def clear_ga_vasp_ingredient(self, ingred_name="", new_seed_file=""):
"""Clear the Genetic Algorithm VASP ingredient.
Assumes that the VASP ingredient has already
been evaluated and the result passed
to the child ingredient.
Args:
ingred_name <str>: Ingredient name to clear.
Match this carefully with a name from
the recipe.
new_seed_file <str>: New seed file to put
in the cleared ingredient.
"""
if ingred_name == "":
self.logger.error("Needs an ingredient name!")
return None
fullpath = os.path.join(os.path.dirname(self.keywords['name']), ingred_name)
self.logger.info("Removing directories and files from ingredient specified at %s" % fullpath)
dircontents = os.listdir(fullpath)
subfolders = list()
import shutil
for diritem in dircontents:
fulldir = os.path.join(fullpath,diritem)
if os.path.isdir(fulldir) and diritem.isdigit():
subfolders.append(fulldir)
for subfolder in subfolders:
shutil.rmtree(subfolder)
files_to_remove = list()
files_to_remove.append("starting.xyz")
for filename in files_to_remove:
os.remove(os.path.join(fullpath, filename))
shutil.copy(os.path.join(self.keywords['name'], new_seed_file), os.path.join(fullpath, "starting.xyz"))
from MAST.ingredients import BaseIngredient
cleared_ing = BaseIngredient(name=fullpath)
cleared_ing.change_my_status("W")
return
def __init__(self, **kwargs):
"""Please not modify this init method."""
allowed_keys = {
'name' : (str, str(), 'Name of directory'),
'program': (str, str(), 'Program, e.g. "vasp"'),
'program_keys': (dict, dict(), 'Dictionary of program keywords'),
'structure': (Structure, None, 'Pymatgen Structure object')
}
BaseIngredient.__init__(self, allowed_keys, **kwargs)
def __init__(self, **kwargs):
"""Please not modify this init method."""
allowed_keys = {
'name': (str, str(), 'Name of directory'),
'program': (str, str(), 'Program, e.g. "vasp"'),
'program_keys': (dict, dict(), 'Dictionary of program keywords'),
'structure': (Structure, None, 'Pymatgen Structure object')
}
BaseIngredient.__init__(self, allowed_keys, **kwargs)
def create_ingredient(self, my_ingred_input_options):
"""Create the ingredient directory and metadata file.
Args:
my_ingred_input_options <Input Options>: single ingredient
input options
"""
allowed_keys = {
'name' : (str, str(), 'Name of optimization directory'),
'program': (str, str(), 'DFT program, e.g. "vasp"'),
'program_keys': (dict, dict(), 'Dictionary of program keywords'),
'structure': (Structure, None, 'Pymatgen Structure object')
}
myingred = BaseIngredient(allowed_keys,
name=my_ingred_input_options['name'],
structure=my_ingred_input_options['structure'],
program_keys=my_ingred_input_options['program_keys'])
myingred.write_directory()
return
def create_ingredient(self, my_ingred_input_options):
"""Create the ingredient directory and metadata file.
Args:
my_ingred_input_options <Input Options>: single ingredient
input options
"""
allowed_keys = {
'name': (str, str(), 'Name of optimization directory'),
'program': (str, str(), 'DFT program, e.g. "vasp"'),
'program_keys': (dict, dict(), 'Dictionary of program keywords'),
'structure': (Structure, None, 'Pymatgen Structure object')
}
myingred = BaseIngredient(
allowed_keys,
name=my_ingred_input_options['name'],
structure=my_ingred_input_options['structure'],
program_keys=my_ingred_input_options['program_keys'])
myingred.write_directory()
return
def clear_ga_vasp_ingredient(self, ingred_name="", new_seed_file=""):
"""Clear the Genetic Algorithm VASP ingredient.
Assumes that the VASP ingredient has already
been evaluated and the result passed
to the child ingredient.
Args:
ingred_name <str>: Ingredient name to clear.
Match this carefully with a name from
the recipe.
new_seed_file <str>: New seed file to put
in the cleared ingredient.
"""
if ingred_name == "":
self.logger.error("Needs an ingredient name!")
return None
fullpath = os.path.join(os.path.dirname(self.keywords['name']),
ingred_name)
self.logger.info(
"Removing directories and files from ingredient specified at %s" %
fullpath)
dircontents = os.listdir(fullpath)
subfolders = list()
import shutil
for diritem in dircontents:
fulldir = os.path.join(fullpath, diritem)
if os.path.isdir(fulldir) and diritem.isdigit():
subfolders.append(fulldir)
for subfolder in subfolders:
shutil.rmtree(subfolder)
files_to_remove = list()
files_to_remove.append("starting.xyz")
for filename in files_to_remove:
os.remove(os.path.join(fullpath, filename))
shutil.copy(os.path.join(self.keywords['name'], new_seed_file),
os.path.join(fullpath, "starting.xyz"))
from MAST.ingredients import BaseIngredient
cleared_ing = BaseIngredient(name=fullpath)
cleared_ing.change_my_status("W")
return