def _parsing_vasp(paths, id_prefix, iters=True):
entries = []
icount = 0
for path in paths:
f_outcar = os.path.join(path, 'OUTCAR')
f_job = os.path.join(path, 'job.json')
try:
vi = VaspInput.from_directory(path)
if os.path.isfile(f_job):
attrib = loadfn(f_job)
else:
attrib = {}
if iters and attrib:
tmp_ = path.split('/')[-1]
iter_info = tmp_.split('.')[1]
task_info = tmp_.split('.')[-1]
attrib['iter_info'] = iter_info
attrib['task_info'] = task_info
else:
pass
comp = vi['POSCAR'].structure.composition
ls = LabeledSystem(f_outcar)
lss = ls.to_list()
for ls in lss:
if id_prefix:
eid = id_prefix + "_" + str(icount)
else:
eid = str(uuid4())
entry = Entry(comp,
'vasp',
vi.as_dict(),
ls.as_dict(),
attribute=attrib,
entry_id=eid)
entries.append(entry)
icount += 1
except:
dlog.info("failed here : %s" % path)
return entries
def _parsing_vasp(paths, config_info_dict, id_prefix, iters=True):
entries = []
icount = 0
if iters:
iter_record = []
iter_record_new = []
try:
with open("record.database", "r") as f_record:
iter_record = [i.split()[0] for i in f_record.readlines()]
iter_record.sort()
dlog.info("iter_record")
dlog.info(iter_record)
except:
pass
for path in paths:
try:
f_outcar = os.path.join(path, 'OUTCAR')
f_job = os.path.join(path, 'job.json')
tmp_iter = path.split('/')[-3]
if (tmp_iter in iter_record) and (tmp_iter != iter_record[-1]):
continue
if tmp_iter not in iter_record_new:
iter_record_new.append(tmp_iter)
vi = VaspInput.from_directory(path)
if os.path.isfile(f_job):
attrib = loadfn(f_job)
else:
attrib = {}
if iters and attrib:
# generator/Cu/iter.000031/02.fp/task.007.000000
tmp_ = path.split('/')[-1]
#config_info=tmp_.split('.')[1]
task_info = tmp_.split('.')[-1]
tmp_iter = path.split('/')[-3]
iter_info = tmp_iter.split('.')[-1]
sys_info = path.split('/')[-4]
config_info_int = int(tmp_.split('.')[1])
for (key, value) in config_info_dict.items():
if config_info_int in value:
config_info = key
attrib['config_info'] = config_info
attrib['task_info'] = task_info
attrib['iter_info'] = iter_info
attrib['sys_info'] = sys_info
with open(f_outcar, "r") as fin_outcar:
infile_outcar = fin_outcar.readlines()
for line in infile_outcar:
if "running on" in line:
attrib["core"] = int(line.split()[2])
if "Elapse" in line:
attrib["wall_time"] = float(line.split()[-1])
if "executed on" in line:
attrib["date"] = line.split()[-2]
attrib["clocktime"] = line.split()[-1]
dlog.info("Attrib")
dlog.info(attrib)
comp = vi['POSCAR'].structure.composition
ls = LabeledSystem(f_outcar)
lss = ls.to_list()
for ls in lss:
if id_prefix:
eid = id_prefix + "_" + str(icount)
else:
eid = str(uuid4())
entry = Entry(comp,
'vasp',
vi.as_dict(),
ls.as_dict(),
attribute=attrib,
entry_id=eid)
entries.append(entry)
icount += 1
except Exception:
#dlog.info(str(Exception))
dlog.info("failed for %s" % (path))
#pass
if iters:
iter_record.sort()
iter_record_new.sort()
with open("record.database", "w") as fw:
for line in iter_record:
fw.write(line + "\n")
for line in iter_record_new:
fw.write(line + "\n")
return entries