Re: [SIESTA-L] Problem in transiesta run

[Ankita Joshi]

Dear Nick,Thanks..I will follow these steps...Regards,AnkitaOn 23/09/17, Nick 
Papior   wrote:> From the provided information it is hard 
for us to pin down the problem.Could you please follow these steps:> > 
https://answers.launchpad.net/siesta/+faq/2779> > > > such that we can figure 
out what has gone wrong?> > > > 2017-09-20 15:20 GMT+02:00 Ankita Joshi 
:> > > > > > Dear SIESTA users,> > > > > I am using 
SIESTA version 4.0. I am getting the following error in the end of the output 
file for transiesta run. > > > > > > netCDF error: NetCDF: Invalid argument> > 
Stopping Program from Node: 0> > 
--> > 
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD> > with 
errorcode 1.> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI 
processes.> > You may or may not see output from other processes, depending on> 
> exactly when Open MPI kills them.> > --
 

Re: [SIESTA-L] Problem in transiesta run

[Nick Papior]

>From the provided information it is hard for us to pin down the problem.
Could you please follow these steps:

https://answers.launchpad.net/siesta/+faq/2779

such that we can figure out what has gone wrong?

2017-09-20 15:20 GMT+02:00 Ankita Joshi :

> Dear SIESTA users,
>
> I am using SIESTA version 4.0.  I am getting the following error in the
> end of the output file for transiesta run.
>
>
>
>
>
> *netCDF error: NetCDF: Invalid argumentStopping Program from Node:
> 0--MPI_ABORT
> was invoked on rank 0 in communicator MPI_COMM_WORLDwith errorcode 1.*
>
>
> *NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.You
> may or may not see output from other processes, depending onexactly when
> Open MPI kills them.*
> --
>
> I think that the problem occur due to improper installation of transiesta
> as I faced the problem during its installation.
>
> After installing siesta (https://pelios.csx.cam.ac.uk/~mc321/siesta.html),
> I tried to install Transiesta but got the error "make: *** No rule to make
> target `libnetcdf_f90.a', needed by `transiesta'.  Stop."
>
> Then, I searched the mailing list and someone has suggested to comment the
> line NDF_INTERFACE in the arch.make file. I did that and successfully
> installed the transiesta but I don't know whether this is correct or not.
> Can anyone suggest something?
>
> Thanks,
>
> With regards
> Ankita
>
>
>


-- 
Kind regards Nick

Re: [SIESTA-L] Problem with Transiesta Run: MINVEC: BASIS VECTORS ARE LINEARLY DEPENDENT

[Nick Papior Andersen]

Try and include the Monkhorst-Pack grid and manually set it to the gamma
point. Siesta has two ways of specifying the k-grid, either MP or via a
cutoff length (see http://dx.doi.org/10.1103/PhysRevB.45.13891).

Kind regards Nick


2013/9/28 Sebastian Caicedo D. sebastian.caic...@correounivalle.edu.co

 Dear and Respected SIESTA/TranSiesta users,

 I'm new to Siesta/TranSiesta and have just performed a couple of tutorials
 and examples quite successfully. Now I'm Trying to perform a calculation of
 my own: Bulk InAs, which I need as an electrode for a larger device I
 intend to work on. I'm performing convergence tests, and Started with just
 a Gamma-point calculation. I faced some problems with the basis set, I
 could solve using the Mailing list info.

 Nevertheless I'm facing another issue. When calculating the unitary cell
 of InAs with Transiesta, I get the following error message:

 MINVEC: BASIS VECTORS ARE LINEARLY DEPENDENT

 So I tried the same calculation using SIESTA (compiled without Transiesta
 support) and it worked out just fine.

 At the end of the output file I found these lines:

 TS kgrid determined first with 3D cell !!!
  Specifying only cutoff in Electrode AND Scattering calculations might
 lead to problems !!

 So I assume this has something to do with the k-grid of the calculation
 (remember I'm performing a Gamma-point only test).

 Is my assumption correct? Does anyone have any ideas of how to deal with
 this problem?

 I attach the input and output files I'm using, so you can check them out.

 Thanks in advance.

 Sebastián Caicedo Dávila
 Bionanoelectronics Research Group
 Universidad del Valle
 Cali-Colombia