def step3():
"""
put aligned & relaxed 2d materials in all possible ways on the
aligned & relaxed slab,
relax interface ionic positions(ISIF=2)
- uses info from step2_sub.json and step2_2d.json
- creates required input files and submits the jobs to the que
- 8(pairs) * 2(atoms in graphene basis) = 16 jobs
- returns: step3.json
"""
seperation = 3 # in angstroms
nlayers_2d = 1
nlayers_sub = 2
hkl_sub = [1,1,1]
hkl_2d = [0,0,1]
#job directory for the runs
name = 'step3'
job_dir = 'step3'
# incar
incar = Incar.from_dict(incar_dict)
incar['ISMEAR'] = 1
incar['ISIF'] = 2
# kpoints
kpoints = Kpoints.monkhorst_automatic(kpts=(18, 18, 1))
# load in previous jobs
relaxed_sub_jobs = Calibrate.jobs_from_file('step2_sub.json')
relaxed_2d_jobs = Calibrate.jobs_from_file('step2_2d.json')
# create list of all substrate poscars
all_poscars = []
# loop over aligned & relaxed substrates and 2d
for jsub, j2d in zip(relaxed_sub_jobs,relaxed_2d_jobs):
# substrate
job_dir_sub = os.path.join(jsub.parent_job_dir, jsub.job_dir)
contcar_file = os.path.join(job_dir_sub, 'CONTCAR')
# read in as structure object
substrate_slab_aligned = Structure.from_file(contcar_file)
species_sub = ''.join([tos.symbol for tos in substrate_slab_aligned.types_of_specie])
# 2d
job_dir_2d = os.path.join(j2d.parent_job_dir, j2d.job_dir)
contcar_file = os.path.join(job_dir_2d, 'CONTCAR')
# read in as structure object
mat2d_slab_aligned = Structure.from_file(contcar_file)
species_2d = ''.join([tos.symbol for tos in mat2d_slab_aligned.types_of_specie])
# position the aligned materials in all possible ways
hetero_interfaces = generate_all_configs(mat2d_slab_aligned,
substrate_slab_aligned,
nlayers_2d,
nlayers_sub,
seperation )
# loop over all hetero-interfaces
for i, iface in enumerate(hetero_interfaces):
sd_flags = CalibrateSlab.set_sd_flags(interface=iface,
n_layers=nlayers_2d+nlayers_sub,
top=True, bottom=False)
poscar = Poscar(iface, selective_dynamics=sd_flags)
poscar.comment = '_'.join([species_sub,species_2d,str(i)])
all_poscars.append(poscar)
# setup calibrate and run'em
turn_knobs = OrderedDict(
[
('POSCAR', all_poscars)
])
qadapter, job_cmd = get_run_cmmnd(nnodes=nnodes, nprocs=nprocs,
walltime=walltime,
job_bin=bin_sub, mem=mem)
run_cal(turn_knobs, qadapter, job_cmd, job_dir,
name, incar=incar, kpoints=kpoints)
return [name+'.json']
def step2():
"""
read in the realxed bulk substrates and relaxed 2d,
create substrate slab,
get aligned substrates and 2d,
relax the aligned structures seperatly(only ionic positions, ISIF=2)
- input from step1_sub.json and step1_2d.json
- 8(pairs) * 2 = 16 jobs
- returns step2.json
"""
nlayers_2d = 1
nlayers_sub = 2
hkl_sub = [1,1,1]
min_thick = 10.0
min_vac = 18.0
hkl_2d = [0,0,1]
#job directory for the runs
job_dir_sub = 'step2_sub'
job_dir_2d = 'step2_2d'
# isif = 2
incar_sub['ISIF'] = 2
incar_2d['ISIF'] = 2
# kpoints
kpoints_sub = Kpoints.monkhorst_automatic(kpts=(18, 18, 1))
kpoints_2d = Kpoints.monkhorst_automatic(kpts=(18, 18, 1))
# CSL settings for each substrate
alignment_settings = { 'Pt': [120, 0.10, 1, 0.5],
'Ag': [120, 0.10, 1, 0.5],
'Al': [120, 0.10, 1, 0.5],
'Au': [120, 0.10, 1, 0.5],
'Pd': [120, 0.10, 1, 0.5],
'Ir': [120, 0.10, 1, 0.5],
'Cu': [50, 0.06, 1, 0.5],
'Ni': [50, 0.06, 1, 0.5] }
# load in previous jobs
relaxed_sub_jobs = Calibrate.jobs_from_file('step1_sub.json')
relaxed_2d_jobs = Calibrate.jobs_from_file('step1_2d.json')
poscars_sub = []
poscars_2d = []
# create list of all aligned substrate and 2d slabs
for jsub in relaxed_sub_jobs:
jdir = os.path.join(jsub.parent_job_dir, jsub.job_dir)
contcar_file = os.path.join(jdir, 'CONTCAR')
relaxed_struct_sub = Structure.from_file(contcar_file)
# create slab
slab_sub = Interface(relaxed_struct_sub, hkl = hkl_sub,
min_thick = min_thick, min_vac = min_vac,
primitive = False, from_ase = True)
species_sub = ''.join([tos.symbol for tos in slab_sub.types_of_specie])
# loop over 2d
for j2d in relaxed_2d_jobs:
jdir = os.path.join(j2d.parent_job_dir, j2d.job_dir)
contcar_file = os.path.join(jdir, 'CONTCAR')
slab_2d = slab_from_file(hkl_2d, contcar_file)
species_2d = ''.join([tos.symbol for tos in slab_2d.types_of_specie])
# align
slab_sub_aligned, slab_2d_aligned = get_aligned_lattices(
slab_sub,
slab_2d,
*alignment_settings[species_sub])
# aligned sub poscar
sd_flags = CalibrateSlab.set_sd_flags(interface=slab_sub_aligned,
n_layers=nlayers_sub)
poscar = Poscar(slab_sub_aligned, selective_dynamics=sd_flags)
poscar.comment = '_'.join([species_sub,species_2d,'sub'])
poscars_sub.append(poscar)
# aligned 2d slab
sd_flags = CalibrateSlab.set_sd_flags(interface=slab_2d_aligned,
n_layers=nlayers_2d)
poscar = Poscar(slab_2d_aligned, selective_dynamics=sd_flags)
poscar.comment = '_'.join([species_sub,species_2d,'2d'])
poscars_2d.append(poscar)
# setup calibrate and run'em
turn_knobs_sub = OrderedDict(
[
('POSCAR', poscars_sub)
])
turn_knobs_2d = OrderedDict(
[
('POSCAR', poscars_2d)
])
qadapter, job_cmd = get_run_cmmnd(nnodes=nnodes, nprocs=nprocs,
walltime=walltime,
job_bin=bin_sub, mem=mem)
run_cal(turn_knobs_sub, qadapter, job_cmd, job_dir_sub,
'step2_sub', incar=incar_sub, kpoints=kpoints_sub)
run_cal(turn_knobs_2d, qadapter, job_cmd, job_dir_2d,
'step2_2d', incar=incar_2d, kpoints=kpoints_2d)
return ['step2_sub.json', 'step2_2d.json']
