def __init__(self,
parameters,
structure=None,
parent_job_dir='.',
job_dir='./cal_lammps',
qadapter=None,
job_cmd='qsub',
wait=True,
is_matrix=False,
turn_knobs=OrderedDict([('STRUCTURES', []),
('PAIR_COEFF', [])]),
checkpoint_file=None,
cal_logger=None):
self.parameters = parameters
self.structure = structure
Calibrate.__init__(self,
None,
None,
None,
None,
parent_job_dir=parent_job_dir,
job_dir=job_dir,
qadapter=qadapter,
job_cmd=job_cmd,
wait=wait,
turn_knobs=turn_knobs,
is_matrix=is_matrix,
checkpoint_file=checkpoint_file,
cal_logger=cal_logger)
def __init__(
self,
parameters,
structure=None,
parent_job_dir=".",
job_dir="./cal_lammps",
qadapter=None,
job_cmd="qsub",
wait=True,
is_matrix=False,
turn_knobs=OrderedDict([("STRUCTURES", []), ("PAIR_COEFF", [])]),
checkpoint_file=None,
cal_logger=None,
):
self.parameters = parameters
self.structure = structure
Calibrate.__init__(
self,
None,
None,
None,
None,
parent_job_dir=parent_job_dir,
job_dir=job_dir,
qadapter=qadapter,
job_cmd=job_cmd,
wait=wait,
turn_knobs=turn_knobs,
is_matrix=is_matrix,
checkpoint_file=checkpoint_file,
cal_logger=cal_logger,
)
def run_cal(turn_knobs, qadapter, job_cmd, job_dir, name,
incar=None, poscar=None, potcar=None, kpoints=None):
"""
setup and run calibrate job
"""
Calibrate.LOG_FILE = name+'.json'
cal = Calibrate(incar, poscar, potcar, kpoints,
turn_knobs=turn_knobs, qadapter=qadapter,
job_cmd = job_cmd, job_dir=job_dir)
cal.setup()
cal.run()
def run_cal(turn_knobs, qadapter, job_cmd, job_dir, checkpoint_file,
incar=None, poscar=None, potcar=None, kpoints=None,
Grid_type='G', functional='PBE', is_matrix=True):
"""
setup and run calibrate job
"""
cal = Calibrate(incar, poscar, potcar, kpoints,
is_matrix=is_matrix,
turn_knobs=turn_knobs, qadapter=qadapter,
job_cmd=job_cmd, job_dir=job_dir,
Grid_type=Grid_type, functional=functional,
checkpoint_file=checkpoint_file, cal_logger=logger)
cal.setup()
cal.run()
def __init__(self, parameters, parent_job_dir='.',
job_dir='./cal_lammps', qadapter=None,
job_cmd='qsub', wait=True,
turn_knobs=OrderedDict([('STRUCTURES',[]),
('PAIR_COEFFS',[])]),
checkpoint_file=None, cal_logger=None):
self.parameters = parameters
Calibrate.__init__(self, None, None, None, None,
parent_job_dir=parent_job_dir,
job_dir=job_dir, qadapter=qadapter,
job_cmd=job_cmd, wait=wait,
turn_knobs = turn_knobs,
checkpoint_file=checkpoint_file,
cal_logger=cal_logger)
def run_cal(turn_knobs,
qadapter,
job_cmd,
job_dir,
checkpoint_file,
incar=None,
poscar=None,
potcar=None,
kpoints=None,
Grid_type='G',
functional='PBE',
is_matrix=True):
"""
setup and run calibrate job
"""
cal = Calibrate(incar,
poscar,
potcar,
kpoints,
is_matrix=is_matrix,
turn_knobs=turn_knobs,
qadapter=qadapter,
job_cmd=job_cmd,
job_dir=job_dir,
Grid_type=Grid_type,
functional=functional,
checkpoint_file=checkpoint_file,
cal_logger=logger)
cal.setup()
cal.run()
def run_cal(turn_knobs,
qadapter,
job_cmd,
job_dir,
logger,
checkpoint_file,
incar_remove=None,
incar=None,
poscar=None,
potcar=None,
kpoints=None,
reuse=None,
Grid_type='G',
pseudopotential='PBE',
is_matrix=True,
cal_type='Cal',
reuse_incar=None,
n_layers=None,
magnetism=False,
database=None,
mappings_override=POTCAR_SPEC):
"""
calibrate job launching function
"""
cal = Calibrate(incar,
poscar,
potcar,
kpoints,
reuse=reuse,
reuse_incar=reuse_incar,
is_matrix=is_matrix,
turn_knobs=turn_knobs,
qadapter=qadapter,
job_cmd=job_cmd,
job_dir=job_dir,
reuse_override=False,
Grid_type=Grid_type,
pseudopotential=pseudopotential,
magnetism=magnetism,
checkpoint_file=checkpoint_file,
cal_logger=logger,
database=database,
mappings_override=mappings_override,
incar_remove=incar_remove)
cal.setup()
cal.run()
turn_knobs = { 'ENCUT' : range(400, 500, 100),
'KPOINTS': [k for k in range(20, 30, 10)]
}
job_dir = 'calBulk'
job_cmd = ['mpirun', '/home/km468/Software/VASP/vasp.5.3.5/vasp']
qparams= dict(nnodes='1', ppnode='16',
job_name='vasp_job', pmem='1000mb',
walltime='24:00:00',
rocket_launch=''.join(job_cmd))
# set qadapter to None to launch via qlaunch
# reserve and launch offline
# qlaunch -r singleshot
# lpad recover_offline
qadapter = None #CommonAdapter(q_type="PBS",**qparams)
cal = Calibrate(incar, poscar, potcar, kpoints,
turn_knobs = turn_knobs,
qadapter = qadapter,
job_dir = job_dir, job_cmd=job_cmd)
caltask = MPINTCalibrateTask(cal.as_dict())
#firework with launch directory set to $FW_JOB_DIR, an environment variable
#spec={'_launch_dir':'$FW_JOB_DIR'},
fw_calibrate = Firework([caltask],
name="fw_test")
wf = Workflow([fw_calibrate], name="mpint_wf_test")
lp = LaunchPad.from_file(LAUNCHPAD_LOC)
print('fireworks in the database before adding the workflow: \n',
lp.get_fw_ids())
lp.add_wf(wf)
print('fireworks in the database: \n', lp.get_fw_ids())
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']
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']
if __name__ == '__main__':
# functions will be run in the order given in the list
steps = [step1, step2, step3]
error_handlers = [VaspErrorHandler()]
# update interval
interval = 300
Calibrate.launch_daemon(steps, interval, error_handlers)