def test_bandgap_check_Vasp(self):
# add the workflow
structure = self.struct_si
# instructs to use db_file set by FWorker, see env_chk
my_wf = get_wf(structure,
"bandstructure.yaml",
vis=MPRelaxSet(structure, force_gamma=True),
common_params={
"vasp_cmd": VASP_CMD,
"db_file": ">>db_file<<"
})
if not VASP_CMD:
my_wf = use_fake_vasp(my_wf, ref_dirs_si)
else:
my_wf = use_custodian(my_wf)
my_wf = add_namefile(my_wf) # add a slug of fw-name to output files
my_wf = add_bandgap_check(my_wf,
check_bandgap_params={"max_gap": 0.1},
fw_name_constraint="structure optimization")
self.lp.add_wf(my_wf)
# run the workflow
# set the db_file variable
rapidfire(self.lp, fworker=_fworker)
# structure optimization should be completed
self.assertEqual(
self.lp.fireworks.find_one({"name": "Si-structure optimization"},
{"state": 1})["state"], "COMPLETED")
self.assertEqual(
self.lp.fireworks.find_one({"name": "Si-static"},
{"state": 1})["state"], "DEFUSED")
def test_bandgap_check_Vasp(self):
# add the workflow
structure = self.struct_si
# instructs to use db_file set by FWorker, see env_chk
my_wf = get_wf(structure, "bandstructure.yaml",
vis=MPRelaxSet(structure, force_gamma=True),
common_params={"vasp_cmd": VASP_CMD,
"db_file": ">>db_file<<"})
if not VASP_CMD:
my_wf = use_fake_vasp(my_wf, ref_dirs_si)
else:
my_wf = use_custodian(my_wf)
my_wf = add_namefile(my_wf) # add a slug of fw-name to output files
my_wf = add_bandgap_check(my_wf, check_bandgap_params={"max_gap": 0.1}, fw_name_constraint="structure optimization")
self.lp.add_wf(my_wf)
# run the workflow
# set the db_file variable
rapidfire(self.lp, fworker=FWorker(env={"db_file": os.path.join(db_dir, "db.json")}))
# structure optimization should be completed
self.assertEqual(self.lp.fireworks.find_one(
{"name": "Si-structure optimization"}, {"state": 1})["state"],
"COMPLETED")
self.assertEqual(self.lp.fireworks.find_one(
{"name": "Si-static"}, {"state": 1})["state"],
"DEFUSED")
def test_bandstructure_Vasp(self):
# add the workflow
structure = self.struct_si
# instructs to use db_file set by FWorker, see env_chk
my_wf = get_wf(structure,
"bandstructure.yaml",
vis=MPRelaxSet(structure, force_gamma=True),
common_params={
"vasp_cmd": VASP_CMD,
"db_file": ">>db_file<<"
})
if not VASP_CMD:
my_wf = use_fake_vasp(my_wf, ref_dirs_si)
else:
my_wf = use_custodian(my_wf)
my_wf = add_namefile(my_wf) # add a slug of fw-name to output files
self.lp.add_wf(my_wf)
# run the workflow
# set the db_file variable
rapidfire(
self.lp,
fworker=FWorker(env={"db_file": os.path.join(db_dir, "db.json")}))
# make sure the structure relaxation ran OK
d = self.get_task_collection().find_one(
{"task_label": "structure optimization"},
sort=[("_id", DESCENDING)])
self._check_run(d, mode="structure optimization")
# make sure the static run ran OK
d = self.get_task_collection().find_one({"task_label": "static"},
sort=[("_id", DESCENDING)])
self._check_run(d, mode="static")
# make sure the uniform run ran OK
d = self.get_task_collection().find_one({"task_label": "nscf uniform"},
sort=[("_id", DESCENDING)])
self._check_run(d, mode="nscf uniform")
# make sure the uniform run ran OK
d = self.get_task_collection().find_one({"task_label": "nscf line"},
sort=[("_id", DESCENDING)])
self._check_run(d, mode="nscf line")
wf = self.lp.get_wf_by_fw_id(1)
self.assertTrue(all([s == 'COMPLETED' for s in wf.fw_states.values()]))
def test_bandstructure_Vasp(self):
# add the workflow
structure = self.struct_si
# instructs to use db_file set by FWorker, see env_chk
my_wf = get_wf(structure, "bandstructure.yaml",
vis=MPRelaxSet(structure, force_gamma=True),
common_params={"vasp_cmd": VASP_CMD,
"db_file": ">>db_file<<"})
if not VASP_CMD:
my_wf = use_fake_vasp(my_wf, ref_dirs_si)
else:
my_wf = use_custodian(my_wf)
my_wf = add_namefile(my_wf) # add a slug of fw-name to output files
self.lp.add_wf(my_wf)
# run the workflow
# set the db_file variable
rapidfire(self.lp, fworker=FWorker(env={"db_file": os.path.join(db_dir, "db.json")}))
# make sure the structure relaxation ran OK
d = self.get_task_collection().find_one({"task_label": "structure optimization"},
sort=[("_id", DESCENDING)])
self._check_run(d, mode="structure optimization")
# make sure the static run ran OK
d = self.get_task_collection().find_one({"task_label": "static"}, sort=[("_id", DESCENDING)])
self._check_run(d, mode="static")
# make sure the uniform run ran OK
d = self.get_task_collection().find_one({"task_label": "nscf uniform"}, sort=[("_id", DESCENDING)])
self._check_run(d, mode="nscf uniform")
# make sure the uniform run ran OK
d = self.get_task_collection().find_one({"task_label": "nscf line"}, sort=[("_id", DESCENDING)])
self._check_run(d, mode="nscf line")
wf = self.lp.get_wf_by_fw_id(1)
self.assertTrue(all([s == 'COMPLETED' for s in wf.fw_states.values()]))
def wf_electron_conductivity(structure,
vasp_input_set_relax=None,
vasp_input_set_fixvol_relax=None,
vasp_input_set_static=None,
vasp_input_set_band=None,
vasp_input_set_diel=None,
vasp_input_set_elastic=None,
vasp_kpoint_set=None,
vasp_cmd=">>vasp_cmd<<",
db_file=">>db_file<<",
mode="standard",
Temp=None,
Doping=None,
strain=None,
ifSB=None):
'''This workflow aims to calculate electronic transport properties.'''
tag = datetime.utcnow().strftime('%Y-%m-%d-%H-%M-%S-%f')
fws = []
# get the input set for the optimization and update it if we passed custom settings
vis_relax = MPRelaxSet(structure,
user_incar_settings=vasp_input_set_relax,
user_kpoints_settings=vasp_kpoint_set)
# Structure optimization firework
fw_opt_equi = MyOptimizeFW(structure=structure,
vasp_input_set=vis_relax,
vasp_cmd=vasp_cmd,
db_file=db_file,
name="equi structure optimization",
count=1,
spec={"_queueadapter": {
"job_name": 'opt'
}})
fws.append(fw_opt_equi) #1
# static calculations firework
fw_static_equi = MyStaticFW(
structure=structure,
vasp_input_set_params=vasp_input_set_static,
prev_calc_loc="equi structure optimization-final",
vasp_cmd=vasp_cmd,
db_file=db_file,
name="equi static",
parents=fws[0],
spec={"_queueadapter": {
"job_name": 'static'
}})
fws.append(fw_static_equi) #2
# Structure optimization firework for 0.1% larger and 0.2% larger structures
fw_opt_05 = MyOptimizeFW(structure=structure,
vasp_input_set_params=vasp_input_set_fixvol_relax,
strain=strain[0],
prev_calc_loc="equi structure optimization-final",
vasp_cmd=vasp_cmd,
db_file=db_file,
name="0.5per structure optimization",
count=1,
parents=fws[0],
spec={"_queueadapter": {
"job_name": 'opt'
}})
fw_opt_10 = MyOptimizeFW(structure=structure,
vasp_input_set_params=vasp_input_set_fixvol_relax,
strain=strain[1],
prev_calc_loc="equi structure optimization-final",
vasp_cmd=vasp_cmd,
db_file=db_file,
name="1.0per structure optimization",
count=1,
parents=fws[0],
spec={"_queueadapter": {
"job_name": 'opt'
}})
fws.append(fw_opt_05) #3
fws.append(fw_opt_10) #4
fw_static_05 = MyStaticFW(
structure=structure,
vasp_input_set_params=vasp_input_set_static,
prev_calc_loc="0.5per structure optimization-final",
vasp_cmd=vasp_cmd,
db_file=db_file,
name="0.5per static",
parents=fws[2],
spec={"_queueadapter": {
"job_name": 'static'
}})
fw_static_10 = MyStaticFW(
structure=structure,
vasp_input_set_params=vasp_input_set_static,
prev_calc_loc="1.0per structure optimization-final",
vasp_cmd=vasp_cmd,
db_file=db_file,
name="1.0per static",
parents=fws[3],
spec={"_queueadapter": {
"job_name": 'static'
}})
fws.append(fw_static_05) #5
fws.append(fw_static_10) #6
# band structure calculation firework
fw_band_equi = MyNonSCFFW(structure=structure,
vasp_input_set_params=vasp_input_set_band,
prev_calc_loc="equi static",
name="equi nscf",
vasp_cmd=vasp_cmd,
db_file=db_file,
parents=fws[1],
spec={"_queueadapter": {
"job_name": 'band'
}})
fw_band_05 = MyNonSCFFW(structure=structure,
vasp_input_set_params=vasp_input_set_band,
prev_calc_loc="0.5per static",
name="0.5per nscf",
vasp_cmd=vasp_cmd,
db_file=db_file,
parents=fws[4],
spec={"_queueadapter": {
"job_name": 'band'
}})
fw_band_10 = MyNonSCFFW(structure=structure,
vasp_input_set_params=vasp_input_set_band,
prev_calc_loc="1.0per static",
name="1.0per nscf",
vasp_cmd=vasp_cmd,
db_file=db_file,
parents=fws[5],
spec={"_queueadapter": {
"job_name": 'band'
}})
fws.append(fw_band_equi) #7
fws.append(fw_band_05) #8
fws.append(fw_band_10) #9
# elastic constant calculation
fw_elastic = MyElasticFW(structure=structure,
vasp_input_set_params=vasp_input_set_elastic,
prev_calc_loc="equi structure optimization-final",
name="elastic",
vasp_cmd=vasp_cmd,
db_file=db_file,
parents=fws[1],
spec={"_queueadapter": {
"job_name": 'elastic'
}})
fws.append(fw_elastic) #10
# dielect constant calculation
fw_dielect = MyDFPTFW(structure=structure,
user_incar_settings=vasp_input_set_diel,
lepsilon=True,
prev_calc_loc="equi static",
name="dielectric",
vasp_cmd=vasp_cmd,
db_file=db_file,
parents=fws[1],
spec={"_queueadapter": {
"job_name": 'dielect'
}})
fws.append(fw_dielect) #11
# effective mass
fw_effectivemass_CBM = MyEffectivemassFW(
structure=structure,
vasp_input_set_params=vasp_input_set_band,
prev_calc_loc="equi static",
whichbnd="CBM",
stepsize=0.01,
name="CBM",
vasp_cmd=vasp_cmd,
db_file=db_file,
parents=fws[6],
spec={"_queueadapter": {
"job_name": 'CBM'
}})
fw_effectivemass_VBM = MyEffectivemassFW(
structure=structure,
vasp_input_set_params=vasp_input_set_band,
prev_calc_loc="equi static",
whichbnd="VBM",
stepsize=0.01,
name="VBM",
vasp_cmd=vasp_cmd,
db_file=db_file,
parents=fws[6],
spec={"_queueadapter": {
"job_name": 'VBM'
}})
fw_effectivemass_CSB = MyEffectivemassFW(
structure=structure,
vasp_input_set_params=vasp_input_set_band,
prev_calc_loc="equi static",
whichbnd="CSB",
stepsize=0.01,
name="CSB",
vasp_cmd=vasp_cmd,
db_file=db_file,
parents=fws[6],
spec={"_queueadapter": {
"job_name": 'CSB'
}})
fw_effectivemass_VSB = MyEffectivemassFW(
structure=structure,
vasp_input_set_params=vasp_input_set_band,
prev_calc_loc="equi static",
whichbnd="VSB",
stepsize=0.01,
name="VSB",
vasp_cmd=vasp_cmd,
db_file=db_file,
parents=fws[6],
spec={"_queueadapter": {
"job_name": 'VSB'
}})
fws.append(fw_effectivemass_CBM) #12
fws.append(fw_effectivemass_VBM) #13
fws.append(fw_effectivemass_CSB) #14
fws.append(fw_effectivemass_VSB) #15
# Call AICON
fw_eleccond = CalElecCondFW(structure=structure,
name="electrical conductivity",
mode=mode,
Temp=Temp,
Doping=Doping,
ifSB=ifSB,
db_file=db_file,
parents=fws[6:15],
spec={"_queueadapter": {
"job_name": 'AICON'
}})
fws.append(fw_eleccond) #16
# finally, create the workflow
wf_electron_conductivity = Workflow(fws)
wf_electron_conductivity.name = "{}:{}".format(
structure.composition.reduced_formula,
"electronic transport properties")
return add_namefile(wf_electron_conductivity)
def wf_phonon_conductivity(structure,
vasp_input_set_relax=None,
vasp_input_set_fixvol_relax=None,
vasp_input_set_dfpt=None,
vasp_kpoint_set=None,
vasp_cmd=">>vasp_cmd<<",
db_file=">>db_file<<",
Temp=None,
ifscale=None,
supercell=None):
""" This workflow aims to calculate lattice thermal conductivity of the structure. """
fws = []
# get the input set for the optimization and update it if we passed custom settings
vis_relax = MPRelaxSet(structure,
user_incar_settings=vasp_input_set_relax,
user_kpoints_settings=vasp_kpoint_set)
# Structure optimization firework
fw_opt_orig = MyOptimizeFW(structure=structure,
vasp_input_set=vis_relax,
vasp_cmd=vasp_cmd,
db_file=db_file,
name="equi structure optimization",
count=1,
spec={"_queueadapter": {
"job_name": 'opt'
}})
fws.append(fw_opt_orig) #1
# Structure optimization firework for 0.4% smaller and 0.4% larger structures
fw_opt_minus = MyOptimizeFW(
structure=structure,
vasp_input_set_params=vasp_input_set_fixvol_relax,
strain=-0.004,
prev_calc_loc="equi structure optimization-final",
vasp_cmd=vasp_cmd,
db_file=db_file,
name="minus structure optimization",
count=1,
parents=fws[0],
spec={"_queueadapter": {
"job_name": 'opt'
}})
fw_opt_plus = MyOptimizeFW(
structure=structure,
vasp_input_set_params=vasp_input_set_fixvol_relax,
strain=0.004,
prev_calc_loc="equi structure optimization-final",
vasp_cmd=vasp_cmd,
db_file=db_file,
name="plus structure optimization",
count=1,
parents=fws[0],
spec={"_queueadapter": {
"job_name": 'opt'
}})
fws.append(fw_opt_minus) #2
fws.append(fw_opt_plus) #3
# 2nd Force Constant calculation using DFPT
fw_dfpt_orig = MyPhononFW(
structure=structure,
user_incar_settings=vasp_input_set_dfpt,
prev_calc_loc="equi structure optimization-final",
supercell=supercell,
name="orig phonon band",
vasp_cmd=vasp_cmd,
db_file=db_file,
parents=fws[0],
spec={"_queueadapter": {
"job_name": 'dfpt',
"ppnode": 8
}})
fw_dfpt_minus = MyPhononFW(
structure=structure,
user_incar_settings=vasp_input_set_dfpt,
prev_calc_loc="minus structure optimization-final",
supercell=supercell,
name="minus phonon band",
vasp_cmd=vasp_cmd,
db_file=db_file,
parents=fws[1],
spec={"_queueadapter": {
"job_name": 'dfpt',
"ppnode": 8
}})
fw_dfpt_plus = MyPhononFW(
structure=structure,
user_incar_settings=vasp_input_set_dfpt,
prev_calc_loc="plus structure optimization-final",
supercell=supercell,
name="plus phonon band",
vasp_cmd=vasp_cmd,
db_file=db_file,
parents=fws[2],
spec={"_queueadapter": {
"job_name": 'dfpt',
"ppnode": 8
}})
fws.append(fw_dfpt_orig) #4
fws.append(fw_dfpt_minus) #5
fws.append(fw_dfpt_plus) #6
# get band.yaml and gruneisen.yaml
fw_phoncond = CalPhonCondFW(structure=structure,
Temp=Temp,
ifscale=ifscale,
supercell=supercell,
name="thermal conductivity",
db_file=db_file,
parents=fws[3:6],
spec={"_queueadapter": {
"job_name": 'AICON'
}})
fws.append(fw_phoncond)
wf_phonon_conductivity = Workflow(fws)
wf_phonon_conductivity.name = "{}:{}".format(
structure.composition.reduced_formula, "phonon transport properties")
return add_namefile(wf_phonon_conductivity)
