Convert to q2. Step 1

parent 12d731c5
# Creates: C5H12-gpaw.csv
from q2.job import Job
def workflow():
return [
Job('C5H12.agts.py@8x25s')]
def agts(queue):
queue.add('C5H12.agts.py',
walltime=25,
......
# Creates: CO_Au111.csv
from q2.job import Job
def workflow():
return [
Job('CO_Au111.agts.py')]
def agts(queue):
queue.add('CO_Au111.agts.py',
creates=['CO_Au111.csv'])
......
# Creates: Cu_bulk.csv
from q2.job import Job
def workflow():
return [
Job('Cu_bulk.agts.py')]
def agts(queue):
queue.add('Cu_bulk.agts.py',
creates=['Cu_bulk.csv'])
......
# Creates: H2-emt.csv, H2-gpaw.csv
from q2.job import Job
def workflow():
return [
Job('H2.agts.py@8x25s')]
def agts(queue):
queue.add('H2.agts.py',
walltime=25,
......
# Creates: N2Cu-N2.csv, N2Cu-surf.csv
from q2.job import Job
def workflow():
return [
Job('N2Cu_relax.agts.py')]
def agts(queue):
queue.add('N2Cu_relax.agts.py',
creates=['N2Cu-N2.csv', 'N2Cu-surf.csv'])
......
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)]
......
# Creates: g2_dzp.csv
from __future__ import print_function
import numpy as np
import ase.db
......
# Creates: nanoparticle.csv
from q2.job import Job
def workflow():
return [
Job('nanoparticle.agts.py@8x2m')]
def agts(queue):
queue.add('nanoparticle.agts.py',
walltime=2 * 60 + 15,
......
# Creates: neb-emt.csv, neb-gpaw.csv
from q2.job import Job
def workflow():
return [
Job('neb.agts.py@12x15m')]
def agts(queue):
queue.add('neb.agts.py',
walltime=15 * 60,
......
# Creates: hybrid.png
import numpy as np
import pylab as plt
......
# Creates: geom.png
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import patches
......
from q2.job import Job
def workflow():
return [
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,
......
# Creates: cl_field.ind_Ffe.png, qm_field.ind_Ffe.png, tot_field.ind_Ffe.png
# -*- coding: utf-8 -*-
from gpaw.mpi import world
assert world.size == 1, 'This script should be run in serial mode (with one process).'
......
from q2.job import Job
def workflow():
return [
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,
......
# Creates: qsfdtd_vs_mie.png
import numpy as np
import pylab as plt
from ase.units import Hartree, Bohr
......
from q2.job import Job
def workflow():
return [
Job('calculate.py@1x1m'),
Job('plot.py', deps=['calculate.py'])]
def agts(queue):
c1 = queue.add('calculate.py',
walltime=60)
......
# Creates: field.ind_Ffe.png
# -*- coding: utf-8 -*-
from gpaw.mpi import world
assert world.size == 1, 'This script should be run in serial mode (with one process).'
......
from q2.job import Job
def workflow():
return [
Job('calculate.py@1x1m'),
Job('plot.py', deps=['calculate.py'])]
def agts(queue):
c1 = queue.add('calculate.py',
walltime=60)
......
# Creates: Au.yml.png
import numpy as np
import matplotlib.pyplot as plt
from ase.units import _hplanck, _c, _e, Hartree
......
from q2.job import Job
def workflow():
return [
Job('plot_permittivity.py')]
def agts(queue):
queue.add('plot_permittivity.py',
creates=['Au.yml.png'])
from q2.job import Job
def workflow():
return [
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)
......
from q2.job import Job
def workflow():
return [
Job('top.py@8x15s'),
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')
......
# Creates: lcaodos.png
import matplotlib.pyplot as plt
import numpy as np
from ase.io import read
......
# Creates: pdos.png
from gpaw import GPAW, restart
import matplotlib.pyplot as plt
......
# Creates: na2_casida_Ffe.png, na2_casida_Frho.png, na2_casida_Fphi.png
# -*- coding: utf-8 -*-
from gpaw.mpi import world
assert world.size == 1, 'This script should be run in serial mode (with one process).'
......
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('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,
......
# Creates: na2_td_Ffe.png, na2_td_Frho.png, na2_td_Fphi.png
# -*- coding: utf-8 -*-
from gpaw.mpi import world
assert world.size == 1, 'This script should be run in serial mode (with one process).'
......
from q2.job import Job
def workflow():
return [
Job('lcaotddft_basis.py@1x10s'),
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)
......
# Creates: ind_1.12.png, ind_2.48.png
# -*- coding: utf-8 -*-
import numpy as np
import matplotlib.pyplot as plt
......
from q2.job import Job
def workflow():
return [
Job('gs.py@8x10s'),
Job('td.py@8x30s', deps=['gs.py']),
Job('tdc.py@8x30s', deps=['td.py']),
Job('td_replay.py@8x30s', deps=['tdc.py']),
Job('spectrum.py@1x2s', deps=['tdc.py']),
Job('td_fdm_replay.py@1x5s', deps=['tdc.py']),
Job('ksd_init.py@1x5s', deps=['gs.py']),
Job('fdm_ind.py@1x2s', deps=['td_fdm_replay.py']),
Job('spec_plot.py@1x2s', deps=['spectrum.py']),
Job('tcm_plot.py@1x2s', deps=['ksd_init.py', 'td_fdm_replay.py', 'spectrum.py']),
Job('ind_plot.py@1x2s', deps=['fdm_ind.py'])]
def agts(queue):
gs = queue.add('gs.py', ncpus=8, walltime=10)
td0 = queue.add('td.py', deps=[gs], ncpus=8, walltime=30)
......
# Creates: spec.png
# -*- coding: utf-8 -*-
import numpy as np
import matplotlib.pyplot as plt
......
# Creates: tcm_1.12.png, tcm_2.48.png, table_1.12.txt, table_2.48.txt
import numpy as np
from matplotlib import pyplot as plt
......
# Creates: fig1.png
import numpy as np
import matplotlib.pyplot as plt
plt.figure(figsize=(6, 6 / 2 ** 0.5))
......
from q2.job import Job
def workflow():
return [
Job('Be_gs_8bands.py@2x20s'),
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,
......
# Creates: Ag.png
from ase.build import bulk
from gpaw import GPAW
......
from q2.job import Job
def workflow():
return [
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',
......
from q2.job import Job
def workflow():
return [
Job('Na2TDDFT.py@2x1m'),
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,
......
from q2.job import Job
def workflow():
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])
......
from q2.job import Job
def workflow():
return [
Job('water/h2o.py'),
Job('wavefunctions/CO.py@8x15s'),
Job('aluminium/Al_fcc.py@2x15s'),
Job('aluminium/Al_bcc.py@2x15s'),
Job('aluminium/Al_fcc_vs_bcc.py@2x15s'),
Job('aluminium/Al_fcc_modified.py@2x15s'),
Job('diffusion/initial.py@2x15s'),
Job('diffusion/solution.py@2x15s'),
Job('diffusion/densitydiff.py', deps=['diffusion/solution.py']),
Job('wannier/si.py@8x15s'),
Job('wannier/wannier-si.py', deps=['wannier/si.py']),
Job('wannier/benzene.py@8x15s'),
Job('wannier/wannier-benzene.py', deps=['wannier/benzene.py']),
Job('band_structure/ag.py'),
Job('vibrations/h2o.py@8x15s'),
Job('vibrations/H2O_vib.py@8x15s', deps=['vibrations/h2o.py']),
Job('vibrations/H2O_vib_2.py@4x15s', deps=['vibrations/H2O_vib.py']),
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('eels/test.py', deps=['band_structure/ag.py']),
Job('gw/test.py'),
Job('rpa/si.pbe.py'),
Job('rpa/si.pbe+exx.py@4x15s', deps=['rpa/si.pbe.py']),
Job('rpa/si.rpa_init_pbe.py'),
Job('rpa/si.rpa.py@4x15s', deps=['rpa/si.rpa_init_pbe.py']),
Job('stress/con_pw.py'),
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)
......
from q2.job import Job
def workflow():
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])
......
# Creates: atomization.txt
from __future__ import print_function
from ase import Atoms, Atom
......
# Creates: optimization.txt
from __future__ import print_function
from gpaw import restart
......
from q2.job import Job
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'])
......
# Creates: all_electron.csv
from __future__ import print_function
import numpy as np
......
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'])
# Creates: ACF.dat
import subprocess
subprocess.call('bader -p all_atom -p atom_index density.cube'.split())
charges = []
......
# Creates: h2o-bader.png
import os
import pickle
import numpy as np
......
from q2.job import Job
def workflow():
return [
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'])
......
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)
# Creates: bandstructure.png
"""Band structure tutorial
Calculate the band structure of Si along high symmetry directions
......
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'])
......
# Creates: 2d_eps.png
import matplotlib.pyplot as plt
import numpy as np
......
# Creates: bse_MoS2.png
import matplotlib.pyplot as plt
import numpy as np
......
# Creates: bse_Si.png
import matplotlib.pyplot as plt
import numpy as np
......
from q2.job import Job
def workflow():
return [
Job('gs_Si.py@4x20s'),
Job('eps_Si.py@4x4m', deps=['gs_Si.py']),
Job('plot_Si.py@1x10s', deps=['eps_Si.py']),
Job('gs_MoS2.py@4x1m'),
Job('pol_MoS2.py@64x33m', deps=['gs_MoS2.py']),
Job('plot_MoS2.py@1x10s', deps=['pol_MoS2.py']),
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)
......
from q2.job import Job
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)
# Creates: graphene_eps.png
import matplotlib.pyplot as plt
import numpy as np
from ase import Atoms
......
# Creates: silicon_ABS.png
import numpy as np
import matplotlib.pyplot as plt
......
# Creates: graphite_EELS.png
import numpy as np
import matplotlib.pyplot as plt
......
# Creates: aluminum_EELS.png
import numpy as np
import matplotlib.pyplot as plt
......
# Creates: nl_freq_grid.png
import numpy as np
import matplotlib.pyplot as plt
......
# Creates: si_abs.png
import numpy as np
from math import pi
import matplotlib.pyplot as plt
......
# Creates: mac_eps.csv
# Refer to G. Kresse, Phys. Rev. B 73, 045112 (2006)
# for comparison of macroscopic and microscopic dielectric constant
# and absorption peaks.
......
from q2.job import Job
def workflow():
return [
Job('plot_freq.py'),
Job('silicon_ABS_simpleversion.py'),
Job('plot_silicon_ABS_simple.py', deps=['silicon_ABS_simpleversion.py']),
Job('silicon_ABS.py@16x1m'),
Job('plot_ABS.py', deps=['silicon_ABS.py']),
Job('aluminum_EELS.py@8x1m'),
Job('plot_aluminum_EELS_simple.py', deps=['aluminum_EELS.py']),
Job('graphite_EELS.py@8x1m'),
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')
......
# Creates: tas2_eps.png
from __future__ import division
from ase import Atoms
from ase.lattice.hexagonal import Hexagonal
......
# Creates: zero.png, periodic.png, corrected.png, pwcorrected.png, slab.png
import numpy as np
import matplotlib.pyplot as plt
from ase.io import write
......