StoBe web distribution, latest news
(Stockholm-Berlin version of deMon, a
Density Functional Theory molecule/cluster package)
Version 3.3 (May 2014, StoBe2014)
Latest news about
On this page we report bugs, features, and announce updates as they become
availabe. Any suggestions to improve this page are welcome.
Note that bug fixes and new features described on this page are usually
published together with StoBe code updates. As a registered scientist you are
entitled to download any updated StoBe version from the download section of
the StoBe home
page using your previously assigned StoBe userid/password. The download
date of the most recent version is always shown in this download section.
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- March 3, 2014: Major update includes NEB calculations
A major update of StoBe has been completed which includes the options of
running multi-image SCF calculations in one StoBe run. Further,
nudged-elastic-band (NEB) calculations to obtain approximate reaction paths
and barrier energies are now possible.
- August 9, 2013: Generate vibrational (IR) spectra, irspec
The new utility irspec allows you to use output files from StoBe runs to
generate total and angle-resolved vibrational (infrared, IR) spectra for
graphical output or for further processing. The spectra include gaussian
broadening where the broadening width (FWHM) can be chosen freely.
Angle-resolved spectra can be computed for any polarization or incident beam
direction. Further, filters may be applied to extract spectra of specific
types or mixtures of vibrational symmetry modes.
- March 16, 2013: Bug fix of supersymmetry option
A bug appearing in combinations of localizing core orbitals and and
freezing orbitals with the supersymmetry option has been fixed. This
affected the evaluation of core excitation spectra.
- March 4, 2013: Version 3.2 released
The StoBe update includes bug fixes in the codes as well as improvements of
the StoBe user manual.
New options StoBe: The print output has been further optimized to
handle large KS orbital energies. The LOCALIZE option to handle core
orbital localization has been introduced.
New options Xrayspec: Partial averaging of angle (polarization and
beam direction) dependent spectra is implemented. Spectra can be globally
shifted and scaled.
- October 18, 2011: Further bug fixes
The StoBe update includes further bug fixes and an minor revision of the
StoBe user manual.
- March 7, 2011: Version 3.1 released
StoBe Version 3.1 includes a number of bug fixes and some new options.
- the maximum overlap option of the SCF interation scheme
has been completely revised,
- the Trust-Region Roothan-Hall minimization
scheme to improve SCF convergence has been implemented,
- a Verlet type short-time molecular dynamics has been included,
- the StoBe user manual has been further improved.
- February 14, 2008: Makefile revision
The Makefile of the linux/unix version of StoBe (StoBe2008_1) has been
revised to account for updated operating systems (e.g. different 32bit and
64bit linux versions) and compiler/library versions.
- February 14, 2008: Instruction pages for XAS calculations
Additional comment and
pages on XAS have been published to assist StoBe users interested in XAS
- June 06, 2007: StoBe upgrade to Version 3.0
The upgrade includes a number of bug fixes. In particular, calculations of
basis set superposition errors (BSSE) for systems with model potential
atoms treated as ghost atoms have been corrected.
- July 19, 2006: StoBe upgrade to Version 2.2
The upgrade includes (parametrized) relativistic effective core potentials
and corresponding valence basis sets according to Dolg et al. for all
elements from Li (Z = 3) to Fermium (Z = 100) following the
parametrization/representation of the Toulouse group (J.-L. Heully).
Further, some minor changes concerning the use of external point charges.
An internal code revision allows to generate fast StoBe executables using
the Intel Fortran compiler V. 9.1 on linux systems.
- December 18, 2005: Bug in Molden format output removed
A bug in the Molden format output routine of StoBe assigned wrong
coefficients to orbital vectors (confusing the orbital visualization inside
Molden). This bug, appearing only in the unix/linux version of StoBe and
when using fortran compilers without integer zero initialization, has been
- December 1, 2005: Basis set library baslib.new6 obsolete
As of Dec. 1, 2005 the basis set library baslib.new6 has become obsolete
and will not be included any longer in the official StoBe distribution. The
updated library baslib.new7 has been greatly revised where all reliable
basis sets of baslib.new6 have been retained with a few minor modifications
introduced for consistency reasons. This includes basis set title changes,
phase changes of contractions, and numerical corrections. Further details
are described separately. In cases
of doubt please contact the StoBe
- November 15, 2005: Bug fix for Dolg pseudopotential runs
A bug in the basis set input routine which could crash StoBe runs using
Dolg pseudopotentials has been fixed.
- June 23, 2005: New utility pcfilt complements utility latsph
Utility pcfilt can be used to identify and remove lattice centers
(generated by untility latsph) which coincide with cluster centers from the
list of lattice centers.
- June 2, 2005: Bug fix for Huzinaga ECPs
A bug in the evaluation of f projection operators of the Huzinaga effective
core potentials (ECP), which could result in a program crash in very rare
cases, has been fixed.
- May 5, 2005: Sum rule for XAS oscillator strengths
A bug in the evaluation of XAS oscillator strengths leading to violation of
the corresponding sum rule has been removed.
- March 10, 2005: Symmetrized point charge environments
The symmetrization of point charge environments has been updated. The new
version is faster and more general.
- March 2, 2005: Utility latsph updated
Utility latsph, used to create point charge environments with crystal
symmetry, is updated to vers. 1.1 with more extended print output and a few
- January 26, 2005: Utility latsph generates atom centers of
A new utility, latsph, can be used to create point charge environments with
crystal symmetry to be used in StoBe calculations of embedded ionic
(surface) clusters, see option PTCHarges of the StoBe manual. The utility
calculates coordinates of all atom centers in a 3-dim. lattice, defined by
lattice vectors and lattice basis vectors, which lie inside a sphere of
given center and radius. In addition, a planar constraint may be imposed to
include only those centers which lie below a plane of given normal
direction and distance from the sphere center.
- January 26, 2005: Bug in geometry optimizations with a point
A bug, causing StoBe to crash in geometry optimizations with a fixed point
charge environment (option PTCHarges, see manual) was fixed.
- November 27, 2004: Gaussian Cube file output
The DRAW keyword of StoBe includes now an option to generate the
electrostatic potential on a 3-dim. grid with file output using the
Gaussian Cube format. Output file can be used by visualizers such as
- November 24, 2004: Opteron compiling
The Linux/Unix version includes compiler options for the 64bit Intel
Fortran compiler > V. 8.0 which can also be applied on AMD Opteron cpu
systems together with the ACML numerical library.
- October 10, 2004: Runtype option
The RUNTYPE keyword includes the option NOOPtimize which is identical in
its meaning with option NO-Optimize and is implemented for compatibility
with older deMon input.
- June 12, 2004: Drawing option
The DRAW option of Stobe allows plotting of potentials, densities, and more
along planar sections whose cartesian coordinates use atomic (Bohr) or
Angstrom length units depending on the initial input of the atom
coordinates. This has been made fully consistent for the use of Angstrom
- June 7, 2004: Orbital selection by maximum overlap
In previous SCF runs where a maximum overlap criterion for the orbital
selection was used a bug could lead to a wrong orbital energy assignment in
the output listing and in the restart file. The bug has been fixed.
Further, overlaps of the occupied orbitals selected in each iteration can
be listed with the new option "MAXOverlap LIST".
- June 5, 2004: Listing of virtual orbitals
The listing of orbitals has been extended so that all orbitals below the
HOMO are included irrespective of their occupation.
- May 18, 2004: Input orbitals listing
A list of all input orbitals with occupations can be included in the output
listing with the new keyword "IORBitals" in keyword line "PRINt ...".
- May 18, 2004: Symmetry bug fixed
A bug that prevented systems with symmetry groups containing 3-dim.
representations (tetrahedral, cubic gruops) from running has been fixed.
Symmetry group labels can be given either with mixed or upper case
characters ( e. g. C4v or C4V).
- April 15, 2004: Restart file bug fixed
A bug connected with restarting StoBe runs where fractional occupation is
included (see smear option) has been fixed. Further, the smear option has
- Feb. 05, 2004: Rotation of rigid groups available
In optimization runs the rotation of rigid groups of atoms about their
centers of gravity is available now in addition to group translation.
- Jan. 09, 2004: Updated basis set library
A completely revised basis set library, baslib.new7, has been added which,
compared with baslib.new6 contains a number of additional basis sets as
well as bug fixes:
- Phases of all orbital basis sets have been made consistent such that for
each contraction the largest component is positive.
- Test basis sets which are unreasonable for production have been removed.
Numerical errors have been corrected in some cases.
- New basis sets from the Pacific Northwest Library have been added.
- New DFT optimized orbital basis sets (N. Russo) have been added.
- All basis sets come with appropriate references.
The old basis set library baslib.new6 has been kept for compatibility reasons.
- Dec. 26, 2003: Full Molekel, generic Molden format file output
- Output of geometric, electronic, and vibrational properties are stored in
a Molekel format file Molekel.mkl which can be viewed with the vizualizer
- Output of geometric, electronic a vibrational properties as well as
convergence behavior are stored in a generic Molden format file Molden.molf
which can be viewed with the vizualizer Molden. This differs from the
previously implemented Gaussian-94 output format, used also in Molden. The
previous format is still available and produces a file GMolden.mdf.
- Keyword MOLDen, see Dec. 18, 2003, is obsolete and is replaced by the
more general keyword FILEoutput, see manual, f.8.
- Dec. 20, 2003: Vibrational analysis output
- Vibrational analysis output lists at the end orbitals and electronic
parameters referring to the equilibrium rather than the latest distorted
- Dec. 18, 2003: MOLDEN (Gaussian-94) file output turned off by default
- Keyword NOMOlden obsolete, new keyword MOLDen enables MOLDEN file output.
- Dec. 15, 2003: Bug in group definition with multi-line indices
- Multi-line input of group indices works now correctly.
- Dec. 13, 2003: New version 2.0 (StoBe2004) published. New features
- Quadrupole transitions for hard X-ray absorption.
- Full vibrational analysis including geometric constraints on atom centers.
- Electric polarizability
- Oct. 15, 2003: FAQ page included on StoBe web home page
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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