StoBe web distribution
StoBe
(Stockholm-Berlin version of deMon, a
Density Functional Theory molecule/cluster package)
Version 3.3 (May 2014, StoBe2014)
PC-based software to evaluate electronic states and
properties of molecules and (atom) clusters
using Density Functional
Theory (DFT).
CONTENTS OF THIS PAGE
PROGRAM DESCRIPTION
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. 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 Microsoft(C) Windows and Linux versions of StoBe which can be easily
made available and used on Personal Computers near experimental sites.
StoBe is copyright protected and distributed as licensed
software. The present distribution refers to the Microsoft Windows
and Linux versions of StoBe only. For Unix versions contact the
authors.
For further information about technical details consult the StoBe manual. A detailed tutorial for XAS calculations
with pyridine (C5H5N) as example including corresponding in/output files (MS
Windows style) can be downloaded here.
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LICENSING AND DISTRIBUTION
The PC Windows version of StoBe is copyright protected and distributed
according to certain restrictions following a license scheme described below.
-
The StoBe software has been developed as part of a joint research
effort and is not considered a professional software package. Its
distribution to interested scientists and academic scientific institutions is
based on an "as is" policy with no further warranties as to
correctness or reliability of the approaches used.
-
The StoBe software is distributed as executable (MS Windows version)
or source code (Linux version) together with auxiliary libraries,
documentation, and example runs, and with an installation procedure.
Software support beyond the existing documentation can be given by the StoBe authors only on an "as available" basis.
-
The use of the StoBe software requires the payment of a licence fee of
Eur. 100.- (single-user license, MS Windows) and Eur. 200.-
(single-user license, Linux), respectively, per PC for academic users ,
before the software can be downloaded and/or used. Administrational handling
costs (Eur. 20.-) are added to each order.
The administrational part of the distribution is carried out at the
Fritz-Haber-Institut, Faradayweg 4-6, D-14195 Berlin (Germany).
To
order a StoBe licence please contact
or one of the StoBe authors by email. Please provide
information about (a) the number and type of license(s), (b) an invoice
address, and (c) an email address for further correspondence. (Your
email address will be used ONLY for notifying you of the download password
and of bugs/changes/updates of the StoBe software.) After administrational
processing of your order you will be sent an invoice. After receipt of the
payment by the Fritz-Haber-Institut administration an email containing the
license ID and password will be sent to your email address. After this you
can download the software (using your ID/password) from this web site below.
Note that distribution of StoBe from this web site is restricted to members
of scientific non-profit organizations. Licenses for commercial use will be
handled separately by the involved institutions. For further information
please contact the StoBe authors.
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HARDWARE / SOFTWARE REQUIREMENTS
The StoBe package requires the following hardware/ software
-
IBM PC, or PC-compatible, with Intel Pentium type cpu (at least
1 GHz)
- at least 512MB memory,
- at least 100MB disk storage (15MB for the installation and examples),
- operating systems
(a) Microsoft Windows version: Windows NT4 / 2000 / XP / Vista / 7
(earlier Windows versions may work but cannot be guaranteed).
(b) Linux versions: Red Hat (> V.9), Suse (> V.8), debian, or
ubuntu.
- ASCII text editor, e. g. vim,
MSWord, for input/ouput file handling,
- (optional) numerical libraries as for example
atlas (for Linux
version only),
- (optional) software for graphical analysis of molecular structure output, e.g.
BALSAC
- (optional) software for StoBe output postprocessing, such as graphical
analysis of molecular orbitals, e.g.
Molden,
Molekel
- (optional) plotting software for graphical spectra output,
e.g. Gnuplot
- (optional) PostScript viewer/printer utility, e. g. ghostview, for graphical
orbital/density output,
Installation of the Linux version 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.
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DOWNLOADING
Latest updates on January 19, 2021
Start downloading the (licensed) StoBe package in
a single file (Windows: 13 MB, Linux: 8MB) by identifying yourself with a
correct license ID and password.
Please enter:
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PROGRAM INSTALLATION AND RUNNING
(A) MICROSOFT WINDOWS VERSION
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.
INSTALLING StoBe requires that you have Administrator status on
your PC and consists of three steps. (Note that your browser may have
download switches set such that one or more of the following steps are
performed automatically.)
- Unpack and install all StoBe files by running StoBe2014_1.exe.
This will ask you for the name of the StoBe package subdirectory where
"c:\Program Files\StoBe2014" is used as a default. The StoBe
package subdirectory directory will be called $StoBe in the following.
At the end of the installation you can inspect the Readme1st.txt file
which describes latest changes and gives further advice
concerning the installation.
- Install the Compaq fortran runtime libraries by running
VFRUN660I.exe in directory $StoBe.
- Clean up. You may leave the original download file
StoBe2014_1.exe for backup purposes.
You can inspect the StoBe users manual in directory
$StoBe\Manual or open it from the Windows Program menu.
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 MS 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 MS 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 StoBe2014
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 spectrum calculations are strongly
advised to read the comment and
instruction
pages on XAS.
The present StoBe version for Microsoft Windows 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.
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(B) LINUX VERSION
If a previous version of StoBe is installed in your PC you have
to delete all system files of the previous version from corresponding
subdirectories before you install the new version. Note that any old
StoBe input/output files should be kept for later use.
INSTALLING StoBe requires that you have root status on
your PC and consists of three steps. (Note that your browser may have
download switches set such that one or more of the following steps are
performed automatically.)
- Rename, uncompress, and unpack all files of the downloaded
package file StoBe2014_1.linux in the present installation directory
(called $StoBe in the following) by
- >mv StoBe2014_1.linux StoBe2014_1.tar.gz
which produces the compressed file StoBe2014_1.tar.gz
- >gunzip StoBe2014_1.tar.gz
which produces the uncompressed file StoBe2014_1.tar
- >tar -xvf StoBe2014_1.tar
which unpacks all files
A file Readme.1st may exist in directory $StoBe describing latest
changes and giving further advice concerning the installation.
- Generate all StoBe executables (*.x files) by running
file Makefile. This may require editing file Makefile of directory
$StoBe in order to adjust compiler / linker options as well as
library subdirectories.
- Clean up by removing all installation *.f, *.o files from
directory $StoBe. (Note that command "make clean" will remove
all object files and executables.) You may leave the original download
file StoBe2014_1.tar. for backup purposes.
You can inspect the StoBe users manual 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 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.
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.
StoBe users doing X-ray absorption spectrum calculations are strongly
advised to read the comment and
instruction
pages on XAS.
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
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HOW TO CONTACT THE AUTHORS
We are open to any suggestions and questions concerning the StoBe software.
You can contact the authors using addresses
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