def setUpClass(cls):
struct_si = PymatgenTest.get_structure("Si")
vis = MPRelaxSet(struct_si, force_gamma=True)
cls.bs_wf = get_wf(struct_si,
"bandstructure.yaml",
vis=vis, common_params={"vasp_cmd": "test_VASP"})
cls.bsboltz_wf = get_wf(struct_si,
"bandstructure_boltztrap.yaml",
vis=vis)
def wf_scan_opt(structure, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
user_incar_settings = c.get("USER_INCAR_SETTINGS", {})
half_kpts = c.get("HALF_KPOINTS_FIRST_RELAX", HALF_KPOINTS_FIRST_RELAX)
ediffg = user_incar_settings.get("EDIFFG", -0.05)
wf = get_wf(structure,
"optimize_only.yaml",
vis=MVLScanRelaxSet(structure,
user_incar_settings=user_incar_settings),
common_params={
"vasp_cmd": vasp_cmd,
"db_file": db_file
})
wf = use_custodian(wf,
custodian_params={
"ediffg": ediffg,
"max_force_threshold": 0,
"half_kpts_first_relax": half_kpts,
"job_type": "metagga_opt_run",
"vasp_cmd": vasp_cmd
})
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
if c.get("REMOVE_WAVECAR", REMOVE_WAVECAR):
wf = clean_up_files(wf)
return wf
def wf_scan_opt(structure, c=None):
"""
Structure optimization using the SCAN metaGGA functional.
This workflow performs a 2-step optmization. The first step
is a conventional GGA run and serves to precondition the geometry and
wavefunctions. The second step is a SCAN structure optimization.
The first optimization is force converged with EDIFFG = -0.05,
and the second optimization is force converged with EDIFFG=-0.02.
"""
c = c or {}
user_incar_settings = c.get("USER_INCAR_SETTINGS", {})
vdw = c.get("vdw")
bandgap = c.get("bandgap", 0)
wf = get_wf(
structure,
"SCAN_optimization.yaml",
vis=MPScanRelaxSet(structure,
user_incar_settings=user_incar_settings,
vdw=vdw,
bandgap=bandgap),
params=[{
"name": "SCAN optimization"
}],
)
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def test_single_Vasp_dbinsertion(self):
# add the workflow
structure = self.struct_si
# instructs to use db_file set by FWorker, see env_chk
my_wf = get_wf(structure,
"optimize_only.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)
# add an msonable object to additional fields
my_wf.fws[0].tasks[-1]['additional_fields'].update(
{"test_additional_field": self.struct_si})
self.lp.add_wf(my_wf)
# run the workflow
rapidfire(self.lp, fworker=_fworker)
d = self.get_task_collection().find_one()
self._check_run(d, mode="structure optimization")
self._check_run(d, mode="additional field")
wf = self.lp.get_wf_by_fw_id(1)
self.assertTrue(all([s == 'COMPLETED' for s in wf.fw_states.values()]))
def test_chgcar_db_read(self):
# add the workflow
structure = self.struct_si
# instructs to use db_file set by FWorker, see env_chk
my_wf = get_wf(structure, "static_only.yaml", vis=MPStaticSet(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)
# set the flags for storing charge densties
my_wf.fws[0].tasks[-1]["parse_chgcar"] = True
my_wf.fws[0].tasks[-1]["parse_aeccar"] = True
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")}))
d = self.get_task_collection().find_one()
self._check_run(d, mode="static")
wf = self.lp.get_wf_by_fw_id(1)
self.assertTrue(all([s == 'COMPLETED' for s in wf.fw_states.values()]))
chgcar_fs_id = d["calcs_reversed"][0]["chgcar_fs_id"]
accar0_fs_id = d["calcs_reversed"][0]["aeccar0_fs_id"]
accar2_fs_id = d["calcs_reversed"][0]["aeccar2_fs_id"]
self.assertTrue(bool(chgcar_fs_id))
self.assertTrue(bool(accar0_fs_id))
self.assertTrue(bool(accar2_fs_id))
def wf_bandstructure_plus_boltztrap(structure, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
params = []
for x in range(4): # everything but BoltzTrap task
params.append({"vasp_cmd": vasp_cmd, "db_file": db_file})
params.append({"db_file": db_file})
wf = get_wf(structure,
"bandstructure_boltztrap.yaml",
vis=MPRelaxSet(structure, force_gamma=True),
params=params)
wf = add_common_powerups(wf, c)
if c.get("SMALLGAP_KPOINT_MULTIPLY", SMALLGAP_KPOINT_MULTIPLY):
wf = add_small_gap_multiply(wf, 0.5, 5, "static")
wf = add_small_gap_multiply(wf, 0.5, 5, "nscf")
if c.get("STABILITY_CHECK", STABILITY_CHECK):
wf = add_stability_check(wf,
fw_name_constraint="structure optimization")
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def test_single_Vasp_dbinsertion(self):
# add the workflow
structure = self.struct_si
# instructs to use db_file set by FWorker, see env_chk
my_wf = get_wf(structure,
"optimize_only.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)
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")}))
d = self.get_task_collection().find_one()
self._check_run(d, mode="structure optimization")
wf = self.lp.get_wf_by_fw_id(1)
self.assertTrue(all([s == 'COMPLETED' for s in wf.fw_states.values()]))
def wf_bandstructure_plus_hse(structure, gap_only=True, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
if gap_only:
wf_src_name = "bandstructure_hsegap.yaml"
else:
wf_src_name = "bandstructure_hse.yaml"
wf = get_wf(structure, wf_src_name,
vis=MPRelaxSet(structure, force_gamma=True),
common_params={"vasp_cmd": vasp_cmd,
"db_file": db_file})
wf = add_common_powerups(wf, c)
if c.get("SMALLGAP_KPOINT_MULTIPLY", SMALLGAP_KPOINT_MULTIPLY):
wf = add_small_gap_multiply(wf, 0.5, 5, "static")
wf = add_small_gap_multiply(wf, 0.5, 5, "nscf")
if c.get("STABILITY_CHECK", STABILITY_CHECK):
wf = add_stability_check(wf, fw_name_constraint="structure optimization")
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def wf_bandstructure_plus_boltztrap(structure, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
params = []
for x in range(4):
params.append({"vasp_cmd": vasp_cmd, "db_file": db_file})
params.append({"db_file": db_file})
wf = get_wf(structure, "bandstructure_boltztrap.yaml",
vis=MPRelaxSet(structure, force_gamma=True),
params=params)
wf = add_common_powerups(wf, c)
if c.get("SMALLGAP_KPOINT_MULTIPLY", SMALLGAP_KPOINT_MULTIPLY):
wf = add_small_gap_multiply(wf, 0.5, 5, "static")
wf = add_small_gap_multiply(wf, 0.5, 5, "nscf")
if c.get("STABILITY_CHECK", STABILITY_CHECK):
wf = add_stability_check(wf, fw_name_constraint="structure optimization")
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
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 wf_bandstructure_hse(structure, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
wf_src_name = "bandstructure_hse_full.yaml"
wf = get_wf(structure,
wf_src_name,
vis=MPHSERelaxSet(structure, force_gamma=True),
common_params={
"vasp_cmd": vasp_cmd,
"db_file": db_file
})
wf = add_common_powerups(wf, c)
if c.get("SMALLGAP_KPOINT_MULTIPLY", SMALLGAP_KPOINT_MULTIPLY):
wf = add_small_gap_multiply(wf, 0.5, 5, "static")
if c.get("STABILITY_CHECK", STABILITY_CHECK):
wf = add_stability_check(wf,
fw_name_constraint="structure optimization")
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def wf_bandstructure_no_opt(structure, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
wf = get_wf(
structure,
"bandstructure_no_opt.yaml",
vis=MPStaticSet(structure, force_gamma=True),
common_params={
"vasp_cmd": vasp_cmd,
"db_file": db_file
},
)
wf = add_common_powerups(wf, c)
if c.get("SMALLGAP_KPOINT_MULTIPLY", SMALLGAP_KPOINT_MULTIPLY):
wf = add_small_gap_multiply(wf, 0.5, 5, "static")
wf = add_small_gap_multiply(wf, 0.5, 5, "nscf")
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def test_single_Vasp_dbinsertion(self):
# add the workflow
structure = self.struct_si
# instructs to use db_file set by FWorker, see env_chk
my_wf = get_wf(structure, "optimize_only.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)
# add an msonable object to additional fields
my_wf.fws[0].tasks[-1]['additional_fields'].update(
{"test_additional_field": self.struct_si})
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")}))
d = self.get_task_collection().find_one()
self._check_run(d, mode="structure optimization")
self._check_run(d, mode="additional field")
wf = self.lp.get_wf_by_fw_id(1)
self.assertTrue(all([s == 'COMPLETED' for s in wf.fw_states.values()]))
def wf_structure_optimization(structure, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
user_incar_settings = c.get("USER_INCAR_SETTINGS")
wf = get_wf(
structure,
"optimize_only.yaml",
vis=MPRelaxSet(structure,
force_gamma=True,
user_incar_settings=user_incar_settings),
common_params={
"vasp_cmd": vasp_cmd,
"db_file": db_file
},
)
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
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_trackers(self):
# add the workflow
structure = self.struct_si
my_wf = get_wf(structure,
"optimize_only.yaml",
vis=MPRelaxSet(structure, force_gamma=True),
common_params={"vasp_cmd": VASP_CMD})
if not VASP_CMD:
my_wf = use_fake_vasp(my_wf, ref_dirs_si)
else:
my_wf = use_custodian(my_wf)
my_wf = add_trackers(my_wf)
self.lp.add_wf(my_wf)
# run the workflow
rapidfire(self.lp, fworker=_fworker)
for x in self.lp.get_tracker_data(1):
for t in x["trackers"]:
self.assertGreater(len(t.content.split("\n")), 20)
wf = self.lp.get_wf_by_fw_id(1)
self.assertTrue(all([s == 'COMPLETED' for s in wf.fw_states.values()]))
def test_SCAN_large_bandgap(self):
# A structure with a large bandgap (LiF) should result in KSPACING
# hitting the maximum allowed value of 0.44
structure = Structure.from_file(
os.path.join(reference_dir,
"SCAN_structure_optimization_LiF/inputs", "POSCAR"))
my_wf = get_wf(structure,
"SCAN_optimization.yaml",
vis=MPScanRelaxSet(structure),
common_params={"vasp_cmd": VASP_CMD})
self._run_scan_relax(my_wf, "SCAN_structure_optimization_LiF")
# Check INCAR.orig generated by the InputSet
incar_orig = Incar.from_file(
os.path.join(self._get_launch_dir(), "INCAR.orig.gz"))
ref_incar = Incar.from_file(
os.path.join(reference_dir,
"SCAN_structure_optimization_LiF/inputs",
"INCAR.orig"))
for p in incar_orig.keys():
if p == "MAGMOM": # Ignore MAGMOM b/c structure initialized from POSCAR cannot have a MAGMOM
pass
else:
self.assertEqual(incar_orig[p], ref_incar[p])
# Check INCAR.relax1 generated by the Workflow
incar = Incar.from_file(
os.path.join(self._get_launch_dir(), "INCAR.relax1.gz"))
self.assertEqual(incar["METAGGA"], "None")
self.assertEqual(incar["EDIFFG"], -0.05)
self.assertEqual(incar["LWAVE"], False)
# Check INCAR.relax2
incar = Incar.from_file(
os.path.join(self._get_launch_dir(), "INCAR.relax2.gz"))
self.assertEqual(incar["METAGGA"], "None")
self.assertEqual(incar["LWAVE"], True)
self.assertEqual(incar["NSW"], 0)
self.assertEqual(incar["EDIFFG"], -0.05)
self.assertEqual(incar["ICHARG"], 1)
self.assertEqual(incar["ISTART"], 0)
# Check INCAR.relax3 for the correct kspacing
incar = Incar.from_file(
os.path.join(self._get_launch_dir(), "INCAR.relax3.gz"))
for p in incar.keys():
if p == "KSPACING":
self.assertEqual(incar[p], 0.44)
elif p == "ICHARG" or p == "ISTART":
self.assertEqual(incar[p], 1)
elif p == "ISMEAR":
self.assertEqual(incar[p], -5)
elif p == "SIGMA":
self.assertEqual(incar[p], 0.05)
else:
self.assertEqual(incar_orig[p], incar[p])
def test_SCAN_small_bandgap(self):
# A structure with a small bandgap (LiH) should result in a KSPACING
# value of 0.351275
structure = Structure.from_file(
os.path.join(reference_dir,
"SCAN_structure_optimization_LiH/inputs", "POSCAR"))
my_wf = get_wf(structure,
"SCAN_optimization.yaml",
vis=MPScanRelaxSet(structure),
common_params={"vasp_cmd": VASP_CMD})
self._run_scan_relax(my_wf, "SCAN_structure_optimization_LiH")
# Check INCAR.orig
incar_orig = Incar.from_file(
os.path.join(self._get_launch_dir(), "INCAR.orig.gz"))
ref_incar = Incar.from_file(
os.path.join(reference_dir,
"SCAN_structure_optimization_LiH/inputs",
"INCAR.orig"))
for p in incar_orig.keys():
if p == "MAGMOM": # Ignore MAGMOM b/c structure initialized from POSCAR cannot have a MAGMOM
pass
else:
self.assertEqual(incar_orig[p], ref_incar[p])
# Check INCAR.relax1
incar = Incar.from_file(
os.path.join(self._get_launch_dir(), "INCAR.relax1.gz"))
self.assertEqual(incar["METAGGA"], "None")
self.assertEqual(incar["EDIFFG"], -0.05)
self.assertEqual(incar["LWAVE"], False)
# Check INCAR.relax2
incar = Incar.from_file(
os.path.join(self._get_launch_dir(), "INCAR.relax2.gz"))
self.assertEqual(incar["METAGGA"], "None")
self.assertEqual(incar["LWAVE"], True)
self.assertEqual(incar["NSW"], 0)
self.assertEqual(incar["EDIFFG"], -0.05)
self.assertEqual(incar["ICHARG"], 1)
self.assertEqual(incar["ISTART"], 0)
# Check INCAR.relax3
incar = Incar.from_file(
os.path.join(self._get_launch_dir(), "INCAR.relax3.gz"))
for p in incar.keys():
if p == "KSPACING":
self.assertAlmostEqual(incar[p], 0.351275, 4)
elif p == "ICHARG" or p == "ISTART":
self.assertEqual(incar[p], 1)
elif p == "ISMEAR":
self.assertEqual(incar[p], -5)
elif p == "SIGMA":
self.assertEqual(incar[p], 0.05)
else:
self.assertEqual(incar_orig[p], incar[p])
def test_SCAN_large_bandgap(self):
# A structure with a large bandgap (LiF) should result in KSPACING
# hitting the maximum allowed value of 0.44
structure = Structure.from_file(
os.path.join(reference_dir, "PBESol_pre_opt_for_SCAN_LiF/inputs",
"POSCAR"))
my_wf = get_wf(structure, "metagga_optimization.yaml")
fw_ids = self._run_scan_relax(my_wf, "LiF")
# Check PBESol INCAR
ref_incar = Incar.from_file(
os.path.join(reference_dir, "PBESol_pre_opt_for_SCAN_LiF/inputs",
"INCAR"))
incar = Incar.from_file(
os.path.join(self._get_launch_dir()[0], "INCAR.gz"))
for p in incar.keys():
if p == "KSPACING":
self.assertEqual(incar[p], 0.22)
elif p == "ICHARG" or p == "ISTART":
self.assertEqual(incar[p], 1)
elif p == "METAGGA":
self.assertEqual(incar[p], "None")
elif p == "GGA":
self.assertEqual(incar[p], "Ps")
elif p == "EDIFFG":
self.assertEqual(incar[p], -0.05)
elif p == "MAGMOM": # Ignore MAGMOM b/c structure initialized from POSCAR cannot have a MAGMOM
pass
else:
self.assertEqual(incar[p], ref_incar[p])
# Check SCAN INCAR
ref_incar = Incar.from_file(
os.path.join(reference_dir,
"SCAN_structure_optimization_LiF/inputs", "INCAR"))
incar = Incar.from_file(
os.path.join(self._get_launch_dir()[1], "INCAR.gz"))
for p in incar.keys():
if p == "KSPACING":
self.assertEqual(incar[p], 0.44)
elif p == "SIGMA":
self.assertEqual(incar[p], 0.05)
elif p == "ICHARG":
self.assertEqual(incar[p], 1)
else:
self.assertEqual(incar[p], ref_incar[p])
# get a fw that can be used to identify the workflow
fw_id = list(fw_ids.values())[0]
# check workflow finished without error
wf = self.lp.get_wf_by_fw_id(fw_id)
is_completed = [s == "COMPLETED" for s in wf.fw_states.values()]
self.assertTrue(all(is_completed))
def test_SCAN_with_vdw(self):
# Verify appropriate changes to the INCAR when VdW is enabled
# VdW should be off for relax1 (GGA) and re-enabled for relax2 (SCAN)
structure = Structure.from_file(os.path.join(reference_dir, "SCAN_structure_optimization_LiF_vdw/inputs", "POSCAR"))
my_wf = get_wf(structure, "SCAN_optimization.yaml", vis=MPScanRelaxSet(structure, vdw="rvv10"),
common_params={"vasp_cmd": VASP_CMD, "vdw_kernel_dir": os.path.join(reference_dir, "SCAN_structure_optimization_LiF_vdw/inputs")})
self._run_scan_relax(my_wf, "SCAN_structure_optimization_LiF_vdw")
# Check INCAR.orig
incar_orig = Incar.from_file(os.path.join(self._get_launch_dir(), "INCAR.orig.gz"))
ref_incar = Incar.from_file(os.path.join(reference_dir, "SCAN_structure_optimization_LiF_vdw/inputs", "INCAR.orig"))
for p in incar_orig.keys():
if p == "MAGMOM": # Ignore MAGMOM b/c structure initialized from POSCAR cannot have a MAGMOM
pass
else:
self.assertEqual(incar_orig[p], ref_incar[p])
# Check INCAR.relax1
incar = Incar.from_file(os.path.join(self._get_launch_dir(), "INCAR.relax1.gz"))
self.assertIsNone(incar.get("LUSE_VDW", None))
self.assertIsNone(incar.get("BPARAM", None))
self.assertEqual(incar["METAGGA"], "None")
self.assertEqual(incar["EDIFFG"], -0.05)
self.assertEqual(incar["LWAVE"], False)
# Check INCAR.relax2
incar = Incar.from_file(os.path.join(self._get_launch_dir(), "INCAR.relax2.gz"))
self.assertEqual(incar["METAGGA"], "None")
self.assertEqual(incar["LWAVE"], True)
self.assertEqual(incar["NSW"], 0)
self.assertEqual(incar["EDIFFG"], -0.05)
self.assertEqual(incar["ICHARG"], 1)
self.assertEqual(incar["ISTART"], 0)
# Check INCAR.relax3
incar = Incar.from_file(os.path.join(self._get_launch_dir(), "INCAR.relax3.gz"))
for p in incar.keys():
if p == "KSPACING":
self.assertEqual(incar[p], 0.44)
elif p == "ICHARG" or p == "ISTART":
self.assertEqual(incar[p], 1)
elif p == "ISMEAR":
self.assertEqual(incar[p], -5)
elif p == "SIGMA":
self.assertEqual(incar[p], 0.05)
elif p == "MAGMOM": # Ignore MAGMOM b/c structure initialized from POSCAR cannot have a MAGMOM
pass
else:
self.assertEqual(incar_orig[p], incar[p])
def wf_thermal_expansion(structure, c=None):
"""
Thermal expansion coefficient workflow from the given structure and config dict.
Args:
structure (Structure): input structure
c (dict): workflow config dict
Returns:
Workflow
"""
c = c or {}
eos = c.get("EOS", "vinet")
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
pressure = c.get("PRESSURE", 0.0)
user_kpoints_settings = {"grid_density": 7000}
# 10 deformations
deformations = [(np.identity(3) * (1 + x)).tolist() for x in np.linspace(-0.1, 0.1, 10)]
tag = "thermal_expansion group: >>{}<<".format(str(uuid4()))
# input set for structure optimization
vis_relax = MPRelaxSet(structure, force_gamma=True)
v = vis_relax.as_dict()
v.update({"user_kpoints_settings": user_kpoints_settings})
vis_relax = vis_relax.__class__.from_dict(v)
# optimization only workflow
wf = get_wf(structure, "optimize_only.yaml",
params=[{"vasp_cmd": vasp_cmd, "db_file": db_file,
"name": "{} structure optimization".format(tag)}],
vis=vis_relax)
wf_thermal = get_wf_thermal_expansion(structure, user_kpoints_settings=user_kpoints_settings,
deformations=deformations, vasp_cmd=vasp_cmd, db_file=db_file,
eos=eos, pressure=pressure, tag=tag)
# chain it
wf.append_wf(wf_thermal, wf.leaf_fw_ids)
wf = add_modify_incar(wf, modify_incar_params={"incar_update": {"ENCUT": 600, "EDIFF": 1e-6}})
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def wf_scan_opt(structure, c=None):
"""
Structure optimization using the SCAN metaGGA functional.
This workflow performs a 2-step optmization. The first step
is a GGA structure optimization using the PBESol functional that serves to
precondition the geometry and charge density. The second step is a
SCAN structure optimization.
The first optimization is force converged with EDIFFG = -0.05,
and the second optimization is force converged with EDIFFG=-0.02.
The bandgap from the first step is used to update the KSPACING parameter,
which sets the appropriate number of k-points for the subsequent SCAN
calculation.
"""
c = c or {}
# override the default R2SCAN functional with SCAN
vasp_input_set_params = {"user_incar_settings": {"METAGGA": "SCAN"}}
if c.get("USER_INCAR_SETTINGS"):
vasp_input_set_params["user_incar_settings"] = c.get(
"USER_INCAR_SETTINGS")
# if the user has supplied METAGGA, respect that setting instead
if not vasp_input_set_params["user_incar_settings"].get("METAGGA"):
vasp_input_set_params["user_incar_settings"]["METAGGA"] = "SCAN"
if c.get("vdw"):
vasp_input_set_params["vdw"] = c.get("vdw")
if c.get("bandgap"):
vasp_input_set_params["bandgap"] = c.get("bandgap")
wf = get_wf(
structure,
"metagga_optimization.yaml",
# override the default FW name to reflect the SCAN functional
params=[{}, {
"name": "SCAN structure optimization"
}],
common_params={"vasp_input_set_params": vasp_input_set_params},
)
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
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_dielectric_constant(structure, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
wf = get_wf(structure, "dielectric_constant.yaml", vis=MPRelaxSet(structure, force_gamma=True),
common_params={"vasp_cmd": vasp_cmd, "db_file": db_file})
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def wf_nmr(structure, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
wf = get_wf(structure, "nmr.yaml",
common_params={"vasp_cmd": vasp_cmd, "db_file": db_file})
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def wf_static(structure, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
wf = get_wf(structure, "static_only.yaml",
vis=MPStaticSet(structure),
common_params={"vasp_cmd": vasp_cmd,
"db_file": db_file})
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def test_SCAN_incar_override(self):
# user incar settings should be passed all the way through the workflow
structure = Structure.from_file(
os.path.join(reference_dir,
"SCAN_structure_optimization_LiH/inputs", "POSCAR"))
my_wf = get_wf(structure,
"SCAN_optimization.yaml",
vis=MPScanRelaxSet(structure,
user_potcar_functional="PBE_52",
user_incar_settings={
"NSW": 10,
"SYMPREC": 1e-6,
"SIGMA": 0.1
}),
common_params={"vasp_cmd": VASP_CMD})
self._run_scan_relax(my_wf, "SCAN_structure_optimization_LiH")
# Check INCAR.orig
incar = Incar.from_file(
os.path.join(self._get_launch_dir(), "INCAR.orig.gz"))
self.assertEqual(incar["NSW"], 10)
self.assertEqual(incar["SYMPREC"], 1e-6)
self.assertEqual(incar["SIGMA"], 0.1)
# Check INCAR.relax1
incar = Incar.from_file(
os.path.join(self._get_launch_dir(), "INCAR.relax1.gz"))
self.assertEqual(incar["NSW"], 10)
self.assertEqual(incar["SYMPREC"], 1e-6)
self.assertEqual(incar["SIGMA"], 0.1)
# Check INCAR.relax2
incar = Incar.from_file(
os.path.join(self._get_launch_dir(), "INCAR.relax2.gz"))
self.assertEqual(incar["NSW"], 0)
self.assertEqual(incar["SYMPREC"], 1e-6)
self.assertEqual(incar["SIGMA"], 0.1)
# Check INCAR.relax3
incar = Incar.from_file(
os.path.join(self._get_launch_dir(), "INCAR.relax3.gz"))
self.assertEqual(incar["NSW"], 10)
self.assertEqual(incar["SYMPREC"], 1e-6)
self.assertEqual(incar["SIGMA"], 0.1)
def wf_dielectric_constant(structure, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
wf = get_wf(structure, "dielectric_constant.yaml",
vis=MPRelaxSet(structure, force_gamma=True),
common_params={"vasp_cmd": vasp_cmd,
"db_file": db_file})
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def wf_elastic_constant(structure, c=None, order=2, sym_reduce=False):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
uis_optimize = {"ENCUT": 700, "EDIFF": 1e-6, "LAECHG": False}
if order > 2:
uis_optimize.update({"EDIFF": 1e-10, "EDIFFG": -0.001,
"ADDGRID": True, "LREAL": False, "ISYM": 0})
# This ensures a consistent k-point mesh across all calculations
# We also turn off symmetry to prevent VASP from changing the
# mesh internally
kpts_settings = Kpoints.automatic_density(structure, 40000, force_gamma=True)
stencils = np.linspace(-0.075, 0.075, 7)
else:
kpts_settings = {'grid_density': 7000}
stencils = None
uis_static = uis_optimize.copy()
uis_static.update({'ISIF': 2, 'IBRION': 2, 'NSW': 99, 'ISTART': 1, "PREC": "High"})
# input set for structure optimization
vis_relax = MPRelaxSet(structure, force_gamma=True, user_incar_settings=uis_optimize,
user_kpoints_settings=kpts_settings)
# optimization only workflow
wf = get_wf(structure, "optimize_only.yaml", vis=vis_relax,
params=[{"vasp_cmd": vasp_cmd, "db_file": db_file,
"name": "elastic structure optimization"}])
vis_static = MPStaticSet(structure, force_gamma=True, lepsilon=False,
user_kpoints_settings=kpts_settings,
user_incar_settings=uis_static)
# deformations wflow for elasticity calculation
wf_elastic = get_wf_elastic_constant(structure, vasp_cmd=vasp_cmd, db_file=db_file,
order=order, stencils=stencils, copy_vasp_outputs=True,
vasp_input_set=vis_static, sym_reduce=sym_reduce)
wf.append_wf(wf_elastic, wf.leaf_fw_ids)
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def wf_structure_optimization(structure, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
user_incar_settings = c.get("USER_INCAR_SETTINGS")
wf = get_wf(structure, "optimize_only.yaml",
vis=MPRelaxSet(structure, force_gamma=True,
user_incar_settings=user_incar_settings),
common_params={"vasp_cmd": vasp_cmd,
"db_file": db_file})
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def test_single_Vasp_dbinsertion(self):
# add the workflow
structure = self.struct_si
# instructs to use db_file set by FWorker, see env_chk
my_wf = get_wf(structure, "optimize_only.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)
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")}))
d = self._get_task_collection().find_one()
self._check_run(d, mode="structure optimization")
def test_single_Vasp(self):
# add the workflow
structure = self.struct_si
my_wf = get_wf(structure, "optimize_only.yaml", vis=MPRelaxSet(structure, force_gamma=True),
common_params={"vasp_cmd": VASP_CMD})
if not VASP_CMD:
my_wf = use_fake_vasp(my_wf, ref_dirs_si)
else:
my_wf = use_custodian(my_wf)
self.lp.add_wf(my_wf)
# run the workflow
rapidfire(self.lp)
fw = self.lp.get_fw_by_id(1)
with open(os.path.join(fw.launches[-1].launch_dir, "task.json")) as f:
d = json.load(f)
self._check_run(d, mode="structure optimization")
def test_single_Vasp(self):
# add the workflow
structure = self.struct_si
my_wf = get_wf(structure, "optimize_only.yaml", vis=MPRelaxSet(structure, force_gamma=True),
common_params={"vasp_cmd": VASP_CMD})
if not VASP_CMD:
my_wf = use_fake_vasp(my_wf, ref_dirs_si)
else:
my_wf = use_custodian(my_wf)
self.lp.add_wf(my_wf)
# run the workflow
rapidfire(self.lp, fworker=_fworker)
d = self.get_task_collection().find_one({"task_label": "structure optimization"})
self._check_run(d, mode="structure optimization")
wf = self.lp.get_wf_by_fw_id(1)
self.assertTrue(all([s == 'COMPLETED' for s in wf.fw_states.values()]))
def test_SCAN_incar_override(self):
# user incar settings should be passed all the way through the workflow
structure = Structure.from_file(
os.path.join(reference_dir, "PBESol_pre_opt_for_SCAN_LiH/inputs",
"POSCAR"))
my_wf = get_wf(structure,
"metagga_optimization.yaml",
common_params={
"vasp_input_set_params": {
"user_potcar_functional": "PBE_52",
"user_incar_settings": {
"NSW": 10,
"SYMPREC": 1e-6,
"SIGMA": 0.1
}
}
})
fw_ids = self._run_scan_relax(my_wf, "LiH")
# Check PBESol INCAR
incar1 = Incar.from_file(
os.path.join(self._get_launch_dir()[0], "INCAR.gz"))
self.assertEqual(incar1["NSW"], 10)
self.assertEqual(incar1["SYMPREC"], 1e-6)
self.assertEqual(incar1["SIGMA"], 0.1)
# Check SCAN INCAR
incar2 = Incar.from_file(
os.path.join(self._get_launch_dir()[1], "INCAR.gz"))
self.assertEqual(incar2["NSW"], 10)
self.assertEqual(incar2["SYMPREC"], 1e-6)
self.assertEqual(incar2["SIGMA"], 0.1)
# get a fw that can be used to identify the workflow
fw_id = list(fw_ids.values())[0]
# check workflow finished without error
wf = self.lp.get_wf_by_fw_id(fw_id)
is_completed = [s == "COMPLETED" for s in wf.fw_states.values()]
self.assertTrue(all(is_completed))
def wf_r2scan_opt(structure, c=None):
"""
Structure optimization using the R2SCAN metaGGA functional.
This workflow performs a 2-step optmization. The first step
is a GGA structure optimization using the PBESol functional that serves to
precondition the geometry and charge density. The second step is a
R2SCAN structure optimization.
The first optimization is force converged with EDIFFG = -0.05,
and the second optimization is force converged with EDIFFG=-0.02.
The bandgap from the first step is used to update the KSPACING parameter,
which sets the appropriate number of k-points for the subsequent R2SCAN
calculation.
"""
c = c or {}
vasp_input_set_params = {}
if c.get("USER_INCAR_SETTINGS"):
vasp_input_set_params["user_incar_settings"] = c.get(
"USER_INCAR_SETTINGS")
if c.get("vdw"):
vasp_input_set_params["vdw"] = c.get("vdw")
if c.get("bandgap"):
vasp_input_set_params["bandgap"] = c.get("bandgap")
wf = get_wf(
structure,
"metagga_optimization.yaml",
common_params={"vasp_input_set_params": vasp_input_set_params},
)
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def test_trackers(self):
# add the workflow
structure = self.struct_si
my_wf = get_wf(structure, "optimize_only.yaml",
vis=MPRelaxSet(structure, force_gamma=True),
common_params={"vasp_cmd": VASP_CMD})
if not VASP_CMD:
my_wf = use_fake_vasp(my_wf, ref_dirs_si)
else:
my_wf = use_custodian(my_wf)
my_wf = add_trackers(my_wf)
self.lp.add_wf(my_wf)
# run the workflow
rapidfire(self.lp)
for x in self.lp.get_tracker_data(1):
for t in x["trackers"]:
self.assertGreater(len(t.content.split("\n")), 20)
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_single_Vasp(self):
# add the workflow
structure = self.struct_si
my_wf = get_wf(structure, "optimize_only.yaml", vis=MPRelaxSet(structure, force_gamma=True),
common_params={"vasp_cmd": VASP_CMD})
if not VASP_CMD:
my_wf = use_fake_vasp(my_wf, ref_dirs_si)
else:
my_wf = use_custodian(my_wf)
self.lp.add_wf(my_wf)
# run the workflow
rapidfire(self.lp)
fw = self.lp.get_fw_by_id(1)
with open(os.path.join(fw.launches[-1].launch_dir, "task.json")) as f:
d = json.load(f)
self._check_run(d, mode="structure optimization")
wf = self.lp.get_wf_by_fw_id(1)
self.assertTrue(all([s == 'COMPLETED' for s in wf.fw_states.values()]))
def wf_scan_opt(structure, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
user_incar_settings = c.get("USER_INCAR_SETTINGS", {})
half_kpts = c.get("HALF_KPOINTS_FIRST_RELAX", HALF_KPOINTS_FIRST_RELAX)
ediffg = user_incar_settings.get("EDIFFG", -0.05)
wf = get_wf(
structure,
"optimize_only.yaml",
vis=MVLScanRelaxSet(
structure, user_incar_settings=user_incar_settings),
common_params={
"vasp_cmd": vasp_cmd,
"db_file": db_file
})
wf = use_custodian(
wf,
custodian_params={
"ediffg": ediffg,
"max_force_threshold": 0,
"half_kpts_first_relax": half_kpts,
"job_type": "metagga_opt_run",
"db_file": db_file,
"vasp_cmd": vasp_cmd
})
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
if c.get("REMOVE_WAVECAR", REMOVE_WAVECAR):
wf = clean_up_files(wf)
return wf
def get_wf_magnetic_deformation(structure, c=None, vis=None):
"""
Minimal workflow to obtain magnetic deformation proxy, as
defined by Bocarsly et al. 2017, doi: 10.1021/acs.chemmater.6b04729
Args:
structure: input structure, must be structure with magnetic
elements, such that pymatgen will initalize ferromagnetic input by
default -- see MPRelaxSet.yaml for list of default elements
c: Workflow config dict, in the same format
as in presets/core.py and elsewhere in atomate
vis: A VaspInputSet to use for the first FW
Returns: Workflow
"""
if not structure.is_ordered:
raise ValueError(
"Please obtain an ordered approximation of the input structure."
)
structure = structure.get_primitive_structure(use_site_props=True)
# using a uuid for book-keeping,
# in a similar way to other workflows
uuid = str(uuid4())
c_defaults = {"vasp_cmd": VASP_CMD, "db_file": DB_FILE}
if c:
c.update(c_defaults)
else:
c = c_defaults
wf = get_wf(structure, "magnetic_deformation.yaml", common_params=c, vis=vis)
fw_analysis = Firework(
MagneticDeformationToDB(
db_file=DB_FILE, wf_uuid=uuid, to_db=c.get("to_db", True)
),
name="MagneticDeformationToDB",
)
wf.append_wf(Workflow.from_Firework(fw_analysis), wf.leaf_fw_ids)
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
wf = add_additional_fields_to_taskdocs(
wf,
{
"wf_meta": {
"wf_uuid": uuid,
"wf_name": "magnetic_deformation",
"wf_version": __magnetic_deformation_wf_version__,
}
},
)
return wf
def get_wf_magnetic_deformation(structure, c=None, vis=None):
"""
Minimal workflow to obtain magnetic deformation proxy, as
defined by Bocarsly et al. 2017, doi: 10.1021/acs.chemmater.6b04729
Args:
structure: input structure, must be structure with magnetic
elements, such that pymatgen will initalize ferromagnetic input by
default -- see MPRelaxSet.yaml for list of default elements
c: Workflow config dict, in the same format
as in presets/core.py and elsewhere in atomate
vis: A VaspInputSet to use for the first FW
Returns: Workflow
"""
if not structure.is_ordered:
raise ValueError(
"Please obtain an ordered approximation of the input structure.")
structure = structure.get_primitive_structure(use_site_props=True)
# using a uuid for book-keeping,
# in a similar way to other workflows
uuid = str(uuid4())
c_defaults = {"vasp_cmd": VASP_CMD, "db_file": DB_FILE}
if c:
c.update(c_defaults)
else:
c = c_defaults
wf = get_wf(structure,
"magnetic_deformation.yaml",
common_params=c,
vis=vis)
fw_analysis = Firework(
MagneticDeformationToDb(db_file=DB_FILE,
wf_uuid=uuid,
to_db=c.get("to_db", True)),
name="MagneticDeformationToDb",
)
wf.append_wf(Workflow.from_Firework(fw_analysis), wf.leaf_fw_ids)
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
wf = add_additional_fields_to_taskdocs(
wf,
{
"wf_meta": {
"wf_uuid": uuid,
"wf_name": "magnetic_deformation",
"wf_version": __magnetic_deformation_wf_version__,
}
},
)
return wf
def test_SCAN_with_vdw(self):
# Verify appropriate changes to the INCAR when VdW is enabled
# VdW should be off for relax1 (GGA) and re-enabled for relax2 (SCAN)
structure = Structure.from_file(
os.path.join(reference_dir,
"PBESol_pre_opt_for_SCAN_LiF_vdw/inputs", "POSCAR"))
my_wf = get_wf(structure,
"metagga_optimization.yaml",
common_params={
"vasp_input_set_params": {
"vdw": "rVV10"
},
"vdw_kernel_dir":
os.path.join(
reference_dir,
"PBESol_pre_opt_for_SCAN_LiF_vdw/inputs")
})
fw_ids = self._run_scan_relax(my_wf, "LiF_vdw")
# Check PBESol INCAR
ref_incar = Incar.from_file(
os.path.join(reference_dir,
"PBESol_pre_opt_for_SCAN_LiF_vdw/inputs", "INCAR"))
incar = Incar.from_file(
os.path.join(self._get_launch_dir()[0], "INCAR.gz"))
self.assertIsNone(incar.get("LUSE_VDW", None))
self.assertIsNone(incar.get("BPARAM", None))
for p in incar.keys():
if p == "KSPACING":
self.assertEqual(incar[p], 0.22)
elif p == "ICHARG":
self.assertEqual(incar[p], 1)
elif p == "METAGGA":
self.assertEqual(incar[p], "None")
elif p == "GGA":
self.assertEqual(incar[p], "Ps")
elif p == "EDIFFG":
self.assertEqual(incar[p], -0.05)
elif p == "MAGMOM": # Ignore MAGMOM b/c structure initialized from POSCAR cannot have a MAGMOM
pass
else:
self.assertEqual(incar[p], ref_incar[p])
# Check SCAN INCAR
ref_incar = Incar.from_file(
os.path.join(reference_dir,
"SCAN_structure_optimization_LiF_vdw/inputs",
"INCAR"))
incar = Incar.from_file(
os.path.join(self._get_launch_dir()[1], "INCAR.gz"))
for p in incar.keys():
if p == "KSPACING":
self.assertEqual(incar[p], 0.44)
elif p == "SIGMA":
self.assertEqual(incar[p], 0.05)
elif p == "ICHARG":
self.assertEqual(incar[p], 1)
else:
self.assertEqual(incar[p], ref_incar[p])
# get a fw that can be used to identify the workflow
fw_id = list(fw_ids.values())[0]
# check workflow finished without error
wf = self.lp.get_wf_by_fw_id(fw_id)
is_completed = [s == "COMPLETED" for s in wf.fw_states.values()]
self.assertTrue(all(is_completed))
def wf_bulk_modulus(structure, c=None):
"""
Bulk modulus workflow from the given structure and config dict.
Args:
structure (Structure): input structure
c (dict): workflow config dict
Returns:
Workflow
"""
c = c or {}
eos = c.get("EOS", "vinet")
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
user_kpoints_settings = {"grid_density": 7000}
# 6 deformations
deformations = [(np.identity(3) * (1 + x)).tolist()
for x in np.linspace(-0.05, 0.05, 6)]
tag = "bulk_modulus group: >>{}<<".format(str(uuid4()))
# input set for structure optimization
vis_relax = MPRelaxSet(structure, force_gamma=True)
v = vis_relax.as_dict()
v.update({"user_kpoints_settings": user_kpoints_settings})
vis_relax = vis_relax.__class__.from_dict(v)
# static input set for the transmute firework
uis_static = {"ISIF": 2, "ISTART": 1, "IBRION": 2, "NSW": 99}
# optimization only workflow
wf = get_wf(structure,
"optimize_only.yaml",
params=[{
"vasp_cmd": vasp_cmd,
"db_file": db_file,
"name": "{} structure optimization".format(tag)
}],
vis=vis_relax)
vis_static = MPStaticSet(structure,
force_gamma=True,
lepsilon=False,
user_kpoints_settings=user_kpoints_settings,
user_incar_settings=uis_static)
# get the deformations wflow for bulk modulus calculation
wf_bm = get_wf_bulk_modulus(structure,
eos=eos,
user_kpoints_settings=user_kpoints_settings,
deformations=deformations,
vasp_cmd=vasp_cmd,
db_file=db_file,
tag=tag,
vasp_input_set=vis_static)
# chain it
wf.append_wf(wf_bm, wf.leaf_fw_ids)
wf = add_modify_incar(
wf,
modify_incar_params={"incar_update": {
"ENCUT": 600,
"EDIFF": 1e-6
}})
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf