def __init__(self, poscar='POSCAR'):
if type(poscar) is str:
try:
poscar_lines = Cabinet.read_file(poscar)
except IOError:
print("error: vaspy.Poscar could not "
"find '{0}' file !!!".format(poscar))
exit()
elif type(poscar) is list:
poscar_lines = poscar
elif poscar is None:
print("POSCAR was not read !!! (Template POSCAR is loaded !!!)")
poscar = os.path.join(MODULE_DIR,
'../sorce/originalsVASP', 'poscar')
poscar_lines = Cabinet.read_file(poscar)
self.poscar_title = poscar_lines[0]
self.cell_scale = float(poscar_lines[1])
self.cell_lattices = Cabinet.conv_lines2array(poscar_lines[2:5])
# self.cell_latticesはarrayとして読み込む
if poscar_lines[5].split()[0].isdigit(): # vasp4
self.elements = None
self.num_atoms = [int(x) for x in poscar_lines[5].split()]
i = sum(self.num_atoms)
sites = [[float(x) for x in y.split()[0:3]]
for y in poscar_lines[7:7+i]]
self.cell_sites = np.array(sites)
self.vasp_version = 4
else:
self.elements = poscar_lines[5].split() # vasp5
self.num_atoms = [int(x) for x in poscar_lines[6].split()]
i = sum(self.num_atoms)
sites = [[float(x) for x in y.split()[0:3]]
for y in poscar_lines[8:8+i]]
self.cell_sites = np.array(sites)
self.vasp_version = 5
def __init__(self, num_run=1, fname_run='list_run',
fname_running='running_jobs'):
self.num_run = num_run
self.list_run_file = fname_run
self.running_jobs_file = fname_running
lines = Cabinet.read_file(fname_run)
self.finished_list = [x.split() for x in lines if x[0] == '#']
self.run_list = [x.split() for x in lines if x[0] != '#']
try:
lines = Cabinet.read_file(fname_running)
self.running_jobs = [x for x in lines if x != '\n']
except IOError:
self.running_jobs = []
def prep_run_file(self, next_run='next_run.sh'):
"""
run_fileを修正してnext_run.shを作成
run_listの実行したjobをコメントアウト
"""
work_path, fname_exe = self.run_list[0]
key = "cd $PBS_O_WORKDIR\n"
# work_pathが相対pathの場合、絶対pathに修正する
if work_path[0] == '/':
alt = "cd {0}\n".format(os.path.join(work_path))
else:
alt = "cd {0}\n".format(os.path.join(os.getcwd(), work_path))
lines = Cabinet.read_file(fname_exe)
# $PBS_O_WORKDIRの記述が無い場合errorメッセージを出力
try:
pos = lines.index(key)
except ValueError:
print("{0}に'cd $PBS_O_WORKDIR'の記述がありません".format(fname_exe))
exit()
lines[pos] = alt
Cabinet.write_file(next_run, lines)
finished = self.run_list.pop(0)
finished[0] = '#' + finished[0]
self.finished_list.append(finished)
tmp_list = self.finished_list + self.run_list
all_list = [" ".join(x) + "\n" for x in tmp_list]
Cabinet.write_file(self.list_run_file, all_list)
def get_results(cls, fname='OSZICAR'):
"""
iterationの回数、nswの数、energy、magをdict形式でreturn
緩和毎にlistに追加する
"""
lines = Cabinet.read_file(fname)
keywords = r"\s*([\d]+)\s+F=\s*([\d\-\.E\+]+)\s+E0=\s+.*\s+"
meta = re.compile(keywords)
keywords2 = r"\s*DAV:\s*([\d]+)\s+.*"
meta2 = re.compile(keywords2)
results = []
for i in range(0, len(lines)):
if meta.match(lines[i]):
relax_num, energy, mag = cls.get_3values(lines[i])
j = 1
while not meta2.match(lines[i-j]):
j += 1
iter_num = lines[i-j].split()[1]
results.append({'iter_num': iter_num, 'nsw_num': relax_num,
'energy': energy, 'mag': mag})
if not results:
last_val = lines[-1].split()
try:
if math.fabs(float(last_val[3])) > 1e-5:
print("{0} is unfinished with error. ".format(fname))
return []
except ValueError:
print("{0} is unfinished with error. ".format(fname))
return []
print("{0} is unfinished but converged. "
"(val. of mag is false)".format(fname))
results.append({'iter_num': int(last_val[1]), 'nsw_num': 1,
'energy': float(last_val[2]), 'mag': -100})
return results
def get_enemag(oszicar='OSZICAR'):
"""
Read energy and magnetic momentum from OSZICAR/OUTCAR.
Judge file type from first line of the read file.
"""
try:
lines = Cabinet.read_file(oszicar)
except IOError:
lines = ['error']
try:
head = lines[0].split()[0]
except IndexError:
print(oszicar)
exit()
if head == 'N': # OSZICAR
output = vaspy.Oszicar(oszicar)
elif head[0:4] == 'vasp': # OUTCAR
output = vaspy.Outcar(oszicar)
else:
print("I cannot read {0}".format(oszicar))
return None, None, False
if not output.results:
print(oszicar)
return None, None, False
energy = output.results[-1]['energy']
mag = output.results[-1]['mag']
return energy, mag, True
def read_outcar(self, fname='OUTCAR_ibzkp'):
"""
Read NGX, NGY, NGZ, NBANDS parameters from OUTCAR.
"""
lines = Cabinet.read_file(fname)
ngx_key = re.compile(r".*WARNING:.*NGX\s*to\s*(\d+)*")
ngy_key = re.compile(r".*WARNING:.*NGY\s*to\s*(\d+)*")
ngz_key = re.compile(r".*WARNING:.*NGZ\s*to\s*(\d+)*")
nbands_key = re.compile(r".*NBANDS\s*=\s*(\d+)*")
ngx_value = None
ngy_value = None
ngz_value = None
for i in range(0, len(lines)):
ngx_meta = ngx_key.match(lines[i])
ngy_meta = ngy_key.match(lines[i])
ngz_meta = ngz_key.match(lines[i])
nbands_meta = nbands_key.match(lines[i])
if ngx_meta:
ngx_value = int(ngx_meta.group(1))
elif ngy_meta:
ngy_value = int(ngy_meta.group(1))
elif ngz_meta:
ngz_value = int(ngz_meta.group(1))
elif nbands_meta:
nbands_value = int(nbands_meta.group(1))
nbands_value += nbands_value % 2 # alt to even
return {'ngx': ngx_value, 'ngy': ngy_value, 'ngz': ngz_value,
'nbands': nbands_value}
def read_origin_file(fname):
"""
self.individualsの作成に用いる
(__init__()で実行)
Originから読み取ったすべてのindividualの情報を
dict形式でreturnする
どの様に進化したか 'background'
世代 'generation'
親 'parents'
子供 'children'(空)を要素に持つ
またmake_family_tree()で使う'blood'(空)を定義
"""
individuals = {}
lines = Cabinet.read_file(fname)
for line in lines:
if line.split()[0] == '-' * 7:
gene = int(line.split()[1].split('generation')[-1])
else:
line = line.split(None, 1)
id_indiv = int(line[0])
line = line[1].split(',')
background = line[0].split('\n')[0]
if background == 'random':
parents = None
else:
line = line[1].split()
parents = [int(x) for x in line[2:]]
individuals.update({id_indiv: {'background': background,
'parents': parents,
'generation': gene,
'blood': None,
'children': []}})
return individuals
def read_potcar(self):
"""
Several POTCAR files lines are loaded based on self.psuedo_pot list.
"""
path_list = [os.path.join(self.VASP_POT_DIR, x, 'POTCAR')
for x in self.psuedo_pot]
potentials_lines = [Cabinet.read_file(x) for x in path_list]
return potentials_lines
def __init__(self, dos):
DataBox.__init__(self, [])
self.dos_lines = Cabinet.read_file(dos)
self.num_atoms = self.get_num_atoms(self.dos_lines[0])
(self.num_energy,
self.fermi_energy) = self.get_parameters(self.dos_lines[5])
print(self.get_parameters(self.dos_lines[5]))
self.dos_data = self.__prep_dos_data(self.num_atoms,
self.labels_orbital)
def get_results(self, fname='OUTCAR'):
"""
energy, magの値を修得
"""
lines = Cabinet.read_file(fname)
energy = self.get_energy(lines)
mag = self.get_mag(lines)
elements = self.get_elements(lines)
results = {'energy': energy, 'mag': mag, 'elements': elements}
return results
def get_elements(path):
"""
元素名を修得
"""
lines = Cabinet.read_file(path)
key = r"\s*There are 3 types of atoms in the system:\s+([\w\s]+)"
meta = re.compile(key)
for line in lines:
if meta.match(line):
elements = meta.match(line).group(1)
return elements.split()
def get_data_single(fname):
"""
一つのoutputファイルからデータ修得
変数が多いので分割することも要検討
"""
lines = Cabinet.read_file(fname)
key_energy = r"\s*total energy=\s*([-\d\.]*)\s*"
meta_energy = re.compile(key_energy)
key_atoms = (r"\s*ntyp=\s*([\d]+)\s+natm=\s*([\d]+)\s+"
r"ncmpx=\s*([\d]+)\s*")
meta_atoms = re.compile(key_atoms)
key_latt = (r"\s*brvtyp=\s*([^\s]+)\s+a=\s*([\d\.]+)\s+"
r"c/a=\s*([\d\.]+)\s+b/a=\s*([\d\.]+)\s*")
meta_latt = re.compile(key_latt)
for line in lines:
if meta_latt.match(line):
latt_a = meta_latt.match(line).group(2)
if meta_atoms.match(line):
ntype = int(meta_atoms.match(line).group(1))
num_atoms = int(meta_atoms.match(line).group(2))
if meta_energy.match(line):
energy = float(meta_energy.match(line).group(1))
pos_compo = lines.index(" type of site\n")
key_type = r"\s*type=([^\s]+)\s+.*"
meta_type = re.compile(key_type)
key_conc = (r"\s*component=\s*([\d]+)\s+anclr=\s*([\d\.]+)\s+"
r"conc=\s*([\d\.]+)\s*")
meta_conc = re.compile(key_conc)
i = 1
site_id = 0
compo = []
while lines[pos_compo+i] != "\n":
if meta_type.match(lines[pos_compo+i]):
site_id += 1
type_name = meta_type.match(lines[pos_compo+i]).group(1)
compo.append({'site_id': site_id, 'type_name': type_name,
'compositions':[]})
if meta_conc.match(lines[pos_compo+i]):
component = meta_conc.match(lines[pos_compo+i]).group(1)
anclr = float(meta_conc.match(lines[pos_compo+i]).group(2))
conc = meta_conc.match(lines[pos_compo+i]).group(3)
compo[-1]['compositions'].append({'Z': int(anclr),
'component': int(component),
'concentration': float(conc)})
i += 1
try:
return {'energy': energy/num_atoms, 'num_atoms': num_atoms,
'latt_a': latt_a, 'compo': compo}
except UnboundLocalError:
print('error {0}'.format(fname))
return None
def get_composition(fname='./POTCAR'):
"""
POTCARから元素を読む
PAW_PBEから始まる行に元素名が記載されているのでそこを読む
空行は例外処理でpassする
"""
lines = Cabinet.read_file(fname)
elements = []
for line in lines:
try:
if line.split()[0] == 'PAW_PBE':
elements.append(line.split()[1].split('_')[0])
except IndexError:
pass
return elements
def read_float(fname):
"""
ファイルをfloatデータとして読み込み
float化できない文字がある行はスキップ
"""
stock = []
rows = Cabinet.read_file(fname)
for row in rows:
row = row.split()
try:
row = [float(x) for x in row] # 全てをfloat化
stock.append(row)
except ValueError:
pass
return stock
def from_file(cls, fname):
"""
Read a Incar file, and make a incar_dict.
"""
lines = Cabinet.read_file(fname)
incar_dict = {}
for line in lines:
if line[0] not in ('#', '\n'):
para_list = line.split('#')[0].split('!')[0]
# ^ remove comment_out ^
para_list = para_list.split()
key = para_list[0].lower()
value_list = para_list[2:]
incar_dict.update({key: value_list})
cls.__fix_dict(incar_dict)
return incar_dict
def fix(modname, fname):
"""
modnameはパッケジされている場合に必要
"""
lines = Cabinet.read_file(fname)
key = r"\s*from\s+(.*)\s+import\s+\*"
meta = re.compile(key)
star_list = [meta.match(x).group(1) for x in lines if meta.match(x)]
for module in star_list:
exec('import {0}{1}'.format(modname, module))
try:
a = eval('{0}{1}.__all__'.format(modname, module))
except AttributeError:
b = eval('dir({0}{1})'.format(modname, module))
a = [x for x in b if x[0] != '_']
print('from {0} import {1}'.format(module, ', '.join(a)))
print()
def get_ene_mag(oszicar='OSZICAR'):
"""
Read energy and magnetic momentum from OSZICAR/OUTCAR.
"""
try:
lines = Cabinet.read_file(oszicar)
except IOError:
lines = ''
if lines[0].split()[0] == 'N': # OSZICAR
output = vaspy.Oszicar(oszicar)
elif lines[0].split()[0][0:4] == 'vasp': # OUTCAR
output = vaspy.Outcar(oszicar)
else:
print("I cannot read {0}".format(oszicar))
return None, None
energy = output.results[-1]['energy']
mag = output.results[-1]['mag']
return energy, mag
def test_readfrom_lines(self):
""" read from lines format"""
posc_lines = Cabinet.read_file(os.path.join(self.path, "POSCAR"))
poscar = vaspy.Poscar(posc_lines)
print(poscar.poscar_title)
def test_outcar(self):
"""for outcar obj"""
outcar = vaspy.Outcar(os.path.join(self.path, "OUTCAR"))
o_lines = Cabinet.read_file(os.path.join(self.path, "OUTCAR"))
print(outcar.get_mag(o_lines))
def __init__(self, fname):
output_lines = Cabinet.read_file(fname)
self.data = self.get_data(output_lines)
def __init__(self, path):
self.path = os.path.dirname(path)
self.bgp_lines = Cabinet.read_file(path)
poscar_lines = self.split_structure()
self.poscars = [{'ID': x['ID'], 'object': vaspy.Poscar(x['lines'])}
for x in poscar_lines]
