scnc
/
phonopy
mirror of https://github.com/phonopy/phonopy.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity
phonopy/doc/changelog.rst

578 lines
20 KiB
ReStructuredText
Raw Blame History

.. _changelog:
Change Log
==========
Apr-5-2014: Version 1.8.4.1
-----------------------------
* Fix irreps for non-zero q-point of nonsymmorphic case
Mar-31-2014: Version 1.8.4
---------------------------
* Implementation of analytical derivative of dynamical matrix in C,
which improves the performance of group velocity calculation.
* Minor change of python module for group velocity.
Feb-17-2014: Version 1.8.3
---------------------------
* A collection of small fixes in interface.
* Spglib update (spglib-1.6.0)
* Change in ``phonopy/file_IO/write_FORCE_SETS_*``.
Feb-8-2014: Version 1.8.2
---------------------------
* ``vasprun.xml`` of VASP 5.2.8 is only specially parsed to treat
special wrong character.
* Python module interface is updated and modified. ``set_post_process``,
``set_force_sets`` will be obsolete. ``set_displacements`` is
obsolete.
Jan-9-2014: Version 1.8.0
---------------------------
This version is dangerous. A lot of code is modified internally.
* Tetrahedron method is implemented for total and partial DOS.
This is activated by ``--thm`` option.
* The display output with ``-v`` option is enriched.
* Symmetrization for ``outcar-born`` is implemented (Experimental).
* Cutoff-frequency ``CUTOFF_FREQUENCY`` (``--cutoff_freq``) is
implemented to ignore frequencies lower than this cutoff frequency
to calculate thermal properties and thermal displacements.
Dec-4-2013: Version 1.7.5
---------------------------
* ``--mass`` option is created to shortcut of the ``MASS`` tag.
* ``--fc_spg_symmetry`` option is created to symmetrize force
constants.
* Symmetry finder update (spglib version 1.5.2)
Oct-3-2013: Version 1.7.4
---------------------------
* Thermal displacement matrix is implemented. See
:ref:`thermal_displacement_matrices_tag` and :ref:`thermal_displacement`.
* PDOS with projection along arbitrary direction was implemented. See
:ref:`projection_direction_tag`.
* ``partial_dos.dat`` format was changed. XYZ projected PDOS is not
output. Instead atom projected PDOS (sum of XYZ projected PDOS)
is written. See :ref:`output_files`.
* DOS and PDOS python interface was modified. The keyword of
``omega_something`` is changed to ``freq_something``.
* ``gruneisen`` didn't run because it didn't follow the move of
the ``file_IO.py`` file location. This is fixed.
* The formula of non-analytical term correction implemented in phonopy
is not translational invariant in reciprocal space. This induces
tiny difference of the choice of equivalent q-points being different
by reciprocal primitive vectors. Now in the mesh sampling mode
(``MP``), q-points are automatically moved to inside
first-Brillouin-zone.
* In the mesh sampling mode, consistency of symmetry of mesh numbers
to crystal symmetry is checked. If the symmetry disagrees with
crystal symmetry, mesh symmetrization (equivalent to ``MESH_SYMMETRY
= .FALSE.``) is disabled.
* Wien2k interface is updated to adapt Wien2k-13.
* Fix the problem that only Vinet EOS worked in phonopy-qha.
Sep-17-2013: Version 1.7.3
---------------------------
* Fix. Segmentation fault happens in some specific systems
(e.g. Kubuntu 12.04 32bit) due to a different behavior of numpy
array creation.
* Group velocity for degenerate phonon mode is calculated slightly
different from older version and now it is symmetrized by
site-symmetry of q-point.
Aug-4-2013: Version 1.7.2
---------------------------
* ``group_velocity/__init__.py`` is moved to ``phonon`` directory.
* ``hphonopy/file_IO.py`` is moved to top directory.
* New ``harmonic/derivative_dynmat.py``: Analytical derivatives of
dynamical matrix
* Group velocity is computed by analytical derivatives of dynamical
matrix in the default configuration instead of previous finite
difference method. Group velocity calculation with the finite
difference method can be still activated by ``--gv_delta_q`` option.
* Force constants solver was partially rewritten. The order and shape
of matrices in the formula is rearranged
(:ref:`force_constants_solver_theory`).
July-14-2013: Version 1.7.1
---------------------------
* ``--pdos`` option was created. This is same as ``PDOS`` tag.
* Group velocity with degenerate modes was improved.
Jun-21-2013: Version 1.7
---------------------------
* The tag ``CHARACTER_TABLE`` was renamed to ``IRREPS``
(:ref:`irreps_tag`), and the option of ``--ct`` was renamed to
``--irreps`` as well. To show Ir-representations along with
characters, ``SHOW_IRREPS`` tag (or ``--show_irreps`` option) is
used. The output file name was also renamed to ``irreps.yaml``. In
the ir-reps calculation, display and file outputs were modified to
show the arguments of complex value characters.
* Numpy array types of 'double' and 'intc' for those arrays
passed to numpy C-API are used.
* ``thermal_displacement.py`` is slightly modified for the preparation
to include thermal displacement matrix.
* Symmetry finder update (spglib 1.4.2).
Apr-13-2013: Version 1.6.4
---------------------------
* Group velocity can be calculated using ``GROUP_VELOCITY`` tag or
``--gv`` option (:ref:`group_velocity_tag`).
* Non-analytical term correction is implemented in C, which
accelerates the calculation speed.
Feb-7-2013: Version 1.6.3
----------------------------
* Arbitral projection direction is allowed for thermal displacements
calculation. (:ref:`thermal_displacements_tag`)
* A new tag `WRITEDM` and an option `--writedm` are
implemented. Dynamical matrices are written into ``qpoints.yaml``
when this is used togather with the ``QPOINTS`` mode. (:ref:`writedm_tag`)
Nov-13-2012: Version 1.6.2
----------------------------
* A small fix of FHIaims.py.
Nov-4-2012: Version 1.6.1
----------------------------
* Implementation of database of character table for another type
of point group -3m.
* A new option ``--irreps`` or ``IRREPS`` tag (Experimental).
* ``character_table.yaml`` output.
* Eigenvectors output in``modulation.yaml`` was recovered.
Oct-22-2012: Version 1.6
----------------------------
* Experimental support of band connection. (:ref:`band_connection_tag`)
* Experimental support of mode Grüneisen parameter calculation. (:ref:`phonopy_gruneisen`)
* Format of ``MODULATION`` tag was modified. (:ref:`modulation_tag`)
* Phonopy is controlled by command line options more than
before. ``--qpoints``, ``--modulation`` and ``--anime`` options are prepared.
* Symmetry finder update.
* Implementation of database of character table for the point
group 32. Fix -3m database.
June-29-2012: Version 1.5
-------------------------
* Bug fix on plotting PDOS with labels.
* The array structures of qpoints, distances, frequencies, eigenvalues,
eigenvectors in BandStructure are changed to the lists of those
values of segments of band paths. For qpoints, frequencies,
eigenvalues, eigenvectors, the previous array structures are
recovered by numpy.vstack and for distances, numpy.hstack.
* Experimental support on thermal displacement.
* Experimental support on fitting DOS to a Debye model
(:ref:`debye_model_tag`) implemented by Jörg Meyer.
May-22-2012: Version 1.4.2
---------------------------
* Bug fix on showing the values of thermal properties. No bug in plot
and yaml.
May-21-2012: Version 1.4.1
---------------------------
* Avoid list comprehension with else statement, because it is not
supported in old python versions.
May-13-2012: Version 1.4
---------------------------
* ``--writefc`` option is implemented.
* In using ``MODULATION`` tag, phase factor for each mode can be
specified as the third value of each mode in degrees.
* Arguments of ``get_modulation`` in Phonopy module were modified.
The phase factor is now included in ``phonon_modes``.
* Class ``Phonopy`` was refactored. All private variables were renamed
as those starting with an underscore. Some basic variables are
obtained with the same variable names without the underscode, which
was implemented by the function ``property``.
* The labels of segments of band structure plot are specified by
``BAND_LABELS`` (:ref:`band_labels_tag`).
* ``--band`` option is implemented.
* ``GAMMA_CENTER`` tag and ``--gc``, ``--gamma_center`` option are
implemented (:ref:`mp_tag`).
* ``phonopy-qha`` was polished. Most of the code was moved to
``phonopy/qha/__init__.py``.
* ``Phonopy::get_mesh`` and ``Phonopy::get_band_structure`` were
modified. Instead of eigenvalues, frequencies are returned.
* The order of return values of ``Phonopy::get_thermal_properties``
was changed as numpy arrays of temperatures, Helmhotlz free
energies, entropies, and heat capacities at constant volume.
* Arguments of the class ``ThermalProperties``, ``Dos``, and
``PartialDOS`` were changed. Instead of eigenvalues, frequencies are
used.
* The default sigma value used for total and partial DOS was changed
to (max_frequency - min_frequency) / 100.
* Symmetry finder update.
Mar-20-2012: Version 1.3
---------------------------
* C implementations of a few parts of ``force_constants.py`` to speed
up.
* spglib update.
* Many small modifications.
* License is changed to the new BSD from the LGPL.
Oct-13-2011: Version 1.2.1
---------------------------
* Bug fix of the option ``--dim`` with 9 elements.
Oct-12-2011: Version 1.2
---------------------------
* Closing support of the ``--nac_old`` option.
* The option ``--nomeshsym`` is available on the manual.
* Symmetry finder update that includes the bug fix of Wyckoff letter
assignment.
* Showing site-symmetry symbols with respective orientations in the output of
``--symmetry`` option.
* Code cleanings of ``settings.py``, ``force_constant.py``, etc.
* Starting implementation of ``character_table.py`` (:ref:`irreps_tag`).
Sep-19-2011: Version 1.1
---------------------------
* ``--readfc`` option is implemented.
* A bit of clean-up of the code ``dynamical_matrix.py``,
``force_constant.py`` and ``_phonopy.c`` to make implementations
similar to the formulations often written in text books.
Sep-5-2011: Version 1.0
---------------------------
* ``settings.py`` is moved to ``phonopy/cui/Phonopy``. The configure
parser from a file and options is modified.
* Usage of ``MODULATION`` tag was changed.
* The option ``--nosym`` is available on the manual.
Aug-8-2011: Version 0.9.6
---------------------------
* Symmetry finder update
* Wyckoff positions are shown with ``--symmetry`` option
Jun-7-2011: Version 0.9.5.1
----------------------------------
* Bug fix of ``get_surrounding_frame`` in ``cells.py`` by Jörg Meyer and Christian Carbogno.
Errata of document
-----------------------------
The cell matrix definition of ``Atoms`` class was transposed.
Jun-3-2011: Version 0.9.5
----------------------------------
* Wien2k interface is updated (:ref:`wien2k_interface`), but this is
still quite experimental support.
* More information is involved in ``disp.yaml``. Along this
modification, supercells with displacements can be created solely
from ``disp.yaml`` using ``dispmanager``.
* Instead of ``TRANSLATION`` tag, ``FC_SYMMETRY`` is created
(:ref:`fc_symmetry_tag`).
* Closing support of ``--fco`` option.
* Add a few more examples in the ``example`` directory.
* Symmetry finder update
* ``propplot`` is updated for the ``--gnuplot`` option.
Errata of document
-----------------------------
The example of ``FORCE_SETS`` was wrong and was fixed. The explanation
of the document is correct.
Apr-18-2011: Version 0.9.4.2
-----------------------------
* In the setting tag ``BAND``, now comma ``,`` can be used to
disconnect the sequence of band paths
(:ref:`band_structure_related_tags`).
* ``dispmanager``, an auxiliary tool for modifying ``disp.yaml``, is
developed (:ref:`dispmanager_tool`).
* Symmetry finder update to spglib-1.0.3.1. Almost perfect casting to
a Bravais lattice is achieved using ``--symmetry`` option.
* The setting tags ``TRANSLATION``, ``PERMUTATION``, and ``MP_REDUCE``
are ceased.
Feb-26-2011: Version 0.9.4.1
-----------------------------
* Wien2k interface bug fix
Feb-20-2011: Version 0.9.4
-----------------------------
* Big phonopy-interface change was imposed. Some of filenames and
formats of input and output files are modified. **There is no
default setting filename** like ``INPHON`` (setting file is passed
as the first argument). Some of tag names and those usage are also
modified. Please first check :ref:`examples_link` for the new usage.
List of changes:
- Setting file has to be passed to phonopy as the first argunment.
- FORCES is replaced by FORCE_SETS (:ref:`file_forces`).
- DISP is replaced by disp.yaml.
- LSUPER tag is removed. Please use -d option.
- NDIM and MATDIM tags are replaced by DIM tag (:ref:`dimension_tag`).
- Band structure setting tags are changed to BAND tag
(:ref:`band_structure_related_tags`).
- DOS tag is renamed to DOS_RANGE tag (:ref:`dos_related_tags`).
These changes are applied only for the phonopy interface. Internal
simulation code has not been touched, so **physical results would not
be affected**. If you have any questions, please send e-mail to
phonopy :ref:`mailinglist`.
* ``phonopy-FHI-aims`` had not worked in some of previous
versions. Now it works by Jörg Meyer and Christian Carbogno.
* Directory structure of the code was changed.
* Symmetry finder update to spglib-1.0.2
* [**Experimental**] Finding Bravais lattice using
``--symmetry`` option.
* [**Experimental**] Modulated structure along specified phonon modes
by ``MODULATION`` tag (:ref:`modulation_tag`).
Jan-21-2011: Version 0.9.3.3
-----------------------------
* Animation file output update (:ref:`animation_tag`). The ``ANIME``
tag format was changed.
Jan-12-2011: Version 0.9.3.2
-----------------------------
* ``phonopy-qha`` is updated. A few options are added
(:ref:`phonopy_qha_options`). Calculation under pressure is
supported by ``--pressure`` option.
* Primitive cell search and Bravais lattice output are integrated into
the symmetry search with ``--symmetry`` option.
Errata of document
-----------------------------
* There were mistakes in the documents for the ``PRIMITIVE_AXIS`` and
``MATDIM``. The 9 values are read from the first three to
the last three as respective rows of the matrices defined.
Dec-30-2010: Version 0.9.3.1
-----------------------------
* Bug fix of ``-f`` option.
* The output filenames of ``phonopy-qha`` are modified and summarized
at :ref:`phonopy_qha_output_files`.
Dec-5-2010: Version 0.9.3
------------------------------------
* The license is changed to LGPL.
* ``MASS`` tag is recreated (:ref:`mass_tag`).
* ``--mp`` option is created. This works like the ``MP`` tag.
* Improvement of ``phonopy-qha`` both in the code and :ref:`manual
<phonopy_qha>`.
* The bug in ``--fco`` option was fixed.
Nov-26-2010: Version 0.9.2
------------------------------------
* spglib update (ver. 1.0.0)
* ASE.py is removed. Compatible class and functions, Atoms,
write_vasp, and read_vasp, are implemented.
* A ``vasprun.xml`` parser wrapper is implemened to avoid the broken
``PRECFOCK`` in vasprun.xml of VASP 5.2.8.
Sep-22-2010: Version 0.9.1.4
------------------------------------
* The new tag ``ANIME_TYPE`` supports ``xyz`` and ``xyz_jmol`` formats
by Jörg Meyer and Christian Carbogno, and also `A set of ``POSCAR``
files corresponding to animation frames.
* Fix bugs in ``trim_cell`` and
``Primitive.__supercell_to_primitive_map`` in ``cells.py``. When
:math:`M_s^{-1}M_p` is not symmetric, the supercell was not created
correctly.
* ``phonopy-FHI-aims`` update by jm.
Aug-24-2010: Version 0.9.1.3
------------------------------------
* Update symmetry finder of spglib. Now precision is in Cartesian distance.
* The animation output for ``arc`` didn't work. Now it works.
* Qpoint mode didn't work with bugs. Now it works.
* ``--vasp`` option is renamed to ``--cell`` or ``-c``.
* The new options ``--symmetry``, ``--displacement`` or ``-d``,
``--dim``, ``--primitive_axis`` are implemented.
* The option ``--ndim`` is replaced with ``--dim`` with ``-d`` option.
June-10-2010: Version 0.9.1.2
------------------------------------
* The code on non-analytical term correction is included in the
``DynamicalMatrix`` class. Data sets read by ``parse_BORN`` are set
by ``set_non_analytical_term`` and gotten by
``get_non_analytical_term``. The q-vector direction (only direction
is used in the non-analytical term correction) is set by
``set_q_non_analytical_term``. However for emprical damping
function, some distance is used, i.e., when a q-point is getting
away, non-analytical term is weaken. For this purpose, the second
argument of ``set_q_non_analytical_term`` is used.
At the same time, a small problem on the previous implementation was
found. When a reduced q-point is out of the first Brillouin zone,
it is not correctly handled. Currently it is fixed so as that when
absolute values of elements of the reduced q-point are over 0.5, they
are reduced into -0.5 < q < 0.5.
[**Attention**] The previous ``--nac`` option is moved to
``--nac_old``. ``--nac`` is used for different method of the
non-analytical term correction at general q-points. This will be
documented soon.
* Bug fix on ``write_FORCES`` in ``file_IO.py``. When order of
displacements in ``DISP`` file is not ascending order of atom indices,
it was not correctly re-ordered. Because the default order of
phonopy is ascending order, usually there is no problem for the most
users.
* ``phonopy-FHI-aims``
- adapted to extensions of dynamical_matrix with respect to
non-analytical corrections
- added support for animation infrastructure
- moved several options to control.in
by Jörg Meyer and Christian Carbogno
May-11-2010: Version 0.9.1.1
------------------------------------
* ``phonopy-FHI-aims`` adapted to split of dos array into the two
seperate omega, dos arrays in TotalDOS class by Jörg Meyer.
May-10-2010: Version 0.9.1
------------------------------------
* The methods of get_partial_DOS and get_total_DOS are added to the
Phonopy class.
Apr-12-2010: Version 0.9.0.2
------------------------------------
* spglib bug was fixed. If the crystal structure has non-standard origin,
the translation was not correctly handled. This problem happened
after version 0.9.0.
Apr-12-2010: Version 0.9.0.1
------------------------------------
* spglib update
Apr-10-2010: Version 0.9.0
------------------------------------
* Phonopy module (``__init.py__``) is heavily revised and the script
``phonopy`` is rewritten using the phonopy module. Therefore there
may be bugs. Be careful. Document of the phonopy module will be
updated gradually.
* A small Wien2k interface document is added (:ref:`wien2k_interface`).
* A script ``phonopy-FHI-aims`` and its examples are added by
Jörg Meyer.
* spglib update
Mar-10-2010: Version 0.7.4
------------------------------------
* spglib update
* Animation mode (:ref:`animation_tag`)
Feb-10-2010: Version 0.7.3
------------------------------------
* Bug fix for Wien2k mode
Jan-12-2010: Version 0.7.2
------------------------------------
* [**Experimental**] Non-analytical term correction
was implemented.
Dec-8-2009: Version 0.7.1 released
------------------------------------
* :ref:`auxiliary_tools` ``propplot`` is added.
* Memory consumption is reduced when using ``-f`` option to handle
large vasprun.xml files.
Nov-24-2009: Version 0.7.0 released
------------------------------------
* :ref:`auxiliary_tools` ``bandplot`` and ``pdosplot`` are prepared.
* Formats of `band.yaml`, `mesh.yaml`, and `qpoints.yaml` are slightly
modified.
* There was bug in ``PERMUTATION`` tag to calculate symmetrized force
constants. Now it is fixed. Usually this is not necessary to set
because this does not affect to result.
* Symmetry finder spglib is updated.
* ``PM`` tag is implemented. See :ref:`setting_tags`. Behaviors in
the previous versions are ``PM = AUTO``.
Oct-14-2009: Version 0.6.2 released
------------------------------------
* Installation process was changed slightly.
See :ref:`install`.
* The command ``phonopy`` is stored in the ``bin``
directory. ``phonopy.py`` is renamed to ``phonopy``.
* setup system is improved by Maxim V. Losev.
* ``--fz`` tag was implemented experimentally. This is supposed to
enable to subtract residual forces on atoms in equilibrium structure
from those in structure with atomic displacements.
.. |sflogo| image:: http://sflogo.sourceforge.net/sflogo.php?group_id=161614&type=1
:target: http://sourceforge.net
|sflogo|
Reference in New Issue View Git Blame Copy Permalink