def __init__(self,save_old_file=False):
# read in what is there
json_filename = 'run_data.json'
try:
with open(json_filename,'r') as f:
data =json.load(f)
except:
print("CANNOT FIND run_data.json: CLASS MUST BE CALLED IN DIRECTORY WHERE FILE IS")
return
last_step = data['relaxation'][-1]
structure = pymatgen.Structure.from_dict(last_step['structure'])
composition = structure.composition
energy = last_step['electronic']['e_0_energy']
set = MPVaspInputSet()
incar = set.get_incar(structure)
poscar = set.get_poscar(structure)
potcar = set.get_potcar(structure)
parameters = self.parse_pseudo_inputs(poscar,incar,potcar)
entry = pymatgen.entries.computed_entries.ComputedEntry(composition, energy, parameters=parameters )
data['ComputedEntry'] = entry
if save_old_file:
shutil.move('run_data.json','run_data_OLD.json')
pmg_dump(data, 'run_data.json')
return
def __init__(self, save_old_file=False):
# read in what is there
json_filename = 'run_data.json'
try:
with open(json_filename, 'r') as f:
data = json.load(f)
except:
print(
"CANNOT FIND run_data.json: CLASS MUST BE CALLED IN DIRECTORY WHERE FILE IS"
)
return
last_step = data['relaxation'][-1]
structure = pymatgen.Structure.from_dict(last_step['structure'])
composition = structure.composition
energy = last_step['electronic']['e_0_energy']
set = MPVaspInputSet()
incar = set.get_incar(structure)
poscar = set.get_poscar(structure)
potcar = set.get_potcar(structure)
parameters = self.parse_pseudo_inputs(poscar, incar, potcar)
entry = pymatgen.entries.computed_entries.ComputedEntry(
composition, energy, parameters=parameters)
data['ComputedEntry'] = entry
if save_old_file:
shutil.move('run_data.json', 'run_data_OLD.json')
pmg_dump(data, 'run_data.json')
return
def get_MaterialsProject_VASP_inputs(structure, workdir, job_name, nproc=16, supplementary_incar_dict=None):
if os.path.exists(workdir):
print 'WORKDIR ALREADY EXISTS. DELETE TO LAUNCH NEW JOB'
return -1
os.mkdir(workdir)
input_set = MPVaspInputSet()
incar = input_set.get_incar(structure)
# set the number of parallel processors to sqrt(nproc),
# as recommended in manual.
incar.update({'NPAR':int(np.sqrt(nproc))})
if supplementary_incar_dict != None:
incar.update(supplementary_incar_dict)
poscar = input_set.get_poscar(structure)
kpoints = input_set.get_kpoints(structure)
potcar = input_set.get_potcar(structure)
incar.write_file(workdir+'INCAR')
poscar.write_file(workdir+'POSCAR', vasp4_compatible = True)
kpoints.write_file(workdir+'KPOINTS')
potcar.write_file(workdir+'POTCAR')
with open(workdir+'job.sh','w') as f:
f.write(submit_template.format(job_name,nproc))
with open(workdir+'clean.sh','w') as f:
f.write(clean_template)
return 0
def get_ModifiedMaterialsProject_VASP_inputs(structure, workdir, job_name, nproc=16,
U_strategy_instance = None, supplementary_incar_dict = None):
"""
Inputs will be inspired by MaterialsProject, but this function is appropriate
when we are seriously modifying the inputs such that they no longer conform to Materials Project.
"""
if os.path.exists(workdir):
print 'WORKDIR ALREADY EXISTS. DELETE TO LAUNCH NEW JOB'
return -1
os.mkdir(workdir)
# let's start with MP
input_set = MPVaspInputSet()
incar = input_set.get_incar(structure)
if U_strategy_instance != None:
# reading the structure here insures consistency, rather
# than having the strategy read the structure outside this driver.
U_strategy_instance.read_structure(structure)
# Generate all LDAU-related variables according to specified strategy.
LDAU_dict, poscar_need_hack, potcar_need_hack = U_strategy_instance.get_LDAU()
incar.update(LDAU_dict)
# set the number of parallel processors to sqrt(nproc),
# as recommended in manual.
incar.update({'NPAR':int(np.sqrt(nproc))})
if supplementary_incar_dict != None:
incar.update(supplementary_incar_dict)
poscar = input_set.get_poscar(structure)
kpoints = input_set.get_kpoints(structure)
potcar = input_set.get_potcar(structure)
incar.write_file(workdir+'INCAR')
poscar.write_file(workdir+'POSCAR', vasp4_compatible = True)
kpoints.write_file(workdir+'KPOINTS')
potcar.write_file(workdir+'POTCAR')
if poscar_need_hack:
# do we need specialized hacking of the poscar because of the U strategy?
new_poscar_lines = U_strategy_instance.get_new_poscar_lines()
with open(workdir+'POSCAR','w') as f:
for line in new_poscar_lines:
print >>f, line.strip()
if potcar_need_hack:
# do we need specialized hacking of the potcar because of the U strategy?
new_potcar_symbols = U_strategy_instance.get_new_potcar_symbols(potcar)
new_potcar = Potcar(new_potcar_symbols)
# overwrite the previous potcar
new_potcar.write_file(workdir+'POTCAR')
with open(workdir+'job.sh','w') as f:
f.write(submit_template.format(job_name,nproc))
with open(workdir+'clean.sh','w') as f:
f.write(clean_template)
return 0
for line in id_expgap:
words=line.split()
print words
id_line=words[0]
os.mkdir(id_line)
os.chdir(id_line)
s = mpr.get_structure_by_material_id(id_line)
# obtain structural information from Materials Project database
#print json.dumps(s.to_dict)
# convert structural infomation into a dictionary and then dump to a json file
user_incar_settings={"ALGO":'Normal',"EDIFF":1E-8,"ENCUT":500,"NSW":0,"LWAVE":True}
mpvis = MPVaspInputSet(user_incar_settings=user_incar_settings)
mpvis.get_incar(s).write_file('INCAR')
# from the GW input set, get the incar parameters, generate INCAR
print mpvis.get_incar(s)
#
kp_density = mpvis.get_kpoints(s).kpts[0]
# from the GW input set, get the k-point density
kpoints = Kpoints.gamma_automatic(kp_density)
# generate Gamma centered k-point mesh
kpoints.write_file('KPOINTS')
# generate KPOINTS file
mpvis.get_poscar(s).write_file('POSCAR')
# generate POSCAR file
mpvis.get_potcar(s).write_file('POTCAR')
# generate POTCAR file
os.chdir('..')
id_expgap.close()
