差分
この文書の現在のバージョンと選択したバージョンの差分を表示します。
| ab_initio:ase_manual 2009/01/24 01:19 | ab_initio:ase_manual 2009/05/19 18:35 現在 | ||
|---|---|---|---|
| ライン 4: | ライン 4: | ||
| from LinearAlgebra import Heigenvalues | from LinearAlgebra import Heigenvalues | ||
| from Numeric import array | from Numeric import array | ||
| - | a = array([[1.0, 0.01j], [-0.01j, 1.0]]) | + | a1 = array([[1.0, 0.01j], [-0.01j, 1.0]]) |
| - | b = Heigenvalues(a) | + | b1 = Heigenvalues(a1) |
| - | print b | + | print b1 |
| </code> | </code> | ||
| ライン 12: | ライン 12: | ||
| <code python> | <code python> | ||
| - | the_filename = 'out.nc' | + | f1 = 'out.nc' |
| from Dacapo import Dacapo | from Dacapo import Dacapo | ||
| - | the_model = Dacapo.ReadAtoms(filename = the_filename) | + | s1 = Dacapo.ReadAtoms(filename = f1) |
| - | the_calculator = the_model.GetCalculator() | + | c1 = s1.GetCalculator() |
| from ASE.Utilities.DOS import DOS | from ASE.Utilities.DOS import DOS | ||
| - | a_dos = DOS(the_calculator) | + | d1 = DOS(c1) |
| - | x = a_dos.GetEnergies() | + | x0 = d1.GetEnergies() |
| - | y1 = a_dos.GetDOS(0) | + | y1 = d1.GetDOS(0) |
| - | y2 = a_dos.GetDOS(1) | + | y2 = d1.GetDOS(1) |
| - | for i in range(len(x)): | + | for i in range(len(x0)): |
| - | print x[i], y1[i], -y2[i] | + | print x0[i], y1[i], -y2[i] |
| </code> | </code> | ||
| + | ===== WriteXYZ ===== | ||
| + | <code python> | ||
| + | from Dacapo import Dacapo | ||
| + | s1 = Dacapo.ReadAtoms(filename = 'out.nc') | ||
| - | ===== 標準ツール trajectory2xyz ソースコード ===== | + | 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> | <code python> | ||
| #!/usr/bin/env python | #!/usr/bin/env python | ||
| ライン 59: | ライン 66: | ||
| <code python> | <code python> | ||
| - | the_filename = 'out.nc' | + | f1 = 'out.nc' |
| from Dacapo import Dacapo | from Dacapo import Dacapo | ||
| - | the_model = Dacapo.ReadAtoms(filename = the_filename) | + | s1 = Dacapo.ReadAtoms(filename = f1) |
| from ASE.Visualization.VTK import VTKPlotAtoms | from ASE.Visualization.VTK import VTKPlotAtoms | ||
| - | a_atom_plot = VTKPlotAtoms(the_model) | + | ap1 = VTKPlotAtoms(s1) |
| </code> | </code> | ||
| <code python> | <code python> | ||
| - | the_filename = 'out.nc' | + | f1 = 'out.nc' |
| - | the_band = 0 | + | |
| from Dacapo import Dacapo | from Dacapo import Dacapo | ||
| - | the_model = Dacapo.ReadAtoms(filename = the_filename) | + | s1 = Dacapo.ReadAtoms(filename = f1) |
| - | the_calculator = the_model.GetCalculator() | + | |
| - | from ASE.Visualization.VTK import VTKPlotAtoms | + | from ASE.Visualization.VTK import VTKPlotDensity |
| - | a_atom_plot = VTKPlotAtoms(the_model) | + | dp1 = VTKPlotDensity(s1, showatoms = True) |
| - | + | ||
| - | from ASE.Visualization.VTK import VTKPlotWaveFunction | + | |
| - | a_wavefunction_plot = VTKPlotWaveFunction(the_model, band = the_band, parent = a_atom_plot) | + | |
| - | a_atom_plot.Update() | + | |
| </code> | </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> | ||
