Commit 1bf70ce6 authored by kuismam's avatar kuismam

Add larger agts test

parent 5f82c7bc
55
Ag 10.103905000389176 10.103905000008758 10.103904999876299
Ag 7.834679336211867 10.103904999352315 8.701370697682759
Ag 7.834679340832878 10.103904999354150 11.506439314621725
Ag 8.701370665688859 7.834679357161356 10.103905007696909
Ag 8.701370665308216 12.373130642197591 10.103905007698188
Ag 10.103904976158379 8.701370686292490 12.373130653292217
Ag 10.103904976157530 11.506439317177399 7.834679353935756
Ag 10.103904976156278 8.701370681789365 7.834679354325114
Ag 10.103904976159003 11.506439312673004 12.373130653681239
Ag 11.506439296195815 7.834679342845536 10.103905007694889
Ag 11.506439296575573 12.373130656515496 10.103905007695612
Ag 12.373130635565678 10.103904999354432 11.506439328570341
Ag 12.373130640188251 10.103904999353622 8.701370683735332
Ag 5.469156666114690 10.103904999354842 10.103905005512239
Ag 5.588478493238041 10.103904999233938 7.312739879070636
Ag 5.588478495850199 10.103904999235979 12.895070137309508
Ag 6.353892546503481 7.786587195926696 8.671410351460853
Ag 6.353892547580336 7.786587194385294 11.536399662804023
Ag 6.353892546538882 12.421222803061172 8.671410351584541
Ag 6.353892547615006 12.421222804601117 11.536399662678935
Ag 7.312739841949994 5.588478517787002 10.103905009100099
Ag 7.312739841749010 14.619331481141657 10.103905009101180
Ag 7.786587177872104 8.671410339353447 6.353892573461263
Ag 7.786587177387537 8.671410340347787 13.853917439738002
Ag 7.786587178005386 11.536399659450783 6.353892573376582
Ag 7.786587177517367 11.536399658456247 13.853917439827566
Ag 8.671410320022330 6.353892568399456 12.421222812032616
Ag 8.671410321487164 13.853917430038301 7.786587200094877
Ag 8.671410321573923 6.353892568847229 7.786587200055542
Ag 8.671410319937563 13.853917430483618 12.421222811991546
Ag 10.103904971805569 7.312739867717672 14.619331491980857
Ag 10.103904971804868 12.895070133267549 5.588478520538273
Ag 10.103904971803416 7.312739865356937 5.588478520758856
Ag 10.103904976215832 10.103904999536681 5.469156690727183
Ag 10.103904976215198 10.103904999536679 14.738653321284643
Ag 10.103904971806967 12.895070130906749 14.619331492201322
Ag 10.103904982922902 5.469156684217877 10.103905007678017
Ag 10.103904982918419 14.738653314772066 10.103905007676579
Ag 11.536399635790955 6.353892565071086 12.421222807257857
Ag 11.536399634320981 13.853917433377452 7.786587204865930
Ag 11.536399634238530 6.353892565517794 7.786587204827500
Ag 11.536399635872016 13.853917433825520 12.421222807218275
Ag 12.421222785164929 8.671410345151649 13.853917438345588
Ag 12.421222784549244 11.536399654642805 6.353892574763493
Ag 12.421222784677941 8.671410344157460 6.353892574853783
Ag 12.421222785039685 11.536399653645935 13.853917438442179
Ag 12.895070107302825 5.588478509698299 10.103905009097678
Ag 12.895070107502168 14.619331489229758 10.103905009099620
Ag 13.853917412593216 7.786587197434970 8.671410348376295
Ag 13.853917411514395 7.786587195896960 11.536399665888940
Ag 13.853917412553468 12.421222801546829 8.671410348511326
Ag 13.853917411478047 12.421222803086360 11.536399665751484
Ag 14.619331464680650 10.103904999236820 12.895070144622364
Ag 14.619331467291348 10.103904999234961 7.312739871757974
Ag 14.738653296671229 10.103904999357042 10.103905005516358
def agts(queue):
basis = queue.add('lcaotddft_basis.py', ncpus=1, walltime=1)
queue.add('lcaotddft_ag55.py', deps=[basis], ncpus=64, walltime=1)
......@@ -278,10 +278,15 @@ require 5p orbitals in the basis set, and thus, we must generate a custom basis
set.
Here is how to generate a double-zeta basis set with 5p orbital in valence for
Silver for GLLB-SC potential
Silver for GLLB-SC potential. We will use GPAW 0.8 setup definition, since semi-core p states are not relevant here.
.. literalinclude:: lcaotddft_basis.py
We calculate the icosahedral Ag55 cluster: :download:`ag55.xyz`
This code uses ScaLAPACK parallelization with 64 cores.
.. literalinclude:: lcaotddft_ag55.py
Advanced tutorial - large organic molecule
==========================================
......
from ase.io import read
from gpaw.tddft import photoabsorption_spectrum
from gpaw import PoissonSolver
from gpaw.lcaotddft import LCAOTDDFT
from gpaw.occupations import FermiDirac
from gpaw import setup_paths
setup_paths.insert(0,'.')
atoms = read('ag55.xyz')
atoms.center(vacuum=5.0)
# Increase accuragy of density for ground state
convergence = {'density':1e-6}
# Increase accuracy of Poisson Solver and apply multipole corrections up to l=2
poissonsolver = PoissonSolver(eps=1e-14, remove_moment=1+3)
td_calc = LCAOTDDFT(xc='GLLBSC', basis='GLLBSC-dz', h=0.3, nbands=352,
convergence=convergence, poissonsolver=poissonsolver,
occupations=FermiDirac(0.1),
parallel={'sl_default':(8,8,32),'band':2})
atoms.set_calculator(td_calc)
# Relax the ground state
atoms.get_potential_energy()
# For demonstration purposes, save intermediate ground state result to a file
td_calc.write('ag55.gpw', mode='all')
# gpw format does not currently save PoissonSolver, so specify it here again
poissonsolver = PoissonSolver(eps=1e-14, remove_moment=1+3)
td_calc = LCAOTDDFT('ag55.gpw', poissonsolver=poissonsolver,
parallel={'sl_default':(8,8,32), 'band':2})
td_calc.absorption_kick([1e-5, 0.0, 0.0])
td_calc.propagate(20, 500, 'ag55.dm')
photoabsorption_spectrum('ag55.dm','ag55.spec', width=0.2)
......@@ -6,7 +6,7 @@ print "Generating setup with following parameters", args
generator = Generator('Ag', 'GLLBSC')
generator.N *= 2 # Increase grid resolution
generator.run(**args)
bm = BasisMaker(generator, name='GLLBSC', run=False)
bm = BasisMaker(generator, name='GLLBSC-dz', run=False)
basis = bm.generate(zetacount=2, polarizationcount=0,
energysplit=0.07,
jvalues=[0,1,2], # include d, s and p
......
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