def compute(self, output_dir):
outcar = os.path.join(output_dir, 'OUTCAR')
if not os.path.isfile(outcar):
dlog.warning("cannot find OUTCAR in " + output_dir + " skip")
return None
else:
ls = LabeledSystem(outcar)
stress = []
with open(outcar, 'r') as fin:
lines = fin.read().split('\n')
for line in lines:
if 'in kB' in line:
stress_xx = float(line.split()[2])
stress_yy = float(line.split()[3])
stress_zz = float(line.split()[4])
stress_xy = float(line.split()[5])
stress_yz = float(line.split()[6])
stress_zx = float(line.split()[7])
stress.append([])
stress[-1].append([stress_xx, stress_xy, stress_zx])
stress[-1].append([stress_xy, stress_yy, stress_yz])
stress[-1].append([stress_zx, stress_yz, stress_zz])
outcar_dict = ls.as_dict()
outcar_dict['data']['stress'] = {
"@module": "numpy",
"@class": "array",
"dtype": "float64",
"data": stress
}
return outcar_dict
def testEntry(self):
entries = []
for i, f in enumerate(self.iter_path):
vi = VaspInput.from_directory(f)
ls = LabeledSystem(os.path.join(f, 'OUTCAR'))
attrib = loadfn(os.path.join(f, 'job.json'))
comp = vi['POSCAR'].structure.composition
entry = Entry(comp,
'vasp',
vi.as_dict(),
ls.as_dict(),
entry_id='pku-' + str(i),
attribute=attrib)
entries.append(entry)
self.assertEqual(len(entries), len(self.ref_entries))
ret0 = entries[0]
r0 = self.ref_entries[0]
self.assertEqual(Incar.from_dict(ret0.inputs['INCAR']),
Incar.from_dict(r0.inputs['INCAR']))
self.assertEqual(str(r0.inputs['KPOINTS']),
str(Kpoints.from_dict(ret0.inputs['KPOINTS'])))
self.assertEqual(ret0.inputs['POTCAR'], r0.inputs['POTCAR'].as_dict())
self.assertEqual(
Poscar.from_dict(ret0.inputs['POSCAR']).structure,
r0.inputs['POSCAR'].structure)
self.assertEqual(ret0.entry_id, 'pku-0')
def test():
from monty.serialization import dumpfn, loadfn
from monty.json import MontyDecoder, MontyEncoder
from pymatgen.io.vasp.inputs import PotcarSingle, Potcar
vi = VaspInput.from_directory('.')
ls = LabeledSystem('OUTCAR', fmt='vasp/outcar')
en0 = Entry('Al',
'vasp',
inputs=vi.as_dict(),
data=ls.as_dict(),
entry_id='pku-1')
print(en0)
fname = 'pku-1.json'
dumpfn(en0.as_dict(), fname, indent=4)
en1 = Entry.load(fname)
#vin=VaspInput.from_dict(en1.inputs)
#vin.write_input('./new')
print(en1)
print(en1.as_dict())
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
