From 36f976a6aba9ad4376f890512601de4bbfef880b Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Sun, 12 Jan 2025 10:16:42 +0900
Subject: [PATCH 1/3] Set version 3.11.1

---
 doc/changelog.md                    |  6 ++
 doc/command-options.md              |  8 ++-
 doc/install.md                      |  1 -
 doc/pypolymlp.md                    | 87 ++++++++++++++++++++++++++++-
 doc/workload-distribution.md        | 12 ++--
 phono3py/api_phono3py.py            | 22 ++++++--
 phono3py/cui/phono3py_argparse.py   | 28 ++++------
 phono3py/cui/phono3py_script.py     | 24 ++++++--
 phono3py/interface/phono3py_yaml.py |  2 +-
 phono3py/version.py                 |  2 +-
 10 files changed, 153 insertions(+), 39 deletions(-)

diff --git a/doc/changelog.md b/doc/changelog.md
index 03458e30..87e4d5ab 100644
--- a/doc/changelog.md
+++ b/doc/changelog.md
@@ -2,6 +2,12 @@
 
 # Change Log
 
+## Jan-12-2024: Version 3.11.1
+
+
+- `-i`, `-o`, `--io` options have been deprecated.
+- `--amplitude` option has been activated for `phono3py-load`.
+
 ## Jan-2-2024: Version 3.11.0
 
 - Release to follow the change of phonopy
diff --git a/doc/command-options.md b/doc/command-options.md
index 8b603d1f..ab845058 100644
--- a/doc/command-options.md
+++ b/doc/command-options.md
@@ -1358,8 +1358,11 @@ set. Other filters (`lzf` or integer values of 0 to 9) may be used, see h5py
 documentation
 (<http://docs.h5py.org/en/stable/high/dataset.html#filter-pipeline>).
 
-(output_filename_option)=
+### `-o`, `-i`, `--io`
 
+These options are deprecated.
+
+<!-- (output_filename_option)=
 ### `-o` (command option only)
 
 This modifies default output file names to write.
@@ -1378,7 +1381,6 @@ This rule is applied to
 * `gamma_detail-xxx.hdf5` (write only)
 
 (input_filename_option)=
-
 ### `-i` (command option only)
 
 This modifies default input file names to read.
@@ -1399,7 +1401,7 @@ This rule is applied to
 
 This modifies default input and output file names.
 
-This is equivalent to setting `-i` and `-o` simultaneously.
+This is equivalent to setting `-i` and `-o` simultaneously. -->
 
 <!-- ## References
 
diff --git a/doc/install.md b/doc/install.md
index 17b6de30..2b383c02 100644
--- a/doc/install.md
+++ b/doc/install.md
@@ -41,7 +41,6 @@ removed.
 If phono3py is compiled with a special compiler or special options, manual
 modification of `CMakeLists.txt` may be needed.
 
-- {ref}`OpenMP library <install_openmp>`: For the multithreding support.
 - {ref}`Linear algebra library <install_lapacke>`: BLAS, LAPACK, and LAPACKE
   (optional, see {ref}`install_with_lapacke`)
 
diff --git a/doc/pypolymlp.md b/doc/pypolymlp.md
index 50e73093..59fba9ca 100644
--- a/doc/pypolymlp.md
+++ b/doc/pypolymlp.md
@@ -230,7 +230,7 @@ Max drift of fc2: -0.000000 (zz) -0.000000 (zz)
 fc3 was written into "fc3.hdf5".
 fc2 was written into "fc2.hdf5".
 ----------- None of ph-ph interaction calculation was performed. -----------
-Dataset generated using MMLPs was written in "phono3py_mlp_eval_dataset.yaml".
+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]-------------------------
                  _
@@ -334,7 +334,7 @@ Max drift of fc2: 0.000000 (xx) 0.000000 (xx)
 fc3 was written into "fc3.hdf5".
 fc2 was written into "fc2.hdf5".
 ----------- None of ph-ph interaction calculation was performed. -----------
-Dataset generated using MMLPs was written in "phono3py_mlp_eval_dataset.yaml".
+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]-------------------------
                  _
@@ -353,6 +353,89 @@ an additional 200 supercells. In total, 400 supercells are created. The forces
 for these supercells are then evaluated. Finally, the force constants are
 calculated using symfc.
 
+### Command options for force constants calculation
+
+After obtaining the MLPs, displacements are generated using those MLPs, and the
+resulting forces are computed accordingly. The displacement distance is set by
+the `--amplitude` option, whose default value is 0.001 Angstrom. When the `--rd`
+option is used, it specifies the number of supercells with random directional
+displacements. Note that to achieve accurate force constants, the actual number
+of generated supercells is twice the specified number. Additionally, when using
+`--rd`, the `--symfc` option must be used together. If `--rd` is omitted,
+systematic displacements are introduced, and thus `--symfc` is not required.
+
+Once the file `phono3py.pmlp` is obtained, force constants can be calculated
+using MLPs from `phono3py.pmlp`. After removing the `fc3.hdf5` and `fc2.hdf5`
+files, `phono3py-load` will detect `phono3py.pmlp` and then compute the force
+constants by loading the MLPs from `phono3py.pmlp` as follows:
+
+```
+% phono3py-load --pypolymlp --rd 100 --symfc --amplitude 0.01 phono3py.yaml
+        _                      _____
+  _ __ | |__   ___  _ __   ___|___ / _ __  _   _
+ | '_ \| '_ \ / _ \| '_ \ / _ \ |_ \| '_ \| | | |
+ | |_) | | | | (_) | | | | (_) |__) | |_) | |_| |
+ | .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, |
+ |_|                                |_|    |___/
+                      3.11.1-dev14+g5f281b65
+
+-------------------------[time 2025-01-12 10:08:31]-------------------------
+Compiled with OpenMP support (max 10 threads).
+Running in phono3py.load mode.
+Python version 3.12.3
+Spglib version 2.5.0
+----------------------------- General settings -----------------------------
+HDF5 data compression filter: gzip
+Crystal structure was read from "phono3py.yaml".
+Supercell (dim): [2 2 2]
+Primitive matrix:
+  [0.  0.5 0.5]
+  [0.5 0.  0.5]
+  [0.5 0.5 0. ]
+Spacegroup: Fm-3m (225)
+Use -v option to watch primitive cell, unit cell, and supercell structures.
+NAC parameters were read from "phono3py.yaml".
+----------------------------- Force constants ------------------------------
+----------------------------- pypolymlp start ------------------------------
+Pypolymlp is a generator of polynomial machine learning potentials.
+Please cite the paper: A. Seko, J. Appl. Phys. 133, 011101 (2023).
+Pypolymlp is developed at https://github.com/sekocha/pypolymlp.
+Load MLPs from "phono3py.pmlp".
+------------------------------ pypolymlp end -------------------------------
+Generate random displacements
+  Twice of number of snapshots will be generated for plus-minus displacements.
+  Displacement distance: 0.01
+Evaluate forces in 200 supercells by pypolymlp
+-------------------------------- Symfc start -------------------------------
+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 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 (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 2025-01-12 10:08:40]-------------------------
+                 _
+   ___ _ __   __| |
+  / _ \ '_ \ / _` |
+ |  __/ | | | (_| |
+  \___|_| |_|\__,_|
+```
+
+
 ## Parameters for developing MLPs
 
 A few parameters can be specified using the `--mlp-params` option for the
diff --git a/doc/workload-distribution.md b/doc/workload-distribution.md
index 6d207f01..90295788 100644
--- a/doc/workload-distribution.md
+++ b/doc/workload-distribution.md
@@ -54,13 +54,11 @@ indices are chosen and executed as follows:
 % phono3py-load --mesh 19 19 19 --br --gp "0,1,2,3,4,5,6,7,8,9,20,21,22,23,24,25" --write-gamma
 ```
 
-Then many `kappa-m191919-gx.hdf5` files are generated. These file
-names should not be altered because in reading the data by phono3py,
-those file names are supposed to be so, though there is a little
-freedom to arrange those file names, for which see {ref}`-o <output_filename_option>` and {ref}`-i <input_filename_option>`
-options. After completing calculations for all irreducible grid-point
-indices, the RTA thermal conductivity is computed by another run in a
-short time from the stored data:
+Then many `kappa-m191919-gx.hdf5` files are generated. These file names should
+not be altered because in reading the data by phono3py, those file names are
+supposed to be so. After completing calculations for all irreducible grid-point
+indices, the RTA thermal conductivity is computed by another run in a short time
+from the stored data:
 
 ```bash
 % phono3py-load --mesh 19 19 19 --br --read-gamma
diff --git a/phono3py/api_phono3py.py b/phono3py/api_phono3py.py
index 4dc2bfbc..cee8b4b6 100644
--- a/phono3py/api_phono3py.py
+++ b/phono3py/api_phono3py.py
@@ -36,6 +36,7 @@
 from __future__ import annotations
 
 import copy
+import warnings
 from collections.abc import Sequence
 from typing import Literal, Optional, Union
 
@@ -2091,13 +2092,26 @@ def run_thermal_conductivity(
             When writing results into files in hdf5, large data are compressed
             by this options. See the detail at h5py documentation.
         input_filename : str, optional, default is None
-            When specified, the string is inserted before filename extension
-            in reading files.
+            Deprecated. When specified, the string is inserted before filename
+            extension in reading files.
         output_filename : str, optional, default is None
-            When specified, the string is inserted before filename extension
-            in writing files.
+            Deprecated. When specified, the string is inserted before filename
+            extension in writing files.
 
         """
+        if input_filename is not None:
+            warnings.warn(
+                "input_filename parameter is deprecated.",
+                DeprecationWarning,
+                stacklevel=2,
+            )
+        if output_filename is not None:
+            warnings.warn(
+                "output_filename parameter is deprecated.",
+                DeprecationWarning,
+                stacklevel=2,
+            )
+
         if self._interaction is None:
             msg = (
                 "Phono3py.init_phph_interaction has to be called "
diff --git a/phono3py/cui/phono3py_argparse.py b/phono3py/cui/phono3py_argparse.py
index 086bb51d..cd61b766 100644
--- a/phono3py/cui/phono3py_argparse.py
+++ b/phono3py/cui/phono3py_argparse.py
@@ -57,16 +57,15 @@ def get_parser(fc_symmetry=False, is_nac=False, load_phono3py_yaml=False):
         dest="use_alm",
         action="store_true",
         default=False,
-        help=("Use ALM for generating 2nd and 3rd force constants " "in one fitting"),
+        help=("Use ALM for generating 2nd and 3rd force constants in one fitting"),
+    )
+    parser.add_argument(
+        "--amplitude",
+        dest="displacement_distance",
+        type=float,
+        default=None,
+        help="Distance of displacements",
     )
-    if not load_phono3py_yaml:
-        parser.add_argument(
-            "--amplitude",
-            dest="displacement_distance",
-            type=float,
-            default=None,
-            help="Distance of displacements",
-        )
     parser.add_argument(
         "--ave-pp",
         dest="use_ave_pp",
@@ -106,8 +105,7 @@ def get_parser(fc_symmetry=False, is_nac=False, load_phono3py_yaml=False):
         type=float,
         default=None,
         help=(
-            "Boundary mean free path in micrometre for thermal conductivity "
-            "calculation"
+            "Boundary mean free path in micrometre for thermal conductivity calculation"
         ),
     )
     parser.add_argument(
@@ -429,8 +427,7 @@ def get_parser(fc_symmetry=False, is_nac=False, load_phono3py_yaml=False):
         action="store_true",
         default=False,
         help=(
-            "Atoms are clamped under applied strain in Gruneisen parameter "
-            "calculation"
+            "Atoms are clamped under applied strain in Gruneisen parameter calculation"
         ),
     )
     parser.add_argument(
@@ -747,7 +744,7 @@ def get_parser(fc_symmetry=False, is_nac=False, load_phono3py_yaml=False):
         dest="scattering_event_class",
         type=int,
         default=None,
-        help=("Scattering event class 1 or 2 to draw imaginary part of self " "energy"),
+        help=("Scattering event class 1 or 2 to draw imaginary part of self energy"),
     )
     parser.add_argument(
         "--sigma",
@@ -787,8 +784,7 @@ def get_parser(fc_symmetry=False, is_nac=False, load_phono3py_yaml=False):
         action="store_true",
         default=False,
         help=(
-            "Show reduced number of triplets to be calculated at "
-            "specified grid points"
+            "Show reduced number of triplets to be calculated at specified grid points"
         ),
     )
     if not load_phono3py_yaml:
diff --git a/phono3py/cui/phono3py_script.py b/phono3py/cui/phono3py_script.py
index d1cf1b2a..5299f87f 100644
--- a/phono3py/cui/phono3py_script.py
+++ b/phono3py/cui/phono3py_script.py
@@ -39,6 +39,7 @@
 import argparse
 import pathlib
 import sys
+import warnings
 from typing import Optional
 
 import numpy as np
@@ -154,12 +155,10 @@ def finalize_phono3py(
     else:
         yaml_filename = filename
 
-    if phono3py.mlp_dataset is not None:
+    if phono3py.mlp is not None and phono3py.dataset is not None:
         mlp_eval_filename = "phono3py_mlp_eval_dataset.yaml"
         if log_level:
-            print(
-                f'Dataset generated using MMLPs was written in "{mlp_eval_filename}".'
-            )
+            print(f'Dataset generated using MLPs was written in "{mlp_eval_filename}".')
         phono3py.save(mlp_eval_filename)
 
     _physical_units = get_default_physical_units(phono3py.calculator)
@@ -307,9 +306,26 @@ def read_phono3py_settings(args, argparse_control, log_level):
 
 def get_input_output_filenames_from_args(args):
     """Return strings inserted to input and output filenames."""
+    if args.input_filename is not None:
+        warnings.warn(
+            "-i option is deprecated and will be removed soon.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
     input_filename = args.input_filename
+    if args.output_filename is not None:
+        warnings.warn(
+            "-o option is deprecated and will be removed soon.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
     output_filename = args.output_filename
     if args.input_output_filename is not None:
+        warnings.warn(
+            "--io option is deprecated and will be removed soon.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
         input_filename = args.input_output_filename
         output_filename = args.input_output_filename
     return input_filename, output_filename
diff --git a/phono3py/interface/phono3py_yaml.py b/phono3py/interface/phono3py_yaml.py
index cc6cc13b..20379854 100644
--- a/phono3py/interface/phono3py_yaml.py
+++ b/phono3py/interface/phono3py_yaml.py
@@ -530,7 +530,7 @@ def _displacements_yaml_lines_type1_info(dataset):
     # 'duplicates' is dict, but written as a list of list in yaml.
     # See the docstring of _parse_fc3_dataset for the reason.
     if "duplicates" in dataset and dataset["duplicates"]:
-        lines.append("  duplicated_supercell_ids: " "# 0 means perfect supercell")
+        lines.append("  duplicated_supercell_ids: # 0 means perfect supercell")
         # Backward compatibility for dict type
         if isinstance(dataset["duplicates"], dict):
             for disp1_id, j in dataset["duplicates"].items():
diff --git a/phono3py/version.py b/phono3py/version.py
index 67dcb157..55ed6e8e 100644
--- 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__ = "3.11.0"
+__version__ = "3.11.1"

From 672702083a0602a44e6a0a5e6e9d159069ce98d6 Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Sun, 12 Jan 2025 10:18:50 +0900
Subject: [PATCH 2/3] Update documentation

---
 doc/changelog.md | 4 ++--
 doc/conf.py      | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/doc/changelog.md b/doc/changelog.md
index 87e4d5ab..ce470e95 100644
--- a/doc/changelog.md
+++ b/doc/changelog.md
@@ -4,9 +4,9 @@
 
 ## Jan-12-2024: Version 3.11.1
 
-
 - `-i`, `-o`, `--io` options have been deprecated.
-- `--amplitude` option has been activated for `phono3py-load`.
+- The `--amplitude` option can now be used to specify the displacement distance
+  for `phono3py-load --pypolymlp`.
 
 ## Jan-2-2024: Version 3.11.0
 
diff --git a/doc/conf.py b/doc/conf.py
index 946af04e..2f6a6cfb 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -60,7 +60,7 @@
 # The short X.Y version.
 version = "3.11"
 # The full version, including alpha/beta/rc tags.
-release = "3.11.0"
+release = "3.11.1"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

From 2afef356dba2766862e805d7d5b96403337e7f01 Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Mon, 13 Jan 2025 10:13:33 +0900
Subject: [PATCH 3/3] Minor fix of show_general_settings

---
 phono3py/cui/show_log.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/phono3py/cui/show_log.py b/phono3py/cui/show_log.py
index c03f90b6..03539979 100644
--- a/phono3py/cui/show_log.py
+++ b/phono3py/cui/show_log.py
@@ -65,7 +65,7 @@ def show_general_settings(
 
     print("-" * 29 + " General settings " + "-" * 29)
     if run_mode:
-        print("Run mode: {run_mode}")
+        print(f"Run mode: {run_mode}")
     if output_filename:
         print(f"Output filename is modified by {output_filename}.")
     if input_filename: