2012-12-14 17:06:27 +08:00
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Input files
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===========
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2016-08-29 16:56:26 +08:00
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.. contents::
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:depth: 2
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:local:
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2012-12-14 17:06:27 +08:00
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Setting file
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-------------
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A setting file contains phonopy settings which are summarized at
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:ref:`setting_tags`. This file is passed to phonopy as an argument,
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e.g.,
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::
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% phonopy phonopy.conf
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where the filename is arbitrary.
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Structure file (``POSCAR``)
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----------------------------
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Crystal structure is written in VASP's manner (for Wien2k interface,
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see :ref:`WIEN2k mode <wien2k_mode>`). The format is
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simple. The first line is for your comment, where you can write
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anything you want. The second line is the ratio for lattice
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parameters. You can multiply by this number. The third to fifth lines
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give the lattice parameters, *a*, *b*, and *c* for the respective
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lines. The sixth line contains the number of atoms for each atomic
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species, which have to correspond to the atomic positions in the
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order. The seventh line should be written as ``Direct``. This means
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that the atomic positions are represented in fractional (reduced)
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2013-11-08 13:02:37 +08:00
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coordinates. When you write chemical symbols in the first line, they
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2012-12-14 17:06:27 +08:00
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are read and those defined by the ``ATOM_NAME`` tag are overwritten.
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.. _example_POSCAR1:
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Example of rutile-type silicon oxide crystal structure (1)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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::
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Si O
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1.00000000000000
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4.2266540199664249 0.0000000000000000 0.0000000000000000
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0.0000000000000000 4.2266540199664249 0.0000000000000000
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0.0000000000000000 0.0000000000000000 2.6888359272289208
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2 4
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Direct
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0.0000000000000000 0.0000000000000000 0.0000000000000000
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0.5000000000000000 0.5000000000000000 0.5000000000000000
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0.3067891334429594 0.3067891334429594 0.0000000000000000
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0.6932108665570406 0.6932108665570406 0.0000000000000000
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0.1932108665570406 0.8067891334429594 0.5000000000000000
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0.8067891334429594 0.1932108665570406 0.5000000000000000
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The VASP 5.x style is also supported. Chemical symbols are inserted
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just before the line of the numbers of atoms. The chemical symbols in
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this line overwrite those defined by the ``ATOM_NAME`` tag and those
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defined by the first line of ``POSCAR``.
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Example of rutile-type silicon oxide crystal structure (2)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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::
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Stishovite
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1.00000000000000
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4.2266540199664249 0.0000000000000000 0.0000000000000000
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0.0000000000000000 4.2266540199664249 0.0000000000000000
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0.0000000000000000 0.0000000000000000 2.6888359272289208
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Si O
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2 4
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Direct
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0.0000000000000000 0.0000000000000000 0.0000000000000000
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0.5000000000000000 0.5000000000000000 0.5000000000000000
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0.3067891334429594 0.3067891334429594 0.0000000000000000
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0.6932108665570406 0.6932108665570406 0.0000000000000000
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0.1932108665570406 0.8067891334429594 0.5000000000000000
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0.8067891334429594 0.1932108665570406 0.5000000000000000
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.. _file_forces:
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2016-08-29 16:56:26 +08:00
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Force file (``FORCE_SETS``)
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----------------------------
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This file gives sets of forces in supercells with finite atomic
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displacements. Each supercell involves one displaced atom. The first
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line is the number of atoms in supercell. The second line gives number
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of calculated supercells with displacements. Below the lines, sets of
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forces with displacements are written. In each set, firstly the atom
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number in supercell is written. Secondary, the atomic displacement in
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**Cartesian coordinates** is written. Below the displacement line,
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atomic forces in **Cartesian coordinates** are successively
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written. This is repeated for the set of displacements. Blank likes
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are simply ignored.
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In the following example, the third line is the displaced atom number
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that corresponds to the atom number in the supercell created by
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phonopy. The fourth line gives the displacements in **Cartesian
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coordinates**. The lines below, the atomic forces in **Cartesian
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coordinates** are written. Once all the forces for a supercell are
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2012-12-14 17:06:27 +08:00
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written, the next set of forces are written. This routine is repeated
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until the forces of all the displacements have been written.
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See also :ref:`vasp_force_sets_option` and
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:ref:`wien2k_force_sets_option` for VASP and Wien2k users.
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Example
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~~~~~~~
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::
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48
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2
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1
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0.0050650623043761 0.0000000000000000 0.0086223630086415
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-0.0347116200 -0.0000026500 -0.0679795200
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0.0050392400 -0.0015711700 -0.0079514600
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0.0027380900 -0.0017851900 -0.0069206400
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... (continue until all the forces for this displacement have written)
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25
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0.0050650623043761 0.0000000000000000 0.0086223630086415
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-0.0017134500 -0.0001539800 0.0017333400
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0.0013248100 0.0001984300 -0.0001203700
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-0.0001310200 -0.0007955600 0.0003889300
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... (continue until all the forces for this displacement have written)
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.. _file_force_constants:
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``FORCE_CONSTANTS``
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-------------------
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2013-11-08 13:02:37 +08:00
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If the force constants of a supercell are known, it is not
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necessary to prepared ``FORCES``. Phonopy has an interface to read and write
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``FORCE_CONSTANTS``. To read and write ``FORCE_CONSTANTS`` are
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controlled by :ref:`force_constants_tag`.
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2012-12-14 17:06:27 +08:00
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VASP users can use :ref:`VASP DFPT interface <vasp_force_constants>`
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to create ``FORCE_CONSTANTS`` from ``vasprun.xml``.
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Format
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~~~~~~
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First line is for the number of atoms in supercell. Below second line,
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force constants between atoms are written by every four lines. In
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first line of the four lines, anything can be written, i.e., just
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ignored. Second to fourth lines of the four lines are for the second
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rank tensor of force constant in Cartesian coordinates, i.e.:::
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xx xy xz
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yx yy yz
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zx zy zz
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Example
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~~~~~~~
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::
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32
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1 1
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4.635786969900131 -0.000000000000000 -0.000000000000000
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-0.000000000000000 4.635786969900130 -0.000000000000000
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-0.000000000000000 -0.000000000000000 4.635786969900130
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1 2
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-0.246720998398056 -0.000000000000000 -0.000000000000000
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-0.000000000000000 0.018256999881458 -0.000000000000000
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-0.000000000000000 -0.000000000000000 0.018256999881458
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...
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1 32
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0.002646999982813 0.018011999883049 -0.000000000000000
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0.018011999883049 0.002646999982813 -0.000000000000000
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-0.000000000000000 -0.000000000000000 0.035303999770773
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2 1
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-0.246720998398056 0.000000000000000 0.000000000000000
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0.000000000000000 0.018256999881458 0.000000000000000
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0.000000000000000 0.000000000000000 0.018256999881458
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...
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32 32
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4.635786969900131 0.000000000000000 0.000000000000000
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0.000000000000000 4.635786969900130 0.000000000000000
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0.000000000000000 0.000000000000000 4.635786969900130
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2016-08-29 16:56:26 +08:00
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``force_constants.hdf5``
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-------------------------
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2016-08-29 16:56:26 +08:00
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This is an alternative of ``FORCE_CONSTANTS`` but the data is stored
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in HDF5 format. See the detail of how to obtain this file, :ref:`hdf5_option`.
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``QPOINTS`` (optional)
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-----------------------
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Specific q-points are calculated using ``QPOINTS = .TRUE.`` tag and
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``QPOINTS`` file. The file format of ``QPOINTS`` is as follows. The
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first line gives the number of q-points. Then the successive lines
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give q-points in reduced coordinate of reciprocal space of the input
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unit cell.
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Example
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~~~~~~~
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::
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512
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-0.437500000000000 -0.437500000000000 -0.437500000000000
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-0.312500000000000 -0.437500000000000 -0.437500000000000
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-0.187500000000000 -0.437500000000000 -0.437500000000000
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...
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2016-02-05 12:32:22 +08:00
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.. _born_file:
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``BORN`` (optional)
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-----------------------
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2013-07-14 15:31:47 +08:00
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This file is used with the ``--nac`` option or ``NAC`` tag.
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2015-09-25 16:22:43 +08:00
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The formula implemented is refered to :ref:`non_analytical_term_correction_theory`.
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2012-12-14 17:06:27 +08:00
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Format
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~~~~~~
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2016-02-05 12:32:22 +08:00
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In the first line, unit conversion factor is given. In versions 1.10.4
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or later, the default value for each calculater can be used if
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characters than numerical number are given. The default values for the
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calculaters are found at :ref:`nac_default_value_interfaces`.
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In the second line, dielectric constant :math:`\epsilon` is specifed
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in Cartesian coordinates. The nine values correspond to the tensor
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elements of xx, xy, xz, yx, yy, yz, zx, zy, and zz.
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From the third line, Born effective charges :math:`Z` for the
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independent atoms in the **primitive cell** have to be written in
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Cartesian coordinates. The independent atoms can be found using the
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``-v`` option. As shown below in the Al2O3 example, the independent
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atoms are marked by ``*`` in front of atomic positions::
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% phonopy --dim="2 2 1" --pa="2/3 -1/3 -1/3 1/3 1/3 -2/3 1/3 1/3 1/3" -v
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_
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_ __ | |__ ___ _ __ ___ _ __ _ _
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| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
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| |_) | | | | (_) | | | | (_) || |_) | |_| |
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| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
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|_| |_| |___/
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1.8.4.2
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Settings:
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Supercell: [2 2 1]
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Primitive axis:
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[ 0.66666667 -0.33333333 -0.33333333]
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[ 0.33333333 0.33333333 -0.66666667]
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[ 0.33333333 0.33333333 0.33333333]
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Spacegroup: R-3c (167)
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---------------------------- primitive cell -------------------------------
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Lattice vectors:
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a 2.403817201137804 1.387844508159565 4.372423306604251
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b -2.403817201137804 1.387844508159565 4.372423306604251
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c 0.000000000000000 -2.775689016319131 4.372423306604251
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Atomic positions (fractional):
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*1 Al 0.35218509422890 0.35218509422890 0.35218509422890 26.982
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2 Al 0.64781490577110 0.64781490577110 0.64781490577110 26.982
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3 Al 0.14781490577110 0.14781490577110 0.14781490577110 26.982
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4 Al 0.85218509422890 0.85218509422890 0.85218509422890 26.982
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*5 O 0.55616739064549 0.94383260935451 0.25000000000000 15.999
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6 O 0.44383260935451 0.05616739064549 0.75000000000000 15.999
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7 O 0.25000000000000 0.55616739064549 0.94383260935451 15.999
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8 O 0.75000000000000 0.44383260935451 0.05616739064549 15.999
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9 O 0.94383260935451 0.25000000000000 0.55616739064549 15.999
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10 O 0.05616739064549 0.75000000000000 0.44383260935451 15.999
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------------------------------ unit cell ----------------------------------
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Lattice vectors:
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a 4.807634402275609 0.000000000000000 0.000000000000000
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b -2.403817201137805 4.163533524478696 0.000000000000000
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c 0.000000000000000 0.000000000000000 13.117269919812754
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Atomic positions (fractional):
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*1 Al 0.00000000000000 0.00000000000000 0.35218509422890 26.982 > 1
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2 Al 0.66666666666666 0.33333333333334 0.68551842756224 26.982 > 1
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3 Al 0.33333333333334 0.66666666666666 0.01885176089557 26.982 > 1
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4 Al 0.00000000000000 0.00000000000000 0.64781490577110 26.982 > 2
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5 Al 0.66666666666666 0.33333333333334 0.98114823910443 26.982 > 2
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6 Al 0.33333333333334 0.66666666666666 0.31448157243776 26.982 > 2
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7 Al 0.00000000000000 0.00000000000000 0.14781490577110 26.982 > 3
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8 Al 0.66666666666666 0.33333333333334 0.48114823910443 26.982 > 3
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9 Al 0.33333333333334 0.66666666666666 0.81448157243776 26.982 > 3
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10 Al 0.00000000000000 0.00000000000000 0.85218509422890 26.982 > 4
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11 Al 0.66666666666666 0.33333333333334 0.18551842756224 26.982 > 4
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12 Al 0.33333333333334 0.66666666666666 0.51885176089557 26.982 > 4
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*13 O 0.30616739064549 0.00000000000000 0.25000000000000 15.999 > 5
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14 O 0.97283405731215 0.33333333333334 0.58333333333334 15.999 > 5
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15 O 0.63950072397883 0.66666666666666 0.91666666666666 15.999 > 5
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16 O 0.69383260935451 0.00000000000000 0.75000000000000 15.999 > 6
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17 O 0.36049927602117 0.33333333333334 0.08333333333334 15.999 > 6
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18 O 0.02716594268785 0.66666666666666 0.41666666666666 15.999 > 6
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19 O 0.00000000000000 0.30616739064549 0.25000000000000 15.999 > 7
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20 O 0.66666666666666 0.63950072397883 0.58333333333334 15.999 > 7
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21 O 0.33333333333334 0.97283405731215 0.91666666666666 15.999 > 7
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22 O 0.00000000000000 0.69383260935451 0.75000000000000 15.999 > 8
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23 O 0.66666666666666 0.02716594268785 0.08333333333334 15.999 > 8
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24 O 0.33333333333334 0.36049927602117 0.41666666666666 15.999 > 8
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25 O 0.69383260935451 0.69383260935451 0.25000000000000 15.999 > 9
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26 O 0.36049927602117 0.02716594268785 0.58333333333334 15.999 > 9
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27 O 0.02716594268785 0.36049927602117 0.91666666666666 15.999 > 9
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28 O 0.30616739064549 0.30616739064549 0.75000000000000 15.999 > 10
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29 O 0.97283405731215 0.63950072397883 0.08333333333334 15.999 > 10
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30 O 0.63950072397883 0.97283405731215 0.41666666666666 15.999 > 10
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------------------------------ supercell ----------------------------------
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...
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If VASP is used as the calculator for Born effective charge, and the
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hexagonal unit cell is used for the calculation, the Born effective
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charge tensors of atoms No. 1 and 13 have to be written in ``BORN``
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file.
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2012-12-14 17:06:27 +08:00
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Example
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~~~~~~~
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::
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2014-06-23 14:56:07 +08:00
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14.400
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3.269 0.000 0.000 0.000 3.269 0.000 0.000 0.000 3.234
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2.981 0.000 0.000 0.000 2.981 0.000 0.000 0.000 2.952
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-1.935 0.000 0.000 0.000 -2.036 -0.261 0.000 -0.261 -1.968
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2016-02-05 12:32:22 +08:00
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or using the default NAC unit conversion factor (version 1.10.4 or later),
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::
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default value
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3.269 0.000 0.000 0.000 3.269 0.000 0.000 0.000 3.234
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2.981 0.000 0.000 0.000 2.981 0.000 0.000 0.000 2.952
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-1.935 0.000 0.000 0.000 -2.036 -0.261 0.000 -0.261 -1.968
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2014-06-23 14:56:07 +08:00
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