water molecule. A comparison of
methods,
J. Comput. Chem. 26 (2005) 97-105.
DOI: 10.1002/jcc.20157
[]'s,
Camps
On Mon, Oct 9, 2017 at 4:44 AM, Ulrich Biedermann wrote:
Dear Dan,
I have noticed similar problems. Mulliken charges depend on the atomic basis
set used. In Sies
Dear Dan,
I have noticed similar problems. Mulliken charges depend on the atomic basis
set used. In Siesta the cutoff radius (of H) seems to be the critical
parameter. I suggest that you check the dipol moment of an isolated water
molecule (10 Angstrom box). It should have the correct magnit
Dear Rishi,
please see the manual, section " Output of structural information"
The keywork "WriteMDXmol" may do what you need, however, there are also other
possibilities described...
best regards, Ulrich.
From: Rishi Sreedhar
To: "siesta-l@uam.es"
Sent: 25.09.2017 6:51
Subject:
Hi Marco,
within the Born-Oppenheimer (SIESTA) hydrogen and deuterium have the same
pseudopotential.
Isotope effects come from the change of mass affecting the zero point
vibrational energy and the thermal occupation of vibrational modes.
The most efficient (standard) way to study isotope effec
Dear Nicolas,
in case you are using the intel compiler, you may have to increase the allowed
stack size.
I recently had segmentation faults for jobs compiled with the Intel2017
compiler, which had been running using the same siesta version compiled with
the gnu compiler. The solution was to i
Hi,
In order to avoid artefacts due to different basis sets and pseudopotentials
(or all-electron calculation with Jaguar) I strongly recommend to do a
"gas-phase" calculation with Siesta: put one molecule in a large cubic
supercell such that there is >> two times the larges cutoff of your bas
Hi Riya,
It is good practice to check the magnitude of the BSSE for at least one or two
configurations.
The BESSE depends on your system, the basis set and the structure. You should
make shure that the BESSE counterpoise correction is smaller than your required
accuracy, and if not, you should
Hi Igor,
one obvious difference between your experimental and calculated densities is
that the diffraction experiment averages over zero-point and thermal vibrations
(what was the temperature ?). The DFT density was (presumably) calculated for
the equilibrium structure, i.e., for atoms at rest.
Hi,
In principle, plane-wave (PW) and atom centered orbital (AO) based codes should
give the same results for physically observable energy differences as, e.g.,
cohesive energies, surface formation energies, adsorption energies, ect.
Prerequisite is ofcourse that the same (or at least comparabl
I think it changes with the orbital cutoff (and the supercell size)
- Original Message -
From: Ilia Sivkov
[mailto:isiv...@mpi-halle.mpg.de]
To: siesta-l@uam.es
[mailto:siesta-l@uam.es]
Sent: Mon, 12 Nov 2012 20:59:54 +0100
Subject:
[SIESTA-L] Change size of auxiliary super cell
> Hello
Do you really want an excited state (SpinPolarized true; SingleExcitation
true) ?
Perhaps you should first try to converge the ground state with SpinPolarized
false and SingleExcitation false.
- Original Message -
From: Giacomo Giorgi
[mailto:g...@thch.unipg.it]
To: siesta-l@uam.es
S
Dear Michael,
Siesta has converted the units of electric field from V/Ang (your input) to
atomic units (Ry/Bohr/e).
Simply double-check that this corresponds to the same value.
Regards, Ulrich.
- Original Message -
From: Michael Shin
[mailto:siesta_h...@yahoo.com]
To: Self-Consistent D
Dear Herbert,
If the unit cell for the ion is sufficiently large, Siesta prints an estimate
of this interaction energy as Emadel (rather than printing the warning). I
have seen values like 2 eV for a 10x10x10 Angstrom cell.
For the slab+ion you will always get the warning.
Your simple approac
Hi Jack,
a simple way of getting a per atom value of the difference spin density is to
look at the Mulliken population analysis in the (long) output (LongOutput
.TRUE.). It gives orbital occupancies for spin up and spin down for each atom
and also the value summed over all orbitals on that ato
Hi Onur,
In order to optimize internal coordinates (the z-components of the third and
fourth atom) you probably should set
MD.NumCGsteps 100 (default is zero)
and either you need to vary the unit cell constants a and c/a manually, or you
have to set
MD.VariableCell .True (default is false)
Dear Lily,
the best approach is to check convergence of your property of interest with
mesh-cutoff,
which often is better (at smaller cutoff) than the convergence of total energy.
The reason is systematic error cancellation.
However, as "early warning indicator" I keep an eye on the line " Tot
Dear Rob,
note that the doubly negative oxygen ion does not have bound states. The
orbital energies are no longer negative for some of the occupied orbitals and
the large r90% and r99% radii indicate that the orbitals are no longer
localized on the atom. Also note the large number of warnings
> Hi all,
>
> I've learned that the single point energy calculation should be the
> most appropriate method for any type of convergence testings (whether
> that be k-point, cutoff, fine grid or cell size). I want to know if
> there are keywords/flags within SIESTA for single point energy calcula
program line_av
c
c LINE_AV version 1.1.1
c
c written by P. Ulrich Biedermann March 2009
C last changed 30.3.2009
c This program LINE_AV reads files written by SIESTA with data stored on the
c mesh used by DHSCF, e.g., R
According to your input, your system is isolated by 10 Angstroms vacuum in all
three directions (the maximum fractional coordinates given are ca. 0.3, 0.65,
and 0.2) and should be recognized by siesta as "molecule" (look for an output
line like "siesta: System type = molecule").
The simplest an
Thank you for this information. I will have a look at SIESTA 3 and otherwise
dive into the adventure of modifying SIESTA 2.0.2
Ulrich.
- Original Message -
From: Alexander Vozny
[mailto:ovoz...@gmail.com]
To: siesta-l@uam.es
Sent: Thu, 27 May 2010
16:19:29 +0200
Subject: Re: [SIESTA-L]
Dear all,
I would like to use pseudo hydrogen atoms with valence 0.5 to saturate dangling
bonds on a semiconductor surface. I have created a pseudopotenital with the
atom program using the input
pg Hpseudo hydrogen 0.5
tm2 2.0
Hpb
0.5 0.0 0.0
Jonas,
I was successfull with the following syntax:
...
LatticeConstant 1.03 Ang
%block LatticeVectors
12.827 0. 0.
0. 10.520 0.
0. 0. 3.838
%endblock LatticeVectors
AtomicCoordinatesFormat Fractional
%block AtomicCoordinatesAndAtomicSpecies
0.953598710.133807980.5000
4.0782 is the experimental fcc lattice constant of gold, 2.8837 the
corresponing bond length or lattice constant of a primitive cell. The bond
length of 2.92311 probably is an optimized value for the DFT/basis set used.
Ulrich Biedermann
> Dear all,
>
> Some fdf files in the director
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