def write(self, name, data):
filename = self.get_filename(ext='json')
try:
self.lock.acquire()
if os.path.isfile(filename):
alldata = read_json(filename)
else:
alldata = {}
alldata[name] = data
write_json(filename, alldata)
finally:
self.lock.release()
def run_single(self, name):
self.log('Running', name)
try:
atoms = self.create_system(name)
except Exception:
self.log(name, 'FAILED')
traceback.print_exc(file=self.logfile)
return
atoms.calc = self.calcfactory(self.get_filename(name), atoms)
tstart = time()
try:
data = self.calculate(name, atoms)
if self.after:
exec self.after
except KeyboardInterrupt:
raise
except Exception:
self.log(name, 'FAILED')
traceback.print_exc(file=self.logfile)
return
tstop = time()
data['time'] = tstop - tstart
filename = self.get_filename(ext='json')
try:
self.lock.acquire()
if os.path.isfile(filename):
alldata = read_json(filename)
else:
alldata = {}
alldata[name] = data
write_json(filename, alldata)
finally:
self.lock.release()
for write in self.write_funcs:
filenamebase = self.get_filename(name)
write(filenamebase, atoms, data)
return atoms
def run_single(self, name):
self.log('Running', name)
try:
atoms = self.create_system(name)
except Exception:
self.log(name, 'FAILED')
traceback.print_exc(file=self.logfile)
return
atoms.calc = self.calcfactory(self.get_filename(name), atoms)
tstart = time()
try:
data = self.calculate(name, atoms)
if self.after:
exec self.after
except KeyboardInterrupt:
raise
except Exception:
self.log(name, 'FAILED')
traceback.print_exc(file=self.logfile)
return
tstop = time()
data['time'] = tstop - tstart
filename = self.get_filename(ext='json')
try:
self.lock.acquire()
if os.path.isfile(filename):
alldata = read_json(filename)
else:
alldata = {}
alldata[name] = data
write_json(filename, alldata)
finally:
self.lock.release()
for write in self.write_funcs:
filenamebase = self.get_filename(name)
write(filenamebase, atoms, data)
return atoms
def run(self, atoms, name):
args = self.args
if self.lock is None:
# Create lock object:
if args.use_lock_file:
self.lock = Lock(self.get_filename(ext='lock'))
else:
self.lock = OpenLock()
skip = False
if args.use_lock_file:
try:
filename = self.get_filename(ext='json')
self.lock.acquire()
if os.path.isfile(filename):
data = read_json(filename)
if name in data:
skip = True
else:
data[name] = {}
write_json(filename, data)
else:
write_json(filename, {name: {}})
finally:
self.lock.release()
if not skip:
self.set_calculator(atoms, name)
tstart = time.time()
try:
data = self.calculate(atoms, name)
except KeyboardInterrupt:
raise
except Exception:
self.log(name, 'FAILED')
traceback.print_exc(file=self.logfile)
else:
tstop = time.time()
data['time'] = tstop - tstart
self.write(name, data)
def clean_json_file(self, names=None):
self.read(skipempty=False)
n = len(self.data)
if names:
for name in names:
del self.data[name]
else:
self.data = dict((key, value) for key, value in self.data.items()
if value)
filename = self.get_filename(ext='json')
try:
self.lock.acquire()
write_json(filename, self.data)
finally:
self.lock.release()
n -= len(self.data)
self.log('Cleaned', n, ['tasks', 'task'][n == 1])
def clean_json_file(self, names=None):
self.read(skipempty=False)
n = len(self.data)
if names:
for name in names:
del self.data[name]
else:
self.data = dict(
(key, value) for key, value in self.data.items() if value)
filename = self.get_filename(ext='json')
try:
self.lock.acquire()
write_json(filename, self.data)
finally:
self.lock.release()
n -= len(self.data)
self.log('Cleaned', n, ['tasks', 'task'][n == 1])
def run(self, names=None):
"""Run task for all names.
The task will be one of these four:
* Open ASE's GUI
* Write configuration to file
* Write summary
* Do the actual calculation
"""
if self.lock is None:
# Create lock object:
self.lock = Lock(self.get_filename(ext='lock'))
if self.clean:
self.clean_json_file(names)
return
if names is None or len(names) == 0:
names = self.collection.keys()
names = self.expand(names)
names = names[self.slice]
names = self.exclude(names)
if self.gui:
for name in names:
view(self.create_system(name))
return
if self.write_to_file:
if self.write_to_file[0] == '.':
for name in names:
filename = self.get_filename(name, self.write_to_file)
write(filename, self.create_system(name))
else:
assert len(names) == 1
write(self.write_to_file, self.create_system(names[0]))
return
if self.write_summary:
self.read()
self.analyse()
self.summarize(names)
return
atoms = None
for name in names:
if self.use_lock_files:
try:
filename = self.get_filename(ext='json')
self.lock.acquire()
if os.path.isfile(filename):
data = read_json(filename)
if name not in data:
data[name] = {}
write_json(filename, data)
else:
self.log('Skipping', name)
continue
else:
write_json(filename, {name: {}})
finally:
self.lock.release()
if atoms is not None:
del atoms.calc
atoms = self.run_single(name)
return atoms
def run(self, names=None):
"""Run task for all names.
The task will be one of these four:
* Open ASE's GUI
* Write configuration to file
* Write summary
* Do the actual calculation
"""
if self.lock is None:
# Create lock object:
self.lock = Lock(self.get_filename(ext='lock'))
if self.clean:
self.clean_json_file(names)
return
if names is None or len(names) == 0:
names = self.collection.keys()
names = self.expand(names)
names = names[self.slice]
names = self.exclude(names)
if self.gui:
for name in names:
view(self.create_system(name))
return
if self.write_to_file:
if self.write_to_file[0] == '.':
for name in names:
filename = self.get_filename(name, self.write_to_file)
write(filename, self.create_system(name))
else:
assert len(names) == 1
write(self.write_to_file, self.create_system(names[0]))
return
if self.write_summary:
self.read()
self.analyse()
self.summarize(names)
return
atoms = None
for name in names:
if self.use_lock_files:
try:
filename = self.get_filename(ext='json')
self.lock.acquire()
if os.path.isfile(filename):
data = read_json(filename)
if name not in data:
data[name] = {}
write_json(filename, data)
else:
self.log('Skipping', name)
continue
else:
write_json(filename, {name: {}})
finally:
self.lock.release()
if atoms is not None:
del atoms.calc
atoms = self.run_single(name)
return atoms
