# /usr/bin/env python
# Copyright (c) The Dpmodeling Team.
import json
import os
from glob import glob
from uuid import uuid4
from dpdata import LabeledSystem
from monty.serialization import dumpfn, loadfn
from dpgen import SHORT_CMD, dlog
from dpgen.database.entry import Entry
from dpgen.database.vasp import VaspInput
OUTPUT = SHORT_CMD + "_db.json"
SUPPORTED_CACULATOR = ["vasp", "pwscf", "gaussian"]
ITERS_PAT = "iter.*/02.fp/task*"
INIT_PAT = "init/*/02.md/sys-*/scale-*/*"
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def db_run(args):
dlog.info("collecting data")
# print(args.ID_PREFIX)
_main(args.PARAM)
dlog.info("finished")
def _main(param):
with open(param) as fp:
jdata = json.load(fp)
calculator = jdata["calculator"]
path = jdata["path"]
calulator = jdata["calculator"]
output = jdata["output"]
config_info_dict = jdata["config_info_dict"]
id_prefix = jdata["id_prefix"]
skip_init = False
if "skip_init" in jdata:
skip_init = jdata["skip_init"]
## The mapping from sys_info to sys_configs
assert calculator.lower() in SUPPORTED_CACULATOR
dlog.info("data collection from: %s" % path)
if calculator == "vasp":
parsing_vasp(path, config_info_dict, skip_init, output, id_prefix)
elif calculator == "gaussian":
parsing_gaussian(path, output)
else:
parsing_pwscf(path, output)
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def parsing_vasp(path, config_info_dict, skip_init, output=OUTPUT, id_prefix=None):
fp_iters = os.path.join(path, ITERS_PAT)
dlog.debug(fp_iters)
f_fp_iters = glob(fp_iters)
dlog.info("len iterations data: %s" % len(f_fp_iters))
fp_init = os.path.join(path, INIT_PAT)
dlog.debug(fp_init)
f_fp_init = glob(fp_init)
if skip_init:
entries = _parsing_vasp(f_fp_iters, config_info_dict, id_prefix)
dlog.info("len collected data: %s" % len(entries))
else:
dlog.info("len initialization data: %s" % len(f_fp_init))
entries = _parsing_vasp(f_fp_init, config_info_dict, id_prefix, iters=False)
entries.extend(_parsing_vasp(f_fp_iters, config_info_dict, id_prefix))
dlog.info("len collected data: %s" % len(entries))
# print(output)
# print(entries)
dumpfn(entries, output, indent=4)
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") 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 Exception:
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) 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
[docs]
def parsing_pwscf(path, output=OUTPUT):
pass
[docs]
def parsing_gaussian(path, output=OUTPUT):
pass