2015-06-26 12:58 GMT+02:00 毛飞 <200921220...@mail.bnu.edu.cn>:
> Dear siesta developers and users
>
>
>
> I find two strange things when using siesta codes. Maybe I have
> misunderstood.
>
> a. Acoording to the manual, the maximum number of SCF iterations
> per time step is 50 by default. But
anual (at least in my versions!
:) )
>
>
> Sincerely
>
>
>
> Fei Mao
>
> University of South China, China
>
> 在2015-06-26，Nick Papior 写道:
>
> -原始邮件-
> *发件人:* Nick Papior
> *发送时间:* 2015年6月26日 星期五
> *收件人:* "siesta-l@uam.es"
> *主题:* Re: [SIESTA-L]
Please check your fdf settings.
If the XV file exists that will have precedence (on using certain flags,
not by default), that should also be visible in the output file.
You could start from a fully clean slate, delete all files but pseudo and
fdf.
Lastly, do you have the block existing more than
Please read the documentation for transiesta.
In the currently released versions these keywords should peak your interest:
TS.BiasContour.Eta
TS.BiasContour.NumPoints
2015-07-03 5:33 GMT+02:00 Nadia Salami :
> Dear Transiesta users,
>
> According to DOI: 10.1103/PhysRevB.65.165401, I know that
on't know how to obtain the optimized value.
>
> Your Guidance will be highly appreciated.
> Thanks a lot.
> Best,
> Nadia Salami
>
> On Fri, Jul 3, 2015 at 10:55 AM, Nick Papior wrote:
>
>> Please read the documentation for transiesta.
>>
>> In t
Have you read the appendix about netcdf addition to the siesta code?
It has all the information you need.
2015-07-09 12:07 GMT+00:00 jv sharma :
> Dear Siesta Users/ Experts,
>
> Could someone please throw some light on how to compile Siesta with netCDF
> supprot?
>
> Best regards,
> JVN Sarma.
>
2015-07-09 17:06 GMT+00:00 Nadia Salami :
> Dear Transiesta users,
>
> I want to calculate the transmission coefficient of electron as a function
> of energy for some systems, I have set up them in same way. But when I do
> transiesta calculations for the scattering region of them, the following
>
s
>
>
> ANANT VIJAY VARMA
> M.Tech. STUDENT
> CENTER FOR CONVERGING TECHNOLOGIES
> UNIVERSITY OF RAJASTHAN
> JAIPUR
>
> On Fri, Jul 10, 2015 at 1:30 AM, Nadia Salami
> wrote:
>
>> Dear Dr. Papior,
>>
>> Thank you very much for your useful guidance.
>&g
APPLICATION terminated looks like an error issued in your intel library,
there is not much we can do about those without more information as to why
:(
Maybe you could try the later version?
2015-07-17 20:29 GMT+00:00 Oleksandr Voznyy :
> Hi all,
> I have problems with the trunk-424 version: I t
You have set sp_kind to 1, I assume you have not used configure to create
the initial arch.make file?
On Intel compilers it should be 4.
Remember to do make clean before rerunning make.
On 21 Jul 2015 12:29, "Boubacar Traore" wrote:
> Dear all,
>
> I am trying to compile siesta-3 in parallel with
Oh, and siesta-3 does not work with openmp.
Please do not use that flag until the documentation says it is supported.
On 21 Jul 2015 14:12, "Nick Papior" wrote:
> You have set sp_kind to 1, I assume you have not used configure to create
> the initial arch.make file?
> On
Siesta is not a graphical tool, please search the mailing list. This kind
of question has been asked many times before.
On 21 Jul 2015 11:59, "Jeetu Donderiya"
wrote:
> Hello SIESTA user
>
> I want to calculate density of state of Z shaped ZNR .i am totally
> confused , how to fix its atomic coor
It does not look like you are using the gnubands program in
siesta-trunk-462, please assert you are...
Line 27 is empty in siesta-trunk-462.
2015-07-21 16:52 GMT+00:00 jv sharma :
> Dear Users and Experts,
>
> I am new to Ubuntu and Siesta.
> I have installed siesta-trunk-462. While trying to con
gt; 13.0.1 for the compilation.
> Attached is my new arch.make file.
>
> Are there some compiler flags that I need to set to avoid these problems?
> Or any optimization?
>
> Thanks,
> Boubacar
>
> On Tue, Jul 21, 2015 at 2:12 PM, Nick Papior wrote:
>
>> You have set
the two things that I may be doing wrong !!!
>
> Thanks !
>
> On Tue, Jul 21, 2015 at 7:50 PM, Nick Papior wrote:
>
>> You are doing at least 2 things wrong in your arch.make for a successful
>> application.
>>
>> Please go through the mailing list about com
atoms) compared to few atom systems.
>
Not surprising as already mentioned on the list.
> Best regards,
>
>
> On Tue, Jul 21, 2015 at 9:58 PM, Nick Papior wrote:
>>
>> You still have two problems in your arch.make.
>>
>> 1) As I said in the second mail, do not u
sic
grasp of linux.
As you are a basic user of unix, this might shed some light of why things
goes wrong, as well as providing some basic insights.
2015-07-22 3:56 GMT+00:00 jv sharma :
> Sorry, I could not catch your point, could you please elaborate?
>
> On Tue, Jul 21, 2015 at 11:13 PM,
Try "./gnubands" instead of "gnubands".
On 23 Jul 2015 06:28, "jv sharma" wrote:
> Attached here the output. Thanks for the link on basics of linux.
>
> Regards,
> JVN.
>
> On Thu, Jul 23, 2015 at 2:06 AM, Nick Papior wrote:
>
>> Do
.dat
> At line 128 of file new.gnubands.f90 (unit = 5, file = 'stdin')
> Fortran runtime error: Bad integer for item 1 in list input
> jv@jv-desktop:~/siesta-trunk-462/Util/Bands$
>
>
> On Thu, Jul 23, 2015 at 12:55 PM, Nick Papior
> wrote:
>
>> Try ".
Ah. Would you please try gfortran instead of f95. Edit your arch.make file.
Bad integer for item 1 in list input
On Thu, Jul 23, 2015 at 2:33 PM, Jean-Joseph Adjizian <
jean.adjiz...@uclouvain.be> wrote:
> Hi,
>
> have you opened your arch.make file?
> I think what Nick Papior is saying is to change your Fortran compiler.
> Instead of using f95 you sho
+00:00 jv sharma :
> Yess, finally got it with si_fatbands.bands. Thanks a lot to all who
> helped!!
>
> On Thu, Jul 23, 2015 at 4:04 PM, Nick Papior wrote:
>
>> I think riccardo is correct, something is wrong with the bands file.
>> Hi,
>>
>> I did like thi
Google is your friend.
Please search there.
On 24 Jul 2015 09:08, "Jeetu Donderiya"
wrote:
> Hello SIESTA user
>
> I forget, how to generate executable file from .f file with the help of
> gfortran compiler. Please anyone can tell that command line.
>
> Thanks in advance
>
>
On 24 Jul 2015 17:08, "jv sharma" wrote:
>
> Do this in the forlder where your .f is located:
>
> gfortran -o filename.f filename
Swap the two last arguments and it should be fine.
>
> I got this from the below link, as rightly said by Dr. Nick:
>
> https://www.mail-archive.com/siesta-l@uam.es/msg
2015-07-25 6:55 GMT+00:00 Nadia Salami :
> Dear Transiesta users,
>
> I don’t know how to determine correct k point sampling for the Transiesta
> as well as Tbtrans calculations.
>
You converge using the same principles as standard DFT, for transport
calculations however, you converge the averaged
dos: no such file or directory
>> >
>> > I can see this file by using ls -x command .I don't know how can it
>> > possible.
>> >
>> >
>> > On Fri, Jul 24, 2015 at 10:30 PM, Nick Papior
>> > wrote:
>> >
>> >>
>
Such calculations will be made available in the next release of transiesta.
On 26 Jul 2015 15:34, "Nayereh Ghobadi" wrote:
> Dear Siesta users
>
>
>
> I have used Transiesta to study a graphene based transistor. I want to
> calculate the gate-bias modulation effect on this structure. When I set
--
Kind regards Nick Papior
On 26 Jul 2015 20:59, "Younas Khan" wrote:
>
> Hi all. I applied electric field to my system using the block:
>
> %block ExternalElectricField
> 0. 0. 0.0004 V/Ang
> %endblock ExternalElectricField
>
> However, in the out
I cannot say for sure, I hope before the end of the year...
--
Kind regards Nick Papior
On 26 Jul 2015 18:01, "Nayereh Ghobadi" wrote:
> Thank you very much for your reply. It will be very kind of you if let me
> know when the next release of transiesta will be available?
&g
You should know which direction is the bulk one, if it becomes zero you
have a fully bulk calculation. So my guess is that you have setup the fdf
file incorrectly.
--
Kind regards Nick Papior
On 27 Jul 2015 07:21, "Younas Khan" wrote:
> Thank You Nick, but I am still having
That seems like an extremely large electrode, I would guess you setup the
calculation incorrectly.
2015-07-27 20:11 GMT+00:00 Fadil Iyikanat :
> Hi all. I am doing transiesta calculation. My sistem is a little big. My
> eletrode and scattering regions consist of 114 and 342 atoms respectively.
>
ind regards Nick Papior
On 27 Jul 2015 23:00, "Fadil Iyikanat" wrote:
> Im sure from my electrodes. They are just big electrodes.
> But I dont know where the unitcell comes from which appeared before the
> last line of output.
>
> Because my unitcell of electrode
How can i be sure whether the program stops
> due to the lack of memory or not. Moreover, why i get completely different
> unitcell before the program stop.
>
> Thanks and regards
>
>
> On Tue, Jul 28, 2015 at 1:14 AM, Nick Papior wrote:
>
>> I would assume your ele
t; Current. Does it right?
>
> Best regards,
>
>
> Shihua Tan
>
>
> 2012-12-13 22:30 GMT+08:00 Nick Papior Andersen :
>
>> Dear all
>>
>> I will here give information about the tbtrans versions.
>> First of all there exists 2 different versions of tbtrans f
Please read the many questions already posed about exactly this.
--
Kind regards Nick Papior
On 4 Aug 2015 21:13, "leoqmc ." wrote:
> Dear siesta/Transiesta users,
>
> I am interested in transport calculations. My system consists of a
> molecule between two gold surface
ide me some guide.
>
> Thank You Very Much.
>
> Leone
>
>
>
> 2015-08-04 17:50 GMT-03:00 Nick Papior :
>
>> Please read the many questions already posed about exactly this.
>>
>> --
>>
>> Kind regards Nick Papior
>> On 4 Aug 2015 21:13,
Vacuum is where no atoms exist in the unit-cell, hence creating a larger
unit-cell is equivalent to vacuum.
--
Kind regards Nick Papior
On 13 Aug 2015 12:29, "ANANT VIJAY" wrote:
> Dear siesta users I am New in SIESTA .Please anyone can guide me how to
> add vacuum in siesta s
You shouldn't need to rename the files, nor delete files, try first and do
the straightforward thing. Do them separately in their own directories:
FCrun_11-11
FCrun_12-12
Then do
Phonons --FCwildcard="./FCrun_*" ...
This should work fine.
2015-08-14 8:26 GMT+00:00 Jingxian Yu :
> Dear All,
>
>
spin true in siesta means FM calculation which in turn means
> spins are parallel or antiparallel, but not mixed.
>
> Thank you
> Jaret
>
>
>
>
> On Wednesday, August 5, 2015 4:20 AM, leoqmc . wrote:
>
>
> Dear Nick,
>
> Thank you for your reply.
>
>
They are spin-up/down.
2015-08-16 17:40 GMT+00:00 Jaret Qi :
> Can you please clarify how collinear spin relates to transiesta.
>
>
>
> On Sunday, August 16, 2015 10:33 AM, Nick Papior
> wrote:
>
>
> Same as siesta. Co-linear spin.
>
> 2015-08-16 16:32 GMT+0
Please search the mailing list, this has been asked before.
2015-08-17 15:53 GMT+02:00 azar ostovan :
> Dear transiesta users
>
> I try on optimization an .fdf file for transiesta calculation
>
> Is it better to fix electrode position or let them to relax during
> optimization?
>
>
> warm regards
You should not pipe into Eig2DOS.
2015-08-18 10:03 GMT+02:00 Saeed Nasiri :
> Dear users
>
> I have problems with Eig2DOS utility. It prints out warning or error and
> the
> output file is empty. first I used this
> sh ../../siesta-3.2/Util/Eig2DOS/Eig2DOS < coronene.EIG | tee coronene.dat
> ../.
2015-08-18 19:27 GMT+00:00 leoqmc . :
> Dear Nick and transiesta users,
>
> I am interested in transport calculations in single-molecule two-probe
> systems[Au(111)-Molecule-Au(111)]. I searched in the list for the following
> questions, but I think that these questions were not explicitly solved
You have a skewed z-direction, that is not allowed.
2015-08-19 5:51 GMT+00:00 Jaret Qi :
> Dear transiesta users,
> I'm working on 4ZGNR to get the IV characteristic, but I have this error
> when I use the trunk version:
>
> >>ERROR: Unitcell has the electrode extend into the transport direction
our.NPoles 16
> TS.ComplexContour.NCircle 30
> TS.ComplexContour.NLine10
> # BIAS OPTIONS
> TS.biasContour.NumPoints 40
>
>
> # TS OPTIONS
> TS.Voltage $i eV
>
> # TBT OPTIONS
> TS.TBT.Emin -3 eV
> TS.TBT.Emax +3 eV
> TS.TBT
> plane containing x & y. And is the "skewed" a matter for the trunk version,
> I still not sure why this issue just appear in the case of trunk version!!
>
>
>
> On Wednesday, August 19, 2015 12:52 AM, Nick Papior
> wrote:
>
>
> there are x and/or y compon
oqmc . :
>
>> Dear Nick,
>>
>> I am very grateful for your help. I will follow the tips.
>>
>> Leone Carmo Garcia
>>
>> 2015-08-18 16:42 GMT-03:00 Nick Papior :
>>
>>>
>>>
>>> 2015-08-18 19:27 GMT+00:00 leoqmc . :
>>
Here
http://www.mail-archive.com/siesta-l@uam.es/
2015-08-20 5:12 GMT+00:00 Altaf Ur Rahman :
> How to search it , Thanks in advance
>
> On Wed, Aug 19, 2015 at 3:51 PM, I. Camps wrote:
>
>> Hello,
>>
>> Please, search in the list for a discussion with the subject: "Spin Orbit
>> Coupling".
>>
>
5918
> 9.353835460203 -0.521458607003 5.528017823710
>10.357615863662 -0.610752357764 4.991778712696
> 8.140904379317 -0.448790345987 4.790777885721
> The electrodes are not situated in the same coordinates. Please correct.
&g
ot know from where these coordinates came from? so siesta
> complaining that the electrode are situated in a different coords.
>
>
>
> On Thursday, August 20, 2015 12:08 AM, Nick Papior
> wrote:
>
>
> What are you asking?
> It says:
> "The electrodes are not
> I do not know from where these coordinates came from? so siesta
> complaining that the electrode are situated in a different coords.
>
>
>
> On Thursday, August 20, 2015 12:08 AM, Nick Papior
> wrote:
>
>
> What are you asking?
> It says:
> "The electrodes are not
Since already very Thank you.
>
> Leone Carmo Garcia
>
>
>
> 2015-08-19 14:51 GMT-03:00 leoqmc . :
>
>> Dear Nick,
>>
>> Thank you. I'll read the paper.
>>
>> Leone Carmo Garcia
>>
>> 2015-08-19 14:36 GMT-03:00 Nick Papior :
>>
is for electrode cell "chain like" (bulk like + 20 Angstroms)
>
> LatticeConstant 1.0 Ang
>
> % block LatticeVectors
> 31.540 0.000 0.000
> 25.770 29.994 0.000
> 0.00.0 7.06705
> % endblock LatticeVectors
>
> Is this right?
>
> N
Yes.
--
Kind regards Nick Papior
On 19 Aug 2015 12:33, "azar ostovan" wrote:
> Dear tranSIESTA users
>
> Is it possible to perform electronic transport properties by tranSIESTA
> for structures have relaxed with different software (NO SIESTA)?
>
>
> Kind regards
>
> Azar Ostovan
>
olumn are quite different, what do these
> columns represent?
>
> On Thursday, August 20, 2015 12:32 AM, Nick Papior
> wrote:
>
>
>
>
> 2015-08-20 8:27 GMT+02:00 Jaret Qi :
>
> and even though, this system worked well with 3.2 version and now trunk
> is complaining a
t 0.000
> 0.000 0.000 corrds?
>
No, only the relative position. Their origin can be wherever you decide.
>
>
>
> On Thursday, August 20, 2015 11:06 AM, Nick Papior
> wrote:
>
>
> *"Structure of the Left electrode"*
> Is, as it says, the structure read in t
This is currently a bug in the gen-basis code.
It has already been fixed for the next release of the trunk version.
Please use another version of siesta to get that utility.
2015-08-21 3:08 GMT+02:00 Hongyi Zhao :
> Hi all,
>
> I've compiled the siesta/transiesta of the siesta-trunk-462 using t
Yes, every available version from the website supports parallel
compilation.
To successfully compile with MPI you need to do this to your arch.make file:
FPPFLAGS += -DMPI
MPI_INTERFACE=libmpi_f90.a
As always, remember to start all over to ensure everything is from scratch.
2015-08-21 16:08 GMT+
.gatech.edu)
>
> Research Scientist II
> Partnership for an Advanced Computing Environment
> Georgia Institute of Technology
> 258 Fourth Street, Rich Building, Room 327
> Atlanta, GA 30332-0700
> Office: (404) 385-0045
>
>
> --
> *Fro
Your
MD.FClast
Is ill defined, please see the manual for how to correctly set its value.
--
Kind regards Nick Papior
On 24 Aug 2015 06:42, "Saeed Nasiri" wrote:
> Dear users
>
> I want to calculate vibration frequency for coronene molecule, so at first
> an
> optimiz
You need to manually edit the file Util/Vibra/Src/vibra.h
file and change "maxa" to something big.
I would suggest you do maxa = 200
which should cover most cases :)
After having done that, do
make clean
make
and re-try with fcbuild.
2015-08-25 7:56 GMT+00:00 Saeed Nasiri :
> Dear users
>
> I wa
The reason is that you "attach" a truly bulk semi-infinite electrode to
your scattering region.
When you do this you want the difference between the actual bulk electrode
and the scattering region electrode to be minimized.
A minimization occurs when the scattering part (non-lead) is fully
screened
pure ZGNRs one cell left/right for the
> electrodes then how they could be extended to the scattering region?
>
>
> Sent from Yahoo Mail for iPhone <https://yho.com/footer0>
>
> On Aug 25, 2015, 1:34:55 PM, Nick Papior wrote:
> The reason is that you "attach"
Do not use that many processors for so few atoms. This may be the reason.
A good advice is to use no more than the number of atoms in your system.
However, in your case you use a lot of k-points.
Then look up the fdf flag Diag.ParallelOverK.
2015-08-26 15:13 GMT+02:00 Barnali Bhattacharya :
> D
I have your comments and suggestions on this calculation? Your help
> will be sincerely appreciated. Cheers!
>
> Jin
>
>
>
> On 14/08/2015 6:11 PM, Nick Papior wrote:
>
> You shouldn't need to rename the files, nor delete files, try first and do
> the straightforward
Yes, that could be one.
2015-08-27 17:15 GMT+02:00 leoqmc . :
> Dear Nick,
>
> you said "output". Such "output" would be the average transmission
> function (*. AVTRANS) ?.
>
> Thank you so much.
>
> Leone
>
> 2015-08-25 17:44 GMT-03:00 N
This you should be able to answer yourself,
1) What does k-points implicitly mean in calculations?
2) Is that meaning compatible with your simulation?
3) In your simulation, what would be the difference between a k-point
simulation and a non k-point simulation?
2015-08-28 14:14 GMT+02:00 leoqmc .
Yes, that could be one.
2015-08-28 16:01 GMT+00:00 azar ostovan :
> Dear, nick
> you mean the spectral Property of scattering region don't change any
> more?
> kind regards
> azar
>
> On Fri, Aug 28, 2015 at 12:50 PM, Nick Papior
> wrote:
>
>> Yes, tha
Please try the latest trunk version available and see if it helps. If not
report the error message that it returned.
2015-09-01 7:26 GMT+02:00 Saeed Nasiri :
> Dear users
>
> I have a problem when I run the vibrator and the familiar "Fortran runtime
> error" caused the code to stop. I have seen m
It seems like a pretty small system, I could be wrong but I would not
assume memory problems, are you oversubscribing the number of processors?
2015-09-02 12:32 GMT+02:00 Morteza Roshankar :
> I guess your workspace has run out of space. maybe!!!
>
> On Wed, Sep 2, 2015 at 2:54 PM, Ludwig, Stepha
If, for instance, you have a left electrode of gold, and a right electrode
of copper.
Then you need buffer atoms to correctly screen the electrode regions from
surfaces to vacuum.
2015-09-02 18:54 GMT+00:00 azar ostovan :
> Dear tranSiesta users
>
>
> What is the purpose by using buffer atoms in
ant for unsimilar
> electrods?
>
>
> kind regards
> azar
>
> On Wed, Sep 2, 2015 at 11:31 PM, Nick Papior wrote:
>
>> If, for instance, you have a left electrode of gold, and a right
>> electrode of copper.
>> Then you need buffer atoms to correctly scr
DM files are siesta restart files
TSDE files are transiesta restart files.
--
Kind regards Nick Papior
On 3 Sep 2015 22:08, "leoqmc ." wrote:
> Dear Nick,
>
> I calculated transport properties using the default TS.ComplexContour*
> options. Now I want converges those par
Transiesta does not per default update the density in the electrode
regions. So unless you have a really long extended electrode region
"on-top" of your bulk electrodes, you should not see any difference.
"Bias" can be anything...
"TS.BiasContour.NumPoints>30" is really an arbitrary number unless
Once you know the length of each electrodes principal layers, so will you
know the minimum distance required between the two electrodes.
--
Kind regards Nick Papior
On 15 Sep 2015 14:30, "azar ostovan" wrote:
> Dear transiesta users
>
> How I could find the suitable d
Short answer, at least that distance, not "exact" , but please understand
the importance of electrode principal layers, then it should become obvious
why the answer is yes.
--
Kind regards Nick Papior
On 16 Sep 2015 17:54, "azar ostovan" wrote:
> dear Nick
> thank
Denchar also reads TSDE files, the density matrix is positioned in the same
way as the DM file.
PS. It is a mailing list. Please address the mailing list accordingly. :)
2015-09-16 17:29 GMT+00:00 leoqmc . :
> Dear Nick,
>
> I am interested in obtain the charge density for the screening region i
parse.F90 is a routine used to "parse" fdf input, hence you have an error
in your fdf input file.
I would suspect your kgrid_monkhorst_pack grid to be ill-defined.
I guess you have
%block kgrid_monkhorst_pack
0
0
0
%endblock
which in reality should be
%block kgrid_monkhorst_pack
0
In the trunk version you can check the file Src/m_hs_matrix.F90, while you
can check the io routines that reads the HSX file on how to
retrieve the sparse matrix in the HSX files.
2015-09-20 2:10 GMT+00:00 peter :
> Hi,
> I need to get the Hamiltonian and Overlap matrix from the HSX file. My
> qu
> Regards
> Rajan
>
> On Sun, Sep 20, 2015 at 12:32 PM, Nick Papior
> wrote:
>
>> In the trunk version you can check the file Src/m_hs_matrix.F90, while
>> you can check the io routines that reads the HSX file on how to
>> retrieve the sparse matrix in the HSX fi
--
Kind regards Nick Papior
On 24 Sep 2015 17:30, "leoqmc ." wrote:
>
> Dear Colleagues,
>
> When I try to use the EIGENCHANNELS option, I get the following error
message:
>
> File ".SOME/PATH/ inelastic / lib / python2.6 / site-packages / inela
You are not stating how many basis orbitals you have in your setup, so it
is hard to tell whether it is a memory problem.
Note that it may as well be limited disk space which _can_ trigger a
SIGSEGV. Writing wave-functions is highly expensive on disk space and the
fact that it runs smoothly till t
Could you try and add -fbacktrace to the flags.
Any way it seems weird that it "suddenly" triggers as all memory have been
allocated.
Could you also attach the fdf files?
--
Kind regards Nick Papior
On 25 Sep 2015 02:34, "Marcos Veríssimo Alves" <
marcos.verissimo.al...@
Ok, so there is a bug in diagk and pdos file when not passing a full weight
of the k array.
This patch fixes it (note the patch also fixes a bug in pdoskp which is
related to Diag.ParallelK.
Apply by:
$> cd
$> patch -p0 < patch_writewave_pdos
2015-09-25 7:25 GMT+02:00 Nick Papior :
ns. Is it also
> valid for Siesta 3.2-pl 5?
>
> Cheers,
>
> Marcos
>
> On Fri, Sep 25, 2015 at 4:40 AM, Nick Papior wrote:
>
>> Ok, so there is a bug in diagk and pdos file when not passing a full
>> weight of the k array.
>>
>> This patch fixes it (no
Please reread the manual, it seems like you are missing obj_setup.sh step.
2015-09-27 10:30 GMT+00:00 RAJAN SINGH :
> Dear Siesta Users
>
> While doing the installation of siesta-3.2 (path level 5) version after
> generation of "arch.make" file using command "../Src/configure" , when I am
> typin
You may have a longer ranging screening length of your electrode.
Try and add more electrode layers. Generally you just want dQ to be as low
as possible, but sometimes it can be hard.
See answer below:
2015-10-01 11:04 GMT+02:00 Seyed Mohammad Tabatabaei :
> Dear all,
>
> I have attached the th
urther?
>
> On 10/1/15, Nick Papior wrote:
> > You may have a longer ranging screening length of your electrode.
> >
> > Try and add more electrode layers. Generally you just want dQ to be as
> low
> > as possible, but sometimes it can be hard.
> >
> > See ans
You are missing the zgesv routine (defined in liblapack.a).
Please search the mailing list, it has been asked before.
2015-10-01 18:27 GMT+00:00 RAJAN SINGH :
>
> Dear Siesta Users
>
> While doing the installation of siesta-3.2 (path level 5) version after
> generation of "arch.make" file using
There is now correct answer, it just have to be "well below".
Test it to get a feel for it.
2015-10-03 16:27 GMT+00:00 Seyed Mohammad Tabatabaei :
> Dear all,
>
> How many electron volts should the TS.ComplexContour.Emin be lower
> than the minimum eigenvalue?
>
> Bests,
> Mohammad,
>
--
Kind
Post your arch.make file, and which version of siesta you are using.
PS. Always supply as much information as possible...
2015-10-05 13:15 GMT+02:00 Aniruddha Kibey :
> Dear all
> I have compiled siesta using openmpi-1.10.0 which was compiled
> using intel parallel studio 2011. The test
FPPFLAGS= $(FPPFLAGS_MPI) $(FPPFLAGS_CDF)
> DUMMY_FOX= --enable-dummy
> #
> .F.o:
> $(FC) -c $(INCFLAGS) $(FFLAGS) $(FPPFLAGS) $<
> .f.o:
> $(FC) -c $(INCFLAGS) $(FFLAGS) $<
> .F90.o:
> $(FC) -c $(INCFLAGS) $(FFLAGS) $(FPPFLAGS) $<
> .f90.o:
> $(
I don't know if vibra can handle restarts, but you simply change the
FCfirst flag.
You possibly have to rename the new files.
--
Kind regards Nick Papior
On 9 Oct 2015 05:52, "Radhika Narayanan"
wrote:
> Dear all,
>
> Could anyone suggest how to restart a Force Constant
Oh and beware of not overwriting the force-constant matrix file. You may
also have to manually fix that one.
--
Kind regards Nick Papior
On 9 Oct 2015 07:22, "Nick Papior" wrote:
> I don't know if vibra can handle restarts, but you simply change the
> FCfirst flag.
&
you have not compiled transiesta (I guess).
Do
cd Obj
make clean
make transiesta
rerun using the transiesta executable.
2015-10-09 9:40 GMT+02:00 RAJAN SINGH :
>
> Dear Siesta Users
>
> While running the transiesta example of simple chain of atoms, I am
> getting error:
>
> siesta: ERROR: wrong
Use the trunk version and the TBTrans_rep code (those examples where
created for the updated tbtrans code).
2015-10-09 11:06 GMT+02:00 RAJAN SINGH :
>
> Dear Siesta Users
>
> I am trying to run simple transiesta example given @
> http://departments.icmab.es/leem/siesta/tlv14/
>
> While running th
Generally it just becomes more heavy. You could look into diagonalization
optimizations:
http://departments.icmab.es/leem/siesta/Documentation/Manuals/siesta-3.1-manual/node51.html
But you have to test it. There is no single _correct_ answer for optimizing
the calculation time. So you have to do
This may or may not be due to your local computer killing your application
for various reasons. We simply do not know.
As this hasn't been reported by any-one else I suspect you are:
1) Going beyond your time-limit (is it a cluster with an admin? Have you
asked him/her first?)
2) Perhaps you are ca
gt; to reach a single CG step. I do not understand about the MKL lapack and
> blas libraries to the MKL_LIBS line. Can you please tell me mor eprecisely
> where and how to add this MKL lapack?
>
> On Thu, Oct 15, 2015 at 12:45 PM, Nick Papior
> wrote:
>
>> This may or m
> Hi.
>
>
> On 10/15/2015 09:15 AM, Nick Papior wrote:
>
>> This may or may not be due to your local computer killing your
>> application for various reasons. We simply do not know.
>> As this hasn't been reported by any-one else I suspect you are:
>> 1) Goin
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