phono3py 3.3.2__tar.gz → 3.3.4__tar.gz

{phono3py-3.3.2 → phono3py-3.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phono3py
-Version: 3.3.2
+Version: 3.3.4
 Summary: This is the phono3py module.
 Author-Email: Atsushi Togo <atztogo@gmail.com>
 License: Copyright (c) 2015-2024, Phonopy. All rights reserved.

phono3py-3.3.4/example/AlN-LDA/README.md

@@ -0,0 +1,69 @@
+This is the example of the wurtzite-type AlN phono3py calculation. The VASP code
+was used with 500 eV and LDA as XC functional. The experimental lattice
+parameters were used and the internal positions of atoms were relaxed by
+calculation. The 3x3x2 and 5x5x3 supercells were chosen for fc3 and fc2. The
+6x6x4, 2x2x2, 1x1x2 k-point sampling meshes with Gamma-centre in the basal plane
+and off-Gamma-centre along c-axis were employed for the unit cell, fc3
+supercell, and fc2 supercell, respectively. For the DFPT calculation of Born
+effective charges and dielectric constant, the 12x12x8 k-point sampling mesh
+with the similar shift was used.
+
+Then the forces were calculated with the above settings. `FORCES_FC3` and
+`FORCES_FC2` were created with subtracting residual forces of perfect supercell
+from all displaced supercell forces.
+
+Perfect and displaced supercells were created by
+
+```bash
+% phono3py --dim 3 3 2 -c POSCAR-unitcell -d
+```
+
+In the example directory, `FORCES_FC3` is compressed to `FORCES_FC3.xz`. After
+unzipping `FORCES_FC3.xz` (e.g., using `xz -d`), to obtain `fc3.hdf5` and
+`fc2.hdf5` using symfc (the results without using symfc, i.e., finite difference
+method, are shown at the bottom of this README)
+
+```bash
+% phono3py-load --symfc -v
+```
+
+Lattice thermal conductivity is calculated by
+
+```bash
+% phono3py-load --mesh 40 --br --ts 300
+```
+
+`kappa-m15158.hdf5` is written as the result. Parameters for non-analytical term
+correction (NAC) is automatically read from those stored in `phono3py_disp.yaml` or
+`BORN` file. The lattice thermal conductivity is calculated as k_xx=242.8 and
+k_zz=226.5 W/m-K at 300 K. Without NAC, k_xx=233.6 and k_zz=222.2.
+
+Use of larger supercell for fc2 may change the shape of phonon band structure.
+To see it, first regenerate `phono3py_disp.yaml` with `--dim-fc2` option,
+
+```bash
+% phono3py --dim 3 3 2 --dim-fc2 5 5 3 -c POSCAR-unitcell -d
+```
+
+Then re-create force constants and calculate thermal conductivity,
+
+```bash
+% phono3py-load --symfc -v
+% phono3py-load --br --mesh=40 --ts 300
+```
+
+If `phono3py_disp.yaml` is renamed to `phono3py_disp_dimfc2.yaml`, it can be
+specified at the first argument of `phono3py-load` command:
+
+```bash
+% phono3py-load phono3py_disp_dimfc2.yaml --symfc -v
+% phono3py-load phono3py_disp_dimfc2.yaml --br --mesh=40 --ts 300
+```
+
+k_xx=240.2 and k_zz=230.1 are obtained. In the case of this example, we can see
+that the larger fc2 supercell contributes little, which means that the 3x3x2
+supercell was good enough to obtain a good shape of phonon band structure.
+
+Using the finite difference method implemented in phono3py, lattice thermal
+conductivities are obtained as k_xx=251.2 and k_zz=233,4 without using the large
+fc2 supercell and k_xx=249.4 k_zz=236.9 using the large fc2 supercell.

{phono3py-3.3.2 → phono3py-3.3.4}/example/NaCl-alm/README.md

@@ -29,4 +29,4 @@ lattice thermal conductivity at 300 K is calculated by
 % phono3py-load phono3py_params_NaCl222.yaml.xz --mesh 50 --ts 300 --br
 ```
 
-The result is ~7.2 W/m-K at 300 K.
+The result is ~7.3 W/m-K at 300 K.

phono3py-3.3.4/example/NaCl-rd/README.md

@@ -0,0 +1,80 @@
+# Example of using random directional displacements
+
+## How to use symfc
+
+This example utilizes an NaCl calculation result from A. Togo and A. Seko, J.
+Chem. Phys. 160, 211001 (2024). Supercells of 2x2x2 and 4x4x4 conventional unit
+cells are chosen for the third-order force constants (fc3) and second-order
+force constants (fc2), respectively. Displacement-force datasets consisting of
+100 supercells for fc3 and 2 supercells for fc2 are extracted and stored in
+`phono3py_params_NaCl.yaml.xz`. Random directional displacements of a constant
+0.03 Angstrom are used.
+
+To calculate force constants, an external force constants calculator is
+necessary. Here, the symfc tool (available at https://github.com/symfc/symfc) is
+used, which can be easily installed via pip or conda.
+
+The `fc3.hdf5` and `fc2.hdf5` are computed using the command:
+
+```
+% phono3py-load phono3py_params_NaCl.yaml.xz --symfc -v
+```
+
+Lattice thermal conductivity (LTC) is calculated with the following command:
+
+```
+% phono3py-load phono3py_params_NaCl.yaml.xz --br --ts 300 --mesh 50
+```
+
+By this, LTC is obtained around 8.3 W/m-k.
+
+
+## How to use pypolymlp
+
+When supercell energies are included in `phono3py_params.yaml` like file, the
+polynomial machine learning potential (poly-MLP) by pypolymlp can be used to
+calculate fc3 by the following command:
+
+```bash
+% phono3py-load phono3py_params_NaCl.yaml.xz --pypolymlp --symfc --rd 400 -v
+```
+
+the procedure below is performed:
+
+1. Poly-MLPs are computed from the displacement-force dataset for fc3. This is
+   activated by `--pypolymlp` option.
+2. 800=400+400 supercells for random directional displacements are generated,
+   where 400+400 means 400 supercells with random displacements (u) and 400
+   supercells with opposite displacement vectors (-u). This is activated by
+   `--rd 400` option. The default displacement distance is 0.001 Angstrom in
+   `--pypolymlp` mode. Since random displacements are generated `--symfc` has to
+   be specified for fc3. In this example, random displacements are used for fc2,
+   too, `--symfc` is applied to both of fc3 and fc2. Without `--rd` option,
+   systematic displacements are generated, for which the option `--fc-calc "symfc|"`
+   has to be specified instead of `--symfc` (equivalent to `--fc-calc "symfc|symfc")`).
+3. Forces on atoms in these 800 supercells are calculated using poly-MLP.
+4. Force constants are calculated.
+
+
+The `fc3.hdf5` and `fc2.hdf5` are obtained. Using these force constants, LTC is
+calculated by
+
+```bash
+% phono3py-load phono3py_params_NaCl.yaml.xz --br --ts 300 --mesh 50
+```
+
+and the LTC value of around 8.2 W/m-k is obtained.
+
+## Generating phono3py_params.yaml from vasprun.xml's
+
+`phono3py_params.yaml` is generated from
+
+```bash
+% phono3py phono3py_disp.yaml --cf3 NaCl-vasprun/vasprun-{00001..00100}.xml --cf2 NaCl-vasprun/vasprun-ph0000{1,2}.xml --sp
+```
+
+This command reads electronic energies of supercells from `vasprun.xml`s and
+writes them into `phono3py_params.yaml`, too. Here, `phono3py_disp.yaml` is not
+included in this example, but `phono3py_params_NaCl.yaml.xz` can be used to run
+this example since corresponding information of displacements is included in
+this file, too.

{phono3py-3.3.2 → phono3py-3.3.4}/example/Si-CRYSTAL/README

@@ -23,7 +23,7 @@ for the CRYSTAL interface, so the -c crystal.o parameter is not needed
 
 4) Create force constant files fc2.hdf5 and fc3.hdf5:
 
-   phono3py --crystal --dim="2 2 2" --dim-fc2="4 4 4" --sym-fc
+   phono3py --crystal --dim="2 2 2" --dim-fc2="4 4 4" --fc-symmetry
 
 5) Thermal conductivity calculation:
 

{phono3py-3.3.2 → phono3py-3.3.4}/example/Si-LDA/README.md

@@ -13,18 +13,18 @@ conventional unit cell to the primitive cell.
 To create `fc3.hdf5` and `fc2.hdf5`,
 
 ```
-% phono3py --sym-fc
+% phono3py-load
 ```
 
 Using 11x11x11 sampling mesh, lattice thermal conductivity is calculated by
 
 ```
-% phono3py --mesh 11 11 11 --fc3 --fc2 --br
+% phono3py-load --mesh 11 11 11 --br --ts 300
 ```
 
 `kappa-m111111.hdf5` is written as the result. The lattice thermal conductivity
-is calculated as 112.5 W/m-K at 300 K. This becomes, with 19x19x19 sampling
-mesh, 127.0 W/m-K.
+is calculated as 112.4 W/m-K at 300 K. This becomes, with 19x19x19 sampling
+mesh, 128.2 W/m-K.
 
 Accumulated lattice thermal conductivity is calculated using `phono3py-kaccum`
 script.

{phono3py-3.3.2 → phono3py-3.3.4}/example/Si-PBE/README.md

@@ -13,18 +13,18 @@ conventional unit cell to the primitive cell.
 To create `fc3.hdf5` and `fc2.hdf5`,
 
 ```
-% phono3py --sym-fc
+% phono3py-load
 ```
 
 Using 11x11x11 sampling mesh, lattice thermal conductivity is calculated by
 
 ```
-% phono3py --mesh 11 11 11 --fc3 --fc2 --br
+% phono3py-load --mesh 11 11 11 --fc3 --fc2 --br
 ```
 
 `kappa-m111111.hdf5` is written as the result. The lattice thermal conductivity
-is calculated as 119.3 W/m-K at 300 K. This becomes, with 19x19x19 sampling
-mesh, 132.4 W/m-K.
+is calculated as 119.5 W/m-K at 300 K. This becomes, with 19x19x19 sampling
+mesh, 130.1 W/m-K.
 
 Accumulated lattice thermal conductivity is calculated using `phono3py-kaccum`
 script.

{phono3py-3.3.2 → phono3py-3.3.4}/example/Si-PBEsol/README.md

@@ -13,18 +13,18 @@ the conventional unit cell to the primitive cell.
 To create `fc3.hdf5` and `fc2.hdf5`,
 
 ```
-% phono3py --sym-fc
+% phono3py-load
 ```
 
 Using 11x11x11 sampling mesh, lattice thermal conductivity is calculated by
 
 ```
-% phono3py --mesh 11 11 11 --fc3 --fc2 --br
+% phono3py-load --mesh 11 11 11 --br
 ```
 
 `kappa-m111111.hdf5` is written as the result. The lattice thermal conductivity
-is calculated as 109.0 W/m-K at 300 K. This becomes, with 19x19x19 sampling
-mesh, 123.2 W/m-K.
+is calculated as 109.1 W/m-K at 300 K. This becomes, with 19x19x19 sampling
+mesh, 124.4 W/m-K.
 
 Accumulated lattice thermal conductivity is calculated using `phono3py-kaccum`
 script.
@@ -80,11 +80,11 @@ In this example directory, the dataset is renamed to
 at `vasprun_xml_fc2/disp-fc2-00001/vasprun.xml`. `FORCES_FC2` is generated by
 
 ```
-% phono3py phono3py_disp_dimfc2.yaml --cf2 vasprun_xml_fc2/disp-fc2-00001/vasprun.xml
+% phono3py -c phono3py_disp_dimfc2.yaml --cf2 vasprun_xml_fc2/disp-fc2-00001/vasprun.xml
 ```
 
 A lattice thermal conductivity calculation is performed by, e.g.,
 ```
 % phono3py-load phono3py_disp_dimfc2.yaml --mesh 11 11 11 --br --ts 300
 ```
-The result is 108.0 W/m-K, and with the 19x19x19 mesh, 125.4 W/m-K.
+The result is 107.9 W/m-K, and with the 19x19x19 mesh, 125.4 W/m-K.

{phono3py-3.3.2 → phono3py-3.3.4}/example/Si-QE/README.md

@@ -13,18 +13,18 @@ the conventional unit cell to the primitive cell.
 To create `fc3.hdf5` and `fc2.hdf5`,
 
 ```
-% phono3py --sym-fc
+% phono3py-load
 ```
 
 Using 11x11x11 sampling mesh, lattice thermal conductivity is calculated by
 
 ```
-% phono3py --mesh 11 11 11 --fc3 --fc2 --br
+% phono3py-load --mesh 11 11 11 --br --ts 300
 ```
 
 `kappa-m111111.hdf5` is written as the result. The lattice thermal conductivity
-is calculated as 118.9 W/m-K at 300 K. This becomes, with 19x19x19 sampling
-mesh, 129.9 W/m-K.
+is calculated as 121.3 W/m-K at 300 K. This becomes, with 19x19x19 sampling
+mesh, 135.4 W/m-K.
 
 The .out files for supercells are found in `supercell_out.tar.lzma`. If phono3py
 is properly installed, the following command should work.

{phono3py-3.3.2 → phono3py-3.3.4}/phono3py/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '3.3.2'
-__version_tuple__ = version_tuple = (3, 3, 2)
+__version__ = version = '3.3.4'
+__version_tuple__ = version_tuple = (3, 3, 4)

{phono3py-3.3.2 → phono3py-3.3.4}/phono3py/api_phono3py.py

@@ -1487,6 +1487,9 @@ class Phono3py:
             fc2 = None
         if fc_calculator_options is not None and "|" in fc_calculator_options:
             fc2 = None
+        # fc2 should not be set if phonon_supercell_matrix is available.
+        if self._phonon_supercell_matrix is not None:
+            fc2 = None
 
         # Normally self._fc2 is overwritten in produce_fc2
         if self._fc2 is None:
@@ -1527,6 +1530,9 @@ class Phono3py:
         else:
             disp_dataset = self._phonon_dataset
 
+        if not forces_in_dataset(disp_dataset):
+            raise RuntimeError("Forces are not set in the dataset.")
+
         if is_compact_fc:
             p2s_map = self._phonon_primitive.p2s_map
         else:
@@ -1548,10 +1554,7 @@ class Phono3py:
             )
         else:
             if "displacements" in disp_dataset:
-                msg = (
-                    "fc_calculator has to be set to produce force "
-                    "constans from this dataset for fc2."
-                )
+                msg = "fc_calculator to solve fc2 has to be set."
                 raise RuntimeError(msg)
             self._fc2 = get_phonopy_fc2(
                 self._phonon_supercell,