Re: [SIESTA-L] About Work Function Calculation on Au

2023-03-22 Thread yh46

Hello SIESTA users,
I found that this is due to choice of PAO.EnergyShift, the work  
function value is very sensitive to the selection of this parameter.  
With PAO.EnergyShift = 0.02 Ry I get 3.5 eV. With PAO.EnergyShift =  
0.001 Ry,  I get 5.1eV.


I know that the role of this parameter is changing the localization of  
the basis functions. Is there an a priori way to determine this  
parameter, beside comparing the results with other sources  
(experiments, other codes etc.)?


Thank you very much!

Best,
Yuefei


Quoting yh46 :


Hello Dear Prof. Garcia,
Thank you very much!

Actually I have tried 30 layers. The work function is very close  
(within 0.2eV, 30 layer even smaller).


I plotted the potential along z direction using  
ElectrostaticPotential.grid.nc. The potential profile is flat in the  
vacuum. The value of the potential is basically the vacuum level in  
the output file, which I subtract the Fermi level in the output file  
to get work function.


Is there any other possible cause that could lead to this strange  
result of work function? Thank you!


Best,
Yuefei


Quoting Alberto Garcia :


Hi,

Your 'slab' is just three layers thick... that is not nearly enough  
to have a good representation of

a "bulk" region in the center and a "surface" region.

After you fix that, you probably need to process the .VH file and  
obtain a potential profile along

z to check that you reach a flat region in the vacuum.

Alberto

- El 15 de Marzo de 2023, a las 11:41, yh46  escribió:

| Hello Dear SIESTA Users,
| I am trying to do a work function calculation of Au 111 surface. The
| work function I get if 3.5 eV, which is quite different from
| experimental results ~ 5.26eV, or Quantum Espresso Result(Physical
| Review B, 2009, 80(23): 235407) ~ 5.15eV, or VASP result from my
| own~4.8eV. I understand that they are different codes, however the
| results are too different. I am wondering if there is anything wrong
| with my input file or the pseudo potential file that I use? I have
| attached the input files. Thank you very much!

| Best,
| Yuefei

| --
| Yuefei Huang
| Graduate Student
| Department of Material Science and NanoEngineering
| Rice University
| email: yuefei.hu...@rice.edu
| phone: +1-832-499-9169

| --
| SIESTA is supported by the Spanish Research Agency (AEI) and by  
the European

| H2020 MaX Centre of Excellence
|  
(https://urldefense.com/v3/__http://www.max-centre.eu/__;!!D9dNQwwGXtA!SR7RKg5wYyo4KC7PNB4i_YnJUjJdXsj-mVehHFyh_ZVKs3VnEZJW6r_lWnes9l149P-x9YbDmN_sXQ$

| )



--
Yuefei Huang
Graduate Student
Department of Material Science and NanoEngineering
Rice University
email: yuefei.hu...@rice.edu
phone: +1-832-499-9169



--
Yuefei Huang
Graduate Student
Department of Material Science and NanoEngineering
Rice University
email: yuefei.hu...@rice.edu
phone: +1-832-499-9169
TACC:  Starting up job 11076108 
TACC:  Starting parallel tasks... 
Siesta Version  : v4.1-b4
Architecture: x86_64-unknown-linux-gnu--Intel
Compiler version: ifort (IFORT) 18.0.2 20180210
Compiler flags  : mpiifort -O2 -fPIC -fp-speculation=strict -fp-model strict 
-I/opt/apps/intel118/impi18_0/parallel-netcdf/4.6.2/x86_64/include
PP flags: -DMPI -DCDF -DNCDF -DNCDF_4 -DNCDF_PARALLEL
Libraries   : libncdf.a libfdict.a   -lmkl_scalapack_lp64 
-lmkl_blacs_intelmpi_lp64 
-L/opt//intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64 
-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core  -liomp5 -lpthread -lm -ldl 
-L/opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64 
-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core  -liomp5 -lpthread -lm -ldl 
-L/opt/apps/intel18/impi18_0/parallel-netcdf/4.6.2/x86_64/lib -lnetcdff 
-lnetcdf -L/opt/apps/intel18/impi18_0/phdf5/1.10.4/x86_64/lib -lhdf5_fortran 
-lhdf5 -lz
PARALLEL version
NetCDF support
NetCDF-4 support
NetCDF-4 MPI-IO support

* Running on 90 nodes in parallel
>> Start of run:  22-MAR-2023   4:10:03

   ***   
   *  WELCOME TO SIESTA  *   
   ***   

reinit: Reading from SIESTA.fdf

reinit: ---
reinit: System Name: Au
reinit: ---
reinit: System Label: SIESTA
reinit: ---

initatom: Reading input for the pseudopotentials and atomic orbitals --
Species number:   1 Atomic number:   79 Label: Au
 
Ground state valence configuration:   6s01  5d10
Reading pseudopotential information in formatted form from Au.psf

Valence configuration for pseudopotential generation:
6s( 1.00) rc: 2.63
6p( 0.00) rc: 2.77
5d(10.00) rc: 2.63
5f( 0.00) rc: 2.63
For Au, standard SIESTA heuristics set lmxkb to 3
 (one more than the basis l, including polarization orbitals).
Use PS.lmax or PS.KBprojectors blocks to override.



Re: [SIESTA-L] about the 'Electrode connectivity is not perfect'

2023-03-22 Thread Nick Papior
Please see this question on matter modelling:
https://urldefense.com/v3/__https://mattermodeling.stackexchange.com/questions/9424/tbt-transiesta-calculation-error__;!!D9dNQwwGXtA!Q0B4ku0Ggr5WGLRlqQanAhMDQgCsmcwv4nk4V4yVTmXyu0RdrGo-Nwh_WVdR97nasmLA7ityvqMRA22Sjg$
 

Den tirs. 21. mar. 2023 kl. 22.03 skrev Bo Xiao :

> Dear siesta users
>
> I meet the problem in carrying out the transiesta simulation.
> The electrode calculation is all right, while it always show the error
> message in calculating the current/voltage curves, 'Electrode connectivity
> is not perfect'.
> When i substitue the metal atoms in electrode by other metals, the
> calculation is all right.
> The attachement is the input and output files.
> I am looking forward to your message.
>
> Best Wishes
> xiaoboy
>
> --
> SIESTA is supported by the Spanish Research Agency (AEI) and by the
> European H2020 MaX Centre of Excellence 
> (https://urldefense.com/v3/__http://www.max-centre.eu/__;!!D9dNQwwGXtA!Q0B4ku0Ggr5WGLRlqQanAhMDQgCsmcwv4nk4V4yVTmXyu0RdrGo-Nwh_WVdR97nasmLA7ityvqPHnOD2nA$
>  )
>


-- 
Kind regards Nick

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