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Merge pull request #332 from phonopy/refactoring
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Refactor CUI for using pypolymlp
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@atztogo
atztogo authored Jan 15, 2025
2 parents 4ac2d78 + bbd2380 commit 394e7e0
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56 changes: 28 additions & 28 deletions doc/pypolymlp.md
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Original file line number Diff line number Diff line change
Expand Up @@ -162,16 +162,16 @@ crystal symmetry.
Having `phono3py_params.yaml`, phono3py is executed with `--pypolymlp` option,

```
% phono3py-load --pypolymlp phono3py_params.yaml
% phono3py-load phono3py_params.yaml --pypolymlp -d
_ _____
_ __ | |__ ___ _ __ ___|___ / _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ |_ \| '_ \| | | |
| |_) | | | | (_) | | | | (_) |__) | |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, |
|_| |_| |___/
3.5.0
3.11.2
-------------------------[time 2024-09-19 15:20:27]-------------------------
-------------------------[time 2025-01-15 16:25:17]-------------------------
Compiled with OpenMP support (max 10 threads).
Running in phono3py.load mode.
Python version 3.12.6
Expand All @@ -187,7 +187,6 @@ Primitive matrix:
Spacegroup: Fm-3m (225)
Use -v option to watch primitive cell, unit cell, and supercell structures.
NAC parameters were read from "phono3py_params.yaml".
----------------------------- Force constants ------------------------------
Displacement dataset for fc3 was read from "phono3py_params.yaml".
----------------------------- pypolymlp start ------------------------------
Pypolymlp is a generator of polynomial machine learning potentials.
Expand All @@ -204,16 +203,17 @@ Clear training X.T @ X
Calculate X.T @ X for test data
Clear test X.T @ X
Regression: model selection ...
- alpha = 1.000e-03 : rmse (train, test) = 9.39542e+14 9.39543e+14
- alpha = 1.000e-02 : rmse (train, test) = 9.39542e+14 9.39543e+14
- alpha = 1.000e-01 : rmse (train, test) = 0.03738 0.04961
- alpha = 1.000e+00 : rmse (train, test) = 0.03900 0.04742
- alpha = 1.000e+01 : rmse (train, test) = 0.04058 0.04584
- alpha = 1.000e-03 : rmse (train, test) = 1.12211e+15 1.12211e+15
- alpha = 1.000e-02 : rmse (train, test) = 1.12211e+15 1.12211e+15
- alpha = 1.000e-01 : rmse (train, test) = 0.00002 0.00002
- alpha = 1.000e+00 : rmse (train, test) = 0.00002 0.00002
- alpha = 1.000e+01 : rmse (train, test) = 0.00002 0.00002
MLPs were written into "phono3py.pmlp"
------------------------------ pypolymlp end -------------------------------
Generate displacements
Displacement distance: 0.001
Evaluate forces in 292 supercells by pypolymlp
----------------------------- Force constants ------------------------------
Computing fc3[ 1, x, x ] using numpy.linalg.pinv.
Displacements (in Angstrom):
[ 0.0010 0.0000 0.0000]
Expand All @@ -225,14 +225,14 @@ Displacements (in Angstrom):
Expanding fc3.
fc3 was symmetrized.
fc2 was symmetrized.
Max drift of fc3: -0.000000 (zzz) -0.000000 (zzz) -0.000000 (zzz)
Max drift of fc2: -0.000000 (zz) -0.000000 (zz)
Max drift of fc3: 0.000000 (xxx) 0.000000 (xxx) 0.000000 (xxx)
Max drift of fc2: 0.000000 (yy) 0.000000 (yy)
fc3 was written into "fc3.hdf5".
fc2 was written into "fc2.hdf5".
----------- None of ph-ph interaction calculation was performed. -----------
Dataset generated using MLPs was written in "phono3py_mlp_eval_dataset.yaml".
Summary of calculation was written in "phono3py.yaml".
-------------------------[time 2024-09-19 15:21:41]-------------------------
-------------------------[time 2025-01-15 16:26:37]-------------------------
_
___ _ __ __| |
/ _ \ '_ \ / _` |
Expand Down Expand Up @@ -269,9 +269,9 @@ Having `phono3py_params.yaml`, phono3py is executed with `--pypolymlp` option,
| |_) | | | | (_) | | | | (_) |__) | |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, |
|_| |_| |___/
3.5.0
3.11.2
-------------------------[time 2024-09-19 15:33:23]-------------------------
-------------------------[time 2025-01-15 16:43:57]-------------------------
Compiled with OpenMP support (max 10 threads).
Running in phono3py.load mode.
Python version 3.12.6
Expand All @@ -287,7 +287,6 @@ Primitive matrix:
Spacegroup: Fm-3m (225)
Use -v option to watch primitive cell, unit cell, and supercell structures.
NAC parameters were read from "phono3py_params.yaml".
----------------------------- Force constants ------------------------------
Displacement dataset for fc3 was read from "phono3py_params.yaml".
----------------------------- pypolymlp start ------------------------------
Pypolymlp is a generator of polynomial machine learning potentials.
Expand All @@ -304,39 +303,40 @@ Clear training X.T @ X
Calculate X.T @ X for test data
Clear test X.T @ X
Regression: model selection ...
- alpha = 1.000e-03 : rmse (train, test) = 9.39542e+14 9.39543e+14
- alpha = 1.000e-02 : rmse (train, test) = 9.39542e+14 9.39543e+14
- alpha = 1.000e-01 : rmse (train, test) = 0.03738 0.04961
- alpha = 1.000e+00 : rmse (train, test) = 0.03900 0.04742
- alpha = 1.000e+01 : rmse (train, test) = 0.04058 0.04584
- alpha = 1.000e-03 : rmse (train, test) = 1.12211e+15 1.12211e+15
- alpha = 1.000e-02 : rmse (train, test) = 1.12211e+15 1.12211e+15
- alpha = 1.000e-01 : rmse (train, test) = 0.00002 0.00002
- alpha = 1.000e+00 : rmse (train, test) = 0.00002 0.00002
- alpha = 1.000e+01 : rmse (train, test) = 0.00002 0.00002
MLPs were written into "phono3py.pmlp"
------------------------------ pypolymlp end -------------------------------
Generate random displacements
Twice of number of snapshots will be generated for plus-minus displacements.
Displacement distance: 0.001
Evaluate forces in 400 supercells by pypolymlp
----------------------------- Force constants ------------------------------
-------------------------------- Symfc start -------------------------------
Symfc is a non-trivial force constants calculator. Please cite the paper:
A. Seko and A. Togo, arXiv:2403.03588.
Symfc is a force constants calculator. See the following paper:
A. Seko and A. Togo, Phys. Rev. B, 110, 214302 (2024).
Symfc is developed at https://github.com/symfc/symfc.
Computing [2, 3] order force constants.
Increase log-level to watch detailed symfc log.
--------------------------------- Symfc end --------------------------------
-------------------------------- Symfc start -------------------------------
Symfc is a non-trivial force constants calculator. Please cite the paper:
A. Seko and A. Togo, arXiv:2403.03588.
Symfc is a force constants calculator. See the following paper:
A. Seko and A. Togo, Phys. Rev. B, 110, 214302 (2024).
Symfc is developed at https://github.com/symfc/symfc.
Computing [2] order force constants.
Increase log-level to watch detailed symfc log.
--------------------------------- Symfc end --------------------------------
Max drift of fc3: -0.000000 (xyx) 0.000000 (zyy) -0.000000 (xyx)
Max drift of fc2: 0.000000 (xx) 0.000000 (xx)
Max drift of fc3: -0.000000 (zxz) -0.000000 (xzz) -0.000000 (xzz)
Max drift of fc2: -0.000000 (yy) -0.000000 (yy)
fc3 was written into "fc3.hdf5".
fc2 was written into "fc2.hdf5".
----------- None of ph-ph interaction calculation was performed. -----------
Dataset generated using MLPs was written in "phono3py_mlp_eval_dataset.yaml".
Summary of calculation was written in "phono3py.yaml".
-------------------------[time 2024-09-19 15:34:41]-------------------------
-------------------------[time 2025-01-15 16:45:15]-------------------------
_
___ _ __ __| |
/ _ \ '_ \ / _` |
Expand Down Expand Up @@ -377,7 +377,7 @@ constants by loading the MLPs from `phono3py.pmlp` as follows:
| |_) | | | | (_) | | | | (_) |__) | |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, |
|_| |_| |___/
3.11.1-dev14+g5f281b65
3.11.2
-------------------------[time 2025-01-12 10:08:31]-------------------------
Compiled with OpenMP support (max 10 threads).
Expand Down
62 changes: 32 additions & 30 deletions phono3py/cui/create_force_constants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -514,6 +514,7 @@ def run_pypolymlp_to_compute_forces(
displacement_distance: Optional[float] = None,
number_of_snapshots: Optional[int] = None,
random_seed: Optional[int] = None,
prepare_dataset: bool = False,
mlp_filename: str = "phono3py.pmlp",
log_level: int = 0,
):
Expand Down Expand Up @@ -546,43 +547,44 @@ def run_pypolymlp_to_compute_forces(
if log_level:
print("-" * 30 + " pypolymlp end " + "-" * 31, flush=True)

if displacement_distance is None:
_displacement_distance = 0.001
else:
_displacement_distance = displacement_distance
if prepare_dataset:
if displacement_distance is None:
_displacement_distance = 0.001
else:
_displacement_distance = displacement_distance

if log_level:
if number_of_snapshots:
print("Generate random displacements")
if log_level:
if number_of_snapshots:
print("Generate random displacements")
print(
" Twice of number of snapshots will be generated "
"for plus-minus displacements."
)
else:
print("Generate displacements")
print(
" Twice of number of snapshots will be generated "
"for plus-minus displacements."
)
else:
print("Generate displacements")
print(
f" Displacement distance: {_displacement_distance:.5f}".rstrip("0").rstrip(
"."
f" Displacement distance: {_displacement_distance:.5f}".rstrip(
"0"
).rstrip(".")
)
ph3py.generate_displacements(
distance=_displacement_distance,
is_plusminus=True,
number_of_snapshots=number_of_snapshots,
random_seed=random_seed,
)
ph3py.generate_displacements(
distance=_displacement_distance,
is_plusminus=True,
number_of_snapshots=number_of_snapshots,
random_seed=random_seed,
)

if log_level:
print(
f"Evaluate forces in {ph3py.displacements.shape[0]} supercells "
"by pypolymlp",
flush=True,
)
if log_level:
print(
f"Evaluate forces in {ph3py.displacements.shape[0]} supercells "
"by pypolymlp",
flush=True,
)

if ph3py.supercells_with_displacements is None:
raise RuntimeError("Displacements are not set. Run generate_displacements.")
if ph3py.supercells_with_displacements is None:
raise RuntimeError("Displacements are not set. Run generate_displacements.")

ph3py.evaluate_mlp()
ph3py.evaluate_mlp()


def run_pypolymlp_to_compute_phonon_forces(
Expand Down
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