Dear Siesta users,
There have been some messages on the list recently about difficulties with the
calculation of optical properties, more specifically
related to an error in routine 'minvec'.
This problem was corrected in mid 2010, and the fix appeared already in
siesta-3.0-rc2.
I strongly sug
Dear Siesta users,
A new development snapshot (siesta-trunk-408.tgz) is available for download by
eligible users at the Siesta website.
This snapshot contains the latest bugfixes, and is a step closer to a
beta-relase that will include the new functionality we have been
working on since the 3.0
Hi, Brad,
Please try the updated version (siesta-3.1-pl11) from the Siesta website.
Best regards,
Alberto
On Sat, Oct 6, 2012 at 6:32 AM, Brad Wells wrote:
> Hi Siesta Users,
>
> I am interested in using the new Hirshfeld code for calculating partial
> charges, as these are very important
Hi Bing,
This is a cosmetic bug that only affects the creation of the optional XML file.
The psf file would still be correct.
The bug has been fixed in siesta-3.1-pl18, available on the Siesta website.
Alberto
On Oct 12, 2012, at 4:01 AM, Huang Bing wrote:
> Hi, siesta users
>
> In ATOM Use
fixes.
We would be grateful for any bug reports. Please follow the guidelines in the
Docs/REPORTING_BUGS file.
Regards,
Alberto
Dr. Alberto Garcia -- Email: alber...@icmab.es
Institut de Ciencia de Materials de Barcelona - CSIC
Campus de la UAB, E-08193 Bellaterra, SPAIN
Tel: +34-93
things to watch out
for and explore in the new version.
To report any remaining issues, see Docs/REPORTING_BUGS
Thanks for your patience and continuous support.
The Siesta team
October 31, 2012
Dr. Alberto Garcia -- Email: alber...@icmab.es
Institut de Ciencia de Materials de Barcelona - C
best
>
>
> Guang-Ping
>
> 2012-11-01
>
> Guangping Zhang
>
> 发件人：Alberto Garcia
> 发送时间：2012-10-31 18:14
> 主题：[SIESTA-L] Enhancements to the TranSiesta/TBTrans code
> 收件人："http://www.uam.es/sie
Liu,
You should upgrade to the latest versions, both along the 3.X branch
and the development ("trunk") branch.
Alberto
On Thu, Nov 8, 2012 at 7:42 AM, liuyunlong0902 wrote:
> Thanks for your suggestion. Here I include the input and output file, which
> is just an example for calculating grap
Dear Siesta users,
We have corrected several bugs and inconsistencies in the development version,
and released a new snapshot (trunk-427).
Some of the improvements affect the new TranSiesta and TBTrans code contributed
recently by Nick Papior Andersen, of the Technical Univ. of Denkmark.
The
We are happy to announce the release of Siesta 3.2.
Users are encouraged to use this version for production runs.
You can find the Siesta 3.2 release in the "Access
to the code" section of the Siesta website.
To report any remaining issues, see Docs/REPORTING_BUGS
Thanks for your patience and c
We have released a new Siesta development snapshot (trunk-433) which includes:
- The implementation (by Fabiano Corsetti) of an orbital-minimization
method without localization that can be used as an alternative to
diagonalization.
- The JobList suite of utilities (by Jose Soler) to organize,
Alex,
You might want to try the development version of Siesta (check the website).
The mesh operations have been overhauled to deal precisely
with the kind of inhomogenous system that you are dealing with. You will
eventually hit the same kind of basic limit, but the load balancing should be
be
Hi Benedikt,
SIESTA does not need projections, as the basis orbitals are localized on
the atoms. You get naturally the "chemical" information one is used to.
Plane-wave codes such as vasp do need projections to get some kind of
"local" information from the delocalized basis.
Alberto
On Mon, J
Hi Herbert,
Siesta is also able (as of 3.2) to do Hirshfeld and Voronoi charge
partitioning analyses.
Alberto
On Thu, Jun 20, 2013 at 3:21 PM, Herbert Fruchtl <
herbert.fruc...@st-andrews.ac.uk> wrote:
> Just to add to the discussion that started with the question about PDOS
> projection ra
Hi,
There is an overflow of the output field for the configuration information,
which is later confusing Siesta when it
tries to check it.
This might be considered as a bug in Atom: those configuration fields are very
small for spin-polarized cases, and it seems that for large shells such as d
Hi Alejandro,
On Jan 3, 2014, at 3:37 PM, Alejandro Suarez wrote:
> ...
> However, I have run into trouble when attempting to run the calculation with
> the adsorbate and ghost atoms substituted for the surface. As was posted
> previously (http://www.mail-archive.com/siesta-l@uam.es/msg01507.h
SIESTA Tutorial
Zaragoza (Spain)
June 16-19 2014
This is a four-day hands-on tutorial on the use of the SIESTA code
(http://www.icmab.es/siesta), aimed at students and researchers from different
disciplines who already use, or plan to use, SIESTA in their work and who would
like to understand
(e.artacho _at_
nanogune.edu)
Alberto Garcia, Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC)
(albertog _at_ icmab.es)
* Instructors:
Jose Soler, Universidad Autonoma de Madrid
Georg Huhs, Barcelona Supercomputing Center
Javier Junquera, Universidad de Cantabria
Emilio Artacho, CIC
Dear Mike,
Thank you for bringing this up.
The authoritative reference manual for each revision can always be found in the
Docs/ directory of the Siesta distribution.
For the latest versions we also make it available for download directly from
the web page.
In the case of the development vers
Hi Mike,
The FoX library does not contain any MPI calls, so it does not need mpif90 for
compilation. However, if you link it with a code (such as Siesta) with MPI
calls, then you do need to link it with mpif90.
Regards,
Alberto
On 11 Jul 2014, at 22:10, Michael R. C. Williams
wrote:
>
Hi,
You want the 'prefix.bands' file. The .BONDS file contains bond-length
information...
By the way, if you use the 'pi/a' option for the k-point scale, make sure that
you
have a
LatticeConstant XX.XX
line in your input file.
Regards,
Alberto
On 16 Jul 2014, at 15:42, toufik esssa
This is a semi-automatic periodic posting to the Siesta mailing list.
The mailing list can be a good resource for everybody, provided that we can
abide by a few common-sense guidelines:
* Before posting, make sure that you have made a fair effort at learning about
the issue in the documentatio
We are happy to announce the availability of a beta version of the
upcoming Siesta 4.0 release.
This version includes the van der Waals functionals, the new
load-balancing code for real-space grid operations, a Wannier90
interface, a new Orbital-Minimization-Method solver, and other
improvements a
Hi,
In the new version siesta-4.0b available at the Siesta website there is an
updated grid2cube (named g2c_ng)
in the Util/Grid directory that can handle non-orthorhombic cells.
Regards,
Alberto
On 31 Dec 2015, at 11:20, Nick Papior wrote:
> I have created a small utility in python for
ng is wrong with my STRUCT file "1Ben_free_0d00V.xyz".
> For your information, I attached the STRUCT file. Would you please comment on
> my operations? It will be great if you can send me an example for the
> executable.
>
> Cheers!
>
> Jin
>
>
>
&g
Please see the "Local Density of States" section of the manual.
On 30 Jan 2016, at 11:35, Anju Saroha wrote:
> Hi to all,
>
> I am having a doubt in plotting charge density in 3D mode. I tried using
> DENCHAR utility program. I want to know how one can plot charge density in
> some specific e
If you are not using an external lapack+blas library, you should use
COMP_LIBS=linalg.a
in the arch.make file to compile all the linear-algebra code in Src/Libs.
Version 4.0 needs extra code that is not in the file Src/Libs/lapack.f.
See Src/Sys/nolibs.make.
Regards,
Alberto
On 04 Feb
aving directory
> `/nfs/disk1/nwzaw2/softwares/SIESTA/siesta-4.0b-485/Obj/SiestaXC'
> make: *** No rule to make target `COMP_LIBS=linalg.a', needed by `siesta'.
> Stop.
>
>
> On Thu, Feb 4, 2016 at 5:32 PM, Alberto Garcia wrote:
> If you are not using an externa
Hi,
It is always advisable to install optimized versions of the libraries.
However, you can compile (the *serial* version only) without any external
libraries
by using the arch.make example in Src/Sys/nolibs.mk, as explained in
the list link you quote.
But note that this only works for the new
Hi,
The spin-orbit interaction is not yet included in the released version of
Siesta. It will be in the next few months.
Regards,
Alberto
On 10 Feb 2016, at 09:32, Abdullahi Lawal wrote:
> Dear Siesta user.
> Please some body should help me, i want to calculate the structural
> propertie
Hi,
There is a subtle point concerning the use of the pseudopotential approximation
with van der Waals functionals. In short, since the vdW xc term
is non-local, the influence of the core can extend beyond the nominal
"pseudopotential cutoff", leading to pseudos that can be pathological (for
ex
On 03 Mar 2016, at 05:02, Anju Saroha wrote:
> Dear Siesta users
>
> I am a new user of Siesta and using siesta-trunk-462. Can somebody please
> help me in knowing how to plot 3-D charge density in specific energy range,
> say between -5.0 eV to 0.0 eV, instead of the complete energy range of
Hi,
Actually, a full F2003 compiler is not necessary for this. Only the
"allocatable array extensions" (TR 15581) feature is needed. All mainstream
compilers have implemented this as an extension of F95 for several years now.
So you seem to be using a very old compiler. If your budget is tight
The SIESTA developers have decided to change the licensing conditions for the
code. From now on, SIESTA will be released under the GPL open-source license
(https://en.wikipedia.org/wiki/GNU_General_Public_License).
In the past SIESTA had always been free for academic use, but re-distribution
w
Hi Aihua,
This problem is corrected in the latest version (4.0-b2) in
http://launchpad.net/siesta
The structure read at the beginning of the calculation is used to generate the
k-points.
Note that it would indeed not be advisable to perform a band-structure
calculation at the end of
a cell-rel
ling after every cell relaxation step?
>
> Best regards
>
> Aihua
>
>
> > -Original Messages-
> > From: "Alberto Garcia"
> > Sent Time: Wednesday, May 18, 2016
> > To: siesta-l@uam.es
> > Cc:
> > Subject: Re: [SIESTA-L] discrepancy
>
>
>
>
>
> On 16-05-13 7:54 AM, "siesta-l-requ...@uam.es on behalf of Alberto Garcia"
> wrote:
>
>> The SIESTA developers have decided to change the licensing conditions for
>> the code. From now on, SIESTA will be released under the GPL open-sourc
> Grigory Shamov
>
> Westgrid/ComputeCanada Site Lead
> University of Manitoba
> E2-588 EITC Building,
> (204) 474-9625
>
>
>
>
>
> On 16-05-13 7:54 AM, "siesta-l-requ...@uam.es on behalf of Alberto Garcia"
> wrote:
>
>> The SIEST
We are pleased to announce the release of Siesta-4.0.
This version should be the default choice for production for most users.
You can read the Release Notes and obtain the tarball in the release page:
http://launchpad.net/siesta/4.0/4.0
Note in particular the BACKWARD COMPATIBILITY ISSUES an
Hi,
Please note that the gnubands program is intended to plot band structures,
i.e., energy values along *lines* in the BZ. The relevant data is obtained with
the "BandLines" option in Siesta. If you use the "BandPoints" option you get
information about a set of *points* in the BZ, which is not
Hi,
Thank you for the report.
There is indeed a bug in the implementation of the -DSIESTA__NO_MRRR option.
A patch is available. See: https://bugs.launchpad.net/siesta/+bug/1622526
Regards,
Alberto
On 09 Sep 2016, at 17:03, Jariyanee Prasongkit
wrote:
> Dear Siesta team,
>
> I am tryin
Dear Mersad,
You have found one of the cases in which the automatic "configure" mechanism
falls short. As explained in the manual, we consider
the "configure" route as just a way to get a first draft of an 'arch.make'
file. For fine-tuning you should take a look at the file
Src/Sys/DOCUMENTED-
Hi,
Indeed, the CONTIGUOUS keyword is a F2008 feature, not implemented yet in all
compilers.
For now you can apply the patch attached to
https://bugs.launchpad.net/siesta/+bug/1619437
to fix this problem, or simply delete the CONTIGUOUS keyword.
Best regards,
Alberto
On 14 Sep 2016, a
The files are of the form SystemLabel.Extension.
In your case, input-ok-og.DIM, etc.
Alberto
On 24 Oct 2016, at 08:14, Marco Fronzi wrote:
> Dear Siesta Users,
>
> I am trying to plot charge density and wavefunction using denchar.
> In the working directory I put the following files from sie
Hi, Mohammad,
Depending on the Siesta version that you are using, and the options used, the
XV file might contain the coordinates
predicted for the next molecular-dynamics or relaxation step, so they will not
be same as those for which the electronic structure (the DM) was computed.
If you want
Hi,
In your arch.make, replace -DNCDF by -DCDF, type “make clean” and “make”.
Alberto
> On 30 Jan 2017, at 11:33, RAJAN SINGH wrote:
>
> Dear Siesta users
>
> I am facing following errors while trying to install 4.1-b1 in parallel mode
> with NETCDF:
>
> Fatal Error: Can't open module file
Dear Mark,
Please look at the example for Ba in the Tutorial/PS_Generation subdirectory of
the Atom distribution.
(see also Guide.txt). The short answer to your question is that you can
generate an appropriate pseudo
for your needs by using an ionized reference configuration.
Best regards,
Hi Ian,
Please make sure that you are using GNU make. We use the VPATH feature to find
source files in other directories.
Also, try to do a “make clean” in case there is some previous corruption.
Best regards,
Alberto
> On 24 Apr 2017, at 13:46, Ian Shuttleworth wrote:
>
> Dear all
>
>
Hi,
I cannot reproduce your problem in my computer. Beyond making sure that your
MPI system is not hitting some internal buffer limit, I can suggest a few
things:
— You are using a lot of processors for a relatively small system
— Your cell is huge, way beyond what is needed for such as system,
Hi Nicolas,
Apart from using the DM restart option, you can set the number of scf
iterations to zero:
dm-use-save-dm T
max-scf-iterations 0
write-voronoi-pop T
This will skip the scf loop completely, and proceed to the “post-scf-work”
subroutine.
In this routine:
— The total energy will be c
Dear Mogus,
The legacy O(N) module is quite delicate, as explained in the manual. You need
to specify the correct value of the chemical potential (in the (sizable) gap)
for the minimization to work correctly.
Unless your system is very large, you might find that the diagonalization
method in
Hi,
This is because the .ion file only contains the PAOs and the “scalar” KB
projectors. The extra information
in the .psf file (SO-part of the semilocal pseudopotentials) is needed to build
the spin-orbit contribution
to the Hamiltonian.
Best regards,
Alberto
> On 15 Mar 2018, at 02:06, Y
To clarify, what Siesta and all the other mentioned packages do is really
“ab-initio molecular dynamics”, as opposed to “molecular dynamics with
classical or effective potentials”.
Alberto
> On 3 Jul 2018, at 01:24, sullah wrote:
>
> Dear Najmeh.
>
> In SIESTA, you can perform MD by solvi
er was accepted only
| when we changed the AIMD to MD in the third round of review. Here, I
| would take the liberty to ask you about the difference in MD between
| SIESTA and the other mentioned code?
|
| Regards,
|
| Saif
|
| Em 05.07.2018 05:03, Alberto Garcia escreveu:
|
|> To clarify, what S
Hi,
You seem to be missing the blacs and pblas libraries. These are sometimes
included in scalapack, but not on all systems, apparently. Since you seem to be
working on an IBM machine, you might get some inspiration from this snippet of
an arch.make file that I used in the past. Details might b
Hi,
You are using the C++ compiler ('g++') instead of 'gcc' (C compiler). This
causes some
extra name mangling in 'sockets.o' that confuses the linking stage.
Best regards,
Alberto
- El 20 de Noviembre de 2018, a las 04:30, Zhiping Xu x...@tsinghua.edu.cn
escribió:
| Dear Siesta dev
Dear Alex,
You are hitting an internal limit in the size of the radial function registry
pool.
If you have access to the code, you can change the line
integer, parameter :: nmax_funcs = 300
in ‘Src/matel_registry.F90’ to make the parameter ‘nmax_funcs’ larger, and
recompile.
In a forthcomin
Hi,
It is not an error, nor a bug in the code. It is just an informational message
that is printed whenever you are running
a calculation without k-point sampling for a system whose unit cell is not
large enough to allow the representation of all orbital interactions (matrix
elements of H and S
Hi,
The code in siesta_init is:
#ifdef MPI
call gridxc_init(comm=MPI_Comm_World,
$ time_mpi_calls=fdf_get('gridxc-time-mpi-calls',.false.))
#else
call gridxc_init()
#endif
Thus, you seem not to have used the -DMPI compilation flag, while you are using
an MPI-enabled version
Dear Azadeh,
No, the current Grimme-D method in Siesta is the one using only two-body
potentials. See:
J Comput Chem 25: 1463–1473, 2004 and J Comput Chem 27: 1787–1799, 2006.
Alberto
- El 22 de Septiembre de 2019, a las 07:34, Azadeh Ayatollahie
azadeh.ayatolla...@gmail.com escribió:
|
Hi,
You seem to have a misconception: phonon calculations for periodic dense
systems need a supercell to account for the forces on "far" atoms (beyond the
primitive cell) when you move an atom in the unit cell. Otherwise your
dynamical matrix will be wrong.
This supercell is just a bookeeping a
Dear Dr. Popov,
Your unit cell is cubic, and the coordinates show a highly symmetric pattern.
If your
atoms happen to be in centrosymmetric positions, the forces must be zero.
- El 26 de Feb de 2020, a las 19:14, popov po...@ipb.ac.rs escribió:
| Dear Siesta users,
|
| I have got all for
The capability to process non-collinear and spin-orbit wave-functions has been
implemented already, and it will appear in a formal release soon. If you
desire, you can download a snapshot of the current code of the 4.1 series from
https://gitlab.com/siesta-project/siesta/tree/rel-4.1
(Click o
Dear Pablo,
It might be that you are using an old version of the PSML-enabled code, since
the psml-support branch is tracking the master developments.
Please note that since Siesta development moved to Gitlab, all updates are done
there, and they are not pushed back to Launchpad.
For an ove
Hi,
You should use 'readwfx' to process the WFSX file directly. The old WFS format
is obsolete, and the conversion programs are there just in case someone needs
to use the data in an old file.
Please read the header in Util/readwfx.f for instructions on how to use.
Newer versions of Siesta (in
in:
http://max-centre.eu/webinar/new-developments-siesta-high-performance-materials-simulations
Information on past and future MaX webinars can be found in:
http://max-centre.eu/webinar/
Best regards,
Alberto Garcia
for the Siesta developers
--
SIESTA is supported by the Spanish
In the absence of more information (you might want to enable debugging symbols
to see where the error occurs):
- It might be that the energy range you specified does not contain any
wavefunctions (the program should anyway not crash... You might check this with
the Util/WFS/readwfx program).
advice ?
|
|
|
| El-abed Haidar | Doctor of Philosophy (Science )
| Condensed Matter Theory (CMT) Group
|| School of Physics
| THE UNIVERSITY OF SYDNEY | NSW | 2006
|
|
|
|
|
|
| From: siesta-l-requ...@uam.es on behalf of Alberto
| Garcia
| Sent: Tuesday, 15 December 2020 7:30 PM
| To
Hi,
Since you are using a recent 'master' version, you might want to look into the
Obj/ARCH-EXPERIMENTAL directory.
There you will find a more structured way of organizing the building.
Alberto
- El 16 de Dic de 2020, a las 10:15, Tamas Karpati tkarp...@gmail.com
escribió:
| Hi,
|
| So
Hi,
You do not give details, but you must be using a very old version...
Try downloading a new one from the psml-support branch in Gitlab.
I hope this helps,
Alberto
- El 3 de Feb de 2021, a las 15:30, I. Camps ica...@gmail.com escribió:
| Hello SIESTers,
|
| I am trying to compile all
In Siesta you can have different species "names" with the same atomic number.
This can be used to assign different basis orbitals, and in your case
pseudopotentials, to atoms in different environments.
You will have to generate appropriate pseudopotentials for your different
pseudo-H atoms. Yo
Hi,
You can follow the standard procedure of carrying out the ground-state
calculation first, and then re-using the density-matrix to start a new
calculation for
the analysis you require. That will save you the work of re-converging the
electronic structure. Please see the manual for the option
Hi,
For this simple kind of constraint, you should not need to write your own
constr.f file. You can use the constraint-specification options described in
the manual.
Best regards,
Alberto
- El 20 de Mayo de 2021, a las 10:40, Pablo Álvarez Rodríguez
pablo96carnic...@gmail.com escr
Hi,
You can use the program 'grid2val' in the directory Util/Grid of the Siesta
distribution:
c Usage:
c
cgrid2val gridfile(gridfile is, for example, a .RHO file)
c
c Points where the function is to be evaluated are read from
c standard input, in the following (free) format
Hi,
In your arch.make you have defined the symbol NETCDF_INTERFACE, but the symbol
whose value you append to INCFLAGS is NETCDF_INCLAGS.
Please change NETCDF_INTERFACE to NETCDF_INCFLAGS.
Also, regarding your related post: 'make lib' should not be used to compile
Siesta. Just use 'make'.
Alb
Hi,
You do not say which exact version you are using, nor specify the nature of
your problem.
I would advise you to use the latest version along any of the branches with
support for PSML files. See the guide to Siesta versions in
https://gitlab.com/siesta-project/siesta/-/wikis/Guide-to-Sies
Hi,
A few things to note (others might be at work):
- Your DM tolerance might be too coarse, leading to inaccurate forces and
patchy relaxation convergence.
- You do not say which relaxation algorithm you are using. You might try the
"quenched molecular dynamics" approach
mentioned at the end o
Hi, Karen,
There are several facets in this issue:
* When a finite temperature (smearing) is used just for convergence
acceleration, the free energy is a
computational artifact that is formally needed to restore the variational
property. Tests for the size of the smearing and
for the fineness
Hi,
As explained in
https://gitlab.com/siesta-project/siesta/-/wikis/Guide-to-Siesta-versions
you need to use the rel-MaX-1 branch, which contains both PSML support and the
ELSI interface.
Best regards,
Alberto
- El 17 de Ene de 2022, a las 02:50, Chong Wang ch-w...@outlook.com
e
Hi,
You have a number of errors in your input file:
-- The atomic number of C is 6, not 12
-- For C and N, the d orbital should have n=3
-- For H the p orbital should have n=2
I hope this helps. You must have made changes to Simune's files...
Alberto
- El 2 de Feb de 2022, a las 09:49, K
Thank you, Danny,
I might add that a few days ago we merged the PSML functionality into the main
('master') branch of Siesta in Gitlab.
(For a guide to the various Siesta versions, see:
https://gitlab.com/siesta-project/siesta/-/wikis/Guide-to-Siesta-versions).
Compilation is now relatively str
Hi,
The units are indeed Bohr^-1. But in the .bands file (assuming you are using
the 'bandlines' option), what is printed is
the cumulative path length in reciprocal space.
I hope this helps.
Alberto
- El 10 de Feb de 2022, a las 04:39, Pasan Henadeera henadeer...@gmail.com
escribió:
Hi Francisco,
You need to run a new (SOC) calculation, but you can re-use the DM file
(density matrix) from the previous run to initialize the SOC calculation, thus
typically reducing the number of steps needed for convergence.
Regards,
Alberto
- El 27 de Marzo de 2022, a las 09:34, Fr
Hi,
There must be some issue with your input. Could you share it?
Regards,
Alberto
- El 28 de Marzo de 2022, a las 02:52, Francisco Garcia
garcia.ff@gmail.com escribió:
| Dear Users
|
| I performed a series of single point energy calculations on an FCC crystal by
| varying the lat
Hi,
The problem originates in a mismatch between the valence configuration of Sm as
given in Siesta's tables, and most periodic tables (6s2 6p0 5d0 4f6) and
Pseudo-Dojo's choice for configuration, which is [Xe] 6s2 5d1 4f5. In
addition, the pseudo-dojo pseudopotential (in the NC SR+3 table) ha
Hi,
As the error message suggests, you can try the non-perturbative options (see
manual).
I hope this helps.
Regards,
Alberto
- El 13 de Junio de 2022, a las 12:22, Reza Behjatmanesh-Ardakani
reza.b@gmail.com escribió:
| Hi,
| I used following fdf file for Li unit cell:
| =
Hi,
I cannot reproduce your results. Which version of Siesta are you using? Can you
show your output?
The expected behavior is something like this (obtained with the 4.1 branch
version):
[...]
siesta: Electric dipole (a.u.) = -0.000.558297 -0.00
siesta: Electric dipole (Debye)
Hello,
You seem to be missing the BLAS library in your link statement. It could be as
simple as adding -lblas to your link line, but it would depend
on your installation.
Best regards,
Alberto
- El 22 de Junio de 2022, a las 23:14, Ghazanfari, Sarah
sarah.ghazanf...@ndsu.edu escribió:
Hello,
We are writing a section on GPUs in the documentation, but until it is ready
you can use the ideas below:
There are two ways to take advantage of GPUs (enabled only for the solver
stage, which typically takes up the most time):
-- Using the ELPA library and its native interface in Sies
Hi Roberto,
The first reference is the closest in spirit, except that we incorporate the
mix as the pseudopotential of a new "alchemical" species
instead of keeping separate "pure" ghost atoms and using a weight factor for
each.
The second reference imposes extra conditions on the pseudopotenti
Dear Rajesh,
I quote from (the source of) the Siesta manual:
\item The default perturbative scheme for polarization orbitals
can fail in very specific cases. When the polarization orbital
has to have a node due to the presence of a lower-lying orbital
with the same $l$, the program can (if e
Hi,
You should remove the comment character from:
#%endblock LatticeVectors
Alberto
- El 21 de Septiembre de 2022, a las 12:23, Amal Yassin
escribió:
| Dear Siesta Users
| I make run to carbone nanotube armchair, but i find an error, can anyone helle
| me to solve this error? ( I ad
Hi,
For some reason, you are using commas (",") instead of dots (".") as decimal
separators. In fortran,
a comma in an input line separates items. This confuses the program. You should
check your 'locale' settings.
Alberto
- El 7 de Noviembre de 2022, a las 17:18, Amal Yassin
escribi
Hi,
This is something that we are planning to implement.
For now, if file space is a problem, you could use symbolic links from a
central location to each execution directory.
Best regards,
Alberto
- El 3 de Feb de 2023, a las 19:33, Daniel Bennett
escribió:
| Hi all,
| I was wond
Hi,
Your 'slab' is just three layers thick... that is not nearly enough to have a
good representation of
a "bulk" region in the center and a "surface" region.
After you fix that, you probably need to process the .VH file and obtain a
potential profile along
z to check that you reach a flat
Hi,
Please note that the master branch has received a lot of new commits in the
past week. You might have downloaded a version with a temporary glitch.
I suggest you now re-run the build step in the same directory with the option
'-j 1' instead of '-j 44', so that the compilation's last messa
Hi Daniel,
In Siesta 5.0 the CMake system builds all the utilities by default. If you
install the package after building they will all be in the
/path/to/installation/bin
directory, together with the siesta executable itself. If you do not install,
they will be in _build/Util/, where _buil
Hi Francisco,
You could indeed modify the constr.f file to include what you need, but first
check the section of the manual entitled "Auxiliary Force Field". In there you
can find a discussion of the MM.Potentials block, in which you can define the
parameters of, among others, a harmonic poten
ic potential to selected atoms.
| Any assistance would be appreciated.
| Thanks!
| Francisco
| On Mon, Nov 13, 2023 at 1:51 AM Alberto Garcia < [ mailto:alber...@icmab.es |
| alber...@icmab.es ] > wrote:
|| Hi Francisco,
|| You could indeed modify the constr.f file to include what you need, b
You compiler (gnu 4.8.5) is *very* old. Please upgrade to a modern version.
Best regards,
Alberto
- El 6 de Junio de 2024, a las 19:09, Boubacar Traore
escribió:
| I finally sorted out the issue of scalapack linking by adding its path to
| LIBRARY_PATH instead of LD_LIBRARY_PATH (more
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