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6
doc/changelog.rst
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@ -184,7 +184,7 @@ Jan-4-2015: Version 1.9.2
without a unit cell structure file. The unit cell structure file is
specified using ``--cell`` (``-c``) option or ``CELL_FILENAME``
tag. See :ref:`force_calculators`, :ref:`wien2k_interface`,
:ref:`abinit_interface`, and :ref:`pwscf_interface`.
:ref:`abinit_interface`, and :ref:`qe_interface`.
* For the ``gruneisen`` command, ``--factor``, ``--nomeshsym``,
``--wien2k``, ``--abinit``, and ``--pwscf`` options are
implemented. See :ref:`gruneisen_calculators` and
@ -197,8 +197,8 @@ Jan-4-2015: Version 1.9.2
Oct-30-2014: Version 1.9.1.3
-----------------------------
* Experimental support for Abinit. See :ref:`pwscf_mode` and
:ref:`pwscf_force_sets_option`.
* Experimental support for Abinit. See :ref:`qe_mode` and
:ref:`qe_force_sets_option`.
Oct-29-2014: Version 1.9.1.2
-----------------------------

60
doc/command-options.rst
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@ -80,11 +80,11 @@ tags.
Choice of force calculator
---------------------------
Currently interfaces for VASP, Wien2k, Pwscf, Abinit, and Elk are
prepared. Wien2k, Pwscf, Abinit, Elk and CRYSTAL interfaces are invoked with
``--wienk2``, ``--pwscf``, ``--abinit``, ``--elk`` and ``--crystal`` options,
respectively, and if none of these options or ``--vasp`` option is
specified, VASP mode is invoked.
Currently interfaces for VASP, WIEN2k, Quantum ESPRESSO (QE), ABINIT,
Elk, SIESTA, and CRYSTAL are prepared. These interfaces are invoked
with ``--vasp``, ``--wienk2``, ``--qe``, ``--abinit``, ``--elk``,
``--siesta``, and ``--crystal`` options, respectively, and nothing is
specified, ``--vasp`` is selected as the default interface.
The details about these interfaces are found at :ref:`calculator_interfaces`.
@ -127,18 +127,19 @@ e.g.,
% phonopy --abinit -c NaCl.in band.conf
.. _pwscf_mode:
.. _qe_mode:
``--pwscf``
``--qe``
~~~~~~~~~~~~
Pwscf mode is invoked with this option. Usually this option is used
with ``--cell`` (``-c``) option or ``CELL_FILENAME`` tag to read Pwscf
input file that contains the unit cell crystal structure, e.g.,
Quantum ESPRESSO mode is invoked with this option. Usually this option
is used with ``--cell`` (``-c``) option or ``CELL_FILENAME`` tag to
read QE/PWscf input file that contains the unit cell crystal structure,
e.g.,
::
% phonopy --pwscf -c NaCl.in band.conf
% phonopy --qe -c NaCl.in band.conf
.. _siesta_mode:
@ -208,12 +209,12 @@ Unit cell crystal structure file is specified with this tag.
Without specifying this tag, default file name is searched in current
directory. The default file names for the calculators are as follows::
VASP | POSCAR
Wien2k | case.struct
Abinit | unitcell.in
Pwscf | unitcell.in
Elk | elk.in
CRYSTAL| crystal.o
VASP | POSCAR
WIEN2k | case.struct
ABINIT | unitcell.in
PWscf | unitcell.in
Elk | elk.in
CRYSTAL | crystal.o
Create ``FORCE_SETS``
----------------------
@ -252,11 +253,11 @@ Attention:
.. _abinit_force_sets_option:
Abinit interface
ABINIT interface
^^^^^^^^^^^^^^^^
``FORCE_SETS`` file is created from ``disp.yaml`` and Abinit output
files (``*.out``). In the reading of forces in Abinit output files,
``FORCE_SETS`` file is created from ``disp.yaml`` and ABINIT output
files (``*.out``). In the reading of forces in ABINIT output files,
forces in eV/Angstrom are read. The unit conversion factor is
determined with this unit.
@ -265,19 +266,20 @@ determined with this unit.
% phonopy --abinit -f disp-001/supercell.out disp-002/supercell.out ...
.. _pwscf_force_sets_option:
.. _qe_force_sets_option:
Pwscf interface
^^^^^^^^^^^^^^^^
Quantum ESPRESSO interface
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
``FORCE_SETS`` file is created from ``disp.yaml`` and Pwscf output
``FORCE_SETS`` file is created from ``disp.yaml`` and PWscf output
files.
::
% phonopy --pwscf -f disp-001/supercell.out disp-002/supercell.out ...
% phonopy --qe -f disp-001/supercell.out disp-002/supercell.out ...
Here ``*.out`` files are the saved texts of standard outputs of Pwscf calculations.
Here ``*.out`` files are the saved texts of standard outputs of PWscf
calculations.
.. _wien2k_force_sets_option:
@ -294,7 +296,7 @@ http://www.wien2k.at/reg_user/unsupported/.
file when creating supercell with displacements, and
``case.scf``'s, which are the WIEN2k output files. The order of
displacements in ``disp.yaml`` file and the order of ``case.scf``'s
have to be same. **For Wien2k struct file, only negative atom index
have to be same. **For WIEN2k struct file, only negative atom index
with the P lattice format is supported.**
::
@ -446,5 +448,5 @@ printed out and phonopy stops without going to phonon analysis.
% phonopy --symmetry
This tag can be used together with the ``--cell`` (``-c``),
``--abinit``, ``--pwscf``, ``--elk``, ``--wien2k``, ``--crystal`` or
``--primitive_axis`` option.
``--abinit``, ``--qe``, ``--elk``, ``--wien2k``, ``--siesta``,
``--crystal`` or ``--primitive_axis`` option.

40
doc/crystal.rst
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@ -3,7 +3,7 @@
CRYSTAL & phonopy calculation
=========================================
CRYSTAL program package has a robust built-in phonon calculation
CRYSTAL program package has a robust built-in phonon calculation
workflow. However, the Phonopy interface enables convenient access
to many phonon-related properties, such as subsequent Phono3py
calculations of lattice thermal conductivity.
@ -17,7 +17,7 @@ For optimization outputs, the final geometry in the file is read.
If dielectric tensor and effective Born charges are present, the interface
creates a BORN file for Non-analytical correction (:ref:`nac_tag`).
The recommended strategy is to carry out a Gamma-point frequency calculation
The recommended strategy is to carry out a Gamma-point frequency calculation
with INTENS and INTCPHF. This produces all required quantities and also confirms that
the structure optimization has converged to a true local minimum.
@ -28,10 +28,10 @@ How to run
----------
The workflow for a CRYSTAL-Phonopy calculation is outlined here using the
Si example found in ``example/Si-CRYSTAL``.
Si example found in ``example/Si-CRYSTAL``.
In this example, the CRYSTAL output file is ``crystal.o``.
This is the default for the CRYSTAL interface, so, the ``-c crystal.o``
In this example, the CRYSTAL output file is ``crystal.o``.
This is the default for the CRYSTAL interface, so, the ``-c crystal.o``
parameter is not needed
1) Create supercells with :ref:`crystal_mode` option::
@ -39,19 +39,19 @@ parameter is not needed
% phonopy --crystal -d --dim="4 4 4"
In this example, 4x4x4 supercells are created. For every supercell file, the
interface creates a .d12 input file and an .ext structure file. The files
interface creates a .d12 input file and an .ext structure file. The files
``supercell.d12/.ext`` contain the perfect supercell. The files
``supercell-xxx.d12/.ext`` (``xxx`` are numbers) contain the supercells
with displacements. File ``disp.yaml`` is also generated, containing information
with displacements. File ``disp.yaml`` is also generated, containing information
about the supercell and the displacements.
In the case of the Si example, files ``supercell-001.d12`` and
In the case of the Si example, files ``supercell-001.d12`` and
``supercell-001.ext`` will be created.
2) To make valid CRYSTAL input files, there are two possible options:
a) Manually: modify the generated supercell-xxx.d12 files by replacing
the line ``Insert basis sets and parameters here`` with the
a) Manually: modify the generated supercell-xxx.d12 files by replacing
the line ``Insert basis sets and parameters here`` with the
basis set and computational parameters.
b) Recommended option: before generating the supercells, include a file named
@ -60,8 +60,8 @@ parameter is not needed
When phonopy finds this file, it automatically generates complete
CRYSTAL input files in the step 1
Note that supercells with displacements must not be relaxed in the
force calculations, because atomic forces induced by a small atomic
Note that supercells with displacements must not be relaxed in the
force calculations, because atomic forces induced by a small atomic
displacement are what we need for phonon calculation. To get accurate
forces, TOLDEE parameter should be 10 or higher. Phonopy includes this
parameter and the necessary GRADCAL keyword automatically in the inputs.
@ -71,19 +71,18 @@ parameter is not needed
% runcry14 supercell-001.d12
3) To create ``FORCE_SETS``, that is used by phonopy,
3) To create ``FORCE_SETS``, that is used by phonopy,
the following phonopy command is executed::
% phonopy --crystal -f supercell-001.o
Here ``.o`` files are the CRYSTAL output files from the force
calculations. saved text files of standard outputs of the
Pwscf calculations. All ``.o`` files corresponding to the generated
``supercell-xxx.d12`` files have to be given in the above command.
To run this command, ``disp.yaml`` has to be located in 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:`crystal_force_sets_option`.
calculations. All ``.o`` files corresponding to the generated
``supercell-xxx.d12`` files have to be given in the above command.
To run this command, ``disp.yaml`` has to be located in 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:`crystal_force_sets_option`.
4) Now, Phonopy post-prcessing commands can be run. ``FORCE_SETS`` is
automatically read in. Create phonon dispersion plot with:
@ -187,4 +186,3 @@ The workflow is very similar to the Si example below:
.. |crystal-band-nac| image:: NaCl-crystal-band-NAC.png
:width: 33%

130
doc/examples.rst
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@ -17,29 +17,29 @@ Si
``FORCE_SETS`` file creation for VASP
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
For the other calculators such as pwscf, abinit, etc, the way to
For the other calculators such as PWscf, ABINIT, etc, the way to
create ``FORCE_SETS`` is found following :ref:`calculator_interfaces`.
::
% phonopy -f vasprun.xml
_
_ __ | |__ ___ _ __ ___ _ __ _ _
% phonopy -f vasprun.xml
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
0.9.4
counter (file index): 1 (1)
counter (file index): 1 (1)
FORCE_SETS has been created.
_
_
___ _ __ __| |
/ _ \ '_ \ / _` |
| __/ | | | (_| |
\___|_| |_|\__,_|
where ``vasprun.xml`` is the VASP output.
@ -49,13 +49,13 @@ DOS
::
% phonopy -p mesh.conf
_
_ __ | |__ ___ _ __ ___ _ __ _ _
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
0.9.4
Mesh sampling mode
Settings:
@ -70,7 +70,7 @@ DOS
|Si-DOS|
Thermal properties
~~~~~~~~~~~~~~~~~~
@ -78,13 +78,13 @@ Thermal properties
% phonopy -t -p mesh.conf
_
_ __ | |__ ___ _ __ ___ _ __ _ _
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
0.9.4
Mesh sampling mode
Settings:
@ -111,7 +111,7 @@ Thermal properties
:width: 50%
|Si-props|
NaCl
----
@ -121,13 +121,13 @@ Band structure
::
% phonopy -p band.conf
_
_ __ | |__ ___ _ __ ___ _ __ _ _
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
0.9.1.4
Band structure mode
Settings:
@ -151,21 +151,21 @@ Band structure
Band structure with non-analytical term correction
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This requires to prepare BORN file.
::
% phonopy -p --nac band.conf
_
_ __ | |__ ___ _ __ ___ _ __ _ _
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
1.4
Band structure mode
Settings:
Non-analytical term correction: on
@ -198,15 +198,15 @@ PDOS
::
% phonopy -p pdos.conf
_
_ __ | |__ ___ _ __ ___ _ __ _ _
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
1.6.2
Mesh sampling mode
Settings:
Sampling mesh: [41 41 41]
@ -218,12 +218,12 @@ PDOS
Spacegroup: Fm-3m (225)
Calculating force constants...
Number of irreducible q-points: 1771
_
_
___ _ __ __| |
/ _ \ '_ \ / _` |
| __/ | | | (_| |
\___|_| |_|\__,_|
.. |NaCl-PDOS| image:: NaCl-PDOS.png
:width: 50%
@ -233,19 +233,19 @@ PDOS
With non-analytical term correction, the PDOS may not change very much
because it mainly affects phonon modes in the reciprocal
region close to :math:`\Gamma` point.
::
% phonopy --nac -p pdos.conf
_
_ __ | |__ ___ _ __ ___ _ __ _ _
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
1.6.2
Mesh sampling mode
Settings:
Non-analytical term correction: on
@ -258,7 +258,7 @@ region close to :math:`\Gamma` point.
Spacegroup: Fm-3m (225)
Calculating force constants...
Number of irreducible q-points: 1771
_
_
___ _ __ __| |
/ _ \ '_ \ / _` |
| __/ | | | (_| |
@ -283,9 +283,9 @@ profile than that given by the smearing method.
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
1.9.2.1
Mesh sampling mode
Settings:
Non-analytical term correction: on
@ -325,9 +325,9 @@ Band structure and DOS or PDOS can be plotted on one figure together by
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
1.9.2
Band structure and mesh sampling mode
Settings:
Non-analytical term correction: on
@ -350,7 +350,7 @@ Band structure and DOS or PDOS can be plotted on one figure together by
___ _ __ __| |
/ _ \ '_ \ / _` |
| __/ | | | (_| |
\___|_| |_|\__,_|
\___|_| |_|\__,_|
.. |NaCl-band-PDOS-NAC| image:: NaCl-band-PDOS-NAC.png
:width: 50%
@ -371,7 +371,7 @@ MgB2 characters of ireducible representations
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
1.11.10
Python version 3.6.0
Spglib version 1.9.9
Ir-representation mode
@ -379,115 +379,115 @@ MgB2 characters of ireducible representations
Supercell: [3 3 2]
Spacegroup: P6/mmm (191)
Computing force constants...
-------------------------------
Irreducible representations
-------------------------------
q-point: [ 0. 0. 0.]
Point group: 6/mmm
Original rotation matrices:
1 2 3 4 5 6
-------- -------- -------- -------- -------- --------
1 0 0 -1 0 0 1 -1 0 -1 1 0 0 -1 0 0 1 0
0 1 0 0 -1 0 1 0 0 -1 0 0 1 -1 0 -1 1 0
0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1
7 8 9 10 11 12
-------- -------- -------- -------- -------- --------
-1 0 0 1 0 0 -1 1 0 1 -1 0 0 1 0 0 -1 0
0 -1 0 0 1 0 -1 0 0 1 0 0 -1 1 0 1 -1 0
0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1
13 14 15 16 17 18
-------- -------- -------- -------- -------- --------
0 -1 0 0 1 0 -1 0 0 1 0 0 -1 1 0 1 -1 0
-1 0 0 1 0 0 -1 1 0 1 -1 0 0 1 0 0 -1 0
0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1
19 20 21 22 23 24
-------- -------- -------- -------- -------- --------
0 1 0 0 -1 0 1 0 0 -1 0 0 1 -1 0 -1 1 0
1 0 0 -1 0 0 1 -1 0 -1 1 0 0 -1 0 0 1 0
0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1
Transformation matrix:
1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
Rotation matrices by transformation matrix:
E i C6 S3 C3 S6
-------- -------- -------- -------- -------- --------
1 0 0 -1 0 0 1 -1 0 -1 1 0 0 -1 0 0 1 0
0 1 0 0 -1 0 1 0 0 -1 0 0 1 -1 0 -1 1 0
0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1
C2 sgh C3 S6 C6 S3
-------- -------- -------- -------- -------- --------
-1 0 0 1 0 0 -1 1 0 1 -1 0 0 1 0 0 -1 0
0 -1 0 0 1 0 -1 0 0 1 0 0 -1 1 0 1 -1 0
0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1
C2' sgd C2'' sgv C2' sgd
-------- -------- -------- -------- -------- --------
0 -1 0 0 1 0 -1 0 0 1 0 0 -1 1 0 1 -1 0
-1 0 0 1 0 0 -1 1 0 1 -1 0 0 1 0 0 -1 0
0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1
C2'' sgv C2' sgd C2'' sgv
-------- -------- -------- -------- -------- --------
0 1 0 0 -1 0 1 0 0 -1 0 0 1 -1 0 -1 1 0
1 0 0 -1 0 0 1 -1 0 -1 1 0 0 -1 0 0 1 0
0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1
Character table:
1 ( -0.019): A2u
( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0)
( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0)
( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0)
( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0)
2 ( 0.004): E1u
( 2, 0.0) ( 2, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 0.0)
( 2, 180.0) ( 2, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 0.0) ( 1, 180.0)
( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0)
( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0)
4 ( 9.953): E1u
( 2, 0.0) ( 2, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 0.0)
( 2, 180.0) ( 2, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 0.0) ( 1, 180.0)
( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0)
( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0)
6 ( 11.982): A2u
( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0)
( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0)
( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0)
( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0)
7 ( 17.269): E2g
( 2, 0.0) ( 2, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 180.0) ( 1, 180.0)
( 2, 0.0) ( 2, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 180.0) ( 1, 180.0)
( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0)
( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0)
9 ( 20.565): B2g
( 1, 0.0) ( 1, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 0.0) ( 1, 0.0)
( 1, 180.0) ( 1, 180.0) ( 1, 0.0) ( 1, 0.0) ( 1, 180.0) ( 1, 180.0)
( 1, 180.0) ( 1, 180.0) ( 1, 0.0) ( 1, 0.0) ( 1, 180.0) ( 1, 180.0)
( 1, 0.0) ( 1, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 0.0) ( 1, 0.0)
_
___ _ __ __| |
/ _ \ '_ \ / _` |
| __/ | | | (_| |
\___|_| |_|\__,_|
Al-QHA
-------

24
doc/gruneisen.rst
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@ -13,7 +13,7 @@ How to run
It is necessary to run three phonon calculations. One is calculated at
the equilibrium volume and the remaining two are calculated at the
slightly larger volume and smaller volume than the equilibrium
volume. The unitcells at these volumes have to be fully relaxed under
volume. The unitcells at these volumes have to be fully relaxed under
the constraint of each volume.
Let files named ``POSCAR-unitcell``, ``FORCE_SETS`` (or ``FORCE_CONSTANTS``
@ -64,13 +64,13 @@ plot.
.. _gruneisen_calculators:
Abinit, Pwscf, Wien2k, and CRYSTAL interfaces
---------------------------------------------
Abinit, Quantum ESPRESSO, Wien2k, and CRYSTAL interfaces
----------------------------------------------------------
``--abinit``, ``--pwscf``, ``--wien2k``, or ``--crystal`` options can be specified
for corresponding calculators and the crystal structure file format
should be different from that of the VASP format. An Abinit example is
as follows::
``--abinit``, ``--qe``, ``--wien2k``, or ``--crystal`` options can be
specified for corresponding calculators and the crystal structure file
format should be different from that of the VASP format. An Abinit
example is as follows::
% 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
@ -80,11 +80,11 @@ as follows::
Command options
----------------
If one of ``--abinit``, ``--pwscf``, ``--wien2k``, or ``--crystal`` options is
specified, the interface mode is changed to it. The unit conversion
factor to THz is appropriately selected and its crystal structure file
format is accepted. If none of them is specified, as the VASP
interface mode is invoked as the default interface.
If one of ``--abinit``, ``--qe``, ``--wien2k``, or ``--crystal``
options is specified, the interface mode is changed to it. The unit
conversion factor to THz is appropriately selected and its crystal
structure file format is accepted. If none of them is specified, as
the VASP interface mode is invoked as the default interface.
The following command options can be used for all interface
modes. They work similarly to those for ``phonopy`` script.

10
doc/index.rst
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@ -46,12 +46,12 @@ The following features of phonopy are highlighted:
- :ref:`Interfaces to calculators <calculator_interfaces>`:
:ref:`VASP <tutorial>`,
:ref:`VASP DFPT <vasp_dfpt_interface>`,
:ref:`Abinit <abinit_interface>`,
:ref:`Pwscf <pwscf_interface>`,
:ref:`Siesta <siesta_interface>`,
:ref:`ABINIT <abinit_interface>`,
:ref:`Quantu ESPRESSO <qe_interface>`,
:ref:`SIESTA <siesta_interface>`,
:ref:`Elk <elk_interface>`,
:ref:`FHI-aims <FHI_aims_interface>`,
:ref:`Wien2k <wien2k_interface>`,
:ref:`WIEN2k <wien2k_interface>`,
:ref:`CRYSTAL <crystal_interface>`
- :ref:`Python APIs <phonopy_module>`
@ -104,7 +104,7 @@ Mailing list
For questions, bug reports, and comments, please visit
https://lists.sourceforge.net/lists/listinfo/phonopy-users to
subscribe the phonopy mailing list
subscribe the phonopy mailing list
and send them to phonopy-users@lists.sourceforge.net.
Message body including attached files has to be smaller than 300 KB.

56
doc/interfaces.rst
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@ -3,9 +3,10 @@
Interfaces to calculators
==========================
The interfaces for VASP, Wien2k, Pwscf, Abinit, Elk and CRYSTAL are built in
to the usual phonopy command. See the command options and how to
invoke each of them at :ref:`force_calculators`.
The interfaces for VASP, WIEN2k, Quantum ESPRESSO (QE), ABINIT, Elk,
SIESTA, and CRYSTAL are built in to the usual phonopy command. See the
command options and how to invoke each of them at
:ref:`force_calculators`.
Physical unit system for calculator
------------------------------------
@ -15,11 +16,11 @@ Physical unit systems used for the calculators are as follows::
| Distance Atomic mass Force Force constants
-----------------------------------------------------------------
VASP | Angstrom AMU eV/Angstrom eV/Angstrom^2
Wien2k | au (bohr) AMU mRy/au mRy/au^2
Pwscf | au (bohr) AMU Ry/au Ry/au^2
Abinit | au (bohr) AMU eV/Angstrom eV/Angstrom.au
Siesta | au (bohr) AMU eV/Angstrom eV/Angstrom.au
elk | au (bohr) AMU hartree/au hartree/au^2
WIEN2k | au (bohr) AMU mRy/au mRy/au^2
QE | au (bohr) AMU Ry/au Ry/au^2
ABINIT | au (bohr) AMU eV/Angstrom eV/Angstrom.au
SIESTA | au (bohr) AMU eV/Angstrom eV/Angstrom.au
Elk | au (bohr) AMU hartree/au hartree/au^2
CRYSTAL | Angstrom AMU eV/Angstrom eV/Angstrom^2
For these sets of physical properties, phonon frequency is calculated
@ -35,10 +36,10 @@ Without specifying ``-c`` option, default file name for unit cell is
used as shown below::
VASP | POSCAR
Wien2k | case.struct
Pwscf | unitcell.in
Abinit | unitcell.in
Siesta | input.fdf
WIEN2k | case.struct
QE | unitcell.in
ABINIT | unitcell.in
SIESTA | input.fdf
Elk | elk.in
CRYSTAL | crystal.o
@ -52,13 +53,28 @@ option. The default value is dependent on calculator, and the list is
shown below::
VASP | 0.01 Angstrom
Wien2k | 0.02 au (bohr)
Pwscf | 0.02 au (bohr)
Abinit | 0.02 au (bohr)
Siesta | 0.02 au (bohr)
WIEN2k | 0.02 au (bohr)
QE | 0.02 au (bohr)
ABINIT | 0.02 au (bohr)
SIESTA | 0.02 au (bohr)
Elk | 0.02 au (bohr)
CRYSTAL | 0.01 Angstrom
.. _frequency_default_value_interfaces:
Default unit conversion factor of phonon frequency to THz
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
::
VASP | 15.633302
WIEN2k | 3.44595837
QE | 108.97077
ABINIT | 21.49068
SIESTA | 21.49068
Elk | 154.10794
CRYSTAL | 15.633302
.. _nac_default_value_interfaces:
Default unit conversion factor for non-analytical term correction
@ -67,10 +83,10 @@ Default unit conversion factor for non-analytical term correction
::
VASP | 14.399652
Wien2k | 2000
Pwscf | 2
Abinit | 51.422090
Siesta | 51.422090
WIEN2k | 2000
QE | 2
ABINIT | 51.422090
SIESTA | 51.422090
Elk | 1
CRYSTAL | 14.399652

4
doc/procedure.rst
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@ -3,6 +3,6 @@
Short tutorials
================
Tutorials for different force calculators, VASP, WIEN2k, PWscf (QE),
ABINIT, SIESTA, Elk, and, CRYSTAL, are found at
Tutorials for different force calculators, VASP, WIEN2k, Quantum
ESPRESSO, ABINIT, SIESTA, Elk, and, CRYSTAL, are found at
:ref:`tutorials_for_calculators`.

38
doc/pwscf.rst
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@ -1,9 +1,9 @@
.. _pwscf_interface:
.. _qe_interface:
Pwscf & phonopy calculation
=========================================
Quantum ESPRESSO (QE) & phonopy calculation
============================================
Quantum espresso package itself has a set of the phonon calculation
Quantum ESPRESSO package itself has a set of the phonon calculation
system. But the document here explains how to calculate phonons using
phonopy, i.e., using the finite displacement and supercell approach.
@ -16,7 +16,7 @@ More tags may be supported on request.
::
nat, ntyp, ATOMIC_SPECIES, ATOMIC_POSITIONS, CELL_PARAMETERS
nat, ntyp, celldm(1), ATOMIC_SPECIES, ATOMIC_POSITIONS, CELL_PARAMETERS
How to run
----------
@ -25,9 +25,9 @@ The procedure of Pwscf-phonopy calculation is shown below using the
NaCl example found in ``example/NaCl-pwscf`` directory.
1) Read a Pwscf input file and create supercells with
:ref:`pwscf_mode` option::
:ref:`qe_mode` option::
% phonopy --pwscf -d --dim="2 2 2" -c NaCl.in
% 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
@ -57,10 +57,10 @@ NaCl example found in ``example/NaCl-pwscf`` directory.
% mpirun pw.x -i NaCl-001.in |& tee NaCl-001.out
% mpirun pw.x -i NaCl-002.in |& tee NaCl-002.out
3) To create ``FORCE_SETS``, that is used by phonopy,
3) To create ``FORCE_SETS``, that is used by phonopy,
the following phonopy command is executed::
% phonopy --pwscf -f NaCl-001.out NaCl-002.out
% phonopy --qe -f NaCl-001.out NaCl-002.out
Here ``.out`` files are the saved text files of standard outputs of the
Pwscf calculations. If more supercells with displacements were
@ -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
@ -77,7 +77,7 @@ NaCl example found in ``example/NaCl-pwscf`` directory.
::
% phonopy --pwscf -c NaCl.in -p band.conf
% phonopy --qe -c NaCl.in -p band.conf
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
@ -85,7 +85,7 @@ NaCl example found in ``example/NaCl-pwscf`` directory.
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
1.11.0
Python version 2.7.12
Spglib version 1.9.2
Calculator interface: pwscf
@ -113,15 +113,15 @@ NaCl example found in ``example/NaCl-pwscf`` directory.
|pwscf-band|
.. |pwscf-band| image:: NaCl-pwscf-band.png
:width: 50%
: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
@ -206,13 +206,13 @@ be something like below::
1.105385 0 0 0 1.105385 0 0 0 1.105385
-1.105385 0 0 0 -1.105385 0 0 0 -1.105385
Once this is made, the non-analytical term correction is included
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|
.. |pwscf-band-nac| image:: NaCl-pwscf-band-NAC.png
:width: 50%
:width: 50%

10
doc/setting-tags.rst
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@ -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
--------------------------