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| ab_initio:ase_manual 2020/08/17 16:10 | — 現在 | ||
|---|---|---|---|
| ライン 1: | ライン 1: | ||
| - | ====== ASEマニュアル ====== | ||
| - | ===== 行列の固有値 ===== | ||
| - | <code python> | ||
| - | from LinearAlgebra import Heigenvalues | ||
| - | from Numeric import array | ||
| - | a1 = array([[1.0, 0.01j], [-0.01j, 1.0]]) | ||
| - | b1 = Heigenvalues(a1) | ||
| - | print b1 | ||
| - | </code> | ||
| - | ===== 状態密度 ===== | ||
| - | |||
| - | <code python> | ||
| - | f1 = 'out.nc' | ||
| - | |||
| - | from Dacapo import Dacapo | ||
| - | s1 = Dacapo.ReadAtoms(filename = f1) | ||
| - | c1 = s1.GetCalculator() | ||
| - | |||
| - | from ASE.Utilities.DOS import DOS | ||
| - | d1 = DOS(c1) | ||
| - | x0 = d1.GetEnergies() | ||
| - | y1 = d1.GetDOS(0) | ||
| - | y2 = d1.GetDOS(1) | ||
| - | |||
| - | for i in range(len(x0)): | ||
| - | print x0[i], y1[i], -y2[i] | ||
| - | </code> | ||
| - | ===== WriteXYZ ===== | ||
| - | <code python> | ||
| - | from Dacapo import Dacapo | ||
| - | s1 = Dacapo.ReadAtoms(filename = 'out.nc') | ||
| - | |||
| - | from ASE.IO.xyz import WriteXYZ | ||
| - | WriteXYZ('out.xyz', atoms = s1) | ||
| - | </code> | ||
| - | |||
| - | ==== 標準ツール trajectory2xyz ソースコード ==== | ||
| - | <code python> | ||
| - | #!/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]) | ||
| - | </code> | ||
| - | |||
| - | ===== VTK (Visual Tool Kit) ===== | ||
| - | |||
| - | <code python> | ||
| - | f1 = 'out.nc' | ||
| - | |||
| - | from Dacapo import Dacapo | ||
| - | s1 = Dacapo.ReadAtoms(filename = f1) | ||
| - | |||
| - | from ASE.Visualization.VTK import VTKPlotAtoms | ||
| - | ap1 = VTKPlotAtoms(s1) | ||
| - | </code> | ||
| - | |||
| - | <code python> | ||
| - | f1 = 'out.nc' | ||
| - | |||
| - | from Dacapo import Dacapo | ||
| - | s1 = Dacapo.ReadAtoms(filename = f1) | ||
| - | |||
| - | from ASE.Visualization.VTK import VTKPlotDensity | ||
| - | dp1 = VTKPlotDensity(s1, showatoms = True) | ||
| - | </code> | ||
| - | |||
| - | <code python> | ||
| - | f1 = 'out.nc' | ||
| - | m1 = 0 | ||
| - | |||
| - | from Dacapo import Dacapo | ||
| - | s1 = Dacapo.ReadAtoms(filename = f1) | ||
| - | |||
| - | from ASE.Visualization.VTK import VTKPlotWaveFunction | ||
| - | wp1 = VTKPlotWaveFunction(s1, band = m1, showatoms = True) | ||
| - | </code> | ||
