Energy in dataset

phono3py/cui/create_force_sets.py

@@ -0,0 +1,359 @@
+"""Command line user interface to create force sets files."""
+
+# Copyright (C) 2024 Atsushi Togo
+# All rights reserved.
+#
+# This file is part of phono3py.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions
+# are met:
+#
+# * Redistributions of source code must retain the above copyright
+#   notice, this list of conditions and the following disclaimer.
+#
+# * Redistributions in binary form must reproduce the above copyright
+#   notice, this list of conditions and the following disclaimer in
+#   the documentation and/or other materials provided with the
+#   distribution.
+#
+# * Neither the name of the phonopy project nor the names of its
+#   contributors may be used to endorse or promote products derived
+#   from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+# COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
+# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+
+from __future__ import annotations
+
+import copy
+import sys
+from typing import Optional
+
+from phonopy.cui.create_force_sets import check_number_of_force_files
+from phonopy.cui.load_helper import get_nac_params
+from phonopy.cui.phonopy_script import file_exists, files_exist, print_error
+from phonopy.file_IO import parse_FORCE_SETS, write_FORCE_SETS
+from phonopy.interface.calculator import get_calc_dataset
+
+from phono3py.file_IO import (
+    get_length_of_first_line,
+    parse_FORCES_FC2,
+    write_FORCES_FC2,
+    write_FORCES_FC3,
+)
+from phono3py.interface.phono3py_yaml import (
+    Phono3pyYaml,
+    displacements_yaml_lines_type1,
+)
+
+
+def create_FORCES_FC3_and_FORCES_FC2(
+    settings,
+    cell_filename: Optional[str],
+    log_level: int = 0,
+):
+    """Create FORCES_FC3 and FORCES_FC2 or phono3py_params.yaml from files.
+
+    With settings.save_params=True, phono3py_params.yaml is created instead of
+    FORCES_FC3 and FORCES_FC2. To create phono3py_params.yaml, at least fc3
+    forces have to be collected.
+
+    """
+    interface_mode = settings.calculator
+    disp_filename_candidates = [
+        "phono3py_disp.yaml",
+    ]
+    if cell_filename is not None:
+        disp_filename_candidates.insert(0, cell_filename)
+    disp_filenames = files_exist(disp_filename_candidates, log_level, is_any=True)
+    disp_filename = disp_filenames[0]
+    ph3py_yaml = Phono3pyYaml(settings={"force_sets": True})
+    ph3py_yaml.read(disp_filename)
+    if ph3py_yaml.calculator is not None:
+        interface_mode = ph3py_yaml.calculator  # overwrite
+
+    if settings.create_forces_fc3 or settings.create_forces_fc3_file:
+        calc_dataset_fc3 = _get_force_sets_fc3(
+            settings, ph3py_yaml.dataset, disp_filename, interface_mode, log_level
+        )
+        if not calc_dataset_fc3["forces"]:
+            if log_level:
+                print("%s could not be created." % "FORCES_FC3")
+                print_error()
+            sys.exit(1)
+
+    if settings.create_forces_fc2:
+        calc_dataset_fc2 = _get_force_sets_fc2(
+            settings,
+            ph3py_yaml.phonon_dataset,
+            disp_filename,
+            interface_mode,
+            log_level,
+        )
+        if not calc_dataset_fc2["forces"]:
+            if log_level:
+                print("%s could not be created." % "FORCES_FC2")
+                print_error()
+            sys.exit(1)
+
+    if settings.save_params:
+        fc3_yaml_filename = "phono3py_params.yaml"
+        if not (settings.create_forces_fc3 or settings.create_forces_fc3_file):
+            if log_level:
+                print(f'When creating "{fc3_yaml_filename}" with force sets for fc2, ')
+                print("force sets for fc3 have to be collected simultaneously.")
+                print(f'"{fc3_yaml_filename}" could not be created.')
+                print("")
+                print_error()
+            sys.exit(1)
+
+        _set_forces_and_nac_params(
+            ph3py_yaml, settings, calc_dataset_fc3, calc_dataset_fc2
+        )
+
+        with open(fc3_yaml_filename, "w") as w:
+            w.write(str(ph3py_yaml))
+            if log_level:
+                print(f'"{fc3_yaml_filename}" has been created.')
+    else:
+        if settings.create_forces_fc3 or settings.create_forces_fc3_file:
+            write_FORCES_FC3(
+                ph3py_yaml.dataset,
+                forces_fc3=calc_dataset_fc3["forces"],
+                filename="FORCES_FC3",
+            )
+            if log_level:
+                print("%s has been created." % "FORCES_FC3")
+
+        if settings.create_forces_fc2:
+            write_FORCES_FC2(
+                ph3py_yaml.phonon_dataset,
+                forces_fc2=calc_dataset_fc2["forces"],
+                filename="FORCES_FC2",
+            )
+            if log_level:
+                print("%s has been created." % "FORCES_FC2")
+
+
+def create_FORCES_FC2_from_FORCE_SETS(log_level):
+    """Convert FORCE_SETS to FORCES_FC2."""
+    filename = "FORCE_SETS"
+    file_exists(filename, log_level)
+    disp_dataset = parse_FORCE_SETS(filename=filename)
+    write_FORCES_FC2(disp_dataset)
+
+    if log_level:
+        print("")
+        print("FORCES_FC2 has been created from FORCE_SETS.")
+        print("The following yaml lines should replace respective part of")
+        print("phono3py_disp.yaml made with --dim-fc2=dim_of_FORCE_SETS.")
+
+        print("")
+        print("\n".join(displacements_yaml_lines_type1(disp_dataset)))
+
+
+def create_FORCE_SETS_from_FORCES_FCx(
+    phonon_smat, input_filename: Optional[str], cell_filename: Optional[str], log_level
+):
+    """Convert FORCES_FC3 or FORCES_FC2 to FORCE_SETS."""
+    if cell_filename is not None:
+        disp_filename = cell_filename
+    elif input_filename is None:
+        disp_filename = "phono3py_disp.yaml"
+    else:
+        disp_filename = f"phono3py_disp.{input_filename}.yaml"
+    if phonon_smat is not None:
+        forces_filename = "FORCES_FC2"
+    else:
+        forces_filename = "FORCES_FC3"
+
+    if log_level:
+        print(f'Displacement dataset is read from "{disp_filename}".')
+        print(f'Forces are read from "{forces_filename}"')
+
+    with open(forces_filename, "r") as f:
+        len_first_line = get_length_of_first_line(f)
+
+    if len_first_line == 3:
+        file_exists(disp_filename, log_level)
+        file_exists(forces_filename, log_level)
+        ph3yml = Phono3pyYaml()
+        ph3yml.read(disp_filename)
+        if phonon_smat is None:
+            dataset = copy.deepcopy(ph3yml.dataset)
+            smat = ph3yml.supercell_matrix
+        else:
+            dataset = copy.deepcopy(ph3yml.phonon_dataset)
+            smat = ph3yml.phonon_supercell_matrix
+
+        if smat is None or (phonon_smat is not None and (phonon_smat != smat).any()):
+            if log_level:
+                print("")
+                print("Supercell matrix is inconsistent.")
+                print(f'Supercell matrix read from "{disp_filename}":')
+                print(smat)
+                print("Supercell matrix given by --dim-fc2:")
+                print(phonon_smat)
+                print_error()
+            sys.exit(1)
+
+        parse_FORCES_FC2(dataset, filename=forces_filename)
+        write_FORCE_SETS(dataset)
+
+        if log_level:
+            print("FORCE_SETS has been created.")
+    else:
+        if log_level:
+            print(
+                "The file format of %s is already readable by phonopy."
+                % forces_filename
+            )
+
+
+def _get_force_sets_fc2(
+    settings, disp_dataset, disp_filename, interface_mode, log_level
+) -> dict:
+    interface_mode = settings.calculator
+    if log_level:
+        print(f'FC2 displacement dataset was read from "{disp_filename}".')
+    num_atoms = disp_dataset["natom"]
+    num_disps = len(disp_dataset["first_atoms"])
+    force_filenames = settings.create_forces_fc2
+    for filename in force_filenames:
+        file_exists(filename, log_level)
+
+    if log_level > 0:
+        print(f"  Number of displacements: {num_disps}")
+        print(f"  Number of supercell files: {len(force_filenames)}")
+
+    calc_dataset = get_calc_dataset(
+        interface_mode,
+        num_atoms,
+        force_filenames,
+        verbose=(log_level > 0),
+    )
+    force_sets = calc_dataset["forces"]
+
+    if settings.subtract_forces:
+        force_filename = settings.subtract_forces
+        file_exists(force_filename, log_level)
+        calc_dataset_zero = get_calc_dataset(
+            interface_mode,
+            num_atoms,
+            [
+                force_filename,
+            ],
+            verbose=(log_level > 0),
+        )
+        force_set_zero = calc_dataset_zero["forces"][0]
+        for fs in force_sets:
+            fs -= force_set_zero
+
+        if log_level > 0:
+            print("Forces in '{force_filename}' were subtracted from supercell forces.")
+
+    if log_level > 0:
+        print("")
+
+    return calc_dataset
+
+
+def _get_force_sets_fc3(
+    settings, disp_dataset, disp_filename, interface_mode, log_level
+) -> dict:
+    if log_level:
+        print("")
+        print(f'FC3 Displacement dataset was read from "{disp_filename}".')
+
+    num_atoms = disp_dataset["natom"]
+    num_disps = len(disp_dataset["first_atoms"])
+    for d1 in disp_dataset["first_atoms"]:
+        for d2 in d1["second_atoms"]:
+            if "included" not in d2 or d2["included"]:
+                num_disps += 1
+
+    if settings.create_forces_fc3_file:
+        file_exists(settings.create_forces_fc3_file, log_level)
+        force_filenames = [x.strip() for x in open(settings.create_forces_fc3_file)]
+    else:
+        force_filenames = settings.create_forces_fc3
+
+    for filename in force_filenames:
+        file_exists(filename, log_level)
+
+    if log_level > 0:
+        print(f"  Number of displacements: {num_disps}")
+        print(f"  Number of supercell files: {len(force_filenames)}")
+
+    if not check_number_of_force_files(num_disps, force_filenames, disp_filename):
+        calc_dataset = {"forces": []}
+    else:
+        calc_dataset = get_calc_dataset(
+            interface_mode,
+            num_atoms,
+            force_filenames,
+            verbose=(log_level > 0),
+        )
+        force_sets = calc_dataset["forces"]
+
+    if settings.subtract_forces:
+        force_filename = settings.subtract_forces
+        file_exists(force_filename, log_level)
+        calc_dataset = get_calc_dataset(
+            interface_mode,
+            num_atoms,
+            [
+                force_filename,
+            ],
+            verbose=(log_level > 0),
+        )
+        force_set_zero = calc_dataset["forces"][0]
+        for fs in force_sets:
+            fs -= force_set_zero
+
+        if log_level > 0:
+            print(
+                f"Forces in '{force_filename}' were subtracted from supercell forces."
+            )
+
+    if log_level > 0:
+        print("")
+
+    return calc_dataset
+
+
+def _set_forces_and_nac_params(
+    ph3py_yaml: Phono3pyYaml, settings, calc_dataset_fc3: dict, calc_dataset_fc2: dict
+):
+    count = len(ph3py_yaml.dataset["first_atoms"])
+    for i, d1 in enumerate(ph3py_yaml.dataset["first_atoms"]):
+        d1["forces"] = calc_dataset_fc3["forces"][i]
+        if "energies" in calc_dataset_fc3:
+            d1["energy"] = float(calc_dataset_fc3["energies"][i])
+        for d2 in d1["second_atoms"]:
+            if "included" not in d2 or d2["included"]:
+                d2["forces"] = calc_dataset_fc3["forces"][count]
+                if "energies" in calc_dataset_fc3:
+                    d2["energy"] = float(calc_dataset_fc3["energies"][count])
+                count += 1
+
+    if settings.create_forces_fc2:
+        for i, d in enumerate(ph3py_yaml.phonon_dataset["first_atoms"]):
+            d["forces"] = calc_dataset_fc2["forces"][i]
+            if "energies" in calc_dataset_fc2:
+                d["energy"] = float(calc_dataset_fc2["energies"][i])
+
+    nac_params = get_nac_params(primitive=ph3py_yaml.primitive)
+    if nac_params:
+        ph3py_yaml.nac_params = nac_params

phono3py/cui/create_supercells.py

@@ -1,4 +1,4 @@
-"""Utilities of main CUI script."""
+"""Command line user interface to create supercells."""
 
 # Copyright (C) 2015 Atsushi Togo
 # All rights reserved.
@@ -48,7 +48,6 @@ def create_phono3py_supercells(
     cell_info,
     settings,
     symprec,
-    output_filename=None,
     interface_mode="vasp",
     log_level=1,
 ):
@@ -121,7 +120,7 @@ def create_phono3py_supercells(
         )
         write_supercells_with_displacements(
             interface_mode,
-            phono3py.supercell,
+            phono3py.phonon_supercell,
             phono3py.phonon_supercells_with_displacements,
             optional_structure_info,
             zfill_width=5,

phono3py/cui/phono3py_argparse.py

@@ -681,6 +681,14 @@ def get_parser(fc_symmetry=False, is_nac=False, load_phono3py_yaml=False):
         default=False,
         help="Calculate real part of self energy",
     )
+    parser.add_argument(
+        "--sp",
+        "--save-params",
+        dest="save_params",
+        action="store_true",
+        default=None,
+        help="Save parameters that can run phono3py in phono3py_params.yaml.",
+    )
     parser.add_argument(
         "--scattering-event-class",
         dest="scattering_event_class",