Some softwares developed so far by Ken Sakai.
Gloabl Tooll for Gaussian 03/09/16
<<2021-08-28; Complied with Rad Studioi 10.3>>
Reading Gaussian03/09/16 Output files.
1. Coverting Coordinates Files
2. Picking up the SCF-Done Energies during the optimization, although there is no meaning in chemical viewpoints. However, this allows you to quickly monitor whether the optimization procedures are going ok or not. These energies can also be viewed graphically. Can extract the final atomic coordinates in a cartesian format and save them as a file for further use. Maximum and RMS Force together with Maximum and RMS Displacement during the optimization can now be graphically viewed.
3. This tool can extract the final coordinates in Z-matrix format and save them in a Gaussian input format file in the Z-matrix format.
4. This is a powerful tool now because it can automatically produce a report which can be utilized for supplementary materials preparation.
5. Comparison of Multiple MO Energy Diagrams can be graphically viewed.
6. Projected Density Of States can be plotted. This is useful for studying the density of states of metal clusters (requires PW to activate).
7. MO Coefficients can be read but with the Log files generated using Pop=Full is required. After reading the Log file, the corresponding FCH file can be read to be replaced with the data in the FCH file (requires PW to activate).
#MO Coeff Handling Routine (PDOS routine bug fixation done 20210828)
KenX2023.exe, CrsyTab.exe, CifConv.exe, and HKLConv.exe, Updated October 11, 2023
KenX2023 is supplied here free of charge to academics (including students), provided it is acknowledged. Commercial users require a special permission of the author. The users should quote the following reference:
Sakai, K. (2023). Kyushu University, Japan. KenX.
This program package was originally developed as a Graphical User Interface for Shelxl97. However, various multipurpose tools for structure development are implemented. Especially, initial structure development tasks for DFT calculations are largely supported. We do develop many of model structures using this program.It also involves some CIF utilities for publication (CifConv.exe), a tool generating crystallographic table with multiple columns (CrysTab.exe), and a tool to convert HKLF data by defining a transformation matrix (HKLConv.exe).
KenX was greatly changed from the former versions. KenX2020 can be used to convert molecular structures to be handled in DFT calculation. It reads a cartesian coordinate file, allows deformation of structures, exports Gaussian Input Files, etc. The last Gaussian-com-file saving routine has been greatly improved from this version. You can prepare some standard input codes to be inserted into your creating input files, before saving.
Bug Fix Report
### May 29, 2016 ### Naming Routine Error in Action when Applied Fixed.
### June 14, 2016 ### Distances and Angles Data Display Routine Revised.
### Sept 20, 2016 ### Bug Fixed for Coordinates Generation by the Shift Rountine.
### May 21, 2017 ### Some routines for Molecular Treatments for the structure development Revised.
### Oct 02, 2018 ### Translational structure moving events revised to enable a little smaller shift (fine tue of position can be done from this version).
### April 20, 2020 ### Remember Unselected. This is added to memorize the unselected part of atoms in a memory, which can be restored by the ReSelect button. This is used for make some rotations along the selected axes of interest in order to make various conformers in a logical way.
### April 20, 2020 ### The problems about the window tasks and display regions have been greatly solved.
### April 28, 2020 ### More options added; Align Vector, Remember Unselected, Reverse Selection. Moreover, the Locate Option has largely improved to make the user able to locate fragments stored in KenX/fragments folder. File saving routine for producing fragment files have also been added.
### May 8, 2020 ### The problem about the accessing folder memorizing strategy has been solved. Now, multiple KenX windows can momorize their individual accessing folder separately so that the individual task may be done much more effectively. The previous version had a problem of memorizing the accessing folder using a single path recording file within a KenX program folder.
$$$ July 07, 2021 $$$ The hydrogen atom lable display error plus a trivial graphic display error upon the symmetry expansion process have been solved to disply them correctly. Especially, the H atom names (described by Brush.Style := bsBold in an unexpected error by the complier has been avoided by inserting Brush.Style := bsClear before all H-name descpription task treatments.
### October 11, 2023 ### The least-squares calculations on the individually defined planes in molecules or crystals can now be performed by simply clicking the atoms. The plane calculation results can be saved into an ASCII file to be imiported into Excel file for detailed examinations.
IR/Raman Spectral Subtraction Program (vibsp_subtract2018.exe). The program directly reads Gaussian log files containg the results of frequency calculations. The frequency calculations conducted with a defalt setup only provides IR intensity data so that such files should be used to see the IR data. If Freq=Raman is suggested in the job command code, Raman data can be computed. For the latter case, both IR and Raman data simulation can be performed. Gaussian, Lorentzian, and G/L-mixed functions are available.
A program activity coefficients of ions in aqueous solutions (debyehuckel_calc.exe).
A program assisting the analysis of elemental compositions of chemicals. The data given from the combustion analysis (CHN%) and other analytical techniques can be used to evaluate the elemental compositions. The program also generates simulating isotopic distribution patterns, which can be compared with those observed in the mass spectrometry, such as ESI-TOF MS, FAB MS (SIMS), or MALDI-TOF MS spectroscopy. WinCHNMS2016 (EAnalysis2016.exe).
Renewed 2016-09-30
Bug Fixed 2016-10-26
ESR Simulation Program (esr_simulator.exe). In this new version, simulation of ESR spectra for non-100%-abandance nuclei like Pt-195 (33.8%) can be simulated. This version also can deal with I=5/2 Mn and all other Nuclei, though all of them have not been implemented as yet. At present, only 1H, 2H, 14N, 15N, 55Mn, and 195Pt have been installed for our use. Those who need to add other nuclei can contact KS........
Updated on 2017-06-04: Parameters saving routines added. Blank lines auto-deleting routines added.
Updated on 2017-06-07: A routine adding an additional broad gaussian feature has been introduced.
Moreover, the values with two decimals can now be defined for the coupling constants.
Updated on 2017-06-13: Scroll Bars (Automatic) have been added.
Just read the file named "solar_irradiance.txt" which involves the solar irradiance as a function of the wavelenght of light, supplied from NREL (National Renewable Energy Laboratory). Then the distribution of light involved in the solar irradiance can be analyzed in detail.
This is to conduct Monte Carlo Simulation for the partial reduction of viologen oligomers based on the statistical law. More than one branches of multiviologens tethers can be defined and the partial reduction of these acceptor sites can be done by delivering electrons in a random fashion. If there is more than 2 electrons delivered over a certain branch, diradicals are supposed to be preferentially formed within each branch. Simulation can be automatically repeated many times to obtain the averaged values for the repeated trials together with the standard deviations for the values estimated.
This is developed to carry out deconvolution of two spectral components hidden in a series of spectral data (at least two spectra involving two components in different intensity ratios must be obtained).
This is a special program developed to estimate the absorption-inhibition effect for a certain pigment used in photochemical reactions.
Simulation Program for Some Complicated Ion-Pair Formation Equilibria in Solution.
This has been developed to regenerate the observed molar conductivity data for highly charged molecular species.
The program simplifies the stepwise formation constants in a reasonable scheme and carries out the fitting experiments.
The molar conductivity data should be supplied and imported into the program as the products of molar conductivity and the molar concentration,
which should be also given as a function of the molar concentration. Please see the ReadMe.txt file for details.
The program has been developed using the Delphi 5 program package, and all the source files are also supplied here with a single ZIP file.
This is a multipurpose utility to handle spectrophotometric data. The main usage is to produce 2D-sheet data that can be imported into a global kinetic analysis software called SPECFIT. This program is a commercial package which has been thus far developed by Dr. Robert A. Binstead, USA (Spectrum Research Associate. The merit of using this software is that multiwavelengths data sets can be analyzed to yield an absorptivity spectrum of each chemical species hidden in spectral changes. The singular value decomposition method (factor analysis) also facilitates one to predict the number of chemical species involved in each reaction. Moreover, relatively complicated systems can be analyzed to determine the rate or the equilibrium constants defined in one's model. Since the author has long been a user of spectrophotometers from Shimadzu, file formats that can be handled in the present version of SpecfitV.exe are limited. It reads three or four types of files at the moment. One is ASCII files (*.ASC) generated by a Shimadzu Multispec1500 photodiode array detector. Another is ASCII files (*.ASC) generated by a Shimadzu UV3150K UV-visible-NIR spectrophotometer. It also handles ASCII files (*.ASC) produced by a Shimadzu RF5300PC spectrofluorometer. The program also reads files consisting of conma-separated (nm,absorbance) lines. The program also accepts files in other formats, but let me just stop here. Recently, the program has been recompiled to handle the data from a Hitachi Fluorophotometer, for the use of Dr. Ishida, Kitazato University. In addition, some other tools are also implemented.
(1) Added a routine to generate FIX files for known spectra for the Shimadzu UV 2450, 3100PC, 3150PC, which use the UVProbe package for the control software (for Yoshimi Yokoyama, September 13, 2005).
A stand-alone program simulating Isotope Patterns for the data analysis in Mass Spectrometry (WinMassSpec.exe). Since the older versions of the program (WinMass.exe) suffered from a bug, I made a completely revised version of the simulation program. Isotopic abundances data for almost all the well-known elements have now been implemented in 'Elem.txt' and 'abundances.txt'. If you need or would like to modify the basic numerical parameters concerning the abundances, you can easily do so by editting the files mentioned above.
A Simulation Program for the ESR Spectra of Organic Radicals (WinESR2.exe).
This is to read your output files generated during the geometry optimization. Transfer your log files from your workstations and open them with this tool. There are two ways to open each log file. One is to automatically extract the final atomic coordinates in a cartesian format. The other is to automatically pick up the potential energies during the optimization procedures. (GeomOptGaussian2020.exe). Some revisions have been made. Energy profile data can be extracted (which was done by use of SCAN). This software can extract the final coordinates in Z-matrix format and save them in a Gaussian input format file (September 2, 2013). The program was compiled in Delphi 10 (the newest Delphi version).
Potential energy graphics display mode revised (Bug Fixation Done) (2017-07-18).
Spartan PDF file conversion routine revised to have no integer values in the ressulting files (2017-11-11).
The graphic treatment routine for potential energy change during optimization has been further revised (2017-12-02).
Complied with the latest version of Rad Studio 10.3.3 (2020-02-15)
Window Tasks Improved with regard to Energy Picker while geomoptimization. (2020-02-15)
Potential Energy Change Picking Routine for the geomoptimization has been largely revised. (2020-02-2)
This is a Tool to generate Calculated Spectra based on the calculated oscilator strengths (f values) that are written in an output file of Gaussian 98/03/09. It is also possible to import a data file in a simple text format which merely contains energy and f values separated with tabs. Example datasets for making tables for publication purposes are also supplied within a single ZIP file.
The new version now provides much smarter routine enabling direct access to the log files produced by Gaussian 09 when carrying out the standard TD-DFT (Time-Dependent Density Functional Theory) calculaitons. I have not checked if it works well with the output files from the newer version of Gaussian (ver16). However, I expect it is not very difficult to give further revision to support the files from the G16 package.
2017-11-18 Some errors and bugs fixed. Screen Size modifed. Two different screen sizes are now available.
These have been separately complied by giving them different sizes. SpectraF6s.exe should be good for the use by lap top PCs.
2017-12-03 Minor Revisions given in the ESI table saving routines.
This program reads cartesian coordinates of molecules and you can define two vectors. The origin can be located at a certain atom of interest. You can make such a translation. You can also rotate your molecule to fit these vectors onto particular axes. For instance, your vector may be adjusted to be parallel to the X axis. This is originally developed when we did some EHMO-level of MO calculations to adjust the orbital location in an appropriate way. For example, dz2 could be located parallel to the z axis. dx2-y2 orbital may also be located along the x and y orbitals. Finally you should save your new cartesian coordinates. An example of cartesian coordinate file comes with this tool. (MolRot.exe).
This is to convert a powder X-ray diffraction data obtained by Rigaku or Mac-Science Instruments into a file to be used in XFIT or GSAS programs. With converted files, unit cell constants could be searched by use of other softwares (XFIT, CRYSFIRE, etc.) available at the CCP14 site. (XRDConv.exe).
CS decay profiles predicted based on the Monte Carlo simulation technique. This program supposes that several equivalent branches involving a few equivalent viologen acceptor sites are tethered to a single Ru(bpy)32+-type photosensitizer.
Simple tool to generate your password using a randomized scheme. Number of characters for your PW can be freely decided. PW's using alphabets in lower and upper cases together with numbers (0,1,2,3,4,5,6,7,8,9) are to be included. No special character codes are to be included.......
This is about the single-crystal X-ray crsytallography practice (June 2023)