def perturb_wf_setup(perovskite,
structure_type='111',
Nstruct=100,
perturbamnt=None,
max_strain=0.06,
nimages=8,
tags=[]):
if perturbamnt is None:
perturbamnt = perovskite.lattconst * 0.04
print(
"Setting up {} different perturbation polarization approaches\nMax strain = {}, "
"Perturbation amount = {}".format(Nstruct, max_strain, perturbamnt))
allowed_struct_type = ['111', '211', 's2s21', 's2s22']
if structure_type not in allowed_struct_type:
raise ValueError("{} not in {}".format(structure_type,
allowed_struct_type))
fws = []
pert_N_structs = [
perovskite.get_struct_from_structure_type(structure_type).as_dict()
]
user_incar_settings = {"ADDGRID": True, 'EDIFF': 1e-8, "NELMIN": 6}
for nind in range(Nstruct):
sclass = PerfectPerovskite(Asite=perovskite.eltA,
Bsite=perovskite.eltB,
Osite=perovskite.eltC,
lattconst=perovskite.lattconst)
strain_class = StrainedPerovskite.generate_random_strain(
sclass,
structure_type=structure_type,
max_strain=max_strain,
perturb_amnt=perturbamnt)
tmp_wf = polarization_wf(strain_class.structure,
strain_class.base,
submit=False,
nimages=nimages,
user_incar_settings=user_incar_settings,
tags=tags)
fws.extend(tmp_wf.fws)
pert_N_structs.append(strain_class.structure.as_dict())
print("Submitting Polarization workflow with {} fireworks".format(
len(fws)))
wf = Workflow(fws)
lp = LaunchPad().from_file(lpad_file_path)
lp.add_wf(wf)
def born():
fw = Firework(
[
Cry(),
Eat(),
Sleep(),
Poop(),
],
spec={"name": "BabyJain"}
)
launchpad = LaunchPad()
launchpad.add_wf(Workflow([fw]))
def polarization_wf(polar_structure,
nonpolar_structure,
submit=False,
nimages=8,
user_incar_settings={},
tags=[]):
"""
:param polar_structure: structure of polar structure
:param nonpolar_structure: structure of nonpolar structure
:param submit: boolean for submitting
:param tags: list of string tags
:return:
"""
if polar_structure.species != nonpolar_structure.species:
raise ValueError("WRONG ORDER OF SPECIES: {} vs {}".format(
polar_structure.species, nonpolar_structure.species))
vasp_input_set_params = {'user_incar_settings': user_incar_settings}
wf = get_wf_ferroelectric(
polar_structure,
nonpolar_structure,
vasp_cmd=">>vasp_cmd<<",
db_file='>>db_file<<',
vasp_input_set_polar="MPStaticSet",
vasp_input_set_nonpolar="MPStaticSet",
relax=False,
vasp_relax_input_set_polar=vasp_input_set_params,
vasp_relax_input_set_nonpolar=vasp_input_set_params,
nimages=nimages,
hse=False,
add_analysis_task=True,
tags=tags)
print('workflow created with {} fws'.format(len(wf.fws)))
if submit:
print("\tSubmitting Polarization workflow")
lp = LaunchPad().from_file(lpad_file_path)
lp.add_wf(wf)
else:
return wf
def generate_lattconst_wf(list_elt_sets,
functional='PBE',
vasp_cmd='>>vasp_cmd<<',
db_file='>>db_file<<',
submit=False,
scan_smart_lattice=None):
"""Generates a workflow which calculates lattice constants
through optimization fireworks for a given functional type
NOTE: that the SCAN functionality might be reliant on some Custodian features from Danny's Custodian
"""
if functional in ['PBE', 'LDA']:
job_type = 'double_relaxation_run'
potcar_type = functional
incar_settings = {"ADDGRID": True, 'EDIFF': 1e-8}
elif functional in ['SCAN']:
job_type = 'metagga_opt_run'
potcar_type = 'PBE' #this is the POTCAR that needs to be used for SCAN...
incar_settings = {'EDIFF': 1e-8, 'ISIF': 7}
if scan_smart_lattice is None:
raise ValueError("Need to provide a smarter starting point "
"for SCAN lattice constants...")
fws = []
for elt_set in list_elt_sets:
if functional == 'SCAN':
compkey = Composition({
elt_set[0]: 1,
elt_set[1]: 1,
elt_set[2]: 3
})
lattconst = scan_smart_lattice[compkey]
else:
lattconst = None
pp = PerfectPerovskite(Asite=elt_set[0],
Bsite=elt_set[1],
Osite=elt_set[2],
lattconst=lattconst)
s = pp.get_111_struct()
vis = MPRelaxSet(s,
user_incar_settings=incar_settings,
potcar_functional=potcar_type)
fw = OptimizeFW(s,
name="{} {} structure optimization".format(
s.composition.reduced_formula, functional),
vasp_input_set=vis,
vasp_cmd=vasp_cmd,
db_file=db_file,
job_type=job_type,
auto_npar=">>auto_npar<<")
fws.append(fw)
wf = Workflow(fws, name='{} latt const workflow'.format(functional))
if submit:
print('Submitting workflow with {} fws for {}'.format(
len(list_elt_sets), functional))
lpad = LaunchPad().from_file(lpad_file_path)
lpad.add_wf(wf)
else:
print('Workflow created with {} fws for {}'.format(
len(list_elt_sets), functional))
return wf
"""
This code is described in the Dynamic Workflow tutorial, https://materialsproject.github.io/fireworks/dynamic_wf_tutorial.html
"""
from fireworks import ScriptTask
from fireworks.core.firework import Firework, Workflow
from fireworks.core.launchpad import LaunchPad
from fireworks.core.rocket_launcher import rapidfire
from fw_tutorials.dynamic_wf.printjob_task import PrintJobTask
if __name__ == "__main__":
# set up the LaunchPad and reset it
launchpad = LaunchPad()
# launchpad.reset('', require_password=False)
# create the Workflow that passes job info
fw1 = Firework([ScriptTask.from_str('echo "This is the first FireWork"')],
spec={"_pass_job_info": True},
fw_id=1)
fw2 = Firework([PrintJobTask()], parents=[fw1], fw_id=2)
wf = Workflow([fw1, fw2])
# store workflow and launch it locally
launchpad.add_wf(wf)
rapidfire(launchpad)
elif args.command == 'detect_fizzled':
# TODO: report when fixed
print lp.detect_fizzled(args.time, args.fix)
elif args.command == 'detect_unreserved':
# TODO: report when fixed
print lp.detect_unreserved(args.time, args.fix)
elif args.command == 'add':
# TODO: make this cleaner, e.g. make TAR option explicit
# fwf = Workflow.from_FireWork(FireWork.from_file(args.wf_file))
# lp.add_wf(fwf)
try:
fwf = Workflow.from_FireWork(FireWork.from_file(args.wf_file))
lp.add_wf(fwf)
except:
try:
if '.tar' in args.wf_file:
fwf = Workflow.from_tarfile(args.wf_file)
else:
fwf = Workflow.from_file(args.wf_file)
lp.add_wf(fwf)
except:
print 'Error reading FireWork/Workflow file.'
traceback.print_exc()
elif args.command == 'get_fw':
fw = lp.get_fw_by_id(args.fw_id)
fw_dict = fw.to_dict()
if args.filename:
elif args.command == 'detect_fizzled':
# TODO: report when fixed
print lp.detect_fizzled(args.time, args.fix)
elif args.command == 'detect_unreserved':
# TODO: report when fixed
print lp.detect_unreserved(args.time, args.fix)
elif args.command == 'add':
# TODO: make this cleaner, e.g. make TAR option explicit
# fwf = Workflow.from_FireWork(FireWork.from_file(args.wf_file))
# lp.add_wf(fwf)
try:
fwf = Workflow.from_FireWork(FireWork.from_file(args.wf_file))
lp.add_wf(fwf)
except:
try:
if '.tar' in args.wf_file:
fwf = Workflow.from_tarfile(args.wf_file)
else:
fwf = Workflow.from_file(args.wf_file)
lp.add_wf(fwf)
except:
print 'Error reading FireWork/Workflow file.'
traceback.print_exc()
elif args.command == 'get_fw':
fw = lp.get_fw_by_id(args.fw_id)
fw_dict = fw.to_dict()
if args.filename:
"""
This code is described in the Dynamic Workflow tutorial, https://materialsproject.github.io/fireworks/dynamic_wf_tutorial.html
"""
from fireworks import ScriptTask
from fireworks.core.firework import Firework, Workflow
from fireworks.core.launchpad import LaunchPad
from fireworks.core.rocket_launcher import rapidfire
from fw_tutorials.dynamic_wf.printjob_task import PrintJobTask
if __name__ == "__main__":
# set up the LaunchPad and reset it
launchpad = LaunchPad()
# launchpad.reset('', require_password=False)
# create the Workflow that passes job info
fw1 = Firework([ScriptTask.from_str('echo "This is the first FireWork"')], spec={"_pass_job_info": True}, fw_id=1)
fw2 = Firework([PrintJobTask()], parents=[fw1], fw_id=2)
wf = Workflow([fw1, fw2])
# store workflow and launch it locally
launchpad.add_wf(wf)
rapidfire(launchpad)
