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Release v3.3.3

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Atsushi Togo 2024-08-06 15:21:47 +09:00
parent 5f2fac89ad
commit 326b112679
8 changed files with 172 additions and 50 deletions
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8
doc/changelog.md
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@ -2,6 +2,14 @@
# Change Log
## Jul-22-2024: Version 3.3.3
- Provide functionality by `--cf3` and `--cf2` command options to create force
constants from displacement-force dataset of random displacements when
an external force constants calculator is specified.
- New command line options `--rd`, `--rd-fc2`, `--fc-calc`, `--fc-calc-opt` and
`--sp` to support random displacements.
## Jul-22-2024: Version 3.3.2
- Minor fix of `phono3py.load` function for reading displacements from

5
doc/command-options.md
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@ -174,6 +174,8 @@ created from `FORCES_FC2` and `phono3py_disp.yaml` instead of `FORCES_FC3` and
% phono3py --cfs --dim-fc2="x x x"
```
(sp_option)=
### `--sp` or `--save-params`
Instead of `FORCES_FC3`, `phono3py_params.yaml` is generated. This option must
@ -296,7 +298,7 @@ very accurate.
The default value depends on calculator. See
{ref}`default_displacement_distance_for_calculator`.
(fc_calculator_options_option)=
(fc_calculator_option)=
### `--fc-calc`, `--fc-calculator` (`FC_CALCULATOR`)
Choice of force constants calculator.
@ -313,6 +315,7 @@ Those for fc2 and fc3 are seprated by `|` such as `symfc|` . Blank means to
employ the finite difference method for systematic displacements generated by
the option `-d`.
(fc_calculator_options_option)=
### `--fc-calc-opt`, `--fc-calculator-options` (`FC_CALCULATOR_OPTIONS`)
Special options for force constants calculators.

2
doc/conf.py
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@ -60,7 +60,7 @@ copyright = "2015, Atsushi Togo"
# The short X.Y version.
version = "3.3"
# The full version, including alpha/beta/rc tags.
release = "3.3.2"
release = "3.3.3"
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.

6
doc/cutoff-pair.md
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@ -2,7 +2,11 @@
# Force constants calculation with cutoff pair-distance
Here the detail of the command option {ref}`--cutoff_pair <cutoff_pair_option>`
Since this calculation is a little bit tricky. It may be recommended to try
{ref}`random-displacements` with `--fc-calc-opt "cutoff = VAL"` before trying
this option.
Here the detail of the command option {ref}`--cutoff-pair <cutoff_pair_option>`
is explained.
<!-- See also reference {cite}`Mizokami-PRB-2018`. -->

91
doc/random-displacements.md
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@ -1,5 +1,5 @@
(random-displacements)=
# Randan displacements
# Force constants calculation with randan displacements of atoms
Random displacements and corresponding forces in supercells can be employed as a
displacement-force dataset for computing force constants. This requires an
@ -34,3 +34,92 @@ If random directional displacements for fc2 are expected, `--rd-fc2` and
```
where `--dim` is necessary but `--rd` is not.
## Create `FORCES_FC3` and `FORCES_FC2`
`FORCES_FC3` and optionally `FORCES_FC2`, which contains forces corresponding to
displacements, can be created by
```bash
% phono3py --cf3 vasprun_xmls/vasprun-00{001..100}.xml
```
Here it is assumed that the forces were calculated by VASP, and the output files
(`vasprun.xml`) are stored in `vasprun_xmls` directory after renaming. When
running this command, `phono3py_disp.yaml` is automatically read. For the
different file name, e.g. `phono3py_disp_rd.yaml`, it is specified with `-c`
option:
```bash
% phono3py -c phono3py_disp_rd.yaml --cf3 vasprun_xmls/vasprun-00{001..100}.xml
```
`FORCES_FC2` is created similarly, e.g., from the VASP output stored as
`vasprun_xmls/vasprun-ph000{1,2}.xml`,
```bash
% phono3py --cf2 vasprun_xmls/vasprun-ph000{1,2}.xml
```
## Create `phono3py_params.yaml`
Instead of creating `FORCES_FC3` and `FORCES_FC2`, more convenient data file to
store displacement-force dataset is created by `--sp` option:
```bash
% phono3py --cf3 vasprun_xmls/vasprun-00{001..100}.xml --cf2 vasprun_xmls/vasprun-ph0000{1,2}.xml --sp
```
The advantage to employ `phono3py_params.yaml` is that this file can contain all
the information required to run phono3py such as crystal structure, supercell
information, displacements, forces, and parameters for non-analytical term
correction. This file is immediately usable for `phono3py-load` command ({ref}`phono3py_load_command`).
## Calculation of force constants
If `phono3py_disp.yaml` is located in current directory, force constants are
calculated from `FORCES_FC3` (and optionally `FORCES_FC2`) and
`phono3py_disp.yaml` by
```bash
% phono3py --symfc -v
```
or with `phono3py_params.yaml`
```bash
% phono3py -c phono3py_params.yaml --symfc -v
```
Similarly, it is performed by also using `phono3py-load` command,
```bash
% phono3py-load --symfc -v
```
or
```bash
% phono3py-load phono3py_params.yaml --symfc -v
```
## Cutoff pair-distance for fc3 calculation
The number of supercells required for calculating fc3 depends on crystal
structure, crystal symmetry, and supercell size. For larger supercells, the
number can be very large. In addition, the required computational time and
memory space can also become large. In such case, it may be good to consider
introducing cutoff distance for pairs of atoms. It is performed by
`--fc-calc-opt` option as
```bash
% phono3py --symfc -v --fc-calc-opt "cutoff=8"
```
The shortcut of `--fc-calc-opt "cutoff=8"` is `--cutoff-pair 8`.
The convergence of fc3 has to be checked. With the same input of
displacement-force dataset, calculated force constants gradually converge by
increasing cutoff pair-distance. The convergence may be checked by lattice
thermal conductivity, but it may depend on quantity that is expected to be
calculated.

64
phono3py/cui/create_force_constants.py
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@ -168,14 +168,9 @@ def create_phono3py_force_constants(
if settings.read_fc2:
_read_phono3py_fc2(phono3py, symmetrize_fc2, input_filename, log_level)
else:
if phono3py.phonon_supercell_matrix is None:
force_filename = "FORCES_FC3"
else:
force_filename = "FORCES_FC2"
_create_phono3py_fc2(
phono3py,
ph3py_yaml,
force_filename,
symmetrize_fc2,
settings.is_compact_fc,
fc_calculator,
@ -219,20 +214,22 @@ def parse_forces(
"""
filename_read_from: Optional[str] = None
dataset = None
calculator = phono3py.calculator
# Get dataset from ph3py_yaml. dataset can be None.
# physical_units can be overwritten if calculator is found in ph3py_yaml.
dataset = _extract_dataset_from_ph3py_yaml(ph3py_yaml, fc_type)
if ph3py_yaml:
dataset = _extract_dataset_from_ph3py_yaml(ph3py_yaml, fc_type)
if dataset and ph3py_yaml.calculator:
calculator = ph3py_yaml.calculator
physical_units = get_default_physical_units(calculator)
if fc_type == "phonon_fc2":
natom = len(phono3py.phonon_supercell)
else:
if phono3py.phonon_supercell is None or fc_type == "fc3":
natom = len(phono3py.supercell)
else:
natom = len(phono3py.phonon_supercell)
if dataset:
filename_read_from = phono3py_yaml_filename
@ -269,20 +266,18 @@ def parse_forces(
assert dataset is not None
if "natom" in dataset and dataset["natom"] != natom:
msg = (
raise RuntimeError(
"Number of atoms in supercell is not consistent with "
'"%s".' % filename_read_from
f'"{filename_read_from}".'
)
raise RuntimeError(msg)
if log_level and filename_read_from is not None:
print(
'Displacement dataset for %s was read from "%s".'
% (fc_type, filename_read_from)
f'Displacement dataset for {fc_type} was read from "{filename_read_from}".'
)
# Overwrite dataset['cutoff_distance'] when necessary.
if cutoff_pair_distance:
if fc_type == "fc3" and cutoff_pair_distance:
if "cutoff_distance" not in dataset or (
"cutoff_distance" in dataset
and cutoff_pair_distance < dataset["cutoff_distance"]
@ -295,10 +290,10 @@ def parse_forces(
# dataset comes either from disp_fc*.yaml or phono3py*.yaml.
if not forces_in_dataset(dataset):
if force_filename is not None:
if fc_type == "phonon_fc2":
parse_FORCES_FC2(dataset, filename=force_filename)
else:
if fc_type == "fc3":
parse_FORCES_FC3(dataset, filename=force_filename)
else:
parse_FORCES_FC2(dataset, filename=force_filename)
if log_level:
print(
@ -452,10 +447,8 @@ def read_type2_dataset(natom, filename="FORCES_FC3", log_level=0) -> Optional[di
if len_first_line == 6:
dataset = get_dataset_type2(f, natom)
if log_level:
print(
"%d snapshots were found in %s."
% (len(dataset["displacements"]), "FORCES_FC3")
)
n_disp = len(dataset["displacements"])
print(f'{n_disp} snapshots were found in "{filename}".')
else:
dataset = None
return dataset
@ -663,7 +656,6 @@ def run_pypolymlp_to_compute_phonon_forces(
def _create_phono3py_fc2(
phono3py: Phono3py,
ph3py_yaml: Optional[Phono3pyYaml],
force_filename,
symmetrize_fc2,
is_compact_fc,
fc_calculator,
@ -675,6 +667,11 @@ def _create_phono3py_fc2(
force_filename is either "FORCES_FC2" or "FORCES_FC3".
"""
if phono3py.phonon_supercell_matrix is None:
force_filename = "FORCES_FC3"
else:
force_filename = "FORCES_FC2"
_ph3py_yaml = _get_default_ph3py_yaml(ph3py_yaml)
try:
@ -682,7 +679,7 @@ def _create_phono3py_fc2(
phono3py,
ph3py_yaml=_ph3py_yaml,
force_filename=force_filename,
fc_type="fc2",
fc_type="phonon_fc2",
log_level=log_level,
)
except RuntimeError as e:
@ -752,12 +749,13 @@ def _to_ndarray(array, dtype="double"):
return array
def _extract_dataset_from_ph3py_yaml(ph3py_yaml: Optional[Phono3pyYaml], fc_type):
dataset = None
if fc_type == "phonon_fc2":
if ph3py_yaml and ph3py_yaml.phonon_dataset is not None:
dataset = copy.deepcopy(ph3py_yaml.phonon_dataset)
def _extract_dataset_from_ph3py_yaml(
ph3py_yaml: Optional[Phono3pyYaml], fc_type
) -> Optional[dict]:
if ph3py_yaml.phonon_supercell is None or fc_type == "fc3":
if ph3py_yaml.dataset is not None:
return copy.deepcopy(ph3py_yaml.dataset)
else:
if ph3py_yaml and ph3py_yaml.dataset is not None:
dataset = copy.deepcopy(ph3py_yaml.dataset)
return dataset
if ph3py_yaml.phonon_dataset is not None:
return copy.deepcopy(ph3py_yaml.phonon_dataset)
return None

44
phono3py/cui/phono3py_script.py
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@ -517,11 +517,13 @@ def grid_addresses_to_grid_points(grid_addresses, bz_grid):
return bz_grid.grg2bzg[grid_points]
def create_supercells(
def create_supercells_with_displacements(
settings: Phono3pySettings,
cell_info: dict,
confs_dict: dict,
unitcell_filename: str,
interface_mode: Optional[str],
load_phono3py_yaml: bool,
symprec: float,
log_level: int,
):
@ -539,6 +541,16 @@ def create_supercells(
log_level=log_level,
)
store_nac_params(
phono3py,
settings,
cell_info["phonopy_yaml"],
unitcell_filename,
log_level,
nac_factor=Hartree * Bohr,
load_phonopy_yaml=load_phono3py_yaml,
)
if log_level:
if phono3py.supercell.magnetic_moments is None:
print("Spacegroup: %s" % phono3py.symmetry.get_international_table())
@ -971,8 +983,15 @@ def main(**argparse_control):
# Create supercells with displacements and then exit #
######################################################
if not settings.use_pypolymlp:
create_supercells(
settings, cell_info, confs_dict, interface_mode, symprec, log_level
create_supercells_with_displacements(
settings,
cell_info,
confs_dict,
unitcell_filename,
interface_mode,
load_phono3py_yaml,
symprec,
log_level,
)
#######################
@ -1091,15 +1110,16 @@ def main(**argparse_control):
##################################
# Non-analytical term correction #
##################################
store_nac_params(
phono3py,
settings,
cell_info["phonopy_yaml"],
unitcell_filename,
log_level,
nac_factor=Hartree * Bohr,
load_phonopy_yaml=load_phono3py_yaml,
)
if settings.is_nac:
store_nac_params(
phono3py,
settings,
cell_info["phonopy_yaml"],
unitcell_filename,
log_level,
nac_factor=Hartree * Bohr,
load_phonopy_yaml=load_phono3py_yaml,
)
###################
# Force constants #

2
phono3py/version.py
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@ -34,4 +34,4 @@
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
__version__ = "3.3.2"
__version__ = "3.3.3"