@surface

この文書は読取専用です。文書のソースを閲覧することは可能ですが、変更はできません。もし変更したい場合は管理者に連絡してください。
====== Tips and Chips ======



[[Not_Chip|「チップじゃないんだ、ティップなんだよ！」]]

===== General =====
  * [[linux:clear_DNS_cache|DNSキャッシュのクリア]]
  * [[linux:ssh_keygen|SSHキーの削除]]
  * [[大文字小文字変換]]
  * 
===== macOS =====
  * 最新の[[chromedriver]]をインストールする
  * [[ログインスクリーン画像の在り処]]
  * [[iconファイルの在り処]]
  * [[Joplinデータの在り処]]
  * [[なんでlsできへんねん！]]
===== iOS =====
  * [[iPhoneのパケット通信を禁止する]]
===== Linux =====
  * [[linux:logind_conf|ノーパソサーバにして蓋したら寝ちゃったんですよ]]
  * [[linux:lsb_release|ubuntuのバージョン知りたいんですが]]
  * [[linux:etc_netplan|今時固定IPっすか]]
  * [[linux:hostnamectl|hostname後から変えたいんですが]]
  * [[linux:usage_of_systemctl|systemctlの使い方]]
  * [[MySQLシステムに新しいデータベース]]

===== Web contents =====
  * [[jmolテスト]]
===== Error Handling =====

  *Use_https:Security Token did not match. Possible CSRF attack.
    * httpsを使え！





===== From NetCDF to XYZ =====
// Mon, 09 Nov 2009 13:06:28 +0000 //

<code lang="python">
#!/usr/bin/env python
import os
import tempfile
from optparse import OptionParser
 
from Dacapo import Dacapo
from ASE.Trajectories.NetCDFTrajectory import NetCDFTrajectory
from ASE.IO.xyz import WriteXYZ
 
cmd = OptionParser(usage = '%prog [-r R1 R2 R3] input_nc_file output_xyz_file')
cmd.add_option('-r', '--repeat', type = 'int', nargs = 3,
               help = 'Repeat R1, R2, R3 times along the three axes',
               metavar = 'R1 R2 R3')
 
(opt, argv) = cmd.parse_args()
 
if len(argv) != 2:
    cmd.print_help()
    raise SystemExit
 
ncfile = argv[0]
xyzfile = argv[1]
 
try:
  model = Dacapo.ReadAtoms(ncfile, index = 1)
  trajectory = True
except IndexError:
  trajectory = False
 
if not trajectory:
  model = Dacapo.ReadAtoms(ncfile)
  WriteXYZ(xyzfile, atoms = model, repeat = opt.repeat, id = ncfile)
else:
  model = Dacapo.ReadAtoms(ncfile, index = 0) 
  model.SetCalculator(None)
  tmpfile = tempfile.mktemp()
  xyzpath = NetCDFTrajectory(tmpfile, model)
  xyzpath.Update()
 
  frame = 0 
  error = False
  while not error: 
    frame += 1
    try: 
        atoms = Dacapo.ReadAtoms(ncfile, index = frame) 
        model.SetCartesianPositions(atoms.GetCartesianPositions())
        xyzpath.Update()
    except IndexError: 
        error = True
 
  xyzpath.Close()    
  xyzpath = NetCDFTrajectory(tmpfile)
  WriteXYZ(xyzfile, trajectory = xyzpath, repeat = opt.repeat, id = ncfile)
  os.remove(tmpfile)
</code>

===== From NetCDF to DOS =====
// Tue, 10 Nov 2009 13:51:22 +0000 //

<code lang="python">
#!/usr/bin/env python
from optparse import OptionParser</code>

<code lang="python">from Dacapo import Dacapo
from ASE.Utilities.DOS import DOS</code>

<code lang="python">cmd = OptionParser(usage = '%prog [-r] input_nc_file output_text_file')
cmd.add_option('-r', '--reverse', action = "store_true", default = False,
help = 'reverse out put for minor spin states')
(opt, argv) = cmd.parse_args()

if len(argv) != 2:
  cmd.print_help()
  raise SystemExit

  ncfile = argv[0]
  textfile = argv[1]
  sfmt0 = '%-15s %-15s\n'
  sfmt1 = '%-15s %-15s %-15s %-15s\n'
  efmt0 = '%15.7E %15.7E\n'
  efmt1 = '%15.7E %15.7E %15.7E %15.7E\n'

</code>

<code lang="python">  atoms = Dacapo.ReadAtoms(ncfile)
  calc = atoms.GetCalculator()
  isSpinPolarized = calc.GetSpinPolarized()
  dos = DOS(calc)
  x0 = dos.GetEnergies()
  if isSpinPolarized:
    y0 = dos.GetDOS(0)
    y1 = dos.GetDOS(1)
    fp = open(textfile, 'w')
    if opt.reverse:
      fp.write(sfmt1 % ('Energy', 'DOS0', 'DOS1', 'DIFF'))
    else:
      fp.write(sfmt1 % ('Energy', 'DOS0', 'DOS1', 'TOTAL'))
      for i in range(len(x0)):
        if opt.reverse:
          fp.write(efmt1 % (x0[i], y0[i], -y1[i], y0[i] - y1[i]))
        else:
          fp.write(efmt1 % (x0[i], y0[i],  y1[i], y0[i] + y1[i]))
      fp.close()
  else:
    y0 = dos.GetDOS(0)
    fp = open(textfile, 'w')
    fp.write(sfmt0 % ('Energy', 'DOS'))
    for i in range(len(x0)):
      fp.write(efmt0 % (x0[i], y0[i]))
    fp.close()
</code>

===== From NetCDF to CUBE (1) =====
// Tue, 10 Nov 2009 13:55:13 +0000 //

==== Total density of states ====
<code lang="python">
#!/usr/bin/env python
import string
from math import log10
from optparse import OptionParser

from Dacapo import Dacapo
from ASE.IO.Cube import WriteCube

cmd = OptionParser(usage = '%prog input_nc_file output_cube_file')

(opt, argv) = cmd.parse_args()

if len(argv) != 2:
  cmd.print_help()
  raise SystemExit

ncfile = argv[0]
cubefile = argv[1]
basename = string.split(cubefile, '.cube')

model = Dacapo.ReadAtoms(ncfile)
calculator = model.GetCalculator()

if not calculator.GetSpinPolarized():
  filename_total= basename[0] + '.cube'
else:
  filename_total= basename[0] + '_total.cube'
  filename_diff= basename[0] + '_diff.cube'
  filename_spin0= basename[0] + '_spin0.cube'
  filename_spin1= basename[0] + '_spin1.cube'
  density0 = calculator.GetDensityArray(spin = 0)
  density1 = calculator.GetDensityArray(spin = 1)
  WriteCube(model, density0, filename_spin0)
  WriteCube(model, density1, filename_spin1)
  diff = density1 - density0
  WriteCube(model, diff, filename_diff)

density = calculator.GetDensityArray()
WriteCube(model, density, filename_total)
</code>