以前のリビジョンの文書です


ASEマニュアル

行列の固有値

from LinearAlgebra import Heigenvalues
from Numeric import array
a = array([[1.0, 0.01j], [-0.01j, 1.0]])
b = Heigenvalues(a)
print b

状態密度

the_filename = 'out.nc'
 
from Dacapo import Dacapo
the_model = Dacapo.ReadAtoms(filename = the_filename)
the_calculator = the_model.GetCalculator()
 
from ASE.Utilities.DOS import DOS
a_dos = DOS(the_calculator)
x  = a_dos.GetEnergies()
y1 = a_dos.GetDOS(0)
y2 = a_dos.GetDOS(1)
 
for i in range(len(x)):
  print x[i], y1[i], -y2[i]

標準ツール trajectory2xyz ソースコード

#!/usr/bin/env python
from optparse import OptionParser
 
from ASE.IO.xyz import WriteXYZ
from ASE.Trajectories.NetCDFTrajectory import NetCDFTrajectory
 
 
 
parser = OptionParser(usage='%prog [-r R1 R2 R3] trajectory xyzfile',
                      version='%prog 0.1')
parser.add_option('-r', '--repeat', type='int', nargs=3,
                  help='Repeat R1, R2, R3 times along the three axes',
                  metavar='R1 R2 R3')
 
options, args = parser.parse_args()
 
if len(args) != 2:
    parser.print_help()
    raise SystemExit
 
print 'Creating xyz file:' ,args[1]
trajectory = NetCDFTrajectory(args[0])
WriteXYZ(args[1],trajectory=trajectory,repeat=options.repeat,id=args[0])

VTK (Visual Tool Kit)

<code python>

band = 0 'CO_in_a_box.nc'

from ASE import ListOfAtoms from ASE import Atom from ASE.Visualization.VTK import VTKPlotWaveFunction from ASE.Visualization.VTK import VTKPlotAtoms

from Dacapo import Dacapo atoms = Dacapo.ReadAtoms(filename='CO_in_a_box.nc') calc = atoms.GetCalculator()

# make a combined plot of the wavefunction and the atoms atomplot = VTKPlotAtoms(atoms) wfplot = VTKPlotWaveFunction(atoms,band=band,parent=atomplot) atomplot.Update()

# The appearence of the individual atomic elements can also be changed. # Finding aluminium atom avatar (found in the dictionary of species avatars) p1_O=atomplot.GetDictOfSpecies()['O'] p1_C=atomplot.GetDictOfSpecies()['C']

# Change the radius to 2.0 AA and set the color to blue p1_C.SetRadius(0.5) p1_O.SetRadius(0.7)

#The color is given in an rgb (red,green,blue) scale p1_C.SetColor1) p1_O.SetColor2) atomplot.Render()

# The unitcell can be removed unitcell=atomplot.unitcell atomplot.RemoveAvatar(unitcell) atomplot.Render()

1) 1,0,0
2) 0,1,0
ab_initio/ase_manual.1232726954.txt.gz · 最終更新: 2009/01/24 01:09 by kimi
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