--tdm_cif) for CIF output for thermal displacement is added (TDISPMAT_CIF).
--fpicth) is made (FMIN, FMAX, and FPITCH).
phonopy_disp.yamlare written when running phonopy.
generate_displacementsmethod has to be called explicitely along with the
distanceargument. See Using phonopy as a python module.
qpoints.hdf5is written with the
--hdf5option. Dynamical matrices are also stored in
WRITEDM = .TRUE.(
--hdf5option. Some output files can be written in hdf5 format. See –hdf5.
--elkoption) was added (Elk & phonopy calculation).
MESH_SYMMETRY = .FALSE.(
--nomeshsym) when PDOS is invoked.
--pwscfoptions have been changed. Now they are just to invoke those calculator modes without a unit cell structure file. The unit cell structure file is specified using
-c) option or
CELL_FILENAMEtag. See Choice of force calculator, Wien2k & phonopy calculation, Abinit & phonopy calculation, and Pwscf & phonopy calculation.
--pwscfoptions are implemented. See Abinit, Pwscf, Wien2k, and CRYSTAL interfaces and Command options.
Supercellclass to build supercell
--fc_computation_algorithm="regression"to compute force constants from forces and displacements using linear regression with displaying standard deviation, by KL(m).
-voption shows Born effective charges and dielectric constants when NAC is set.
vasprun.xmlof VASP 5.2.8 is only specially parsed to treat special wrong character.
set_force_setswill be obsolete.
This version is dangerous. A lot of code is modified internally.
-voption is enriched.
outcar-bornis implemented (Experimental).
--cutoff_freq) is implemented to ignore frequencies lower than this cutoff frequency to calculate thermal properties and thermal displacements.
--massoption is created to shortcut of the
--fc_spg_symmetryoption is created to symmetrize force constants.
partial_dos.datformat was changed. XYZ projected PDOS is not output. Instead atom projected PDOS (sum of XYZ projected PDOS) is written. See Output files.
omega_somethingis changed to
gruneisendidn’t run because it didn’t follow the move of the
file_IO.pyfile location. This is fixed.
MP), q-points are automatically moved to inside first-Brillouin-zone.
MESH_SYMMETRY = .FALSE.) is disabled.
group_velocity/__init__.pyis moved to
hphonopy/file_IO.pyis moved to top directory.
harmonic/derivative_dynmat.py: Analytical derivatives of dynamical matrix
--pdosoption was created. This is same as
CHARACTER_TABLEwas renamed to
IRREPS(IRREPS), and the option of
--ctwas renamed to
--irrepsas well. To show Ir-representations along with characters,
--show_irrepsoption) 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.
thermal_displacement.pyis slightly modified for the preparation to include thermal displacement matrix.
--gvoption (Group velocity).
MODULATIONtag was modified. (Create modulated structure)
--animeoptions are prepared.
--writefcoption is implemented.
MODULATIONtag, phase factor for each mode can be specified as the third value of each mode in degrees.
get_modulationin Phonopy module were modified. The phase factor is now included in
Phonopywas 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
--bandoption is implemented.
--gamma_centeroption are implemented (MESH, MP, or MESH_NUMBERS).
phonopy-qhawas polished. Most of the code was moved to
Phonopy::get_band_structurewere modified. Instead of eigenvalues, frequencies are returned.
Phonopy::get_thermal_propertieswas changed as numpy arrays of temperatures, Helmhotlz free energies, entropies, and heat capacities at constant volume.
PartialDOSwere changed. Instead of eigenvalues, frequencies are used.
force_constants.pyto speed up.
--dimwith 9 elements.
--nomeshsymis available on the manual.
--readfcoption is implemented.
_phonopy.cto make implementations similar to the formulations often written in text books.
settings.pyis moved to
phonopy/cui/Phonopy. The configure parser from a file and options is modified.
MODULATIONtag was changed.
--nosymis available on the manual.
cells.pyby Jörg Meyer and Christian Carbogno.
The cell matrix definition of
Atoms class was transposed.
disp.yaml. Along this modification, supercells with displacements can be created solely from
FC_SYMMETRYis created (FC_SYMMETRY).
propplotis updated for the
The example of
FORCE_SETS was wrong and was fixed. The explanation
of the document is correct.
BAND, now comma
,can be used to disconnect the sequence of band paths (Band structure tags).
dispmanager, an auxiliary tool for modifying
disp.yaml, is developed (dispmanager).
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 Examples for the new usage.
List of changes:
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 Mailing list.
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
[Experimental] Modulated structure along specified phonon modes
MODULATION tag (Create modulated structure).
ANIMEtag format was changed.
phonopy-qhais updated. A few options are added (Options). Calculation under pressure is supported by
MATDIM. The 9 values are read from the first three to the last three as respective rows of the matrices defined.
phonopy-qhaare modified and summarized at Output files.
vasprun.xmlparser wrapper is implemened to avoid the broken
PRECFOCKin vasprun.xml of VASP 5.2.8.
xyz_jmolformats by Jörg Meyer and Christian Carbogno, and also A set of ``POSCAR` files corresponding to animation frames.
cells.py. When is not symmetric, the supercell was not created correctly.
phonopy-FHI-aimsupdate by jm.
arcdidn’t work. Now it works.
--vaspoption is renamed to
--ndimis replaced with
The code on non-analytical term correction is included in the
DynamicalMatrix class. Data sets read by
parse_BORN are set
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
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 is used for different method of the
non-analytical term correction at general q-points. This will be
Bug fix on
file_IO.py. When order of
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
by Jörg Meyer and Christian Carbogno
phonopy-FHI-aimsadapted to split of dos array into the two seperate omega, dos arrays in TotalDOS class by Jörg Meyer.
__init.py__) is heavily revised and the script
phonopyis rewritten using the phonopy module. Therefore there may be bugs. Be careful. Document of the phonopy module will be updated gradually.
phonopy-FHI-aimsand its examples are added by Jörg Meyer.
-foption to handle large vasprun.xml files.
PERMUTATIONtag to calculate symmetrized force constants. Now it is fixed. Usually this is not necessary to set because this does not affect to result.
PMtag is implemented. See Setting tags. Behaviors in the previous versions are
PM = AUTO.
phonopyis stored in the
phonopy.pyis renamed to
--fztag was implemented experimentally. This is supposed to enable to subtract residual forces on atoms in equilibrium structure from those in structure with atomic displacements.