@surface - script
http://sstweb.ee.ous.ac.jp/
2026-04-18T15:07:15+00:00
@surface
http://sstweb.ee.ous.ac.jp/
http://sstweb.ee.ous.ac.jp/lib/exe/fetch.php?media=wiki:logo.png
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text/html
2022-08-23T04:34:32+00:00
Anonymous (anonymous@undisclosed.example.com)
getatoms
http://sstweb.ee.ous.ac.jp/doku.php?id=script:getatoms&rev=1661229272&do=diff
getatoms
#!/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…
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2022-08-23T04:34:32+00:00
Anonymous (anonymous@undisclosed.example.com)
getdensity
http://sstweb.ee.ous.ac.jp/doku.php?id=script:getdensity&rev=1661229272&do=diff
getdensity
#!/usr/bin/env python
from sys import exit
from optparse import OptionParser
def getIndexedDansity(idx, calc):
if index_error(idx, calc):
exit()
(nb, nk, ns) = idx
wf = calc.GetWaveFunctionArray(band = nb, kpt = nk, spin = ns)
density = abs(wf)*abs(wf)
return density
def index_error(idx, calc):
(nband, nkpt, nspin) = idx
NumberOfBands = calc.GetNumberOfBands()
NumberOfKpoints = len(calc.GetIBZKPoints())
isSpinPolarized = calc.GetSpinPolarized()
error = Fals…
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2022-08-23T04:34:32+00:00
Anonymous (anonymous@undisclosed.example.com)
getdos
http://sstweb.ee.ous.ac.jp/doku.php?id=script:getdos&rev=1661229272&do=diff
getdos
#!/usr/bin/env python
from optparse import OptionParser
from Dacapo import Dacapo
from ASE.Utilities.DOS import DOS
cmd = OptionParser(usage = '%prog [-s] 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 = '%…
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2022-08-23T04:34:32+00:00
Anonymous (anonymous@undisclosed.example.com)
gettotaldensity
http://sstweb.ee.ous.ac.jp/doku.php?id=script:gettotaldensity&rev=1661229272&do=diff
gettotaldensity
#!/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 calculato…
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2022-08-23T04:34:32+00:00
Anonymous (anonymous@undisclosed.example.com)
getwfs
http://sstweb.ee.ous.ac.jp/doku.php?id=script:getwfs&rev=1661229272&do=diff
getwfs
#!/usr/bin/env python
from sys import exit
import string
from optparse import OptionParser
from math import log10
from Numeric import sign
from Dacapo import Dacapo
from ASE.IO.Cube import WriteCube
def getNumberOfSpins(calc):
if (calc.GetSpinPolarized()):
return 2
else:
return 1
def index_error(idx, calc):
(nband, nkpt, nspin) = idx
NumberOfBands = calc.GetNumberOfBands()
NumberOfKpoints = len(calc.GetIBZKPoints())
isSpinPolarized = calc.GetSpinPolarized()
erro…
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2022-08-23T04:34:32+00:00
Anonymous (anonymous@undisclosed.example.com)
makevestafile
http://sstweb.ee.ous.ac.jp/doku.php?id=script:makevestafile&rev=1661229272&do=diff
makevestafile
#!/usr/bin/env python
from optparse import OptionParser
from math import sqrt, acos, pi
from Dacapo import Dacapo
from ASE.ChemicalElements import Element
def getabs(v):
_av = sqrt(v[0]**2 + v[1]**2 + v[2]**2)
return _av
def getangle(v1, v2):
_av1 = getabs(v1)
_av2 = getabs(v2)
_ang = acos((v1[0]*v2[0] + v1[1]*v2[1] + v1[2]*v2[2])/(_av1*_av2))*180/pi
return _ang
def WriteVESTA(filename, atoms, cubefile = None):
natoms = len(atoms)
(a1, a2, a3) = atoms.GetUnit…
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2022-08-23T04:34:32+00:00
Anonymous (anonymous@undisclosed.example.com)
traj2xyz
http://sstweb.ee.ous.ac.jp/doku.php?id=script:traj2xyz&rev=1661229272&do=diff
traj2xyz
#!/usr/bin/env python
import os
import tempfile
from optparse import OptionParser
from ase.io.trajectory import PickleTrajectory
from ase.io import write
cmd = OptionParser(usage = '%prog input_traj_file output_xyz_file')
(opt, argv) = cmd.parse_args()
if len(argv) != 2:
cmd.print_help()
raise SystemExit
trajfile = argv[0]
xyzfile = argv[1]
traj1 = PickleTrajectory(trajfile)
atoms1 = []
for it in traj1:
atoms1.append(it)
write(xyzfile, images = atoms1, format =…