Re: [SIESTA-L] Block Chemical_species_label does not exist.

Dear, The link is broken. Could you please fix the link, otherwise we don't know what you are referring to. 2017-09-12 21:30 GMT+02:00 Jingchao Zhang : > Dear support, > > We are having the same issue as this user described in an earlier post: >

Re: [SIESTA-L] SCF convergence problem in Transiesta 4.1-b3

Dear Esmaeil, You have a very large vacuum gap behind your electrode, this may cause problems in the SCF convergence. Then a couple of comments: 1) There is practically no point in having k-points along the transport direction for the scattering calculation. So set the last diagonal k-point to

Re: [SIESTA-L] an issue in tbtran-sisl calculation

can plot this however you wish. I really appreciate your help in advance. Best regards, Zara Kind regards Nick On Sun, Aug 13, 2017 at 11:36 PM, Nick Papior <nickpap...@gmail.com> wrote: > They are (very!) rarely equal. The vector current is a vector sum of > vectors w

Re: [SIESTA-L] Thermopower measurements in molecular junctions

-2630/16/9/093029/pdf 2017-08-11 17:46 GMT+02:00 zabih allah bolboli nojini <zb.noj...@gmail.com>: > Dear Nick Papior, > > I am trying to study the temperature effect on the conductance of my devices > at different bias as well as > the thermoelectric properties.

Re: [SIESTA-L] electrostatic potential

If your system is a semi-conductor (gapped nano-ribbon) then the fermi level of the electrodes and the device need not coincide. In such cases there is an intrinsic offset in the potential between the two calculations and the band-bending you see is introduced. This is what I *presume* is the

Re: [SIESTA-L] an issue in tbtran-sisl calculation

They are (very!) rarely equal. The vector current is a vector sum of vectors with norms equal to their respective bond current. The atomic current is a sum of the norm of each of those vectors that add up to each of the atoms. I.e. this mathematical inequality holds: atomic current >= |vector

Re: [SIESTA-L] Restarting previously failed transiesta calculation

If the *.TSDE file exists, and the fdf-flag DM.UseSaveDM is true, then it will restart. The output when running transiesta will tell you whether it read the DM from a TSDE file, or not. Secondly, please update to siesta-4.1-b3. When trying beta releases it is paramount that you follow the

Re: [SIESTA-L] orbital current calculation

Are you using 4.1-b3? If not, try with that version. 2017-08-03 9:18 GMT+02:00 Zara Nosh : > Dear siesta users, > I am using siesta4.1 (with Netcdf support) to calculate the i-v > characteristic of my nanoribbon system. > When I add the following lines to my fdf file to

Re: [SIESTA-L] Transiesat error + The integer value of the kT offset for the Gauss-Fermi integral is not valid

file in the attached file. > > Kind regards, > Anita > > > > On 1 August 2017 at 10:33, Nick Papior <nickpap...@gmail.com> wrote: > >> You have probably changed the default values in the equilibrium contours >> to something that isn't allowed. >> >> Howev

Re: [SIESTA-L] Transiesat error + The integer value of the kT offset for the Gauss-Fermi integral is not valid

You have probably changed the default values in the equilibrium contours to something that isn't allowed. However, I can't see what your input is. PS. Always, ALWAYS, attach your fdf file. 2017-07-31 20:41 GMT+02:00 anita dameh : > Dear Transiesta users, > > > I tried

Re: [SIESTA-L] Bandstructure calculations with changing unit cell size

Dear Ritwik, 1. If you increase the cell-size you are effectively shrinking the Brillouin zone. The number of bands will then increase due to band-folding. If you want a figure to show this, you can read a small section of my thesis (see p. 10 and 11)

Re: [SIESTA-L] Help for arch.make n libraries for Siesta installation

The minimal siesta installation in serial requires these libraries: BLAS and LAPACK. The minimal siesta installation in parallel requires these libraries: BLAS and LAPACK and ScaLAPACK. Please ensure that all libraries are present when compiling your desired version. 2017-07-23 2:05

[SIESTA-L] Which version of openmpi is suitable for compilation

Dear Ankita, Please do not reply in other people's questions, it will detour the topic. Secondly, any version of OpenMPI is usable with Siesta (I have been using OpenMPI since 1.6 up through 2.1). I would suggest you either take 1.8.7 or 2.1.1. Note that Siesta uses the MPI API, and hence _any_

Re: [SIESTA-L] SCF did not converge in maximum number of steps.

Dear Andy, 1. Update to siesta 4.1-b3. 2. Convergence of transiesta is not guaranteed. You should continue to "play" with the parameters to achieve convergence. 3. One way of improving convergence may be to create smaller differences of bias'. I.e. start with V=0, copy TSDE to V=0.25, then copy

Re: [SIESTA-L] << full static SIESTA binary >>

Yes, it is possible. You should refer to your compiler on how to link statically libraries. For instance, for gfortran it is -static. If you encounter problems, the best bet is that some of your linked libraries hasn't been compiled into static libraries. If you do not use MPI, it is rather easy,

Re: [SIESTA-L] Error found in transmission curve of (7,0)-CNT

It is not clear at all how you have converged your full system. 1. The output of transiesta is just as important (if not more important) to check for inconsistencies. Check that both the electrodes and the scattering region have converged sufficiently, 2. You are applying a bias across a

Re: [SIESTA-L] It cannot generated *.TSHS after the TRANSIESTA calculation

I am guessing you are using siesta 4.1? If so then the TSHS file is *only* generated if the SCF step has successfully completed. Also please look through the output of transiesta. Always do this, it typically provides hints as to why something went wrong. 2017-07-04 10:38 GMT+02:00 成爱强

[SIESTA-L] Release of siesta-4.0.1

We are pleased to announce the release of Siesta-4.0.1. This version should be the default choice for production for most users. You can read the Release Notes, fixed bugs and obtain the tarball in the release page: http://launchpad.net/siesta/4.0/4.0.1 Note in particular the BACKWARD

[SIESTA-L] Beta-release of siesta-4.1 (b3)

We are pleased to announce the release of Siesta-4.1-b3. This third beta release of the 4.1 series fixes a number of bugs reported for the 4.1-b2 release, and adds some new features. If you were using 4.1-b1 or 4.1-b2 you are HIGHLY encouraged to update to 4.1-b3. We encourage all users to test

Re: [SIESTA-L] Help for arch.make n libraries for Siesta installation

ya1...@gmail.com>: > Dear Dr Nick Sir, > > If both paths are given which is preferred for lapack n blas during > installation? > > Regards > Anaya > > On 25 Jun 2017 1:31 a.m., "Nick Papior" <nickpap...@gmail.com> wrote: > >> You shouldn't

Re: [SIESTA-L] tbtran output in TranSiesta4.1

Please see equation 31 in the latest transiesta paper: http://www.sciencedirect.com/science/article/pii/S001046551630306X That should also highlight why the power may become negative. 2017-06-24 11:25 GMT+02:00 Zara Nosh : > Dear all > I have done the tbtran calculation using

Re: [SIESTA-L] Help for arch.make n libraries for Siesta installation

You shouldn't need to specify these variables (they are already defined in COMP_LIBS) BLAS_LIBS=libsiestaBLAS.a LAPACK_LIBS=libsiestaLAPACK.a Otherwise, it looks ok. Also, please note that the 4.1 series is a beta release and if using the beta release series it is imperative to keep using the

Re: [SIESTA-L] problem converging transiesta

There is not much to do other than trial an error. Typically one can get a better convergence by increasing the number of layers that separate the junction and the electrodes. I.e. if the electrostatics are long-range. Also, when you have vacuum regions as terminations of the buffer layers you

Re: [SIESTA-L] problem writting Transiesta TSHS file as NetCDF format

.4 > 2013 Free Software Foundation, Inc." as gfortran compiler. > > I attached make file and TSHS file for you. > May the siesta version I have used made this problem?(I have used > siesta3.2) > > Sincerely yours, > > On Sat, Jun 10, 2017 at 2:24 PM, Nick Papior <nick

Re: [SIESTA-L] problem writting Transiesta TSHS file as NetCDF format

>: >> >>> Dear Nick, >>> >>> I have installed sisl manually by "$> python setup.py install" as you >>> said. But the mentioned error appeared again in the terminal. I attach the >>> installation log file. >>> >>> Be

Re: [SIESTA-L] Segmentation fault

This may be the case where you run out of memory. You could try with 4.0 which should accommodate some memory reduction. Secondly, when 4.0.1 is released there has been a further fix for memory consumption, see e.g. https://bugs.launchpad.net/siesta/+bug/1665294 which seems to be related to your

Re: [SIESTA-L] How to get the value of the current based on Siesta4.1-b2

It seems like you have compiled tbtrans previously without NetCDF4 support, then you have added NetCDF4 support and simply typed: make again. This will not work. You have to: make clean make in the Util/TS/TBtrans directory. PS. the output of tbtrans says: tbt: Saving down-folded self-energies

Re: [SIESTA-L] problem writting Transiesta TSHS file as NetCDF format

llation log file. > > Best Regards, > > > > > > On Sun, May 28, 2017 at 12:41 AM, Nick Papior <nickpap...@gmail.com> > wrote: > >> It seems like you are installing using pip? >> >> As I mentioned in the previous mail, you should download the tarb

Re: [SIESTA-L] problem writting Transiesta TSHS file as NetCDF format

).read_es() > File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 89, in > read_es > File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 50, in > read_geom > File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", l

Re: [SIESTA-L] TRANSIESTA: How can I design Gaussian quadrature with FD distribution

Hi Jeonghun Yun, Implementing a different contour for this may be rather difficult. First of all, it depends on whether you use 4.0, or 4.1? For 4.0 you should look into file: m_ts_contour.F90 While for 4.1 you should look into file: m_ts_contour_eq.F90 If you _only_ wish to change the weights

Re: [SIESTA-L] problem writting Transiesta TSHS file as NetCDF format

; I installed sisl via pip command. And it was successfully installed > without any errors. > Also i installed pre-requisite before installing sisl such as : > setuptools, numpy (>=1.9), scipy, netcdf4-python. > > ‌Best Regards, > > On Mon, May 22, 2017 at 5:44 PM, Nick Papio

Re: [SIESTA-L] problem writting Transiesta TSHS file as NetCDF format

Could you tell us how you have installed sisl? Also, I think I made a mistake in the script, it should be: >>> script begin <<< #!/usr/bin/env python import sys import sisl # Read the electronic structure from the file H = sisl.get_sile(sys.argv[1]).read_es() H.write('output.nc') >>> script end

Re: [SIESTA-L] restarting tbtrans calculations

At the moment one cannot restart tbtrans calcluations. So you have to restart the calculation. 2017-05-19 14:56 GMT+02:00 Ankita Joshi : > Dear siesta users, > > I am using SIESTA 4.1 beta2 version. For my system, I want to restart > tbtrans calculations. Does anyone

Re: [SIESTA-L] Compilation of parallel version of siesta-4.1beta2 with netcdf4 in workstation

Please search the mailing list, several people have listed their arch.make file for parallel compilation. 2017-05-18 9:21 GMT+02:00 Ankita Joshi : > Dear Siesta users, > > I have serial version of SIESTA 4.1 beta2 with TranSIESTA and TBtrans > modules installed in my

Re: [SIESTA-L] thermoelectric calculation

Dear Yosida, In the paper you may find Fig. 10b which is a plot of the current as a function of bias with a temperature gradient (for 3 different cases). The Seebeck coefficient can then be calculated via: S = - dV / dT @ I = 0 Thus you need to calculate the current for a number of bias' for

Re: [SIESTA-L] error in pdos calculations

That has already been fixed for the new release. Also, when reporting these things it is imperative to specify the version of siesta used to help the developers. Thanks. -- Kind regards Nick Papior On 12 Apr 2017 22:04, "Ahmad Ali" <mphysicis...@gmail.com> wrote: i have th

Re: [SIESTA-L] the length of the electrodes in Transiesta

basis range. Your basis range is the minimum length of your electrode along the semi-infinite direction. However, periodicity will often force you to use a longer one. 2017-04-07 11:05 GMT+02:00 MB MB <mb201...@gmail.com>: > Dear Nick Papior, > > I am simulating the transport proper

Re: [SIESTA-L] TranSiesta charge distribution

This is an expected entry if you have a periodic system where the left/right electrode are periodically connected. Essentially "Other" means all the charge sitting in between layers that are disconnected, so these two terms are the content: 1) Electrode-buffer charge 2) electrode-electrode charge

Re: [SIESTA-L] transiesta+The self-energy cannot be calculated with a zero transfer matrix!

You have either requested the semi-infinite direction along a non-periodic direction or your electrode calculation is erroneously setup. To calculate the self-energy transiesta requires a supercell. The transfer matrix is equivalent to the coupling matrix between the unit-cell and the

Re: [SIESTA-L] << compiling siesta-4.1-b2 with Intel Compiler >>

First, did you try my suggestion? It is not clear at all whether you did and you still have the problem? Secondly, those libraries are dependencies normal to the intel compiler. Intel isn't a completely separate compiler, it still relies on system libraries. Lastly, the pthread dependency is

Re: [SIESTA-L] how to install Netcdf4 for compilation of tbtrans in siesta 4.1b2

age? >> > >> > 2017-03-23 7:26 GMT+03:00 berna uyanık <bernauya...@gmail.com>: >> > >> >> Hi. I wonder why have siesta been coming with netcdf? >> >> >> >> 23 Mar 2017 00:00 tarihinde "Nick Papior" <nickpap...@gma

Re: [SIESTA-L] Parallel method by siesta

1:216 1:216 1:40 2 1:216 1:216 41:80 Thanks. I appreciate your help. > > Yangchuan > ME | UT Austin > > On Fri, Feb 24, 2017 at 1:56 AM, Nick Papior <nickpap...@gmail.com> wrote: > >> Those output numbers are not intended for the users. They are mainly used >> by

Re: [SIESTA-L] how to install Netcdf4 for compilation of tbtrans in siesta 4.1b2

Please see this post which contains a script to install netcdf4. http://www.mail-archive.com/siesta-l@uam.es/msg09275.html If you have problems with it consult your local administrator or ask on the NetCDF mailing lists. 2017-03-21 10:00 GMT+01:00 Ankita Joshi : >

Re: [SIESTA-L] Transiesta error+Error in setup. Atoms are having two types, check for electrode and buffer atom overlap.

You have defined some atoms to be both an electrode and a buffer atom. I.e. TS.Atoms.Buffer is probably ill-defined, otherwise is your electrode ill-defined. Please carefully go through your input to check the atoms region (Buffer, Electrode, Device). 2017-03-16 16:03 GMT+01:00 anita dameh

Re: [SIESTA-L] different energies for transiesta calculations in 4.1 and 4.0

The two versions (4.0 and 4.1) have diverged, greatly. Hence energies cannot be compared between the two. There are a variety of reasons for this, one is the choice of reference (ts-Vha as printed out in the output) which has changed, another is the precision of the contours and their integrands.

Re: [SIESTA-L] Different initial spin configurations in v3.2 and v4.1

Please see whether this bug-report has corrected your problems. The bug-report highlights that this is only a matter of printing the initial spin configuration, not how the actual spin-configuration is "seen" by siesta. https://bugs.launchpad.net/siesta/+bug/1648053 2017-03-06 17:27 GMT+01:00

Re: [SIESTA-L] Problem siesta 4 + openmpi

Your fdf input is more than likely corrupted. For instance, some OS's requires that the fdf input ends on a newline character. Secondly, it may be good practice to delete all fdf-*.log and INPUT_TMP.* files before execution. 2017-02-26 22:43 GMT+01:00 Gee Ufpi : > Hi

Re: [SIESTA-L] siesta-4.0-b2 installation error

Your question on Launchpad has been answered, secondly. Please use the latest version, 4.0-b2 is a beta release, the stable 4.0 is released. 2017-02-24 5:38 GMT+01:00 Sunetra Das : > Dear All, > I am getting the following error while trying to install siesta-4.0-b2: > >

Re: [SIESTA-L] Parallel method by siesta

Those output numbers are not intended for the users. They are mainly used by developers iff bugs occur. So an end user can easily neglect the output you refer to. However, the line: InitMesh: MESH = 216 x 216 x80 = 3732480 tells you the real space grid used internally (1st, 2nd, 3rd

Re: [SIESTA-L] Command for k-averaged transmission

Please see this recent answer regarding tbtrans http://www.mail-archive.com/siesta-l@uam.es/msg09576.html -- Kind regards Nick Papior On 22 Feb 2017 22:04, "Ankita Joshi" <joshi.dcy2...@iitr.ac.in> wrote: > Hello SIESTA users, > > I am using SIESTA 4.1 beta-2 a

Re: [SIESTA-L] siesta-4.1-b2 MPI spin-orbit crashes with Error in Cholesky factorisation in cdiag

Please see (a new answer here to your LP question): https://answers.launchpad.net/siesta/+question/465719 2017-02-20 18:34 GMT+01:00 Aurelio Gallardo Caparrós : > Hi! > > I'm using siesta-4.1-b2 MPI compiled in a cluster. > spin-orbit calculations with more than one core

Re: [SIESTA-L] VIBRA package

Could you please update to siesta 4.0? If the error persists, please let us know. 2017-02-19 5:07 GMT+01:00 Sunetra Das : > Hello SIESTA users, > > I am new to SIESTA and trying to calculate the phonon dispersion curves > for a given optimized structure using the VIBRA

Re: [SIESTA-L] Is it must to install siesta 4.1b1 with netcdf

the Hamiltonian in a tbtrans compatible format) - Maybe I have forgotten some things... So I would say NetCDF is almost a requirement for the new tbtrans... 2017-02-17 0:57 GMT+01:00 berna uyanık <bernauya...@gmail.com>: > Has netcdf to be installed for tbtrans? > > 2017-02-16 0:06 GMT+03

Re: [SIESTA-L] Is it must to install siesta 4.1b1 with netcdf

It is not a must, but it is highly recommendable. Also, the second beta release of siesta 4.1 has been released. When testing with a beta release you are encouraged to follow the new releases, closely. 2017-02-15 15:25 GMT+01:00 Riya Rogers : > Dear All > > Is it must

Re: [SIESTA-L] siesta 4.1 error

Please read the output. It clearly states: " Electrode: Left has very few k-points in the semi-infinite direction, at least 20 is recommended. " You need more k-points in the semi-infinite direction. 2017-02-02 14:38 GMT+01:00 AAKANKSHA SUD : > Dear users > I am

Re: [SIESTA-L] PDOS or LDOS in Transiesta

Dear Lee, In transiesta 4.0 it is not possible to further analyse the DOS distribution among orbitals. If you want to do PDOS you need to recalculate for each PDOS region you are interested in. See the TS.TBT.PDOSFrom and TS.TBT.PDOSTo flags. Let me note that since 4.1 this is now possible in a

Re: [SIESTA-L] Error in parallel siesta 4.1b1

Could you please try the latest beta release 4.1-b2, it should have fixed this problem. 2017-01-30 19:05 GMT+01:00 RAJAN SINGH : > Dear Dr Nick > > after this step I have this error > > Error: Different types in pointer assignment at (1); attempted assignment > of

Re: [SIESTA-L] Error in the end of simulation Siesta 4.1 b1

This is the last call before siesta stops. So if this is the only "error" you get, you may disregard it completely. I will fix this in the 4.1-b3 release so that it simply creates a file. May I suggest you to try 4.1-b2 instead of b1? Numerous bug-fixes has already been added to the 4.1 release

Re: [SIESTA-L] NETCDF error

You are trying to compile with netcdf, however, the compiler cannot find the appropriate netcdf module. Either: 1) You have added -DCDF erroneously, or 2) You have forgotten to add the netcdf include directory. 2017-01-30 11:33 GMT+01:00 RAJAN SINGH : > Dear Siesta

Re: [SIESTA-L] Problem with siesta-4.0 and mkl

There are multiple questions regarding compilation of siesta with MKL. Could you please search the mailing list for these. Secondly, you haven't supplied your arch.make file. 2017-01-26 16:55 GMT+01:00 Colin Bannister : > I am having difficulty running Siesta

Re: [SIESTA-L] Empty DOS and PDOS files..!!!

The energy specification in the ProjectedDensityOfStates block *must* be identified as real's, i.e. append an "." to make it a floating number instead of an integer: %block ProjectedDensityOfStates -10.0 20.0 0.1 2000 eV %endblock ProjectedDensityOfStates this should work. 2017-01-18 16:02

Re: [SIESTA-L] Transiesta error: No electrode found in compilation of .fdf file for scattering region

The transiesta examples in the Examples directory, haven't been updated. I didn't realize this until lately. To find some test systems, go to the Tests/TranSiesta-TBTrans folder where you will find the details of the new transiesta. 2017-01-13 8:12 GMT+01:00 Ankita Joshi

Re: [SIESTA-L] Fragmented Core Charges

Have you tried with the larger mesh-cutoff? The one you have attached in the forum have a smaller mesh than the one you supply here. 2017-01-12 15:46 GMT+01:00 Seyed Mohammad Tabatabaei : > Can this core charge fragmentation issue be attributed to some parts of > the SIESTA

Re: [SIESTA-L] ExternalElectricField in Siesta

Hi Ruslan, It is via the sawtooth potential method. -- Kind regards Nick Papior On 10 Nov 2016 15:40, "Руслан Жачук" <zhac...@gmail.com> wrote: Dear siesta users, does someone know how how the module of ExternalElectricField is implemented in SIESTA? Is it via an external sa

Re: [SIESTA-L] Bader Charge Analysis

The bader analysis program is not developed by the siesta project. Please consult the bader developers for details regarding this. 2017-01-02 16:58 GMT+01:00 Seyed Mohammad Tabatabaei : > Dear all, > > I get the following error when I use the bader program with siesta .RHO >

Re: [SIESTA-L] << error compiling Siesta 4.1 (b2) >>

netcdf-fortran/lib -lnetcdff > -L/software/lib/netcdf/lib64 -L/software/lib/pnetcdf/lib > -L/software/lib/hdf5/lib64 -lnetcdf -lnetcdf -lhdf5_hl -lhdf5 -lz -lcurl > --has-f90 -> no > --has-f03 -> yes > > --has-nc2 -> yes > --has-nc4 -> yes > > --pre

Re: [SIESTA-L] Transiesta DOS Units

Currently there are 3 different versions of tbtrans in circulation: 4.0/Util/TBTrans: I do not know the DOS units in this one, you will have to check the code your-self. 4.0/Util/TBTrans_rep: The DOS is in 1/Ry summed over all orbitals in the device region. 4.1/Util/TS/TBtrans: If you have

Re: [SIESTA-L] << error compiling Siesta 4.1 (b2) >>

com>: > Hi Nick, > > I recompile all libraries with the same Fortran compiler/MPI/MKL. The > error persist. > > Here is my arch.make. > > Thanks in advance. > > > []'s, > > Camps > > On Tue, Nov 29, 2016 at 6:33 PM, Nick Papior <nickpap...@gmail

Re: [SIESTA-L] DM versus H convergence

Hi Simona, 2016-11-29 12:15 GMT+01:00 Simona Achilli : > Dear developers, > I’m using the 4.1-b1 version of SIESTA/TRANSIESTA with the default Mixing > of the Hamiltonian and convergence of H. > Although the manual suggest to adopt these criteria for a faster >

Re: [SIESTA-L] Transmission Coefficients

carefully examine the output of transiesta and check the convergence,perhaps charge is leaving the system. Lastly, you should also converge the number of screening layers between your device and electrodes to ensure a continuous potential. Maybe this may be the root cause. -- Kind regards Nick Papior

Re: [SIESTA-L] Fwd: Transiesta error in electrode size

this error message your self-energies may be incorrectly calculated. I.e. I would NOT recommend this. -- Kind regards Nick Papior On 5 Dec 2016 22:08, "anita dameh" <anita.da@gmail.com> wrote: Yes, I got the same warning with Siesta 4.0 and 4.1. b.1 but there is no such war

Re: [SIESTA-L] Fwd: Transiesta error in electrode size

The new transiesta version introduces many more checks regarding the setup of the transiesta calculation. Indeed if the latest transiesta calculation states that the electrodes is too short, then essentially the electrode self-energy cannot be correctly calculated (i.e. the physics is wrong). One

Re: [SIESTA-L] Stars in the output file

It means that the number of digits is too large, so it can't be printed. As a rule of thumb, if this happens you are so far from the minimum that self-consistency will "never" happen. You need to change settings, mixing parameters etc. See manual for details on controlling the convergence.

Re: [SIESTA-L] Error in siesta: corrupted double-linked list- Why does this problem occur and what's the solution?

Please follow these steps to help us help you: https://answers.launchpad.net/siesta/+faq/2779 -- Kind regards Nick Papior On 30 Nov 2016 9:02 pm, "Bahareh Fakhraei" <fakhraei.baha...@gmail.com> wrote: > Hello every one, > > I was relaxing a structure with siesta pro

Re: [SIESTA-L] << error compiling Siesta 4.1 (b2) >>

It seems your netcdf module has been compiled with another compiler. Please ensure correct library and include paths. PS. Always include arch.make file if you have problems compiling, regardless of whether it works for previous versions. 2016-11-29 21:14 GMT+01:00 I. Camps :

[SIESTA-L] Beta-release of Siesta 4.1 (b2)

We are pleased to announce the release of Siesta-4.1-b2. This version is a major step in development for Siesta and introduces many new features. We encourage all users to test this beta version but advice to compare against Siesta 4.0 as this is a beta release. Please read the Release Notes

Re: [SIESTA-L] Fwd: Question on grid2cdf function.

Dear Aaron, It is in Ry. 2016-11-26 0:33 GMT+01:00 Qing Shi : > Dear users, > > Sorry to bother you guys. > I was wondering what the unit is for the electrostatic potential written > in SystemName.VH file. Ry or eV? > And also, I have used the function

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

You may use sisl which is a command line and python scripting utility. The command in sisl is `sgeom input.XV -o output.xsf -o output.xyz`. I also know of Inelastica which should do this with geom2geom command. 2016-11-16 7:17 GMT+01:00 AAKANKSHA SUD : > dear users

Re: [SIESTA-L] error in installation

If you want to compile with mpi, you must use the scalapack library. You have not supplied this library on the link line. -- Kind regards Nick Papior On 17 Nov 2016 6:56 pm, "Tanya Gupta" <gptatanya1...@gmail.com> wrote: > Hello to siesta developers and siesta users > &g

Re: [SIESTA-L] Submit parallel siesta job using SLURM schedular

Ask your cluster administrator. I bet there is guidelines you should follow. -- Kind regards Nick Papior On 15 Nov 2016 8:42 pm, "RAJAN SINGH" <singhrajan.i...@gmail.com> wrote: > Dear Siesta Users > > How to submit siesta job into parallel environment using SLURM?

Re: [SIESTA-L] TRANSIESTA

Yes, with transiesta and inelastica. Please search the mailing list and/or the inelastica website: http://dipc.ehu.es/frederiksen/inelastica/index.php/Main_Page -- Kind regards Nick Papior On 15 Nov 2016 7:31 pm, "amin hamidi" <amin.hamidi1...@gmail.com> wrote: > I want to

Re: [SIESTA-L] k-point in transiesta

> for example 100*100*1 k-point; am I right? > > Thank you very much in advance. > > On Mon, Nov 14, 2016 at 12:48 PM, Nick Papior <nickpap...@gmail.com> > wrote: > >> >> >> 2016-11-12 19:53 GMT+01:00 Zara Nosh <z.nr...@gmail.com>: >> >>>

Re: [SIESTA-L] << polarized spin transport output >>

2016-11-10 20:05 GMT+01:00 I. Camps : > Hello, > > I am following the examples from the tutorial "Siesta/TranSiesta Tutorial, > Tel Aviv, September 8-11, 2014" at SIESTA site (link > ). > > From this tutorial, in example

Re: [SIESTA-L] k-point in transiesta

2016-11-12 19:53 GMT+01:00 Zara Nosh : > Dear siesta users > > I have seen several transiesta examples in siesta package (Test and > Example directories); in all examples the value of k-point in z-direction, > for the scattering and tbtran runs are not equal to one and it has

Re: [SIESTA-L] Error in parallel siesta 4.1b1

Add ", save" right after public and try again, none this has been fixed for the next release. -- Kind regards Nick Papior On 9 Nov 2016 4:23 pm, "RAJAN SINGH" <singhrajan.i...@gmail.com> wrote: > Dear siesta users > > I tried to install parallel versio

Re: [SIESTA-L] Left electrode file does not exist. Please create electrode 'NOT REQUESTED' first.

You are most likely using the 4.0 transiesta executable. Please check your environment and use the 4.1-b1 executable. 2016-11-07 15:40 GMT+01:00 toufik esssakhri : > Dear transiesta users, > > > i am using SIESTA 4.1-b1 to do transport calculations. > > for scattering

Re: [SIESTA-L] compilation error for siesta trunk 572

1 > Error: Object 'spin' at (1) must have the SAVE attribute for default > initialization of a component > make: *** [m_spin.o] Error 1 > > Regards, > Tao > > > > On 2016-10-18 15:02, Nick Papior wrote: > >> With intel compilers you should probably not compile

Re: [SIESTA-L] noncollinear

Please see this bug-report: https://bugs.launchpad.net/siesta/+bug/1636100 This will be fixed in the next release of 4.0 (4.0.1). You may download the patch and apply it in your source if so desired. 2016-10-22 18:30 GMT+02:00 Raha khalili : > Dear all, > > I am

Re: [SIESTA-L] << problem with electrodes >>

The short answer is that transiesta requires a strict input sequence of atoms. In pre-4.1 versions transiesta requires the first atoms to be left-buffer+left-electrodes, and the last atoms to be right-electrode+right-buffer atoms. In 4.1 and beyond, this restriction has been lifted while it still

Re: [SIESTA-L] NetCharge and doping

2016-10-21 9:05 GMT+02:00 Ernesto Ruiz : > Dear SIESTA users, > > I am currently trying to use the NetCharge and SimulateDoping options > (SIESTA 4.1), but I cannot understand some of the explanations given in the > manual. From what I can understand, NetCharge sets a charge in

Re: [SIESTA-L] compilation error for siesta trunk 572

8 0.22 > 8.5 > H 2 > n=1 0 2 E 50. 8.3 > 8.5 2.2 > n=2 1 1 E 20. 7.8 Q 6.5 0.9 > 8.0 > %endblock PAO.Basis > > DM.Tolerance 0.10E-04 > MD.MaxForceTol 0.001 eV/Ang > MD.MaxStressTol 0.01 GPa > > MD.VariableCell T

Re: [SIESTA-L] compilation error for siesta trunk 572

mpirun -np 16 /home/tl439/~siesta-maint/siesta/trunk/Obj/siesta < > h2o.relax.fdf > h2o.relax.out > it doesn't work neither. > > I used same execution command for siesta 4.0, it works. > > Regards, > Tao > > > > On 2016-10-18 13:13, Nick Papior wrote: > >> P

Re: [SIESTA-L] compilation error for siesta trunk 572

l64 -lmkl_scalapack_lp64 > -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lmkl_blacs_intelmpi_lp64 > -lpthread -lm > PARALLEL version > > Could you suggest what to do please? > > Regards, > Tao > > > > > > > On 2016-10-14 12:18, T. Liu wrote: > &g

Re: [SIESTA-L] error in siesta 4.b installation

Please change dc_lapack.a to libsiestaLAPACK.a in your arch.make file. 2016-10-17 4:13 GMT+02:00 anita dameh : > Dear siesta and transiesta users, > I have tried to compile siesta 4,b but I got the following error > > ranlib libSiestaXC.a > cp *.mod *.a .. > make[1]:

Re: [SIESTA-L] compilation error for siesta trunk 572

Try add .c to the SUFFIXES list. 2016-10-14 12:32 GMT+02:00 T. Liu : > Dear all, > > I can compile 4.0 with the following arch.make > > arch.make > > # > # Copyright (C) 1996-2016 The SIESTA group > # This file is distributed under the terms

Re: [SIESTA-L] Noncollinear SpinPolarized calculation

vance. > Best regards, > Raha > > On Tue, Sep 27, 2016 at 11:22 PM, Nick Papior <nickpap...@gmail.com> > wrote: > >> Please try siesta-4.0 instead. >> >> 2016-09-27 8:57 GMT+02:00 Raha khalili <khadije.khal...@gmail.com>: >> >>> Dear Nic

Re: [SIESTA-L] Installation of NetCDF with CDF4 support (also installation of HDF5 and zlib)

/www.facebook.com/groups/1482411542018575/)? > > > []'s, > > Camps > > On Tue, Sep 27, 2016 at 4:39 PM, Nick Papior <nickpap...@gmail.com> wrote: > >> Dear list, >> >> Several have asked questions about installation of NetCDF4 successfully. >> >> I

Re: [SIESTA-L] Noncollinear SpinPolarized calculation

nput and output files > are attached here. Could you give a look at them please? > > Thank you in advance, > Best regards > Raha > > On Mon, Sep 26, 2016 at 7:52 PM, Nick Papior <nickpap...@gmail.com> wrote: > >> Yes, you can use non colinear spin configuration.

Re: [SIESTA-L] *.TBTGFL and *.TBTGFR files

bias and they take a lot of space. > > > -- > *De :* siesta-l-requ...@uam.es <siesta-l-requ...@uam.es> de la part de > Nick Papior <nickpap...@gmail.com> > *Envoyé :* mardi 27 septembre 2016 10:27 > *À :* siesta-l@uam.es >

[SIESTA-L] Installation of NetCDF with CDF4 support (also installation of HDF5 and zlib)

Dear list, Several have asked questions about installation of NetCDF4 successfully. If you simply download NetCDF and install it using configure without any flags you will only get support for CDF-3. Although you have downloaded NetCDF-4.4.1 it will NOT intrinsically install NetCDF with CDF-4

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