Convert to q2. Step 2

parent d5008e05
Pipeline #20645868 failed with stage
in 88 minutes and 59 seconds
# Creates: C5H12-gpaw.csv
from q2.job import Job
def workflow():
from q2.job import Job
return [
Job('C5H12.agts.py@8x25s')]
def agts(queue):
queue.add('C5H12.agts.py',
walltime=25,
ncpus=8,
creates=['C5H12-gpaw.csv'])
if __name__ == "__main__":
if __name__ == '__main__':
from ase.optimize.test.C5H12 import *
# Creates: CO_Au111.csv
from q2.job import Job
def workflow():
from q2.job import Job
return [
Job('CO_Au111.agts.py')]
def agts(queue):
queue.add('CO_Au111.agts.py',
creates=['CO_Au111.csv'])
if __name__ == "__main__":
if __name__ == '__main__':
from ase.optimize.test.CO_Au111 import *
# Creates: Cu_bulk.csv
from q2.job import Job
def workflow():
from q2.job import Job
return [
Job('Cu_bulk.agts.py')]
def agts(queue):
queue.add('Cu_bulk.agts.py',
creates=['Cu_bulk.csv'])
if __name__ == "__main__":
if __name__ == '__main__':
from ase.optimize.test.Cu_bulk import *
# Creates: H2-emt.csv, H2-gpaw.csv
from q2.job import Job
def workflow():
from q2.job import Job
return [
Job('H2.agts.py@8x25s')]
def agts(queue):
queue.add('H2.agts.py',
walltime=25,
ncpus=8,
creates=['H2-emt.csv', 'H2-gpaw.csv'])
if __name__ == "__main__":
if __name__ == '__main__':
from ase.optimize.test.H2 import *
# Creates: N2Cu-N2.csv, N2Cu-surf.csv
from q2.job import Job
def workflow():
from q2.job import Job
return [
Job('N2Cu_relax.agts.py')]
def agts(queue):
queue.add('N2Cu_relax.agts.py',
creates=['N2Cu-N2.csv', 'N2Cu-surf.csv'])
if __name__ == "__main__":
if __name__ == '__main__':
from ase.optimize.test.N2Cu_relax import *
......@@ -2,20 +2,5 @@ from q2.job import Job
def workflow():
return [
Job('g2_dzp.py 0@4x13m'),
Job('g2_dzp.py 1@4x13m'),
Job('g2_dzp.py 2@4x13m'),
Job('g2_dzp.py 3@4x13m'),
Job('g2_dzp.py 4@4x13m'),
Job('g2_dzp.py 5@4x13m'),
Job('g2_dzp.py 6@4x13m'),
Job('g2_dzp.py 7@4x13m'),
Job('g2_dzp.py 8@4x13m'),
Job('g2_dzp.py 9@4x13m'),
Job('g2_dzp_csv.py', deps=['g2_dzp.py 0', 'g2_dzp.py 1', 'g2_dzp.py 2', 'g2_dzp.py 3', 'g2_dzp.py 4', 'g2_dzp.py 5', 'g2_dzp.py 6', 'g2_dzp.py 7', 'g2_dzp.py 8', 'g2_dzp.py 9'])]
def agts(queue):
jobs = [queue.add('g2_dzp.py ' + str(i), ncpus=4, walltime=800)
for i in range(10)]
queue.add('g2_dzp_csv.py', deps=jobs, creates='g2_dzp.csv')
jobs = [Job('g2_dzp.py+{}@4x13m'.format(i)) for i in range(10)]
return jobs + [Job('g2_dzp_csv.py', deps=jobs)]
# Creates: nanoparticle.csv
from q2.job import Job
def workflow():
from q2.job import Job
return [
Job('nanoparticle.agts.py@8x2m')]
def agts(queue):
queue.add('nanoparticle.agts.py',
walltime=2 * 60 + 15,
ncpus=8,
creates=['nanoparticle.csv'])
if __name__ == "__main__":
if __name__ == '__main__':
from ase.optimize.test.nanoparticle import *
# Creates: neb-emt.csv, neb-gpaw.csv
from q2.job import Job
def workflow():
from q2.job import Job
return [
Job('neb.agts.py@12x15m')]
def agts(queue):
queue.add('neb.agts.py',
walltime=15 * 60,
ncpus=12,
creates=['neb-emt.csv', 'neb-gpaw.csv'])
if __name__ == '__main__':
from ase.optimize.test.neb import *
......@@ -6,16 +6,3 @@ def workflow():
Job('calculate.py@8x1m'),
Job('plot_geom.py', deps=['calculate.py']),
Job('plot.py', deps=['calculate.py'])]
def agts(queue):
c1 = queue.add('calculate.py',
ncpus=8,
walltime=60)
queue.add('plot_geom.py',
deps=c1,
creates=['geom.png'])
queue.add('plot.py',
deps=[c1],
creates=['hybrid.png'])
......@@ -6,18 +6,3 @@ def workflow():
Job('calculate.py@8x1m'),
Job('postprocess.py@8x10s', deps=['calculate.py']),
Job('plot.py', deps=['postprocess.py'])]
def agts(queue):
c1 = queue.add('calculate.py',
ncpus=8,
walltime=60)
c2 = queue.add('postprocess.py',
ncpus=8,
walltime=10,
deps=c1)
queue.add('plot.py',
deps=c2,
creates=['cl_field.ind_Ffe.png', 'qm_field.ind_Ffe.png',
'tot_field.ind_Ffe.png'])
......@@ -5,11 +5,3 @@ def workflow():
return [
Job('calculate.py@1x1m'),
Job('plot.py', deps=['calculate.py'])]
def agts(queue):
c1 = queue.add('calculate.py',
walltime=60)
queue.add('plot.py',
deps=c1,
creates=['qsfdtd_vs_mie.png'])
......@@ -5,11 +5,3 @@ def workflow():
return [
Job('calculate.py@1x1m'),
Job('plot.py', deps=['calculate.py'])]
def agts(queue):
c1 = queue.add('calculate.py',
walltime=60)
queue.add('plot.py',
deps=c1,
creates=['field.ind_Ffe.png'])
......@@ -4,7 +4,3 @@ from q2.job import Job
def workflow():
return [
Job('plot_permittivity.py')]
def agts(queue):
queue.add('plot_permittivity.py',
creates=['Au.yml.png'])
......@@ -6,9 +6,3 @@ def workflow():
Job('basisgeneration.py@1x10s'),
Job('lcao_h2o.py@1x10s'),
Job('lcao_opt.py@1x10s')]
def agts(queue):
queue.add('basisgeneration.py', ncpus=1, walltime=10)
queue.add('lcao_h2o.py', ncpus=1, walltime=10)
queue.add('lcao_opt.py', ncpus=1, walltime=10)
......@@ -7,10 +7,3 @@ def workflow():
Job('pdos.py', deps=['top.py']),
Job('lcaodos_gs.py@8x15s'),
Job('lcaodos_plt.py', deps=['lcaodos_gs.py'])]
def agts(queue):
top = queue.add('top.py', ncpus=8)
queue.add('pdos.py', deps=top, creates='pdos.png')
calc = queue.add('lcaodos_gs.py', ncpus=8)
queue.add('lcaodos_plt.py', deps=calc, creates='lcaodos.png')
......@@ -4,46 +4,12 @@ from q2.job import Job
def workflow():
return [
Job('timepropagation_calculate.py@8x1m'),
Job('timepropagation_continue.py@8x1m', deps=['timepropagation_calculate.py']),
Job('timepropagation_postprocess.py@8x5s', deps=['timepropagation_continue.py']),
Job('timepropagation_plot.py@1x5s', deps=['timepropagation_postprocess.py']),
Job('timepropagation_continue.py@8x1m',
deps=['timepropagation_calculate.py']),
Job('timepropagation_postprocess.py@8x5s',
deps=['timepropagation_continue.py']),
Job('timepropagation_plot.py@1x5s',
deps=['timepropagation_postprocess.py']),
Job('casida_calculate.py@8x1m'),
Job('casida_postprocess.py@8x5s', deps=['casida_calculate.py']),
Job('casida_plot.py@1x5s', deps=['casida_postprocess.py'])]
def agts(queue):
calc1 = queue.add('timepropagation_calculate.py',
ncpus=8,
walltime=60)
calc2 = queue.add('timepropagation_continue.py',
ncpus=8,
walltime=60,
deps=calc1)
calc3 = queue.add('timepropagation_postprocess.py',
ncpus=8,
walltime=5,
deps=calc2)
calc4 = queue.add('timepropagation_plot.py',
ncpus=1,
walltime=5,
deps=calc3,
creates=['na2_td_Ffe.png', 'na2_td_Frho.png', 'na2_td_Fphi.png'])
calc5 = queue.add('casida_calculate.py',
ncpus=8,
walltime=60)
calc6 = queue.add('casida_postprocess.py',
ncpus=8,
walltime=5,
deps=calc5)
calc7 = queue.add('casida_plot.py',
ncpus=1,
walltime=5,
deps=calc6,
creates=['na2_casida_Ffe.png', 'na2_casida_Frho.png', 'na2_casida_Fphi.png'])
......@@ -7,9 +7,3 @@ def workflow():
Job('lcaotddft_ag55.py@48x1m', deps=['lcaotddft_basis.py']),
Job('lcaotddft_fig1.py', deps=['lcaotddft_ag55.py']),
Job('lcaotddft.py@4x40s')]
def agts(queue):
basis = queue.add('lcaotddft_basis.py', ncpus=1, walltime=10)
ag55 = queue.add('lcaotddft_ag55.py', deps=[basis], ncpus=48, walltime=100)
queue.add('lcaotddft_fig1.py', deps=[ag55], creates='fig1.png')
queue.add('lcaotddft.py', ncpus=4, walltime=40)
......@@ -7,19 +7,3 @@ def workflow():
Job('Be_8bands_lrtddft.py@2x20s', deps=['Be_gs_8bands.py']),
Job('Be_8bands_lrtddft_dE.py@2x20s', deps=['Be_gs_8bands.py']),
Job('Na2_relax_excited.py@4x8m')]
def agts(queue):
calc1 = queue.add('Be_gs_8bands.py',
ncpus=2,
walltime=20)
queue.add('Be_8bands_lrtddft.py',
ncpus=2,
walltime=20,
deps=calc1)
queue.add('Be_8bands_lrtddft_dE.py',
ncpus=2,
walltime=20,
deps=calc1)
queue.add('Na2_relax_excited.py',
ncpus=4,
walltime=500)
from q2.job import Job
def workflow():
from q2.job import Job
return [
Job('dos.agts.py', deps=['../iron/PBE.py', '../wavefunctions/CO.py', '../wannier/si.py', '../aluminium/Al_fcc.py'])]
Job('dos.agts.py',
deps=['../iron/PBE.py', '../wavefunctions/CO.py',
'../wannier/si.py', '../aluminium/Al_fcc.py'])]
def agts(queue):
queue.add('dos.agts.py', ncpus=1,
deps=['../iron/PBE.py',
'../wavefunctions/CO.py',
'../wannier/si.py',
'../aluminium/Al_fcc.py'])
if __name__ == '__main__':
import os
......
......@@ -7,11 +7,3 @@ def workflow():
Job('part2.py', deps=['Na2TDDFT.py']),
Job('ground_state.py@8x15s'),
Job('spectrum.py', deps=['ground_state.py'])]
def agts(queue):
calc1 = queue.add('Na2TDDFT.py',
ncpus=2,
walltime=60)
queue.add('part2.py', deps=calc1)
gs = queue.add('ground_state.py', ncpus=8)
queue.add('spectrum.py', deps=gs)
from q2.job import Job
def workflow():
from q2.job import Job
return [
Job('HAl100.py'),
Job('stm.agts.py', deps=['HAl100.py'])]
def agts(queue):
job = queue.add('HAl100.py')
queue.add('stm.agts.py', ncpus=1, deps=[job])
if __name__ == '__main__':
import sys
......
......@@ -23,7 +23,8 @@ def workflow():
Job('iron/ferro.py@4x15s'),
Job('iron/anti.py@4x15s'),
Job('iron/non.py@2x15s'),
Job('iron/PBE.py', deps=['iron/ferro.py', 'iron/anti.py', 'iron/non.py']),
Job('iron/PBE.py',
deps=['iron/ferro.py', 'iron/anti.py', 'iron/non.py']),
Job('eels/test.py', deps=['band_structure/ag.py']),
Job('gw/test.py'),
Job('rpa/si.pbe.py'),
......@@ -34,38 +35,5 @@ def workflow():
Job('stress/stress.py'),
Job('transport/pt_h2_tb_transport.py'),
Job('transport/pt_h2_lcao_manual.py'),
Job('transport/pt_h2_lcao_transport.py', deps=['transport/pt_h2_lcao_manual.py'])]
def agts(queue):
queue.add('water/h2o.py', ncpus=1)
queue.add('wavefunctions/CO.py', ncpus=8)
queue.add('aluminium/Al_fcc.py', ncpus=2)
queue.add('aluminium/Al_bcc.py', ncpus=2)
queue.add('aluminium/Al_fcc_vs_bcc.py', ncpus=2)
queue.add('aluminium/Al_fcc_modified.py', ncpus=2)
queue.add('diffusion/initial.py', ncpus=2)
sol = queue.add('diffusion/solution.py', ncpus=2)
queue.add('diffusion/densitydiff.py', deps=[sol])
si = queue.add('wannier/si.py', ncpus=8)
queue.add('wannier/wannier-si.py', deps=[si])
benzene = queue.add('wannier/benzene.py', ncpus=8)
queue.add('wannier/wannier-benzene.py', deps=[benzene])
band = queue.add('band_structure/ag.py', ncpus=1, creates='Ag.png')
h2o = queue.add('vibrations/h2o.py', ncpus=8)
h2ovib = queue.add('vibrations/H2O_vib.py', ncpus=8, deps=[h2o])
queue.add('vibrations/H2O_vib_2.py', ncpus=4, deps=[h2ovib])
ferro = queue.add('iron/ferro.py', ncpus=4)
anti = queue.add('iron/anti.py', ncpus=4)
non = queue.add('iron/non.py', ncpus=2)
queue.add('iron/PBE.py', deps=[ferro, anti, non])
queue.add('eels/test.py', deps=band)
queue.add('gw/test.py')
rpa_si_exxgs = queue.add('rpa/si.pbe.py')
queue.add('rpa/si.pbe+exx.py', deps=rpa_si_exxgs, ncpus=4)
rpa_si_rpags = queue.add('rpa/si.rpa_init_pbe.py')
queue.add('rpa/si.rpa.py', deps=rpa_si_rpags, ncpus=4)
queue.add('stress/con_pw.py', ncpus=1)
queue.add('stress/stress.py', ncpus=1)
queue.add('transport/pt_h2_tb_transport.py')
t1 = queue.add('transport/pt_h2_lcao_manual.py')
queue.add('transport/pt_h2_lcao_transport.py', deps=t1)
Job('transport/pt_h2_lcao_transport.py',
deps=['transport/pt_h2_lcao_manual.py'])]
from q2.job import Job
def workflow():
from q2.job import Job
return [
Job('surface.agts.py'),
Job('work_function.py', deps=['surface.agts.py'])]
def agts(queue):
al = queue.add('surface.agts.py')
queue.add('work_function.py', ncpus=1, deps=[al])
if __name__ == '__main__':
exec(open('Al100.py').read(), {'k': 6, 'N': 5})
......@@ -5,12 +5,3 @@ def workflow():
return [
Job('atomize.py@1x30s'),
Job('relax.py@1x30s', deps=['atomize.py'])]
def agts(queue):
a = queue.add('atomize.py', ncpus=1, walltime=30,
creates=['atomization.txt'])
queue.add('relax.py', deps=a, ncpus=1, walltime=30,
creates=['optimization.txt'])
if 0: # https://trac.fysik.dtu.dk/projects/gpaw/ticket/250
queue.add('ensembles.py', deps=a, ncpus=1, walltime=30,
creates=['ensemble_energies.txt', 'ensemble.dat'])
......@@ -4,7 +4,3 @@ from q2.job import Job
def workflow():
return [
Job('NaCl.py@1x30s')]
def agts(queue):
queue.add('NaCl.py', ncpus=1, walltime=30, creates=['all_electron.csv'])
......@@ -6,8 +6,3 @@ def workflow():
Job('h2o.py'),
Job('bader.py', deps=['h2o.py']),
Job('plot.py', deps=['bader.py'])]
def agts(queue):
h2o = queue.add('h2o.py')
bader = queue.add('bader.py', deps=h2o, creates=['ACF.dat'])
queue.add('plot.py', deps=bader, creates=['h2o-bader.png'])
......@@ -4,6 +4,3 @@ from q2.job import Job
def workflow():
return [
Job('gllbsc_band_gap.py@1x30s')]
def agts(queue):
queue.add('gllbsc_band_gap.py', ncpus=1, walltime=30)
......@@ -4,8 +4,3 @@ from q2.job import Job
def workflow():
return [
Job('bandstructure.py@1x5s')]
def agts(queue):
queue.add('bandstructure.py', ncpus=1, walltime=5,
creates=['bandstructure.png'])
......@@ -12,20 +12,3 @@ def workflow():
Job('get_2d_eps.py@1x8m', deps=['gs_MoS2.py']),
Job('plot_2d_eps.py@1x10s', deps=['get_2d_eps.py']),
Job('alpha_MoS2.py@1x10s', deps=['gs_MoS2.py'])]
def agts(queue):
gs_si = queue.add('gs_Si.py', ncpus=4, walltime=20)
bse_si = queue.add('eps_Si.py', ncpus=4, walltime=240, deps=gs_si)
queue.add('plot_Si.py', ncpus=1, walltime=10, deps=bse_si,
creates='bse_Si.png')
gs_mos2 = queue.add('gs_MoS2.py', ncpus=4, walltime=100)
bse_mos2 = queue.add('pol_MoS2.py', ncpus=64, walltime=2000, deps=gs_mos2)
queue.add('plot_MoS2.py', ncpus=1, walltime=10, deps=bse_mos2,
creates='bse_MoS2.png')
eps = queue.add('get_2d_eps.py', ncpus=1, walltime=500, deps=gs_mos2)
queue.add('plot_2d_eps.py', ncpus=1, walltime=10, deps=eps,
creates='2d_eps.png')
queue.add('alpha_MoS2.py', ncpus=1, walltime=10, deps=gs_mos2)
......@@ -5,7 +5,3 @@ def workflow():
return [
Job('ethanol_in_water.py@4x10s'),
Job('check.py', deps=['ethanol_in_water.py'])]
def agts(queue):
h2o = queue.add('ethanol_in_water.py', ncpus=4, walltime=10)
queue.add('check.py', deps=h2o)
......@@ -14,26 +14,3 @@ def workflow():
Job('plot_EELS.py', deps=['graphite_EELS.py']),
Job('tas2_dielectric_function.py@8x15s'),
Job('graphene_dielectric_function.py@8x15s')]
def agts(queue):
queue.add('plot_freq.py', creates='nl_freq_grid.png')
simple_si = queue.add('silicon_ABS_simpleversion.py')
queue.add('plot_silicon_ABS_simple.py', creates='si_abs.png',
deps=simple_si)
si = queue.add('silicon_ABS.py', creates='mac_eps.csv',
ncpus=16, walltime=100)
queue.add('plot_ABS.py', deps=si, creates='silicon_ABS.png')
al = queue.add('aluminum_EELS.py', ncpus=8, walltime=100)
queue.add('plot_aluminum_EELS_simple.py', deps=al,
creates=['aluminum_EELS.png'])
GR = queue.add('graphite_EELS.py', ncpus=8, walltime=100)
queue.add('plot_EELS.py', deps=GR, creates='graphite_EELS.png')
queue.add('tas2_dielectric_function.py', ncpus=8, creates='tas2_eps.png')
queue.add('graphene_dielectric_function.py', ncpus=8,
creates='graphene_eps.png')
......@@ -7,11 +7,3 @@ def workflow():
Job('pwdipole.py'),
Job('plot.py', deps=['dipole.py', 'pwdipole.py']),
Job('check.py', deps=['dipole.py', 'pwdipole.py'])]
def agts(queue):
d = [queue.add('dipole.py', ncpus=4, walltime=60),
queue.add('pwdipole.py')]
queue.add('plot.py', deps=d,
creates=['zero.png', 'periodic.png', 'corrected.png',
'pwcorrected.png', 'slab.png'])
queue.add('check.py', deps=d)
......@@ -15,21 +15,3 @@ def workflow():
Job('MoS2_GWG.py@8x20s', deps=['MoS2_gs_GW.py']),
Job('MoS2_bs_plot.py', deps=['MoS2_GWG.py']),
Job('check_gw.py', deps=['MoS2_GWG.py'])]
def agts(queue):
conv = queue.add('C_ecut_k_conv_GW.py', ncpus=8, walltime=20 * 60)
queue.add('C_ecut_k_conv_plot_GW.py', deps=conv, creates='C_GW.png')
queue.add('C_ecut_extrap.py', deps=conv, creates='C_GW_k8_extrap.png')
freq = queue.add('C_frequency_conv.py', walltime=30)
queue.add('C_frequency_conv_plot.py', deps=freq, creates='C_freq.png')
queue.add('C_equal_test.py', deps=[conv, freq])
bn = queue.add('BN_GW0.py', walltime=70)
queue.add('BN_GW0_plot.py', deps=bn, creates='BN_GW0.png')
mos2 = queue.add('MoS2_gs_GW.py', walltime=70)
mos2_gwg = queue.add('MoS2_GWG.py', deps=mos2, ncpus=8, walltime=20)
queue.add('MoS2_bs_plot.py', deps=mos2_gwg, creates='MoS2_bs.png')
queue.add('check_gw.py', deps=mos2_gwg)
......@@ -6,9 +6,3 @@ def workflow():
Job('nio.py'),
Job('n.py'),
Job('check.py', deps=['n.py'])]
def agts(queue):
queue.add('nio.py')
n = queue.add('n.py')
queue.add('check.py', deps=n, creates='gaps.csv')
# Creates: h.png
from q2.job import Job
def workflow():
from q2.job import Job
return [
Job('h.py'),
Job('h.agts.py', deps=['h.py'])]
def agts(queue):
ae = queue.add('h.py')
queue.add('h.agts.py', deps=ae, creates='h.png')
if __name__ == '__main__':
import numpy as np
......
......@@ -7,9 +7,3 @@ def workflow():
Job('surface.py@4x6s'),
Job('sigma.py', deps=['bulk.py', 'surface.py']),
Job('fig2.py', deps=['sigma.py'])]
def agts(queue):
bulk = queue.add('bulk.py', ncpus=4, walltime=6)
surf = queue.add('surface.py', ncpus=4, walltime=6)
sigma = queue.add('sigma.py', deps=[bulk, surf])
queue.add('fig2.py', deps=sigma, creates='fig2.png')
......@@ -5,7 +5,3 @@ def workflow():
return [
Job('mnsi.py'),
Job('plot2d.py', deps=['mnsi.py'])]
def agts(queue):
mnsi = queue.add('mnsi.py')
queue.add('plot2d.py', deps=mnsi, creates='pot_contour.png')
......@@ -6,9 +6,3 @@ def workflow():
Job('diffusion1.py@4x10s'),
Job('neb.py@12x1m', deps=['diffusion1.py']),
Job('check.py', deps=['neb.py'])]
def agts(queue):
d = queue.add('diffusion1.py', ncpus=4, walltime=10)
n = queue.add('neb.py', deps=d, ncpus=12, walltime=60)
queue.add('check.py', deps=n)
......@@ -6,8 +6,3 @@ def workflow():
Job('gaps.py'),
Job('eos.py@4x10m'),
Job('plot_a.py', deps=['eos.py'])]
def agts(queue):
queue.add('gaps.py', creates='si-gaps.csv')
eos = queue.add('eos.py', ncpus=4, walltime=600)
queue.add('plot_a.py', deps=eos, creates='si-a.png')
......@@ -6,8 +6,3 @@ def workflow():
Job('CO.py@1x10s'),
Job('CO2cube.py@1x10s', deps=['CO.py']),
Job('CO2plt.py@1x10s', deps=['CO.py'])]
def agts(queue):
d = queue.add('CO.py', ncpus=1, walltime=10)
queue.add('CO2cube.py', deps=d, ncpus=1, walltime=10)
queue.add('CO2plt.py', deps=d, ncpus=1, walltime=10)
......@@ -9,16 +9,3 @@ def workflow():
Job('bb_WSe2.py@16x20m', deps=['gs_WSe2.py']),
Job('interpolate_bb.py', deps=['bb_MoS2.py', 'bb_WSe2.py']),
Job('interlayer.py', deps=['interpolate_bb.py'])]
def agts(queue):
gs_MoS2 = queue.add('gs_MoS2.py', ncpus=16, walltime=25)