Release v3.3.3

phonopy · Aug 6, 2024 · 326b112 · 326b112
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diff --git a/doc/changelog.md b/doc/changelog.md
@@ -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

diff --git a/doc/command-options.md b/doc/command-options.md
@@ -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.

diff --git a/doc/conf.py b/doc/conf.py
@@ -60,7 +60,7 @@
 # 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.

diff --git a/doc/cutoff-pair.md b/doc/cutoff-pair.md
@@ -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`. -->

diff --git a/doc/random-displacements.md b/doc/random-displacements.md
@@ -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.
diff --git a/phono3py/cui/create_force_constants.py b/phono3py/cui/create_force_constants.py
@@ -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,
@@ -675,14 +667,19 @@ 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:
         dataset = parse_forces(
             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
diff --git a/phono3py/cui/phono3py_script.py b/phono3py/cui/phono3py_script.py
@@ -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 #

diff --git a/phono3py/version.py b/phono3py/version.py
@@ -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"