def __init__(self, allowed_keys, **kwargs):
allowed_keys_base = dict()
allowed_keys_base.update(allowed_keys)
MASTObj.__init__(self, allowed_keys_base, **kwargs)
work_dir = '/'.join(self.keywords['name'].split('/')[:-1])
topmeta = Metadata(metafile='%s/metadata.txt' % work_dir)
data = topmeta.read_data(self.keywords['name'].split('/')[-1])
self.meta_dict = dict()
if data:
for datum in data.split(';'):
self.meta_dict[datum.split(':')[0]] = datum.split(':')[1].strip()
self.metafile = Metadata(metafile='%s/metadata.txt' % self.keywords['name'])
self.program = self.keywords['program_keys']['mast_program'].lower()
self.logger = loggerutils.get_mast_logger(self.keywords['name'])
sdir=os.path.join(os.path.dirname(self.keywords['name']),"structure_index_files")
if os.path.exists(sdir):
self.atomindex = AtomIndex(structure_index_directory=sdir)
else:
self.atomindex = None
if self.program == 'vasp':
self.checker = VaspChecker(name=self.keywords['name'],
program_keys = self.keywords['program_keys'],
structure = self.keywords['structure'])
self.errhandler = VaspError(name=self.keywords['name'],
program_keys = self.keywords['program_keys'],
structure = self.keywords['structure'])
elif self.program == 'vasp_neb':
self.checker = VaspNEBChecker(name=self.keywords['name'],
program_keys = self.keywords['program_keys'],
structure = self.keywords['structure'])
self.errhandler = VaspNEBError(name=self.keywords['name'],
program_keys = self.keywords['program_keys'],
structure = self.keywords['structure'])
elif self.program == 'phon':
self.checker = PhonChecker(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
self.errhandler = PhonError(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
elif self.program == 'lammps':
self.checker = LammpsChecker(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
self.errhandler = GenericError(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
elif self.program =='structopt':
self.checker = StructoptChecker(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
self.errhandler = GenericError(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
else:
allowed_keys={'name','program_keys','structure'}
self.checker = GenericChecker(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
self.errhandler = GenericError(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
def __init__(self, allowed_keys, **kwargs):
allowed_keys_base = dict()
allowed_keys_base.update(allowed_keys)
MASTObj.__init__(self, allowed_keys_base, **kwargs)
work_dir = '/'.join(self.keywords['name'].split('/')[:-1])
topmeta = Metadata(metafile='%s/metadata.txt' % work_dir)
data = topmeta.read_data(self.keywords['name'].split('/')[-1])
self.meta_dict = dict()
if data:
for datum in data.split(';'):
self.meta_dict[datum.split(':')[0]] = datum.split(
':')[1].strip()
self.metafile = Metadata(metafile='%s/metadata.txt' %
self.keywords['name'])
self.program = self.keywords['program_keys']['mast_program'].lower()
self.logger = loggerutils.get_mast_logger(self.keywords['name'])
sdir = os.path.join(os.path.dirname(self.keywords['name']),
"structure_index_files")
if os.path.exists(sdir):
self.atomindex = AtomIndex(structure_index_directory=sdir)
else:
self.atomindex = None
if self.program == 'vasp':
self.checker = VaspChecker(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
self.errhandler = VaspError(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
elif self.program == 'vasp_neb':
self.checker = VaspNEBChecker(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
self.errhandler = VaspNEBError(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
elif self.program == 'phon':
self.checker = PhonChecker(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
self.errhandler = PhonError(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
elif self.program == 'lammps':
self.checker = LammpsChecker(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
self.errhandler = GenericError(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
elif self.program == 'structopt':
self.checker = StructoptChecker(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
self.errhandler = GenericError(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
else:
allowed_keys = {'name', 'program_keys', 'structure'}
self.checker = GenericChecker(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
self.errhandler = GenericError(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
class BaseIngredient(MASTObj):
"""Base Ingredient class
Attributes:
self.meta_dict <dict>: Metadata dictionary
self.metafile <Metadata>: Metadata file
self.program <str>: program name, all lowercase,
from 'mast_program' in input
file
self.checker <VaspChecker, PhonChecker, etc.>:
program-dependent checker object
self.errhandler <VaspError, PhonError, etc.>:
program-dependent handler object
self.atomindex <AtomIndex>: atom index object
"""
def __init__(self, allowed_keys, **kwargs):
allowed_keys_base = dict()
allowed_keys_base.update(allowed_keys)
MASTObj.__init__(self, allowed_keys_base, **kwargs)
work_dir = '/'.join(self.keywords['name'].split('/')[:-1])
topmeta = Metadata(metafile='%s/metadata.txt' % work_dir)
data = topmeta.read_data(self.keywords['name'].split('/')[-1])
self.meta_dict = dict()
if data:
for datum in data.split(';'):
self.meta_dict[datum.split(':')[0]] = datum.split(
':')[1].strip()
self.metafile = Metadata(metafile='%s/metadata.txt' %
self.keywords['name'])
self.program = self.keywords['program_keys']['mast_program'].lower()
self.logger = loggerutils.get_mast_logger(self.keywords['name'])
sdir = os.path.join(os.path.dirname(self.keywords['name']),
"structure_index_files")
if os.path.exists(sdir):
self.atomindex = AtomIndex(structure_index_directory=sdir)
else:
self.atomindex = None
if self.program == 'vasp':
self.checker = VaspChecker(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
self.errhandler = VaspError(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
elif self.program == 'vasp_neb':
self.checker = VaspNEBChecker(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
self.errhandler = VaspNEBError(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
elif self.program == 'phon':
self.checker = PhonChecker(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
self.errhandler = PhonError(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
elif self.program == 'lammps':
self.checker = LammpsChecker(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
self.errhandler = GenericError(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
elif self.program == 'structopt':
self.checker = StructoptChecker(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
self.errhandler = GenericError(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
else:
allowed_keys = {'name', 'program_keys', 'structure'}
self.checker = GenericChecker(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
self.errhandler = GenericError(
name=self.keywords['name'],
program_keys=self.keywords['program_keys'],
structure=self.keywords['structure'])
def write_directory(self):
try:
os.makedirs(self.keywords['name'])
self.metafile.write_data('directory created', time.asctime())
self.metafile.write_data('name',
self.keywords['name'].split('/')[-1])
self.metafile.write_data('program', self.program)
self.metafile.write_data('ingredient type',
self.__class__.__name__)
#if 'mast_charge' in self.keywords['program_keys']:
# self.metafile.write_data('charge', self.keywords['program_keys']['mast_charge'])
for key, value in self.meta_dict.items():
self.metafile.write_data(key, value)
except OSError:
self.logger.info("Directory for %s already exists." %
self.keywords['name'])
return
def close_logger(self):
"""Close logger handlers
(prevents IOError from too many handlers being open)
"""
handlerlist = list(
self.logger.handlers) #TTM 428; also deleted return after OSError
for myhandler in handlerlist:
self.logger.removeHandler(myhandler)
myhandler.flush()
myhandler.close()
return
def is_complete(self):
'''Function to check if Ingredient is ready'''
if not self.checker.is_started():
return False #hasn't started running yet
complete = self.checker.is_complete()
frozen = self.checker.is_frozen()
if complete or frozen:
errct = self.errhandler.loop_through_errors()
if errct > 0:
if os.path.isfile(
os.path.join(self.keywords['name'], 'error.5.tar.gz')):
self.logger.error(
"Ingredient directory already has 5 error zip files. A manual look is required."
)
self.change_my_status("E")
return False
if 'mast_auto_correct' in self.keywords['program_keys'].keys():
if str(self.keywords['program_keys']
['mast_auto_correct']).strip()[0].lower() == 'f':
self.change_my_status("E")
else:
self.change_my_status("S")
else:
self.change_my_status("S")
self.errhandler.clean_up_directory()
return False
else:
if complete:
self.metafile.write_data('completed on', time.asctime())
if 'get_energy_from_energy_file' in dirutil.list_methods(
self.checker, 0):
energy = self.checker.get_energy_from_energy_file()
self.metafile.write_data('energy', energy)
return True
else:
return False
else:
return False
def directory_is_locked(self):
return dirutil.directory_is_locked(self.keywords['name'])
def lock_directory(self):
return dirutil.lock_directory(self.keywords['name'])
def unlock_directory(self):
return dirutil.unlock_directory(self.keywords['name'])
def wait_to_write(self):
return dirutil.wait_to_write(self.keywords['name'])
def is_ready_to_run(self):
if self.directory_is_locked():
return False
return self.checker.is_ready_to_run()
def getpath(self):
'''getpath returns the directory of the ingredient'''
return self.keywords['name']
def write_submit_script(self):
from MAST.submit import script_commands
script_commands.write_submit_script(self.keywords)
return
def run(self, mode='serial', curdir=os.getcwd()):
if "dagman" in dirutil.get_mast_platform():
return
from MAST.submit import queue_commands
if mode.lower() == 'noqsub':
curdir = os.getcwd()
os.chdir(self.keywords['name'])
programpath = queue_commands.direct_shell_command()
p = subprocess.Popen(programpath,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
p.wait()
os.chdir(curdir)
self.metafile.write_data('run', time.asctime())
elif mode.lower() == 'serial':
queuesub = queue_commands.write_to_submit_list(
self.keywords['name'])
#runme = subprocess.Popen(queuesub, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
#runme.wait()
# for scheduling other jobs
#runme.wait()
self.metafile.write_data('queued', time.asctime())
return
def get_name(self):
return self.keywords['name'].split('/')[-1]
@property
def name(self):
return self.get_name()
def get_keywords(self):
return self.keywords.copy()
def __repr__(self):
return 'Ingredient %s of type %s' % (
self.keywords['name'].split('/')[-1], self.__class__.__name__)
def get_my_label(self, label):
"""Get the value of a label in the metadata file.
Args:
label <str>: Label to search for.
Returns:
<str>: Value of the label as a string, stripped.
"""
myname = self.keywords['name']
mymeta = Metadata(metafile=os.path.join(myname, "metadata.txt"))
mylabel = mymeta.search_data(label)
if mylabel == "":
raise MASTError(self.__class__.__name__,
"No metadata for tag %s" % label)
return mylabel[1]
def change_my_status(self, newstatus):
"""Change an ingredient status by writing the new status to
change_status.txt in the ingredient folder, to get picked
up by the recipe plan.
Args:
newstatus <str>: New status to which to change the ingredient.
"""
ingdir = self.keywords['name']
oneup = os.path.dirname(ingdir)
tryrecipe = os.path.basename(oneup)
statuspath = ""
if dirutil.dir_is_in_scratch(tryrecipe):
statuspath = "%s/change_status.txt" % ingdir
else:
twoup = os.path.dirname(oneup)
tryrecipe = os.path.basename(twoup)
if dirutil.dir_is_in_scratch(tryrecipe):
statuspath = "%s/change_status.txt" % oneup
else:
raise MASTError(
self.__class__.__name__,
"Cannot change status of ingredient %s as recipe %s or %s is not found in $MAST_SCRATCH."
% (self.keywords['name'], oneup, twoup))
if os.path.isfile(statuspath):
statusfile = MASTFile(statuspath)
else:
statusfile = MASTFile()
statusfile.data.append("%s:recommend:%s" % (newstatus, time.asctime()))
statusfile.to_file(statuspath)
self.logger.info("Recommending status change to %s" % newstatus)
class BaseIngredient(MASTObj):
"""Base Ingredient class
Attributes:
self.meta_dict <dict>: Metadata dictionary
self.metafile <Metadata>: Metadata file
self.program <str>: program name, all lowercase,
from 'mast_program' in input
file
self.checker <VaspChecker, PhonChecker, etc.>:
program-dependent checker object
self.errhandler <VaspError, PhonError, etc.>:
program-dependent handler object
self.atomindex <AtomIndex>: atom index object
"""
def __init__(self, allowed_keys, **kwargs):
allowed_keys_base = dict()
allowed_keys_base.update(allowed_keys)
MASTObj.__init__(self, allowed_keys_base, **kwargs)
work_dir = '/'.join(self.keywords['name'].split('/')[:-1])
topmeta = Metadata(metafile='%s/metadata.txt' % work_dir)
data = topmeta.read_data(self.keywords['name'].split('/')[-1])
self.meta_dict = dict()
if data:
for datum in data.split(';'):
self.meta_dict[datum.split(':')[0]] = datum.split(':')[1].strip()
self.metafile = Metadata(metafile='%s/metadata.txt' % self.keywords['name'])
self.program = self.keywords['program_keys']['mast_program'].lower()
self.logger = loggerutils.get_mast_logger(self.keywords['name'])
sdir=os.path.join(os.path.dirname(self.keywords['name']),"structure_index_files")
if os.path.exists(sdir):
self.atomindex = AtomIndex(structure_index_directory=sdir)
else:
self.atomindex = None
if self.program == 'vasp':
self.checker = VaspChecker(name=self.keywords['name'],
program_keys = self.keywords['program_keys'],
structure = self.keywords['structure'])
self.errhandler = VaspError(name=self.keywords['name'],
program_keys = self.keywords['program_keys'],
structure = self.keywords['structure'])
elif self.program == 'vasp_neb':
self.checker = VaspNEBChecker(name=self.keywords['name'],
program_keys = self.keywords['program_keys'],
structure = self.keywords['structure'])
self.errhandler = VaspNEBError(name=self.keywords['name'],
program_keys = self.keywords['program_keys'],
structure = self.keywords['structure'])
elif self.program == 'phon':
self.checker = PhonChecker(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
self.errhandler = PhonError(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
elif self.program == 'lammps':
self.checker = LammpsChecker(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
self.errhandler = GenericError(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
elif self.program =='structopt':
self.checker = StructoptChecker(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
self.errhandler = GenericError(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
else:
allowed_keys={'name','program_keys','structure'}
self.checker = GenericChecker(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
self.errhandler = GenericError(name=self.keywords['name'],program_keys=self.keywords['program_keys'],structure=self.keywords['structure'])
def write_directory(self):
try:
os.makedirs(self.keywords['name'])
self.metafile.write_data('directory created', time.asctime())
self.metafile.write_data('name', self.keywords['name'].split('/')[-1])
self.metafile.write_data('program', self.program)
self.metafile.write_data('ingredient type', self.__class__.__name__)
#if 'mast_charge' in self.keywords['program_keys']:
# self.metafile.write_data('charge', self.keywords['program_keys']['mast_charge'])
for key, value in self.meta_dict.items():
self.metafile.write_data(key, value)
except OSError:
self.logger.info("Directory for %s already exists." % self.keywords['name'])
return
def close_logger(self):
"""Close logger handlers
(prevents IOError from too many handlers being open)
"""
handlerlist = list(self.logger.handlers) #TTM 428; also deleted return after OSError
for myhandler in handlerlist:
self.logger.removeHandler(myhandler)
myhandler.flush()
myhandler.close()
return
def is_complete(self):
'''Function to check if Ingredient is ready'''
if not self.checker.is_started():
return False #hasn't started running yet
complete = self.checker.is_complete()
frozen = self.checker.is_frozen()
if complete or frozen:
errct = self.errhandler.loop_through_errors()
if errct > 0:
if os.path.isfile(os.path.join(self.keywords['name'],'error.5.tar.gz')):
self.logger.error("Ingredient directory already has 5 error zip files. A manual look is required.")
self.change_my_status("E")
return False
if 'mast_auto_correct' in self.keywords['program_keys'].keys():
if str(self.keywords['program_keys']['mast_auto_correct']).strip()[0].lower() == 'f':
self.change_my_status("E")
else:
self.change_my_status("S")
else:
self.change_my_status("S")
self.errhandler.clean_up_directory()
return False
else:
if complete:
self.metafile.write_data('completed on', time.asctime())
if 'get_energy_from_energy_file' in dirutil.list_methods(self.checker,0):
energy = self.checker.get_energy_from_energy_file()
self.metafile.write_data('energy', energy)
return True
else:
return False
else:
return False
def directory_is_locked(self):
return dirutil.directory_is_locked(self.keywords['name'])
def lock_directory(self):
return dirutil.lock_directory(self.keywords['name'])
def unlock_directory(self):
return dirutil.unlock_directory(self.keywords['name'])
def wait_to_write(self):
return dirutil.wait_to_write(self.keywords['name'])
def is_ready_to_run(self):
if self.directory_is_locked():
return False
return self.checker.is_ready_to_run()
def getpath(self):
'''getpath returns the directory of the ingredient'''
return self.keywords['name']
def write_submit_script(self):
from MAST.submit import script_commands
script_commands.write_submit_script(self.keywords)
return
def run(self, mode='serial', curdir=os.getcwd()):
if "dagman" in dirutil.get_mast_platform():
return
from MAST.submit import queue_commands
if mode.lower() == 'noqsub':
curdir = os.getcwd()
os.chdir(self.keywords['name'])
programpath = queue_commands.direct_shell_command()
p = subprocess.Popen(programpath, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
p.wait()
os.chdir(curdir)
self.metafile.write_data('run', time.asctime())
elif mode.lower() == 'serial':
queuesub = queue_commands.write_to_submit_list(self.keywords['name'])
#runme = subprocess.Popen(queuesub, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
#runme.wait()
# for scheduling other jobs
#runme.wait()
self.metafile.write_data('queued', time.asctime())
return
def get_name(self):
return self.keywords['name'].split('/')[-1]
@property
def name(self):
return self.get_name()
def get_keywords(self):
return self.keywords.copy()
def __repr__(self):
return 'Ingredient %s of type %s' % (self.keywords['name'].split('/')[-1], self.__class__.__name__)
def get_my_label(self, label):
"""Get the value of a label in the metadata file.
Args:
label <str>: Label to search for.
Returns:
<str>: Value of the label as a string, stripped.
"""
myname = self.keywords['name']
mymeta = Metadata(metafile=os.path.join(myname, "metadata.txt"))
mylabel = mymeta.search_data(label)
if mylabel == "":
raise MASTError(self.__class__.__name__,
"No metadata for tag %s" % label)
return mylabel[1]
def change_my_status(self, newstatus):
"""Change an ingredient status by writing the new status to
change_status.txt in the ingredient folder, to get picked
up by the recipe plan.
Args:
newstatus <str>: New status to which to change the ingredient.
"""
ingdir = self.keywords['name']
oneup = os.path.dirname(ingdir)
tryrecipe = os.path.basename(oneup)
statuspath = ""
if dirutil.dir_is_in_scratch(tryrecipe):
statuspath = "%s/change_status.txt" % ingdir
else:
twoup = os.path.dirname(oneup)
tryrecipe = os.path.basename(twoup)
if dirutil.dir_is_in_scratch(tryrecipe):
statuspath = "%s/change_status.txt" % oneup
else:
raise MASTError(self.__class__.__name__, "Cannot change status of ingredient %s as recipe %s or %s is not found in $MAST_SCRATCH." % (self.keywords['name'],oneup, twoup))
if os.path.isfile(statuspath):
statusfile = MASTFile(statuspath)
else:
statusfile=MASTFile()
statusfile.data.append("%s:recommend:%s" % (newstatus, time.asctime()))
statusfile.to_file(statuspath)
self.logger.info("Recommending status change to %s" % newstatus)