. O'Boyle, A. L. Tenderholt and K. M. Langner. J. Comp. Chem., 2008, 29, 839-845.
Here is a list of some papers that cite GaussSum from 2004 to 2009. There are many more papers since 2009 and I thank you for your continued support.
Ligand-Selective Photodissociation from [Ru(bpy)(4AP)4]2+: a Spectroscopic and Computational Study
Luca Salassa, Claudio Garino, Giovanni Salassa, Carlo Nervi, Roberto Gobetto, Carlo Lamberti, Diego Gianolio, Ranieri Bizzarri and Peter J. Sadler
Inorg. Chem., 2009, 48 (4), pp 1469-1481
Localised to intraligand charge-transfer states in cyclometalated platinum complexes: an experimental and theoretical study into the influence of electron-rich pendants and modulation of excited states by ion binding
David L. Rochester, Stephanie Develay, Stanislav Zali, J. A. Gareth Williams, Dalton Trans., 2009, (10),1728-1741
Synthetic, structural, photophysical and computational studies of -conjugated bis- and tris-1,3,2-benzodiazaboroles and related bis(boryl) dithiophenes
Lothar Weber, Vanessa Werner, Mark A. Fox, Todd B. Marder, Stefanie Schwedler, Andreas Brockhinke, Hans-Georg Stammler, Beate Neumann, Dalton Trans., 2009, (8),1339-1351
The Chromophore Structure of the Cyanobacterial Phytochrome Cph1 As Predicted by Time-Dependent Density Functional Theory
Ricardo A. Matute and Renato Contreras, Guillermo Prez-Hernndez and Leticia Gonzlez
J. Phys. Chem. B, 2008, 112 (51), pp 16253-16256
Comparison of adsorption mechanism on colloidal silver surface of alafosfalin and its analogs
Journal of Raman Spectroscopy
Edyta Podstawka, Marcin Andrzejak, Pawelstrok Kafarski, Leonard M. Proniewicz
Volume 39, Issue 9, Date: September 2008, Pages: 1238-1249
Computational and Spectroscopic Studies of New Rhenium(I) Complexes Containing Pyridylimidazo[1,5-a]pyridine Ligands: Charge Transfer and Dual Emission by Fine-Tuning of Excited States
Luca Salassa, Claudio Garino, Andrea Albertino, Giorgio Volpi, Carlo Nervi, Roberto Gobetto and Kenneth I. Hardcastle
Organometallics, 2008, 27 (7), pp 1427-1435
A Computational Study of the Ground and Excited State Structure and Absorption Spectra of Free-Base N-Confused Porphine and Free-Base N-Confused Tetraphenylporphyrin
Shubham Vyas, Christopher M. Hadad and David A. Modarelli
J. Phys. Chem. A, 2008, 112 (29), pp 6533-6549
Determination of Absolute Configuration of Chiral Hemicage Metal Complexes Using Time-Dependent Density Functional Theory
Frederick J. Coughlin, Karl D. Oyler, Robert A. Pascal, Jr., and Stefan Bernhard
Inorg. Chem., 2008, 47 (3), pp 974-979
Effect of an aliphatic spacer group on the adsorption mechanism of phosphonodipeptides containing N-terminal glycine on the colloidal silver surface
Journal of Raman Spectroscopy
Volume 39, Issue 10, Date: October 2008, Pages: 1396-1407
Edyta Podstawka, Pawelstrok Kafarski, Leonard M. Proniewicz
Effect of an aliphatic spacer group on the adsorption mechanism on the colloidal silver surface of L-proline phosphonodipeptides
Journal of Raman Spectroscopy
Edyta Podstawka, Pawelstrok Kafarski, Leonard M. Proniewicz
Volume 39, Issue 12, Date: December 2008, Pages: 1726-1739
Electronic structure and reactivity analysis for a set of Zn-chelates with substituted 8-hydroxyquinoline ligands and their application in OLED
Ricardo Vivas-Reyes, Francisco Nunez-Zarur, Emiliano Martinez
Organic Electronics, Volume 9, Issue 5, October 2008, Pages 625-634
A laser flash photolysis, matrix isolation, and DFT investigation of (?6-C6H5Y)Cr(CO)3 (Y = NH2, OCH3, H, CHO, or CO2CH3)
Mohammed A.H. Alamiry, Peter Brennan, Conor Long, Mary T. Pryce, Journal of Organometallic Chemistry, Volume 693, Issue 17, 15 August 2008, Pages 2907-2914
Mechanism of Forster-type hopping of charge transfer and excitation energy transfer along blocked oligothiophenes by Si-atoms
Yong Ding, Xiangsi Wang, Fengcai Ma
Chemical Physics, Volume 348, Issues 1-3, 2 June 2008, Pages 31-38
Mechanism of Ligand Photodissociation in Photoactivable [Ru(bpy)2L2]2+ Complexes: A Density Functional Theory Study
Luca Salassa, Claudio Garino, Giovanni Salassa, Roberto Gobetto and Carlo Nervi
J. Am. Chem. Soc., 2008, 130 (29), pp 9590-9597
Nature of Charge Carriers in Long Doped Oligothiophenes: The Effect of Counterions
Natalia Zamoshchik, Ulrike Salzner and Michael Bendikov
J. Phys. Chem. C, 2008, 112 (22), pp 8408-8418
Photoinduced Se?C Insertion Following Photolysis of (?5-C4H4Se)Cr(CO)3. A Picosecond and Nanosecond Time-Resolved Infrared, Matrix Isolation, and DFT Investigation
Peter Brennan, Michael W. George, Omar S. Jina, Conor Long, Jennifer McKenna, Mary T. Pryce, Xue-Zhong Sun and Khuong Q. Vuong
Organometallics, 2008, 27 (15), pp 3671-3680
Quantum chemical studies on the potentially important imidates
Tarek M. El-Gogary
Journal of Molecular Structure: THEOCHEM, Volume 861, Issues 1-3, 30 July 2008, Pages 62-67
Reversible Intramolecular C?C Bond Formation/Breaking and Color Switching Mediated by a N,C-Chelate in (2-ph-py)BMes2 and (5-BMes2-2-ph-py)BMes2
Ying-Li Rao, Hazem Amarne, Shu-Bin Zhao, Theresa M. McCormick, Sanela Marti, Yi Sun, Rui-Yao Wang and Suning Wang
J. Am. Chem. Soc., 2008, 130 (39), pp 12898-12900
Ruthenium-carbonyl complexes of 1-alkyl-2-(arylazo)imidazoles: Synthesis, structure, spectra and redox properties
T.K. Mondal, S.K. Sarker, P. Raghavaiah, C. Sinha
Polyhedron, Volume 27, Issue 13, 10 September 2008, Pages 3020-3028
Spectroscopic and theoretical studies on axial coordination of bis(pyrrol-2-ylmethyleneamine)phenyl complexes
Jia-Mei Chen, Wen-Juan Ruan, Liang Meng, Feng Gao, Zhi-Ang Zhu
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, Volume 71, Issue 1, 1 November 2008, Pages 191-198
Structural Properties of l-X-l-Met-l-Ala Phosphonate Tripeptides: A Combined FT-IR, FT-RS, and SERS Spectroscopy Studies and DFT Calculations
Edyta Podstawka, Pawe? Kafarski and Leonard M. Proniewicz
J. Phys. Chem. A, 2008, 112 (46), pp 11744-11755
Structures and Bonding on a Colloidal Silver Surface of the Various Length Carboxyl Terminal Fragments of Bombesin
Edyta Podstawka, Yukihiro Ozaki and Leonard M. Proniewicz
Langmuir, 2008, 24 (19), pp 10807-10816
Structure?Property Relationships of Polyselenoethers [?(CH2)ySe?]x (y = 1, 2, and 3) and Related Polyethers and Polysulfides
Yuji Sasanuma, Akinori Watanabe and Kenta Tamura
J. Phys. Chem. B, 2008, 112 (32), pp 9613-9624
Structure, spectra and electrochemistry of ruthenium-carbonyl complexes of naphthylazoimidazole
Inorganica Chimica Acta, Volume 361, Issue 8, 2 June 2008, Pages 2431-2438
Tapan Kumar Mondal, Joydev Dinda, Jack Cheng, Tian-Huey Lu, Chittaranjan Sinha
Structure, Stereodynamics and Absolute Configuration of the Atropisomers of Hindered Arylanthraquinones
Lodovico Lunazzi, Michele Mancinelli and Andrea Mazzanti
J. Org. Chem., 2009, 74 (3), pp 1345-1348
Synthesis, Separation, and Circularly Polarized Luminescence Studies of Enantiomers of Iridium(III) Luminophores
Frederick J. Coughlin, Michael S. Westrol, Karl D. Oyler, Neal Byrne, Christina Kraml, Eli Zysman-Colman, Michael S. Lowry and Stefan Bernhard
Inorg. Chem., 2008, 47 (6), pp 2039-2048
Theoretical analysis on the electronic structures and properties of PPV fused with electron-withdrawing unit: Monomer, oligomer and polymer
Yangwu Fu, Wei Shen, Ming Li
Polymer, Volume 49, Issue 10, 13 May 2008, Pages 2614-2620
Computational Study of Iron(II) Systems Containing Ligands with Nitrogen Heterocyclic Groups
R. A. Kirgan and D. P. Rillema
J. Phys. Chem. A, 2007, 111 (50), pp 13157-13162
Electronic Spectroscopy of Nonalternant Hydrocarbons Inside Helium Nanodroplets
Ozgur Birer, Paolo Moreschini, Kevin K. Lehmann, and Giacinto Scoles
J. Phys. Chem. A, 2007, 111 (49), pp 12200-12209
Spectroscopic and Computational Studies of a Ru(II) Terpyridine Complex: The Importance of Weak Intermolecular Forces to Photophysical Properties
Claudio Garino, Roberto Gobetto, Carlo Nervi, Luca Salassa, Edward Rosenberg, J. B. Alexander Ross, Xi Chu, Kenneth I. Hardcastle, and Cristiana Sabatini
Inorg. Chem., 2007, 46 (21), pp 8752-8762
Influence of the Substituted Side Group on the Molecular Structure and Electronic Properties of TPP and Related Implications on Organic Zeolites Use
Godefroid Gahungu, Bin Zhang, and Jingping Zhang
J. Phys. Chem. B, 2007, 111 (19), pp 5031-5033
Syntheses and structures of mononuclear lutetium imido complexes with very short Lu-N bonds
Tarun K. Panda, Soren Randoll, Cristian G. Hrib, Peter G. Jones, Thomas Bannenberg, Matthias Tamm, Chem. Commun., 2007, (47),5007-5009
A DFT/TDDFT study of the structural and spectroscopic properties of Al(III) complexes with 4-nitrocatechol in acidic aqueous solution
Jean-Paul Cornard, Christine Lapouge, Jean-Claude Merlin
Chemical Physics, Volume 340, Issues 1-3, 9 November 2007, Pages 273-282
Adsorption mechanism of physiologically active l-phenylalanine phosphonodipeptide analogues: Comparison of colloidal silver and macroscopic silver substrates
E. Podstawka, A. Kudelski, L.M. Proniewicz
Surface Science, Volume 601, Issue 21, 1 November 2007, Pages 4971-4983
Theoretical studies on electrochemistry of p-aminophenol
Yuanzhi Song
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, Volume 67, Issues 3-4, July 2007, Pages 611-618
Intramolecular hydrogen bonding and photoinduced intramolecular proton and electron transfer in 2-(2'-hydroxyphenyl)benzothiazole
Dongjie Sun, Jinghai Fang, Guanghua Yu, Fengcai Ma
Journal of Molecular Structure: THEOCHEM, Volume 806, Issues 1-3, 31 March 2007, Pages 105-112
Photophysical properties and computational investigations of tricarbonylrhenium(I)[2-(4-methylpyridin-2-yl)benzo[d]-X-azole]L and tricarbonylrhenium(I)[2-(benzo[d]-X-azol-2-yl)-4-methylquinoline]L derivatives (X = N-CH3, O, or S; L = Cl-, pyridine)
Andrea Albertino, Claudio Garino, Simona Ghiani, Roberto Gobetto, Carlo Nervi, Luca Salassa, Edward Rosenberg, Ayesha Sharmin, Guido Viscardi, Roberto Buscaino, Gianluca Croce, Marco Milanesio
Journal of Organometallic Chemistry, Volume 692, Issue 6, 15 February 2007, Pages 1377-1391
A Density Functional Theory Study of the Electronic Properties of Os(II) and Os(III) Complexes Immobilized on Au(111).
O'Boyle, N. M.; Albrecht, T.; Murgida, D. H.; Cassidy, L.; Ulstrup, J.; Vos, J. G.,
Inorg. Chem., 2007, 46, 117.
Photophysical and electrochemical properties of new ortho-metalated complexes of rhodium(III) containing 2,2-dipyridylketone and 2,2-dipyridylamine. An experimental and theoretical study
Wei Lin Su, Yu Cheng Yu, Mei Ching Tseng, Shao Pin Wang and Wen Liang Huang
Dalton Trans., 2007, 3440.
Photochemical cis-trans Isomerization of
cis-(eta6-1,2-Diphenylethene)Cr(CO)3 and the Molecular Structure of
trans-(eta6-1,2-Diphenylethene)Cr(CO)3
A. Coleman, S.M. Draper, C. Long, and M.T. Pryce
Organometallics, 2007, 26, 4128.
Density Functional Studies on the Effects of Hydrogen Bonding on the Formation of a Charge-Transfer Complex between p-Benzoquinone and 2,6-Dimethoxyphenol
Bangal, P. R.
J. Phys. Chem. A.; (Article); 2007; 111(25); 5536-5543.
Lone Pair-pi and pi-pi Interactions Play an Important Role in Proton-Coupled Electron Transfer Reactions
DiLabio, G. A.; Johnson, E. R.
J. Am. Chem. Soc.; (Article); 2007; 129(19); 6199-620
Intramolecular hydrogen bonding and photoinduced intramolecular proton and electron transfer in 2-(2'-hydroxyphenyl)benzothiazole.
D. Sun, J. Fang, G. Yu and F. Ma.
J. Mol. Struct. THEOCHEM, 2007, 806, 105.
Photophysical properties and computational investigations of tricarbonylrhenium(I)[2-(4-methylpyridin-2-yl)benzo[d]-X-azole]L and tricarbonylrhenium(I)[2-(benzo[d]-X-azol-2-yl)-4-methylquinoline]L derivatives (X = N--CH3, O, or S; L = Cl-, pyridine).
A. Albertino, C. Garino, S. Ghiani, R. Gobetto, C. Nervi, L. Salassa, E. Rosenberg, A. Sharmin, G. Viscardi, R. Buscaino, G. Croce, and M. Milanesio,
J. Organomet. Chem., 2007, 692, 1377.
Electronic transitions and bonding properties in a series of five-coordinate "16-electron" complexes [Mn(CO)3(L2)]- (L2 = chelating redox-active p-donor ligand).
F. Hartl, P. Rosa, L. Ricard, P. Le Floch and S. Zalis.
Coord. Chem. Rev., 2007, 251, 557.
Theoretical studies on electrochemistry of p-aminophenol
Y. Song
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2007, 67, 611.
The electronic and structural properties of nonclassical bicyclic thiophene: Monomer, oligomer and polymer
W. Shen, M. Li, R. He, J. Zhang and W. Lei
Polymer, 2007, 48, 3912-3918
Spectroscopic and computational studies on self-assembly complexes of bis(pyrrol-2- ylmethyleneamine) ligands linked by alkyl spacers with Cu(II)
W. Li, Y. Wang, L. Yang, A. Szeghalmi, Y. Ye, J. Ma, M. Luo, J.-m. Hu and W. Kiefer
J. Raman. Spectros., 2007, 38, 483-495.
CO2 Fixation and Transformation by a Dinuclear Copper Cryptate under Acidic Conditions
J.-M. Chen, W. W., X.-L. Feng and T.-B. Lu
Chemistry - An Asian Journal, 2007, 2, 710-719.
A DFT study of the chemisorption of methoxy on clean and low oxygen precovered Ru(0 0 0 1) surfaces
M.N.D.S. Cordeiro, A.S.S. Pinto and J.A.N.F. Gomes
Surface Science, 2007, 601, 2473-2485
Syntheses, crystallography and spectroelectrochemical studies of ruthenium azomethine complexes
M.Z. Al-Noaimi, H. Saadeh, S.F. Haddad, M.I. El-Barghouthi, M. El-khateeb and R.J. Crutchley
Polyhedron, 2007, 26, 3675.
Field-induced conformational changes in bimetallic oligoaniline junctions
J.C. Sotelo, L. Yan, M. Wang and J.M. Seminario
Phys. Rev. A, 2007, 75, 022511
Density functional theoretical study of Cun, Aln (n = 4-31) and copper doped aluminum clusters: Electronic properties and reactivity with atomic oxygen
C. Lacaze-Dufaure, C. Blanc, G. Mankowski and C. Mijoule
Surface Science, 2007, 601, 1544-1553
Electronic Structure and Excited States of Rhenium(I) Amido and Phosphido Carbonyl-Bipyridine Complexes Studied by Picosecond Time-Resolved IR Spectroscopy and DFT Calculations.
Gabrielsson, A.; Busby, M.; Matousek, P.; Towrie, M.; Hevia, E.; Cuesta, L.; Perez, J.; Zalis, S.; Vlcek, A., Jr.,
Inorg. Chem., 2006, 45, 9789.
Spectroscopic and Computational Studies on the Coordination-Driven Self-Assembly Complexes (ZnL)2 and (NiL)2 [L= Bis(2,4-dimethyldipyrrin-3-yl)methane].
Li, W.; Wang, Y.-B.; Yang, L.-Y.; Shan, X.-F.; Cai, X.; Szeghalmi, A.; Ye, Y.; Ma, J.-S.; Luo, M.-D.; Hu, J.; Kiefer, W.,
J. Phys. Chem. B., 2006, 110, 21958.
The hydrogen bond in the acetylene-2(HF) complex: A theoretical study about intramolecular and unusual PI...H interactions using DFT and AIM calculations.
B.G. Oliveira, R.C.M.U. Araujo, A.B. Carvalho, E.F. Lima, W.L.V. Silva, M.N. Ramos and A.M. Tavares,
J. Mol. Struct. THEOCHEM, 2006, 775, 39.
Calculation of standard electrode potential of half reaction for benzoquinone and hydroquinone.
Y. Song, J. Xie, Y. Song, H. Shu, G. Zhao, X. Lv and W. Xie,
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2006, 65, 333.
A theoretical quantum study on the distribution of electrophilic
and nucleophilic active sites on Ag(100) surfaces modeled as Finite Clusters.
C. H. Rios-Reyes, R. L. Camacho-Mendoza and L. H. Mendoza-Huizar,
J. Mex. Chem. Soc., 2006, 50, 19.
Computational studies of the interactions
between emeraldine and palladium atom.
B. Bialek, Surf. Sci., 2006, 600, 1679.
Excited States of Nitro-Polypyridine Metal Complexes and Their Ultrafast Decay.
Time-Resolved IR Absorption, Spectroelectrochemistry, and TD-DFT Calculations of
fac-[Re(Cl)(CO)3(5-Nitro-1,10-phenanthroline)].
A. Gabrielsson, P. Matousek, M. Towrie, F. Hartl,
S. Zalis, and A. Vlcek, Jr.,
J. Phys. Chem. A, 2005, 109, 6147.
Molecular geometry, electronic structure and optical properties study of meridianal tris(8-hydroxyquinolinato)gallium(III) with ab initio and DFT methods. G. Gahungu, and J. Zhang, J. Mol. Struct. THEOCHEM, 2005, 755, 19.
CH/N Substituted mer-Gaq3 and mer-Alq3 Derivatives: An Effective Approach for the
Tuning of Emitting Color.
G. Gahungu and J. Zhang. J. Phys. Chem. B, 2005, 109, 17762.
Ground- and excited-state electronic structure of an emissive pyrazine-bridged ruthenium(II) dinuclear complex.
W.R. Browne, N.M. O'Boyle, W. Henry, A.L. Guckian, S. Horn, T. Fett, C.M. O'Connor, M. Duati, L. De Cola, C.G. Coates, K.L. Ronayne, J.J. McGarvey, and J.G. Vos,
J. Am. Chem. Soc., 2005, 127, 1229.
Bimetallic Clusters Pt6Au: Geometric and Electronic Structures within Density Functional
Theory
W. Quan Tian, M. Ge, F. Gu, and Y. Aoki, J. Phys. Chem. A, 2005, 109, 9860.
Ground vs. excited state interaction in ruthenium-thienyl dyads: implications for through bond interactions in multicomponent systems. W. Henry, W.R. Browne, K.L. Ronayne, N.M. O'Boyle, J.G. Vos, and J.J. McGarvey, J. Mol. Struct., 2005, 735-736, 123.
(NH3CH2CH2NH3)Ag2SnS4: a quaternary sulfide-containing chiral layers.
Y. An, B. Menghe, L. Ye, M. Ji, X. Liu, and G. Ning,
Inorg. Chem. Commun.,
2005, 8, 301.
Ligand-to-Diimine/Metal-to-Diimine Charge-Transfer Excited States of [Re(NCS)(CO)3(alpha-diimine)] (alpha-diimine = 2,2'-bipyridine, di-iPr-N,N-1,4-diazabutadiene). A Spectroscopic and Computational Study.
A.M. Blanco Rodriguez, A. Gabrielsson, M. Motevalli, P. Matousek, M. Towrie, J. Syebera, S. Zalis, and Antonin Vlcek, Jr., J. Phys. Chem. A, 2005, 109, 5016.
DFT and HF Studies of the Geometry, Electronic Structure, and Vibrational Spectra of
2-Nitrotetraphenylporphyrin and Zinc 2-Nitrotetraphenylporphyrin.
W. Li, Y.-B. Wang, I. Pavel, Y. Ye, Z.-P. Chen, M.-D. Luo,
J.-M. Hu, and W. Kiefer, J. Phys. Chem. A, 2004, 108, 6052.
Assessment of intercomponent interaction in phenylene bridged dinuclear ruthenium(II) and osmium(II) polypyridyl complexes.
A.L. Guckian, M.Doering, M. Ciesielski, O. Walter, J. Hjelm, N.M. O'Boyle, W. Henry, W.R. Browne, J.J. McGarvey, and J.G. Vos, Dalton Trans., 2004, 3943.
Ab initio study of the electronic and structural properties of the crystalline polyethyleneimine polymer. G. Herlem and B. Lakard, J. Chem. Phys., 2004, 120, 9376.
A number of people provided helpful feedback during the development of GaussSum. The following names are listed in no particular order:
shaloncai reported an error in the data written in UVData.txt.
Rudy Coquet reported an error in the data written in CDSpectrum.txt.
Fabrizia Fabrizi de Biani reported an error in the labels used in UVData.txt.
Tong Glenna reported an error in the major and minor contributions in UVData.txt.
Christos Garoufalis reported a problem parsing PC-GAMESS files with large basis sets.
Emmanuel Koukaras reported a bug in the output of DOS_spectrum.txt, as well as a problem plotting the COOP.
Xinyu Huang reported a bug plotting the PDOS.
Yafei Dai reported problems parsing Gaussian files with "pop=regular".
Charles Bradshaw reported problems plotting the vibrational frequencies for GAMESS calculations.
Juan Sotelo-Campos pointed out that the COOP was only being calculated for alpha orbitals in unrestricted calculations.
Dr. Carlo Nervi, Torino, who found a bug in EDDM.py
James Hepburn, Aberdeen, who found that Hyperchem code had been neglected
Prof Ziyang Liu, Zhejiang University, P.R.China, who found a bug in the output of MO.py for unrestricted calculations
Fred Coughlin, Princeton, U.S., who found a couple of bugs in my code for CD spectra
Li Daobing and Jordan Mantha who have packaged GaussSum up for Debian and Ubuntu users
Neil Berry, Liverpool, who helped to increase GaussSum support for GAMESS files
Julien Chiron, Faculté des Sciences de Saint Jérôme, Marseille, France helped me add support for GAMESS and is perhaps the first Mac user of GaussSum (see screenshots)
Avril Coghlan, formerly of Trinity College Dublin, Ireland, thought of the name (it rhymes with awesome!) and suggested various web page improvements
Elmar Gerwalin, University of Kaiserslautern, Germany, who helped me enormously in getting GaussSum (a) to run in Linux and (b) to work for other people's calculations
Denis G. Golovanov, Russian Academy of Sciences, Moscow and his non-symmetry-containing logfile provided another challenge to GaussSum
Guillaume Herlam, Université de Franche-Comté, Besançon, France who requested and tested COOP diagrams
Roma Oakes, Queens University Belfast, made many useful comments regarding the initial development, especially regarding IR_Raman.py
Ullrich Siehl, University of Ulm, Germany, who made a number of suggestions that lead to the creation of version 0.9.
In order to create GaussSum, I had to learn a few things. I found the following resources very helpful:
GaussSum-3.0.2/Docs/style.css 0000666 0001750 0001750 00000001346 13222437274 014517 0 ustar noel noel p {
font-size: 90%;
color: #333300;
line-height: 160%;
font-family: Verdana,Arial,Helvetica,Sans-Serif,MS Sans Serif, sans-serif;
text-align: justify;
}
a {
font-size: 100%;
line-height: 160%;
font-family: Verdana,Arial,Helvetica,Sans-Serif,MS Sans Serif, sans-serif;
text-align: justify
}
.application {
color: red;
}
.year {
font-weight: bold;
}
.journal {
font-style: italic;
}
.volume {
text-decoration: underline;
}
h2 {
font-size: 110%;
color: black;
font-family: Georgia, Verdana, sans-serif;
text-align: justify;
line-height:50%;
}
GaussSum-3.0.2/GaussSum.ico 0000666 0001750 0001750 00000022676 13222437274 014231 0 ustar noel noel 00 % ( 0 ` % ! !!! !!! !!! !!! !!! !!! ! !! !!! !! !! !! ! ! ! ! ! !!!! ! ! ! ! ! ! ! ! ! ! ! ! ! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!kikRUR 1RQZ! ! km{{ 1 ! ! ! 9Z]U )(9{189 ) 0RE{m mQ1u RQZ{{{sy{s}{s}{s}RYZ 49Mc]{U{UUaueJ}{yJIR!(1) ces{}{}sysususu{sy{s}{s}{sskqs ,1iki]Y{]}}qaIs!(9) ! 1km{sususususqsq{sy{s}{sy{ky{ky!UZ!i{]s]{emem] 4Z 9ARsqsususqsukq{kq{Zy{J1!!!!u{ek]ke{e{Y{U{]M $J JMR !R]kcm{RisBes1ek!akikqs!!!qsecYc]ke{e{Y{Q{Q{ B JMZJMR ! ) ()0189
#
# This program is free software; you can redistribute and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 2, or (at your option) any later
# version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY, without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
import os
import sys
if getattr(sys, 'frozen', False):
# frozen
here = os.path.dirname(sys.executable)
os.chdir(here)
from tkinter import * # GUI stuff
import gausssum.gausssumgui
if __name__=="__main__":
root = Tk()
root.title("GaussSum")
app = gausssum.gausssumgui.App(root,sys.argv) # Set up the app...
mainloop() # ...and sit back
GaussSum-3.0.2/gausssum/ 0000777 0001750 0001750 00000000000 13222436700 013611 5 ustar noel noel GaussSum-3.0.2/gausssum/__init__.py 0000666 0001750 0001750 00000000000 13222437274 015717 0 ustar noel noel GaussSum-3.0.2/gausssum/aboutbox.py 0000666 0001750 0001750 00000006156 13222437274 016025 0 ustar noel noel #
# GaussSum (http://gausssum.sf.net)
# Copyright (C) 2006-2015 Noel O'Boyle
#
# This program is free software; you can redistribute and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 2, or (at your option) any later
# version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY, without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
from tkinter import * # GUI stuff
import webbrowser
import tkinter.simpledialog
import traceback
import copy # For deepcopy...until I find a better way of doing this
from cclib.parser import ADF, GAMESS, Gaussian
import os, sys
if hasattr(sys, "frozen"): # i.e. if using py2exe
installlocation = os.path.dirname(sys.executable)
else:
import gausssum
installlocation = gausssum.__path__[0]
class AboutPopupBox(tkinter.simpledialog.Dialog):
def __init__(self, parent, title = None): # Override (just to set the geometry!)
Toplevel.__init__(self, parent)
self.transient(parent)
if title:
self.title(title)
self.parent = parent
self.result = None
body = Frame(self)
self.initial_focus = self.body(body)
body.pack(padx=5, pady=5)
self.buttonbox()
self.grab_set()
if not self.initial_focus:
self.initial_focus = self
self.protocol("WM_DELETE_WINDOW", self.cancel)
self.initial_focus.focus_set()
self.wait_window(self)
def body(self,master): # Override
self.resizable(False,False)
self.canvas2 = Canvas(master,width=340,height=260)
self.canvas2.pack(side=TOP)
self.photo2 = PhotoImage(file=os.path.join(installlocation,"mesh.gif"))
self.item2 = self.canvas2.create_image(11,11,anchor=NW,image=self.photo2)
Label(master,text="(c) 2006-2016 Noel O'Boyle").pack(side=TOP)
Label(master,text="http://gausssum.sf.net").pack(side=TOP)
Label(master,text="").pack(side=TOP) # Creates a bit of spacing at the bottom
Label(master,text="Support GaussSum by citing:").pack(side=TOP)
Label(master,text="N.M. O'Boyle, A.L. Tenderholt and K.M. Langner.",font=("Times",10,"bold")).pack(side=TOP)
Label(master,text="J. Comp. Chem. 2008, 29, 839-845.",font=("Times",10,"bold")).pack(side=TOP)
# Label(master,text="").pack(side=TOP) # Creates a bit of spacing at the bottom
width, height = 354, 455
x = (652-width)//2 + self.parent.winfo_rootx()
y = (480-height)//2 + self.parent.winfo_rooty()
self.geometry("%dx%d+%d+%d" % (width, height, x, y)) # Place it in the centre of the root window
def openmybrowser(self): # New
webbrowser.open("http://gausssum.sf.net")
def buttonbox(self): # Override
box = Frame(self)
w = Button(box, text="OK", width=10, command=self.ok, default=ACTIVE)
w.pack(side=LEFT, padx=5, pady=5)
self.bind("", self.ok)
box.pack()
GaussSum-3.0.2/gausssum/electrontrans.py 0000666 0001750 0001750 00000045265 13222437274 017071 0 ustar noel noel #
# GaussSum (http://gausssum.sf.net)
# Copyright (C) 2006-2013 Noel O'Boyle
#
# This program is free software; you can redistribute and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 2, or (at your option) any later
# version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY, without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details
import os
import sys
import math
import stat
import numpy
import glob
from gausssum.utils import GaussianSpectrum, levelname, percent
from cclib.parser.utils import convertor
# from Tkinter import *
from .mpl import MPLPlot
from .plot import DisplayPlot
from .folder import folder
def createEDDM(screen, logfile, contrib, gaussdir, unres):
def cubman(cmds):
if cmds[0] == "sc":
output.write("echo Scaling %s by %s\n" % (cmds[1], cmds[-1]))
elif cmds[0] == "a":
output.write("echo Adding to %s\n" % cmds[3])
elif cmds[0] == "sq":
output.write("echo Squaring %s\n" % cmds[1])
elif cmds[0] == "su":
output.write("echo Subtracting %s from %s\n" % (cmds[1], cmds[3]))
lines = []
lines.append("echo %s > tmp.txt" % cmds[0])
for cmd in cmds[1:]:
lines.append("echo %s >> tmp.txt" % cmd)
cmdname = syscmd[CAT]
lines.append("%s tmp.txt | %s%scubman > tmp2.txt\n" % (cmdname, envvar('G03DIR'), os.sep))
output.write("\n".join(lines))
def envvar(x):
if windows:
return "%" + x + "%"
else:
return "${" + x + "}"
def createcubes(mo):
cube = "mo%s.cub" % getmo(mo)
report = "echo Creating cubefile %s" % cube
orb = mo[0] + 1
if unres:
calctype = ['alpha', 'beta'][mo[1]]
orb += len(logfile.moenergies[0]) * mo[1]
cmd = "%s%scubegen 0 MO=%d %s %s -2 h\n" % (
envvar('G03DIR'), os.sep, orb, fchkpoint, cube)
if windows:
line = "if not exist %s %s & %s\n" % (cube, report, cmd)
else:
line = 'if [ ! -e "%s" ]\nthen\n %s\n %s\nfi\n' % (cube, report, cmd)
output.write(line)
def getmo(mo):
suffix = ""
if unres:
suffix = ["A", "B"][mo[1]]
return "%d%s" % (mo[0] + 1, suffix)
def createsquares(mo):
cube = "mo%s.cub" % getmo(mo)
sq = "sq%s.cub" % getmo(mo)
if windows:
output.write("if not exist %s (\n" % sq)
else:
output.write("if [ ! -e %s ]\nthen\n" % sq)
cubman(["sq", cube, "y", sq, "y"])
if windows:
output.write(")\n")
else:
output.write("fi\n")
def formchk(filename):
filename = filename.split(fakeossep)[-1]
fchkpoint = filename.replace('.chk', '.fck')
report = "echo Formatting %s to %s" % (filename, fchkpoint)
cmd = "%s%sformchk %s %s > tmp2.txt\n" % (envvar('G03DIR'), os.sep, filename,
fchkpoint)
if windows:
line = "if not exist %s %s & %s\n" % (fchkpoint, report, cmd)
else:
line = 'if [ ! -e "%s" ]\nthen\n %s\n %s\nfi\n' % (fchkpoint, report, cmd)
return fchkpoint, line
windows = sys.platform == "win32"
## windows = False
fakeossep = os.sep
## fakeossep = "\\"
## os.sep = "/"
COPY, DELETE, CAT, MOVE = range(4)
syscmd = ['cp', 'rm', 'cat', 'mv']
if windows:
syscmd = ['copy', 'del', 'type', 'move']
fchkpoint = glob.glob(os.path.join(gaussdir, "*.fck")) + glob.glob(os.path.join(gaussdir, "*.fchk"))
line = ""
if len(fchkpoint) == 0:
chkpoint = glob.glob(os.path.join(gaussdir, "*.chk"))
fchkpoint, line = formchk(chkpoint[0])
else:
fchkpoint = fchkpoint[0].split(fakeossep)[-1]
# Error!
screen.write("Creating the EDDM script file for %s\n" % fchkpoint)
if windows:
output = open(os.path.join(gaussdir, "eddm.bat"), "w")
output.write("@echo off\n")
else:
finalsection = []
output = open(os.path.join(gaussdir, "eddm.sh"), "w")
os.chmod(os.path.join(gaussdir, "eddm.sh"), stat.S_IRWXU) # Make executable
if line:
output.write(line)
output.write("echo === Using formatted checkpoint %s ===\n" % fchkpoint)
for i in range(len(logfile.etenergies)): # For each transition
if windows:
output.write("""if "%%1" == "%d" goto :tran%d\n""" % (i+1, i+1))
else:
finalsection.append("""if [ "$1" == "%d" ]\nthen\n tran%d\nfi\n""" % (i+1, i+1))
line = "echo You need to specify a transition in the range 1 to %d\n" % len(logfile.etenergies)
if windows:
output.write("%s\ngoto :end\n" % line)
else:
finalsection.append(line)
for i in range(len(logfile.etenergies)): # For each transition
if windows:
output.write(":tran%d\n" % (i+1))
else:
output.write("function tran%d\n{\n" % (i+1))
totalcon = sum(contrib[i])
scales = [x / float(totalcon) for x in contrib[i]]
minimum_scale = 0 # Don't include contributions that don't contribute!
# Create any necessary cube and squared files
alreadydone = set()
for sec, scale in zip(logfile.etsecs[i], scales):
if scale > minimum_scale:
for M in range(2):
if sec[M] not in alreadydone:
createcubes(sec[M])
createsquares(sec[M])
alreadydone.add(sec[M])
N = 0 # Find the first transition with non-zero scale
while N < len(scales) and scales[N] <= minimum_scale:
N += 1
if N < len(scales):
scale = scales[N]
cubman(["sc","sq%s.cub" % getmo(logfile.etsecs[i][N][0]),"y","before.cub","y",str(scale)])
cubman(["sc","sq%s.cub" % getmo(logfile.etsecs[i][N][1]),"y","after.cub","y",str(scale)])
created_tmp = False
for j in range(N + 1, len(logfile.etsecs[i])):
scale = scales[j]
if scale > minimum_scale:
created_tmp = True
cubman(["sc","sq%s.cub" % getmo(logfile.etsecs[i][j][0]),"y","tmp.cub","y",str(scale)])
cubman(["a","tmp.cub","y","before.cub","y","tmp2.cub","y"])
output.write("%s tmp2.cub before.cub\n" % syscmd[MOVE])
cubman(["sc","sq%s.cub" % getmo(logfile.etsecs[i][j][1]),"y","tmp.cub","y",str(scale)])
cubman(["a","tmp.cub","y","after.cub","y","tmp2.cub","y"])
output.write("%s tmp2.cub after.cub\n" % syscmd[MOVE])
if created_tmp:
output.write("%s tmp.cub\n" % syscmd[DELETE])
cubman(["su","before.cub","y","after.cub","y",
"trans%d.cub" % (i+1,),"y"])
else:
output.write("echo No significant contributions found")
if windows:
output.write("goto :end\n")
else:
output.write("}\n")
if windows:
output.write(":end\n")
else:
output.write("\n".join(finalsection))
output.close()
def readorbital_data(inputfile):
# Reads in all data from orbital_data.txt
line=inputfile.readline(); NBasis=int(line.split()[1])
line=inputfile.readline().split(); HOMO=[int(line[1])-1]
unres=False
if len(line)==3:
unres=True # This is an unrestricted calculation
HOMO.append(int(line[2])-1)
line=inputfile.readline(); NGroups=int(line.split()[1])
groupname=[]; groupatoms=[]
for i in range(NGroups): # Read in group info
line=inputfile.readline()
temp=line.split('\t')
groupname.append(temp[0])
groupatoms.append(map(int,temp[1].split()))
line=inputfile.readline()
headers = inputfile.readline()
# Contribs for orbital#1 will be in contrib[0][0-->NGroups]
if not unres:
contrib = numpy.zeros((1,NBasis,NGroups), "d")
else:
contrib = numpy.zeros((2,NBasis,NGroups), "d")
evalues=[]
for i in range(NBasis-1,-1,-1):
line=inputfile.readline().split()
evalue = [float(line[2])]
more = line[4+NGroups:4+NGroups*2] # Strip off the crud at the start
contrib[0,i,:] = [float(x) for x in more]
if unres:
evalue.append(float(line[6+NGroups*2]))
more = line[8+NGroups*3:8+NGroups*4]
contrib[1,i,:] = [float(x) for x in more]
evalues.append(evalue)
evalue.reverse() # Because you're reading them in backwards
return HOMO,NBasis,NGroups,groupname,groupatoms,contrib,evalues
def ET(root,screen,logfile,logfilename,
start,end,numpts,FWHM,UVplot,
EDDM):
screen.write("Starting to analyse the electronic transitions\n")
# Create output directory if necessary
gaussdir=folder(screen,logfilename)
unres = len(logfile.homos) > 1
CIS = logfile.etsecs
if UVplot==True:
#######################################################
# UV-Visible section #
#######################################################
# Read in orbital_data.txt if it exists(which contains info on the contribs)
NGroups=0
orbdata = False
try:
inputfile=open(os.path.join(gaussdir,"orbital_data.txt"),"r")
except IOError:
screen.write("orbital_data.txt not found\n")
else:
thisHOMO,NBasis,NGroups,groupname,groupatoms,contrib,evalue=readorbital_data(inputfile)
inputfile.close()
orbdata=True
screen.write("Using orbital_data.txt\n")
if thisHOMO != list(logfile.homos):
screen.write("Disagreement on HOMO...orbital_data.txt says "+str(thisHOMO)+"\n"+logfile.filename+" says "+str(logfile.homos)+"\n")
return False
screenCD=[]
for i in range(len(logfile.etenergies)): # For each transition
screenCD.append("")
# charge density [before, after] for each of the groups for each of the transitions
majorCIS, minorCIS = [[] for x in logfile.etenergies], [[] for x in logfile.etenergies]
allpercent = [[] for x in logfile.etenergies]
for i in range(len(logfile.etenergies)): # For each transition
if orbdata:
CD=[ [0, 0] for x in range(NGroups)]
totcontribs = 0
for j in range(len(CIS[i])): # For each contribution
thisCIS = CIS[i][j]
mycontrib = thisCIS[2] ** 2
totcontribs += mycontrib # tot up the contribs
percontrib = int(mycontrib * 100 + .5)
if orbdata:
for k in range(NGroups):
CD[k][0] += mycontrib * contrib[thisCIS[0][1], thisCIS[0][0], k] # Add to 'before' charge density
CD[k][1] += mycontrib * contrib[thisCIS[1][1], thisCIS[1][0], k] # Add to 'after' charge density
alphabeta = ["", ""]
if unres:
alphabeta = [["(A)", "(B)"][thisCIS[0][1]], ["(A)", "(B)"][thisCIS[1][1]]]
CIStext = "%s%s->%s%s (%d%%)" % (levelname(thisCIS[0][0], logfile.homos[thisCIS[0][1]]), alphabeta[0],
levelname(thisCIS[1][0], logfile.homos[thisCIS[1][1]]), alphabeta[1],
percontrib)
if percontrib >= 10: # Major contributions (>=10%)
majorCIS[i].append(CIStext)
elif percontrib >= 2: #Minor contributions (>=2%)
minorCIS[i].append(CIStext)
allpercent[i].append(percontrib)
if orbdata:
for j in range(len(groupname)): # The charge densities are scaled so that they add to one
CD[j][0]=CD[j][0]/totcontribs
CD[j][1]=CD[j][1]/totcontribs
screenCD[i]=screenCD[i]+percent(CD[j][0])+"-->"+percent(CD[j][1])+" ("+percent(round(CD[j][1],2)-round(CD[j][0],2))+")\t"
if EDDM:
createEDDM(screen, logfile, allpercent, gaussdir, unres)
# Write UVData.txt containing info on the transitions
fileoutput = ""
for i in range(len(logfile.etenergies)): # For each transition
temp = [i+1,logfile.etenergies[i],
convertor(logfile.etenergies[i],"cm-1","nm"),
logfile.etoscs[i],logfile.etsyms[i],
", ".join(majorCIS[i]),", ".join(minorCIS[i])]
if orbdata:
temp.append(screenCD[i])
fileoutput += "\t".join(map(str,temp)) + "\n"
screen.write("Writing the transition info to UVData.txt\n")
outputfile=open(os.path.join(gaussdir,"UVData.txt"),"w")
outputfile.write("HOMO is "+str(logfile.homos[0]+1))
if unres:
outputfile.write("\t%d" % (logfile.homos[1] + 1,))
outputfile.write("\nNo.\tEnergy (cm-1)\tWavelength (nm)\tOsc. Strength\tSymmetry\tMajor contribs\tMinor contribs")
for i in range(NGroups):
outputfile.write("\t"+groupname[i])
outputfile.write("\n"+fileoutput)
outputfile.close()
endwaveno = convertor(start,"nm","cm-1")
startwaveno = convertor(end,"nm","cm-1")
t = GaussianSpectrum(startwaveno,endwaveno,numpts,
( logfile.etenergies,[[x*2.174e8/FWHM for x in logfile.etoscs]] ),
FWHM)
screen.write("Writing the spectrum to UVSpectrum.txt\n")
outputfile=open(os.path.join(gaussdir,"UVSpectrum.txt"),"w")
outputfile.write("Energy (cm-1)\tWavelength (nm)\tAbs\t<--UV Spectrum\tUV-Vis transitions-->\tEnergy (cm-1)\tWavelength (nm)\tOsc. strength\n")
width=endwaveno-startwaveno
for x in range(numpts):
realx=width*x/numpts+startwaveno
outputfile.write(str(realx)+"\t"+str(convertor(realx,"cm-1","nm"))+"\t"+str(t.spectrum[0,x]))
if x\tWavelength (nm)\tEnergy (cm-1)\tR(length)\n")
width = endwaveno - startwaveno
for x in range(numpts):
# Need to use float, otherwise it's an integer
# realx = float(width)*x/numpts+start
realx = width * x / numpts + startwaveno
outputfile.write("%f\t%f\t%f" % (realx, 1.0e7/realx, t.spectrum[0,x]))
if x < len(logfile.etenergies): # Write the R values out also
outputfile.write( "\t\t\t%f\t%f\t%f" % (convertor(logfile.etenergies[x], "cm-1", "nm"),
logfile.etenergies[x],logfile.etrotats[x]) )
outputfile.write("\n")
outputfile.close()
if root:
# Plot the UV Spectrum using Gnuplot
screen.write("Plotting using Gnuplot\n")
if max(t.spectrum[0,:])<1E-8: # Gnuplot won't draw it if the spectrum is flat
screen.write("There are no peaks in this wavelength range!\n")
else:
g = MPLPlot()
g.setlabels("Wavelength (nm)", r"$\epsilon$")
xvalues_nm = [convertor(x,"cm-1","nm") for x in t.xvalues]
g.data(zip(xvalues_nm,t.spectrum[0,:]))
energies_nm = [convertor(x,"cm-1","nm") for x in logfile.etenergies]
oscdata = [(x, y) for x, y in zip(energies_nm, logfile.etrotats) if start < x < end]
g.data(oscdata, vlines=True, y2axis="R (length) / $10^{-40}$")
g.subplot.set_xlim(left=start, right=end)
g.secondaxis.set_ylim(bottom=0)
DisplayPlot(root, g, "Circular dichroism spectrum")
screen.write("Finished")
#######################################################
# End of main #
#######################################################
GaussSum-3.0.2/gausssum/folder.py 0000666 0001750 0001750 00000002257 13222437274 015453 0 ustar noel noel #
# GaussSum (http://gausssum.sf.net)
# Copyright (C) 2006-2009 Noel O'Boyle
#
# This program is free software; you can redistribute and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 2, or (at your option) any later
# version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY, without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
# Creates a new output folder if it doesn't already exist
# The folder is created in the same directory as the input file
import os
def folder(screen, logfilename, create=True):
# Create the output directory if necessary
logdir=os.path.dirname(logfilename)
logname=os.path.basename(logfilename)
gaussdir=os.path.join(logdir,"gausssum3")
if create:
if not os.path.isdir(gaussdir):
screen.write("Creating new output folder\n")
os.mkdir(gaussdir)
else:
screen.write("Using old output folder\n")
return gaussdir
GaussSum-3.0.2/gausssum/gausssumgui.py 0000666 0001750 0001750 00000064521 13222437274 016556 0 ustar noel noel #
# GaussSum (http://gausssum.sf.net)
# Copyright (C) 2006-2009 Noel O'Boyle
#
# This program is free software; you can redistribute and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 2, or (at your option) any later
# version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY, without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
from tkinter import * # GUI stuff
import tkinter.messagebox # For the About Dialog
import tkinter.filedialog # For the Open File and Save File
import webbrowser
import tkinter.simpledialog
import traceback
import copy # For deepcopy...until I find a better way of doing this
import configparser # For writing the settings to an .ini file
import logging
import glob
from cclib.parser import ADF, GAMESS, Gaussian, ccopen
from gausssum.preferencesbox import PreferencesPopupBox
from gausssum.aboutbox import AboutPopupBox
from gausssum.popanalysis import Popanalysis
from gausssum.electrontrans import ET
from gausssum.geoopt import GeoOpt
from gausssum.search import Search
from gausssum.vibfreq import Vibfreq
from gausssum.scf import SCF
from gausssum.utils import *
from gausssum.folder import folder
import os, sys
if hasattr(sys, "frozen"): # i.e. if using cx_Freeze
installlocation = os.path.dirname(sys.executable)
else:
import gausssum
installlocation = gausssum.__path__[0]
class App: # This sets up the GUI
def __init__(self,root,argv):
self.root = root
self.root.resizable(False,False)
self.addmenubar()
self.frame1=Frame(self.root)
self.frame1.grid()
frame2=Frame(self.root)
frame2.grid(row=1)
self.scrollbar=Scrollbar(frame2)
self.scrollbar.pack(side=RIGHT,fill=Y)
if sys.platform == "win32":
self.txt=Text(frame2,font=("Courier New",8),yscrollcommand=self.scrollbar.set,width=90,height=21)
else: # Avoid font problems (? I don't remember the reason for this)
self.txt=Text(frame2,yscrollcommand=self.scrollbar.set,width=90,height=21)
self.txt.pack(expand=1,fill=Y)
self.scrollbar.config(command=self.txt.yview)
self.screen=Redirect(self.txt.insert,self.root,[END,self.txt]) # Oh yeah! Could I have done it in a more roundabout way?
self.screen.write("Support GaussSum by citing:\nN.M. O'Boyle, A.L. Tenderholt and K.M. Langner. J. Comp. Chem. 2008, 29, 839-845.\n")
frame3=Frame(self.frame1,relief=GROOVE,borderwidth=3)
frame3.pack(side=LEFT,anchor=W)
self.middleframe=Frame(self.frame1,width=380,height=140)
self.middleframe.pack(side=LEFT)
# Thanks to the students from Ulm for the next line
# which prevents self.middleframe resizing when you choose a different option
self.middleframe.pack_propagate(0)
self.frame4=Frame(self.middleframe)
self.frame4.pack(side=LEFT)
self.script = StringVar()
self.b3=Radiobutton(frame3, text="Search file", variable=self.script, value="FIND",command=self.option,state=DISABLED)
self.b3.pack(anchor=W)
self.b0=Radiobutton(frame3, text="Monitor SCF", variable=self.script, value="SCF",command=self.option,state=DISABLED)
self.b0.pack(anchor=W)
self.b1=Radiobutton(frame3, text="Monitor GeoOpt", variable=self.script, value="GEOOPT",command=self.option,state=DISABLED)
self.b1.pack(anchor=W)
self.b2=Radiobutton(frame3, text="Frequencies", variable=self.script, value="IR_RAMAN",command=self.option,state=DISABLED)
self.b2.pack(anchor=W)
self.b5=Radiobutton(frame3, text="Orbitals", variable=self.script, value="MO",command=self.option,state=DISABLED)
self.b5.pack(anchor=W)
self.b4=Radiobutton(frame3, text="Electronic transitions", variable=self.script, value="UVVIS",command=self.option,state=DISABLED)
self.b4.pack(anchor=W)
## self.b6=Radiobutton(frame3, text="EDDM.py", variable=self.script, value="EDDM", command=self.option,state=DISABLED)
## self.b6.pack(anchor=W)
## self.b7=Radiobutton(frame3, text="NMR.py (beta)", variable=self.script, value="NMR", command=self.option,state=DISABLED)
## self.b7.pack(anchor=W)
self.b3.select()
self.frame5=Frame(self.frame1)
self.frame5.pack(side=LEFT)
self.photo = PhotoImage(file=os.path.join(installlocation,"mesh2.gif")) # Doesn't work if don't use self.
Button(self.frame5,image=self.photo,command=self.runscript).pack(side=LEFT)
self.root.bind("", self.runscript)
x = (self.root.winfo_screenwidth()-652)//2 # The window is 652x480
y = (self.root.winfo_screenheight()-580)//2
self.root.geometry("652x480+"+str(x)+"+"+str(y)) # Get the window dead-centre
self.error=ErrorCatcher()
# Read in the preferences from the preferences file.
# If it doesn't exist, create one using the defaults.
self.readprefs()
if len(argv)>1: # What to do if a filename is passed as an argument
if os.path.isfile(argv[1]): # Does it exist?
self.inputfilename=os.path.basename(argv[1])
t=os.path.dirname(argv[1])
if t:
os.chdir(t)
# Create an instance of the parser
self.logfile = ccopen(self.inputfilename)
self.fileopenednow()
else:
self.screen.write(argv[1]+" does not exist or is not a valid filename\n")
self.inputfilename=None
else:
self.inputfilename=None
### Read in the nmr standards file (if it exists)
## self.nmrstandards = NMRstandards(self.settings['nmr.data'])
def option(self):
# What to do when they choose a script
s=self.script.get()
self.frame4.destroy()
self.frame4=Frame(self.middleframe,width=380)
self.frame4.pack(side=LEFT)
if s=="SCF" or s=="GEOOPT":
Label(self.frame4,text="Leave out the first n points").pack(side=LEFT)
self.numpts=Entry(self.frame4,width=3)
self.numpts.pack(side=LEFT)
self.numpts.insert(0,"0")
self.reparse = IntVar()
ckb = Checkbutton(self.frame4, text="Reparse first?",
variable=self.reparse)
ckb.pack(side=LEFT)
elif s=="IR_RAMAN":
frame5=Frame(self.frame4)
frame5.pack(side=TOP)
frame6=Frame(self.frame4)
frame6.pack(side=TOP)
frame7=Frame(self.frame4)
frame7.pack(side=TOP)
frame8=Frame(self.frame4)
frame8.pack(side=TOP)
frame9=Frame(self.frame4)
frame9.pack(side=TOP)
Label(frame5,text="Start:").pack(side=LEFT)
self.start=Entry(frame5,width=5)
self.start.pack(side=LEFT)
self.start.insert(0,self.settings['ir_raman.start'])
Label(frame5,text="End:").pack(side=LEFT)
self.end=Entry(frame5,width=5)
self.end.pack(side=LEFT)
self.end.insert(0,self.settings['ir_raman.end'])
Label(frame5,text="Num pts:").pack(side=LEFT)
self.numpts=Entry(frame5,width=6)
self.numpts.pack(side=LEFT)
self.numpts.insert(0,self.settings['ir_raman.numpoints'])
Label(frame5,text="FWHM").pack(side=LEFT)
self.FWHM=Entry(frame5,width=3)
self.FWHM.pack(side=LEFT)
self.FWHM.insert(0,self.settings['ir_raman.fwhm'])
Label(frame6,text="Scaling factors:").pack(side=LEFT)
self.scale=StringVar()
r=Radiobutton(frame6,text="General",variable=self.scale,value="Gen")
r.pack(side=LEFT)
self.scalefactor=Entry(frame6,width=5)
self.scalefactor.insert(0,'1.00')
self.scalefactor.pack(side=LEFT)
r2=Radiobutton(frame6,text="Individual",variable=self.scale,value="Indiv")
r2.pack(side=LEFT)
r.select()
Label(frame7, text="The following are used to calculate Raman intensities:").pack()
Label(frame8, text="Exc. wavelength (nm)").pack(side=LEFT)
self.excitation = Entry(frame8, width=6)
self.excitation.pack(side=LEFT)
self.excitation.insert(0, self.settings['ir_raman.excitation'])
Label(frame8, text="Temp. (K)").pack(side=LEFT)
self.temperature = Entry(frame8,width=6)
self.temperature.pack(side=LEFT)
self.temperature.insert(0, self.settings['ir_raman.temperature'])
if not hasattr(self.data, "vibramans"):
self.excitation.configure(state=DISABLED)
self.temperature.configure(state=DISABLED)
elif s=="FIND":
frame6=Frame(self.frame4)
frame6.pack(side=LEFT)
frame7=Frame(self.frame4)
frame7.pack(side=LEFT)
self.searchrad=StringVar()
for i in range(4):
t="find.text%d" % (i+1)
Radiobutton(frame6, text=self.settings[t], variable=self.searchrad, value=self.settings[t]).grid(sticky=W)
r=Radiobutton(frame6, text="Custom", variable=self.searchrad, value="Custom")
r.grid(sticky=W)
r.select()
self.customsearch=Entry(frame6,width=15)
self.customsearch.grid(row=4,column=1)
self.customsearch.insert(END,"Enter phrase here")
self.casesensitive=IntVar()
casetick=Checkbutton(frame6,text="Case sensitive",variable=self.casesensitive)
casetick.grid(row=4,column=2)
elif s=="MO":
frame8=Frame(self.frame4)
frame6=Frame(self.frame4)
frame7=Frame(self.frame4)
frame8.pack()
frame6.pack(side=TOP)
frame7.pack(side=TOP)
self.MOplot=IntVar()
self.MODOS=Radiobutton(frame8, text="DOS", variable=self.MOplot, value=False)
self.MODOS.pack(anchor=W)
self.MOCOOP=Radiobutton(frame8, text="COOP", variable=self.MOplot, value=True)
self.MOCOOP.pack(anchor=W)
self.MODOS.select()
Label(frame6,text="Start:").pack(side=LEFT)
self.start=Entry(frame6,width=5)
self.start.pack(side=LEFT)
self.start.insert(0,self.settings['mo.start'])
Label(frame6,text="End:").pack(side=LEFT)
self.end=Entry(frame6,width=5)
self.end.pack(side=LEFT)
self.end.insert(0,self.settings['mo.end'])
Label(frame6,text="FWHM:").pack(side=LEFT)
self.FWHM=Entry(frame6,width=5)
self.FWHM.pack(side=LEFT)
self.FWHM.insert(0,self.settings['mo.fwhm'])
self.makeorigin=IntVar()
self.makeoriginbtn=Checkbutton(frame7,text="Create originorbs.txt?",variable=self.makeorigin)
self.makeoriginbtn.pack(anchor=W)
elif s=="UVVIS":
frame7=Frame(self.frame4)
frame7.pack(side=TOP)
frame6=Frame(self.frame4)
frame6.pack()
self.UVplot=IntVar()
self.UVbox=Radiobutton(frame7, text="UV-Visible", variable=self.UVplot, command=self.UVupdate, value=True)
self.UVbox.pack(anchor=W)
self.CDbox=Radiobutton(frame7, text="Circular dichroism", variable=self.UVplot, command=self.UVupdate, value=False)
self.CDbox.pack(anchor=W)
self.UVbox.select()
Label(frame6,text="Start:").grid(row=0,column=0)
Label(frame6,text="nm").grid(row=1,column=1)
self.start=Entry(frame6,width=5)
self.start.grid(row=0,column=1)
self.start.insert(0,self.settings['uvvis.start'])
Label(frame6,text="End:").grid(row=0,column=2)
Label(frame6,text="nm").grid(row=1,column=3)
self.end=Entry(frame6,width=5)
self.end.grid(row=0,column=3)
self.end.insert(0,self.settings['uvvis.end'])
Label(frame6,text="Num pts:").grid(row=0,column=4)
self.numpts=Entry(frame6,width=5)
self.numpts.grid(row=0,column=5)
self.numpts.insert(0,self.settings['uvvis.numpoints'])
self.fwhmlabel=Label(frame6,text="FWHM",width=6)
self.fwhmlabel.grid(row=0,column=6)
self.fwhmunits=Label(frame6,text="1/cm")
self.fwhmunits.grid(row=1,column=7)
self.FWHM=Entry(frame6,width=5)
self.FWHM.grid(row=0,column=7)
self.FWHM.insert(0,self.settings['uvvis.fwhm'])
self.eddm = IntVar()
self.eddmbtn = Checkbutton(frame7, text="Create EDDM script?", variable=self.eddm)
self.eddmbtn.pack(anchor=W)
gaussdir = folder(self.screen, self.logfile.filename, create=False)
if (len(glob.glob(os.path.join(gaussdir, "*.fck"))) == 0 and
len(glob.glob(os.path.join(gaussdir, "*.fchk"))) == 0 and
len(glob.glob(os.path.join(gaussdir, "*.chk"))) == 0):
self.eddmbtn.configure(state=DISABLED)
def createnmrpanel(self,parent):
# Sets up the Panel for the NMR options
frame6=Frame(parent)
frame6.grid(row=0,column=0)
# Set up the Radiobuttons
self.nmrrb = StringVar() # Extract, Comment, Listbox
self.nmrrb1=Radiobutton(frame6, text="Just extract NMR data", variable=self.nmrrb, value="Extract",command=self.nmrrbcb)
self.nmrrb1.pack(anchor=W)
self.nmrrb2=Radiobutton(frame6, text="Take level of theory from comment", variable=self.nmrrb, value="Comment",command=self.nmrrbcb)
self.nmrrb2.pack(anchor=W)
self.nmrrb3=Radiobutton(frame6, text="Take level of theory from listbox", variable=self.nmrrb, value="Listbox",command=self.nmrrbcb)
self.nmrrb3.pack(anchor=W)
self.nmrrb1.select()
# Set up the Listbox
frame7=Frame(parent)
frame7.grid(row=1,column=0)
nmrscrlbar=Scrollbar(frame7,orient=VERTICAL)
self.nmrlbx1=Listbox(frame7,yscrollcommand=nmrscrlbar.set,height=5)
nmrscrlbar.config(command=self.nmrlbx1.yview)
nmrscrlbar.pack(side=RIGHT,fill=Y)
self.nmrlbx1.pack(side=LEFT,fill=BOTH,expand=1)
for x in self.nmrstandards:
self.nmrlbx1.insert(END,x['theory'])
self.nmrlbx1.select_set(0)
self.nmrlbx1.configure(state=DISABLED)
# Set up more Radiobuttons
frame8=Frame(parent)
frame8.grid(row=0,column=1)
self.nmrrb2 = StringVar() # Calculate, Standard
self.nmrrb2a=Radiobutton(frame8, text="Calculate relative ppm", variable=self.nmrrb2, value="Calculate")
self.nmrrb2a.pack(anchor=W)
self.nmrrb2b=Radiobutton(frame8, text="Add new standard", variable=self.nmrrb2, value="Standard")
self.nmrrb2b.pack(anchor=W)
self.nmrrb2a.select()
self.nmrrb2a.configure(state=DISABLED)
self.nmrrb2b.configure(state=DISABLED)
def nmrrbcb(self):
# What to do when the user chooses one of the NMR radiobuttons
# (NMR RadioButton CallBack)
value=self.nmrrb.get()
if value=="Listbox": # Configure the listbox
self.nmrlbx1.configure(state=NORMAL)
else:
self.nmrlbx1.configure(state=DISABLED)
if value=="Extract": # Configure everything
self.nmrrb2a.configure(state=DISABLED)
self.nmrrb2b.configure(state=DISABLED)
elif value=="Listbox":
self.nmrrb2a.configure(state=NORMAL)
self.nmrrb2b.configure(state=DISABLED)
else:
self.nmrrb2a.configure(state=NORMAL)
self.nmrrb2b.configure(state=NORMAL)
def UVupdate(self):
# What to do when the user chooses UVVis or CD for UVVis.py
if self.UVplot.get()==False:
# Choose CD
self.fwhmlabel.configure(text="sigma:")
self.fwhmunits.configure(text="eV")
self.FWHM.delete(0,END)
self.FWHM.insert(0,self.settings['uvvis.sigma'])
else:
# Choose UVVis
self.fwhmlabel.configure(text="FWHM:")
self.fwhmunits.configure(text="1/cm")
self.FWHM.delete(0,END)
self.FWHM.insert(0,self.settings['uvvis.fwhm'])
def runscript(self,event=None):
# What to do when the user clicks on the GaussSum logo
# to run the script
if not self.inputfilename:
self.screen.write("You need to open a log file first\n")
return # Do nothing if no file opened
s = self.script.get()
self.txt.delete(1.0, END)
worked=False
try:
if s=="SCF":
if self.reparse.get():
self.data = self.logfile.parse()
worked = SCF(self.root,self.screen,self.data,int(self.numpts.get()))
elif s=="GEOOPT":
if self.reparse.get():
self.data = self.logfile.parse()
worked = GeoOpt(self.root,self.screen,self.data,int(self.numpts.get()))
elif s=="IR_RAMAN":
worked = Vibfreq(self.root,self.screen,self.data,self.logfile.filename,int(self.start.get()),int(self.end.get()),int(self.numpts.get()),float(self.FWHM.get()),self.scale.get(),float(self.scalefactor.get()),float(self.excitation.get()),float(self.temperature.get()))
elif s=="FIND":
if self.searchrad.get()=="Custom":
worked = Search(self.screen,self.logfile.filename,self.customsearch.get(),self.casesensitive.get())
else:
worked = Search(self.screen,self.logfile.filename,self.searchrad.get(),1)
elif s=="MO":
worked = Popanalysis(self.root,self.screen,self.data,self.logfile.filename,float(self.start.get()),float(self.end.get()),self.MOplot.get(),float(self.FWHM.get()),self.makeorigin.get())
elif s=="UVVIS":
worked = ET(self.root,self.screen,self.data,self.logfile.filename,int(self.start.get()),int(self.end.get()),int(self.numpts.get()),float(self.FWHM.get()),self.UVplot.get(),self.eddm.get())
## elif s=="NMR":
## listboxvalue=self.nmrlbx1.curselection()
## try: # Works for both list of strings and list of ints (see Tkinter documentation for details)
## listboxvalue=map(int,listboxvalue)
## except ValueError: pass
## if len(listboxvalue)>0:
## selected = self.nmrlbx1.get(listboxvalue[0])
## else:
## selected = []
## worked=GaussSum.NMR.NMR(self.screen,self.logfile,self.nmrrb.get(),
## selected,self.nmrrb2.get(),self.nmrstandards)
except:
traceback.print_exc(file=self.error) # Catch errors from the python scripts (user GIGO errors, of course!)
messagebox.showerror(title="The script is complaining...",message=self.error.log)
self.error.clear()
self.root.update()
def addmenubar(self):
"""Set up the menubar."""
menu = Menu(self.root)
self.root.config(menu=menu)
filemenu = Menu(menu)
menu.add_cascade(label="File", underline=0, menu=filemenu)
filemenu.add_command(label="Open...", underline=0, command=self.fileopen)
filemenu.add_command(label="Settings...",underline=0, command=self.preferences)
filemenu.add_separator()
filemenu.add_command(label="Exit", underline=1, command=self.fileexit)
viewmenu=Menu(menu)
menu.add_cascade(label="View", underline=0, menu=viewmenu)
viewmenu.add_command(label="Error messages", underline=1, command=self.showerrors)
helpmenu = Menu(menu)
menu.add_cascade(label="Help", underline=0, menu=helpmenu)
helpmenu.add_command(label="Documentation",underline=0, command=self.webdocs)
helpmenu.add_separator()
helpmenu.add_command(label="About...", underline=0, command=self.aboutdialog)
def aboutdialog(self,event=None): # Soaks up event if provided
d=AboutPopupBox(self.root,title="About GaussSum")
def showerrors(self):
self.screen.write("Log of error messages\n%s\n%s\n" % ('*'*20,self.error.longlog) )
def fileexit(self):
self.root.destroy()
def fileopen(self):
if self.inputfilename!=None:
mydir=os.path.dirname(self.inputfilename)
else:
mydir="."
inputfilename = tkinter.filedialog.askopenfilename(
filetypes=[
("All files",".*"),
("Output Files",".out"),
("Log Files",".log"),
("ADF output",".adfout")
],
initialdir=mydir
)
if inputfilename!="":
self.inputfilename=os.path.basename(inputfilename)
os.chdir(os.path.dirname(inputfilename))
# Create an instance of the parser
if hasattr(self, "logfile") and self.logfile!=None:
self.logfile.logger.removeHandler(self.logfile.logger.handlers[0])
self.logfile = ccopen(self.inputfilename)
self.fileopenednow()
def fileopenednow(self):
"""What to do once a file is opened."""
if self.logfile==None:
messagebox.showerror(
title="Not a valid log file",
message=("cclib does not recognise %s as a valid logfile.\n\n"
"If the file *is* valid, please send an email to "
"gausssum-help@lists.sourceforge.net\n describing the problem." % self.inputfilename)
)
for button in [self.b0, self.b1, self.b2, self.b3, self.b4, self.b5]:
button.configure(state=DISABLED)
return
# Prevent the logger writing to stdout; instead, write to screen
self.logfile.logger.removeHandler(self.logfile.logger.handlers[0])
newhandler = logging.StreamHandler(self.screen)
newhandler.setFormatter(logging.Formatter("[%(name)s %(levelname)s] %(message)s"))
self.logfile.logger.addHandler(newhandler)
try:
self.data = self.logfile.parse()
except:
messagebox.showerror(
title="Problems parsing the logfile",
message=("cclib has problems parsing %s.\n\n"
"If you think it shouldn't, please send an email to "
"gausssum-help@lists.sourceforge.net\n describing the problem." % self.inputfilename)
)
for button in [self.b0, self.b1, self.b2, self.b3, self.b4, self.b5]:
button.configure(state=DISABLED)
return
self.screen.write("Opened and parsed %s.\n" % self.inputfilename)
has = lambda x: hasattr(self.data, x)
self.b3.configure(state=NORMAL) # Search
if has("scftargets") and has("scfvalues"):
self.b0.configure(state=NORMAL)
else:
self.b0.configure(state=DISABLED)
if has("geotargets") and has("geovalues"):
self.b1.configure(state=NORMAL)
else:
self.b1.configure(state=DISABLED)
if has("vibfreqs") and (has("vibirs") or has("vibramans")):
self.b2.configure(state=NORMAL)
else:
self.b2.configure(state=DISABLED)
if has("etenergies") and has("etoscs"):
self.b4.configure(state=NORMAL)
else:
self.b4.configure(state=DISABLED)
self.b5.configure(state=NORMAL) # Orbitals
## self.b6.configure(state=NORMAL) # EDDM
## self.b7.configure(state=NORMAL) # NMR
self.b3.invoke() # Click on Find.py
self.root.title("GaussSum - "+self.inputfilename)
def preferences(self):
# The Preferences Dialog Box
oldsettings=copy.deepcopy(self.settings) # Remember the old settings
d=PreferencesPopupBox(self.root,self.settings,title="Settings")
if self.settings!=oldsettings: # if there are any changes
self.saveprefs()
def getsettingsfile(self):
# Check for GaussSum.ini in $APPDATA/GaussSum2.2 (XP)
# or $HOME/.GaussSum2.2 (Linux)
if sys.platform == "win32":
settingsfile = os.path.join(os.getenv("APPDATA"),"GaussSum2.2","GaussSum.ini")
else:
settingsfile = os.path.join(os.getenv("HOME"), ".GaussSum2.2","GaussSum.ini")
return settingsfile
def saveprefs(self):
# Save the settings
settingsfile = self.getsettingsfile()
writeoutconfigfile(self.settings,settingsfile)
def readprefs(self):
# The default settings are overwritten by any existing stored
# settings.
self.settings = {
'find.text1':'SCF Done',
'find.text2':'k 501%k502',
'find.text3':'imaginary',
'find.text4':'Framework',
'ir_raman.start':'0',
'ir_raman.end':'4000',
'ir_raman.numpoints':'500',
'ir_raman.fwhm':'10',
'ir_raman.excitation':'785',
'ir_raman.temperature':'293.15',
'mo.start':'-20',
'mo.end':'0',
'mo.fwhm':'0.3',
'uvvis.start':'300',
'uvvis.end':'800',
'uvvis.numpoints':'500',
'uvvis.fwhm':'3000',
'uvvis.sigma':'0.2',
}
settingsfile = self.getsettingsfile()
if os.path.isfile(settingsfile): # Check for settings file
# Found it! - so read it in.
self.settings.update(readinconfigfile(settingsfile))
else: # Initialise the settings file (and directory)
settingsdir = os.path.dirname(settingsfile)
if not os.path.isdir(settingsdir):
os.mkdir(settingsdir)
self.saveprefs() # Save the inital settings file
def webdocs(self):
if hasattr(sys, "frozen"): # Using cx_Freeze
webbrowser.open(os.path.join(installlocation, "Docs", "index.html"))
else:
webbrowser.open(os.path.join(installlocation, "..", "Docs", "index.html"))
GaussSum-3.0.2/gausssum/geoopt.py 0000666 0001750 0001750 00000003724 13222437274 015475 0 ustar noel noel #
# GaussSum (http://gausssum.sf.net)
# Copyright (C) 2006-2013 Noel O'Boyle
#
# This program is free software; you can redistribute and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 2, or (at your option) any later
# version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY, without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
import os
import sys
import math
# from Tkinter import *
from .plot import DisplayPlot
from .mpl import MPLPlot
def GeoOpt(root, screen, logfile, numpts):
screen.write("Starting GeoOpt.py\n")
deviation = []
for i in range(len(logfile.geovalues)):
dev = 0
for j in range(len(logfile.geotargets)):
if abs(logfile.geovalues[i][j]) > logfile.geotargets[j]:
dev += math.log(abs(logfile.geovalues[i][j]) / logfile.geotargets[j])
deviation.append(dev)
if len(logfile.scfenergies) >= numpts+2: # If there are two points to plot
g = MPLPlot()
g.setlabels("Optimisation Step", "Energy")
data = list(zip(range(len(logfile.scfenergies)-numpts), logfile.scfenergies[numpts:]))
g.data(data)
g.data(data, lines=False)
DisplayPlot(root, g, "Geometry optimisation")
if len(deviation) >= numpts+2:
h = MPLPlot()
h.setlabels("Optimisation Step", "Deviation from targets")
data = list(zip(range(len(deviation)-numpts), deviation[numpts:]))
h.data(data)
h.data(data, lines=False)
h.subplot.set_ylim(bottom=0)
DisplayPlot(root, h, "Deviation from targets")
else:
screen.write("I need at least two points to plot\n")
screen.write("Finishing GeoOpt.py\n")
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P ˾}0zO ; GaussSum-3.0.2/gausssum/mpl.py 0000666 0001750 0001750 00000003744 13222437274 014772 0 ustar noel noel #
# GaussSum (http://gausssum.sf.net)
# Copyright (C) 2006-2013 Noel O'Boyle
#
# This program is free software; you can redistribute and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 2, or (at your option) any later
# version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY, without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
from matplotlib.figure import Figure
from matplotlib import rcParams
from matplotlib import pyplot
rcParams.update({'figure.autolayout': True})
# Uncomment the following for XKCD-style plots
# pyplot.xkcd()
colors = "bgrcmyk"
class MPLPlot(object):
def __init__(self):
self.figure = Figure(figsize=(6,5), dpi=100)
self.subplot = self.figure.add_subplot(111)
self.cindex =0
def data(self, mtuples, lines=True, title=None, vlines=False, y2axis=""):
color = colors[self.cindex]
if y2axis:
new_axis = self.subplot.twinx()
new_axis.set_ylabel(y2axis)
self.secondaxis = new_axis
axis = new_axis
else:
axis = self.subplot
if not mtuples: return
xvals, yvals = zip(*mtuples)
if not lines:
axis.plot(xvals, yvals, "x", color=color, label=title)
else:
if not vlines:
axis.plot(xvals, yvals, color=color, label=title)
else:
for i, (xval, yval) in enumerate(zip(xvals, yvals)):
axis.vlines(xval, yval, 0, color=color, label=title if i==0 else "")
self.cindex += 1
if self.cindex == len(colors):
self.cindex = 0
def setlabels(self, xaxis, yaxis):
self.subplot.set_xlabel(xaxis)
self.subplot.set_ylabel(yaxis)
GaussSum-3.0.2/gausssum/plot.py 0000666 0001750 0001750 00000004060 13222437274 015150 0 ustar noel noel #
# GaussSum (http://gausssum.sf.net)
# Copyright (C) 2006-2013 Noel O'Boyle
#
# This program is free software; you can redistribute and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 2, or (at your option) any later
# version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY, without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
import os
from tkinter import *
# Matplotlib imports
import matplotlib
matplotlib.use('TkAgg')
from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2TkAgg
from matplotlib.backend_bases import key_press_handler
from matplotlib.figure import Figure
class DisplayPlot(object):
def __init__(self, root, g, title):
self.popup = Toplevel(root)
self.popup.focus_set()
self.popup.title(title)
self.title = title # do this better
self.popup.resizable(False,False)
self.frame1 = Frame(self.popup)
self.frame1.pack()
canvas = FigureCanvasTkAgg(g.figure, master=self.frame1)
canvas.show()
canvas.get_tk_widget().pack(side=TOP, fill=BOTH, expand=1)
toolbar = NavigationToolbar2TkAgg( canvas, self.frame1 )
toolbar.update()
canvas._tkcanvas.pack(side=TOP, fill=BOTH, expand=1)
frame2 = Frame(self.frame1)
frame2.pack(side=TOP)
def on_key_event(event):
key_press_handler(event, canvas, toolbar)
def close(event=None):
self.popup.destroy()
Button(frame2, text="Close", underline=0, command=close).pack(side=LEFT)
canvas.mpl_connect('key_press_event', on_key_event)
self.popup.bind("",close)
self.popup.bind("",close)
self.popup.bind("",close)
self.popup.protocol("WM_DELETE_WINDOW", close)
GaussSum-3.0.2/gausssum/popanalysis.py 0000666 0001750 0001750 00000050536 13222437274 016545 0 ustar noel noel #
# GaussSum (http://gausssum.sf.net)
# Copyright (C) 2006-2013 Noel O'Boyle
#
# This program is free software; you can redistribute and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 2, or (at your option) any later
# version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY, without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
import string
import os
import sys
import numpy
from math import exp, log
from .plot import DisplayPlot
from .mpl import MPLPlot
from .folder import folder
from gausssum.utils import levelname
from gausssum.utils import GaussianSpectrum
from gausssum.utils import Groups
def repr_of_evalue(evalue):
if numpy.isnan(evalue):
return "-"
else:
return "%.2f" % evalue
def Popanalysis(root,screen,logfile,logfilename,start,end,COOP,FWHM,makeorigin):
def DOSconvolute(orb_MPA,evalue):
"""Convolute the DOS spectrum"""
heights = [x for x in numpy.swapaxes(orb_MPA,0,1)]
# Remove any NAN eigenvalues from the convolution
not_nans = ~numpy.isnan(evalue)
nevalue = evalue[not_nans]
nheights = []
for h in heights:
nheights.append(h[not_nans])
spectrum = GaussianSpectrum(start, end, 1000,
(nevalue, nheights),
FWHM)
return spectrum
def tidy(num): # Changes +-0.155648 into +-0.16
if num>=0:
rounded=int(num*100+.5)/100.
return str(rounded)[:4]
else:
rounded=int(num*100-.5)/100.
return str(rounded)[:5]
def originoutput(MPA):
"""Write a file suitable for reading with Origin."""
outputfile=open(os.path.join(gaussdir,"origin_orbs.txt"),"w")
for i in range(len(evalue[0])):
if numgroups>0 and pop:
total=0
for j in range(numgroups):
outputfile.write(str(total)+"\t"+str(evalue[0][i])+"\t")
total += MPA[0][i,j]
outputfile.write("\n")
total=0
for j in range(numgroups):
total += MPA[0][i,j]
outputfile.write(str(total)+"\t"+str(evalue[0][i])+"\t")
outputfile.write("\n")
else:
outputfile.write("0\t"+str(evalue[0][i])+"\n")
outputfile.write("1\t"+str(evalue[0][i])+"\n")
if unres:
for i in range(len(evalue[1])):
if numgroups>0 and pop:
total=0
for j in range(numgroups):
outputfile.write(str(total)+"\t"+str(evalue[1][i])+"\t")
total += MPA[1][i,j]
outputfile.write("\n")
total=0
for j in range(numgroups):
total += MPA[1][i,j]
outputfile.write(str(total)+"\t"+str(evalue[1][i])+"\t")
outputfile.write("\n")
else:
outputfile.write("0\t"+str(evalue[1][i])+"\n")
outputfile.write("1\t"+str(evalue[1][i])+"\n")
outputfile.close()
def densityofstates():
"""Do the density of status calculation."""
groupnames = list(groups.groups.keys()) if groups else []
if groups and pop:
contrib = [x * numpy.dot(x,overlap) for x in MOCoeff]
if not unres:
MPA = [numpy.zeros( (logfile.nmo,numgroups), "d")]
else:
MPA = [numpy.zeros( (logfile.nmo,numgroups), "d")
for x in range(2)]
for i,groupname in enumerate(groupnames):
for basisfn in groups.groups[groupname]:
MPA[0][:,i] += contrib[0][:,basisfn]
if unres:
MPA[1][:,i] += contrib[1][:,basisfn]
else: # Set MPA to be all ones
MPA = [numpy.ones( (logfile.nmo,1), "d")]
if unres:
MPA = [numpy.ones( (logfile.nmo,1), "d")
for x in range(2)]
# Write DOS and PDOS data to orbital_data.txt
screen.write("Writing orbital data to orbital_data.txt\n")
outputfile=open(os.path.join(gaussdir,"orbital_data.txt"),"w")
outputfile.write("NBasis:\t"+str(NBsUse)+"\n")
outputfile.write("HOMO:\t%s" % "\t".join([str(x+1) for x in HOMO]))
if not (groups and pop):
# No point outputting group info since we don't have the %contribs
outputfile.write("\nGroups:\t0\n")
else:
outputfile.write("\nGroups:\t"+str(len(groups.groups))+"\n")
line = []
for groupname in groupnames:
v = groups.groups[groupname]
line.append("%s\t%s" % (groupname," ".join(map(str,v))))
outputfile.write("\n".join(line) + "\n")
if unres:
outputfile.write("\nAlpha MO\t\teV\tSymmetry")
else:
outputfile.write("\nMO\t\teV\tSymmetry")
if groups and pop:
t = "\t".join(groupnames)
outputfile.write("\t" + t+"\tAccurate values (for the Electronic Transitions module)")
if unres:
if groups and pop:
outputfile.write("\t"*(len(groups.groups)-1))
outputfile.write("\tBeta MO\t\teV\tSymmetry")
if groups and pop:
outputfile.write(t+"\tAccurate values (for UVVis.py)")
outputfile.write("\n")
for i in range(max([len(x) for x in evalue])-1,-1,-1): # Print them out backwards
line=str(i+1)+"\t"+levelname(i, HOMO[0])+"\t"+repr_of_evalue(evalue[0][i])+"\t"+symmetry[0][i]
if groups and pop:
for j in range(len(groups.groups)):
line=line+"\t"+str(int(MPA[0][i,j]*100+.5))
for j in range(len(groups.groups)):
line=line+"\t"+str(MPA[0][i,j])
if unres and i=len(evalue[1]):
continue
output.write(str(k+1)+"\t"+levelname(k, HOMO[j])+"\t"+str(evalue[j][k]))
for fragx in range(len(groups.groups)-1):
for fragy in range(fragx+1,len(groups.groups)):
output.write("\t"+str(groupoverlap[j][k,fragx,fragy]))
output.write("\n")
output.close()
# Convolute the COOP spectrum
spectrum = []
for j in range(len(HOMO)):
overlaps = []
for fragx in range(numgroups - 1):
for fragy in range(fragx+1, numgroups):
overlaps.append(groupoverlap[j][:,fragx,fragy])
spectrum.append(GaussianSpectrum(start, end, 1000,
(evalue[j], overlaps), FWHM))
# Create COOP_spectrum.txt
output = open(os.path.join(gaussdir,"COOP_spectrum.txt"),"w")
output.write("\t")
if unres:
output.write("Alpha%sBeta%s" % ("\t"*numoverlaps,"\t"*numoverlaps))
output.write("Total\n")
output.write("eV\t%s" % listofoverlaps)
if unres:
output.write("\t%s\t%s" % (listofoverlaps, listofoverlaps))
output.write("\n")
for i in range(len(spectrum[0].xvalues)):
output.write("%f" % spectrum[0].xvalues[i])
for k in range(len(spectrum)):
for j in range(len(spectrum[k].spectrum[:,0])):
output.write("\t%f" % spectrum[k].spectrum[j,i])
if unres:
output.write("\t%f" % sum([spectrum[x].spectrum[j,i] for x in [0,1]]))
output.write("\n")
output.close()
g = MPLPlot()
i = 0
for fragx in range(numgroups-1):
for fragy in range(fragx+1, numgroups):
for j in range(len(spectrum)):
if not unres:
g.data( zip(spectrum[j].xvalues,spectrum[j].spectrum[i,:]),
title='overlap of %s with %s' % (groupnames[fragx], groupnames[fragy]))
else:
g.data( zip(spectrum[j].xvalues,spectrum[j].spectrum[i,:]),
title='%s overlap of %s with %s' % (['Alpha','Beta'][j], groupnames[fragx], groupnames[fragy]))
## if unres: # Plot the total or not?
## g.data( zip(spectrum[j].xvalues,spectrum[0].spectrum[i,:] + spectrum[1].spectrum[i,:]),
## title='Total overlap of %s with %s' % ( groupnames[fragx], groupnames[fragy]))
i += 1
g.setlabels("Energy (eV)", "")
g.subplot.set_xlim(left=start, right=end)
g.subplot.legend(loc="upper right", prop={'size':8})
DisplayPlot(root,g,"COOP spectrum")
return # End of crystalorbital()
############### START OF MAIN ##################
screen.write("Starting to analyse the molecular orbitals\n")
groupatoms=[]; groupname=[]; atomorb=[]
# Create the output directory if necessary
gaussdir=folder(screen,logfilename)
# Read in the groups (if they exist!)
filename = os.path.join(gaussdir,"Groups.txt")
groups = False
numgroups = 0
if not os.path.isfile(filename):
screen.write("Groups.txt not found\n")
elif not (hasattr(logfile, "atombasis") and hasattr(logfile, "atomnos")):
screen.write("Groups.txt found but not used as logfile does not have"
" atombasis or atomnos\n") # not necessary depending on the groups
else:
screen.write("Reading Groups.txt\n")
if not hasattr(logfile, "aonames"):
groups = Groups(filename, logfile.atomnos, None, logfile.atombasis)
else:
groups = Groups(filename, logfile.atomnos, logfile.aonames, logfile.atombasis)
numgroups = len(groups.groups)
screen.write("There are %d groups\n" % numgroups)
NAtoms = logfile.natom
NBasis = logfile.nbasis
NBsUse = logfile.nmo
# Verify that groups.txt is okay
if groups:
if COOP==False:
status = groups.verify("DOS")
else:
status = groups.verify("COOP")
if status:
screen.write(status)
return 1
screen.write("The number of atoms is "+str(NAtoms)+"\n")
screen.write("NBasis is "+str(NBasis)+"\n")
screen.write("NBsUse is "+str(NBsUse)+"\n")
pop=False
if hasattr(logfile, "aooverlaps") and hasattr(logfile, "mocoeffs"):
screen.write("Found an overlap matrix and MO coefficients\n")
pop=True # Assuming you never get an overlap matrix without the MOCoeffs
MOCoeff = logfile.mocoeffs
overlap = logfile.aooverlaps
atomorb = logfile.aonames
if len(MOCoeff)==2:
screen.write("This is an unrestricted calculation - found the Beta MO coefficents\n")
unres=False
HOMO = logfile.homos
if len(HOMO)==2:
screen.write("This is an unrestricted calculation\n")
unres=True
evalue = logfile.moenergies
if hasattr(logfile,"mosyms"):
symmetry = logfile.mosyms
else:
symmetry = [["?" for x in evalue[0]]]
if unres:
symmetry.append(["?" for x in evalue[1]])
screen.write("Number of evalues found: %s\n" %
" ".join([str(len(x)) for x in evalue]))
screen.write("Number of orbital symmetries found: %s\n" %
" ".join([str(len(x)) for x in symmetry]))
if COOP==True:
if not (groups and pop):
screen.write("To calculate the COOP spectrum, you need Groups.txt and a log file containing a full population analysis\n")
return 1
crystalorbital()
else: # Density of States
densityofstates()
screen.write("Finished\n")
GaussSum-3.0.2/gausssum/preferencesbox.py 0000666 0001750 0001750 00000022031 13222437274 017202 0 ustar noel noel #
# GaussSum (http://gausssum.sf.net)
# Copyright (C) 2006-2013 Noel O'Boyle
#
# This program is free software; you can redistribute and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 2, or (at your option) any later
# version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY, without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
from tkinter import * # GUI stuff
import tkinter.messagebox # For the About Dialog
import tkinter.simpledialog
import os
class PreferencesPopupBox(simpledialog.Dialog):
def __init__(self, parent, settings, title = None): # Override (just to set the geometry!)
Toplevel.__init__(self, parent)
self.transient(parent)
self.settings=settings # Note that changes to self.settings will affect the global self.settings thru 'settings'
self.oldsettings = settings.copy() # Remember the current settings
if title:
self.title(title)
self.parent = parent
self.result = None
body = Frame(self)
self.initial_focus = self.body(body)
body.pack(padx=5, pady=5)
self.buttonbox()
if not self.initial_focus:
self.initial_focus = self
self.protocol("WM_DELETE_WINDOW", self.cancel)
self.initial_focus.focus_set()
self.wait_window(self)
def body(self,master): # Override
# The content of the settings dialog box
# Creation of the main sections
self.resizable(False,False)
self.frame1=Frame(master,relief=SUNKEN,borderwidth=2)
self.frame1.pack()
Label(self.frame1,text="Search file").pack()
self.frame3=Frame(self.frame1)
self.frame3.pack()
Label(self.frame1,text="").pack()
Label(self.frame1,text="Frequencies").pack()
self.frame4=Frame(self.frame1)
self.frame4.pack()
Label(self.frame1,text="").pack()
Label(self.frame1,text="Orbitals").pack()
self.frame5=Frame(self.frame1)
self.frame5.pack()
Label(self.frame1,text="").pack()
Label(self.frame1,text="Electronic transitions").pack()
self.frame6=Frame(self.frame1)
self.frame6.pack()
Label(self.frame1,text="").pack()
# The Find.py section
Label(self.frame3,text="Search for:").grid(row=0,column=0)
self.find=[None]*4
self.find[0]=Entry(self.frame3,width=15)
self.find[1]=Entry(self.frame3,width=15)
self.find[2]=Entry(self.frame3,width=15)
self.find[3]=Entry(self.frame3,width=15)
self.find[0].grid(row=0,column=1)
self.find[1].grid(row=1,column=1)
self.find[2].grid(row=0,column=2)
self.find[3].grid(row=1,column=2)
for i in range(4):
self.find[i].delete(0,END)
self.find[i].insert(0,self.settings[ 'find.text%d'%(i+1) ])
# The IR_Raman.py section
self.frame4a = Frame(self.frame4)
self.frame4a.pack()
self.irraman=[None]*6
Label(self.frame4a,text="Start:").grid(row=0,column=0)
self.irraman[0]=Entry(self.frame4a,width=5)
self.irraman[0].grid(row=0,column=1)
Label(self.frame4a,text="End:").grid(row=0,column=2)
self.irraman[1]=Entry(self.frame4a,width=5)
self.irraman[1].grid(row=0,column=3)
Label(self.frame4a,text="Num pts:").grid(row=0,column=4)
self.irraman[2]=Entry(self.frame4a,width=5)
self.irraman[2].grid(row=0,column=5)
Label(self.frame4a,text="FWHM:").grid(row=0,column=6)
self.irraman[3]=Entry(self.frame4a,width=5)
self.irraman[3].grid(row=0,column=7)
self.frame4b = Frame(self.frame4)
self.frame4b.pack()
Label(self.frame4b,text="Exc. wavelength:").grid(row=0,column=0)
self.irraman[4]=Entry(self.frame4b,width=5)
self.irraman[4].grid(row=0,column=1)
Label(self.frame4b,text="Temp:").grid(row=0,column=2)
self.irraman[5]=Entry(self.frame4b,width=6)
self.irraman[5].grid(row=0,column=3)
a=['start','end','numpoints','fwhm','excitation','temperature']
for i in range(6):
self.irraman[i].delete(0,END)
self.irraman[i].insert(0,self.settings[ 'ir_raman.%s'%a[i] ])
# The MO.py section
self.mo=[None]*3
Label(self.frame5,text="Start:").grid(row=0,column=0)
self.mo[0]=Entry(self.frame5,width=5)
self.mo[0].grid(row=0,column=1)
Label(self.frame5,text="End:").grid(row=0,column=2)
self.mo[1]=Entry(self.frame5,width=5)
self.mo[1].grid(row=0,column=3)
Label(self.frame5,text="FWHM").grid(row=0,column=4)
self.mo[2]=Entry(self.frame5,width=5)
self.mo[2].grid(row=0,column=5)
a=['start','end','fwhm']
for i in range(3):
self.mo[i].delete(0,END)
self.mo[i].insert(0,self.settings['mo.%s'%(a[i])])
# UVVis.py section
self.uvvis=[None]*5
Label(self.frame6,text="Start:").grid(row=0,column=0)
self.uvvis[0]=Entry(self.frame6,width=5)
self.uvvis[0].grid(row=0,column=1)
Label(self.frame6,text="End:").grid(row=0,column=2)
self.uvvis[1]=Entry(self.frame6,width=5)
self.uvvis[1].grid(row=0,column=3)
Label(self.frame6,text="Num pts:").grid(row=0,column=4)
self.uvvis[2]=Entry(self.frame6,width=5)
self.uvvis[2].grid(row=0,column=5)
Label(self.frame6,text="FWHM:").grid(row=0,column=6)
self.uvvis[3]=Entry(self.frame6,width=5)
self.uvvis[3].grid(row=0,column=7)
Label(self.frame6,text="sigma:").grid(row=0,column=8)
self.uvvis[4]=Entry(self.frame6,width=5)
self.uvvis[4].grid(row=0,column=9)
a=['start','end','numpoints','fwhm','sigma']
for i in range(5):
self.uvvis[i].delete(0,END)
self.uvvis[i].insert(0,self.settings['uvvis.%s'%(a[i])])
x = (652-450)//2 + self.parent.winfo_rootx()
y = (480-410)//2 + self.parent.winfo_rooty()
self.geometry("450x460+"+str(x)+"+"+str(y)) # Place it in the centre of the root window
def buttonbox(self): # Override
box = Frame(self)
cancel=Button(box,text="Cancel",width=10,command=self.cancel,default=ACTIVE)
cancel.pack(side=LEFT,padx=5,pady=5)
self.save = Button(box, text="Save", width=10, command=self.ok, default=ACTIVE)
self.save.pack(side=LEFT, padx=5, pady=5)
self.bind("",self.ok)
self.bind("",self.cancel)
box.pack()
def checkcubman(self, event=None): # Checks for existence of cubman at specificed location
if not os.path.isfile(self.cubman.get()):
messagebox.showerror(title="No such file",
message='''
There isn't any file with this name.
Make sure you include the full path, filename and extension (if any).
For example (in Windows): C:\\Program Files\\Gaussian\\cubman.exe'''
)
def checkformchk(self, event=None): # Checks for existence of formchk at specificed location
if not os.path.isfile(self.formchk.get()):
messagebox.showerror(title="No such file",
message='''
There isn't any file with this name.
Make sure you include the full path, filename and extension (if any).
For example (in Windows): C:\\Program Files\\Gaussian\\formchk.exe'''
)
def checkcubegen(self, event=None): # Checks for existence of formchk at specificed location
if not os.path.isfile(self.cubegen.get()):
messagebox.showerror(title="No such file",
message='''
There isn't any file with this name.
Make sure you include the full path, filename and extension (if any).
For example (in Windows): C:\\Program Files\\Gaussian\\cubegen.exe'''
)
def ok(self, event=None): # Override
# Remembers the settings
# If they are different from before, they will be saved by 'preferences()'
a=['start','end','numpoints','fwhm','excitation','temperature']
for i in range(6):
self.settings['ir_raman.%s'%(a[i])]=self.irraman[i].get()
a=['start','end','numpoints','fwhm']
for i in range(4):
self.settings['find.text%d'%(i+1)]=self.find[i].get()
self.settings['uvvis.%s'%(a[i])]=self.uvvis[i].get()
self.settings['uvvis.sigma']=self.uvvis[4].get()
a=['start','end','fwhm']
for i in range(3):
self.settings['mo.%s'%(a[i])]=self.mo[i].get()
if not self.validate():
self.initial_focus.focus_set() # put focus back
return
self.withdraw()
self.update_idletasks()
self.apply()
self.cancel()
GaussSum-3.0.2/gausssum/scf.py 0000666 0001750 0001750 00000003324 13222437274 014747 0 ustar noel noel #
# GaussSum (http://gausssum.sf.net)
# Copyright (C) 2006-2013 Noel O'Boyle
#
# This program is free software; you can redistribute and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 2, or (at your option) any later
# version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY, without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
import os
import sys
import math
from .plot import DisplayPlot
from .mpl import MPLPlot
def SCF(root,screen,logfile,numpoints):
screen.write("Starting to analyse the progress of the SCF\n")
scfvalues = logfile.scfvalues[-1] # The most recent in the logfile
scftargets = logfile.scftargets[-1] # Ditto
deviation = []
for i in range(len(scfvalues)): # Which SCF cycle
dev = 0
for j in range(len(scftargets)): # Which target
if abs(scfvalues[i][j]) > scftargets[j]:
dev += math.log(abs(scfvalues[i][j]) / scftargets[j])
deviation.append(dev)
if len(deviation)>=numpoints+2: # If there are two points to plot
h = MPLPlot()
h.setlabels("SCF convergence step", "Deviation from targets")
data = list(zip(range(len(deviation)-numpoints),deviation[numpoints:]))
h.data(data)
h.data(data, lines=False)
h.subplot.set_ylim(bottom=0)
DisplayPlot(root,h,"Plot of SCF deviation vs Iteration")
else:
screen.write("I need at least two points to plot\n")
screen.write("Finished\n")
GaussSum-3.0.2/gausssum/search.py 0000666 0001750 0001750 00000002542 13222437274 015442 0 ustar noel noel #
# GaussSum (http://gausssum.sf.net)
# Copyright (C) 2006-2009 Noel O'Boyle
#
# This program is free software; you can redistribute and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 2, or (at your option) any later
# version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY, without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
def Search(screen, logfilename, searchstring, case_sensitive):
screen.write("Starting to search\n")
searchterm = searchstring.split("%")
inputfile = open(logfilename, "r")
if not case_sensitive:
# change all the searchterms to lowercase
temp=[]
for x in searchterm:
temp.append(x.lower())
searchterm=temp
screenoutput = []
for line in inputfile:
searchline = line
if not case_sensitive:
searchline = line.lower()
for x in searchterm:
if searchline.find(x) >= 0:
screenoutput.append(line)
break
inputfile.close()
screen.write("".join(screenoutput))
screen.write("Finished searching\n")
GaussSum-3.0.2/gausssum/utils.py 0000666 0001750 0001750 00000031305 13222437274 015334 0 ustar noel noel #
# GaussSum (http://gausssum.sf.net)
# Copyright (C) 2006-2013 Noel O'Boyle
#
# This program is free software; you can redistribute and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 2, or (at your option) any later
# version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY, without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
from tkinter import *
import configparser # For writing the settings to an .ini file
from cclib.parser.utils import PeriodicTable
import numpy
import os
import sys
import math
# This class allows Find.py, etc. to write directly to the 'console screen'
# in GaussSum.py.
# It also allows Find.py, etc. to write to stdout when testing.
class Redirect:
def __init__(self,write_function,root,other):
self.outputfn=write_function
self.args=other
self.root=root
def write(self,text):
if self.args=="None":
self.outputfn(text)
else:
self.outputfn(self.args[0],text)
self.root.update() # so it shows it immediately
self.args[1].see(END) # scroll if necessary to see last text inserted
def flush(self):
pass
def readinconfigfile(inifile):
# Taken from the Python Cookbook (O'Reilly):
# reads in configuration information from a
# Windows-style .ini file, and returns a
# dictionary of settings.
#
# Uses the Python module configparser for the complicated stuff.
cp = configparser.ConfigParser(interpolation=None)
cp.read(inifile)
config={}
for sec in cp.sections():
name = sec.lower()
for opt in cp.options(sec):
config[name+"."+opt.lower()] = cp.get(sec,opt).strip()
return config
def writeoutconfigfile(config,inifile):
# The companion to readinconfigile
# Written by me!
cp = configparser.ConfigParser(interpolation=None)
for key,value in config.items():
sec=key.split('.')[0]
opt=key.split('.')[1]
if not cp.has_section(sec):
cp.add_section(sec)
cp.set(sec,opt,value)
out=open(inifile,"w")
cp.write(out)
out.close()
class NMRstandards(object):
def __init__(self,location):
"""
Read in the nmr standards file (if it exists)
Returns a list of dictionaries:
nmrdata=[dict_1,dict_2,dict_3...]
dict_n=['theory':'B3LYP/6-31G(d)','name':'TMS','C':12.23,'H':123]
"""
self.location = location
self.nmrdata = []
# Check for nmr standards file in location described in settings
try:
readin = open(self.location,"r")
except IOError:
# File does not exist - i.e. no settings yet
pass
else:
for line in readin:
if not line.lstrip().startswith("#"): # Ignore comments
temp=line.split("\t")
adict={}
adict['theory']=temp[0]
adict['name']=temp[1]
for i in range(2,len(temp),2): # Read in the calculated shifts
adict[temp[i]]=float(temp[i+1])
self.nmrdata.append(adict)
readin.close()
def __getitem__(self,index):
"""Shortcut to access the data directly."""
return self.nmrdata[index]
def save(self):
"""Write the NMR standards to disk."""
outputfile = open(self.location,"w")
lines = []
for adict in self.nmrdata:
output = [adict['theory'],adict['name']]
for k,v in adict.items():
if k not in ["theory","name"]:
output.append(k)
output.append(str(v))
lines.append("\t".join(output))
outputfile.write("\n".join(lines))
outputfile.close()
class ErrorCatcher:
def __init__(self):
self.log=""
self.longlog=""
def write(self,text):
self.log=self.log+text
def clear(self):
self.longlog=self.longlog+self.log
self.log=""
def percent(number):
return str(int(round(number*100))) # round leaves .0 at the end of a number
def levelname(i,HOMO):
if iHOMO+1:
level='L+'+str(i-HOMO-1)
elif i==HOMO+1:
level="LUMO"
else:
level="HOMO"
return level
def lorentzian(x,peak,height,width):
"""The lorentzian curve.
f(x) = a/(1+a)
where a is FWHM**2/4
"""
a = width**2./4.
return float(height)*a/( (peak-x)**2 + a )
class Spectrum(object):
"""Convolutes and stores spectrum data.
Usage:
Spectrum(start,end,numpts,peaks,width,formula)
where
peaks is [(pos,height),...]
formula is a function such as gaussianpeak or delta
>>> t = Spectrum(0,50,11,[[(10,1),(30,0.9),(35,1)]],5,delta)
>>> t.spectrum
array([[ 0. ],
[ 1. ],
[ 1. ],
[ 1. ],
[ 0. ],
[ 0.89999998],
[ 1.89999998],
[ 1.89999998],
[ 1. ],
[ 0. ],
[ 0. ]],'d')
"""
def __init__(self,start,end,numpts,peaks,width,formula):
self.start = start
self.end = end
self.numpts = numpts
self.peaks = peaks
self.width = width
self.formula = formula
# len(peaks) is the number of spectra in this object
self.spectrum = numpy.zeros( (numpts,len(peaks)),"d")
self.xvalues = numpy.arange(numpts)*float(end-start)/(numpts-1) + start
for i in range(numpts):
x = self.xvalues[i]
for spectrumno in range(len(peaks)):
for (pos,height) in peaks[spectrumno]:
self.spectrum[i,spectrumno] = self.spectrum[i,spectrumno] + formula(x,pos,height,width)
class GaussianSpectrum(object):
"""An optimised version of Spectrum for convoluting gaussian curves.
Usage:
GaussianSpectrum(start,end,numpts,peaks,width)
where
peaks -- ( [List of peaks],[ [list of heights],[list of heights],..] )
"""
def __init__(self,start,end,numpts,peaks,width):
self.start = start
self.end = end
self.numpts = numpts
self.peaks = peaks[0]
self.heights = peaks[1]
self.width = width
# make heights a local variable as it's accessed in the inner loop
heights = self.heights
# len(heights) is the number of spectra in this object
data = []
self.xvalues = numpy.arange(self.numpts)*float(self.end-self.start)/(self.numpts-1) + self.start
A = -2.7726/self.width**2
for x in self.xvalues:
tot = [0]*len(self.heights) # The total for each spectrum for this x value
for peakno in range(len(self.peaks)): # For each peak
pos = self.peaks[peakno]
exponent = math.exp(A*(pos-x)**2)
for spectrumno in range(len(heights)):
tot[spectrumno] += heights[spectrumno][peakno]*exponent
data.append(tot)
self.spectrum = numpy.swapaxes(numpy.array(data),0,1)
class Groups(object):
"""Stores the groups to be used for a DOS or COOP calculation
Essentially, the groups are a partitioning of the orbitals among
atoms or a group of atoms.
Usage:
Groups(filename, atomnos, aonames, atombasis)
where
atomnos is a list of the atomic numbers of the atoms
aonames is a list of the 'names' of each atomic orbital
atombasis is a list for each atom of the indices of the basis fns on that atom
Attributes:
groups -- a dictionary of the partition of the orbitals among groups
"""
def __init__(self, filename, atomnos, aonames, atombasis):
self.atomnos = atomnos
self.aonames = aonames
self.atombasis = atombasis
self._makeatomnames()
if not self.aonames:
self._makeaonames()
self._readfile(filename)
self._setup()
def _readfile(self,filename):
"""Read group info from a file.
File format:
First line must be one of "orbitals","atoms","allorbitals","allatoms".
The remainder of the file is ignored in the case of allatoms/allorbitals.
Otherwise a series of groups must be described with a name by itself on one line
and a list of group members on the following line.
As an example:
atoms
Phenyl ring
1,4-6,8
The rest
2,3,7
"""
inputfile = open(filename,"r")
grouptype = next(inputfile).strip()
while not grouptype: # Ignore blank lines
grouptype = next(inputfile).strip()
groups = {}
for line in inputfile:
if not line.strip(): continue # Ignore blank lines
groupname = line.strip()
atoms = []
line = next(inputfile)
parts = line.split(",")
for x in parts:
temp = x.split("-")
if len(temp)==1:
atoms.append(int(temp[0]))
else:
atoms.extend(range(int(temp[0]),int(temp[1])+1))
groups[groupname] = atoms
inputfile.close()
self.filegroups = groups
self.grouptype = grouptype
def _makeatomnames(self):
"""Create unique names for the atoms"""
pt = PeriodicTable()
d = {}
names = []
for atomno in self.atomnos:
if atomno in d:
d[atomno] += 1
else:
d[atomno] = 1
names.append(pt.element[atomno] + str(d[atomno]))
self.atomnames = names
def _makeaonames(self):
"""Create unique names for the atomic basis if needed"""
d = {}
for atomname, ab in zip(self.atomnames, self.atombasis):
names.extend([atomname + "_" + x for x in range(len(ab))])
self.aonames = names
def __str__(self):
"""Return a string representation of this object."""
ans = []
for k,v in self.groups.items():
ans.append("%s: %s" % (k,",".join(map(str,v))))
return "\n".join(ans)
def _setup(self):
"""Create the groups attribute."""
type = self.grouptype.lower()
if not self.filegroups:
if type=="allorbitals":
self.groups = {}
for i in range(len(self.aonames)):
orbital = self.aonames[i]
self.groups[orbital] = [i]
elif type=="allatoms":
self.groups = dict(zip(self.atomnames, self.atombasis))
else:
raise TypeError("You need to specify groups")
else:
if type=="orbitals":
self.groups = {}
for k,v in self.filegroups.items():
# Convert the indices to start from 0
self.groups[k] = [x-1 for x in v]
elif type=="atoms":
self.groups = {}
for k,v in self.filegroups.items():
self.groups[k] = []
for x in v:
# Convert the indices to start from 0
self.groups[k].extend(self.atombasis[x - 1])
else:
raise TypeError("%s is not a valid type of group" % type)
def verify(self,purpose):
"""Verify that the groups attribute is consistent.
purpose is one of "DOS" or "COOP"
"""
status = ""
# Create one big list of all of the atom orbitals in the groups
all = []
for x in self.groups.values():
all += x
all.sort()
if purpose=="DOS": # Each atom orb must appear exactly once
ok = (all==list(range(len(self.aonames))))
if not ok:
status = "Problem with Groups.txt!\n(1)Every atom/orbital must " \
"be listed as a member of some group\n(2)No " \
"atom/orbital can be listed twice"
elif purpose=="COOP":
# No atom can appear twice (and cannot have any crazy atoms either)
badatom = [x for x in all if x not in range(len(self.aonames))]
if badatom:
status = "Atomic orb number out of range in Groups.txt\n"
else:
for i in range(len(all)-1):
if all[i]==all[i+1]:
status += "Atomic orb %d has been included twice\n" % all[i]
return status
if __name__=="__main__":
import doctest
doctest.testmod(verbose=True)
GaussSum-3.0.2/gausssum/vibfreq.py 0000666 0001750 0001750 00000015147 13222437274 015640 0 ustar noel noel #
# GaussSum (http://gausssum.sf.net)
# Copyright (C) 2006-2013 Noel O'Boyle
#
# This program is free software; you can redistribute and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 2, or (at your option) any later
# version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY, without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
import os
import math
import gausssum.utils
from .plot import DisplayPlot
from .mpl import MPLPlot
from .folder import folder
def activity_to_intensity(activity, frequency, excitation, temperature):
"""Convert Raman acitivity to Raman intensity according to
Krishnakumar et al, J. Mol. Struct., 2004, 702, 9."""
excitecm = 1 / (1e-7 * excitation)
f = 1e-13
above = f * (excitecm - frequency)**4 * activity
exponential = -6.626068e-34 * 299792458 * frequency / (1.3806503e-23 * temperature)
below = frequency * (1 - math.exp(exponential))
return above / below
def get_scaling_factors(filename, scale):
"""Read in scaling factors from an existing output file.
Note: Scale is prepopulated with the general scaling factor
"""
inputfile = open(filename, "r")
line = inputfile.readline()
line = inputfile.readline()
i = 0
line = inputfile.readline().split('\t')
while len(line) > 6: # Read in the individual scaling factors
sf = line[-2]
if sf != '':
scale[i] = float(sf)
i += 1
line = inputfile.readline().split('\t')
inputfile.close()
return scale
def Vibfreq(root,screen,logfile,logfilename,start,end,numpts,FWHM,typeofscale,scalefactor,excitation,temperature):
def dofreqs(name,act):
screen.write("\n************* Doing the "+name+" *****************\n")
filename=name+"Spectrum.txt"
freq = logfile.vibfreqs.copy() # Copy so that it won't be changed by the routine
if hasattr(logfile, "vibsyms"):
vibsyms = logfile.vibsyms
else:
vibsyms = ['?'] * len(freq)
# Handle the scaling of the frequencies
scale = [scalefactor] * len(freq)
if typeofscale == "Gen":
screen.write("Going to scale with a scaling factor of "+str(scalefactor)+"\n")
general = True
else:
screen.write("Going to use individual scaling factors\n")
screen.write("Looking for scaling factors in "+filename+"...")
inputfilename = os.path.join(gaussdir,filename)
if not os.path.isfile(inputfilename):
screen.write("not found\nGoing to use general scale factor of "+str(scalefactor)+" instead\n")
general = True
else:
screen.write("found\n")
general = False
get_scaling_factors(inputfilename, scale) # Update scaling factors in 'scale' from file
for i in range(len(freq)): # Scale the freqs
freq[i] = freq[i]*scale[i]
# Convolute the spectrum
spectrum = gausssum.utils.Spectrum(start,end,numpts,
[list(zip(freq,act))],
FWHM,gausssum.utils.lorentzian)
if name == "Raman":
intensity = [activity_to_intensity(activity, frequency, excitation, temperature)
for activity, frequency in zip(act, freq)]
spectrum_intensity = gausssum.utils.Spectrum(start,end,numpts,
[list(zip(freq, intensity))],
FWHM,gausssum.utils.lorentzian)
outputfile = open(os.path.join(gaussdir,filename),"w")
screen.write("Writing scaled spectrum to "+filename+"\n")
outputfile.write("Spectrum\t%s\t\tNormal Modes\n" % ["", "\t"][name=="Raman"])
outputfile.write("Freq (cm-1)\t%s act\t%s\tMode\tLabel\tFreq (cm-1)\t%s act\t" % (name, ["", "Intensity\t"][name=="Raman"],name))
outputfile.write("%sScaling factors\tUnscaled freq\n" % ["", "Intensity\t"][name=="Raman"])
width = end-start
for x in range(0,numpts):
if spectrum.spectrum[x,0]<1e-20:
spectrum.spectrum[x,0] = 0.
realx = width*(x+1)/numpts+start
outputfile.write(str(realx)+"\t"+str(spectrum.spectrum[x,0]))
if name == "Raman":
outputfile.write("\t%f" % spectrum_intensity.spectrum[x,0])
if x>KEJH
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