Re: [SIESTA-L] supercell

[T. Liu]

Thanks, Nick.

On 2016-07-27 08:31, Nick Papior wrote:

Currently you cannot perform supercell expansions using off-diagonal
components.

2016-07-27 9:23 GMT+02:00 T. Liu :


Dear All,

I am trying to use 'supercell' block to make a
2 0 1
0 1 0
0 0 2
supercell, but Siesta stopped and showed that

Not safe to use non-diagonal supercells
Stopping Program from Node: 0

Program aborted. Backtrace:
#0 0x10e968729
#1 0x10e9693a4
#2 0x10ea3e7a8
#3 0x10da4a74a
#4 0x10d9160fa
#5 0x10d906a39
#6 0x10d904e15
#7 0x10db02bce
Abort trap: 6

Could you please tell me if it is possible to make non-diagonal
supercell by 'supercell' block? It seems no more detail in the
manual.

Regards,
Tao


--

Kind regards Nick

Re: [SIESTA-L] supercell

[Nick Papior]

Currently you cannot perform supercell expansions using off-diagonal
components.

2016-07-27 9:23 GMT+02:00 T. Liu :

> Dear All,
>
> I am trying to use 'supercell' block to make a
> 2 0 1
> 0 1 0
> 0 0 2
> supercell, but Siesta stopped and showed that
>
> Not safe to use non-diagonal supercells
> Stopping Program from Node:0
>
> Program aborted. Backtrace:
> #0  0x10e968729
> #1  0x10e9693a4
> #2  0x10ea3e7a8
> #3  0x10da4a74a
> #4  0x10d9160fa
> #5  0x10d906a39
> #6  0x10d904e15
> #7  0x10db02bce
> Abort trap: 6
>
>
> Could you please tell me if it is possible to make non-diagonal supercell
> by 'supercell' block? It seems no more detail in the manual.
>
> Regards,
> Tao
>



-- 
Kind regards Nick

[SIESTA-L] supercell

[T. Liu]

Dear All,

I am trying to use 'supercell' block to make a
2 0 1
0 1 0
0 0 2
supercell, but Siesta stopped and showed that

Not safe to use non-diagonal supercells
Stopping Program from Node:0

Program aborted. Backtrace:
#0  0x10e968729
#1  0x10e9693a4
#2  0x10ea3e7a8
#3  0x10da4a74a
#4  0x10d9160fa
#5  0x10d906a39
#6  0x10d904e15
#7  0x10db02bce
Abort trap: 6


Could you please tell me if it is possible to make non-diagonal 
supercell by 'supercell' block? It seems no more detail in the manual.


Regards,
Tao

Re: [SIESTA-L] script for energy vs lattice constant convergence.

[Mayuri Vaghela]

thank you so much I Camp

On Tue, Jul 26, 2016 at 7:11 AM, I. Camps  wrote:

> Hello Mayuri,
>
> You can use the Atomic Simulation Environment (ASE:
> https://wiki.fysik.dtu.dk/ase/index.html) and do a file with the exported
> data you need, or can use a batch script similar to the one bellow. I use
> this script to do mesh cutoff convergence studies. In your case, you can
> export the Lattice constants and the energy and do the graph.
>
>
> Script:
> **
> #!/bin/bash
> #rm E_vs_h.dat
> tmp=0
> # Numero de pontos para fazer a curva Energia vs h
> for i in 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
> do
> tmp=`echo "$i" | bc`
> dx=`echo "150+$i*25" | bc`
> cat > Fase_1-$i.fdf <
> SystemLabel  Fase_1-$i
> SystemName   Fase_1-$i
> NumberOfAtoms19
>
> NumberOfSpecies  4
> %block ChemicalSpeciesLabel
> 11  H
> 26  C
> 38  O
> 457 La
> %endblock ChemicalSpeciesLabel
>
> LatticeConstant 1.0 Ang
> %block LatticeParameters
>   10.210800 13.731200 14.740600  90.00  90.00  90.00
> %endblock LatticeParameters
>
> AtomicCoordinatesFormat Fractional
>
> %block AtomicCoordinatesAndAtomicSpecies
>  0.58180  0.79890  0.48710  1
>  0.70480  0.81720  0.48590  1
> -0.06120  0.43740  0.30310  1
> -0.06120  0.43740  0.19690  1
>  0.12630  0.92250  0.48580  1
>  0.61630  0.73390  0.22540  1
>  0.61440  0.62940  0.21840  1
>  0.32520  0.92300  0.46540  2
>  0.19440  0.97170  0.48320  2
>  0.16190  1.04440  0.40990  2
> -0.16260  0.99060  0.25000  3
>  0.58340  0.67980  0.25000  3
> -0.05730  0.81080  0.40310  3
>  0.65110  0.76630  0.46620  3
>  0.14710  0.54670  0.25000  3
>  0.07700  0.69600  0.25000  3
> -0.23110  0.84040  0.25000  3
>  0.02596  0.87346  0.25000  4
>  0.33514  0.68258  0.25000  4
> %endblock AtomicCoordinatesAndAtomicSpecies
>
> PAO.BasisSize DZP
> MD.TypeOfRun  CG
> MD.NumCGsteps 0
> MaxSCFIterations  1000
> SpinPolarized true
> *MeshCutoff$dx Ry*
> DM.MixingWeight   0.01
> DM.NumberPulay3
> XC.functional GGA
> XC.authorsPBE
> SolutionMethod diagon
>
> %block PAO.Basis # Define Basis set
> La4   3.000# Label, l-shells, ionic net
> charge
>  n=5   0   2 # n, l, Nzeta
>3.515  3.063
>1.000  1.000
>  n=5   1   2 # n, l, Nzeta
>3.884  3.063
>1.000  1.000
>  n=5   2   2 # n, l, Nzeta
>4.864  3.741
>1.000  1.000
>  n=4   3   2 # n, l, Nzeta
>3.102  1.812
>1.000  1.000
> %endblock PAO.Basis
>
>
> # Fim do input para o SIESTA
> !
> *mpirun -np 8 siesta < Fase_1-$i.fdf > Fase_1-$i.out*
>
> *E=$(grep "E_KS" Fase_1-$i.out | grep '='| awk '{printf "%12.6f
> \n",$6}')echo $dx $E $i >> E_vs_mesh.dat*
> done
>
>
> **
>
> []'s,
>
> Camps
>
>
>
>
> On Wed, Jul 20, 2016 at 5:28 AM, Mayuri Vaghela  > wrote:
>
>> hi all siesta users,
>> i want energy vs lattice constant graph. so i need script which is
>> compatible with siesta, i search about how to make script to get minima in
>> ene vs Latt. Cons. but proper result is not obtained.
>> please help me..
>>
>
>