Python commopy.Bash类代码示例

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()