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How to read the results stored in hdf5 files

How to read the results stored in hdf5 files#

How to use HDF5 python library#

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. Usually for running interactive python, ipython is recommended to use but not the plain python. In the following example, an MgO result of thermal conductivity calculation 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)

Details of kappa-*.hdf5 file#

Files name, e.g. kappa-m323220.hdf5, is determined by some specific options. mxxx, show the numbers of sampling mesh. sxxx and gxxx appear optionally. sxxx gives the smearing width in the smearing method for Brillouin zone integration for phonon lifetime, and gxxx denotes the grid number. Using the command option of -o, the file name can be modified slightly. For example -o nac gives kappa-m323220.nac.hdf5 to memorize the option --nac was used.

Currently kappa-*.hdf5 file (not for the specific grid points) contains the properties shown below.

mesh#

(Versions 1.10.11 or later)

The numbers of mesh points for reciprocal space sampling along reciprocal axes, \(a^*, b^*, c^*\).

frequency#

Phonon frequencies. The physical unit is THz, where THz is in the ordinal frequency not the angular frequency.

The array shape is (irreducible q-point, phonon band).

gamma#

Imaginary part of self energy of phonon bubble diagram (phonon-phonon scattering). The physical unit is THz, where THz is in the ordinal frequency not the angular frequency.

The array shape for all grid-points (irreducible q-points) is (temperature, irreducible q-point, phonon band).

The array shape for a specific grid-point is (temperature, phonon band).

Phonon lifetime (\(\tau_\lambda=1/2\Gamma_\lambda(\omega_\lambda)\)) may be estimated from gamma. \(2\pi\) has to be multiplied with gamma values in the hdf5 file to convert the unit of ordinal frequency to angular frequency. Zeros in gamma values mean that those elements were not calculated such as for three acoustic modes at \(\Gamma\) point. The below is the copy-and-paste from the previous section to show how to obtain phonon lifetime in pico second:

In [8]: g = f['gamma'][30]

In [9]: import numpy as np

In [10]: g = np.where(g > 0, g, -1)

In [11]: lifetime = np.where(g > 0, 1.0 / (2 * 2 * np.pi * g), 0)

gamma_isotope#

Isotope scattering of \(1/2\tau^\mathrm{iso}_\lambda\). The physical unit is same as that of gamma.

The array shape is same as that of frequency.

group_velocity#

Phonon group velocity, \(\nabla_\mathbf{q}\omega_\lambda\). The physical unit is \(\text{THz}\cdot\text{Angstrom}\), where THz is in the ordinal frequency not the angular frequency.

The array shape is (irreducible q-point, phonon band, 3 = Cartesian coordinates).

heat_capacity#

Mode-heat-capacity defined by

\[ C_\lambda = k_\mathrm{B} \left(\frac{\hbar\omega_\lambda}{k_\mathrm{B} T} \right)^2 \frac{\exp(\hbar\omega_\lambda/k_\mathrm{B} T)}{[\exp(\hbar\omega_\lambda/k_\mathrm{B} T)-1]^2}. \]

The physical unit is eV/K.

The array shape is (temperature, irreducible q-point, phonon band).

kappa#

Thermal conductivity tensor. The physical unit is W/m-K.

The array shape is (temperature, 6 = (xx, yy, zz, yz, xz, xy)).

mode-kappa#

Thermal conductivity tensors at k-stars (\({}^*\mathbf{k}\)):

\[ \sum_{\mathbf{q} \in {}^*\mathbf{k}} \kappa_{\mathbf{q}j}. \]

The sum of this over \({}^*\mathbf{k}\) corresponding to irreducible q-points divided by number of grid points gives \(\kappa\) (kappa), e.g.,:

kappa_xx_at_index_30 = mode_kappa[30, :, :, 0].sum()/ weight.sum()

Be careful that until version 1.12.7, mode-kappa values were divided by number of grid points.

The physical unit is W/m-K. Each tensor element is the sum of tensor elements on the members of \({}^*\mathbf{k}\), i.e., symmetrically equivalent q-points by crystallographic point group and time reversal symmetry.

The array shape is (temperature, irreducible q-point, phonon band, 6 = (xx, yy, zz, yz, xz, xy)).

gv_by_gv#

Outer products of group velocities for k-stars (\({}^*\mathbf{k}\)) for each irreducible q-point and phonon band (\(j\)):

\[ \sum_{\mathbf{q} \in {}^*\mathbf{k}} \mathbf{v}_{\mathbf{q}j} \otimes \mathbf{v}_{\mathbf{q}j}. \]

The physical unit is \(\text{THz}^2\cdot\text{Angstrom}^2\), where THz is in the ordinal frequency not the angular frequency.

The array shape is (irreducible q-point, phonon band, 6 = (xx, yy, zz, yz, xz, xy)).

q-point#

Irreducible q-points in reduced coordinates.

The array shape is (irreducible q-point, 3 = reduced coordinates in reciprocal space).

temperature#

Temperatures where thermal conductivities are calculated. The physical unit is K.

weight#

Weights corresponding to irreducible q-points. Sum of weights equals to the number of mesh grid points.

ave_pp#

Averaged phonon-phonon interaction in \(\text{eV}^2, \)P_{\mathbf{q}j}$:

\[ P_{\mathbf{q}j} = \frac{1}{(3n_\mathrm{a})^2} \sum_{\lambda'\lambda''} |\Phi_{\lambda\lambda'\lambda''}|^2. \]

This is not going to be calculated in the RTA thermal coductivity calculation mode by default. To calculate this, --full-pp option has to be specified (see --full-pp (FULL_PP = .TRUE.)).

boundary_mfp#

A value specified by --boundary-mfp, --bmfp (BOUNDARY_MFP). The physical unit is micrometre.

When --boundary-mfp option is explicitly specified, its value is stored here.

kappa_unit_conversion#

This is used to convert the physical unit of lattice thermal conductivity made of heat_capacity, group_velocity, and gamma, to W/m-K. In the single mode relaxation time (SMRT) method, a mode contribution to the lattice thermal conductivity is given by

\[ \kappa_\lambda = \frac{1}{V_0} C_\lambda \mathbf{v}_\lambda \otimes \mathbf{v}_\lambda \tau_\lambda^{\mathrm{SMRT}}. \]

For example, \(\kappa_{\lambda,{xx}}\) is calculated by:

In [1]: import h5py

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

In [3]: kappa_unit_conversion = f['kappa_unit_conversion'][()]

In [4]: weight = f['weight'][:]

In [5]: heat_capacity = f['heat_capacity'][:]

In [6]: gv_by_gv = f['gv_by_gv'][:]

In [7]: gamma = f['gamma'][:]

In [8]: kappa_unit_conversion * heat_capacity[30, 2, 0] * gv_by_gv[2, 0] / (2 * gamma[30, 2, 0])

Out[8]:
array([  1.02050241e+03,   1.02050241e+03,   1.02050241e+03,
         4.40486382e-15,   0.00000000e+00,  -4.40486382e-15])

In [9]: f['mode_kappa'][30, 2, 0]
Out[9]:
array([  1.02050201e+03,   1.02050201e+03,   1.02050201e+03,
         4.40486209e-15,   0.00000000e+00,  -4.40486209e-15])

How to know grid point index number corresponding to grid address#

Runngin with --write-gamma, hdf5 files are written out with file names such as kappa-m202020-g4448.hdf5. You may want to know the grid point index number with given grid address. This is done as follows:

In [1]: import phono3py

In [2]: ph3 = phono3py.load("phono3py_disp.yaml")

In [3]: ph3.mesh_numbers = [20, 20, 20]

In [4]: ph3.grid.get_indices_from_addresses([0, 10, 10])
Out[4]: 4448

This index number is different between phono3py version 1.x and 2.x. To get the number corresponding to the phono3py version 1.x, store_dense_gp_map=False should be specified in phono3py.load,

In [5]: ph3 = phono3py.load("phono3py_disp.yaml", store_dense_gp_map=False)

In [6]: ph3.mesh_numbers = [20, 20, 20]

In [7]: ph3.grid.get_indices_from_addresses([0, 10, 10])
Out[7]: 4200
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