1.. _output_files: 2 3Output files 4============ 5 6.. contents:: 7 :depth: 2 8 :local: 9 10The output data are stored in the following files on the current 11directory. 12 13List of files 14-------------- 15 16``band.yaml`` 17^^^^^^^^^^^^^^ 18 19Sets of phonon frequencies on band paths calculated by the 20:ref:`band-structure mode <band_structure_related_tags>` 21(e.g. ``BAND`` tag) are stored in the YAML format. 22 23``band.yaml`` is viewed using the tool ``phonopy-bandplot`` 24(:ref:`bandplot_tool`). ``phonopy-bandplot`` can convert the data in the YAML 25format to that in the gnuplot-style format using the ``--gnuplot`` option. 26 27``mesh.yaml`` 28^^^^^^^^^^^^^^ 29 30A set of frequencies on irreducible q-points of a q-point mesh by the 31:ref:`mesh-sampling mode <dos_related_tags>` (``MESH`` tag) is stored in 32the YAML format. 33 34``qpoints.yaml`` 35^^^^^^^^^^^^^^^^^ 36 37A set of frequencies calculated by the 38:ref:`q-points mode <qpoints_tag>` 39(``QPOINTS`` tag) is stored in the YAML format. 40 41``thermal_properties.yaml`` 42^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 43 44:ref:`Thermal properties <thermal_properties_tag>` calculated 45are stored in the YAML format. 46 47The auxiliary tool ``phonopy-propplot`` (:ref:`propplot_tool`) can be used to 48plot the content of ``thermal_properties.yaml``. 49 50``thermal_displacements.yaml`` 51^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 52 53:ref:`Mean square displcements of atoms <thermal_displacements_tag>` 54are stored in the YAML format. Without projecting eigenvectors along a 55specific direction, the results projected along Cartesianl 56coordinates, therefore three values for each atom at a temperature, 57are written into the file. 58 59``thermal_displacement_matrices.yaml`` 60^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 61 62:ref:`Mean square displacement matricies of atoms 63<thermal_displacement_matrices_tag>` are stored in the YAML 64format. Since the matrix for each atom at a temperature is symmetric, 65only six elements of it, xx, yy, zz, yz, xz, xy, are written in this 66order. 67 68``total_dos.dat`` and ``projected_dos.dat`` 69^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 70 71:ref:`Total and projected DOS <dos_related_tags>` are stored in the 72simple format, respectively. 73 74``total_dos.dat`` and ``projected_dos.dat`` are viewed using the 75auxiliary tool ``phonopy-pdosplot`` (:ref:`pdosplot_tool`). 76 77File format of ``projected_dos.dat`` 78~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 80The first column is the phonon frequency. The following colums are the 81projected density of states for atoms in the primitive cell. In the 82:ref:`NaCl example <example_pdos>`, there are two atoms in the 83primitive cell, which are one Na and one Cl atoms. The order of atoms 84in the primitive cell is confirmed running phonopy with the ``-v`` 85option. The ``projected_dos.dat`` of this example is starting with the 86following lines:: 87 88 # Sigma = 0.063253 89 -0.6695362607 0.0000000000 0.0000000000 90 -0.6379098952 0.0000000000 0.0000000000 91 -0.6062835296 0.0000000000 0.0000000000 92 -0.5746571641 0.0000000000 0.0000000000 93 -0.5430307986 0.0000000000 0.0000000000 94 -0.5114044331 0.0000000000 0.0000000000 95 -0.4797780675 0.0000000000 0.0000000000 96 -0.4481517020 0.0000000000 0.0000000000 97 -0.4165253365 0.0000000000 0.0000000000 98 -0.3848989710 0.0000000000 0.0000000000 99 -0.3532726054 0.0000000004 0.0000000006 100 -0.3216462399 0.0000000044 0.0000000066 101 -0.2900198744 0.0000000370 0.0000000551 102 -0.2583935089 0.0000002410 0.0000003596 103 -0.2267671433 0.0000012239 0.0000018260 104 ... 105 106where from the left to right in each line, frequency, PDOS of Na and 107PDOS of Cl. The first line is just a comment to remember the sigma 108value used. 109 110With :ref:`xyz_projection_tag` tag specified, the format changes to 111represent x, y, and z components:: 112 113 # Sigma = 0.063253 114 -0.6695362607 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 115 -0.6315846221 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 116 -0.5936329834 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 117 -0.5556813448 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 118 -0.5177297062 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 119 -0.4797780675 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 120 -0.4418264289 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 121 -0.4038747903 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 122 -0.3659231516 0.0000000000 0.0000000000 0.0000000000 0.0000000001 0.0000000001 0.0000000001 123 -0.3279715130 0.0000000009 0.0000000009 0.0000000009 0.0000000014 0.0000000014 0.0000000014 124 -0.2900198744 0.0000000123 0.0000000123 0.0000000123 0.0000000184 0.0000000184 0.0000000184 125 ... 126 127``phonopy.yaml`` and ``phonopy_disp.yaml`` 128^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 129 130Phonopy configurations and crystal structures are stored in these 131files when running pre-process (``phonopy_disp.yaml``) or post-process 132(``phonopy.yaml``). 133 134``phonopy_disp.yaml`` contains information used to create supercells 135with displacements. The format is hopefully understood just looking 136into it. ``displacement`` is written in Cartesian coordinates. 137 138``.hdf5`` files 139^^^^^^^^^^^^^^^^^ 140 141See :ref:`hdf5_tag`. 142 143 144How to read phonopy YAML files 145------------------------------- 146 147Most phonopy results are written in the YAML format. YAML files are 148easily translated to the combination of lists and dictionaries in the 149python case. For each computer language, e.g., Ruby, each YAML parser 150is prepared and you can use those libraries to parse YAML files and 151analyze the data easily in conjunction with your favorite 152language. See http://www.yaml.org/. The basic of the YAML format is 153found easily on the web. In python, it is very easy to parse phonopy's 154yaml files, e.g., 155 156:: 157 158 import yaml 159 with open("band.yaml") as f: 160 data = yaml.load(f) 161 162``mesh.yaml``, ``band.yaml``, ``qpoints.yaml`` 163^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 164 165 166General 167~~~~~~~~~~~ 168 169============== ======================================================= 170============== ======================================================= 171nqpoint Number of q-points calculated. 172natom Number of atoms in the primitive cell. 173phonon Key name of list for q-points. 174q-position Position of q-vector in reduced coordinates. 175band Key name of list for bands. 176frequency Phonon frequency in a specified unit at each phonon 177 mode 178eigenvector Eigenvector at each phonon mode. 179 Each eigenvector :math:`\mathbf{e}` of 180 :ref:`dynamical matrix <dynacmial_matrix_theory>` 181 is shown as sets of three 182 complex values of each atom along the Cartesian axes in 183 the primitive cell. The real and imaginary values 184 correspond to the left and right, respectively. 185 A set of eigenvectors comprising all bands at a q-point 186 forms a unitary matrix obtained as the result of 187 numpy.linalg.eigh, i.e., LAPACK of routine _heevd. 188 Therefore eigenvectors correspond to the column vectors 189 of the unitary matrix. 190group_velocity Group velocity at each phonon mode in the 191 Cartesian coordinates defined in the unit cell. 192============== ======================================================= 193 194Mesh sampling mode 195~~~~~~~~~~~~~~~~~~~ 196 197============== ======================================================= 198============== ======================================================= 199mesh Numbers of mesh sampling points along axes of the 200 primitive cell. 201weight In the mesh sampling mode, only phonons at irreducible 202 q-points are calculated in the default behavior. This 203 value means the multiplicity of a q-point in the 204 reciprocal space of the primitive cell. 205============== ======================================================= 206 207Band structure mode 208~~~~~~~~~~~~~~~~~~~ 209 210============== ======================================================= 211============== ======================================================= 212distance In the band structure mode, this value means the 213 distance from the origin in the reciprocal space of the 214 primitive cell. The unit is the reciprocal of length 215 unit used in the real space. 216============== ======================================================= 217 218 219``thermal_properties.yaml`` 220^^^^^^^^^^^^^^^^^^^^^^^^^^^ 221 222The physical units of the thermal properties are given in the unit 223section of this YAML file. However the physical units are only correct 224when phonopy ran with proper physical units. See 225:ref:`thermal_properties_tag`. 226