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Atsushi Togo
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@ -16,6 +16,9 @@ Si
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``FORCE_SETS`` file creation for VASP
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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For the other calculators such as pwscf, abinit, etc, the way to
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create ``FORCE_SETS`` is found following :ref:`calculator_interfaces`.
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::
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% phonopy -f vasprun.xml
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@ -215,35 +215,6 @@ This file is used with the ``--nac`` option or ``NAC`` tag.
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The formula implemented is refered to :ref:`non_analytical_term_correction_theory`.
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.. ``--nac_old`` option
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.. ~~~~~~~~~~~~~~~~~~~~~
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.. When using the ``--nac_old`` option, a damping function is multiplied
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.. with the non-analytical term to obtain the dynamical matrix at
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.. geneneral **q**-points (:ref:`reference_NAC`), which is written
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.. by,
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.. .. math::
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.. D_{\alpha\beta}(jj',\mathbf{q}) =
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.. D_{\alpha\beta}^{\mathrm{N}}(jj',\mathbf{q}) + \frac{4\pi}{\sqrt{m_j m_j}\Omega_0}
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.. \frac{[\sum_{\gamma}q_{\gamma}Z^{*}_{j,\gamma\alpha}][\sum_{\gamma'}q_{\gamma'}Z^{*}_{j',\gamma'\beta}]}
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.. {\sum_{\alpha\beta}q_{\alpha}\epsilon_{\alpha\beta}^{\infty}
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.. q_{\beta}} \times \exp(-\frac{|\mathbf{q}|^2}{\sigma^2}) \times
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.. \mathrm{unit\ conversion\ factor}.
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.. This equation is directly implemented. Therefore unit conversion of
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.. the non-analytical term is necessary. The variables are implemented
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.. that :math:`m` (mass) is in the amu, :math:`\Omega` (volume of
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.. primitive cell) is determined in the input structure file, and
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.. :math:`Z` (Born effective charge) and :math:`\epsilon` (dielectric
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.. constant) are determined in the ``BORN`` file. In
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.. :math:`\exp(-|\mathbf{q}|^2/\sigma^2)`, :math:`\sigma` is the
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.. parameter, and :math:`\mathbf{q}` is the wave vector in reduced
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.. reciprocal coordinate without :math:`2\pi`. The
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.. reciprocal primitive vectors are calculated by
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.. :math:`[\mathbf{a}^*\,\mathbf{b}^*\,\mathbf{c}^*]=[\mathbf{a}\,\mathbf{b}\,\mathbf{c}]^{-T}`.
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Format
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~~~~~~
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@ -6,9 +6,12 @@ VASP & phonopy calculation
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Pre-process
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~~~~~~~~~~~~
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The input stureture of ``POSCAR`` is supposed to be :ref:`this<example_POSCAR1>`.
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The input stureture of ``POSCAR`` (:ref:`this <example_POSCAR1>`) is
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used as an example here. Most files are found at `SiO2-HP example <https://github.com/atztogo/phonopy/tree/master/example/SiO2-HP/>`_.
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In the pre-process, supercell structures with (or without) displacements are created from a unit cell fully consiering crystal symmetry.
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In the pre-process, supercell structures with (or without)
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displacements are created from a unit cell fully consiering crystal
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symmetry.
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To obtain supercells (:math:`2\times 2\times 3`) with displacements,
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run phonopy::
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@ -43,7 +46,6 @@ In the case of VASP, the calculations for the finite displacement method can be
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ISMEAR = 0; SIGMA = 0.01
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IALGO = 38
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LREAL = .FALSE.
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ADDGRID = .TRUE.
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LWAVE = .FALSE.
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LCHARG = .FALSE.
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@ -115,14 +117,77 @@ In either case, by setting the ``-s`` option, the plot is going to be saved in t
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format. If you don't need to plot DOS, the (partial) DOS
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is just calculated using the ``--dos`` option.
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Non-analytical term correction (Optional)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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To activate non-analytical term correction, :ref:`born_file` is
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required. This file contains the information of Born effective charge
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and dielectric constant. These physical values are also obtained from
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the first-principles calculations, e.g., by using VASP, pwscf, etc. In
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the case of VASP, an example of ``INCAR`` will be as shown below::
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PREC = Accurate
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IBRION = -1
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NELMIN = 5
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ENCUT = 500
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EDIFF = 1.000000e-08
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ISMEAR = 0
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SIGMA = 1.000000e-02
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IALGO = 38
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LREAL = .FALSE.
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LWAVE = .FALSE.
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LCHARG = .FALSE.
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LEPSILON = .TRUE.
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In addition, it is recommended to increase the number of k-points to
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be sampled. Twice the number for each axis may be a choice. After
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running this VASP calculation, ``BORN`` file has to be created
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following the ``BORN`` format (:ref:`born_file`). However for VASP, an
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auxiliary tool is prepared, which is ``outcar-born``. There is an
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option ``--pa`` for this command to set a transformation matrix from
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supercell or unit cell with centring to the primitive cell. Since this
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rutile-type SiO2 has the primitive lattice, it is unnecessary to set
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this option. Running ``outcar-born`` in the directory containing
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``OUTCAR`` of this VASP calculation::
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% outcar-born
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# epsilon and Z* of atoms 1 3
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3.2605670 0.0000000 0.0000000 0.0000000 3.2605670 0.0000000 0.0000000 0.0000000 3.4421330
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3.7558600 0.3020100 0.0000000 0.3020100 3.7558600 0.0000000 0.0000000 0.0000000 3.9965200
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-1.8783900 -0.5270900 0.0000000 -0.5270900 -1.8783900 0.0000000 0.0000100 0.0000100 -1.9987900
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To employ symmetry constraints, ``--st`` option may used as follows::
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% outcar-born --st
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# epsilon and Z* of atoms 1 3
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3.2605670 0.0000000 0.0000000 0.0000000 3.2605670 0.0000000 0.0000000 0.0000000 3.4421330
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3.7561900 0.3020100 0.0000000 0.3020100 3.7561900 0.0000000 0.0000000 0.0000000 3.9968733
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-1.8780950 -0.5270900 0.0000000 -0.5270900 -1.8780950 0.0000000 0.0000000 0.0000000 -1.9984367
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The values are slightly modified by symmetry, but we can see the
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original values obtained directly from VASP was already very good.
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To put ``BORN`` file in the current directly, and running phonopy with
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``--nac`` option, non-analytical term correction is activated, such as::
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% phonopy -p --nac band.conf
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Please watch the example of NaCl with and without ``--nac`` option shown in
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:ref:`examples_link`.
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.. _details_of_procedure:
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Details
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--------
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Some more details
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------------------
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The structure file names are different in different force calculators,
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see :ref:`calculator_interfaces`. To notify this, (*) is put
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after the structure file name. By refering
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:ref:`calculator_interfaces`, please read the file name according to
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those for the other calculators.
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Following files are required in your working directory.
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- ``POSCAR``, and ``FORCE_SETS`` or ``FORCE_CONSTANTS``
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- ``POSCAR`` (*), and ``FORCE_SETS`` or ``FORCE_CONSTANTS``
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- ``disp.yaml`` is required to create ``FORCE_SETS``.
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In the case of finite difference approach, there are three steps.
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@ -131,20 +196,16 @@ In the case of finite difference approach, there are three steps.
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supercell contains one atomic displacement. It is done by using
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``-d`` option with ``--dim`` option that specifies supercell
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dimension. The files of supercells with atomic displacements like
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as ``POSCAR-001``, ``POSCAR-002``, ..., are created in current
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directory (the file format and names are different in :ref:`WIEN2k
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mode <wien2k_mode>`.) by running phonopy. The files ``disp.yaml``
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and ``SPOSCAR`` are also created. The file ``SPOSCAR`` is the
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perfect supercell that contains no atomic displacement. This file
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is not usually used.
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as ``POSCAR-001``, ``POSCAR-002``, ..., (*) are created in current
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directory by running phonopy. The files ``disp.yaml`` and
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``SPOSCAR`` are also created. The file ``SPOSCAR`` is the perfect
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supercell that contains no atomic displacement. This file is not
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usually used.
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2. Calculate forces on atoms of the supercells with atomic
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displacements. Currently phonopy has :ref:`VASP
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<vasp_force_sets_option>` and :ref:`WIEN2k <wien2k_interface>`
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interfaces to create ``FORCE_SETS``. After obtaining forces on
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atoms that calculated by some calculator (it's out of phonopy), the
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forces are summarized in ``FORCE_SETS`` file following the
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:ref:`format <file_forces>`.
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displacements. After obtaining forces on atoms that calculated by
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some calculator (it's out of phonopy), the forces are summarized in
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``FORCE_SETS`` file following the :ref:`format <file_forces>`.
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3. Calculate phonon related properties. See :ref:`analyze_phonon`.
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@ -3,6 +3,10 @@
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Pwscf & phonopy calculation
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=========================================
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Quantum espresso package itself has a set of the phonon calculation
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system. But the document here explains how to calculate phonons using
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phonopy, i.e., using the finite displacement and supercell approach.
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Supported Pwscf tags
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---------------------------
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@ -123,3 +127,92 @@ NaCl example found in ``example/NaCl-pwscf`` directory.
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:ref:`setting_tags` and :ref:`command_options`, respectively, and
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for examples, see :ref:`examples_link`.
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Non-analytical term correction (Optional)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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To activate non-analytical term correction, :ref:`born_file` is
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required. This file contains the information of Born effective charge
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and dielectric constant. These physical values are also obtained from
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the pwscf (``pw.x``) & phonon (``ph.x``) codes in quantum-espresso
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package. There are two steps. The first step is usual self-consistent
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field (SCF) calculation
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by and the second step is running its response function calculations
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under DFPT.
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For the SCF calculation, the input file ``NaCl.in`` looks like::
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&control
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calculation = 'scf'
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tprnfor = .true.
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tstress = .true.
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pseudo_dir = '/home/togo/espresso/pseudo/'
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/
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&system
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ibrav = 0
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nat = 8
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ntyp = 2
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ecutwfc = 70.0
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/
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&electrons
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diagonalization = 'david'
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conv_thr = 1.0d-9
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/
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ATOMIC_SPECIES
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Na 22.98976928 Na.pbe-spn-kjpaw_psl.0.2.UPF
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Cl 35.453 Cl.pbe-n-kjpaw_psl.0.1.UPF
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ATOMIC_POSITIONS crystal
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Na 0.0000000000000000 0.0000000000000000 0.0000000000000000
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Na 0.0000000000000000 0.5000000000000000 0.5000000000000000
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Na 0.5000000000000000 0.0000000000000000 0.5000000000000000
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Na 0.5000000000000000 0.5000000000000000 0.0000000000000000
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Cl 0.5000000000000000 0.5000000000000000 0.5000000000000000
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Cl 0.5000000000000000 0.0000000000000000 0.0000000000000000
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Cl 0.0000000000000000 0.5000000000000000 0.0000000000000000
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Cl 0.0000000000000000 0.0000000000000000 0.5000000000000000
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CELL_PARAMETERS angstrom
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5.6903014761756712 0 0
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0 5.6903014761756712 0
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0 0 5.6903014761756712
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K_POINTS automatic
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8 8 8 1 1 1
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where more the k-point mesh numbers are specified. This may be exectued as::
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mpirun ~/espresso/bin/pw.x -i NaCl.in |& tee NaCl.out
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Many files whose names stating with ``pwscf`` should be created. These
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are used for the next calculation. The input file for the response
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function calculations, ``NaCl.ph.in``, is
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created as follows::
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&inputph
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tr2_ph = 1.0d-14,
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epsil = .true.
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/
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0 0 0
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Similary ``ph.x`` is executed::
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% mpirun ~/espresso/bin/ph.x -i NaCl.ph.in |& tee NaCl.ph.out
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Finally the Born effective charges and dielectric constant are
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obtained in the output file ``NaCl.ph.out``. The ``BORN`` file has to
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be created manually following the ``BORN`` format
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(:ref:`born_file`). The ``BORN`` file for this NaCl calculation would
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be something like below::
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default value
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2.472958201 0 0 0 2.472958201 0 0 0 2.472958201
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1.105385 0 0 0 1.105385 0 0 0 1.105385
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-1.105385 0 0 0 -1.105385 0 0 0 -1.105385
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Once this is made, the non-analytical term correction is included
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just adding the ``--nac`` options as follows::
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% phonopy --pwscf -c NaCl.in -p band.conf
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|pwscf-band-nac|
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.. |pwscf-band-nac| image:: NaCl-pwscf-band-NAC.png
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:width: 50%
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