Merge branch 'master' of https://gitlab.mpcdf.mpg.de/nomad-lab/parser-phonopy

Updated the phonopy parser to the right commit-tmk

phonopyparser/FHIaims.py

+# FHIaims.py - IO routines for phonopy-FHI-aims
+# methods compatible with the corresponding ones from ase.io.aims
+# only minimal subset of functionality required within phonopy context is implemented
+#
+# Copyright (C) 2009-2011 Joerg Meyer (jm)
+# All rights reserved.
+#
+# This file is part of phonopy.
+#
+# 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 phonopy.structure.atoms import PhonopyAtoms
+
+def read_aims(filename):
+    """Method to read FHI-aims geometry files in phonopy context."""
+
+    lines = open(filename, 'r').readlines()
+
+    cell = []
+    is_frac = []
+    positions = []
+    symbols = []
+    magmoms = []
+    for line in lines:
+        fields = line.split()
+        if not len(fields):
+            continue
+        if fields[0] == "lattice_vector":
+            vec = [float(x) for x in fields[1:4]]
+            cell.append(vec)
+        elif fields[0][0:4] == "atom":
+            if fields[0] == "atom":
+                frac = False
+            elif fields[0] == "atom_frac":
+                frac = True
+            pos = [float(x) for x in fields[1:4]]
+            sym = fields[4]
+            is_frac.append(frac)
+            positions.append(pos)
+            symbols.append(sym)
+            magmoms.append(None)
+        # implicitly assuming that initial_moments line adhere to FHI-aims geometry.in specification,
+        # i.e. two subsequent initial_moments lines do not occur
+        # if they do, the value specified in the last line is taken here - without any warning
+        elif fields[0] == "initial_moment":
+            magmoms[-1] = float(fields[1])
+
+    for (n,frac) in enumerate(is_frac):
+        if frac:
+            pos = [ sum( [ positions[n][l] * cell[l][i] for l in range(3) ] ) for i in range(3) ]
+            positions[n] = pos
+    if None in magmoms:
+        atoms = PhonopyAtoms(cell=cell, symbols=symbols, positions=positions)
+    else:
+        atoms = PhonopyAtoms(cell=cell, symbols=symbols, positions=positions, magmoms=magmoms)
+
+    return atoms
+
+
+def write_aims(filename, atoms):
+    """Method to write FHI-aims geometry files in phonopy context."""
+
+    lines = ""
+    lines += "# geometry.in for FHI-aims \n"
+    lines += "# | generated by phonopy.FHIaims.write_aims() \n"
+
+    lattice_vector_line = "lattice_vector " + "%16.16f "*3 + "\n"
+    for vec in atoms.get_cell():
+        lines += lattice_vector_line % tuple(vec)
+
+    N = atoms.get_number_of_atoms()
+
+    atom_line = "atom " + "%16.16f "*3 + "%s \n"
+    positions = atoms.get_positions()
+    symbols = atoms.get_chemical_symbols()
+
+    initial_moment_line = "initial_moment %16.6f\n"
+    magmoms = atoms.get_magnetic_moments()
+
+    for n in range(N):
+        lines += atom_line % (tuple(positions[n]) + (symbols[n],))
+        if magmoms is not None:
+            lines += initial_moment_line % magmoms[n]
+
+    f = open(filename, 'w')
+    f.write(lines)
+    f.close()
+
+
+
+class Atoms_with_forces(PhonopyAtoms):
+    """ Hack to phonopy.atoms to maintain ASE compatibility also for forces."""
+
+    def get_forces(self):
+        return self.forces
+
+
+def read_aims_output(filename):
+    """ Read FHI-aims output and 
+        return geometry, energy and forces from last self-consistency iteration"""
+
+    lines = open(filename, 'r').readlines()
+
+    l = 0
+    N = 0
+    while l < len(lines):
+        line = lines[l]
+        if "Number of atoms" in line:
+            N = int(line.split()[5])
+        elif "| Unit cell:" in line:
+            cell = []
+            for i in range(3):
+                l += 1
+                vec = [float(x) for x in lines[l].split()[1:4]]
+                cell.append(vec)
+        elif ("Atomic structure:" in line) or ("Updated atomic structure:" in line):
+            if "Atomic structure:" in line:
+                i_sym = 3
+                i_pos_min = 4 ; i_pos_max = 7
+            elif "Updated atomic structure:" in line:
+                i_sym = 4
+                i_pos_min = 1 ; i_pos_max = 4
+            l += 1
+            symbols = []
+            positions = []
+            for n in range(N):
+               l += 1
+               fields = lines[l].split()
+               sym = fields[i_sym]
+               pos = [float(x) for x in fields[i_pos_min:i_pos_max]]
+               symbols.append(sym)
+               positions.append(pos)
+        elif "Total atomic forces" in line:
+            forces = []
+            for i in range(N):
+                l += 1
+                force = [float(x) for x in lines[l].split()[2:5]]
+                forces.append(force)
+        l += 1
+    
+    atoms = Atoms_with_forces(cell=cell, symbols=symbols, positions=positions)
+    atoms.forces = forces
+
+    return atoms

phonopyparser/Get_Force_Constants.py

-# Copyright 2016-2018 Fawzi Mohamed, Danio Brambila
-#
-#   Licensed under the Apache License, Version 2.0 (the "License");
-#   you may not use this file except in compliance with the License.
-#   You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-#   Unless required by applicable law or agreed to in writing, software
-#   distributed under the License is distributed on an "AS IS" BASIS,
-#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-#   See the License for the specific language governing permissions and
-#   limitations under the License.
-
-#### phonopy parser written by Hagen-Henrik Kowalski and based on the original work of Joerg Mayer on phonopy-FHI-aims
-
-import numpy as np
-from phonopyparser.PhononModulesNomad import *
-from fnmatch import fnmatch
-import sys
-import math
-import os
-import argparse
-import logging
-
-
-from phonopy.interface.FHIaims import read_aims, write_aims, read_aims_output
-from phonopyparser.con import Control
-# Note this Phonopy is the NOMAD-lab version. Not the open source package on PYPI.
-from phonopy import Phonopy, __version__
-from phonopy.structure.symmetry import Symmetry
-from phonopy.file_IO import write_FORCE_CONSTANTS
-from phonopy.harmonic.forces import Forces
-from phonopy.harmonic.force_constants import get_force_constants
-from phonopy.units import *
-from nomadcore.unit_conversion.unit_conversion import convert_unit_function
-from nomadcore.parser_backend import *
-from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
-from phonopy.structure.atoms import PhonopyAtoms as Atoms
-
-import nomad.config
-
-phonopy_version = __version__
-parser_info = {"name": "parser_phonopy", "version": "1.0"}
-
-
-class PhonopyParserWrapper():
-    """ A proper class envolop for running this parser using Noamd-FAIRD infra. """
-    def __init__(self, backend, **kwargs):
-        self.backend_factory = backend
-
-    def parse(self, mainfile):
-        logging.info('phonopy parser started')
-        logging.getLogger('nomadcore').setLevel(logging.WARNING)
-        backend = self.backend_factory("phonopy.nomadmetainfo.json")
-        # Call the old parser without a class.
-        mainDir = os.path.dirname(os.path.dirname(os.path.abspath(mainfile)))
-        cwd = os.getcwd()
-        os.chdir(mainDir)
-        try:
-            return parse_without_class(mainfile, backend)
-        finally:
-            os.chdir(cwd)
-
-
-def parse_without_class(name, backend):
-    cell_obj = read_aims("geometry.in")
-    cell = cell_obj.get_cell()
-    positions = cell_obj.get_positions()
-    symbols = np.array(cell_obj.get_chemical_symbols())
-    control = Control()
-    if (len(control.phonon["supercell"]) == 3):
-                    supercell_matrix = np.diag(control.phonon["supercell"])
-    elif (len(control.phonon["supercell"]) == 9):
-                    supercell_matrix = np.array(control.phonon["supercell"]).reshape(3,3)
-    displacement = control.phonon["displacement"]
-    sym = control.phonon["symmetry_thresh"]
-    ####
-
-    #### constructing FORCE_CONSTANTS
-    set_of_forces, phonopy_obj, Relative_Path = Collect_Forces_aims(cell_obj, supercell_matrix, displacement, sym)
-    Prep_Path = name.split("phonopy-FHI-aims-displacement-")
-    Whole_Path = []
-
-    # Try to resolve references as paths relative to the upload root.
-    try:
-        for Path in Relative_Path:
-            abs_path = "%s%s" % (Prep_Path[0], Path)
-            rel_path = abs_path.split(nomad.config.fs.staging + "/")[1].split("/", 3)[3]
-            Whole_Path.append(rel_path)
-    except Exception:
-        logging.warn("Could not resolve path to a referenced calculation within the upload.")
-    phonopy_obj.set_forces(set_of_forces)
-    phonopy_obj.produce_force_constants()
-    FC2 = phonopy_obj.get_force_constants()
-    ####
-
-    #### obtaining information about supercell
-    super_c=phonopy_obj.supercell
-    s_cell = super_c.get_cell()
-    super_pos = super_c.get_positions()
-    super_sym = np.array(super_c.get_chemical_symbols())
-    ####
-
-    #### Converting properties to Si unitis
-    converter_FC2 = convert_unit_function('eV*angstrom**-2', 'joules*meter**-2')
-    convert_angstrom = convert_unit_function('angstrom', 'meter')
-    FC2 = converter_FC2(FC2)
-    cell = convert_angstrom(cell)
-    s_cell = convert_angstrom(s_cell)
-    super_pos = convert_angstrom(super_pos)
-    positions = convert_angstrom(positions)
-    displacement = convert_angstrom(displacement)
-
-    #### parsing
-    pbc = np.array((1, 1, 1), bool)
-    Parse = backend
-    Parse.startedParsingSession(name, parser_info)
-    sRun = Parse.openSection("section_run")
-    Parse.addValue("program_name", "Phonopy")
-    Parse.addValue("program_version", phonopy_version)
-    Basesystem = Parse.openSection("section_system")
-    Parse.addArrayValues("configuration_periodic_dimensions", pbc)
-    Parse.addArrayValues("atom_labels", symbols)
-    Parse.addArrayValues("atom_positions", positions)
-    Parse.addArrayValues("simulation_cell", cell)
-    Parse.closeSection("section_system", Basesystem)
-    Supercellsystem = Parse.openSection("section_system")
-    sysrefs = Parse.openSection("section_system_to_system_refs")
-    Parse.addValue("system_to_system_kind", "subsystem")
-    Parse.addValue("system_to_system_ref", Basesystem)
-    Parse.closeSection("section_system_to_system_refs", sysrefs)
-    Parse.addArrayValues("configuration_periodic_dimensions", pbc)
-    Parse.addArrayValues("atom_labels", super_sym)
-    Parse.addArrayValues("atom_positions", super_pos)
-    Parse.addArrayValues("simulation_cell", s_cell)
-    Parse.addArrayValues("SC_matrix", supercell_matrix)
-    Parse.addValue("x_phonopy_original_system_ref", Basesystem)
-    Parse.closeSection("section_system", Supercellsystem)
-    method = Parse.openSection("section_method")
-    Parse.addValue("x_phonopy_symprec", sym)
-    Parse.addValue("x_phonopy_displacement", displacement)
-    Parse.closeSection("section_method", method)
-    results = Parse.openSection("section_single_configuration_calculation")
-    Parse.addValue("single_configuration_calculation_to_system_ref", Supercellsystem)
-    Parse.addValue("single_configuration_to_calculation_method_ref", method)
-    Parse.addArrayValues("hessian_matrix", FC2)
-    GP = Get_Properties(FC2, cell, positions, symbols, supercell_matrix, sym, displacement)
-    GP.prem_emit(Parse, results)
-    GP.prep_ref(Whole_Path, Parse)
-    Parse.closeSection("section_single_configuration_calculation", results)
-    Parse.closeSection("section_run", sRun)
-    Parse.finishedParsingSession("ParseSuccess", None)
-
-    return backend

phonopyparser/Get_Properties.py

-# Copyright 2016-2018 Fawzi Mohamed, Danio Brambila
-#
-#   Licensed under the Apache License, Version 2.0 (the "License");
-#   you may not use this file except in compliance with the License.
-#   You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-#   Unless required by applicable law or agreed to in writing, software
-#   distributed under the License is distributed on an "AS IS" BASIS,
-#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-#   See the License for the specific language governing permissions and
-#   limitations under the License.
-
-#### phonopy parser based on the original work of Joerg Mayer on phonopy-FHI-aims
-
-import numpy as np
-from phonopyparser.PhononModulesNomad import *
-from fnmatch import fnmatch
-import sys
-import math
-import os, logging
-from phonopy.interface.FHIaims import read_aims, write_aims, read_aims_output
-from phonopyparser.con import Control
-from phonopy import Phonopy
-from phonopy.structure.symmetry import Symmetry
-from phonopy.file_IO import parse_FORCE_CONSTANTS
-from phonopy.harmonic.forces import Forces
-from phonopy.harmonic.force_constants import get_force_constants
-from phonopy.units import *
-from phonopy.structure.atoms import Atoms
-from nomadcore.unit_conversion.unit_conversion import convert_unit_function
-from nomadcore.parser_backend import *
-from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
-
-parser_info = {"name": "parser_phonopy", "version": "0.1"}
-
-path = "../../../../nomad-meta-info/meta_info/nomad_meta_info/phonopy.nomadmetainfo.json"
-metaInfoPath = os.path.normpath(
-    os.path.join(os.path.dirname(os.path.abspath(__file__)), path))
-metaInfoEnv, warns = loadJsonFile(filePath=metaInfoPath,
-                                  dependencyLoader=None,
-                                  extraArgsHandling=InfoKindEl.ADD_EXTRA_ARGS,
-                                  uri=None)
-if __name__ == "__main__":
-    import sys
-    name = sys.argv[1]
-    #### Reading basic properties from JSON
-    with open(name) as FORCES:
-            data = json.load(FORCES)
-    hessian= np.array(data["sections"]["section_single_configuration_calculation-0"]["hessian_matrix"])
-    SC_matrix = np.array(data["sections"]["section_system-1"]["SC_matrix"])
-    cell = np.array(data["sections"]["section_system-0"]["simulation_cell"])
-    symbols = np.array(data["sections"]["section_system-0"]["atom_labels"])
-    positions = np.array(data["sections"]["section_system-0"]["atom_positions"])
-    displacement = np.array(data["sections"]["section_method-0"]["x_phonopy_displacement"])
-    symmetry_thresh = np.array(data["sections"]["section_method-0"]["x_phonopy_symprec"])
-    ####
-
-
-    #### omitting
-    get_properties = get_properties(hessian, cell, positions, symbols, SC_matrix, symmetry_thresh, displacement, file_name, metaInfoEnv, parser_info)
-    get_properties.omit_properties()

phonopyparser/__init__.py

@@ -12,4 +12,21 @@
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
 
-from phonopyparser.Get_Force_Constants import PhonopyParserWrapper
+from phonopyparser.phonopy_calculators import PhonopyCalculatorInterface
+
+from nomad.parsing.parser import FairdiParser
+from .metainfo import m_env
+
+
+class PhonopyParser(FairdiParser):
+    def __init__(self):
+        super().__init__(
+            name='parsers/phonopy', code_name='Phonopy', code_homepage='https://phonopy.github.io/phonopy/',
+            mainfile_name_re=(r'(.*/phonopy-FHI-aims-displacement-0*1/control.in$)|(.*/phonon.yaml)')
+        )
+
+    def parse(self, filepath, archive, logger=None):
+        self._metainfo_env = m_env
+
+        interface = PhonopyCalculatorInterface(filepath, archive, logger)
+        interface.parse()

phonopyparser/__main__.py

+# Copyright 2016-2018 Markus Scheidgen
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+
+import sys
+import json
+
+from phonopyparser import PhonopyParser
+
+if __name__ == "__main__":
+    archive = PhonopyParser.main(sys.argv[1])
+    json.dump(archive.m_to_dict(), sys.stdout, indent=2)

phonopyparser/con.py → phonopyparser/fhiaims_io.py

@@ -12,19 +12,16 @@
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
 
-#### phonopy parser based on the original work of Joerg Mayer on phonopy-FHI-aims
+# phonopy parser based on the original work of Joerg Mayer on phonopy-FHI-aims
 
 import numpy as np
-from phonopy.units import VaspToTHz as AimsToTHz, VaspToCm as AimsToCm, VaspToEv as AimsToEv, THzToCm, THzToEv
-from phonopy.interface.FHIaims import read_aims, write_aims, read_aims_output
-# from phonopy.structure.cells import get_equivalent_smallest_vectors
-from phonopy.harmonic.dynamical_matrix import  DynamicalMatrix, DynamicalMatrixNAC, get_equivalent_smallest_vectors
-from phonopy.structure.cells import get_reduced_bases
-import numpy as np
+import math
+import os
+import logging
+from fnmatch import fnmatch
 from phonopy import Phonopy
-from phonopy.structure.cells import Primitive
-
 
+from phonopyparser.FHIaims import read_aims_output
 
 class Control:
     def __init__(self, file=None):
@@ -53,7 +50,7 @@ class Control:
                         if (nfields >= 11):
                             s = map(int, fields[2:11])
                             s = list(s)
-                            Smat = np.array(s).reshape(3,3)
+                            Smat = np.array(s).reshape(3, 3)
                         elif (nfields >= 5):
                             s = map(int, fields[2:5])
                             s = list(s)
@@ -66,7 +63,7 @@ class Control:
                         # this consistency check is not strictly necessary, since int function above used to transform the input
                         # already throws an exception when decimal numbers are encountered
                         # keep for consistency (and future changes to that spot?) nevertheless...
-                        elif (abs(det_Smat-round(det_Smat)) > 1.0e-6):
+                        elif (abs(det_Smat - round(det_Smat)) > 1.0e-6):
                             raise Exception("determinant of supercell differs from integer by more than numerical tolerance of 1.0e-6")
                         self.phonon["supercell"] = s
                     if (fields[1] == "displacement"):
@@ -82,17 +79,89 @@ class Control:
                             delta = (0.1, 0.1, 0.1)
                         if (delta[0] == 0.0) and (delta[1] == 0.0) and (delta[2] == 0.0):
                             raise Exception("evaluation of frequencies with non-analytic corrections must be shifted by delta away from Gamma")
-                        parameters = { "file" : fields[2],
-                                       "method" : fields[3].lower(),
-                                       "delta" : delta }
+                        parameters = {
+                            "file": fields[2], "method": fields[3].lower(), "delta": delta}
                         self.phonon["nac"].update(parameters)
 
-        except Exception:
-            #print (line,)
-            #print ("|-> line triggered exception: ") + str(Exception)
-            raise
+        except Exception as e:
+            raise(e)
+
         # supercell is mandatory for all what follows
         if not self.phonon["supercell"]:
             raise Exception("no supercell specified in %s" % self.file)
         f.close()
 
+
+def clean_position(scaled_positions):
+    scaled_positions = list(scaled_positions)
+    for sp in range(len(scaled_positions)):
+        for i in range(len(scaled_positions[sp])):
+            if np.float(np.round(scaled_positions[sp][i], 7)) >= 1:
+                scaled_positions[sp][i] -= 1.0
+            elif scaled_positions[sp][i] <= -1e-5:
+                scaled_positions[sp][i] += 1.0
+    scaled_positions = np.array(scaled_positions)
+
+    return scaled_positions
+
+
+def read_forces_aims(cell_obj, supercell_matrix, displacement, sym, tol=1e-6, logger=None):
+    if logger is None:
+        logger = logging
+
+    phonopy_obj = Phonopy(cell_obj, supercell_matrix, symprec=sym)
+    phonopy_obj.generate_displacements(distance=displacement)
+    supercells = phonopy_obj.get_supercells_with_displacements()
+    directories = []
+    digits = int(math.ceil(math.log(len(supercells) + 1, 10))) + 1
+    for i in range(len(supercells)):
+        directories.append(("phonopy-FHI-aims-displacement-%0" + str(digits) + "d") % (i + 1))
+    set_of_forces = []
+    Relative_Path = []
+    for directory, supercell in zip(directories, supercells):
+        aims_out = os.path.join(directory, directory + ".out")
+        if not os.path.isfile(aims_out):
+            logger.warn("!!! file not found: %s" % aims_out)
+            cwd = os.getcwd()
+            con_list = os.listdir(cwd)
+            check_var = False
+            for name in con_list:
+                if fnmatch(name, '*.out'):
+                    aims_out = '%s/%s' % (directory, name)
+                    logger.warn(
+                        "Your file seems to have a wrong name proceeding with %s" % aims_out
+                    )
+                    check_var = True
+                    break
+            if not check_var:
+                raise Exception("No phonon calculations found")
+            os.chdir("../")
+        Relative_Path.append(aims_out)
+        supercell_calculated = read_aims_output(aims_out)
+        if (
+            (supercell_calculated.get_number_of_atoms() == supercell.get_number_of_atoms()) and
+            (supercell_calculated.get_atomic_numbers() == supercell.get_atomic_numbers()).all() and
+            (abs(supercell_calculated.get_positions() - supercell.get_positions()) < tol).all() and
+            (abs(supercell_calculated.get_cell() - supercell.get_cell()) < tol).all()):
+            # read_aims_output reads in forces from FHI-aims output as list structure,
+            # but further processing below requires numpy array
+            forces = np.array(supercell_calculated.get_forces())
+            drift_force = forces.sum(axis=0)
+            for force in forces:
+                force -= drift_force / forces.shape[0]
+            set_of_forces.append(forces)
+        elif (
+            (supercell_calculated.get_number_of_atoms() == supercell.get_number_of_atoms()) and
+            (supercell_calculated.get_atomic_numbers() == supercell.get_atomic_numbers()).all() and
+            (abs(clean_position(supercell_calculated.get_scaled_positions()) - clean_position(supercell.get_scaled_positions())) < tol).all() and
+            (abs(supercell_calculated.get_cell() - supercell.get_cell()) < tol).all()):
+            logger.warn("!!! there seems to be a rounding error")
+            forces = np.array(supercell_calculated.get_forces())
+            drift_force = forces.sum(axis=0)
+            for force in forces:
+                force -= drift_force / forces.shape[0]
+            set_of_forces.append(forces)
+        else:
+            raise Exception("calculated varies from expected supercell in FHI-aims output %s" % aims_out)
+
+    return set_of_forces, phonopy_obj, Relative_Path

phonopyparser/phonopy_calculators.py

+import os
+import numpy as np
+import phonopy
+from phonopy.units import THzToEv
+
+from phonopyparser.fhiaims_io import Control, read_forces_aims
+from phonopyparser.phonopy_properties import PhononProperties
+from phonopyparser.FHIaims import read_aims
+
+from nomadcore.unit_conversion.unit_conversion import convert_unit_function
+
+from nomad.datamodel.metainfo.public import section_run, section_system,\
+    section_system_to_system_refs, section_method, section_single_configuration_calculation,\
+    section_k_band, section_k_band_segment, section_dos, section_frame_sequence,\
+    section_thermodynamical_properties, section_sampling_method, Workflow, Phonon, \
+    section_calculation_to_calculation_refs
+
+
+class PhonopyCalculatorInterface: