Using phono3py hdf5 files

Using phono3py hdf5 files#

Using h5py in ipython#

It is assumed that python-h5py is installed on the computer you interactively use. In the following, how to see the contents of .hdf5 files in the interactive mode of Python. The basic usage of reading .hdf5 files using h5py is found at here. In the following example, an MgO result of thermal conductivity calculation stored in kappa-m111111.hdf5 (see kappa-*.hdf5) is loaded and thermal conductivity tensor at 300 K is watched.

In [1]: import h5py

In [2]: f = h5py.File("kappa-m111111.hdf5")

In [3]: list(f)
Out[3]:
['frequency',
 'gamma',
 'group_velocity',
 'gv_by_gv',
 'heat_capacity',
 'kappa',
 'kappa_unit_conversion',
 'mesh',
 'mode_kappa',
 'qpoint',
 'temperature',
 'weight']

In [4]: f['kappa'].shape
Out[4]: (101, 6)

In [5]: f['kappa'][:]
Out[5]:
array([[  0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
          0.00000000e+00,   0.00000000e+00,   0.00000000e+00],
       [  2.11702476e+05,   2.11702476e+05,   2.11702476e+05,
          6.64531043e-13,   6.92618921e-13,  -1.34727352e-12],
       [  3.85304024e+04,   3.85304024e+04,   3.85304024e+04,
          3.52531412e-13,   3.72706406e-13,  -7.07290889e-13],
       ...,
       [  2.95769356e+01,   2.95769356e+01,   2.95769356e+01,
          3.01803322e-16,   3.21661793e-16,  -6.05271364e-16],
       [  2.92709650e+01,   2.92709650e+01,   2.92709650e+01,
          2.98674274e-16,   3.18330655e-16,  -5.98999091e-16],
       [  2.89713297e+01,   2.89713297e+01,   2.89713297e+01,
          2.95610215e-16,   3.15068595e-16,  -5.92857003e-16]])

In [6]: f['temperature'][:]
Out[6]:
array([    0.,    10.,    20.,    30.,    40.,    50.,    60.,    70.,
          80.,    90.,   100.,   110.,   120.,   130.,   140.,   150.,
         160.,   170.,   180.,   190.,   200.,   210.,   220.,   230.,
         240.,   250.,   260.,   270.,   280.,   290.,   300.,   310.,
         320.,   330.,   340.,   350.,   360.,   370.,   380.,   390.,
         400.,   410.,   420.,   430.,   440.,   450.,   460.,   470.,
         480.,   490.,   500.,   510.,   520.,   530.,   540.,   550.,
         560.,   570.,   580.,   590.,   600.,   610.,   620.,   630.,
         640.,   650.,   660.,   670.,   680.,   690.,   700.,   710.,
         720.,   730.,   740.,   750.,   760.,   770.,   780.,   790.,
         800.,   810.,   820.,   830.,   840.,   850.,   860.,   870.,
         880.,   890.,   900.,   910.,   920.,   930.,   940.,   950.,
         960.,   970.,   980.,   990.,  1000.])

In [7]: f['kappa'][30]
Out[7]:
array([  1.09089896e+02,   1.09089896e+02,   1.09089896e+02,
         1.12480528e-15,   1.19318349e-15,  -2.25126057e-15])

In [8]: f['mode_kappa'][30, :, :, :].sum(axis=0).sum(axis=0) / weight.sum()
Out[8]:
array([  1.09089896e+02,   1.09089896e+02,   1.09089896e+02,
         1.12480528e-15,   1.19318349e-15,  -2.25126057e-15])

In [9]: g = f['gamma'][30]

In [10]: import numpy as np

In [11]: g = np.where(g > 0, g, -1)

In [12]: lifetime = np.where(g > 0, 1.0 / (2 * 2 * np.pi * g), 0)
Contents