def test_lsorbit_magmom(self):
magmom1 = [[0.0, 0.0, 3.0], [0, 1, 0], [2, 1, 2]]
magmom2 = [-1,-1,-1, 0, 0, 0, 0 ,0 ]
ans_string1 = "LSORBIT = True\nMAGMOM = 0.0 0.0 3.0 0 1 0 2 1 2\n"
ans_string2 = "LSORBIT = True\nMAGMOM = 3*3*-1 3*5*0\n"
ans_string3 = "LSORBIT = False\nMAGMOM = 2*-1 2*9\n"
incar = Incar({})
incar["MAGMOM"] = magmom1
incar["LSORBIT"] = "T"
self.assertEqual(ans_string1, str(incar))
incar["MAGMOM"] = magmom2
incar["LSORBIT"] = "T"
self.assertEqual(ans_string2, str(incar))
incar = Incar.from_string(ans_string1)
self.assertEqual(incar["MAGMOM"], [[0.0, 0.0, 3.0], [0, 1, 0], [2, 1, 2]])
incar = Incar.from_string(ans_string2)
self.assertEqual(incar["MAGMOM"], [[-1, -1, -1], [-1, -1, -1],
[-1, -1, -1], [0, 0, 0],
[0, 0, 0], [0, 0, 0],
[0, 0, 0], [0, 0, 0]])
incar = Incar.from_string(ans_string3)
self.assertFalse(incar["LSORBIT"])
self.assertEqual(incar["MAGMOM"], [-1, -1, 9, 9])
def test_lsorbit_magmom(self):
magmom1 = [[0.0, 0.0, 3.0], [0, 1, 0], [2, 1, 2]]
magmom2 = [-1, -1, -1, 0, 0, 0, 0, 0]
ans_string1 = "LSORBIT = True\nMAGMOM = 0.0 0.0 3.0 0 1 0 2 1 2\n"
ans_string2 = "LSORBIT = True\nMAGMOM = 3*3*-1 3*5*0\n"
ans_string3 = "LSORBIT = False\nMAGMOM = 2*-1 2*9\n"
incar = Incar({})
incar["MAGMOM"] = magmom1
incar["LSORBIT"] = "T"
self.assertEqual(ans_string1, str(incar))
incar["MAGMOM"] = magmom2
incar["LSORBIT"] = "T"
self.assertEqual(ans_string2, str(incar))
incar = Incar.from_string(ans_string1)
self.assertEqual(incar["MAGMOM"], [[0.0, 0.0, 3.0], [0, 1, 0], [2, 1, 2]])
incar = Incar.from_string(ans_string2)
self.assertEqual(
incar["MAGMOM"],
[[-1, -1, -1], [-1, -1, -1], [-1, -1, -1], [0, 0, 0], [0, 0, 0], [0, 0, 0], [0, 0, 0], [0, 0, 0]],
)
incar = Incar.from_string(ans_string3)
self.assertFalse(incar["LSORBIT"])
self.assertEqual(incar["MAGMOM"], [-1, -1, 9, 9])
def test_lsorbit_magmom(self):
magmom1 = [[0.0, 0.0, 3.0], [0, 1, 0], [2, 1, 2]]
magmom2 = [-1, -1, -1, 0, 0, 0, 0, 0]
magmom4 = [Magmom([1.0, 2.0, 2.0])]
ans_string1 = (
"LANGEVIN_GAMMA = 10 10 10\nLSORBIT = True\n"
"MAGMOM = 0.0 0.0 3.0 0 1 0 2 1 2\n"
)
ans_string2 = "LANGEVIN_GAMMA = 10\nLSORBIT = True\n" "MAGMOM = 3*3*-1 3*5*0\n"
ans_string3 = "LSORBIT = False\nMAGMOM = 2*-1 2*9\n"
ans_string4_nolsorbit = "LANGEVIN_GAMMA = 10\nLSORBIT = False\nMAGMOM = 1*3.0\n"
ans_string4_lsorbit = (
"LANGEVIN_GAMMA = 10\nLSORBIT = True\nMAGMOM = 1.0 2.0 2.0\n"
)
incar = Incar({})
incar["MAGMOM"] = magmom1
incar["LSORBIT"] = "T"
incar["LANGEVIN_GAMMA"] = [10, 10, 10]
self.assertEqual(ans_string1, str(incar))
incar["MAGMOM"] = magmom2
incar["LSORBIT"] = "T"
incar["LANGEVIN_GAMMA"] = 10
self.assertEqual(ans_string2, str(incar))
incar["MAGMOM"] = magmom4
incar["LSORBIT"] = "F"
self.assertEqual(ans_string4_nolsorbit, str(incar))
incar["LSORBIT"] = "T"
self.assertEqual(ans_string4_lsorbit, str(incar))
incar = Incar.from_string(ans_string1)
self.assertEqual(incar["MAGMOM"], [[0.0, 0.0, 3.0], [0, 1, 0], [2, 1, 2]])
self.assertEqual(incar["LANGEVIN_GAMMA"], [10, 10, 10])
incar = Incar.from_string(ans_string2)
self.assertEqual(
incar["MAGMOM"],
[
[-1, -1, -1],
[-1, -1, -1],
[-1, -1, -1],
[0, 0, 0],
[0, 0, 0],
[0, 0, 0],
[0, 0, 0],
[0, 0, 0],
],
)
self.assertEqual(incar["LANGEVIN_GAMMA"], [10])
incar = Incar.from_string(ans_string3)
self.assertFalse(incar["LSORBIT"])
self.assertEqual(incar["MAGMOM"], [-1, -1, 9, 9])
def test_quad_efg(self):
incar1 = Incar({})
incar1["LEFG"] = True
incar1["QUAD_EFG"] = [0.0, 146.6, -25.58]
ans_string1 = "LEFG = True\nQUAD_EFG = 0.0 146.6 -25.58\n"
self.assertEqual(ans_string1, str(incar1))
incar2 = Incar.from_string(ans_string1)
self.assertEqual(ans_string1, str(incar2))
def test_quad_efg(self):
incar1 = Incar({})
incar1["LEFG"] = True
incar1["QUAD_EFG"] = [0.0, 146.6, -25.58]
ans_string1 = "LEFG = True\nQUAD_EFG = 0.0 146.6 -25.58\n"
self.assertEqual(ans_string1, str(incar1))
incar2 = Incar.from_string(ans_string1)
self.assertEqual(ans_string1, str(incar2))
def test_lsorbit_magmom(self):
magmom1 = [[0.0, 0.0, 3.0], [0, 1, 0], [2, 1, 2]]
magmom2 = [-1, -1, -1, 0, 0, 0, 0, 0]
magmom4 = [Magmom([1.0, 2.0, 2.0])]
ans_string1 = "LANGEVIN_GAMMA = 10 10 10\nLSORBIT = True\n" \
"MAGMOM = 0.0 0.0 3.0 0 1 0 2 1 2\n"
ans_string2 = "LANGEVIN_GAMMA = 10\nLSORBIT = True\n" \
"MAGMOM = 3*3*-1 3*5*0\n"
ans_string3 = "LSORBIT = False\nMAGMOM = 2*-1 2*9\n"
ans_string4_nolsorbit = "LANGEVIN_GAMMA = 10\nLSORBIT = False\nMAGMOM = 1*3.0\n"
ans_string4_lsorbit = "LANGEVIN_GAMMA = 10\nLSORBIT = True\nMAGMOM = 1.0 2.0 2.0\n"
incar = Incar({})
incar["MAGMOM"] = magmom1
incar["LSORBIT"] = "T"
incar["LANGEVIN_GAMMA"] = [10, 10, 10]
self.assertEqual(ans_string1, str(incar))
incar["MAGMOM"] = magmom2
incar["LSORBIT"] = "T"
incar["LANGEVIN_GAMMA"] = 10
self.assertEqual(ans_string2, str(incar))
incar["MAGMOM"] = magmom4
incar["LSORBIT"] = "F"
self.assertEqual(ans_string4_nolsorbit, str(incar))
incar["LSORBIT"] = "T"
self.assertEqual(ans_string4_lsorbit, str(incar))
incar = Incar.from_string(ans_string1)
self.assertEqual(incar["MAGMOM"],
[[0.0, 0.0, 3.0], [0, 1, 0], [2, 1, 2]])
self.assertEqual(incar["LANGEVIN_GAMMA"], [10, 10, 10])
incar = Incar.from_string(ans_string2)
self.assertEqual(incar["MAGMOM"], [[-1, -1, -1], [-1, -1, -1],
[-1, -1, -1], [0, 0, 0],
[0, 0, 0], [0, 0, 0],
[0, 0, 0], [0, 0, 0]])
self.assertEqual(incar["LANGEVIN_GAMMA"], [10])
incar = Incar.from_string(ans_string3)
self.assertFalse(incar["LSORBIT"])
self.assertEqual(incar["MAGMOM"], [-1, -1, 9, 9])
def GW_step1(name,
spin_polarized=True,
submit=True,
incar_dict={},
force_overwrite=False):
#name is the name of the job that will be used in submit file
incar = Incar.from_string("""ISMEAR = 1 ; SIGMA = 0.2
ALGO = Exact ; NELM = 1 # exact diagonalization one step suffices
EDIFF = 1E-8 # high precision for groundstate calculation
NBANDS = 96 # need for a lot of bands in GW
LOPTICS = .TRUE. # we need d phi/ d k for GW calculations
KPAR = 2""")
if spin_polarized:
if os.path.exists('POSCAR'):
incar.update({
'LORBIT':
11,
'ISPIN':
2,
'MAGMOM':
get_magmom_string(Structure.from_file('POSCAR'))
})
else:
raise IOError('No POSCAR found at ' + os.getcwd())
if os.path.isdir('step1'):
os.chdir('step1')
else:
os.mkdir('step1')
os.chdir('step1')
if force_overwrite:
os.system('rm -rf *')
incar.update(incar_dict)
incar.write_file('INCAR')
os.system('cp ../{KPOINTS,POSCAR,CONTCAR,POTCAR} .')
if os.path.exists('CONTCAR') and os.stat('CONTCAR').st_size > 10:
shutil.move('CONTCAR', 'POSCAR')
submit_builder(update_dict={
'--mem-per-cpu': '3gb',
'--job-name': name,
'--nodes': 2,
'--ntasks': 32
})
if submit:
os.system('sbatch submit')
os.chdir('../')
def test_types(self):
incar_str = """ALGO = Fast
ECUT = 510
EDIFF = 1e-07
EINT = -0.85 0.85
IBRION = -1
ICHARG = 11
ISIF = 3
ISMEAR = 1
ISPIN = 1
LPARD = True
NBMOD = -3
PREC = Accurate
SIGMA = 0.1"""
i = Incar.from_string(incar_str)
self.assertIsInstance(i["EINT"], list)
self.assertEqual(i["EINT"][0], -0.85)
incar_str += "\nLHFCALC = .TRUE. ; HFSCREEN = 0.2"
incar_str += "\nALGO = All;"
i = Incar.from_string(incar_str)
self.assertTrue(i["LHFCALC"])
self.assertEqual(i["HFSCREEN"], 0.2)
self.assertEqual(i["ALGO"], "All")
def test_types(self):
incar_str = """ALGO = Fast
ECUT = 510
EDIFF = 1e-07
EINT = -0.85 0.85
IBRION = -1
ICHARG = 11
ISIF = 3
ISMEAR = 1
ISPIN = 1
LPARD = True
NBMOD = -3
PREC = Accurate
SIGMA = 0.1"""
i = Incar.from_string(incar_str)
self.assertIsInstance(i["EINT"], list)
self.assertEqual(i["EINT"][0], -0.85)
incar_str += "\nLHFCALC = .TRUE. ; HFSCREEN = 0.2"
incar_str += "\nALGO = All;"
i = Incar.from_string(incar_str)
self.assertTrue(i["LHFCALC"])
self.assertEqual(i["HFSCREEN"], 0.2)
self.assertEqual(i["ALGO"], "All")
def write_wannier_input_file(S, spin_polarized=True, write_incar=True):
string = """Begin Projections
random
End Projections
guiding_centres=true
bands_plot = true
begin kpoint_path\n"""
string += get_kpoints_wannier(S) + '\n'
string += 'end kpoint_path\n'
if spin_polarized:
string += 'spinors=true\n'
w = open('wannier90.win', 'w')
w.write(string)
w.close()
#write INCAR
if write_incar:
incar = Incar.from_string("""ISMEAR = -5
# usefull energy range for density of states
ALGO = None ; NELM = 1 # exact diagonalization one step suffices
NBANDS = 96 # need for a lot of bands in GW
LORBIT = 11
LWRITE_MMN_AMN = TRUE
LWANNIER90_RUN = .TRUE.""")
try:
NBANDS = Incar.from_file('../../step1/INCAR')['NBANDS']
except:
NBANDS = Incar.from_file('../INCAR')['NBANDS']
if spin_polarized:
if os.path.exists('POSCAR'):
incar.update({
'LORBIT':
11,
'ISPIN':
2,
'MAGMOM':
get_magmom_string(Structure.from_file('POSCAR'))
})
else:
raise IOError('No POSCAR found at ' + os.getcwd())
incar.update({'NBANDS': NBANDS})
incar.write_file('INCAR')
def test_types(self):
incar_str = """ALGO = Fast
ECUT = 510
EDIFF = 1e-07
EINT = -0.85 0.85
IBRION = -1
ICHARG = 11
ISIF = 3
ISMEAR = 1
ISPIN = 1
LPARD = True
NBMOD = -3
PREC = Accurate
SIGMA = 0.1"""
i = Incar.from_string(incar_str)
self.assertIsInstance(i["EINT"], list)
self.assertEqual(i["EINT"][0], -0.85)
def test_types(self):
incar_str = """ALGO = Fast
ECUT = 510
EDIFF = 1e-07
EINT = -0.85 0.85
IBRION = -1
ICHARG = 11
ISIF = 3
ISMEAR = 1
ISPIN = 1
LPARD = True
NBMOD = -3
PREC = Accurate
SIGMA = 0.1"""
i = Incar.from_string(incar_str)
self.assertIsInstance(i["EINT"], list)
self.assertEqual(i["EINT"][0], -0.85)
def get_wf_single(structure,
WORKFLOW="get_wf_gibbs",
settings={},
db_file=None):
"""
Get a single workflow
Parameters
structure: pymatgen.Structure
The structure
WORKFLOW: str
The name of the workflow, now only gibbs energy workflow(get_wf_gibbs) is supported
settings: dict
User settings for the workflow
Return
"""
################ PARAMETERS FOR WF #############################
#str, the absolute path of db.json file, e.g. /storage/home/mjl6505/atomate/config/db.json
# If None, it will use the configuration in fireworks
if db_file is None:
db_file = settings.get('db_file', None)
#list, the MAGMOM of the structure, e.g. [4.0, 4.0, -4.0, -4.0]
magmom = settings.get('magmom', None)
magmom = parse_magmom(magmom=magmom, nvalue=len(structure.sites))
#int, the number of initial deformations, e.g. 7
num_deformations = settings.get('num_deformations', 7)
#list/tuple(min, max) or float(-max, max), the maximum amplitude of deformation, e.g. (-0.15, 0.15) means (0.95, 1.1) in volume
deformation_fraction = settings.get('deformation_fraction', (-0.15, 0.20))
#float, minimum ratio of Volumes spacing, e.g. 0.05
volume_spacing_min = settings.get('volume_spacing_min', 0.05)
#bool, run phonon(True) or not(False)
phonon = settings.get('phonon', False)
#list(3x3), the supercell matrix for phonon, e.g. [[2.0, 0, 0], [0, 2.0, 0], [0, 0, 2.0]]
phonon_supercell_matrix = settings.get('phonon_supercell_matrix', None)
phonon_supercell_matrix_min = settings.get('phonon_supercell_matrix_min',
None)
phonon_supercell_matrix_max = settings.get('phonon_supercell_matrix_max',
None)
optimize_sc = settings.get('optimize_sc', False)
#run phonon always, no matter ISIF=4 passed or not
force_phonon = settings.get('force_phonon', False)
#The tolerance for phonon stable
stable_tor = settings.get('stable_tor', 0.01)
#float, the mimimum of temperature in QHA process, e.g. 5
t_min = settings.get('t_min', 5)
#float, the maximum of temperature in QHA process, e.g. 2000
t_max = settings.get('t_max', 2000)
#float, the step of temperature in QHA process, e.g. 5
t_step = settings.get('t_step', 5)
#float, acceptable value for average RMS, recommend >= 0.005
eos_tolerance = settings.get('eos_tolerance', 0.01)
#str, the vasp command, if None then find in the FWorker configuration
vasp_cmd = settings.get('vasp_cmd', None)
#dict, metadata to be included, this parameter is useful for filter the data, e.g. metadata={"phase": "BCC_A2", "tag": "AFM"}
metadata = settings.get('metadata', None)
#It is for RobustOptimizeFW, if run ISIF=4 followed ISIF=7
isif4 = settings.get('isif4', False)
#The level for robust optimization
level = settings.get('level', 1)
#float, the tolerannce for symmetry, e.g. 0.05
symmetry_tolerance = settings.get('symmetry_tolerance', 0.05)
#bool, set True to pass initial VASP running if the results exist in DB, use carefully to keep data consistent.
passinitrun = settings.get('passinitrun', False)
#bool, Whether run isif=2 calculation before isif=4 running
run_isif2 = settings.get('run_isif2', False)
#bool, Whether pass isif=4 calculation.
pass_isif4 = settings.get('pass_isif4', False)
#Set the path already exists for new static calculations; if set as '', will try to get the path from db_file
relax_path = settings.get('relax_path', '')
#The symmetry tolerance, including three keys,
#e.g. override_symmetry_tolerances={'tol_strain': 0.05, 'tol_energy': 0.025, 'tol_bond': 0.10}
override_symmetry_tolerances = settings.get('override_symmetry_tolerances',
None)
#Global settings for all vasp job, e.g.
#override_default_vasp_params = {'user_incar_settings': {}, 'user_kpoints_settings': {}, 'user_potcar_functional': str}
#If some value in 'user_incar_settings' is set to None, it will use vasp's default value
override_default_vasp_params = settings.get('override_default_vasp_params',
{})
#dict, dict of class ModifyIncar with keywords in Workflow name. e.g.
"""
modify_incar_params = { 'Full relax': {'incar_update': {"LAECHG":False,"LCHARG":False,"LWAVE":False}},
'PreStatic': {'incar_update': {"LAECHG":False,"LCHARG":False,"LWAVE":False}},
'PS2': {'incar_update': {"LAECHG":False,"LCHARG":False,"LWAVE":False}},
'static': {'incar_update': {"LAECHG":False,"LCHARG":False,"LWAVE":False}},
"""
modify_incar_params = settings.get('modify_incar_params', {})
#check if fworker_name is assigned
powerups = settings.get('powerups', {})
"""
if len(powerups)>0:
if 'user_incar_settings' not in override_default_vasp_params:
override_default_vasp_params.update({'user_incar_settings':{}})
override_default_vasp_params['user_incar_settings'].update({'powerups':powerups})
modify_incar_params.update({'powerups':powerups})
"""
#dict, dict of class ModifyKpoints with keywords in Workflow name, similar with modify_incar_params
modify_kpoints_params = settings.get('modify_kpoints_params', {})
#bool, print(True) or not(False) some informations, used for debug
verbose = settings.get('verbose', False)
#Save the volume data or not ("chgcar", "aeccar0", "aeccar2", "elfcar", "locpot")
store_volumetric_data = settings.get('store_volumetric_data', False)
## The following settings only work for elastic constants workflow
strain_states = settings.get('strain_states', None)
stencils = settings.get('stencils', None)
analysis = settings.get('analysis', True)
sym_reduce = settings.get('sym_reduce', False)
order = settings.get('order', 2)
conventional = settings.get('conventional', False)
"""
stencils = settings.get('stencils', [0.01])
#sym_reduce = settings.get('sym_reduce', True)
stencils = settings.get('stencils', [-0.01,0.01])
#conventional = settings.get('conventional', True)
"""
#Set the default value for phonon_supercell_matrix_min/max
if isinstance(phonon_supercell_matrix,
str) and (phonon_supercell_matrix_min is None):
if phonon_supercell_matrix.lower().startswith('a'):
phonon_supercell_matrix_min = 60
phonon_supercell_matrix_max = 130
elif phonon_supercell_matrix.lower().startswith('l'):
phonon_supercell_matrix_min = 8
phonon_supercell_matrix_max = 12
elif phonon_supercell_matrix.lower().startswith('v'):
phonon_supercell_matrix_min = 512
phonon_supercell_matrix_max = 1728
else:
raise ValueError(
"Unknown parameters for phonon_supercell_matrix({}), support 'atoms', 'lattice' or 'volume' or 3x3 list."
.format(phonon_supercell_matrix))
uis = override_default_vasp_params.get('user_incar_settings', {})
if magmom:
structure.add_site_property('magmom', magmom)
elif 'MAGMOM' in uis:
magmom = uis['MAGMOM']
if isinstance(magmom, str):
magmom = Incar.from_string(
'MAGMOM={}'.format(magmom)).as_dict()['MAGMOM']
magmom = parse_magmom(magmom=magmom, nvalue=len(structure.sites))
structure.add_site_property('magmom', magmom)
if not db_file:
#from fireworks.fw_config import config_to_dict
#db_file = loadfn(config_to_dict()["FWORKER_LOC"])["env"]["db_file"]
db_file = ">>db_file<<"
"""
if WORKFLOW == "get_wf_gibbs":
#Currently, only this workflow is supported
wf = get_wf_gibbs(structure, num_deformations=num_deformations, deformation_fraction=deformation_fraction,
phonon=phonon, phonon_supercell_matrix=phonon_supercell_matrix, t_min=t_min, t_max=t_max,
t_step=t_step, eos_tolerance=eos_tolerance, volume_spacing_min=volume_spacing_min,vasp_cmd=vasp_cmd,
db_file=db_file, metadata=metadata, name='EV_QHA', symmetry_tolerance=symmetry_tolerance,
run_isif2=run_isif2, pass_isif4=pass_isif4, passinitrun=passinitrun, relax_path=relax_path,
modify_incar_params=modify_incar_params, modify_kpoints_params=modify_kpoints_params,
verbose=verbose, store_volumetric_data=store_volumetric_data)
elif WORKFLOW == "eos":
"""
if WORKFLOW == "eos":
wf = get_wf_EV_bjb(
structure,
deformation_fraction=deformation_fraction,
store_volumetric_data=store_volumetric_data,
num_deformations=num_deformations,
settings=settings,
override_symmetry_tolerances=override_default_vasp_params,
metadata=metadata)
elif WORKFLOW == "singleV":
wf = get_wf_singleV(
structure,
store_volumetric_data=store_volumetric_data,
metadata=metadata,
override_default_vasp_params=override_default_vasp_params,
settings=settings)
elif WORKFLOW == "crosscom":
wf = get_wf_crosscom(structure, metadata=metadata, settings=settings)
elif WORKFLOW == "robust" or WORKFLOW == "get_wf_gibbs":
wf = get_wf_gibbs_robust(
structure,
num_deformations=num_deformations,
deformation_fraction=deformation_fraction,
phonon=phonon,
phonon_supercell_matrix=phonon_supercell_matrix,
t_min=t_min,
t_max=t_max,
t_step=t_step,
eos_tolerance=eos_tolerance,
volume_spacing_min=volume_spacing_min,
vasp_cmd=">>vasp_cmd<<",
db_file=">>db_file<<",
isif4=isif4,
metadata=metadata,
name='EV_QHA',
override_symmetry_tolerances=override_symmetry_tolerances,
override_default_vasp_params=override_default_vasp_params,
modify_incar_params=modify_incar_params,
modify_kpoints_params=modify_kpoints_params,
verbose=verbose,
phonon_supercell_matrix_min=phonon_supercell_matrix_min,
phonon_supercell_matrix_max=phonon_supercell_matrix_max,
optimize_sc=optimize_sc,
level=level,
force_phonon=force_phonon,
stable_tor=stable_tor,
store_volumetric_data=store_volumetric_data,
settings=settings)
elif WORKFLOW == "born":
wf = get_wf_borncharge(
structure=structure,
metadata=metadata,
db_file=db_file,
isif=2,
name="born charge",
vasp_cmd=">>vasp_cmd<<",
override_default_vasp_params=override_default_vasp_params,
modify_incar=modify_incar_params,
settings=settings)
elif WORKFLOW == 'elastic':
wf = get_wf_elastic(
structure=structure,
metadata=metadata,
vasp_cmd=">>vasp_cmd<<",
db_file=">>db_file<<",
name="elastic",
override_default_vasp_params=override_default_vasp_params,
settings=settings,
strain_states=strain_states,
stencils=stencils,
analysis=analysis,
sym_reduce=sym_reduce,
order=order,
conventional=conventional)
else:
raise ValueError(
"Currently, only the gibbs energy workflow is supported.")
return wf
def GW_step2(name,
submit=True,
spin_polarized=True,
incar_dict={},
force_overwrite=False):
#Calculation is supposed to be run in parent directory (step1 should be there as well)
#incar_dict should not have NBANDS tag, since it will be extracted from step1/INCAR
incar = Incar.from_string("""
ISMEAR = -5
NBANDS = 96 # need for a lot of bands in GW
ALGO = GW0 #
NELM = 1
PRECFOCK = Fast
ENCUTGW = 100
NOMEGA = 200
KPAR = 2""")
if not os.path.isdir('step1'):
raise ValueError(
'It is not possible to run step2 before step1. Check if you are in right directory.'
)
os.chdir('step1')
if os.path.exists('WAVECAR') and os.path.exists('WAVEDER') and os.stat(
'WAVECAR').st_size > 100 and os.stat('WAVEDER').st_size > 100:
os.chdir('../')
try:
os.mkdir('step2')
os.chdir('step2')
except:
os.chdir('step2')
else:
raise ValueError(
'step1 calculation did not finish properly. WAVECAR and/or WAVEDER files are not written properly.'
)
if force_overwrite:
os.system('rm -rf *')
os.system('cp ../step1/{WAVE*,KPOINTS,POSCAR,POTCAR} .')
NBANDS = Incar.from_file('../step1/INCAR')['NBANDS']
incar.update({'NBANDS': NBANDS})
if spin_polarized:
if os.path.exists('POSCAR'):
incar.update({
'LORBIT':
11,
'ISPIN':
2,
'MAGMOM':
get_magmom_string(Structure.from_file('POSCAR'))
})
else:
raise IOError('No POSCAR found at ' + os.getcwd())
incar.write_file('INCAR')
submit_builder(update_dict={
'--mem-per-cpu': '3gb',
'--job-name': name,
'--nodes': 2,
'--ntasks': 32
})
if submit:
os.system('sbatch submit')
os.chdir('../')
