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Document update following user interface change for force calculators

This commit is contained in:
Atsushi Togo 2014-10-31 12:38:57 +09:00
parent fb664b914e
commit 0b0d4a6f2d
6 changed files with 149 additions and 124 deletions
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8
doc/abinit.rst
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@ -21,7 +21,7 @@ A procedure of Abinit-phonopy calculation is as follows:
1) Read an Abinit main input file and create
supercells with :ref:`abinit_mode` option::
% phonopy -d --dim="2 2 2" --abinit=NaCl.in
% phonopy --abinit -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
@ -43,7 +43,7 @@ A procedure of Abinit-phonopy calculation is as follows:
::
% phonopy --abinit=unitcell.in -f disp-001/supercell-001.out disp-002/supercell-002.out ...
% phonopy --abinit -f disp-001/supercell-001.out disp-002/supercell-002.out ...
To run this command, ``disp.yaml`` has to be located in the current
directory because the atomic displacements are written into the
@ -54,11 +54,11 @@ A procedure of Abinit-phonopy calculation is as follows:
4) Run post-process of phonopy with the Abinit main input file for the
unit cell used in the step 1::
% phonopy --abinit=NaCl.in -p band.conf
% phonopy --abinit -c NaCl.in -p band.conf
or::
% phonopy --abinit=NaCl.in --dim="2 2 2" [other-OPTIONS] [setting-file]
% phonopy --abinit -c NaCl.in --dim="2 2 2" [other-OPTIONS] [setting-file]
.. |sflogo| image:: http://sflogo.sourceforge.net/sflogo.php?group_id=161614&type=1
:target: http://sourceforge.net

155
doc/command-options.rst
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@ -8,6 +8,7 @@ tags:
* ``--amplitude`` (``DISPLACEMENT_DISTANCE``)
* ``--anime`` (``ANIME``)
* ``-c``, ``--cell`` (``CELL_FILENAME``)
* ``-d`` (``CREATE_DISPLACEMENTS = .TRUE.``
* ``--dim`` (``DIM``)
* ``--mp``, ``--mesh`` (``MP``)
@ -46,10 +47,89 @@ When both of command-line option and setting tag for the same purpose
are set simultaneously, the command-line options overide the setting
tags.
Help (``-h`` or ``--help``)
---------------------------
Force calculator
----------------
Review of options is shown.
If none of the following calculators are specified, VASP mode is invoked.
The physical unit system used for the calculators are shown below.
::
: energy, distance, atomic mass, force
-------------------------------------------------------
VASP : eV, Angstrom, AMU, eV/Angstrom
Wien2k : Ry, au, AMU, mRy/au
Pwscf : Ry, au, AMU, Ry/au
Abinit : hartree, au(=bohr), AMU, eV/Angstrom
.. _wien2k_mode:
``--wien2k``
~~~~~~~~~~~~
This option invokes the WIEN2k mode.In this mode. 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.,
::
% phonopy --wien2k -c case.struct band.conf
**Only the WIEN2k struct with the P lattice is supported**. See more
information :ref:`wien2k_interface`.
.. _abinit_mode:
``--abinit``
~~~~~~~~~~~~
Abinit mode is invoked with this option. Usually this option is used
with ``--cell`` (``-c``) option or ``CELL_FILENAME`` tag to read
Abinit main input file that contains the unit cell crystal structure,
e.g.,
::
% phonopy --abinit -c unitcell.in band.conf
.. _pwscf_mode:
``--pwscf``
~~~~~~~~~~~~
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.,
::
% phonopy --pwscf -c unitcell.in band.conf
.. _cell_filename_option:
Input cell
----------
``-c`` or ``--cell``
~~~~~~~~~~~~~~~~~~~~
Unit cell crystal structure file is specified with this tag.
::
% phonopy --cell=UPOSCAR band.conf
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
Create ``FORCE_SETS``
----------------------
@ -237,16 +317,8 @@ case of VASP mode, it is calculated by
:math:`\sqrt{\text{eV/AMU}}`/(:math:`\text{\AA}\cdot2\pi\cdot10^{12}`)
(=15.633302) in SI base unit. The default conversion factors for
``wien2k``, ``abinit``, and ``pwscf`` are 3.44595, 21.49068 and
108.9708, respectively. These are determined by the unit systems as
follows:
::
Physical units: energy, distance, atomic mass, force
vasp : eV, Angstrom, AMU, eV/Angstrom
wien2k : Ry, au, AMU, mRy/au
pwscf : Ry, au, AMU, Ry/au
abinit : hartree, au(=bohr), AMU, eV/Angstrom
108.9708, respectively. These are determined following the physical
unit systems of the calculators.
When calculating thermal property, the factor to THz is
required. Otherwise the calculated thermal properties have wrong
@ -297,63 +369,6 @@ This tag can be used together with the ``--cell``, ``--abinit``,
``--pwscf``, ``--wien2k``, or ``--primitive_axis`` option.
Input cell
----------
``-c`` or ``--cell``
~~~~~~~~~~~~~~~~~~~~
Phonopy searches the ``POSCAR`` file in the current directory. Using
this tag, you can specify another filename than ``POSCAR`` as the
input unit cell.
::
% phonopy --cell=UPOSCAR band.conf
.. _abinit_mode:
``--abinit``
~~~~~~~~~~~~
Abinit mode is invoked with this option. This option is used with an
Abinit main input file name that contains the unit cell crystal
structure, e.g.,
::
% phonopy --abinit=unitcell.in band.conf
.. _pwscf_mode:
``--pwscf``
~~~~~~~~~~~~
Pwscf mode is invoked with this option. This option is used with a
Pwscf input file name that contains the unit cell crystal structure,
e.g.,
::
% phonopy --pwscf=unitcell.in band.conf
.. _wien2k_mode:
``--wien2k``
~~~~~~~~~~~~
This option with WIEN2k struct file, phonopy runs with the WIEN2k
mode. In this mode, you don't need to prepare ``POSCAR``. The
supercells with displacements in WIEN2k struct format are created
using ``-d`` option. The physical
unit is changed to mRydberg and Bohr. **Only the WIEN2k struct with
the P lattice is supported**. See more information
:ref:`wien2k_interface`.
::
% phonopy --wien2k=case.struct band.conf
.. |sflogo| image:: http://sflogo.sourceforge.net/sflogo.php?group_id=161614&type=1
:target: http://sourceforge.net

4
doc/conf.py
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@ -46,9 +46,9 @@ copyright = u'2009, Atsushi Togo'
# built documents.
#
# The short X.Y version.
version = '1.9.1'
version = '1.9.2'
# The full version, including alpha/beta/rc tags.
release = '1.9.1'
release = '1.9.2'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.

8
doc/pwscf.rst
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@ -22,7 +22,7 @@ A procedure of Pwscf-phonopy calculation is as follows:
1) Read an Pwscf input file and create supercells with
:ref:`pwscf_mode` option::
% phonopy -d --dim="2 2 2" --pwscf=NaCl.in
% phonopy --pwscf -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
@ -43,7 +43,7 @@ A procedure of Pwscf-phonopy calculation is as follows:
::
% phonopy --pwscf=unitcell.in -f disp-001/supercell-001.out disp-002/supercell-002.out ...
% phonopy --pwscf -f disp-001/supercell-001.out disp-002/supercell-002.out ...
Here ``*.out`` files are the saved texts of standard outputs of
Pwscf calculations. To run this command, ``disp.yaml`` has to be
@ -55,11 +55,11 @@ A procedure of Pwscf-phonopy calculation is as follows:
4) Run post-process of phonopy with the Pwscf input file for the
unit cell used in the step 1::
% phonopy --pwscf=NaCl.in -p band.conf
% phonopy --pwscf -c NaCl.in -p band.conf
or::
% phonopy --pwscf=NaCl.in --dim="2 2 2" [other-OPTIONS] [setting-file]
% phonopy --pwscf -c NaCl.in --dim="2 2 2" [other-OPTIONS] [setting-file]
.. |sflogo| image:: http://sflogo.sourceforge.net/sflogo.php?group_id=161614&type=1
:target: http://sourceforge.net

92
doc/setting-tags.rst
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@ -13,47 +13,6 @@ have space among characters (e.g. ``1 / 3``) are not allowed.
Basic tags
----------
``ATOM_NAME``
~~~~~~~~~~~~~
Chemical symbols ::
ATOM_NAME = Si O
The number of chemical symbols have to be same as that of the numbers
in the sixth line of ``POSCAR``.
Chemical symbols read by phonopy are overwritten by those written in
``POSCAR``. See ``POSCAR`` examples. In WIEN2k mode,
you don't need to set this tag, i.e., chemical symbols are read from
the structure file.
``EIGENVECTORS``
~~~~~~~~~~~~~~~~
When this tag is '.TRUE.', eigenvectors are calculated. With ``-p``
option, partial density of states are calculated.
.. _mass_tag:
``MASS``
~~~~~~~~
This tag is not necessary to use usually, because atomic masses are
automatically set from the chemical symbols.
Atomic masses of a **primitive cell** are overwritten by the values
specified. The order of atoms in the primitive cell that is defined by
``PRIMITIVE_AXIS`` tag can be shown using ``-v`` option. It must be
noted that this tag does not affect to the symmetry search.
For example, when there are six atoms in a primitive cell, ``MASS`` is
set as follows ::
MASS = 28.085 28.085 16.000 16.000 16.000 16.000
.. _dimension_tag:
``DIM``
~~~~~~~~~~
@ -150,6 +109,57 @@ Be careful that the axes in ``POSCAR`` is defined by three row
vectors, i.e., :math:`( \mathbf{a}_\mathrm{u} \; \mathbf{b}_\mathrm{u}
\; \mathbf{c}_\mathrm{u} )^T`.
``ATOM_NAME``
~~~~~~~~~~~~~
Chemical symbols ::
ATOM_NAME = Si O
The number of chemical symbols have to be same as that of the numbers
in the sixth line of ``POSCAR``.
Chemical symbols read by phonopy are overwritten by those written in
``POSCAR``. See ``POSCAR`` examples. In WIEN2k mode,
you don't need to set this tag, i.e., chemical symbols are read from
the structure file.
``EIGENVECTORS``
~~~~~~~~~~~~~~~~
When this tag is '.TRUE.', eigenvectors are calculated. With ``-p``
option, partial density of states are calculated.
.. _mass_tag:
``MASS``
~~~~~~~~
This tag is not necessary to use usually, because atomic masses are
automatically set from the chemical symbols.
Atomic masses of a **primitive cell** are overwritten by the values
specified. The order of atoms in the primitive cell that is defined by
``PRIMITIVE_AXIS`` tag can be shown using ``-v`` option. It must be
noted that this tag does not affect to the symmetry search.
For example, when there are six atoms in a primitive cell, ``MASS`` is
set as follows ::
MASS = 28.085 28.085 16.000 16.000 16.000 16.000
.. _dimension_tag:
``CELL_FILENAME``
------------------
::
CELL_FILENAME = UPOSCAR
See :ref:`cell_filename_option`.
Displacement creation tags
--------------------------

6
doc/wien2k.rst
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@ -9,7 +9,7 @@ The Wien2k-phonopy calculation works as follows:
supercells with the Wien2k struct format of P lattice using
``--wien2k`` option (:ref:`wien2k_mode`)::
% phonopy -d --dim="2 2 2" --wien2k=case.struct
% phonopy --wien2k -d --dim="2 2 2" -c case.struct
In this example, 2x2x2 supercells are created. ``case.structS`` and
``case.structS-xxx`` (``xxx`` are numbers) are the perfect
@ -32,7 +32,7 @@ The Wien2k-phonopy calculation works as follows:
http://www.wien2k.at/reg_user/unsupported/.
* Or try experimetal support of ``-f`` option::
% phonopy --wien2k=case.struct -f case-001.scf case-002.scf ...
% phonopy --wien2k -f case-001.scf case-002.scf ...
where ``case-xxx.scf`` are the Wien2k results for the
supercells. ``case-xxx.scf`` has to contain ``FGLxxx`` lines with
@ -55,7 +55,7 @@ The Wien2k-phonopy calculation works as follows:
4) Run post-process of phonopy with the Wien2k unit cell struct file
used in the step 1::
% phonopy --wien2k=case.struct --dim="2 2 2" [other-OPTIONS] [setting-file]
% phonopy --wien2k -c case.struct --dim="2 2 2" [other-OPTIONS] [setting-file]
Phonopy can read only the **P lattice format**. Therefore you have to
convert your struct file to that with the P lattice format. This may