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Update documentation
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Atsushi Togo
parent
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commit
a4eb10c68b
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@ -184,7 +184,7 @@ Jan-4-2015: Version 1.9.2
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without a unit cell structure file. The unit cell structure file is
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specified using ``--cell`` (``-c``) option or ``CELL_FILENAME``
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tag. See :ref:`force_calculators`, :ref:`wien2k_interface`,
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:ref:`abinit_interface`, and :ref:`pwscf_interface`.
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:ref:`abinit_interface`, and :ref:`qe_interface`.
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* For the ``gruneisen`` command, ``--factor``, ``--nomeshsym``,
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``--wien2k``, ``--abinit``, and ``--pwscf`` options are
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implemented. See :ref:`gruneisen_calculators` and
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@ -197,8 +197,8 @@ Jan-4-2015: Version 1.9.2
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Oct-30-2014: Version 1.9.1.3
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-----------------------------
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* Experimental support for Abinit. See :ref:`pwscf_mode` and
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:ref:`pwscf_force_sets_option`.
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* Experimental support for Abinit. See :ref:`qe_mode` and
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:ref:`qe_force_sets_option`.
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Oct-29-2014: Version 1.9.1.2
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-----------------------------
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@ -80,11 +80,11 @@ tags.
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Choice of force calculator
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---------------------------
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Currently interfaces for VASP, Wien2k, Pwscf, Abinit, and Elk are
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prepared. Wien2k, Pwscf, Abinit, Elk and CRYSTAL interfaces are invoked with
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``--wienk2``, ``--pwscf``, ``--abinit``, ``--elk`` and ``--crystal`` options,
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respectively, and if none of these options or ``--vasp`` option is
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specified, VASP mode is invoked.
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Currently interfaces for VASP, WIEN2k, Quantum ESPRESSO (QE), ABINIT,
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Elk, SIESTA, and CRYSTAL are prepared. These interfaces are invoked
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with ``--vasp``, ``--wienk2``, ``--qe``, ``--abinit``, ``--elk``,
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``--siesta``, and ``--crystal`` options, respectively, and nothing is
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specified, ``--vasp`` is selected as the default interface.
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The details about these interfaces are found at :ref:`calculator_interfaces`.
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@ -127,18 +127,19 @@ e.g.,
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% phonopy --abinit -c NaCl.in band.conf
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.. _pwscf_mode:
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.. _qe_mode:
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``--pwscf``
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``--qe``
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~~~~~~~~~~~~
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Pwscf mode is invoked with this option. Usually this option is used
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with ``--cell`` (``-c``) option or ``CELL_FILENAME`` tag to read Pwscf
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input file that contains the unit cell crystal structure, e.g.,
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Quantum ESPRESSO mode is invoked with this option. Usually this option
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is used with ``--cell`` (``-c``) option or ``CELL_FILENAME`` tag to
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read QE/PWscf input file that contains the unit cell crystal structure,
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e.g.,
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::
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% phonopy --pwscf -c NaCl.in band.conf
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% phonopy --qe -c NaCl.in band.conf
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.. _siesta_mode:
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@ -209,11 +210,11 @@ Without specifying this tag, default file name is searched in current
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directory. The default file names for the calculators are as follows::
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VASP | POSCAR
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Wien2k | case.struct
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Abinit | unitcell.in
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Pwscf | unitcell.in
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WIEN2k | case.struct
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ABINIT | unitcell.in
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PWscf | unitcell.in
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Elk | elk.in
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CRYSTAL| crystal.o
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CRYSTAL | crystal.o
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Create ``FORCE_SETS``
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----------------------
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@ -252,11 +253,11 @@ Attention:
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.. _abinit_force_sets_option:
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Abinit interface
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ABINIT interface
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^^^^^^^^^^^^^^^^
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``FORCE_SETS`` file is created from ``disp.yaml`` and Abinit output
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files (``*.out``). In the reading of forces in Abinit output files,
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``FORCE_SETS`` file is created from ``disp.yaml`` and ABINIT output
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files (``*.out``). In the reading of forces in ABINIT output files,
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forces in eV/Angstrom are read. The unit conversion factor is
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determined with this unit.
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@ -265,19 +266,20 @@ determined with this unit.
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% phonopy --abinit -f disp-001/supercell.out disp-002/supercell.out ...
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.. _pwscf_force_sets_option:
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.. _qe_force_sets_option:
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Pwscf interface
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^^^^^^^^^^^^^^^^
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Quantum ESPRESSO interface
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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``FORCE_SETS`` file is created from ``disp.yaml`` and Pwscf output
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``FORCE_SETS`` file is created from ``disp.yaml`` and PWscf output
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files.
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::
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% phonopy --pwscf -f disp-001/supercell.out disp-002/supercell.out ...
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% phonopy --qe -f disp-001/supercell.out disp-002/supercell.out ...
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Here ``*.out`` files are the saved texts of standard outputs of Pwscf calculations.
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Here ``*.out`` files are the saved texts of standard outputs of PWscf
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calculations.
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.. _wien2k_force_sets_option:
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@ -294,7 +296,7 @@ http://www.wien2k.at/reg_user/unsupported/.
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file when creating supercell with displacements, and
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``case.scf``'s, which are the WIEN2k output files. The order of
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displacements in ``disp.yaml`` file and the order of ``case.scf``'s
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have to be same. **For Wien2k struct file, only negative atom index
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have to be same. **For WIEN2k struct file, only negative atom index
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with the P lattice format is supported.**
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::
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@ -446,5 +448,5 @@ printed out and phonopy stops without going to phonon analysis.
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% phonopy --symmetry
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This tag can be used together with the ``--cell`` (``-c``),
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``--abinit``, ``--pwscf``, ``--elk``, ``--wien2k``, ``--crystal`` or
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``--primitive_axis`` option.
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``--abinit``, ``--qe``, ``--elk``, ``--wien2k``, ``--siesta``,
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``--crystal`` or ``--primitive_axis`` option.
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@ -77,13 +77,12 @@ parameter is not needed
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% phonopy --crystal -f supercell-001.o
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Here ``.o`` files are the CRYSTAL output files from the force
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calculations. saved text files of standard outputs of the
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Pwscf calculations. All ``.o`` files corresponding to the generated
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calculations. All ``.o`` files corresponding to the generated
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``supercell-xxx.d12`` files have to be given in the above command.
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To run this command, ``disp.yaml`` has to be located in the current
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directory because the information on atomic displacements stored in
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``disp.yaml`` are used to generate ``FORCE_SETS``. See some more detail at
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:ref:`crystal_force_sets_option`.
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``disp.yaml`` are used to generate ``FORCE_SETS``. See some more
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detail at :ref:`crystal_force_sets_option`.
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4) Now, Phonopy post-prcessing commands can be run. ``FORCE_SETS`` is
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automatically read in. Create phonon dispersion plot with:
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@ -187,4 +186,3 @@ The workflow is very similar to the Si example below:
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.. |crystal-band-nac| image:: NaCl-crystal-band-NAC.png
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:width: 33%
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@ -17,7 +17,7 @@ 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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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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@ -64,13 +64,13 @@ plot.
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.. _gruneisen_calculators:
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Abinit, Pwscf, Wien2k, and CRYSTAL interfaces
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---------------------------------------------
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Abinit, Quantum ESPRESSO, Wien2k, and CRYSTAL interfaces
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----------------------------------------------------------
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``--abinit``, ``--pwscf``, ``--wien2k``, or ``--crystal`` options can be specified
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for corresponding calculators and the crystal structure file format
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should be different from that of the VASP format. An Abinit example is
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as follows::
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``--abinit``, ``--qe``, ``--wien2k``, or ``--crystal`` options can be
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specified for corresponding calculators and the crystal structure file
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format should be different from that of the VASP format. An Abinit
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example is as follows::
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% phonopy-gruneisen orig plus minus --abinit --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --band="1/2 1/4 3/4 0 0 0 1/2 1/2 1/2 1/2 0.0 1/2" -p -c Si.in
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@ -80,11 +80,11 @@ as follows::
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Command options
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----------------
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If one of ``--abinit``, ``--pwscf``, ``--wien2k``, or ``--crystal`` options is
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specified, the interface mode is changed to it. The unit conversion
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factor to THz is appropriately selected and its crystal structure file
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format is accepted. If none of them is specified, as the VASP
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interface mode is invoked as the default interface.
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If one of ``--abinit``, ``--qe``, ``--wien2k``, or ``--crystal``
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options is specified, the interface mode is changed to it. The unit
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conversion factor to THz is appropriately selected and its crystal
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structure file format is accepted. If none of them is specified, as
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the VASP interface mode is invoked as the default interface.
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The following command options can be used for all interface
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modes. They work similarly to those for ``phonopy`` script.
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@ -46,12 +46,12 @@ The following features of phonopy are highlighted:
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- :ref:`Interfaces to calculators <calculator_interfaces>`:
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:ref:`VASP <tutorial>`,
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:ref:`VASP DFPT <vasp_dfpt_interface>`,
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:ref:`Abinit <abinit_interface>`,
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:ref:`Pwscf <pwscf_interface>`,
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:ref:`Siesta <siesta_interface>`,
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:ref:`ABINIT <abinit_interface>`,
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:ref:`Quantu ESPRESSO <qe_interface>`,
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:ref:`SIESTA <siesta_interface>`,
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:ref:`Elk <elk_interface>`,
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:ref:`FHI-aims <FHI_aims_interface>`,
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:ref:`Wien2k <wien2k_interface>`,
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:ref:`WIEN2k <wien2k_interface>`,
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:ref:`CRYSTAL <crystal_interface>`
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- :ref:`Python APIs <phonopy_module>`
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@ -3,9 +3,10 @@
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Interfaces to calculators
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==========================
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The interfaces for VASP, Wien2k, Pwscf, Abinit, Elk and CRYSTAL are built in
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to the usual phonopy command. See the command options and how to
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invoke each of them at :ref:`force_calculators`.
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The interfaces for VASP, WIEN2k, Quantum ESPRESSO (QE), ABINIT, Elk,
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SIESTA, and CRYSTAL are built in to the usual phonopy command. See the
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command options and how to invoke each of them at
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:ref:`force_calculators`.
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Physical unit system for calculator
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------------------------------------
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@ -15,11 +16,11 @@ Physical unit systems used for the calculators are as follows::
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| Distance Atomic mass Force Force constants
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-----------------------------------------------------------------
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VASP | Angstrom AMU eV/Angstrom eV/Angstrom^2
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Wien2k | au (bohr) AMU mRy/au mRy/au^2
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Pwscf | au (bohr) AMU Ry/au Ry/au^2
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Abinit | au (bohr) AMU eV/Angstrom eV/Angstrom.au
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Siesta | au (bohr) AMU eV/Angstrom eV/Angstrom.au
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elk | au (bohr) AMU hartree/au hartree/au^2
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WIEN2k | au (bohr) AMU mRy/au mRy/au^2
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QE | au (bohr) AMU Ry/au Ry/au^2
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ABINIT | au (bohr) AMU eV/Angstrom eV/Angstrom.au
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SIESTA | au (bohr) AMU eV/Angstrom eV/Angstrom.au
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Elk | au (bohr) AMU hartree/au hartree/au^2
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CRYSTAL | Angstrom AMU eV/Angstrom eV/Angstrom^2
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For these sets of physical properties, phonon frequency is calculated
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@ -35,10 +36,10 @@ Without specifying ``-c`` option, default file name for unit cell is
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used as shown below::
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VASP | POSCAR
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Wien2k | case.struct
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Pwscf | unitcell.in
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Abinit | unitcell.in
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Siesta | input.fdf
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WIEN2k | case.struct
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QE | unitcell.in
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ABINIT | unitcell.in
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SIESTA | input.fdf
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Elk | elk.in
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CRYSTAL | crystal.o
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@ -52,13 +53,28 @@ option. The default value is dependent on calculator, and the list is
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shown below::
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VASP | 0.01 Angstrom
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Wien2k | 0.02 au (bohr)
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Pwscf | 0.02 au (bohr)
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Abinit | 0.02 au (bohr)
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Siesta | 0.02 au (bohr)
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WIEN2k | 0.02 au (bohr)
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QE | 0.02 au (bohr)
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ABINIT | 0.02 au (bohr)
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SIESTA | 0.02 au (bohr)
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Elk | 0.02 au (bohr)
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CRYSTAL | 0.01 Angstrom
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.. _frequency_default_value_interfaces:
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Default unit conversion factor of phonon frequency to THz
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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::
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VASP | 15.633302
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WIEN2k | 3.44595837
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QE | 108.97077
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ABINIT | 21.49068
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SIESTA | 21.49068
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Elk | 154.10794
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CRYSTAL | 15.633302
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.. _nac_default_value_interfaces:
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Default unit conversion factor for non-analytical term correction
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@ -67,10 +83,10 @@ Default unit conversion factor for non-analytical term correction
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::
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VASP | 14.399652
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Wien2k | 2000
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Pwscf | 2
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Abinit | 51.422090
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Siesta | 51.422090
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WIEN2k | 2000
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QE | 2
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ABINIT | 51.422090
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SIESTA | 51.422090
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Elk | 1
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CRYSTAL | 14.399652
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@ -3,6 +3,6 @@
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Short tutorials
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================
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Tutorials for different force calculators, VASP, WIEN2k, PWscf (QE),
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ABINIT, SIESTA, Elk, and, CRYSTAL, are found at
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Tutorials for different force calculators, VASP, WIEN2k, Quantum
|
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ESPRESSO, ABINIT, SIESTA, Elk, and, CRYSTAL, are found at
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:ref:`tutorials_for_calculators`.
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|
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@ -1,9 +1,9 @@
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.. _pwscf_interface:
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.. _qe_interface:
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Pwscf & phonopy calculation
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=========================================
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Quantum ESPRESSO (QE) & 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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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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@ -16,7 +16,7 @@ More tags may be supported on request.
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|||
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||||
::
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||||
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||||
nat, ntyp, ATOMIC_SPECIES, ATOMIC_POSITIONS, CELL_PARAMETERS
|
||||
nat, ntyp, celldm(1), ATOMIC_SPECIES, ATOMIC_POSITIONS, CELL_PARAMETERS
|
||||
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How to run
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----------
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@ -25,9 +25,9 @@ The procedure of Pwscf-phonopy calculation is shown below using the
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NaCl example found in ``example/NaCl-pwscf`` directory.
|
||||
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1) Read a Pwscf input file and create supercells with
|
||||
:ref:`pwscf_mode` option::
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||||
:ref:`qe_mode` option::
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||||
% phonopy --pwscf -d --dim="2 2 2" -c NaCl.in
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||||
% phonopy --qe -d --dim="2 2 2" -c NaCl.in
|
||||
|
||||
In this example, 2x2x2 supercells are created. ``supercell.in`` and
|
||||
``supercell-xxx.in`` (``xxx`` are numbers) give the perfect
|
||||
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|
@ -60,7 +60,7 @@ NaCl example found in ``example/NaCl-pwscf`` directory.
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3) To create ``FORCE_SETS``, that is used by phonopy,
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||||
the following phonopy command is executed::
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% phonopy --pwscf -f NaCl-001.out NaCl-002.out
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% phonopy --qe -f NaCl-001.out NaCl-002.out
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Here ``.out`` files are the saved text files of standard outputs of the
|
||||
Pwscf calculations. If more supercells with displacements were
|
||||
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|
@ -69,7 +69,7 @@ NaCl example found in ``example/NaCl-pwscf`` directory.
|
|||
the current directory because the information on atomic
|
||||
displacements stored in ``disp.yaml`` are used to generate
|
||||
``FORCE_SETS``. See some more detail at
|
||||
:ref:`pwscf_force_sets_option`.
|
||||
:ref:`qe_force_sets_option`.
|
||||
|
||||
4) Now post-process of phonopy is ready to run. The unit cell file
|
||||
used in the step 1 has to be specified but ``FORCE_SETS`` is
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||||
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|
@ -77,7 +77,7 @@ NaCl example found in ``example/NaCl-pwscf`` directory.
|
|||
|
||||
::
|
||||
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||||
% phonopy --pwscf -c NaCl.in -p band.conf
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||||
% phonopy --qe -c NaCl.in -p band.conf
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||||
_
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||||
_ __ | |__ ___ _ __ ___ _ __ _ _
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||||
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
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||||
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|
@ -115,13 +115,13 @@ NaCl example found in ``example/NaCl-pwscf`` directory.
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|||
.. |pwscf-band| image:: NaCl-pwscf-band.png
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||||
:width: 50%
|
||||
|
||||
``--pwscf -c NaCl.in`` is specific for the Pwscf-phonopy
|
||||
``--qe -c NaCl.in`` is specific for the Pwscf-phonopy
|
||||
calculation but the other settings are totally common among calculator
|
||||
interfaces such as
|
||||
|
||||
::
|
||||
|
||||
% phonopy --pwscf -c NaCl.in --dim="2 2 2" [other-OPTIONS] [setting-file]
|
||||
% phonopy --qe -c NaCl.in --dim="2 2 2" [other-OPTIONS] [setting-file]
|
||||
|
||||
For settings and command options, see
|
||||
:ref:`setting_tags` and :ref:`command_options`, respectively, and
|
||||
|
|
@ -133,7 +133,7 @@ Non-analytical term correction (Optional)
|
|||
To activate non-analytical term correction, :ref:`born_file` is
|
||||
required. This file contains the information of Born effective charge
|
||||
and dielectric constant. These physical values are also obtained from
|
||||
the pwscf (``pw.x``) & phonon (``ph.x``) codes in quantum-espresso
|
||||
the pwscf (``pw.x``) & phonon (``ph.x``) codes in Quantum ESPRESSO
|
||||
package. There are two steps. The first step is usual self-consistent
|
||||
field (SCF) calculation
|
||||
by and the second step is running its response function calculations
|
||||
|
|
@ -209,7 +209,7 @@ be something like below::
|
|||
Once this is made, the non-analytical term correction is included
|
||||
just adding the ``--nac`` option as follows::
|
||||
|
||||
% phonopy --pwscf --nac -c NaCl.in -p band.conf
|
||||
% phonopy --qe --nac -c NaCl.in -p band.conf
|
||||
|
||||
|
||||
|pwscf-band-nac|
|
||||
|
|
|
|||
|
|
@ -198,11 +198,11 @@ it doesn't work for derived values like thermal properties and
|
|||
mean square displacements.
|
||||
|
||||
The default values for calculators are those to convert frequency
|
||||
units to THz. The default conversion factors for ``wien2k``,
|
||||
``abinit``, ``pwscf``, ``elk``, and CRYSTAL are 3.44595, 21.49068, 108.9708,
|
||||
154.1079, and 15.633302 respectively. These are determined following the physical
|
||||
unit systems of the calculators. How to calcualte these conversion
|
||||
factors is explained at :ref:`physical_unit_conversion`.
|
||||
units to THz. The default conversion factors are shown at
|
||||
:ref:`frequency_default_value_interfaces`. These are determined
|
||||
following the physical unit systems of the calculators. How to
|
||||
calcualte these conversion factors is explained at
|
||||
:ref:`physical_unit_conversion`.
|
||||
|
||||
Displacement creation tags
|
||||
--------------------------
|
||||
|
|
|
|||
Loading…
Reference in New Issue