def generate_doc(self, dir_name, lmps_input, log, dumps):
"""
Args:
dir_name (str): path to the run dir.
lmps_input (LammpsInput/LammpsInputSet):
log (LammpsLog):
dumps ([(filename, LammpsDump)]): list of (dump filename, dump) tuples
Returns:
dict
"""
try:
fullpath = os.path.abspath(dir_name)
if self.use_full_uri:
fullpath = get_uri(dir_name)
d = {k: v for k, v in self.additional_fields.items()}
d["schema"] = {"code": "atomate", "version": LammpsDrone.__version__}
d["completed_at"] = str(datetime.fromtimestamp(os.path.getmtime(log.log_file)))
d["dir_name"] = fullpath
d["last_updated"] = datetime.utcnow()
d["input"] = lmps_input.as_dict()
d["output"] = {"log": log.as_dict()}
d["output"]["dumps"] = dict([(dump_fname, dmp.as_dict()) for dump_fname, dmp in dumps])
return d
except:
import traceback
logger.error(traceback.format_exc())
logger.error("Error in " + os.path.abspath(dir_name) + ".\n" + traceback.format_exc())
return None
def post_process(self, dir_name, d):
"""
Post-processing for various files other than the vasprun.xml and OUTCAR.
Looks for files: transformations.json and custodian.json. Modify this if other
output files need to be processed.
Args:
dir_name:
The dir_name.
d:
Current doc generated.
"""
logger.info("Post-processing dir:{}".format(dir_name))
fullpath = os.path.abspath(dir_name)
# VASP input generated by pymatgen's alchemy has a transformations.json file that tracks
# the origin of a particular structure. If such a file is found, it is inserted into the
# task doc as d["transformations"]
transformations = {}
filenames = glob.glob(os.path.join(fullpath, "transformations.json*"))
if len(filenames) >= 1:
with zopen(filenames[0], "rt") as f:
transformations = json.load(f)
try:
m = re.match("(\d+)-ICSD", transformations["history"][0]["source"])
if m:
d["icsd_id"] = int(m.group(1))
except Exception as ex:
logger.warning("Cannot parse ICSD from transformations file.")
pass
else:
logger.warning("Transformations file does not exist.")
other_parameters = transformations.get("other_parameters")
new_tags = None
if other_parameters:
# We don't want to leave tags or authors in the
# transformations file because they'd be copied into
# every structure generated after this one.
new_tags = other_parameters.pop("tags", None)
new_author = other_parameters.pop("author", None)
if new_author:
d["author"] = new_author
if not other_parameters: # if dict is now empty remove it
transformations.pop("other_parameters")
d["transformations"] = transformations
# Calculations done using custodian has a custodian.json,
# which tracks the jobs performed and any errors detected and fixed.
# This is useful for tracking what has actually be done to get a
# result. If such a file is found, it is inserted into the task doc
# as d["custodian"]
filenames = glob.glob(os.path.join(fullpath, "custodian.json*"))
if len(filenames) >= 1:
with zopen(filenames[0], "rt") as f:
d["custodian"] = json.load(f)
# Convert to full uri path.
if self.use_full_uri:
d["dir_name"] = get_uri(dir_name)
if new_tags:
d["tags"] = new_tags
# Calculations using custodian generate a *.orig file for the inputs
# This is useful to know how the calculation originally started
# if such files are found they are inserted into orig_inputs
filenames = glob.glob(os.path.join(fullpath, "*.orig*"))
if len(filenames) >= 1:
d["orig_inputs"] = {}
for f in filenames:
if "INCAR.orig" in f:
d["orig_inputs"]["incar"] = Incar.from_file(f).as_dict()
if "POTCAR.orig" in f:
d["orig_inputs"]["potcar"] = Potcar.from_file(f).as_dict()
if "KPOINTS.orig" in f:
d["orig_inputs"]["kpoints"] = Kpoints.from_file(f).as_dict()
if "POSCAR.orig" in f:
d["orig_inputs"]["poscar"] = Poscar.from_file(f).as_dict()
logger.info("Post-processed " + fullpath)
def test_get_uri(self):
self.assertTrue(MODULE_DIR in get_uri(MODULE_DIR))
def test_get_uri(self):
self.assertTrue(MODULE_DIR in get_uri(MODULE_DIR))
