Re: [SIESTA-L] Siesta calculation for helical structure

[Zeila Zanolli]

Dear Fanmiao
you can make a supercell large enough to host one period of oscillation.

Best
Zeila

On Tue, Feb 8, 2022 at 10:04 PM Fanmiao Kong <
fanmiao.k...@materials.ox.ac.uk> wrote:

> Hi All,
>
>
>
> I am wondering if there’s a way to calculate helical structures in Siesta?
> There’s no translational periodic boundary condition but the repeating unit
> is twisted by an angle.
>
>
>
> Best wishes,
>
>
>
> Fanmiao
>
>
>
> Fanmiao Kong
>
> Department of Materials, Trinity College, University of Oxford
>
> Tel: +44 (0)7529931806 / +86 13162054601
>
> 16 Parks Road, OX1 3PH, Oxford, UK
>
>
>
> --
> SIESTA is supported by the Spanish Research Agency (AEI) and by the
> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
>


-- 

---
*Zeila Zanolli *| associate professor, Utrecht University
Steering Committee, European Theoretical Spectroscopy Facility
http://www.etsf.eu/
Treasurer and Board Member, Young Academy of Europe http://yacadeuro.org/

http://zeilazanolli.wordpress.com/home
Twitter: @ZeilaZanolli
<https://vpn.icn2.cat/proxy/32d9bc05/http/intranet/Lists/Institutional%20signature/@ZeilaZanolli>


-- 
SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)

Re: [SIESTA-L] Bandlines regarding

[Zeila Zanolli]

Dear Rahul,
search for "BandLines" in the SIESTA manual and you'll find the answer to
your question.

Best
Zeila

On Thu, May 13, 2021 at 10:00 PM RAHUL SURESH 
wrote:

> Hi Users,
> So my question was for the following tag in a SIESTA input file. *What
> exactly do the values in the first column mean? Why are they in an
> increasing order?*
>
> # -- BAND-STRUCTURE-ANALYSIS --
>
> BandLinesScale pi/a
>
> %block BandLines
> 1   0. 0. 0.5000 A
> 20 0.5000 0. 0.5000 L
> 25 0.5000 0. 0. M
> 30 0. 0. 0. \Gamma
> 35 0. 0. 0.5000 A
> 40 0. 0. 0.5000 H
> 45 0. 0. 0. K
> 50 0. 0. 0. \Gamma
> %endblock BandLines
>
> --
> *Regards,*
> *Rahul *
>
> --
> SIESTA is supported by the Spanish Research Agency (AEI) and by the
> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
>


-- 

---
*Zeila Zanolli *| associate professor, Utrecht University
Steering Committee, European Theoretical Spectroscopy Facility
http://www.etsf.eu/
Treasurer and Board Member, Young Academy of Europe http://yacadeuro.org/

http://zeilazanolli.wordpress.com/home
Twitter: @ZeilaZanolli
<https://vpn.icn2.cat/proxy/32d9bc05/http/intranet/Lists/Institutional%20signature/@ZeilaZanolli>


-- 
SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)

Re: [SIESTA-L] Spin polarised band structure

[Zeila Zanolli]

On Mon, Apr 30, 2018 at 11:10 AM, Sunetra Das 
wrote:

> Dear fellow SIESTA users,
>
> I would like to know if SIESTA can plot spin-polarized band structure of a
> given system?
>
yes


> In which of the latest version of the software can I find the feature to
> draw spin-polarized band structure?
>
any version will do it. See the "gnubands" program in Util/Bands/


> Any help is highly appreciated.
>
> Thanks in advance.
>
> Regards,
> Sunetra Das
>

best,
Z

[SIESTA-L] fatbands for SOC

[Zeila Zanolli]

Dear all,

I would like to run the fatbands analysis for a system with Spin Orbit
Coupling.
The Util/COOP/fat program works well for collinear calculations,  but not
for SOC ones:
The  Systemlabel.fullBZ.WFSX file is not written and a warning is reported
in the output:
writewave: WARNING: wavefunctions printed is only
implemented for nspin = 1 or 2

A file Systemlabel.bands.WFSX is produced, but "fat" crashes in the attempt
of reading.


I tested with the Test/si_fatband with a relativistic pseudopotential.

Does anybody has a fat version for SOC calculations?

Thanks and happy new year!
 Zeila


---
Dr. Zeila Zanolli

RWTH Aachen, Institute for Theoretical Solid State Physics
ETSF Research Team Leader (http://www.etsf.eu/)
Fellow Young Academy of Europe (http://yacadeuro.org/)

Mobile: +32 487 556699
Office (RWTH): +49 241 80 27030
Office (ULg): +32 (0)4 366 3636
e-mail: zano...@physik.rwth-aachen.de
web: http://zeilazanolli.wordpress.com/home
ResearcherID: http://www.researcherid.com/rid/F-9568-2010

Re: [SIESTA-L] << compiling siesta-4.1-b1 with NetCDF >>

[Zeila Zanolli]

Hi Jean-Joseph,

have you tried gfortran?
Sometimes intel does not work properly, but gfortran worked well.

cheers
Zeila
---
Dr. Zeila Zanolli

RWTH Aachen, Institute for Theoretical Solid State Physics
ETSF Research Team Leader (http://www.etsf.eu/)

Mobile: +32 487 556699
Office (RWTH): +49 241 80 27030
Office (ULg): +32 (0)4 366 3636
e-mail: zano...@physik.rwth-aachen.de
web: http://zeilazanolli.wordpress.com/home
ResearcherID: http://www.researcherid.com/rid/F-9568-2010



On Tue, Sep 27, 2016 at 1:53 PM, Jean-Joseph Adjizian
<jean.adjiz...@uclouvain.be> wrote:
> Hello,
>
> Sorry, but it seems that I keep struggling with tbtrans installation.
>
> I have installed netcdf.4.4.1 and netcdf-fortran.
>
> I have used the arch.make given in the previous email.
>
> I compile transiesta with no problem but when I compile tbtrans I get the
> following error when it tries to compile m_tbt_sigma_save.F90.
>
> "
>
> mpiifort -c -O1 -I/projects/acad/ucl-naps/software/netcdf_Tbtrans/include
> -I/projects/acad/ucl-naps/software/netcdf_Tbtrans/include -DCDF -DNCDF_4
> -DNCDF_PARALLEL  -DTBTRANS  m_tbt_sigma_save.F90
> m_tbt_sigma_save.F90(260): error #6404: This name does not have a type, and
> must have an explicit type.   [MPI_COMM_WORLD]
> comm = MPI_COMM_WORLD, &
> ---^
> compilation aborted for m_tbt_sigma_save.F90 (code 1)
> make: *** [m_tbt_sigma_save.o] Error 1
>
> "
>
> I am not really an expert in compilation error, could someone guide me
> please?
>
> Thanks a lot in advance,
>
>
> Jean-Jo
>
>
>
> Le 23/09/16 à 16:25, Nick Papior a écrit :
>
> It should be placed at the end of the arch.make.
>
> Try the attached arch.make file.
>
> 2016-09-23 16:15 GMT+02:00 I. Camps <ica...@gmail.com>:
>>
>> Sorry, it didn't work :(
>>
>>
>> []'s,
>>
>> Camps
>>
>> On Fri, Sep 23, 2016 at 11:09 AM, Nick Papior <nickpap...@gmail.com>
>> wrote:
>>>
>>> Ah, ok. Now I see.
>>>
>>> You should (both) do this in your arch.make.
>>>
>>> You may track it on launchpad:
>>> https://bugs.launchpad.net/siesta/+bug/1627041
>>>
>>> The easy fix is this:
>>>
>>> FFLAGS += $(INCFLAGS) $(NETCDF_INCFLAGS)
>>>
>>> which should work (disclaimer I haven't tested this).
>>>
>>> 2016-09-23 15:54 GMT+02:00 I. Camps <ica...@gmail.com>:
>>>>
>>>> Yes, I compiled everything with the same intel compiler.
>>>>
>>>>
>>>> []'s,
>>>>
>>>> Camps
>>>>
>>>> On Fri, Sep 23, 2016 at 10:51 AM, Nick Papior <nickpap...@gmail.com>
>>>> wrote:
>>>>>
>>>>> Have you compiled the netcdf and hdf5 with the same intel compiler?
>>>>> That is necessary.
>>>>>
>>>>> Sadly, this is one of the inconveniences of fortran.
>>>>>
>>>>> 2016-09-23 15:23 GMT+02:00 I. Camps <ica...@gmail.com>:
>>>>>>
>>>>>> Here is the arch.make:
>>>>>> ##
>>>>>> # source /opt/intel/parallel_studio_xe_2015/psxevars.sh
>>>>>> # source /opt/intel/parallel_studio_xe_2017.0.035/psxevars.sh
>>>>>> # source /opt/intel/Compiler/11.0/083/bin/ifortvars.sh intel64
>>>>>> # source /opt/intel/impi_5.0.2/bin64/mpivars.sh
>>>>>> # This file is part of the SIESTA package.
>>>>>> #
>>>>>> # Copyright (c) Fundacion General Universidad Autonoma de Madrid:
>>>>>> # E.Artacho, J.Gale, A.Garcia, J.Junquera, P.Ordejon, D.Sanchez-Portal
>>>>>> # and J.M.Soler, 1996- .
>>>>>> #
>>>>>> # Use of this software constitutes agreement with the full conditions
>>>>>> # given in the SIESTA license, as signed by all legitimate users.
>>>>>> #
>>>>>> # 
>>>>>> # Description:
>>>>>> #  Intel compiler/mkl  V11 on atto
>>>>>> #  OpenMPI with support for Intel compiler V11
>>>>>> #  MKL V11 libraries, including a version of BLACS
>>>>>> provided
>>>>>> # by Intel for the openmpi framework,
>>>>>> # and Intel's own Scalapack, Lapack, and
>>>>

Re: [SIESTA-L] COMPILATION ERROR

[Zeila Zanolli]

I don't know how intel2011 will work with the latest siesta version [I
am not trying all the compilers just for fun :) ]. You can try and see
what happens.
I can tell that for my case of study on JURECA the gfortran worked
well, so this could be a wise alternative to ifort.

best
Z



On Fri, Jul 1, 2016 at 9:54 AM, Anju Saroha <anju@gmail.com> wrote:
> Thanks a lot Zeila Zanolli. We don't have Intel 2015. What about Intel 2011,
> is this version of Intel campatible with siesta?
>
>
> On Fri, Jul 1, 2016 at 3:27 AM, Zeila Zanolli <zeilazano...@gmail.com>
> wrote:
>>
>> I mean: on JURECA
>>
>> http://www.fz-juelich.de/ias/jsc/EN/Expertise/Supercomputers/JURECA/JURECA_node.html
>> siesta compiles but does not run with intel2016
>> siesta compiles and runs well with intel2015 and runs even better with
>> gfortran. (personal experience)
>>
>> cheers
>> z
>>
>>
>> On Thu, Jun 30, 2016 at 11:54 PM, Zeila Zanolli <zeilazano...@gmail.com>
>> wrote:
>> > Yes. There are issues with the intel 2016 compiler.
>> > Try to recompile with intel 2015  or gfortran.
>> >
>> > Cheers,
>> > Zeila
>> > ---
>> > Dr. Zeila Zanolli
>> >
>> > RWTH Aachen, Institute for Theoretical Solid State Physics
>> > ETSF Research Team Leader (http://www.etsf.eu/)
>> >
>> > Mobile: +32 487 556699
>> > Office (RWTH): +49 241 80 27030
>> > Office (ULg): +32 (0)4 366 3636
>> > e-mail: zeilazano...@gmail.com
>> > web: http://zeilazanolli.wordpress.com/home
>> > ResearcherID: http://www.researcherid.com/rid/F-9568-2010
>> >
>> > Announcements:
>> > 21st ETSF Workshop on Electronic Excitations:
>> > Dynamics and spectroscopy of correlated systems
>> > 19 - 23 September 2016, Lund, Sweden
>> > website: https://workshop.etsf.eu/
>> >
>> > NanoteC16
>> > Carbon Nanoscience and Nanotechnology
>> > 31 August - 03 September 2016, Trinity College Dublin, Dublin, Ireland
>> > website: http://nanotec-conference.net/
>> > 
>> >
>> >
>> > On Thu, Jun 30, 2016 at 11:46 PM, Anju Saroha <anju@gmail.com>
>> > wrote:
>> >> Hi,
>> >>
>> >> I have installed the parallel version using intel 2016 and intelmpi
>> >> libraries. When I am giving a test run for ZnO, it is giving an error.
>> >> Both
>> >> error file and arch.make are attached herewith. Please find the files.
>> >> I
>> >> don't understand why this error has come.
>> >>
>> >> Has anyone faced the same error before? Please help me in resolving the
>> >> issue.
>> >> Looking forward for an help.
>> >>
>> >> Thanks and regards
>> >> Anju Saroha
>> >>
>> >> On Tue, Jun 28, 2016 at 3:34 PM, Nick Papior <nickpap...@gmail.com>
>> >> wrote:
>> >>>
>> >>> Please follow these instructions so that we may be able to help you:
>> >>>
>> >>> https://answers.launchpad.net/siesta/+faq/2779
>> >>>
>> >>> 2016-06-28 11:45 GMT+02:00 Anju Saroha <anju@gmail.com>:
>> >>>>
>> >>>> Dear Nick,
>> >>>>
>> >>>> Same error is coming with the new version also. What can be a
>> >>>> possible
>> >>>> way out?
>> >>>>
>> >>>>
>> >>>>
>> >>>> On Tue, Jun 28, 2016 at 2:35 PM, Anju Saroha <anju@gmail.com>
>> >>>> wrote:
>> >>>>>
>> >>>>> Thanks a lot Nick.
>> >>>>>
>> >>>>>
>> >>>>> On Tue, Jun 28, 2016 at 2:28 PM, Nick Papior <nickpap...@gmail.com>
>> >>>>> wrote:
>> >>>>>>
>> >>>>>> No, currently LDA+U is only in the trunk series.
>> >>>>>>
>> >>>>>> 2016-06-28 10:49 GMT+02:00 Anju Saroha <anju@gmail.com>:
>> >>>>>>>
>> >>>>>>> Dear Nick,
>> >>>>>>>
>> >>>>>>> That's true. Still may I know whether U is there in any series?
>> >>>>>>>
>> >>>>>>>
>> >>>

Re: [SIESTA-L] COMPILATION ERROR

[Zeila Zanolli]

I mean: on JURECA
http://www.fz-juelich.de/ias/jsc/EN/Expertise/Supercomputers/JURECA/JURECA_node.html
siesta compiles but does not run with intel2016
siesta compiles and runs well with intel2015 and runs even better with
gfortran. (personal experience)

cheers
z


On Thu, Jun 30, 2016 at 11:54 PM, Zeila Zanolli <zeilazano...@gmail.com> wrote:
> Yes. There are issues with the intel 2016 compiler.
> Try to recompile with intel 2015  or gfortran.
>
> Cheers,
> Zeila
> -------
> Dr. Zeila Zanolli
>
> RWTH Aachen, Institute for Theoretical Solid State Physics
> ETSF Research Team Leader (http://www.etsf.eu/)
>
> Mobile: +32 487 556699
> Office (RWTH): +49 241 80 27030
> Office (ULg): +32 (0)4 366 3636
> e-mail: zeilazano...@gmail.com
> web: http://zeilazanolli.wordpress.com/home
> ResearcherID: http://www.researcherid.com/rid/F-9568-2010
>
> Announcements:
> 21st ETSF Workshop on Electronic Excitations:
> Dynamics and spectroscopy of correlated systems
> 19 - 23 September 2016, Lund, Sweden
> website: https://workshop.etsf.eu/
>
> NanoteC16
> Carbon Nanoscience and Nanotechnology
> 31 August - 03 September 2016, Trinity College Dublin, Dublin, Ireland
> website: http://nanotec-conference.net/
> 
>
>
> On Thu, Jun 30, 2016 at 11:46 PM, Anju Saroha <anju@gmail.com> wrote:
>> Hi,
>>
>> I have installed the parallel version using intel 2016 and intelmpi
>> libraries. When I am giving a test run for ZnO, it is giving an error. Both
>> error file and arch.make are attached herewith. Please find the files. I
>> don't understand why this error has come.
>>
>> Has anyone faced the same error before? Please help me in resolving the
>> issue.
>> Looking forward for an help.
>>
>> Thanks and regards
>> Anju Saroha
>>
>> On Tue, Jun 28, 2016 at 3:34 PM, Nick Papior <nickpap...@gmail.com> wrote:
>>>
>>> Please follow these instructions so that we may be able to help you:
>>>
>>> https://answers.launchpad.net/siesta/+faq/2779
>>>
>>> 2016-06-28 11:45 GMT+02:00 Anju Saroha <anju@gmail.com>:
>>>>
>>>> Dear Nick,
>>>>
>>>> Same error is coming with the new version also. What can be a possible
>>>> way out?
>>>>
>>>>
>>>>
>>>> On Tue, Jun 28, 2016 at 2:35 PM, Anju Saroha <anju@gmail.com> wrote:
>>>>>
>>>>> Thanks a lot Nick.
>>>>>
>>>>>
>>>>> On Tue, Jun 28, 2016 at 2:28 PM, Nick Papior <nickpap...@gmail.com>
>>>>> wrote:
>>>>>>
>>>>>> No, currently LDA+U is only in the trunk series.
>>>>>>
>>>>>> 2016-06-28 10:49 GMT+02:00 Anju Saroha <anju@gmail.com>:
>>>>>>>
>>>>>>> Dear Nick,
>>>>>>>
>>>>>>> That's true. Still may I know whether U is there in any series?
>>>>>>>
>>>>>>>
>>>>>>> Thanks
>>>>>>>
>>>>>>> On Tue, Jun 28, 2016 at 2:13 PM, Nick Papior <nickpap...@gmail.com>
>>>>>>> wrote:
>>>>>>>>
>>>>>>>> Please, remark that the trunk version is a development version and it
>>>>>>>> should be treated as such. :)
>>>>>>>>
>>>>>>>> 2016-06-28 10:33 GMT+02:00 Anju Saroha <anju@gmail.com>:
>>>>>>>>>
>>>>>>>>> Dear Nick,
>>>>>>>>>
>>>>>>>>> I have understood it. Now only I have checked. Thanks a lot.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Tue, Jun 28, 2016 at 1:59 PM, Nick Papior <nickpap...@gmail.com>
>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>> Please follow this site for the trunk version
>>>>>>>>>> https://launchpad.net/siesta
>>>>>>>>>> Currently, 526 is the latest version.
>>>>>>>>>>
>>>>>>>>>> 2016-06-28 10:24 GMT+02:00 Anju Saroha <anju@gmail.com>:
>>>>>>>>>>>
>>>>>>>>>>> Dear Nick,
>>>

Re: [SIESTA-L] COMPILATION ERROR

[Zeila Zanolli]

Yes. There are issues with the intel 2016 compiler.
Try to recompile with intel 2015  or gfortran.

Cheers,
Zeila
---
Dr. Zeila Zanolli

RWTH Aachen, Institute for Theoretical Solid State Physics
ETSF Research Team Leader (http://www.etsf.eu/)

Mobile: +32 487 556699
Office (RWTH): +49 241 80 27030
Office (ULg): +32 (0)4 366 3636
e-mail: zeilazano...@gmail.com
web: http://zeilazanolli.wordpress.com/home
ResearcherID: http://www.researcherid.com/rid/F-9568-2010

Announcements:
21st ETSF Workshop on Electronic Excitations:
Dynamics and spectroscopy of correlated systems
19 - 23 September 2016, Lund, Sweden
website: https://workshop.etsf.eu/

NanoteC16
Carbon Nanoscience and Nanotechnology
31 August - 03 September 2016, Trinity College Dublin, Dublin, Ireland
website: http://nanotec-conference.net/



On Thu, Jun 30, 2016 at 11:46 PM, Anju Saroha <anju@gmail.com> wrote:
> Hi,
>
> I have installed the parallel version using intel 2016 and intelmpi
> libraries. When I am giving a test run for ZnO, it is giving an error. Both
> error file and arch.make are attached herewith. Please find the files. I
> don't understand why this error has come.
>
> Has anyone faced the same error before? Please help me in resolving the
> issue.
> Looking forward for an help.
>
> Thanks and regards
> Anju Saroha
>
> On Tue, Jun 28, 2016 at 3:34 PM, Nick Papior <nickpap...@gmail.com> wrote:
>>
>> Please follow these instructions so that we may be able to help you:
>>
>> https://answers.launchpad.net/siesta/+faq/2779
>>
>> 2016-06-28 11:45 GMT+02:00 Anju Saroha <anju@gmail.com>:
>>>
>>> Dear Nick,
>>>
>>> Same error is coming with the new version also. What can be a possible
>>> way out?
>>>
>>>
>>>
>>> On Tue, Jun 28, 2016 at 2:35 PM, Anju Saroha <anju@gmail.com> wrote:
>>>>
>>>> Thanks a lot Nick.
>>>>
>>>>
>>>> On Tue, Jun 28, 2016 at 2:28 PM, Nick Papior <nickpap...@gmail.com>
>>>> wrote:
>>>>>
>>>>> No, currently LDA+U is only in the trunk series.
>>>>>
>>>>> 2016-06-28 10:49 GMT+02:00 Anju Saroha <anju@gmail.com>:
>>>>>>
>>>>>> Dear Nick,
>>>>>>
>>>>>> That's true. Still may I know whether U is there in any series?
>>>>>>
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> On Tue, Jun 28, 2016 at 2:13 PM, Nick Papior <nickpap...@gmail.com>
>>>>>> wrote:
>>>>>>>
>>>>>>> Please, remark that the trunk version is a development version and it
>>>>>>> should be treated as such. :)
>>>>>>>
>>>>>>> 2016-06-28 10:33 GMT+02:00 Anju Saroha <anju@gmail.com>:
>>>>>>>>
>>>>>>>> Dear Nick,
>>>>>>>>
>>>>>>>> I have understood it. Now only I have checked. Thanks a lot.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Tue, Jun 28, 2016 at 1:59 PM, Nick Papior <nickpap...@gmail.com>
>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>> Please follow this site for the trunk version
>>>>>>>>> https://launchpad.net/siesta
>>>>>>>>> Currently, 526 is the latest version.
>>>>>>>>>
>>>>>>>>> 2016-06-28 10:24 GMT+02:00 Anju Saroha <anju@gmail.com>:
>>>>>>>>>>
>>>>>>>>>> Dear Nick,
>>>>>>>>>>
>>>>>>>>>> In my knowledge, siesta-trunk-515 is the latest version. Is there
>>>>>>>>>> any version latest than this?
>>>>>>>>>>
>>>>>>>>>> Thanks and regards
>>>>>>>>>>
>>>>>>>>>> On Tue, Jun 28, 2016 at 12:26 PM, Nick Papior
>>>>>>>>>> <nickpap...@gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>> Could you please try the latest trunk version, there have been
>>>>>>>>>>> certain fixes for the LDA+U implementation.
>>>>>>>>>>>

[SIESTA-L] [***Posible SPAM***]Re: siesta

[Zeila Zanolli]

Hi,

you edit the gnubands fortran code and increase the corresponding
number (for example, number of bands). Recompile and enjoy.

Cheers
Z
---
Dr. Zeila Zanolli

RWTH Aachen, Institute for Theoretical Solid State Physics
ETSF Research Team Leader (http://www.etsf.eu/)

Mobile: +32 487 556699
Office (RWTH): +49 241 80 27030
Office (ULg): +32 (0)4 366 3636
e-mail: zeilazano...@gmail.com
web: http://zeilazanolli.wordpress.com/home
ResearcherID: http://www.researcherid.com/rid/F-9568-2010

Announcements:
21st ETSF Workshop on Electronic Excitations:
Dynamics and spectroscopy of correlated systems
19 - 23 September 2016, Lund, Sweden
website: https://workshop.etsf.eu/

NanoteC16
Carbon Nanoscience and Nanotechnology
31 August - 03 September 2016, Trinity College Dublin, Dublin, Ireland
website: http://nanotec-conference.net/



On Mon, Jun 27, 2016 at 10:48 AM, 木材 <zyyni...@foxmail.com> wrote:
> when I deal with the computed result of siesta and  input order
> "gnubands",it show that
> Dimensions  in gnubands too small. how should I do to solve the problem,I
> hope for geting your help

Re: [SIESTA-L] LDA + U calculation

[Zeila Zanolli]

it is in the launchpad, as Javier said. Just... one has to search for it.

Cheers
Z



On Sun, Jun 12, 2016 at 11:50 PM, Anju Saroha <anju@gmail.com> wrote:
> Dear Zeila Zanolli,
>
> Thanks a lot for sending me the link.
>
> Regards
>
> On Mon, Jun 13, 2016 at 3:01 AM, Anju Saroha <anju@gmail.com> wrote:
>>
>> Dear Javier,
>>
>> In the link which you have send, if I am going to the trunk link, it is
>> showing as Trunk has no download files.
>> Sorry to bother you this much but I am so helpless in the case that I have
>> no other option except to ask you.
>>
>> Regards
>>
>> On Mon, Jun 13, 2016 at 2:39 AM, Anju Saroha <anju@gmail.com> wrote:
>>>
>>> Dear Javier,
>>>
>>> The link you have send to me has only the option to download
>>> siesta-4.0-b2. Even in the link to icmab siesta-trunk-462 is showing the
>>> latest trunk. Rest are all showing as series.
>>>
>>> Even in the link there is no option for downloading any trunk version. I
>>> will be thankful if you will send me the name of the trunk version. I am not
>>> seeing any released version of trunk other than trunk-462.
>>>
>>> Thanks and regards
>>>
>>> On Mon, Jun 13, 2016 at 2:17 AM, Anju Saroha <anju@gmail.com> wrote:
>>>>
>>>> Thanks Javier.
>>>>
>>>>
>>>> On Sun, Jun 12, 2016 at 11:32 PM, Javier Junquera
>>>> <javier.junqu...@unican.es> wrote:
>>>>>
>>>>>
>>>>>  Dear Anju:
>>>>>
>>>>>  First of all, you need to download the trunk, not the version
>>>>> siesta-4.0-b2.
>>>>>
>>>>>  Then, the parameters to run with LDA+U are fully described in the
>>>>> Docs/siesta.tex file, Section 8.
>>>>>
>>>>>  They are the same as the in the former siesta-ldau-308 version.
>>>>>
>>>>>   Hope this helps,
>>>>>
>>>>>Javier
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Dear Javier,
>>>>>
>>>>> I have download the new version ( siesta-4.0-b2) as you suggested. But
>>>>> I have not found any option for U parameter in the manual. The
>>>>> exchange-correlation block is also not having anything related to U
>>>>> parameter.
>>>>>
>>>>> Can you please suggest me which section I need to see, as I have gone
>>>>> through the complete manual but I didn't find anything related to U
>>>>> parameter.
>>>>>
>>>>> I am really helpless in this situation, please suggest me a solution.
>>>>>
>>>>> Thanks and regards
>>>>>
>>>>>
>>>>> On Fri, Jun 10, 2016 at 11:44 PM, Anju Saroha <anju@gmail.com>
>>>>> wrote:
>>>>>>
>>>>>> Dear Javier,
>>>>>>
>>>>>> Please direct me a way for one more problem, i.e, whether the
>>>>>> installation commands and pattern remains same for all siesta versions? 
>>>>>> Or
>>>>>> do they vary for different versions? I mean to ask that the commands 
>>>>>> which I
>>>>>> used for installation of siesta-trunk-462 will remain same for 
>>>>>> siesta-4.0-b2
>>>>>> also.
>>>>>>
>>>>>> Thanks and regards
>>>>>> Anju Saroha
>>>>>>
>>>>>> On Fri, Jun 10, 2016 at 10:28 PM, Anju Saroha <anju@gmail.com>
>>>>>> wrote:
>>>>>>>
>>>>>>> Dear Javier, thanks a lot for your valuable suggestion. I will
>>>>>>> install this new version.
>>>>>>>
>>>>>>> Regards
>>>>>>>
>>>>>>> On Fri, Jun 10, 2016 at 8:15 PM, Javier Junquera
>>>>>>> <javier.junqu...@unican.es> wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>  Dear Anju:
>>>>>>>>
>>>>>>>>  The LDA+U has been recently merged in the main trunk in Siesta.
>>>>>>>>
>>>>>>>>  You can get it through the new development and distribution
>>>>>>>> platform http://launchpad.net/siesta.
>>&

Re: [SIESTA-L] LDA + U calculation

[Zeila Zanolli]

http://bazaar.launchpad.net/~siesta-maint/siesta/trunk/revision/515?start_revid=515

dowload tarball

Z
---
Dr. Zeila Zanolli

RWTH Aachen, Institute for Theoretical Solid State Physics
ETSF Research Team Leader (http://www.etsf.eu/)

Mobile: +32 487 556699
Office (RWTH): +49 241 80 27030
Office (ULg): +32 (0)4 366 3636
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31 August - 03 September 2016, Trinity College Dublin, Dublin, Ireland
website: http://nanotec-conference.net/



On Sun, Jun 12, 2016 at 11:09 PM, Anju Saroha <anju@gmail.com> wrote:
> Dear Javier,
>
> The link you have send to me has only the option to download siesta-4.0-b2.
> Even in the link to icmab siesta-trunk-462 is showing the latest trunk. Rest
> are all showing as series.
>
> Even in the link there is no option for downloading any trunk version. I
> will be thankful if you will send me the name of the trunk version. I am not
> seeing any released version of trunk other than trunk-462.
>
> Thanks and regards
>
> On Mon, Jun 13, 2016 at 2:17 AM, Anju Saroha <anju@gmail.com> wrote:
>>
>> Thanks Javier.
>>
>>
>> On Sun, Jun 12, 2016 at 11:32 PM, Javier Junquera
>> <javier.junqu...@unican.es> wrote:
>>>
>>>
>>>  Dear Anju:
>>>
>>>  First of all, you need to download the trunk, not the version
>>> siesta-4.0-b2.
>>>
>>>  Then, the parameters to run with LDA+U are fully described in the
>>> Docs/siesta.tex file, Section 8.
>>>
>>>  They are the same as the in the former siesta-ldau-308 version.
>>>
>>>   Hope this helps,
>>>
>>>Javier
>>>
>>>
>>>
>>>
>>> Dear Javier,
>>>
>>> I have download the new version ( siesta-4.0-b2) as you suggested. But I
>>> have not found any option for U parameter in the manual. The
>>> exchange-correlation block is also not having anything related to U
>>> parameter.
>>>
>>> Can you please suggest me which section I need to see, as I have gone
>>> through the complete manual but I didn't find anything related to U
>>> parameter.
>>>
>>> I am really helpless in this situation, please suggest me a solution.
>>>
>>> Thanks and regards
>>>
>>>
>>> On Fri, Jun 10, 2016 at 11:44 PM, Anju Saroha <anju@gmail.com> wrote:
>>>>
>>>> Dear Javier,
>>>>
>>>> Please direct me a way for one more problem, i.e, whether the
>>>> installation commands and pattern remains same for all siesta versions? Or
>>>> do they vary for different versions? I mean to ask that the commands which 
>>>> I
>>>> used for installation of siesta-trunk-462 will remain same for 
>>>> siesta-4.0-b2
>>>> also.
>>>>
>>>> Thanks and regards
>>>> Anju Saroha
>>>>
>>>> On Fri, Jun 10, 2016 at 10:28 PM, Anju Saroha <anju@gmail.com>
>>>> wrote:
>>>>>
>>>>> Dear Javier, thanks a lot for your valuable suggestion. I will install
>>>>> this new version.
>>>>>
>>>>> Regards
>>>>>
>>>>> On Fri, Jun 10, 2016 at 8:15 PM, Javier Junquera
>>>>> <javier.junqu...@unican.es> wrote:
>>>>>>
>>>>>>
>>>>>>  Dear Anju:
>>>>>>
>>>>>>  The LDA+U has been recently merged in the main trunk in Siesta.
>>>>>>
>>>>>>  You can get it through the new development and distribution platform
>>>>>> http://launchpad.net/siesta.
>>>>>>
>>>>>>  I strongly recommend you to use this latest version from now on.
>>>>>>
>>>>>>  Please, keep in mind that the results are not fully backwards
>>>>>> compatible with those obtained with version siesta-ldau-308 because there
>>>>>> are small differences in the generation of the basis set.
>>>>>>
>>>>>>  Best regards,
>>>>>>
>>>>>>  

Re: [SIESTA-L] When is convergence reached?

[Zeila Zanolli]

Dears,

if you are testing the mesh cutoff you should also be careful in using
a cutoff high enough to avoid the eggbox effect.
See here:

http://personales.unican.es/junqueraj/JavierJunquera_files/Metodos/Convergence/Convergence.html

Best,
   Zeila


---
Dr. Zeila Zanolli

ETSF Research Team Leader (http://www.etsf.eu/)

Mobile: +32 487 556699
e-mail: zeilazano...@gmail.com
web: http://zeilazanolli.wordpress.com/home
ResearcherID: http://www.researcherid.com/rid/F-9568-2010



On Wed, Aug 12, 2015 at 7:52 PM, Ludwig, Stephan
stephan.lud...@pi1.physik.uni-stuttgart.de wrote:
 Thank you Zacharias


 -Original message-
 From: fthe...@iesl.forth.gr fthe...@iesl.forth.gr
 Sent: Wednesday 12th August 2015 19:45
 To: siesta-l@uam.es
 Subject: RE: [SIESTA-L] When is convergence reached?

 Try to find the convergence in terms of energy per atom. What you will
 find is that your energy is converged with accuracy less than 1meV/atom.
 This accuracy is good enough for band structure calculations. Therefore,
 convergence has already been reached for a 200 mesh cutoff.

 Zacharias Fthenakis


 Hi,

 thank you for the reply my unit cell is rather big (at least for a solid).
 Its an organic salt with 236 atoms.

 Cell volume = 2905.615438 Ang**3

 : Cell vector modules (Ang) : 32.783000 11.179003 7.999052



 In the first step I want to study bandstructure DOS and PDOS.

 Later optical excitations.



 Can you tell when I can call the system convergent wrt the total energy.



 Thanks and Regards

 Stephan



 -Original message-
 From: fthe...@iesl.forth.gr fthe...@iesl.forth.gr
 Sent: Tuesday 11th August 2015 18:52
 To: siesta-l@uam.es
 Subject: Re: [SIESTA-L] When is convergence reached?


 Hi Stephan,
 it depends on how big is your unit cell and what you want to study.

 Hi,

 I've a question concerning the convergence criterion.

 Let's say I want to examine convergence of the total energy a system
 with
 respect to the meshcutoff.

 When is convergence reached? Is it reached when there is no change in
 the
 first digit after the comma

 like in the following example:

 meshcutoff total energy

 150  -42994.1019

 170  -42994.116

 190  -42994.127

 210  -42994.133



 or is it usefull to continue the test till there is no change in the
 second digit after the comma?

 What is a sensible criterion for convergence?



 Thanks and regards



 Stephan Ludwig




 *
 Dr Zacharias G. Fthenakis
 Research Associate
 Institute of Electronic Structure and Laser (I.E.S.L.)
 Foundation for Research and Technology Hellas (FO.R.T.H.)
 Vassilika Vouton P.O. Box 1527 71003 Heraklion Crete Greece
 Phone +30 2810 391824
 FAX   +30 2810 391305
 webpage: http://esperia.iesl.forth.gr/˜fthenak
 **





 *
 Dr Zacharias G. Fthenakis
 Research Associate
 Institute of Electronic Structure and Laser (I.E.S.L.)
 Foundation for Research and Technology Hellas (FO.R.T.H.)
 Vassilika Vouton P.O. Box 1527 71003 Heraklion Crete Greece
 Phone +30 2810 391824
 FAX   +30 2810 391305
 webpage: http://esperia.iesl.forth.gr/˜fthenak
 **

Re: [SIESTA-L] Plotting professional looking bandstructure

[Zeila Zanolli]

Dear Thomas,

I use xmgrace to plot the data. It is flexible and powerful.

Cheers
   Zeila



---
Dr. Zeila Zanolli

ETSF Research Team Leader (http://www.etsf.eu/)

Mobile: +32 487 556699
e-mail: zeilazano...@gmail.com
web: http://zeilazanolli.wordpress.com/home
ResearcherID: http://www.researcherid.com/rid/F-9568-2010



On Wed, Apr 29, 2015 at 3:50 PM, Thomas Mathew mathew.phys...@gmail.com wrote:
 Dear All,

 After extracting the band-structure data from .bands file using gnubands
 utility, I used gnuplot for plotting the data.

 With just the basic options of gnuplot, the plot doesn't look so
 professional as found on publications.

 Is there any utility/script for plotting the band-structure data with a
 professional look? If not what are the gnuplot options used for doing the
 same

 Thanking you

 Thomas Mathew
 Assistant Professor
 Dept of Physics
 St Pius X College Rajapuram
 Kerala, India
 Mob: +91 8129473653

Re: [SIESTA-L] GGA pseudopotential of Cr ,Fe ,Mn

[Zeila Zanolli]

Dear Swati,

If you want to be sure about your pseudopotentials, you can test them
for the individual atoms. For instance bulk Cr and some bulk made of
C. You can easily find in the literature experimental and theoretical
data concerning the individual components.

Then, for the CrC6 I would make sure all the calculation parameters
(kinetic energy cutoff, k-mesh, ...) in both SIESTA and VASP are
properly converged (as also mentioned by Federico) and - most
important - that you require the same level of accuracy in both codes.

The VASP calculation are done in your group or are from the literature?
If so, is there anything else in the literature for this system? Other
calculations?

btw, I would compare the magnetic moment on the individual atoms, not
just the total value.

Best,
   Zeila
---
Dr. Zeila Zanolli

Marie Curie Fellow
Peter Grünberg Institut (PGI)
Institute for Advanced Simulation (IAS)
Forschungszentrum Jülich
D-52425 Jülich, Germany

ETSF Research Team Leader (http://www.etsf.eu/)

Mobile (Belgian): +32 487 556699
Landline (Germany).: +49 (0)2461 615193
e-mail: zeilazano...@gmail.com
web: http://zeilazanolli.wordpress.com/home
ResearcherID: http://www.researcherid.com/rid/F-9568-2010



On Thu, May 29, 2014 at 9:12 AM, Swati Khatta swati.kha...@gmail.com wrote:
 First : the density of states correctly described by Siesta compared to the
 theoretical value given by VASP.
 Second : We are using double zeta polarisation.
 Third : Xc type is GGA and PBE  for bulk CrC6. And we are comparing our
 results with theoretical calculation of VASP. Experimental evidences not
 found yet.

 Regards
 swati


 On Thu, May 29, 2014 at 12:11 PM, Federico Iori federico.i...@unimore.it
 wrote:

 Hi.
 State first of all that I really do not know the state-of-the-art
 concerning your system, here my two cents:

 First question: is the density of state correctly described by Siesta
 compared to the experimental and theoretical (Vasp, PW or another code)
 data?

 Second: plane wave and localized basis codes can give different results,
 and for my experience it can come mostly from the cutoff on planewaves (for
 VASP) and from the kind of basis used (single, double polarized etc...) for
 Siesta ad example.

 Third: if you are converged  with respect to the size of the cell (if you
 have an isolated molecule), the size of the basis or the planewave energy
 cutoff, then
  the choice of the exchange correlation functional XC can really affect
 your results, especially if you compare them with experimental values.

 When do you talk about lattice constant: are these theoretical values
 optimized no? or do you use by chance experimental values?
 Anyway the two values are the same for me, so geomtry is ok.

 I will focused the attention on the kind of basis use and on the XC used
 (LDA, GGAor others).

 Good luck!
 ff


 On 05/29/2014 07:02 AM, Swati Khatta wrote:

 My system contains 14 atoms in primitive unit cell of CrC6. The lattice
 constant comes out to be a=b=4.32 A and c= 7.18 which is very much close to
 vasp results a=b=4.36 and c=7.12. I have set the spin polarised flag true
 and Write Mulliken Pop 1. The output it is shown that Total spin
 polarization (Qup- Qdown) = 7.620502 so the magnetic moment per mole of the
 system is 3.81.this magnetic moment is much lager than the magnetic moments
 comes from VASP code which is 2.43 .I perfomed same for FeC6 and MnC6 the
 magnetic moments again higher than the value calculated by Vasp code .


 On Wed, May 28, 2014 at 2:09 PM, Federico Iori federico.i...@unimore.it
 wrote:

 Which systems and which quantities are you looking at?

 And also, '' not getting good results'' compared to what? to theory or to
 experimental values?
 This is important to know.

 Best regards
 Federico Iori.


 On 05/28/2014 09:03 AM, Swati Khatta wrote:

 yes Sir I tried this also but not getting good results .I generated by
 myself also , tested it but it also not working  correctly .


 Regards,
 swati


 On Wed, May 28, 2014 at 12:28 PM, Sonu Kumar 1009uku...@gmail.com
 wrote:

 Did you try this ?

 http://departments.icmab.es/leem/siesta/Databases/Pseudopotentials/periodictable-gga-abinit.html
 !!!

 regards,
 sonu



 On Wed, May 28, 2014 at 9:12 AM, Swati Khatta swati.kha...@gmail.com
 wrote:

 Dear siesta Users,

 I am working on the magnetic properties with GGA approximation using
 siesta-3.1. But I am not getting good results of my calculations Please
 provide me the correct input file of GGA pseudopotential of  Cr, Fe ,Mn.
 I'll be thankful of your positive response .

 Regards
 swati





 --
 Dr. Federico Iori, PhD!

 Dipartimento di Scienze e Metodi per l' Ingegneria (DISMI)
 Universita' di Modena e Reggio Emilia
 Via Amendola,2
 Pad. Morselli
 42122 Reggio Emilia (Italy)




 --
 Dr. Federico Iori, PhD!

 Dipartimento di Scienze e Metodi per l

[SIESTA-L] MPI_ERR_TRUNCATE error

[Zeila Zanolli]

Dear siesta list,

I have compiled siesta-3.2-pl-4 on the RWTH Bull computer cluster:
https://sharepoint.campus.rwth-aachen.de/units/rz/HPC/public/Lists/Bull%20Cluster%20Configuration%20Phase%202%20October%202011/AllItems.aspx

I have used intel compiler 14.0 and  openMPI 1.6.5.
I have linked using the
http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/

After submitting a parallel job the code start running but
it stops at the moment of initializing the DM with the error:

*** An error occurred in MPI_Recv
*** on communicator MPI COMMUNICATOR 10 DUP FROM 9
*** MPI_ERR_TRUNCATE: message truncated
*** MPI_ERRORS_ARE_FATAL: your MPI job will now abort

The very same input file works well on another machine (with intel MPI).
However, on the Bull cluster a compilation with intel MPI produces an executable
whose output file 'freezes' for incompatibility between Intel MPI and
the LSF batch system.

I have contacted the cluster support center and they suggest that the
problem is related to the SIESTA code.

Any hint on how to solve this?

Thanks in advance,
   Zeila


---
Dr. Zeila Zanolli

Marie Curie Fellow
Peter Grünberg Institut (PGI)
Institute for Advanced Simulation (IAS)
Forschungszentrum Jülich
D-52425 Jülich, Germany

ETSF Research Team Leader (http://www.etsf.eu/)

Mobile (Belgian): +32 487 556699
Landline (Germany).: +49 (0)2461 615193
e-mail: zeilazano...@gmail.com
web: http://zeilazanolli.wordpress.com/home
ResearcherID: http://www.researcherid.com/rid/F-9568-2010