def run_task(self, fw_spec):
"""
Required Parameters:
folder (str path): Location where vasp inputs
are to be written
custodian_params (dict **kwargs): Contains the job and the
scratch directory for a custodian run
vaspdbinsert_parameters (dict **kwargs): Contains
informations needed to acess a DB, eg, host,
port, password etc.
Optional Parameters:
min_vac_size (float): Size of vacuum layer of slab in Angstroms
min_slab_size (float): Size of slab layer of slab in Angstroms
angle_tolerance (int): See SpaceGroupAnalyzer in analyzer.py
user_incar_settings (dict): See launch_workflow() method in
CreateSurfaceWorkflow class
k_product (dict): See launch_workflow() method in
CreateSurfaceWorkflow class
potcar_functional (dict): See launch_workflow() method in
CreateSurfaceWorkflow class
symprec (float): See SpaceGroupAnalyzer in analyzer.py
terminations (bool): Determines whether or not to consider
different terminations in a slab. If true, each slab with a
specific shift value will have its own Firework and each of the
slab calculations will run in parallel. Defaults to false which
sets the shift value to 0.
"""
dec = MontyDecoder()
folder = dec.process_decoded(self.get("folder"))
cwd = dec.process_decoded(self.get("cwd"))
symprec = dec.process_decoded(self.get("symprec", 0.001))
angle_tolerance = dec.process_decoded(self.get("angle_tolerance", 5))
terminations = dec.process_decoded(self.get("terminations", False))
custodian_params = dec.process_decoded(self.get("custodian_params"))
vaspdbinsert_parameters = \
dec.process_decoded(self.get("vaspdbinsert_parameters"))
user_incar_settings = \
dec.process_decoded(self.get("user_incar_settings",
MPSlabVaspInputSet().incar_settings))
k_product = \
dec.process_decoded(self.get("k_product", 50))
potcar_functional = \
dec.process_decoded(self.get("potcar_fuctional", 'PBE'))
min_slab_size = dec.process_decoded(self.get("min_slab_size", 10))
min_vacuum_size = dec.process_decoded(self.get("min_vacuum_size", 10))
miller_index = dec.process_decoded(self.get("miller_index"))
print 'about to make mplb'
mplb = MPSlabVaspInputSet(user_incar_settings=user_incar_settings,
k_product=k_product,
potcar_functional=potcar_functional,
ediff_per_atom=False)
# Create slabs from the relaxed oriented unit cell. Since the unit
# cell is already oriented with the miller index, entering (0,0,1)
# into SlabGenerator is the same as obtaining a slab in the
# orienetation of the original miller index.
print 'about to copy contcar'
contcar = Poscar.from_file("%s/CONTCAR.relax2.gz" %(cwd+folder))
relax_orient_uc = contcar.structure
print 'made relaxed oriented structure'
print relax_orient_uc
print 'making slab'
slabs = SlabGenerator(relax_orient_uc, (0,0,1),
min_slab_size=min_slab_size,
min_vacuum_size=min_vacuum_size,
max_normal_search=max(miller_index))
# Whether or not to create a list of Fireworks
# based on different slab terminations
print 'deciding terminations'
slab_list = slabs.get_slabs() if terminations else [slabs.get_slab()]
qe = QueryEngine(**vaspdbinsert_parameters)
optional_data = ["state"]
print 'query bulk entry for job completion'
bulk_entry = qe.get_entries({'chemsys': relax_orient_uc.composition.reduced_formula,
'structure_type': 'oriented_unit_cell', 'miller_index': miller_index},
optional_data=optional_data)
print 'chemical formula', relax_orient_uc.composition.reduced_formula
print 'fomular data type is ', type(relax_orient_uc.composition.reduced_formula)
print 'checking job completion'
print bulk_entry
for entry in bulk_entry:
print 'for loop'
print entry.data['state']
if entry.data['state'] != 'successful':
print "%s bulk calculations were incomplete, cancelling FW" \
%(relax_orient_uc.composition.reduced_formula)
return FWAction()
else:
print entry.data['state']
FWs = []
for slab in slab_list:
print slab
new_folder = folder.replace('bulk', 'slab')+'_shift%s' \
%(slab.shift)
# Will continue an incomplete job from a previous contcar file if it exists
print 'cwd is %s' %(os.getcwd())
print 'the folder is %s' %(new_folder)
print os.path.join(os.getcwd(), new_folder)
print cwd+'/'+new_folder
path = cwd+'/'+new_folder
# path = os.path.join(os.getcwd(), folder)
newfolder = os.path.join(path, 'prev_run')
# print 'check if conditions for continuing calculations have been satisfied'
# print 'check for the following path: %s' %(path)
# print os.path.exists(path)
# print os.path.exists(os.path.join(path, 'CONTCAR.gz'))
# print os.stat(os.path.join(path, 'CONTCAR.gz')).st_size !=0
def continue_vasp(contcar):
print folder, 'already exists, will now continue calculation'
print 'making prev_run folder'
os.system('mkdir %s' %(newfolder))
print 'moving outputs to prev_run'
os.system('mv %s/* %s/prev_run' %(path, path))
print 'moving outputs as inputs for next calculation'
os.system('cp %s/%s %s/INCAR %s/POTCAR %s/KPOINTS %s'
%(newfolder, contcar, newfolder, newfolder, newfolder, path))
print 'unzipping new inputs'
os.system('gunzip %s/*' %(path))
print 'copying contcar as new poscar'
if contcar == 'CONTCAR.relax1.gz':
os.system('mv %s/CONTCAR.relax1 %s/POSCAR' %(path , path))
else:
os.system('mv %s/CONTCAR %s/POSCAR' %(path , path))
if os.path.exists(path) and \
os.path.exists(os.path.join(path, 'CONTCAR')) and \
os.stat(os.path.join(path, 'CONTCAR')).st_size !=0:
continue_vasp('CONTCAR')
elif os.path.exists(path) and \
os.path.exists(os.path.join(path, 'CONTCAR.gz')) \
and os.stat(os.path.join(path, 'CONTCAR.gz')).st_size !=0:
continue_vasp('CONTCAR.gz')
elif os.path.exists(path) and \
os.path.exists(os.path.join(path, 'CONTCAR.relax1.gz')) and \
os.stat(os.path.join(path, 'CONTCAR.relax1.gz')).st_size !=0:
continue_vasp('CONTCAR.relax1.gz')
else:
mplb.write_input(slab, cwd+new_folder)
# Writes new INCAR file based on changes made by custodian on the bulk's INCAR.
# Only change in parameters between slab and bulk should be MAGMOM and ISIF
if os.path.exists("%s/INCAR.relax2.gz" %(cwd+folder)):
incar = Incar.from_file(cwd+folder +'/INCAR.relax2.gz')
else:
incar = Incar.from_file(cwd+folder +'/INCAR.relax2')
if os.path.exists("%s/OUTCAR.relax2.gz" %(cwd+folder)):
out = Outcar(cwd+folder+'/OUTCAR.relax2.gz')
else:
out = Outcar(cwd+folder+'/OUTCAR.relax2')
out_mag = out.magnetization
tot_mag = [mag['tot'] for mag in out_mag]
magmom = np.mean(tot_mag)
mag= [magmom for i in slab]
incar.__setitem__('MAGMOM', mag)
incar.__setitem__('ISIF', 2)
incar.__setitem__('AMIN', 0.01)
incar.__setitem__('AMIX', 0.2)
incar.__setitem__('BMIX', 0.001)
incar.__setitem__('NELMIN', 8)
incar.__setitem__('ISTART', 0)
incar.write_file(cwd+new_folder+'/INCAR')
fw = Firework([RunCustodianTask(dir=new_folder, cwd=cwd,
**custodian_params),
VaspSlabDBInsertTask(struct_type="slab_cell",
loc=new_folder, cwd=cwd, shift=slab.shift,
surface_area=slab.surface_area,
vsize=slabs.min_vac_size,
ssize=slabs.min_slab_size,
miller_index=miller_index,
**vaspdbinsert_parameters)],
name=new_folder)
FWs.append(fw)
return FWAction(additions=FWs)
def run_task(self, fw_spec):
"""
Required Parameters:
oriented_unit_cell (Structure): Generated with surface.py
folder (str path): Location where vasp inputs
are to be written
Optional Parameters:
angle_tolerance (int): See SpaceGroupAnalyzer in analyzer.py
user_incar_settings (dict): See launch_workflow() method in
CreateSurfaceWorkflow class
k_product (dict): See launch_workflow() method in
CreateSurfaceWorkflow class
potcar_functional (dict): See launch_workflow() method in
CreateSurfaceWorkflow class
symprec (float): See SpaceGroupAnalyzer in analyzer.py
"""
dec = MontyDecoder()
oriented_ucell = dec.process_decoded(self.get("oriented_ucell"))
folder = dec.process_decoded(self.get("folder"))
cwd = dec.process_decoded(self.get("cwd"))
symprec = dec.process_decoded(self.get("symprec", 0.001))
angle_tolerance = dec.process_decoded(self.get("angle_tolerance", 5))
user_incar_settings = \
dec.process_decoded(self.get("user_incar_settings",
MPSlabVaspInputSet().incar_settings))
k_product = \
dec.process_decoded(self.get("k_product", 50))
potcar_functional = \
dec.process_decoded(self.get("potcar_fuctional", 'PBE'))
# Will continue an incomplete job from a previous contcar file if it exists
print 'cwd is %s' %(os.getcwd())
print 'the folder is %s' %(folder)
print os.path.join(os.getcwd(), folder)
print cwd+'/'+folder
path = cwd+'/'+folder
# path = os.path.join(os.getcwd(), folder)
newfolder = os.path.join(path, 'prev_run')
# print 'check if conditions for continuing calculations have been satisfied'
# print 'check for the following path: %s' %(path)
# print os.path.exists(path)
# print os.path.exists(os.path.join(path, 'CONTCAR.gz'))
# print os.stat(os.path.join(path, 'CONTCAR.gz')).st_size !=0
def continue_vasp(contcar):
print folder, 'already exists, will now continue calculation'
print 'making prev_run folder'
os.system('mkdir %s' %(newfolder))
print 'moving outputs to prev_run'
os.system('mv %s/* %s/prev_run' %(path, path))
print 'moving outputs as inputs for next calculation'
os.system('cp %s/%s %s/INCAR %s/POTCAR %s/KPOINTS %s'
%(newfolder, contcar, newfolder, newfolder, newfolder, path))
print 'unzipping new inputs'
os.system('gunzip %s/*' %(path))
print 'copying contcar as new poscar'
if contcar == 'CONTCAR.relax1.gz':
os.system('mv %s/CONTCAR.relax1 %s/POSCAR' %(path , path))
else:
os.system('mv %s/CONTCAR %s/POSCAR' %(path , path))
if os.path.exists(path) and \
os.path.exists(os.path.join(path, 'CONTCAR')) and \
os.stat(os.path.join(path, 'CONTCAR')).st_size !=0:
continue_vasp('CONTCAR')
elif os.path.exists(path) and \
os.path.exists(os.path.join(path, 'CONTCAR.gz')) \
and os.stat(os.path.join(path, 'CONTCAR.gz')).st_size !=0:
continue_vasp('CONTCAR.gz')
elif os.path.exists(path) and \
os.path.exists(os.path.join(path, 'CONTCAR.relax1.gz')) and \
os.stat(os.path.join(path, 'CONTCAR.relax1.gz')).st_size !=0:
continue_vasp('CONTCAR.relax1.gz')
else:
mplb = MPSlabVaspInputSet(user_incar_settings=user_incar_settings,
k_product=k_product, bulk=True,
potcar_functional=potcar_functional,
ediff_per_atom=False)
mplb.write_input(oriented_ucell, cwd+folder)