Stockholm-Berlin version of deMon, a Density Functional Theory molecule/cluster package
PC-based software to evaluate electronic states and properties of molecules and (atom) clusters using Density Functional Theory (DFT).
CONTENTS OF THIS PAGE
- Program capabilities
- Hardware/Software requirements
- Installation and running
- Latest news
- Contact the authors
The software package StoBe (Stockholm-Berlin) is a numerical program package to evaluate and analyze the electronic structure as well as spectroscopic and other properties of molecules and atom clusters. The approach is based on self-consistent solutions of the Kohn-Sham Density Functional Theory equations using a Linear Combinations of Gaussian Type Orbitals (LCAO) approach. The theory and numerical details of this implementation can be found in references of the StoBe manual included in the Balsac download package, see below. The initial version of StoBe was based on the deMon program code, originally written under the direction of D. R. Salahub at the University of Montreal. StoBe has been re-developed in major parts where the present version offers as advanced features in particular
- the evaluation of near-edge-Xray-absorption-fine-structure and Xray emission spectra (NEXAFS, XES) ,
- use of molecular symmetry,
- extended properties package
- full portability to different computer platforms.
Due to these features, the StoBe package can be used as a valuable theoretical tool to analyze and interpret experimental Xray spectra that are obtained at many synchrotron facilities worldwide. This is particularly true for the Windows and Linux versions of StoBe which can be easily made available and used on PCs near experimental sites. StoBe is distributed as executable (Windows version) or source code (Linux version) together with auxiliary libraries, documentation, and example runs.
For further information about technical details please consult the Balsac manual. The manual together with all tutorials as well as Latest news and FAQs files are included in the StoBe download package (both Windows and Linux) or can be downloaded separately.
The StoBe package requires the following hardware / software
- IBM PC with Pentium or higher cpu (at least 1 GHz) and at least 4 GB memory
- Windows up to V. 10 (Windows version)
- Linux Red Hat, V.9 or later, Suse, V.8 or later, debian, or ubuntu (Linux version)
- (optional) numerical libraries
You may also download selected files of the corresponding StoBe package ( Windows or Linux) separately.
The StoBe package is open source software and offered "as is" . No resposibilities will be taken by the authors as to programming or scientific errors in the codes.
You can register StoBe by email identifying yourself with your name and institution. Registered users will receive announcements of major update releases and bug reports. Their email addresses will be treated confidentially and will NOT be passed on to others.
After having downloaded the installation file, StoBeWindows.zip or StoBeLinux.zip, you may install StoBe on your PC. For instructions see the installation section on this page.
If a previous version of StoBe is installed in your PC you have to remove all system files of the previous version with the uninstall feature of your Windows system before you install the new version. Note that any old StoBe input/output files should be kept for later use.
(A) WINDOWS VERSION
The INSTALLATION of StoBe is straightforward. It requires that you have Administrator status on your PC and and consists in the most general case of five steps. (Note that your browser may have download switches set such that one or more of the following steps are performed automatically.)
- Unpack all files by copying the downloaded file StoBeWindows.zip to an installation subdirectory, e.g. c:\Install (or any other temporary directory, which must be different from the permanent directory where you wish Balsac to be installed). Unzip StoBeWindows.zip inside c:\Install to obtain all system installation files, manuals, tutorials, and possibly a file Readme.1st which describes latest changes and gives further advice concerning the installation. Note that the installation directory cannot be used as the final StoBe directory, see step 2.
- Unpack and install all StoBe files by running StoBe2014_1Windows.exe. This will ask you for the name of the StoBe package subdirectory where "c:\Program Files\StoBe2014" is used as a default. This directory, called $StoBe below, will contain the complete StoBe executable package. Move the help file StoBeMAN.html, tutorials C5H5N_Tutorial.zip, XAS1.html, XAS2.html, and files whatsnew.html, facs.html to $StoBe\Manual. Unzip C5H5N_Tutorial.zip in directory $StoBe\Manual to obtain the tutorial directory C5H5N_Tutorial.
- Install the Compaq fortran runtime libraries by running VFRUN660I.exe in directory $StoBe.
- Set an icon of the StoBe executable on the desktop using e.g. the MS Windows Explorer (create a shortcut of StoBe.exe in directory $StoBe and move it to the desktop.) Set an icon of the StoBe manual (create a shortcut of StoBeMAN.html in directory $StoBe\Manual and move it to the desktop.)
- Clean up by removing all installation files from the installation directory c:\Install. You may leave the original download file StoBeWindows.zip for backup purposes.
NOTE that when unpacking the installation package with Windows 10, depending on the security settings, you may get an opening screen "Windows protected your PC" suggesting to abort the installation with a bold text "Don't run" at the bottom. You can ignore this warning by clicking at the "More info" text which shows another bold text "Run anyway" at the bottom. Clicking this button allows you to proceed with the installation. Microsoft considers any software not registered with Microsoft and not available in the Microsoft Store as "unrecognized" and and risky to run.
NOTE that the installation package includes Windows system components where some may be versions older than those in your present Windows installation. Always keep your latest component version, i.e. in each case when prompted, DO NOT replace your existing system components by older versions of the oSSD installation package.
You can inspect the StoBe users manual as well as all tutorial files, including whatsnew.html, facs.html in directory $StoBe\Manual.
RUNNING StoBe requires input files (basis set and symmetry libraries, keyword and numerical input specific of the molecule/cluster) to be combined with the corresponding executable where correct directories must be provided. This is achieved most conveniently inside the Windows operating system by using batch run files (*.bat). A typical StoBe run consists of a batch run file (called StoBe.bat in the following) and a numerical input file and generates output in ASCII/binary output files. It can be started
- from the Windows file explorer:
double-click at the corresponding batch run file StoBe.bat of the listing.
- from the Command Prompt Window (DOS box):
Open the Command Prompt Window (DOS box) inside Windows. Move to the directory where StoBe.bat exists and type "StoBe.bat" followed by <Enter>.
- from the Windows command line:
choose "Start | Run..." from the taskbar; then type "\$dir\StoBe.bat" where $dir denotes the directory path where StoBe.bat exists and press <enter>.
Typical StoBe run examples together with output are contained in directory $StoBe\Examples. All examples are listed and explained briefly in file examples.txt of the $StoBe\Examples directory. You can run the StoBe examples by copying the corresponding files *.bat, *.inp from directory $StoBe\Examples into an executable directory and then running the corresponding *.bat file.
StoBe users doing X-ray absorption or excitation spectrum calculations are strongly advised to read the instruction pages on XAS, XAS1.html, XAS2.html, in directory $StoBe\Manual. Further, the tutorial project C5H5N_Tutorial.zip in StoBe\Manual can help to get started. (Copy C5H5N_Tutorial.zip to a working directory $dir, unzip C5H5N_Tutorial.zip yielding directory "$dir\C5H5N_Tutorial", read C5H5N_Tutorial.pdf inside the directory and follow the necessary steps.)
The present StoBe Windows version runs for clusters/molecules of up to
- 60 atoms
- 26624 primitive / 850 contracted gaussians for orbitals
- 1700 primitive gaussians for auxiliary functions
- 10000 external point charges
NOTE that StoBe will work successfully in your national (other than US) Windows environment ONLY if real numbers follow the US convention of using "." (period) as the decimal separator symbol and "," (comma) as the digit grouping symbol. Number symbols, like the decimal separator and digit grouping symbol, can be reset in the Regional Settings part of your Microsoft Windows Control Panel.
(B) LINUX VERSION
The INSTALLATION of StoBe requires a fortran77 compiler (for example f77, g77, or ifort) and linker. Depending on the Linux system the provided Make file may have to be modified in details (compiler/library names, system selection) which requires some system administration knowledge. Further, you must have root status on your PC. The installation consists of five steps. (Note that your browser may have download switches set such that one or more of the following steps are performed automatically.)
- Unpack all files by copying the downloaded file StoBeLinux.zip to an installation directory, called $Install in the following. Unzip StoBeLinux.zip inside $Install to obtain all system installation files, manuals, tutorials, and possibly a file Readme.1st which describes latest changes and gives further advice concerning the installation.
- Uncompress, and unpack all files of the downloaded package file StoBe2014_1Linux.tar.gz in directory $Install by
- >gunzip StoBe2014_1Linux.tar.gz
which produces the uncompressed file StoBe2014_1.tar
- >tar -xvf StoBe2014_1.tar
which unpacks all files to a directory StoBeExport with subdirectories
- StoBeExport/Basis containing all basis set libraries
- StoBeExport/Examples containing typical StoBe run examples with input together with output files. All examples are listed and explained briefly in file examples.txt. The examples can be run by copying the corresponding files *.bat, *.inp from directory StoBeExport/Examples to an executable directory and then running the corresponding *.bat file.
- StoBeExport/Manual containing the StoBe manual in html format.
- StoBeExport/Source containing the complete source code of the StoBe package together with a Makefile for compiling.
- StoBeExport/Basis containing all basis set libraries
- >gunzip StoBe2014_1Linux.tar.gz
- Create all StoBe executables (*.x files) by running file Makefile in subdirectory StoBeExport/Source. This may require editing file Makefile of directory StoBeExport/Source in order to adjust compiler / linker options as well as library subdirectories. The compiled/linked executables reside in subdirectory StoBeExport/Source and may be copied to any other directory for subsequent use.
- Move the help file StoBeMAN.html, tutorials C5H5N_Tutorial.zip, XAS1.html, XAS2.html, and files whatsnew.html, facs.html from $Install to a final directory $StoBeManTut. Unzip C5H5N_Tutorial.zip in directory $StoBeManTut to obtain the tutorial directory C5H5N_Tutorial.
- Clean up by removing all installation *.f, *.o files from directory StoBeExport/Source. (Note that command "make clean" will remove all object files, but also all executables.) You may leave the original download file StoBe2014_1.tar. for backup purposes.
You can inspect the StoBe users manual as well as all tutorial files, including whatsnew.html, facs.html in directory StoBeExport/Manual or in directory $StoBeManTut, see above.
RUNNING StoBe requires input files (basis set and symmetry libraries, keyword and numerical input specific of the molecule/cluster) to be combined with the corresponding executables where correct directories must be provided. This is achieved most conveniently inside the Linux operating system by using batch run files (*.run) which combine file assignments and executable calls with numerical input and generates output in ASCII/binary output files, see examples in StoBeExport/Examples.
StoBe users doing X-ray absorption or excitation spectrum calculations are strongly advised to read the instruction pages on XAS, XAS1.html, XAS2.html, in directory $StoBeManTut. Further, the tutorial project C5H5N_Tutorial.zip in $StoBeManTut can help to get started. (Copy C5H5N_Tutorial.zip to a working directory $dir, unzip C5H5N_Tutorial.zip yielding directory "$dir\C5H5N_Tutorial", read C5H5N_Tutorial.pdf inside the directory and follow the necessary steps.)
The present StoBe version for Linux runs for clusters/molecules of up to
- 140 atoms
- 3800 primitive / 1900 contracted gaussians for orbitals
- 3800 primitive gaussians for auxiliary functions
- 100000 external point charges
For suggestions or questions concerning the StoBe software please contact the authors using addresses