def calculate(self, name, atoms):
data = DeltaCodesDFTTask.calculate(self, name, atoms)
try:
steps = atoms.get_calculator().get_number_of_iterations()
except (AttributeError, NotImplemented):
steps = None
data['calculator steps'] = steps
return data
'ecut':ecut,
'xc':'PBE',
'pps':'fhi',
'nstep':700,
'diemac': 1000,
'width':w,
'kpts':kd,
'chksymbreak':0,
'ecutsm':0.05,
'nsym':1,
}
calcfactory = Factory(Abinit, 'Abinit', 'label', **calcopts)
taskopts = {}
task = Task(
calcfactory=calcfactory,
tag=tag,
fit=fit,
use_lock_files=True,
**taskopts)
if __name__ == '__main__':
keys = task.collection.names
for m in ['Mn']:
keys.remove(m) # EOS fails: reason unknown
# run just only system to check if scripts work
#task.run(keys)
task.run(['Si'])
def __init__(self, **kwargs):
DeltaCodesDFTTask.__init__(self, **kwargs)
fit = (5, 0.02)
w = 0.06
ecut = 1200
kd = 8.0
tag = 'dcdft_%s_gpaw_pw' % xc.lower()
task = Task(
calcfactory=Factory(xc=xc,
mode=PW(ecut),
occupations=FermiDirac(w),
maxiter=250,
kptdensity=kd,
),
tag=tag,
fit=fit,
use_lock_files=True,
)
if __name__ == '__main__':
if element is None:
keys = set(parameters.keys()).intersection(set(task.collection.names))
for s in elements_slow:
keys.remove(s) # those are slow, run separately
else:
keys = [element]
task.run(keys)
return calculator
calcopts = {
"toldfe": 1.0e-7,
"ecut": ecut,
"xc": "PBE",
"pps": "fhi",
"nstep": 700,
"diemac": 1000,
"width": w,
"kpts": kd,
"chksymbreak": 0,
"ecutsm": 0.05,
"nsym": 1,
}
calcfactory = Factory(Abinit, "Abinit", "label", **calcopts)
taskopts = {}
task = Task(calcfactory=calcfactory, tag=tag, fit=fit, use_lock_files=True, **taskopts)
if __name__ == "__main__":
keys = task.collection.names
for m in ["Mn"]:
keys.remove(m) # EOS fails: reason unknown
# run just only system to check if scripts work
# task.run(keys)
task.run(["Si"])
z = zipfile.ZipFile(name)
try: # new in 2.6
z.extractall()
except AttributeError:
# http://stackoverflow.com/questions/7806563/how-to-unzip-a-zip-file-with-python-2-4
for f in z.namelist():
fd = open(f, "w")
fd.write(z.read(f))
fd.close()
# AttributeError if unzip not found
except (urllib2.HTTPError, AttributeError):
raise NotAvailable('Retrieval of zip failed')
os.chdir('..')
task = Task(
tag=tag,
use_lock_files=True,
)
# header
h = ['#element', 'V0', 'B0', 'B1']
if not os.path.exists('%s_raw.csv' % tag):
# read calculated results from json file and write into csv
task.read()
task.analyse()
f1 = open('%s_raw.csv' % tag, 'wb')
csvwriter1 = csv.writer(f1)
csvwriter1.writerow(h)
for n in task.collection.names:
#'occupation':0.001, # 0.001
#'maxsteps':None,
#'maxtime':None
#},
ft=w,
symmetry=True,
spinpol=True, # must set explicitly
calculate_stress=False,
deletenc=True, # start fresh every time
kptdensity=kd,
)
taskopts = {}
task = Task(
calcfactory=calcfactory,
tag=tag,
fit=fit,
use_lock_files=True,
**taskopts)
if __name__ == '__main__':
keys = set(psp.keys()).intersection(set(task.collection.names))
for m in ['Be', 'Cr', 'Kr', 'Xe']:
keys.remove(m) # EOS fails: maybe need higher ecut?
for m in ['Zn', 'Zr']:
keys.remove(m) # do not converge
# run just only system to check if scripts work
keys = ['Si']
task.run(keys)
z = zipfile.ZipFile(name)
try: # new in 2.6
z.extractall()
except AttributeError:
# http://stackoverflow.com/questions/7806563/how-to-unzip-a-zip-file-with-python-2-4
for f in z.namelist():
fd = open(f, "w")
fd.write(z.read(f))
fd.close()
# AttributeError if unzip not found
except (urllib.error.HTTPError, AttributeError):
raise NotAvailable('Retrieval of zip failed')
os.chdir('..')
task = Task(
tag=tag,
use_lock_files=True,
)
# header
h = ['#element', 'V0', 'B0', 'B1']
if not os.path.exists('%s_raw.csv' % tag):
# read calculated results from json file and write into csv
task.read()
task.analyse()
f1 = open('%s_raw.csv' % tag, 'wb')
csvwriter1 = csv.writer(f1)
csvwriter1.writerow(h)
for n in task.collection.names:
def __init__(self, inititer=0, **kwargs):
DeltaCodesDFTTask.__init__(self, **kwargs)
self.inititer = inititer
def __init__(self, inititer=0, **kwargs):
DeltaCodesDFTTask.__init__(self, **kwargs)
self.inititer = inititer
