Dear Jianwei Wei,
the problem is that you mix up different versions of Sies2xsf
in the same directory, notably
subroutine test_ani
appears in the file test_md.f of the old version
and test_ani.f of the new version.
I don't know which other problems might follow.
Try to compile the new version in a
Has anyone had experience using SIESTA to calculate degenerate
frequencies?
Even if I force exact symmetry in the unit cell, I get very non-degenerate
frequencies when they should be identical. Could I be doing something
wrong
or is this a numerical limitation with SIESTA?
Thanks,
Ben
which are
provided along with the main code.
You should better
compile it using make (after changing the compiler options
in Makefile if necessary)
Check if you get an updated version from
http://www.home.uni-osnabrueck.de/apostnik/download.html
- Sies2xsf
(it has not been actualized since long
Dear Shi,
the problem is incompatibility of the DM file as was previously stored
with the new calculation. If you don't see
an obvious reason why it might have occur, simply remove (or rename)
your .DM file and start from scratch.
However, starting OrderN from scratch can result in other problems,
Dear Shi,
it was not a good idea to send your 3 MB or so of data
to the mailing list, and twice.
If you want to show an example, show it short.
To your question: yes, you got the arithmetics right.
Only that, for systems with gap SIESTA sets the Fermi energy
more or less in the middle of the gap,
Dear Andrei,
You said in your SIESTA-tuto that the frozen phonon calculations usually
proceed after CG relaxation.
Dear Zhongli,
this is not obligatory, techniclly speaking, but any book on phonons
tells you how they are introduced from Taylor expansion arond
the equilibrium. So, this
Dear Siesta users,
recently Andrei Postnikov wrote a small tutorial on Siesta
http://www.home.uni-osnabrueck.de/apostnik/Lectures/SIESTA-tuto.pdf
He wrote:
one cannot a priori expect equally good performance of basis over
a large range of bond lengths and, say, pressures: as the pressure
Dear Siesta community,
a small document composed by me with the primary aim
of giving to students a broader introduction to the concepts of Siesta,
is accessible at
http://www.home.uni-osnabrueck.de/apostnik/Lectures/SIESTA-tuto.pdf
It is more than one month old, in which time I hoped to update
Hi,everybody
Hi, Shi
I use vib2xsf to visualize the phonons ,but I get some Problems.
First mode : 27
Last mode : 28
Cannot vizualize for q.ne.0 !
Then it stops.
Can you help me?
Yes. It stops because the script cannot vizualize eigenvecors
for q different from (0,0,0). The reason
Dear users,
After reading the siesta papers, I clearly understand the concept of
atomic-like orbitals (radial function times spherical harmonics). However,
I don't quite understand the phrase the radial shape of every orbital is
numerical. Can someone kindly give me a simple explanation?
Dear Andrei
Thanks a lot for your answer; unfortunately you've confirmed my
fears on the real meaning of negative frequencies.
The forces level of the configuration is not larger than 0.02 eV/Ang,
which is half the default (zero) value. I thus expected to be on the
safe side,
Hi Roberto,
apart from checking MeshCutoff, I'd have two suggestions:
1. Look in your .FC file at the on-site terms
(the force induced on a given atom when this atom is displaced).
It may happen that for some atoms, these terms are markedly,
I mean really markedly,
asymmetric with respect to
Dear Pablo,
I see from your data that the crossing/no crossing happens
between the argument values 0.020781 and 0.24937:
.016625 -.069279
.020781 -.026979 ( up to here increasing )
.024937 -.040879 ( from here on decreasing )
.029093 -.077879
Dear Roberto,
the frequencies appearing in VIBRA as negative are in fact imaginary.
The reason for their appearance is too bad forces
(big numerical noise in forces because of unsufficient MeshCutoff)
and/or calculation of phonos too far from equilibrium
(unsufficient structure relaxation prior to
I have managed to plot my graphs with xmgrace. But I am not quite familiar
with the setting of my data on the graphs.
xmgrace is quite well documented; see
http://plasma-gate.weizmann.ac.il/Grace/doc/UsersGuide.html
Do you have any idea of how to :
1. set the fermi level to zero in the
Dear all users :
I have got the result about mulliken population by SIESTA,but I don't
know if it is a wrong result,please help me ,the mulliken population of
boron atom is 3.826and 3.624,I think that the mulliken population of boron
atom should be less than 3, my result as follows:
I doing a convergence test on the meshcutoff values for a cellobiose -
ionic liquid - water system.(So we're using Cl, O, N, C, H in the
system)I'm using LDA CA Single Zeta Basis Sets, and there are 292
atoms(643 orbitals) in the box.I performed single step CG with different
Mesh cutoff
Dear Zubaer,
these differences (which are in fact not that large!) are numerical,
and might come from whatever can be different in different supercells,
namely
i) mesh cutoff
ii) k-points.
Probably you thought already about both factors. However,
The max force on any atom in the supercells is
Dear Haci,
there is no such thing as utlimately correct band structure,
there is always your free choice how to choose the path along which
the bands are shown. But, usually it makes sense to explore
a path connecting several symmetric points. Let's think together
how to get them.
Back to
Dear Haci,
I can only repeat what I suggested before:
A possible reason:
wrong units; remember that you can define k-points in units
of 2*pi/(lattice constant) or in absolute units.
You input contains
BandLinesScale pi/a
and what is your a??
How to figure out what's going on:
look at the
Can you teach how to compile the rho2xsf.f?
You must have got it with the whole directory of tools (Sies2xsf),
including other necessary Fortran sources, and Makefile.
Correct two lines in the Makefile, FC = ... and FFLAGS = ... ,
to you needs (as in arch.make of Siesta)
and type make.
Read the
I have recently performed a calculation of the PDOS for a system with 323
atoms. Actually, not only for this one, but for other 30 systems as well
(thank the heavens the other 30 systems have 90 atoms, at most...).
However, I noticed that I had compiled siesta without the -DWXML_INIT_FLAG
Dear Siesta User,
I am making some calculation on a slab. I enter a Monkhorst Pack grid
that generates 40 k points and it is suggested to think of
shifting this k-point by the program as the following
lines from the .out file suggest it.
I am a bit puzzled by this k-point shifting. To my
Dear Asa,
1. You set up magnetism in the DM.InitSpin block
for atoms 1 and 2 only; consequently the rest of your atoms,
3 through 18, are initialized non-magnetic.
You must be able to see it in the Mulliken populations block since
they are printed over all atoms. Looking at it you can find out
Dear Asa,
it is difficult to guess without knowing the details, but here are
some condensed remarks concerning magnetism in Siesta:
1. If you set SpinPolarized flag True (as you should) and do
nothing else, the initial spin values will be set to maximum
on all atoms. This might be OK for your
Dear Min Cheol Kim,
in order to get a reasonable result on your (magnetic) system,
you should of course run it spin-polarized, and not just as you say
even tried the spinpolarization
but this is the main (and almoet the only) thing that you really need.
Forget playing around with the basis - it is
Dear SIESTA users,
I have difficulties trying to converge calculation with respect to
PAO.EnergyShift.
The system is 8 layers silicon slab, hydrogenated.
The total energy varies strongly with PAO.EnergyShift parameter:
PAO.EnergyShift Etot
300 meV -21007.7361 eV
250 meV
Dear Andrei,
thank you for quick reply.
I have some experience with AIMPRO which is also based on atom-centered
basis functions,
but it does not have parameters like EnergyShift, EnergySplit, nothing
similar.
Dear Ruslan,
exactly as I say: atom-centered basis functions are your free
To all respected siesta users:
Considering
an article on a hexagonal lattice, written by authors who have worked
with siesta, I have encountered that they have used 6x6x2 supercell for
their bulk system !!!
Dear Catrina:
if it is really supercell used in their calculation and not just
Dear Andrei Postnikov,
I am sorry if my words were confusing. Actually, it is not the matter
of imitating at all. I just wanted to know if having supercell for some
systems like bulk hexagonal helps to get better answers.
Dear Catrina,
OK, so you do not care about constructing supercell as
To all respected siesta users,
Thank you very much for helping me.
I have used the usual way (not supercell) for hexagonal system of mine,
using the method mostly discussed here in mailing list. In the .out file
of variable cell, I have Naive supercell factors: 885.
OK, so you
Dear all,
As you know, there is a pseudopotential file database in this website.
Are pseudopotential files in the database reasonable?
As I tested a simple h2o calculation to compare H and O pseudopotential
files in siesta with H and O pseudopotential files in the database, the
Energy value
Hello all,
I have a question concerning the broadening parameter within the PDOS
block. I understand that the larger this value,
the smoother the resulting PDOS curve
Dear Tom,
this is correct.
and the larger the possibility one loses information concerning
peaks that may have been
Deal All,
I know tried to replace the V atom with a C instead. After many CG steps,
the same problem in the SCF run suddenly occured. Can it be an issue of
compilation?
-Joachim
Dear Joachim,
let's be systematic:
1) can you please confirm that the problem is not due to what I suggested
to
Hi all,
I've got a (silly, I'd say) question regarding the subroutine reclat. I
wanted to see the cartesian components of the reciprocal lattice vectors.
when I take a supercell of graphene with
lattice vectors along x and y, I get:
reclat: Unit cell vectors (Bohr):
a1:
Quoting Joachim Fürst [EMAIL PROTECTED]:
Dear all,
I followed the discussion about the vanadium deposited on a graphene
sheet.
My experience with vanadium is that it is necessary to insert semi-core
states
the 3p with the atom program.
Yes I fully agree -
V3p are important in order to
Hallo,
some questions: in those cases when as youy say you got it converged,
does everything else look reasonable? (vanadium is magnetic,
graphene not, bands in due place, no crazy charge transfers etc.)
My wild guess is that, as you set spin polarization on,
by default (unless you have InitSpin
Dear all :
I have a problem in calculating the energy of single atom. The
energy will drop linearly with respect to decreasing of energy shift.
That is OK. The smaller (the absolute value of) the energy shift
the more extended are your basis functions, better the variational
freedom,
Dear all siesta users:
I have compiled the rho2xsf and Xcrysden succesfully,and I use
the rho2xsf to transform the file.RHO to file.XSF format,
it looks like working well,
but when I use the Xcrysden to display the file.XSF,I can get the
atom structure only,I can't find the charge
Dear all,
Is there anyone who has the experience on phonon calculation by siesta?
I'm trying to calculate the phonon spectrum by siesta. I only want to
calculate the force over two atoms by fixing all the others.
It is not quite clear what you are attempting to do.
The forces are always
Hello everybody,
I'm computing the FC matrix for the first time :), and by now I'm
sure the calculation will hit the wall clock time limit.
I see Siesta's moving each atom back and forth and along the three
coordinate axis, son can guess what's doing.
But what exactly is the
Dear users,
I want to create the triclinic lattice (a=8.194 b=12.897 c=14.190 Ang,
alpha=92.98 beta=115.82 gamma=91.15 degree) and tried as follows.
LatticeConstant 1 Ang
%block LatticeParameters
8.194 12.897 14.190 92.98 115.82 91.15
%endblock LatticeParameters
I am not sure whether it
However, I am not yet familiar well with the way to define the crystal
lattice in SIESTA fdf file, and so I am not sure the below definition of
triclinic crystal lattice is correct.
With best regards,
Chol-Jun Yu
I want to create the triclinic lattice (a=8.194 b=12.897 c=14.190 Ang,
Nidhi:
I just tried it again; the file compiles smoothly with ifort and with g77.
(g77 complained, however, about unresolved reference to eos2
which was declared as external, but is not present. This declaration
should be removed. This does not seem to be your case, though).
Otherwise I don't
Dear users;
How to use 2 different basis for the same element? such as use both
DZP and SZP for different O atoms in CO2. Thank you.
Declare them as different species
and assign to them different labels (O1, O2)
Hello SIESTA users.
I want to optimize the lattice parameters of a tetragonal structure
(TiO2) i.e. a and c/a ratio.
I know SIESTA can optimize it, but I want to do it manually i.e. total
energy vs a and c/a.
I want to follow the following steps.
1. First optimized a for fixed c/a.
Dear Mic:
I don't quite understand how you put it, and your attached .ppt
does not make it simple, either. To my opinion it is easier -
sorry for advertizing one my old publication not related to
TiO2, but it contains several figures which explain the search
of minimum, by hand, of a function of
Sir,
As per your instructions to include 5d in the basis of Te
Nidhi:
who ever gave you instructions to include 5d in the basis of Te?
The previous discussion was about Sm5d, which you now included.
As for d-states of Te - there might be a good reason
to include some if you find it necessary;
Dear Marcel,
just by chance, I optimized the same system quite recently.
The trend you report is indeed (generally?) present, but apparently
to somehow smaller extent: I've got
a=4.212, c=7.016 Ang for EnergyShift = 5 mRy;
a=4.255, c=6.969 Ang for EnergyShift = 200 mRy (default)
The basis I used
Hi!
2008/4/15, Marcel Mohr [EMAIL PROTECTED]:
The smaller energyshift, should in principle be better, and results in
larger basis size.
That's not true. It only has to be better for an isolated atom, who knows
what would happen in condensed phase. However, you could use the
variational
Dear siesta users,
Can anyone help me generating pseudopotential of U as I tried to make its
input file but still some error is coming can just pick out the error init
I am attaching the file or it would be very supporting if anyone is
having its .psf file
thanx in advance to all the users
Hi,
I have made the changes according to u and defined the pseudo of Sm as
Hi -
If u refers to me, mind that I never advised you on the pseudo radii
for Sm...
I only meant that inclusing 4f is technically no error - but it will
probably lead to physically wrong results. Whatever...
Regarding
You mix up several things; I doubt it will help to resolve your problems
but let us address them one by one.
Sm valence configuration. 4f states are quite localized and
probably (in reality, not in DFT the calculation) are not any near
to the band gap. If you include them in valence states and in
Dear users,
I've uploaded the new version of the database.
As always any comments/suggestions are really welcome.
Dear Eduardo,
many thanks for the next piece of a nice job.
Now as you welcome comments, here are some faults I've found.
Hopefully they just concern the documentation
(in both
Subsequently, I set FixSpin to be
true and Totalspin to be 1, it gave rise to siesta: Total spin
polarization (Qup-Qdown) =1.35.
Before, you did not mention that you used FixSpin. Correspondingly,
my earluer comment in the list was not related to this case and might be
disregarded.
Dear all :
I used siesta 2.0 version and system is a Ru
complex(Creutz-Taube ion) which has two redox site on
Ru atom.
One is 4d^6 :
t2g(dxy + dyz + dxz) was supposed to be 6
electrons,
eg(dz2 + dx2-y2) was supposed to be zero .
And the other one is 4d^5 :
t2g was
I am trying to calculate the band structure for 20 or so Ni atoms.
However,
Siesta repeats the cluster I specify and I end up with calculations that
has
more than 500 atoms. Is there anyway, I can stop the periodic repetition?
Choose the unit cell size large enough, so that the basis
Hi Andrei,
I understand the system could converge to metastable states, and of course
Eliseo has the right to expect that the system could converge to a given
one. However, what I understood from Eliseo's message is that he expected
the system to converge to a state in which the individual
://www.home.uni-osnabrueck.de/apostnik/download.html
and if you still encounter a problem try to describe it more precisely
than somthing is wrong somewhere ...
99% of the problems so far were due to different compilation
parameters used in the Siesta installation and in Sies2xsf,
that made binary data
Dear Sir I am new siesta user using a tutorial about silicon
bulk.thereis a problem that is when I go to
plot bands.dat
xmgrace bands.dat
and select the correct range of energy.
Now the problem is what is xmgrace.
Xmgrace is a commonly used plotting program under Unix
( see
Hello
I am using rho2xsf, a script to transform 3-dim grid function
written by Written by Andrei Postnikov
Wehn I run and give the required information i.e system name etc)
at the end I always get this message
Error reading function values on the grid
Does any one
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