1.. _changelog:
2
3Change Log
4==========
5
6Mar-17-2021: Version 1.22.3
7---------------------------
8- Fix ``--read-gamma`` option to work.
9
10Feb-21-2021: Version 1.22.2
11---------------------------
12- Fix PyPI source distribution package
13
14Feb-21-2021: Version 1.22.1
15---------------------------
16- ``phono3py`` command didn't work. This was fixed.
17- Fix behaviour when specifying ``--thm`` and ``--sigma`` simultaneously.
18
19Jan-29-2021: Version 1.22.0
20---------------------------
21- Maintenance release to follow phonopy v2.9.0.
22
23Sep-30-2020: Version 1.21.0
24---------------------------
25
26- Maintenance release to follow the change of phonopy at v2.8.1
27- Improvements of phono3py loader (``phono3py.load``), ``phono3py-load``
28  command, API, and ``phono3py_disp.yaml``.
29- Harmonic phonon calculation on mesh was multithreaded. This is
30  effective when using very dense mesh with non-analytical term
31  correction (probably rare case).
32- Real and imaginary parts of self energy and spectral function of
33  bubble diagram at API level
34
35Mar-3-2020: Version 1.20.0
36--------------------------
37
38- ``phono3py_disp.yaml`` is made when creating displacements in
39  addition to ``disp_fc3.yaml`` and
40  ``disp_fc2.yaml``. ``phono3py_disp.yaml`` will be used instead of
41  ``disp_fc3.yaml`` and ``disp_fc2.yaml`` in the future major release
42  (v2.0).
43
44Mar-3-2020: Version 1.19.1
45--------------------------
46
47- Release for pypi and conda (atztogo channel) packagings
48
49Mar-2-2020: Version 1.19.0
50--------------------------
51
52- Improvements of phono3py loader and API.
53- Improvement of interfaces to calculators. Now it is expected to be
54  much easier to implement calculator interface if it exists in
55  phonopy.
56- Fixed dependency to phonopy v2.6.0.
57
58Dec-22-2019: Version 1.18.2
59---------------------------
60
61- Initial version of phono3py loader (``phono3py.load``) was
62  implemented. See docstring of ``phono3py.load``.
63
64Oct-17-2019: Version 1.18.1
65---------------------------
66
67- Fix of phono3py-kaccum to follow the latest phonopy.
68
69Oct-9-2019: Version 1.18.0
70---------------------------
71
72- Maintenance release
73
74Apr-18-2019: Version 1.17.0
75---------------------------
76- ``--cfz`` option was made to subtract residual forces. See
77  :ref:`cfz_option`.
78- ``--cutoff-pair`` was made to override the cutoff pair distance
79  written in ``disp_fc3.yaml`` when using on calculating force
80  constants. This is useful when checking cutoff distance
81  dependency. So the use case of having fully computed ``FORCES_FC3``
82  is assumed.
83- TURBOMOLE interface is provided by Antti Karttunen
84  (``--turbomole``).
85- Compatibility of ``fc2.hdf5`` and ``force_constants.hdf5`` was
86  improved for all calculators to store physical unit information in
87  the hdf5 file. See :ref:`file_format_compatibility`.
88
89Mar-24-2019: Version 1.16.0
90---------------------------
91- Bug fixes and catching up the updates of phonopy.
92- Most of hdf5 output files are compressed by ``gzip`` as
93  default. This compression can be set off, see
94  :ref:`hdf5_compression_option`.
95- (Experimental) ``phono3py`` command accepts ``phono3py.yaml`` type
96  file as an input crystal structure by ``-c`` option. When ``DIM``
97  and any structure file are not given, ``phono3py_disp.yaml``
98  (primary) or ``phono3py.yaml`` (secondary) is searched in the current
99  directory. Then ``phono3py.yaml`` type file is used as the input.
100  By this, semi-automatic phono3py mode is invocked, which acts as
101
102  (1) ``supercell_matrix`` corresponding to ``DIM`` in the
103      ``phono3py.yaml`` type file is used if it exists.
104  (2) ``phonon_supercell_matrix``  corresponding to ``DIM_FC2`` in the
105      ``phono3py.yaml`` type file is used if it exists.
106  (3) ``primitive_matrix`` in the ``phono3py.yaml`` type file
107      is used if it exists. Otherwise, set ``PRIMITIVE_AXES = AUTO``
108      when ``PRIMITIVE_AXES`` is not given.
109  (4) NAC params are read (``NAC = .TRUE.``) if NAC params are
110      contained (primary) in the ``phono3py.yaml`` type file or if
111      ``BORN`` file exists in the current directory (secondary).
112
113Nov-22-2018: version 1.14.3
114----------------------------
115- Update to work with phonopy v1.14.2.
116- Ph-ph interaction can be read (``--read-pp``) and write
117  (``--write-pp``) in RTA thermal conductivity calculation, too. Mind
118  that the data stored are different with and without
119  ``--full-pp``. Wihtout ``--full-pp`` the data are stored in
120  complicated way to save data side, so it is not considered readable
121  by usual users.
122
123June-20-2018: version 1.13.3
124----------------------------
125
126- ``--lw`` (linewidth) option was removed. Use ``--br`` option and
127  find 2*gamma values as linewidths in ``kappa-xxx.hdf5`` file.
128- Documentation of ``--lbte`` option is available at
129  :ref:`direct_solution`.
130- This version is dependent on phonopy>=1.13.2.
131
132May-17-2018: version 1.13.1
133----------------------------
134
135- Compact force constants are implemented (See :ref:`compact_fc_option`).
136
137Mar-16-2018: version 1.12.9
138----------------------------
139
140- Definition of ``mode_kappa`` values in output hdf5 file is
141  changed. Previously they were divided by number of grid points, but
142  now not. Therefore users who compute ``kappa`` from ``mode_kappa``
143  need to be careful about this change. This does not affect to
144  ``phono3py-kaccum`` results.
145
146Feb-1-2018: version 1.12.7
147----------------------------
148
149- ``--tsym`` option is removed. Now with ``--sym-fc3r`` and
150  ``--sym-fc2`` options,
151  translational invariance symmetry is also applied.
152- ``--sym-fc`` option is added. This is just an alias to specify both
153  ``--sym-fc3r`` and ``--sym-fc2`` together.
154- Documentation on ``--write-phonon`` and ``--read-phonon`` options is
155  written. These options are used to save harmonic phonon infromation
156  on strage.
157
158Nov-22-2017: version 1.12.5
159-----------------------------
160
161- Bug fix of RTA thermal conductivity. This bug exists from version
162  1.10.11.18 (git e40cd059). This bug exhibits when all the following
163  conditions are met:
164
165  1. RTA thermal conductivity calculation.
166  2. Tetrahedron method for Brillouin zone integration is used.
167  3. Number of triplets is smaller than number of bands at each grid point.
168  4. Without using ``--full-pp``.
169
170
171  (3) happens when the primitive cell is relatively large. Number of
172  triplets can be shown using ``--stp`` option. A race condition of
173  OpenMP multithreading is the source of the bug. Therefore, if it
174  occurs, the same calculation comes up with the different thermal
175  conductivity value in every run time, for whcih it behaves like
176  randomly.
177
178- RTA thermal conductivity with smearing method (``--sigma``) is made
179  to run with smaller memory consumption as similar as tetrahedron
180  method (``--thm``).
181
182Nov-17-2017: version 1.12.3
183----------------------------
184
185- Command option parser of the phonopy tools is replaced from
186  ``optparse`` to ``argparse``.
187- The filenames used with these options were the positional arguments
188  previously. Now they are the command-line arguments, i.e., filenames
189  have to be put just after the option name like ``-f vasprun.xml-001
190  vasprun.xml-002 ...``.
191- The names of auxiliary tools (``kdeplot`` and ``kaccum``) are
192  changed, for which the prefix phono3py- is added to the old names to
193  avoid accidental conflict with other script names already existing
194  under bin directory.
195- :ref:`sigma_cutoff_option` option was created.
196
197Jun-18-2017: version 1.11.13
198----------------------------
199
200- :ref:`normal_umklapp_option` option was made.
201- Many minor updates: fixing bugs, improving usabilities.
202- Improve of :ref:`auxiliary_tools_kaccum` and :ref:`auxiliary_tools_kdeplot`.
203
204Mar-31-2017: version 1.11.11
205----------------------------
206
207- Abinit code interface is implemented and now under the testing.
208- Reduction of memory usage in RTA thermal conductivity
209  calculation. This is especially effective for larger unit cell
210  case. Currently combinations with --full_pp, --write_gamma_detail,
211  and --simga(smearing method) are not supported for this. Performance
212  tuning is under going. In some case, computation can be slower than
213  the previous versions.
214
215Feb-9-2017: version 1.11.9
216---------------------------
217
218- This version works coupled with phonopy-1.11.8 or later.
219- CRYSTAL code interface is implemented by Antti J. Karttunen.
220
221Dec-14-2016: version 1.11.7
222------------------------------
223
224- This is a maintenance release. This version must be used with
225  phonopy-1.11.6 or later.
226
227Nov-27-2016: version 1.11.5
228------------------------------
229
230- ``gaccum`` is merged to ``kaccum``. ``gaccum`` is removed. See
231  :ref:`auxiliary_tools_kaccum`.
232- ``kdeplot`` is added. See :ref:`auxiliary_tools_kdeplot`.
233
234Apr-24-2016: version 1.10.9
235------------------------------
236
237- Failure of writing ``kappa-mxxx-gx.hdf5`` was fixed.
238
239Apr-16-2016: version 1.10.7
240------------------------------
241
242- API example is prepared and it is found in ``Si`` example. No
243  doucment yet.
244- Si pwscf example was placed in ``example-phono3py`` directory.
245- User interface bug fix.
246
247Mar-15-2016: version 1.10.5
248------------------------------
249
250- Numbering way of phono3py version was just changed (No big updates
251  were made against previous version.) The number is given based on
252  the phonopy version. For example, the harmonic part of
253  phono3py-1.10.5 is based on the code close to phonopy-1.10.4.
254- Python3 support
255- For the RTA thermal conductivity calculation mode with using the
256  linear tetrahedron method, only necessary part of phonon-phonon
257  interaction strengh among phonons. This improves lifetime
258  calculation performance, but as the drawback, averaged ph-ph
259  interaction strength can not be given. See :ref:`full_pp_option`.
260- Pwscf interface (:ref:`calculator_interfaces`)
261
262Oct-10-2015: version 0.9.14
263------------------------------
264
265- Computational performance tuning for phonon-phonon interaction
266  strength calculation was made by Jonathan Skelton. Depending on
267  systems, but 10-20% performance improvement may be possible.
268- ``--stp`` option is created to show numbers of q-point triplets to
269  be calculated. See :ref:`command_options`.
270- ``--write_gamma`` and ``--read_gamma`` support using with ``--bi``
271  option. Therefore a thermal conductivity calculation can be
272  distributed over band index, too. This may be useful for the system
273  whose unit cell is large.
274
275Sep-26-2015: version 0.9.13
276------------------------------
277
278- Changed so that ``--wgp`` option writes ``grid_address-mxxx.hdf5``
279  instead of ``grid_address-mxxx.dat``.
280- ``--write_detailed_gamma`` is implemented. See :ref:`command_options`.
281- When running without setting ``--thm`` and ``--sigma`` options,
282  linear tetrahedron method corresponding to ``--thm`` is used as the
283  default behavior.
284- ``--ise`` options is created.
285
286Aug-12-2015: version 0.9.12
287------------------------------
288
289- Spglib update to version 1.8.2.1.
290- Improve computational performance of ``kaccum`` and ``gaccum``.
291
292Jun-18-2015: version 0.9.10.1
293------------------------------
294
295- Bug fix of ``gcaccum``
296
297Jun-17-2015: version 0.9.10
298----------------------------
299
300- Fix bug in ``kaccum``. When using with ``--pa`` option, irreducible
301  q-points were incorrectly indexed.
302- ``gaccum`` is implemented. ``gaccum`` is very similar to ``kaccum``,
303  but for :math:`\Gamma_\lambda(\omega_\lambda)`.
304- spglib update.
305
306Changes in version 0.9.7
307-------------------------
308
309- The definition of MSPP is modified so as to be averaged ph-ph
310  interaction defined as :math:`P_{\mathbf{q}j}` in the arXiv
311  manuscript. The key in the kappa hdf5 file is changed from ``mspp``
312  to ``ave_pp``. The physical unit of :math:`P_{\mathbf{q}j}` is set
313  to :math:`\text{eV}^2`.
314
315Changes in version 0.9.6
316------------------------
317
318- Silicon example is put in ``example-phono3py`` directory.
319- Accumulated lattice thermal conductivity is calculated by ``kaccum``
320  script.
321- JDOS output format was changed.
322
323Changes in version 0.9.5
324-------------------------
325
326- In ``kappa-xxx.hdf5`` file, ``heat_capacity`` format was changed
327  from ``(irreducible q-point, temperature, phonon band)`` to
328  ``(temperature, irreducible q-point, phonon band)``. For ``gamma``,
329  previous document was wrong in the array shape. It is
330  ``(temperature, irreducible q-point, phonon band)``
331
332
333Changes in version 0.9.4
334------------------------
335
336- The option of ``--cutoff_mfp`` is renamed to ``--boundary_mfp`` and
337  now it's on the document.
338- Detailed contribution of ``kappa`` at each **q**-point and phonon
339  mode is output to .hdf5 with the keyword ``mode_kappa``.
340
341Changes in version 0.8.11
342-------------------------
343
344- A new option of ``--cutoff_mfp`` for including effective boundary
345  mean free path.
346- The option name ``--cutfc3`` is changed to ``--cutoff_fc3``.
347- The option name ``--cutpair`` is changed to ``--cutoff_pair``.
348- A new option ``--ga`` is created.
349- Fix spectrum plot of joint dos and imaginary part of self energy
350
351Changes in version 0.8.10
352-------------------------
353
354- Different supercell size of fc2 from fc3 can be specified using
355  ``--dim_fc2`` option.
356- ``--isotope`` option is implemented. This is used instead of
357  ``--mass_variances`` option without specifying the values. Mass
358  variance parameters are read from database.
359
360Changes in version 0.8.2
361------------------------
362
363- Phono3py python interface is rewritten and a lot of changes are
364  introduced.
365- ``FORCES_SECOND`` and ``FORCES_THIRD`` are no more used. Instead just
366  one file of ``FORCES_FC3`` is used. Now ``FORCES_FC3`` is generated
367  by ``--cf3`` option and the backward compatibility is simple: ``cat
368  FORCES_SECOND FORCES_THIRD > FORCES_FC3``.
369- ``--multiple_sigmas`` is removed. The same behavior is achieved by
370  ``--sigma``.
371
372Changes in version 0.8.0
373------------------------
374
375- ``--q_direction`` didn't work. Fix it.
376- Implementation of tetrahedron method whcih is activated by
377  ``--thm``.
378- Grid addresses are written out by ``--wgp`` option.
379
380Changes in version 0.7.6
381------------------------
382
383- Cut-off distance for fc3 is implemented. This is activated by
384  ``--cutfc3`` option. FC3 elements where any atomic pair has larger
385  distance than cut-off distance are set zero.
386- ``--cutpair`` works only when creating displacements. The cut-off
387  pair distance is written into ``disp_fc3.yaml`` and FC3 is created
388  from ``FORCES_THIRD`` with this information. Usually sets of pair
389  displacements are more redundant than that needed for creating fc3
390  if index permutation symmetry is considered. Therefore using index
391  permutation symmetry, some elements of fc3 can be recovered even if
392  some of supercell force calculations are missing. In paticular, all
393  pair distances among triplet atoms are larger than cutoff pair
394  distance, any fc3 elements are not recovered, i.e., the element will
395  be zero.
396
397Changes in version 0.7.2
398------------------------
399
400- Default displacement distance is changed to 0.03.
401- Files names of displacement supercells now have 5 digits numbering,
402  ``POSCAR-xxxxx``.
403- Cutoff distance between pair displacements is implemented. This is
404  triggered by ``--cutpair`` option. This option works only for
405  calculating atomic forces in supercells with configurations of pairs
406  of displacements.
407
408Changes in version 0.7.1
409------------------------
410
411- It is changed to sampling q-points in Brillouin zone. Previously
412  q-points are sampled in reciprocal primitive lattice. Usually this
413  change affects very little to the result.
414- q-points of phonon triplets are more carefully sampled when a
415  q-point is on Brillouin zone boundary. Usually this
416  change affects very little to the result.
417- Isotope effect to thermal conductivity is included.
418
419Changes in version 0.6.0
420------------------------
421
422- ``disp.yaml`` is renamed to ``disp_fc3.yaml``. Old calculations with
423  ``disp.yaml`` can be used without any problem just by changing the
424  file name.
425- Group velocity is calculated from analytical derivative of dynamical
426  matrix.
427- Group velocities at degenerate phonon modes are better handled.
428  This improves the accuracy of group velocity and thus for thermal
429  conductivity.
430- Re-implementation of third-order force constants calculation from
431  supercell forces, which makes the calculation much faster
432- When any phonon of triplets can be on the Brillouin zone boundary, i.e.,
433  when a mesh number is an even number, it is more carefully treated.
434