Band structure of Ni: Difference between revisions

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(Created page with "==Input files == * Save two files below as *.py files. ===band.py=== <pre> from gpaw import GPAW, FermiDirac from ase import Atoms from ase.io import read, write from gpaw...")
 
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==Job submission script==
==Run job on ulam==


*Save the following into a file '''jobscript''' within your working directory


<pre>
==Plot the results==
#$ -N band
#$ -o out.log
#$ -e band.err
#$ -pe openmpi 16
#$ -l h_rt=3:00:00
#
source /opt/shared/valet/docs/valet.sh
vpkg_rollback all
vpkg_require numpy/1.6.1-2.7
vpkg_require mkl/10.3.8-64bit
vpkg_require openmpi/1.6.1-intel64
#
export PYTHONPATH=/lustre/scratch/ksaha/gpaw/ase:$PYTHONPATH
export PATH=/lustre/scratch/ksaha/gpaw/ase/tools:$PATH
export GPAW_SETUP_PATH=/lustre/scratch/ksaha/gpaw/gpaw-setups-0.8.7929
export PYTHONPATH=/lustre/scratch/ksaha/gpaw/gpaw:${PYTHONPATH}
export PYTHONPATH=/lustre/scratch/ksaha/gpaw/gpaw/build/lib.linux-x86_64-2.7:${PYTHONPATH}
export PATH=/lustre/scratch/ksaha/gpaw/gpaw/build/bin.linux-x86_64-2.7:/lustre/scratch/ksaha/gpaw/gpaw/tools:${PATH}
#
#
cd /home/1076/FCC-Ni_bandstructure/Wiki
#
mpirun /lustre/scratch/ksaha/gpaw/gpaw/build/bin.linux-x86_64-2.7/gpaw-python band.py
#mpirun /lustre/scratch/ksaha/gpaw/gpaw/build/bin.linux-x86_64-2.7/gpaw-python find_band_as_dat.py
</pre>


==Running the job script==
* If your jobs are successful, you should be able to reproduce this figure (using [http://www.gnuplot.info/ gnuplot] on Mills or transfer data to your Windows PC via sftp and use Origin):
 
*To run '''band.py''' execute:
qsub jobscript
 
*To run '''find_band_as_dat.py''' execute:
 
:'''1.''' modify the 4th line of the jobscript "#$ -pe openmpi 16" to "#$ -pe openmpi 1" -- this means we will be running in a single core.
 
:'''2.''' comment the second last line and uncomment the very last line of the jobscript
 
:'''3.''' then submit job: qsub jobscript
 
:'''4.''' bands should be generated into "out.log" file
 
==Test results==
 
* Once you successfully finish running both jobs, you should be able to reproduce this figure (using [http://www.gnuplot.info/ gnuplot] on Mills or transfer data to your Windows PC via sftp and use Origin):


<pre>  
<pre>  

Revision as of 09:27, 8 November 2014

Input files

  • Save two files below as *.py files.

band.py


from gpaw import GPAW, FermiDirac
from ase import Atoms
from ase.io import read, write
from gpaw import GPAW, PoissonSolver, MixerSum
from ase.structure import bulk

# -------------------------------------------------------------
# Bulk configuration
# -------------------------------------------------------------

a = 3.5249 
atoms = bulk('Ni', 'fcc', a=a)
atoms.center()

write('system.traj', atoms)

for a in atoms:
    if a.symbol == 'Ni':
        a.magmom = 0.6

# Make self-consistent calculation and save results
calc = GPAW(h=0.18,
            mode='lcao',
            xc='PBE',
            basis='dzp',
            kpts=(8,8,8),
            occupations=FermiDirac(width=0.05, maxiter=2000),
            mixer=MixerSum(beta=0.010, nmaxold=8, weight=100.0),
            poissonsolver=PoissonSolver(eps=1e-12),
            txt='band_sc.txt')

atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('band_sc.gpw')


# Calculate band structure along Gamma-X 

from ase.dft.kpoints import ibz_points, get_bandpath
points = ibz_points['fcc']
G = points['Gamma']
X = points['X']
kpts, x, X = get_bandpath([G, X], atoms.cell, 80)

calc = GPAW('band_sc.gpw',
            mode='lcao',
            xc='PBE',
            basis='dzp',
            kpts=kpts,
            txt='band_harris.txt',
            fixdensity=True,
            parallel={'domain': 1},
            usesymm=None,
            convergence={'bands': 'all'})

if calc.input_parameters['mode'] == 'lcao':
    calc.scf.reset()

calc.get_potential_energy()
calc.write('band_harris.gpw')

find_band_as_dat.py

from ase.lattice import bulk
from gpaw import GPAW

calc = GPAW('band_harris', txt=None)
import numpy as np

eps_skn = np.array([[calc.get_eigenvalues(k,s)
                     for k in range(80)]
                    for s in range(2)]) - 10.75103

for n in range(10):
    for k in range(80):
        print k, eps_skn[0, k, n], eps_skn[1, k, n]
    print

Run job on ulam

Plot the results

  • If your jobs are successful, you should be able to reproduce this figure (using gnuplot on Mills or transfer data to your Windows PC via sftp and use Origin):
 
gnuplot> plot "result.dat" using 1:2 with lines title "Spin up", "result.dat" using 1:3 with lines title "Spin down"

FIG. 1: Electronic band structure of fcc-Ni.