def is_ready_to_run(self):
"""Check if single VASP NEB ingredient is
ready to run.
"""
dirname = self.keywords['name']
notready=0
if not(os.path.isfile(dirname + "/KPOINTS")):
notready = notready + 1
if not(os.path.isfile(dirname + "/POTCAR")):
notready = notready + 1
if not(os.path.isfile(dirname + "/INCAR")):
notready = notready + 1
else: #INCAR exists. Now check POSCARs.
subdirs = dirutil.walkdirs(dirname)
if not (len(subdirs) == self.keywords['program_keys']['mast_neb_settings']['images'] + 2):
notready = notready + 1 #bad number of subdirs
subdirs.sort()
if len(subdirs) == 0: #This is an NEB without folders yet
notready = notready + 1
else:
for subdir in subdirs:
if not (os.path.isfile(subdir + "/POSCAR")):
notready = notready + 1
if not os.path.isfile(subdirs[0] + "/OSZICAR"):
notready = notready + 1
if not os.path.isfile(subdirs[-1] + "/OSZICAR"):
notready = notready + 1
if not(os.path.isfile(dirname + "/submit.sh")):
notready = notready + 1
if notready > 0:
return False
else:
return True
def is_ready_to_run(self):
"""Check if single VASP NEB ingredient is
ready to run.
"""
dirname = self.keywords['name']
notready = 0
if not (os.path.isfile(dirname + "/KPOINTS")):
notready = notready + 1
if not (os.path.isfile(dirname + "/POTCAR")):
notready = notready + 1
if not (os.path.isfile(dirname + "/INCAR")):
notready = notready + 1
else: #INCAR exists. Now check POSCARs.
subdirs = dirutil.walkdirs(dirname)
if not (len(subdirs) == self.keywords['program_keys']
['mast_neb_settings']['images'] + 2):
notready = notready + 1 #bad number of subdirs
subdirs.sort()
if len(subdirs) == 0: #This is an NEB without folders yet
notready = notready + 1
else:
for subdir in subdirs:
if not (os.path.isfile(subdir + "/POSCAR")):
notready = notready + 1
if not os.path.isfile(subdirs[0] + "/OSZICAR"):
notready = notready + 1
if not os.path.isfile(subdirs[-1] + "/OSZICAR"):
notready = notready + 1
if not (os.path.isfile(dirname + "/submit.sh")):
notready = notready + 1
if notready > 0:
return False
else:
return True
def run(self, verbose=0, single_recipe=0, single_ingred=0):
"""Run the MAST monitor.
"""
if (single_ingred == 0) and ("dagman" in dirutil.get_mast_platform()):
return None #Do not auto-run from __init__ method for CHTC/DAGMan
curdir = os.getcwd()
try:
os.chdir(self.scratch)
except:
os.chdir(curdir)
errorstr = "Could not change directories to MAST_SCRATCH at %s" % self.scratch
raise MASTError(self.__class__.__name__, errorstr)
#dirutil.lock_directory(self.scratch, 1) # Wait 5 seconds
#Directory is now locked by mast initially, but gets
#unlocked at the end of the mastmon run.
if single_ingred == 0:
recipe_dirs = dirutil.walkdirs(self.scratch,1,1)
else:
recipe_dirs = list()
recipe_dirs.append(single_recipe)
if verbose == 1:
self.logger.info("================================")
self.logger.info("Recipe directories:")
for recipe_dir in recipe_dirs:
self.logger.info(recipe_dir)
self.logger.info("================================")
for recipe_dir in recipe_dirs:
self.check_recipe_dir(recipe_dir, verbose, single_ingred)
dirutil.unlock_directory(self.scratch) #unlock directory
os.chdir(curdir)
def run(self, verbose=0, single_recipe=0, single_ingred=0):
"""Run the MAST monitor.
"""
if (single_ingred == 0) and ("dagman" in dirutil.get_mast_platform()):
return None #Do not auto-run from __init__ method for CHTC/DAGMan
curdir = os.getcwd()
try:
os.chdir(self.scratch)
except:
os.chdir(curdir)
errorstr = "Could not change directories to MAST_SCRATCH at %s" % self.scratch
raise MASTError(self.__class__.__name__, errorstr)
#dirutil.lock_directory(self.scratch, 1) # Wait 5 seconds
#Directory is now locked by mast initially, but gets
#unlocked at the end of the mastmon run.
if single_ingred == 0:
recipe_dirs = dirutil.walkdirs(self.scratch, 1, 1)
else:
recipe_dirs = list()
recipe_dirs.append(single_recipe)
if verbose == 1:
self.logger.info("================================")
self.logger.info("Recipe directories:")
for recipe_dir in recipe_dirs:
self.logger.info(recipe_dir)
self.logger.info("================================")
for recipe_dir in recipe_dirs:
self.check_recipe_dir(recipe_dir, verbose, single_ingred)
dirutil.unlock_directory(self.scratch) #unlock directory
os.chdir(curdir)
def run(self, verbose=0):
"""Run the MAST monitor.
"""
curdir = os.getcwd()
try:
os.chdir(self.scratch)
except:
os.chdir(curdir)
errorstr = "Could not change directories to MAST_SCRATCH at %s" % self.scratch
raise MASTError(self.__class__.__name__, errorstr)
#dirutil.lock_directory(self.scratch, 1) # Wait 5 seconds
#Directory is now locked by mast initially, but gets
#unlocked at the end of the mastmon run.
recipe_dirs = dirutil.walkdirs(self.scratch,1,1)
if verbose == 1:
self.logger.info("================================")
self.logger.info("Recipe directories:")
for recipe_dir in recipe_dirs:
self.logger.info(recipe_dir)
self.logger.info("================================")
for recipe_dir in recipe_dirs:
self.check_recipe_dir(recipe_dir, verbose)
dirutil.unlock_directory(self.scratch) #unlock directory
os.chdir(curdir)
def tearDown(self):
#return
dnames = dirutil.walkdirs("childdir",1,1)
for dname in dnames:
shutil.rmtree(dname)
fnames = dirutil.walkfiles("childdir",1,1)
for fname in fnames:
os.remove(fname)
