def main():
Bash.mkdir('cova')
cova_list = Array.frange_stp(1.0, 1.05, 0.05)
series = series_vasp.Produce('POSCAR', 'cova')
series.set_cova(cova_list)
series.make_files()
series.append_list_run('run_cova.sh')
def from_new(cls):
"""
seq ディレクトリを作成し originals ディレクトリ中に初期ファイルを保存
実行ディレクトリを記憶
"""
seq_list = glob.glob("seq*/")
i = 0
for seq in seq_list:
try:
j = int(seq.split("seq")[-1].split("/")[0])
if i < j:
i = j
except ValueError:
pass
i += 1
dirc = 'seq{0}/originals/'.format(i)
str_files = glob.glob('*.str')
Bash.mkdir(dirc)
for fname in ['IN.CVM', 'def.txt', 'energies.txt'] + str_files:
copyfile(fname, os.path.join(dirc, fname))
seq_dirc = "seq{0}".format(str(i))
print("New directory of '{}' is created".format(seq_dirc))
clus_name = cls.get_clus_name(".")
results = CEMResults([])
return cls(seq_dirc, None, None, clus_name, results)
def view_osz(self):
path = '.'
if self.value.value == 'EV curve':
path = glob.glob('voldep/volume_*')[0]
print(path)
Bash.execute("emacs {0}/OSZICAR".format(path))
def set_condition(self, r, n):
"""
path 中に originals ファイルをコピーして rmax, nmax を def.txt にセットする
"""
if not self.distances:
self.current_label = "RmaxN2"
rmax = r
else:
self.current_label = "R{0}N{1}".format(r, n)
rmax = self.distances[r-1]+0.005
dst = os.path.join(self.seq_dirc, self.current_label)
Bash.copy_dir(os.path.join(self.seq_dirc, "originals"), dst)
deftxt = os.path.join(dst, "def.txt")
with open(deftxt, 'r') as rfile:
lines = rfile.readlines()
meta = re.compile(r"^{0}\s*.*".format(self.clus_name))
i = 0
# print(self.clus_name)
while not meta.match(lines[i]):
# print(i)
# print(lines[i])
i += 1
lines[i] = "{0} RMAX={1} NSMAX={2} PRNTMAXCL=T NMAX=0\n".format(
self.clus_name, rmax, n)
with open(os.path.join(dst, "def.txt"), 'w') as wfile:
wfile.write("".join(lines))
def alt_incvm(src, dst):
"""
CONW, ECLI を書き換えて出力する
"""
call("cat {0}/IN.CVM | sed 's/CONW=T/CONW=F/g' | "
"sed 's/ECLI=T/ECLI=F/g' > tmp".format(src), shell=True)
Bash.move('tmp', os.path.join(dst, "IN.CVM"))
def main():
Bash.mkdir('kp')
kp_list = Array.frange_stp(0.08, 0.24, 0.02)
#kp_list = Array.frange_stp(0.04, 0.07, 0.02)
series = series_vasp.Produce('POSCAR', 'kp')
series.set_kp_relax(kp_list)
series.make_files()
series.make_list_run('run.sh')
def test_plt(self):
clean_prev_dir(self.path, 'output')
Bash.mkdir(os.path.join(self.path, 'output', 'text'))
combi_para = [['Co'], ['Al']]
pathA = os.path.join(self.path, 'typeA')
pathB = os.path.join(self.path, 'typeB')
path_out = os.path.join(self.path, 'output')
self.plt_double(combi_para, pathA, pathB, path_out)
def mkdirs(self):
"""
pathに記された階層ディレクトリを作成
階層の順番はsetした順番となる
"""
for param in self.series:
dst_path = param['path']
Bash.mkdir(dst_path)
def conv2poscar(cif_file, out_path):
"""
A cif file convert to POSCAR
"""
cif_file = os.path.normpath(cif_file)
cmd = 'cif2cell -p vasp -f {0} -o {1}/POSCAR --no-reduce \
--vasp-print-species --vasp-cartesian-lattice-vectors \
--vasp-format=5'.format(cif_file, out_path)
Bash.execute(cmd)
def test_volume(self):
print("SeriesVasp test_volume")
os.chdir(self.path)
clean_prev_dir('.', 'volume')
Bash.mkdir('volume')
volume_list = [5, 6, 7]
series = series_vasp.Produce('POSCAR', 'volume')
series.set_volume(volume_list)
series.make_files()
def stack(args):
"""
hcp-fcc Mg stacking 構造を作成する
"""
path = args
strs = CVMStrs.from_str_file(path)
for structure in strs:
dirc = str(structure.label).split('*')[0]
Bash.mkdir(dirc)
structure.make_stack_poscar(os.path.join(dirc, "POSCAR"))
def for_ferrite():
"""
ferrite系のcombinatorial
"""
Bash.mkdir('combi')
elem_list = ['Ni', 'Mn', 'Cu', 'Zn', 'Cr']
comp_list = [['O', 'Fe', x] for x in elem_list]
series = series_vasp.Produce('POSCAR', 'combi')
series.set_elements(comp_list)
series.make_files()
series.append_list_run('run_combi.sh')
def expand_poscars(self, elements):
"""
self.poscarsのPOSCARをディレクトリ(ID名)に展開
elements名も追記する
self.path中に作成
pathを変えたい場合はself.pathを変更
"""
for poscar in self.poscars:
Bash.mkdir(os.path.join(self.path, poscar['ID']))
poscar['object'].elements = elements
poscar['object'].write_poscar(os.path.join(self.path,
poscar['ID'], 'POSCAR'))
def execute(self):
if self.value == 'EV curve':
Bash.execute("batch_run.sh 100")
else:
Bash.execute("qsub run.sh")
top = tk.Toplevel()
f = tk.Frame(top)
f.pack()
label = tk.Label(f, text="{0} calculation started !".format(self.value))
label.pack()
btn = tk.Button(f, text="OK", command=top.destroy)
btn.pack()
def make_system(self, dirname=None):
os.chdir(CWD)
font = ('Helevetica', 12, 'bold')
self.initial.status.configure(text='None', font=font, fg='red')
if not dirname:
dirname = self.e_dir.get()
dirname = "enshu_" + self.e_dir.get()
path = os.path.join(CWD, dirname)
Bash.mkdir(path)
self.initial.listbox.delete(0, tk.END)
SYSTEMS = [x[6:] for x in glob.glob('enshu_*')]
print(SYSTEMS)
self.initial.listbox.insert(tk.END, *SYSTEMS)
self.top.destroy()
def relax(path, num, vaspcmd):
"""
judgeの結果がTrueの場合終了
それ以外はOSZICAR, OUTCARを保管してVASPを再実行
"""
for i in range(0, num):
judge = judge_oszicar(path)
if judge:
break
else:
shutil.copyfile('OUTCAR', "out.relax.{0}".format(i))
shutil.copyfile('OSZICAR', "osz.relax.{0}".format(i))
shutil.copyfile('CONTCAR', 'POSCAR')
print("Start re-calculation.")
Bash.execute(vaspcmd)
def for_Fe16N2():
"""
perovskite系のcombinatorial
"""
Bash.mkdir('combi')
elem_list = [['Sc', 'As', 'Se', 'Y', 'Mo',
'Tc', 'Ag', 'Cd', 'In', 'Te',
'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir',
'Au', 'Hg', 'Tl', 'Pb', 'Bi'], ['C', 'B', 'N']]
combi = Combinatorial(*elem_list)
comp_list = [['Fe', x['elements'][0], 'Fe', x['elements'][1]]
for x in combi.compositions]
series = series_vasp.Produce('POSCAR', 'combi')
series.set_elements(comp_list)
series.make_files()
series.append_list_run('run_combi.sh')
def for_perovskite():
"""
perovskite系のcombinatorial
"""
Bash.mkdir('combi')
elem_list = [['Al', 'Co', 'Cr', 'Cu', 'Fe', 'Ga',
'Ge', 'Mn', 'Nb', 'Ni', 'Pd', 'Pt',
'Rh', 'Ru', 'Sb', 'Si', 'Sn', 'Ti',
'V', 'Zn', 'Zr'], ['C', 'B', 'N']]
combi = Combinatorial(*elem_list)
comp_list = [['Fe', x['elements'][0], x['elements'][1]]
for x in combi.compositions]
series = series_vasp.Produce('POSCAR', 'combi')
series.set_elements(comp_list)
series.make_files()
series.append_list_run('run_combi.sh')
def extract_strs(self, exch_fix,
src_path="../*/str.out", dst_dirc="extracts"):
"""
src_path 中の等価な全ての構造を genstr から抽出する
"""
for path in glob.glob(src_path):
dst_path = os.path.join(
dst_dirc, os.path.basename(os.path.dirname(path)))
Bash.mkdir(dst_path)
idx = self.get_idx_same_str(os.path.dirname(path), exch_fix=exch_fix)
if idx:
lines = self.lines[idx[0]:idx[1]]
with open(os.path.join(dst_path, "str.out"), 'w') as wfile:
wfile.write("".join(lines))
else:
with open(os.path.join(dst_path, "too_large"), 'w') as wfile:
wfile.write("")
def save_results(temp, plot_data):
Bash.mkdir('results_cv1')
lines = "x\ty\n"
for i in range(len(plot_data[0])):
lines += str(plot_data[0][i]) + "\t"
lines += str(plot_data[1][i]) + "\n"
fname = "raw_" + str(temp)
with open(os.path.join('results_cv1', fname), 'w') as wfile:
wfile.write(lines)
lines = "x_fit\ty_fit\n"
for i in range(len(plot_data[2])):
lines += str(plot_data[2][i]) + "\t"
lines += str(plot_data[3][i]) + "\n"
fname = "fit_" + str(temp)
with open(os.path.join('results_cv1', fname), 'w') as wfile:
wfile.write(lines)
def clean_prev_dir(path, dirc):
"""
既存dirctoryを消去
"""
trush_list = Bash.find_files(path, dirc)
for trush in trush_list:
fname = os.path.join(path, trush)
shutil.rmtree(fname)
print("{0} is removed.".format(fname))
def clean_prev(path, files):
"""
既存filesを消去
"""
trush_list = Bash.find_files(path, files)
for trush in trush_list:
fname = os.path.join(path, trush)
os.remove(fname)
print("{0} is removed.".format(fname))
def convert_all(self, dst_path):
"""
det_path中の5種のINCARファイルを修正し上書きする
追加したパラメータを出力
"""
incar_list = Bash.find_files('INCAR_*soc*')
for incar in incar_list:
self.convert_incar(dst_path, incar)
self.note_update()
def prep_one(cls, cif_file, dst_dir):
"""
The dst_dir is current directory,
this method search POSCAR and reserve it.
If not, it will search whethre dst_dir already exist or not.
If it already exist, this module will do nothing.
If not, new directory make and prepare POSCAR file.
"""
if dst_dir == '.':
Cabinet.reserve_file('POSCAR')
elif glob.glob(dst_dir):
line = ("\'{0}\' directory is already exist.\n"
"Do Nothing...\n".format(dst_dir.split('/')[-1]))
print(line)
return
else:
Bash.mkdir(dst_dir)
cls.conv2poscar(cif_file, dst_dir)
shutil.copy(cif_file, dst_dir)
def all(cls, path, incar_obj=None, kp_rx=0.15, kp_soc=0.11):
"""
All pattern of INCAR files are prepared.
それぞれのパラメータの変更は
class method "cls_add_fixedtag"や"cls_add_extratag"を使うか
incar_objに書き替えたincarを入力
省略した場合、path中のPOSCARをbaseに作成
"""
if not incar_obj:
incar_obj = IncarReadPoscar(os.path.join(path, 'POSCAR'))
cls.make_potcar_kpoints(path, kp_rx, kp_soc)
methods = ['relax', 'cell', 'volume', 'volumeE', 'presoc', 'presoc_nc',
'ibzkp', 'soc',
'dos', 'band', 'static']
for method in methods:
getattr(cls, method)(path, incar_obj)
src_dir = os.path.join(MODULE_DIR, '../sorce/originalsVASP', 'Calc')
dst_dir = os.path.join(path, 'Calc')
Bash.copy_dir(src_dir, dst_dir)
def test_normalize(self):
"""normalize lattice parameter """
print("VaspyPoscar test_normalize")
os.chdir(self.path)
clean_prev_dir(".", "normalize")
Bash.mkdir("normalize")
poscar = vaspy.Poscar("POSCAR")
poscar.normalize_lattice()
poscar.write_poscar("normalize/POSCAR")
poscar1 = vaspy.Poscar("POSCAR")
poscar2 = vaspy.Poscar("normalize/POSCAR")
len1 = poscar1.get_lattice_length()
len2 = poscar2.get_lattice_length()
vol1 = poscar1.get_cell_volume()
vol2 = poscar1.get_cell_volume()
self.assertEqual(len1, len2)
self.assertEqual(vol1, vol2)
self.assertEqual(poscar2.cell_lattices[0, 0], 1)
self.assertEqual(poscar2.cell_lattices[0, 1], 0)
self.assertEqual(poscar2.cell_lattices[0, 2], 0)
def initialize():
"""
seq ディレクトリを作成し originals ディレクトリ中に初期ファイルを保存
"""
seq_list = glob.glob("seq*/")
i = 0
for seq in seq_list:
try:
j = int(seq.split("seq")[-1].split("/")[0])
if i < j:
i = j
except ValueError:
pass
i += 1
dirc = 'seq{0}/originals/'.format(i)
str_files = glob.glob('*.str')
Bash.mkdir(dirc)
for fname in ['IN.CVM', 'def.txt', 'energies.txt'] + str_files:
copyfile(fname, os.path.join(dirc, fname))
return 'seq{0}'.format(i)
def find_cif_files(path):
"""
This method find **.cif or **.cif.txt in path and path/cifs directory.
All cif files are moved in path/cifs/ dirctory
"""
cifs_dir = os.path.join(path, 'cifs')
Bash.mkdir(cifs_dir)
search_cif = glob.glob(os.path.join(path, "*.cif"))
search_ciftxt = glob.glob(os.path.join(path, "*.cif.txt"))
search_cwd = search_cif + search_ciftxt
for cif_file in search_cwd:
Bash.move(cif_file, cifs_dir)
search_cif = glob.glob(os.path.join(cifs_dir, "*.cif"))
search_ciftxt = glob.glob(os.path.join(cifs_dir, "*.cif.txt"))
search_cifs = search_cif + search_ciftxt
if len(search_cifs) == 0:
print('I cannot find any .cif file in {0} and {1}'
.format(path, cifs_dir))
exit()
return search_cifs
def test_latt(self):
print("SeriesVasp test_latt")
os.chdir(self.path)
clean_prev_dir('.', 'scale')
Bash.mkdir('scale')
scale_list = [round(random.uniform(1, 3), 3) for x in range(0, 3)]
series = series_vasp.Produce('POSCAR', 'scale')
series.set_scale(scale_list)
series.make_files()
test_param = random.choice(series.series)
test_path = test_param['path']
test = vaspy.Poscar(os.path.join(test_path, 'POSCAR'))
orig_pos = vaspy.Poscar('POSCAR')
orig_a, _, orig_c = orig_pos.get_lattice_length()
len_a, _, len_c = test.get_lattice_length()
scale = test.cell_scale
self.assertAlmostEqual(len_c/len_a, orig_c/orig_a)
self.assertAlmostEqual(scale, test_param['scale'])
def send(self):
# cwd = os.path.basename(os.getcwd())
for system in SYSTEMS:
drctry = 'enshu_' + system
dst = os.path.join('/cooper', 'KSZM_2016', BASE_DIR, drctry)
Bash.mkdir(dst)
files = ['POSCAR', 'CHGCAR', 'OSZICAR', 'OUTCAR',
'murnaghan_plot.eps', 'band.eps']
for file in files:
try:
shutil.copyfile(os.path.join(CWD, drctry, file),
os.path.join(dst, file))
except IOError:
pass
top = tk.Toplevel()
f = tk.Frame(top)
f.pack()
label = tk.Label(f, text="Data were send !")
label.pack()
btn = tk.Button(f, text="OK", command=top.destroy)
btn.pack()